Science Literature

One of the lasting contributions of Professor Phillip Johnson has been his stress on clarifying the meaning of the word "evolution". He found a variety of definitions in common use, ranging from the "alteration in allele frequency" (which makes everyone an evolutionist), to the all-embracing concept of evolutionism (philosophical naturalism). Debates about the relevant science are muddied by people failing to use the word "evolution" in a consistent manner; for example, the industrial melanism of the peppered moth is often cited as proof of Darwin's theoretical model of evolution by natural selection. In his book, The Edge of Evolution, Professor Mike Behe put great stress on understanding Darwinian mechanisms at a molecular level. It is not good enough to talk about adaptation at a phenotypic level because the mechanisms relate to molecular changes at the genotypic level. When the evidence is examined from that perspective, it becomes clear that Darwinian mechanisms cannot build complexity. In a detailed review paper, Behe makes this point again and proposes the "First Rule of Adaptive Evolution" to summarise the findings of experimental evolution.

Phenotypic change does not necessarily map onto genotypic change (source here)

To qualify for Behe's review, experimental studies of evolution must have involved adaptation and must have included an analysis of genomic changes at the molecular level. He has set out to classify the mutations associated with adaptive change. Significant data matching these criteria relate to bacteria and viruses.

"Since species can evolve to gain, lose, or modify functional features, it is of basic interest to determine whether any of these tends to dominate adaptations whose underlying molecular bases are ascertainable. Here, I survey the results of evolutionary laboratory experiments on microbes that have been conducted over the past four decades. Such experiments exercise the greatest control over environmental variables, and they yield our most extensively characterized results at the molecular level."

The details of the review are of a technical nature and are best read in the paper. There is originality in the perspective Behe brings, because many of the researchers responsible for the experimental work have not discussed whether the mutations lead to a gain, a loss, or a modification of functional features. At this point it is worth referring to FCTs, which is the adopted acronym for Functional Coded elemenTs. Behe's analysis of both individual and aggregated findings represents a significant contribution to the literature.

"As seen in Tables 2 through 4, the large majority of experimental adaptive mutations are loss-of-FCT or modification-of-function mutations. In fact, leaving out those experiments with viruses in which specific genetic elements were intentionally deleted and then restored by subsequent evolution, only two gain-of-FCT events have been reported: the development of the ability of a fucose regulatory protein to respond to d-arabinose, and the antibiotic gene capture by f1."

This is a striking finding and it deserves to be formally labelled. Behe has obliged us by suggesting "the First Rule of Adaptive Evolution". This is a descriptive heuristic (rather than a prescriptive law). Adaptive evolution has the effect of breaking or blunting any FCTs whose loss would yield a net fitness gain.

"It is called the "first" rule because the rate of mutations that diminish the function of a feature is expected to be much higher than the rate of appearance of a new feature, so adaptive loss-of-FCT or modification-of-function mutations that decrease activity are expected to appear first, by far, in a population under selective pressure."

The key point to note here is that this Rule is driven by empirical data rather than by theory. The Rule expresses the findings of intensive research and it informs us about what actually happens. It is not a prediction deduced from theory.

"Except in cases where specific genetic features were first removed, as well as in the case of antibiotic gene capture by f1, all adaptive mutations in laboratory evolution experiments with viruses seem to be loss-of-FCT or modification-of-function mutations. Thus, in general laboratory evolutionary situations (that is, where a microorganism was under a general selective pressure rather than a specific one), adaptive loss-of-FCT or modification-of-function mutations were always available. This cannot be said for gain-of-FCT mutations."

For those familiar with The Edge of Evolution, this puts the spotlight again on the challenge of building complexity. These empirical results show that the great majority of cases of adaptive evolution involve either loss of functionality or a modification of an existing function. Adaptive evolution pre-supposes complexity. There is little evidence to support a model of the origin of species using the mechanisms of random mutation and selection (whether artificial or natural).

"Leaving aside gain-of-FCT for the moment, the work reviewed here shows that organisms do indeed adapt quickly in the laboratory - by loss-of-FCT and modification-of-function mutations. If such adaptive mutations also arrive first in the wild, as they of course would be expected to, then those will also be the kinds of mutations that are first available to selection in nature. This is a significant addition to our understanding of adaptation."

As this paper has been subjected to much critical scrutiny, it is appropriate to add some pointers to help general readers with their own appraisal of its significance. First, some complimentary comments from critics about the way the review has been conducted:

"My overall conclusion: Behe has provided a useful survey of mutations that cause adaptation in short-term lab experiments on microbes." (Professor Gerry Coyne, Department of Ecology and Evolution at the University of Chicago, source here).
"I read the paper in draft form some months ago and have not re-read it, but even then it exhibited an impressive command of the experimental evolution literature, at least the literature on adaptation of whole genomes of bacteria and phages (as opposed to the 'directed' evolution of genes on plasmids and of naked nucleic acids). I consider MB's characterization of most molecular evolution in these experiments as point mutations and/or deletions to be accurate. [. . .] My own view of the MB paper is that it has done a service to the study of evolution by pointing out where the next generation of experiments should focus." (Professor Jim Bull, Section of Integrative Biology, University of Texas at Austin, source here).

Numerous objections have been raised to Behe's analysis. It is claimed that the experimental evolution in laboratories does not represent the real world because there has not been enough time. It is claimed that studies of bacteria and viruses do not properly represent the incidence of 'gain-of-FCT mutations' in eukaryotes. It is claimed that mutations involving horizontal genetic transfer and gene duplication need to be considered to do justice to contemporary evolutionary theory. These objections are addressed here, here and here by Behe.

This blog started by pointing out the strong empirical emphasis which Behe brings to the field of evolutionary biology. There is typically a reluctance of researchers to get to the falsification stage of scientific enquiry. Often, theory is elevated above experiment, because the theory 'must be true'. What we now need are a set of review papers showing how theoretical ideas such as horizontal genetic transfer and gene duplication fare when they are analysed experimentally. Scientists should welcome this public scrutiny of favoured ideas - because this is the only way we can escape from 'normal science' in the Kuhnian sense. But for the present, we should digest the findings of Behe's review - here is his summary of the take-home message:

"The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. [. . .] Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent."

Experimental Evolution, Loss-of-Function Mutations, and "The First Rule of Adaptive Evolution"
Michael J. Behe
The Quarterly Review of Biology, December 2010, 85(4), 419-445.

Abstract: Adaptive evolution can cause a species to gain, lose, or modify a function; therefore, it is of basic interest to determine whether any of these modes dominates the evolutionary process under particular circumstances. Because mutation occurs at the molecular level, it is necessary to examine the molecular changes produced by the underlying mutation in order to assess whether a given adaptation is best considered as a gain, loss, or modification of function. Although that was once impossible, the advance of molecular biology in the past half century has made it feasible. In this paper, I review molecular changes underlying some adaptations, with a particular emphasis on evolutionary experiments with microbes conducted over the past four decades. I show that by far the most common adaptive changes seen in those examples are due to the loss or modification of a pre existing molecular function, and I discuss the possible reasons for the prominence of such mutations.

Although it is common to hear references to the "Cambrian explosion", no-one who uses that expression thinks of it as an instant in time when the fuse was lit and - ZAP! - the phyla were born. It has always been recognised that some phyla appear stratigraphically later than others. The problem for Darwin was that the abrupt and early appearance of phyla in the fossil record did not fit his branching pattern of gradual evolution: his model extrapolates from diversification at the species level to produce the larger taxonomic categories. The different phyla should appear after, not before, extensive speciation. A detailed review paper has recently been published which has much useful information about the data relating to the Cambrian record of animals, but which unfortunately mixes this up with highly contentious interpretation. The authors introduce the issues in this way:

"These observations (of the great radiation of animal life during the Early Cambrian) led scientists to focus in particular on two puzzling aspects of the Cambrian radiation, both encompassed by the term "Cambrian explosion". The first is the dramatic increase in disparity (morphological distinctness) as represented by the supposed appearance of nearly all major animal body plans (equivalent to the animal phyla) within a geologically brief interval of time near the beginning of the Cambrian. This problem was compounded by an apparent lack of evidence for "intermediate" taxa - taxa that lie close to the last common ancestor of different phyla in the metazoan tree. The second difficulty is the high rate of diversification (increase in number of species) in the Early Cambrian, particularly the apparent spike in diversification during the Tommotian and Atdabanian ages, spanning an interval that seemed short relative to subsequent radiations."

"The big question that the Cambrian Explosion poses is where does all that new information come from?" says Dr. Stephen Meyer, a featured expert in the documentary. (source here)

Focussing on the analysis provided of the fossil record, the authors select sites that provide opportunities to do detailed stratigraphical work: in Morocco, Siberia, Mongolia and China. Much of the paper is devoted to fossil appearances and chemical isotope analyses drawn from these localities. They give particular attention to the small shelly fauna that characterises the Early Cambrian (the lowest two stages are the Nemakit-Daldynian and the Tommotian). A strong link is found between fossil appearances and seawater chemistry. This is their summary:

"The time line of small shelly fossil first appearances indicates the following.
(1) All aragonitic taxa appeared in the Nemakit-Daldynian, before the first appearances of calcitic taxa, confirming earlier studies and suggesting that the Mg/Ca ratio of seawater determines skeletal mineralogy at the time that carbonate skeletons first evolve in a clade. [. . .]
(2) The major groups of small shelly fossils appear early; five appear by 540-538 Ma, and all but one appear by 534-532 Ma.
(3) By the middle of the Nemakit-Daldynian (534-532 Ma), nearly half of the total number of small shelly fossil genera recorded in our data set had appeared, and by the end of the Nemakit-Daldynian, nearly three-quarters had appeared, suggesting that diversification of these animals occurred throughout the Nemakit-Daldynian, rather than being concentrated at the end of that time. [. . .]
(4) Three pulses in fossil first appearances, the smallest in the early Nemakit-Daldynian , ca. 540-538 Ma, the largest in the middle Nemakit-Daldynian, ca. 534-530 Ma, and the third in the Tommotian, ca. 524-522 Ma, may reflect peaks in small shelly fossil diversification, but could also reflect the influence of local or global preservational biases."

The pattern reported for the small shelly fossils is mirrored in the other animals studied. The above description is generic: there are three pulses of appearance of skeletal animals: a small one at the base of the Cambrian, the largest in the middle of the Nemakit-Daldynian and an intermediate pulse in the Tommotian. Prior to the Cambrian, the seawater is aragonitic; during the Nemakit-Daldynian it is described as aragonite-calcite transition; and in the Tommotian the seawater is calcitic. There is thus an ecological story to accompany the fossil appearance story: the big issue is whether the environmental change drives evolution or whether it constrains evolution or whether it limits the ecological options for animals to feed and breed. The authors recognise that their paper provides a foundation for such discussion to take place:

"An explanation for the processes responsible for the radiation of animals, and of whether the radiation was a consequence or a cause of associated geochemical changes, requires a thorough understanding of the pattern of that radiation, to which this paper contributes."

However, the authors go much further than this in their conclusions. They consider that Darwin's appeal to the imperfection to the fossil record has "turned out to be closer to the truth". In their judgment, the big puzzles are resolved:

"The problem of missing fossil ancestors was solved by the discovery of the Precambrian fossil record, the problem that nearly all the animal phyla appear in the Lower Cambrian with no evidence of intermediate taxa was solved by the recognition that most Lower Cambrian fossils represent stem-groups of living phyla, and the problem of the explosive diversification of animals at the start of the Tommotian was solved by improved correlation and radiometric dating of Lower Cambrian sequences - to which we contribute here - showing that this diversification was drawn out over more than 20 m.y."

It should be obvious that the problem of the early origin of the phyla is not solved by saying that the earliest Cambrian fossils are stem-group rather than crown-group fossils. The challenge to Darwinism posed by the abrupt origins of body plans is undiminished by this fresh analysis. Furthermore, saying that the diversification of animals was drawn out over 20 Ma may reduce the tension for some lineages, but there are still plenty of others where the diversification is inconsistent with Darwinian gradualism (as recently discussed for the echinoderms).

The authors appear to be too eager to sweep away the "Cambrian Explosion" challenge to Darwinism. They might be advised to refer to Meyer, et al. (2006): The Cambrian Explosion: Biology's Big Bang. They may wish also to refer to the work of Thomas Kuhn, who showed how easy it is for scientists to get in a rut and never subject their own presuppositions to critical scrutiny. This has been a real snare for Darwinists who have become experts at slotting every data element into their all-embracing theory. The remedy is to promote multiple working hypotheses. This allows one's own presuppositions to be challenged more easily - and this is healthy for science. The alternative hypothesis this blog has been exploring is that the fossil record is perfectly capable of an ecological perspective. It is there in the Cambrian Explosion data: as soon as environments were capable of being occupied by marine animals, they were colonised. The animals were not suited to aragonite seas, so they are absent from the Ediacaran. But as soon as calcitic seas became widespread, these animals were everywhere. For more on this, with further links, go here.

The earliest Cambrian record of animals and ocean geochemical change
Adam C. Maloof, Susannah M. Porter, John L. Moore, Frank O. Dudas, Samuel A. Bowring, John A. Higgins, David A. Fike, and Michael P. Eddy
Geological Society of America Bulletin, November 2010, v. 122, p. 1731-1774 | doi:10.1130/B30346.1

Abstract: The Cambrian diversification of animals was long thought to have begun with an explosive phase at the start of the Tommotian Age. Recent stratigraphic discoveries, however, suggest that many taxa appeared in the older Nemakit-Daldynian Age, and that the diversification was more gradual. [. . .] The time line suggests that the diversification of skeletal animals began early in the Nemakit-Daldynian, with much of the diversity appearing by the middle of the age. Fossil first appearances occurred in three pulses, with a small pulse in the earliest Nemakit-Daldynian (ca. 540-538 Ma), a larger pulse in the mid- to late Nemakit-Daldynian (ca. 534-530 Ma), and a moderate pulse in the Tommotian (ca. 524-522 Ma). These pulses are associated with rapid reorganizations of the carbon cycle, and are superimposed on long-term increases in sea level and the hydrothermal flux of Sr.

Some have argued that echinoderm diversity is an Ordovician phenomenon: linked to the Great Ordovician Diversification. Others make the case for the radiation to have initiated earlier. All seem to be agreed that the origin of echinoderms is shrouded in uncertainty. One major problem is that the relevant fossils are unfamiliar and often poorly preserved and there are often doubts about their classification. However, in June 2010, research was reported dealing with Middle Cambrian echinoderms from Spain.

"The new Spanish data suggest that a number of the clades involved in [the Great Ordovician] diversification (such as sucocystid cinctans, cothurnocystid stylophorans, ctenocystoids, and isorophid edrioasteroids) appeared significantly earlier in Gondwanan settings than previously thought. This shows that, even by the earliest middle Cambrian, a variety of novel body plans and ecological strategies already existed among echinoderms, pushing back the timing of important divergences into the lower Cambrian."

A Middle Cambrian echinoid - a stromatocystitid edrioasteroid (source here)

The remarkable aspect of this research is the extent of diversification reported. There are eight different body plans that indicate the animals occupied very different ecological niches. This is the ecological interpretation of the fossil record noted in previous blogs.

"There are low to medium suspension feeders (such as gogiids, lichenoidids, or isorophid edrioasteroids) that lived permanently attached; others are free-living forms, such as cinctans, stylophorans, and "eocystitids". Both gogiids and isorophids were commonly attached to skeletal debris. Previous lichenoidids known rested on the substrate, but the new specimens from Spain were also attached to skeletal debris. Cinctans and stylophorans rested on the seafloor and captured particles from the water-sediment interface."

Whatever else is understood from these data, diversification must have been earlier than previously thought. This puts the spotlight on the Early Cambrian - not just providing us with the Cambrian Explosion of animal phyla, but also the emergence of a diversity of ecosystems and the radiation of animal groups.

"Because many of these taxa appear close to the beginning of the middle Cambrian, it seems likely that their origins must be placed in the early Cambrian."

It should be remembered that the sea urchin, an echinoderm, is one of the animals whose genomes has been sequenced. Two of these genes, pax and BOULE, have been the subject of previous comment (here). Those involved with the sequencing expressed surprise at finding such sophistication, for it was realised that much of the animals genetic makeup is remarkably similar to that possessed by humans. This early appearance of genetic complexity is a major aspect of the Cambrian Explosion - for these animals were not simple or primitive in their genetic makeup. Such a flowering of biological information is inconsistent with the gradualism inherent in darwinian mechanisms.

"Any snorkeler who has ever marvelled at the spherical, almost otherworldly, symmetry of the sea urchin will be amazed to learn that this organism, so different in habitat and body plan from ourselves, actually shares a substantial number of the same genes and pathways," said Francis Collins, director of the National Human Genome Research Institute (NHGRI) which helped fund the project.
"It turns out that the sea urchin is very much like us," said George Weinstock, the co- director of the HGSC. "You wouldn't think it to look at it. But it's closer to us than a fly," he said. (Source here)

Middle Cambrian echinoderms from north Spain show echinoderms diversified earlier in Gondwana
Samuel Zamora
Geology, June 2010, 38(6), 507-510 | doi:10.1130/G30657.1

Abstract: New fossil discoveries in the middle Cambrian of Spain have considerably expanded our knowledge of the temporal and spatial distribution of some major clades of echinoderms including sucocystid cinctans, isorophid edrioasteroids, cothurnocystid stylophorans, ctenocystoids, and a new group of blastozoans ("eocystitids"). Because many of these taxa appear close to the beginning of the middle Cambrian, it seems likely that their origins must be placed in the early Cambrian. These results, based on articulated specimens provided from Echinoderm Lagerstatten, agree with the hidden diversity provided from isolated ossicles from other Gondwanan areas.

Until this year, the Bryozoa were missing from the list of Cambrian organisms. Although some had been previously reported, critical scrutiny showed that they were misidentified and that the oldest known bryozoans came from Lower Ordovician strata. This year, however, Upper Cambrian bryozoans were reported from the lower Tinu Formation, southern Mexico. They were said to be about 8 Ma years older than the oldest Ordovician fossils. This means that Cambrian strata can be said to record examples of all the skeletalized metazoan phyla.

"One mineralized group, the phylum Bryozoa, seems to have "missed" the Cambrian radiation. [. . .] As discussed below, Late Cambrian bryozoans are now known, and have features that suggest they lie near the base of the bryozoan lineage."

"Bryozoa", from Ernst Haeckel's Kunstformen der Natur, 1904 (source here)

In view of the ecological perspective this blog has been giving to the appearance of organisms in the fossil record (see here), it is worth highlighting the ecological significance of bryozoans. This is brought out in the following paragraph:

"Bryozoans are an important Paleozoic-Holocene phylum in substrate stabilization, as a food source and major filter-feeding group, as rock formers, and as a component of a new Late Ordovician habitat - animal-constructed reefs. Late Ordovician bryozoan-coral-stromatoporoid reefs were colonized by high-diversity faunas. These reefs replaced earlier, microbially formed, thrombolite reefs. The Tinu Formation shows that Bryozoa, as all other mineralized metazoan phyla, had a Cambrian origin, although Bryozoa formed only small Early Ordovician reefs."

The Cambrian, then was a remarkable period of Earth history. In the Precambrian, we have only soft-bodied organisms. At the end of the Cambrian, we have all the skeletalized metazoan phyla and much more besides. Subsequent periods of Earth history may have had more dramatic radiations at the Order, Class or Family level, but there were no further bauplan innovations affecting skeletalized metazoan organisms.

This phenomenon has long been troubling for the Darwinian paradigm. The branching pattern of speciation endorsed by Darwin and his followers implies that Family, Class, Order and Phylum categories emerge as later stage developments of the evolutionary process. What we see in the fossil record, however, is the opposite of this. We start with discontinuity of body plans, followed by diversification - as variation around a theme. Darwinists have never confronted their theory with the facts - they exhibit all the characteristics of Kuhnian 'normal science' that will force-fit anomalous data to theory. For more on this and the 'inverted cone of diversity', go here.

Cambrian origin of all skeletalized metazoan phyla - Discovery of Earth's oldest bryozoans (Upper Cambrian, southern Mexico)
Ed Landing, Adam English and John D. Keppie
Geology, June 2010, 38(6), 547-550 | doi:10.1130/G30870.1

Abstract: Exquisite Pywackia baileyi Landing n. gen. and sp. specimens from the lower Tinu Formation, southern Mexico, extend the bryozoan record into the Upper Cambrian. They are ~8 m.y. older than the purported oldest bryozoans from South China, and show that all skeletalized metazoan phyla appeared in the Cambrian. The new form differs from similar, twig-like cryptostomes by its shallow autozooecia and an elongate axial zooid, which may be homologous to the stolon in nonmineralized ctenostomes. It may morphologically resemble mineralized stem group bryozoans that retained a stolon-like individual, although an ability to bud was acquired by the feeding individuals (autozooids). The latest Cambrian origin of bryozoans, several mollusk classes (polyplacophorans, cephalopods), and euconodonts was a major evolutionary development and can be considered the onset of the Ordovician radiation of more complex marine communities.

Students of the Cambrian Explosion have had much to think about this year. In this blog, and others to follow, several of these will be featured. We start with Nectocaris, one of the 'weird wonders' of Stephen Jay Gould in Wonderful Life. There have been many attempts to locate it within the traditional taxonomic framework. Some have placed it in the arthropods and others have considered it a chordate. However, research published earlier this year, based on 91 specimens (rather than one), has concluded that the animal is a mollusc.

The (reconstructed) ancient squid hunted using its two long tentacles (Source here)

Martin Smith and Jean-Bernard Caron have suggested that Nectocaris displays characters that put it into a relationship with cephalopods. They point to paired camera-type eyes, flexible tentacles and jet propulsion via a 'nozzle'. The reconstructed animal has the appearance of a squid but with two rather than eight or ten tentacles. They suggest that the animal is a stem-group rather than a crown-group cephalopod. It lacks features they consider to be more advanced: there is no shell, only two tentacles and no obvious beak or radula (although the mouthparts are poorly preserved). Their analysis has been accepted by most commentators. The relevance to the Cambrian Explosion is that, before now, the earliest fossil remains of cephalopods are Late Cambrian. Since the studied samples all come from the Middle Cambrian Burgess Shale Formation, Nectocaris "extends the cephalopods' fossil record by over 30 million years".

"The findings make the ancestors of modern squid and octopuses at least 30 million years older. Evolutionary biologist Martin Smith, the main author of the study, told PA news agency that the findings bring cephalopods much closer to the first appearance of complex animals. "We go from very simple pre-Cambrian life-forms to something as complex as a cephalopod in the geological blink of an eye, which illustrates just how quickly evolution can produce complexity," said Mr Smith."

The above quote from Martin Smith illustrates both the significance for the Cambrian Explosion and the conundrum the evidence provides for evolutionary theory. The problem is that everything occurs "in the geological blink of an eye" - whether it be the origins of the phyla with radically different body plans, or whether it be the origins of different classes within a phylum (such as the origin of cephalopods within the mollusca). In a News & Views essay for Nature, Stefan Bengtson provides an insight into these animals.

"To most people, molluscs are rather dull creatures: slugs, snails, clams, mussels and such, at times good for eating but otherwise uninteresting. Yet everyone harbours a fascination for cephalopods, which are also molluscs: the octopus, the chambered nautilus, the cuttlefish and the squid, not least the mythical giant Kraken that Alfred, Lord Tennyson pictured in "ancient, dreamless, uninvaded sleep" in the ocean abyss. Cephalopods are not like other molluscs.
Anything but sluggish, they are capable of instant and rapid movement. Far from being mindless filterers or grazers, they are active predators possessing the most advanced nervous system known among invertebrates. Their brain-to-body ratio exceeds that of most vertebrates (although we have not been smart enough to figure out exactly how smart they are). They are masters of camouflage, changing shape, surface pattern, texture and colour in the blink of an eye - and they do have good eyes. When threatened, they escape by means of a built-in hydro jet that can even send them squirting through the air like little rockets on a tail of water."

At very least, then, if the identification of Nectocaris as a cephalopod is valid, the time available for evolutionary transformation is reduced by 30 Ma. The credibility of gradualist mechanisms, already at breaking point, simply vanishes. It is a cop-out to say that the data "illustrates just how quickly evolution can produce complexity" because it begs the question that evolution can generate complexity at all. Martin Smith's words are the evolutionary biologist's equivalent of the 'god-of-the-gaps' argument. He has no mechanism to explain how it could ever happen, but since evolution is regarded as a 'fact', then evolution must have done it.

It is worth considering whether Nectocaris is primitive or derived. The authors entertain this idea when they write: "Nectocaridids' single pair of tentacles may originate via the fusion of multiple pairs, or represent the primitive state". They also articulate the puzzle of having mineralised ancestors and mineralised descendants - but opt for Nectocaris being primitive because "no obvious precursors" for cephalopods have been found. They resolve their conundrum by postulating that there must have been non-mineralised precursors:

"Given that the highly plastic molluscan secretome has convergently produced similar shell microstructures in unrelated lineages, we suggest that nautiloids evolved from a nonmineralized, coleoid-like ancestor related to the nectocaridids."

Not all are convinced. Christopher Taylor finds reasons for thinking that Nectocaris is not such a primitive animal, but a specialised organism (and that, it should be said, raises even more puzzles for the Darwinian, gradualist paradigm).

"As described in an earlier post, the earliest known stem cephalopods (from the Late Cambrian) possessed shells with large numbers of very tightly packed septa and were unlikely to have been very buoyant. Their generally short conical shape would have been ill-suited for jet-propelled swimming as in modern cephalopods and they were most likely benthic. As other molluscan classes were also ancestrally benthic, it seems unparsimonious that the actively swimming Nectocaris represents the ancestral cephalopod lifestyle.
If Nectocaris is a stem cephalopod (which essentially depends on how strong the siphon is as a supporting apomorphy), then the most likely scenario is that its shell loss and squid-like form is an independent convergence on modern shell-less cephalopods rather than representing the ancestral form for cephalopods as a whole. Nectocaris would not be an ancestor, but a highly specialised side branch of its own."

Primitive soft-bodied cephalopods from the Cambrian
Martin R. Smith and Jean-Bernard Caron
Nature, 465, 469-472, (27 May 2010) | doi:10.1038/nature09068

Abstract: The exquisite preservation of soft-bodied animals in Burgess Shale-type deposits provides important clues into the early evolution of body plans that emerged during the Cambrian explosion. Until now, such deposits have remained silent regarding the early evolution of extant molluscan lineages - in particular the cephalopods. Nautiloids, traditionally considered basal within the cephalopods, are generally depicted as evolving from a creeping Cambrian ancestor whose dorsal shell afforded protection and buoyancy. Although nautiloid-like shells occur from the Late Cambrian onwards, the fossil record provides little constraint on this model, or indeed on the early evolution of cephalopods. Here, we reinterpret the problematic Middle Cambrian animal Nectocaris pteryx as a primitive (that is, stem-group), non-mineralized cephalopod, based on new material from the Burgess Shale. Together with Nectocaris, the problematic Lower Cambrian taxa Petalilium and (probably) Vetustovermis form a distinctive clade, Nectocarididae, characterized by an open axial cavity with paired gills, wide lateral fins, a single pair of long, prehensile tentacles, a pair of non-faceted eyes on short stalks, and a large, flexible anterior funnel. This clade extends the cephalopods' fossil record by over 30 million years, and indicates that primitive cephalopods lacked a mineralized shell, were hyperbenthic, and were presumably carnivorous. The presence of a funnel suggests that jet propulsion evolved in cephalopods before the acquisition of a shell. The explosive diversification of mineralized cephalopods in the Ordovician may have an understated Cambrian 'fuse'.

See also:

Bengtson, S. A little Kraken wakes, Nature, 465, 427-428, (27 May 2010) | doi:10.1038/465427a

Moskvitch, K. Mystery fossil is ancestor of squid, BBC News (27 May 2010)

Taylor, C. Nectocaris: Largely Irrelevant to Cephalopods? Catalogue of Organisms (27 May 2010)

One only has to visit a tropical rainforest to discover a world filled with abundant treasures. It is entirely natural for people to want to protect these regions from any threat. Climate change has been perceived as a threat: cooler climates do not support tropical ecozones - but what about warmer climates? Concerns have been raised about plants being unable to adapt to the heat, and there are potential dangers of rainfall reductions. Geological research has revealed a remarkable period of Earth history at the Paleocene-Eocene Boundary, a very warm period known as the Paleocene-Eocene Thermal Maximum (PETM). Although this has been much studied, little is known of the way the tropics responded to high temperatures globally (temperatures rose by about 5 degrees C) and to higher levels of carbon dioxide (perhaps 2.5 times the present level). One point that is agreed is that this rise in global temperatures was geologically rapid: "one of the most abrupt global warming events of the past 65 million years". New research concludes that, fat from being compromised by heat stress, the tropical regions coped very well.

"Most scientists have assumed that, as carbon dioxide levels increase and the Earth warms, plant species diversity in the rainforests will start to dwindle, with plants unable to adapt to the heat. But a new study suggests that the opposite may be true. In the past, rising atmospheric carbon dioxide and higher temperatures actually drove the evolution of far greater numbers of new rainforest plant species than were wiped out."

Although the study says the Amazon can adapt to a warmer world, it still faces an extreme threat from deforestation. (Image: Gerd Ludwig/Corbis, Source here)

The fieldwork was located in Columbia and Venezuela and led by Carlos Jaramillo, a palaeobiologist at the Smithsonian Tropical Research Institute in Panama, In the late Paleocene, the northern Andes had not been uplifted and most of Central America was still underwater. Pollen recovered from cores was used to gain an understanding of the plants growing at the time.

"To find out how this ancient climate change affected rainforest plants, Jaramillo and his team analysed fossilized pollen trapped in rock cores from rainforests in Colombia and Venezuela. They spent seven years locating appropriate sites and taking samples, then used a battery of dating techniques to ensure that they were examining cores formed before, during and after the thermal maximum - a relatively narrow time window in geological terms. The results are published this week in Science."

The findings were an eye-opener. The researchers were expecting the abrupt warming event to have had adverse effects. However, Jaramillo is reported as saying: "we didn't find any extinction event [in plants] associated with the increase in temperature, we didn't find that the precipitation decreased". Furthermore, diversity increased.

"Although some plant species disappeared, many more new species arose. That included entire families, suggesting that the increased temperatures and carbon dioxide levels actually boosted biodiversity. "What we found was exactly the opposite of what we were expecting," says Jaramillo. "The diversity of the tropical forest increased really fast over a very short amount of time.""

With hindsight, the research outcomes are not so surprising. The authors point out in their paper that "Greenhouse experiments have shown that high levels of CO2 together with high levels of soil moisture improve the performance of plants under high temperatures, and it is possible that higher Paleogene CO2 levels contributed to their success." Fieldwork undertaken in forests has documented increased rates of growth that correlate with increased CO2 concentrations in the atmosphere (go here). The implication is that tropical forests are not as fragile and vulnerable to climate change as many have suggested.

"Indeed, it is possible that rainforest families in general, which have been present in the Neotropics since the Paleocene, have the genetic variability to cope with high temperatures, CO2, and rainfall."

Whilst these conclusions have primary applications in the fields of ecology and the environment, this blog is written to point out the relevance for a design-orientated perspective on the natural world. The clue is in the concept of "genetic variability" that enables animals and plants to adapt to environmental change. Within the Design paradigm, animals and plants are designed to adapt because the world's environments experience change. (Speciation, however, can often lead to a loss of genetic variability, which is why some species reach a state where environmental change threatens them with extinction.) This paradigm expects negative feedback mechanisms to be dominant in ecological systems (as pointed out here and here) so that perturbed systems are restored to an equilibrium state.

There is an important application to all this. Design thinking is relevant to many contemporary issues affecting human societies and the world's environments. I should add that there is no party line on such issues, and every view expressed is ultimately a personal view. Climate models have been developed that incorporate significant positive feedback mechanisms - allowing them to predict avalanche scenarios (whether heating or cooling). This has been accompanied by a strong emphasis on the fragility of the Earth's ecosystems - with consequent apocalyptic scenarios much loved by the media. These emphases have led to the politicisation of science, with climate scientists and many others advocating the expenditure of large sums of money to "save the planet". A design perspective allows us to look at the scientific evidence more dispassionately - and there are good reasons for rejecting climate models with large positive feedback parameters. It also allows us to have more confidence in the self-regulating character of the natural world. We recognise that climate change has always been an aspect of history, so adaptation to a changing world is the way forward.

Having said this, there is no doubt that human activity is affecting the Earth's ecozones in a damaging way. The biggest threat to tropical rainforests is not climate change but unmanaged logging. Governments are often complicit in this, and consumers are at fault whenever wood is purchased without any evidence that is from a managed forest source. Instead of blaming the consumption of fossil fuels, those concerned about tropical rainforests would do well to ensure the wood they purchase has the FSC trademark (or similar).

"Jaramillo believes that there is a more pressing threat to the diversity of tropical rainforests. "Deforestation is the real enemy," he says, "not the increase in temperature and carbon dioxide." "

Effects of Rapid Global Warming at the Paleocene-Eocene Boundary on Neotropical Vegetation
Carlos Jaramillo, Diana Ochoa, Lineth Contreras, Mark Pagani, Humberto Carvajal-Ortiz, Lisa M. Pratt, Srinath Krishnan, Agustin Cardona, Millerlandy Romero, Luis Quiroz, Guillermo Rodriguez, Milton J. Rueda, Felipe de la Parra, Sara Moron, Walton Green, German Bayona, Camilo Montes, Oscar Quintero, Rafael Ramirez, German Mora, Stefan Schouten, Hermann Bermudez, Rosa Navarrete, Francisco Parra, Mauricio Alvaran, Jose Osorno, James L. Crowley, Victor Valencia, and Jeff Vervoort.
Science, 330, 12 November 2010: 957-961

Abstract: Temperatures in tropical regions are estimated to have increased by 3 [deg] to 5[deg]C, compared with Late Paleocene values, during the Paleocene-Eocene Thermal Maximum (PETM, 56.3 million years ago) event. We investigated the tropical forest response to this rapid warming by evaluating the palynological record of three stratigraphic sections in eastern Colombia and western Venezuela. We observed a rapid and distinct increase in plant diversity and origination rates, with a set of new taxa, mostly angiosperms, added to the existing stock of low-diversity Paleocene flora. There is no evidence for enhanced aridity in the northern Neotropics. The tropical rainforest was able to persist under elevated temperatures and high levels of atmospheric carbon dioxide, in contrast to speculations that tropical ecosystems were severely compromised by heat stress.

See also:

Milton, J. Rapid warming boosted ancient rainforest, Nature News, 11 November 2010 | doi:10.1038/news.2010.604

A key concept for Darwinism is adaptation. Traits are identified that confer survival and reproduction advantages to an organism. These traits are supposed to experience selection pressures that drive adaptive change and speciation. Consequently, traits are of central importance for theories of evoplutionary transformation, as is also time. However, when contemplating the flowering plants, even Darwin found them difficult to reconcile with his theory. Writing to J.D. Hooker in 1879, he described the evolutionary success of angiosperms as "an abominable mystery". He was troubled by the abrupt origin and extraordinarily rapid diversification of flowering plants in the mid-Cretaceous.

"The answer to whether any of the above traits are consistent predictors of diversity of a given rate of lineage growth depends more upon geographical rather than biological traits, such as geographical extent (i.e., total area occupied by a clade) and climate. Others have suggested that neither geographical nor biological traits determine diversification on their own but rather certain traits (or combinations thereof) may stimulate diversification within a particular geographical context."

Darwin freely acknowledged weaknesses in his case for evolution by natural selection (Source here).

If branching speciation, as illustrated in Darwin's On the Origin of Species, and if there are no limits to the number of species possible (i.e. gradualism reigns), then a broad prediction can be made that the number of species within a clade will increase with clade age. A recent analysis of all families of flowering plants has looked for correlations like this but has failed to confirm this particular trend. Even allowing for statistical variations from the predicted pattern, the conclusion to be drawn is that clade age is no guide to species diversity.

"Drs. Jana Vamosi and Steven Vamosi of the Department of Biological Sciences have found through extensive statistical analysis that the size of the geographical area is the most important factor when it comes to biodiversity of a particular flowering plant family. The researchers were looking at the underlying forces at work spurring diversity - such as why there could be 22,000 varieties of some families of flowers, orchids for example, while there could be only forty species of others, like the buffaloberry family. In other words, what factors have produced today's biodiversity?"

The research considered all the 409 angiosperm families and amassed data on species richness. Four putative key traits were documented: growth form, fruit type, sexual system and floral symmetry. In addition, the researchers recorded the geographical range of the lineage and the area potentially available for expansion (based on an ecozone classification of biogeographical realms). Phylogenetic relationships were based on published angiosperm family trees and best estimates of their age of origin.

"In total, the procedures used here attempt to incorporate our broadest knowledge of angiosperm systematics to produce the most comprehensive phylogenetic hypothesis."

For people interested in the details of angiosperm diversity, there are some really interesting findings, including useful analyses of tropical ecozones. Our purpose here, though, is to focus on the main findings: species richness is primarily dependent on the geographical area colonised.

"Our analyses reveal that available area for expansion is the most critical determinant of increased diversification in flowering plants, followed by zygomorphy, as revealed by model-averaged estimates. Our best models consistently incorporated these features, explaining up to 51% of the variation in species richness. Age explained little of the variation in species richness, indicating diversity-dependent diversification consistent with previous studies. There was no indication that particular trait combinations, rather than isolated traits, lead to higher diversification rates."

The findings of this study are not out of step with other recent research. Vamosi and Vamosi refer to similar conclusions relating to passerine birds (published in 2006). Land vertebrates are discussed here, drawing the same conclusions. The Darwinian scenario of evolution by natural selection acting on inheritable variations is really a hypothesis that is failing to be validated by these analyses of data. Instead, we are witnessing a 'colonisation' theme emerging, in which animal and plant orders/families experience radiations influenced primarily by geography (and ecology).

"We find that several key traits are associated with species richness and geographical extent but that their effects are best seen when accounting for ecoregion area. These constraints on the 'carrying capacity' of a lineage are emerging as critically important in disparate lineages and placing the most severe bounds on the species richness of a lineage. Geography, thus, determines the species richness of a clade far more than age as lineages rapidly expand and diversify upon a landscape. Certain traits (herbaceousness and tropicality) encourage diversification by expanding the size of the landscape upon which diversification occurs. Once the landscape is 'full' of members of a particular family with a characterizing adaptation, speciation rates decline (or extinction rates increase) leaving both medium-aged and old-aged lineages with equivalent species richness."

For those of us who have questioned the efficacy of the Darwinian mechanisms so prominently promoted in textbooks, these new biodiversity studies are very interesting. They are opening the door for new perspectives on life's history - away from Darwinian adaptationism towards colonisation accompanied by relatively rapid diversification. The fossil record has never provided support for Darwinian transformation, but it does offer some fascinating scenarios of responses to global ecological change: abrupt appearance followed by rapid diversification and colonisation. Recent blogs exploring these issues have considered photosynthesizing plant communities in the late Precambrian, the first land plants (liverworts), land vertebrates, and planktic foraminifera. When these ideas get into the educational curriculum, the tendency to present everything from a Darwinian perspective will be challenged - alternatives are available and they demonstrate a better fit to available data.

Key innovations within a geographical context in flowering plants: towards resolving Darwin's abominable mystery
Jana C. Vamosi and Steven M. Vamosi
Ecology Letters, 13(10), 1270-1279, October 2010 | DOI: 10.1111/j.1461-0248.2010.01521.x

Abstract: Elucidating factors associated with diversification have been attempted in lineages as diverse as birds, mammals and angiosperms, yet has met with limited success. In flowering plants, the ambiguity of associations between traits and diversification has sparked debate since Darwin's description of angiosperm diversification as an 'abominable mystery'. Recent work has found that diversification is often diversity-dependent, suggesting that species richness depends on geographical area available more than on traits or the time available to accumulate species. Here, we undertake phylogenetic generalized least squares analyses that jointly examine the effects of age, ecoregion area and four ecological traits on diversification in 409 angiosperm families. Area explained the most variation, dwarfing the effect of traits and age, suggesting that diversity-dependent diversification is controlled by ecological limits. Within the context of area, however, traits associated with biotic pollination (zygomorphy) exhibited the greatest effect, possibly through the evolution of specialization.

See also:

Toward resolving Darwin's 'abominable mystery', EurekAlert (16 September 2010).

Stephen Hawking has achieved the status of 'celebrity scientist'. He writes books that sell well and has both presented and performed in television series. His latest book, The Grand Design, co-authored with Leonard Mlodinow, has been reviewed widely by both popular press and scientific journals. According to Michael Turner, who wrote the Nature review, these authors:

"offer a brief but thrilling account of some of the boldest ideas in physics - including M-theory and the multiverse - and what these have to say about our existence and the nature of the Universe."

"How do we know that the reality we perceive is true?" - or are we like fish seeing the world from a bowl? (Graphic by Barron Storey, source here).

The media appeared to be stimulated primarily by the claim that physics has made God redundant. "God is unnecessary, science can explain the universe without the need for a creator" (BBC News), "Why God Did Not Create the Universe. There is a sound scientific explanation for the making of our world - no gods required." (Wall Street Journal). The Guardian responded by conducting a poll among its readers, asking the question: "Is physicist Stephen Hawking right that physics, not God, created the universe?" This theme is also picked out in the Nature review: "No miracle in the Multiverse". Some might find the argument to be artificially polarised - for did not the pioneers of science link the existence of laws of nature with the reality of a supreme Lawgiver? More recent research has unearthed evidence for the "fine-tuning" of the Cosmos, so the evidences of design have become more prominent with time. Hawking and Mlodinow recognise this when they write:

"Newton believed that our strangely habitable solar system did not "arise out of chaos by the mere laws of nature." Instead, he maintained that the order in the universe was "created by God at first and conserved by him to this Day in the same state and condition." The discovery recently of the extreme fine-tuning of so many laws of nature could lead some back to the idea that this grand design is the work of some grand Designer."

This brings us to the heart of the argument presented by Hawking and Mlodinow: they are endorsing M-theory and the Multiverse cosmological model. This is how Turner puts it:

"In searching for the holy grail, Hawking and others pinned their hopes first on super-gravity and then on string theory. Both are now seen as different regimes of a grander mathematical framework called M-theory, where M is yet to be determined - is it master, miracle or mirage? M-theory unifies gravity with the other fundamental forces (weak and strong nuclear and electromagnetism), predicts seven additional dimensions of space and suggests that space and time might be emergent phenomena rather than fundamental. It is exciting and important, but much of it remains to be explored."

Using M-theory, cosmologists have suggested that our universe is but one of a vast number of universes, all with different physics and with different life-histories. We happen to be in one that has the parameters that favour life. The fine tuning is not by design, but by chance. When you have an infinity of options, anything is theoretically possible! Hawking and Mlodinow explain it this way:

"As recent advances in cosmology suggest, the laws of gravity and quantum theory allow universes to appear spontaneously from nothing. Spontaneous creation is the reason there is something rather than nothing, why the universe exists, why we exist. It is not necessary to invoke God to light the blue touch paper and set the universe going. Our universe seems to be one of many, each with different laws. That multiverse idea is not a notion invented to account for the miracle of fine tuning. It is a consequence predicted by many theories in modern cosmology. If it is true it reduces the strong anthropic principle to the weak one, putting the fine tunings of physical law on the same footing as the environmental factors, for it means that our cosmic habitat - now the entire observable universe - is just one of many. Each universe has many possible histories and many possible states. Only a very few would allow creatures like us to exist. Although we are puny and insignificant on the scale of the cosmos, this makes us in a sense the lords of creation."

Some of us will continue to think that the multiverse advocates are driven by a theological agenda: the need to account for the miracle of fine tuning. The theories of modern cosmology are being selected by intelligent agents: they have other options. But atheism is driving these agents to find responses to the strong evidences of design which are staring them in the face. This blog is arguing that they are on a road that leads to the destruction of all that we value within science. The first casualty is testability and the falsification criterion. This is where Turner finds a problem (and for more on this point, John Horgan's blog is worth reading):

"The multiverse is possibly the most important idea of our time, and may even be right, but it gives me a headache. Is it science if we cannot test it? The different patches are incommunicado, so we will never be able to observe them. The multiverse displaces rather than answers the question about choice and who chooses, and does not explain why there is something rather than nothing."

Secondly, the concept of realism in science is sacrificed. This is the focus of the article Hawking and Mlodinow wrote for Scientific American. In the quest for a theory of everything (that explains our Cosmos), they have adopted a theory with a seemingly infinite number of solutions. M-theory never leads to a unique set of equations. Every implementation of the theory is accompanied by its own dependent reality. Consequently, it does not make sense to talk of what "reality" actually is.

"In our view, there is no picture- or theory-independent concept of reality. Instead we adopt a view that we call model-dependent realism: the idea that a physical theory or world picture is a model (generally of a mathematical nature) and a set of rules that connect the elements of the model to observations. According to model-dependent realism, it is pointless to ask whether a model is real, only whether it agrees with observation. If two models agree with observation, neither one can be considered more real than the other. A person can use whichever model is more convenient in the situation under consideration."

Thirdly, we are presented with a cosmological extrapolation of quantum mechanics. The authors are so captivated by their theoretical models that they have lost touch with the need to constrain their thinking by reference to empirical data. This is from a review in The Economist:

"The main novelty in "The Grand Design" is the authors' application of a way of interpreting quantum mechanics, derived from the ideas of the late Richard Feynman, to the universe as a whole. According to this way of thinking, "the universe does not have just a single existence or history, but rather every possible version of the universe exists simultaneously." The authors also assert that the world's past did not unfold of its own accord, but that "we create history by our observation, rather than history creating us." They say that these surprising ideas have passed every experimental test to which they have been put, but that is misleading in a way that is unfortunately typical of the authors. It is the bare bones of quantum mechanics that have proved to be consistent with what is presently known of the subatomic world. The authors' interpretations and extrapolations of it have not been subjected to any decisive tests, and it is not clear that they ever could be."

Paradoxically, scientific realism has been used to promote atheism against theism, but Hawking is now leading his band of atheists towards a virtual reality dream-world that is generated by the manipulation of mathematical models. With science developing independently of the empirical world, realism becoming localised and history becoming a construct of observation, post-modernist thinking reigns supreme. Now it is time for theistic realists to quote Sagan's words with conviction:

"For me, it is far better to grasp the Universe as it really is than to persist in delusion, however satisfying and reassuring." (Carl Sagan, The Demon-Haunted World (1995) Chapter 1)

No miracle in the Multiverse
Michael Turner
Nature, 467, 657-658 (7 October 2010) | doi:10.1038/467657a

1st paragraph: Despite publicity to the contrary, The Grand Design does not disprove the existence of God. Science has not had much new to say about God since mathematician Pierre-Simon Laplace remarked to Napoleon that he had no need for "that hypothesis" when asked why he had neglected the deity in his treatise Mecanique celeste (Celestial Mechanics, 1799-1825).

The Elusive Theory of Everything
Stephen Hawking and Leonard Mlodinow
Scientific American, October 2010.

1st paragraph: A few years ago the city council of Monza, Italy, barred pet owners from keeping goldfish in curved fishbowls. The sponsors of the measure explained that it is cruel to keep a fish in a bowl because the curved sides give the fish a distorted view of reality. Aside from the measure's significance to the poor goldfish, the story raises an interesting philosophical question: How do we know that the reality we perceive is true?

See also:

Lennox, J., As a scientist I'm certain Stephen Hawking is wrong. You can't explain the universe without God. The Daily Mail, 3rd September 2010.

Tyler, D. The Metaphysics of Multiverse Theory, ARN Literature Blog (20 November 2008).

According to Massimo Pigliucci and Maarten Boudry, the widespread use of machine-information metaphors is unfortunate and misleading. They complain about textbooks that develop metaphors to a considerable level of detail. As an example, they cite Alberts, who is often quoted for his analogy between a cell and a "miniature factory, complete with assembly lines, messengers, transport vehicles, etc." Another machine metaphor they dislike is that of the genome as a "blueprint", notably in the hype surrounding the Human Genome Project. Whilst these analogies are widely held within the scientific community and by educators, the main target of Pigliucci and Boudry's paper appears to be intelligent design:

"The analogy between living organisms and man-made machines has proven a persuasive rhetorical tool of the ID movement. In fact, for all the technical lingo and mathematical 'demonstrations', in much of their public presentations it is clear that ID theorists actually expect the analogies to do the argumentative work for them. In Darwin's Black Box, Behe takes Alberts' machine analogy to its extreme, describing the living cell as a complicated factory containing cargo-delivery systems, scanner machines, transportation systems and a library full of blueprints."

From the Editorial of Molecular Cell (October 2010): "Looking at a textbook picture of a cell, it all seems perfectly serene within, like a bird's eye view of a beautiful city. Zooming in close, however, a much more dynamic image emerges (see the cover). It soon becomes apparent that cells encounter a wide variety of conditions, many of which can induce stresses. These insults must be carefully and appropriately dealt with to maintain the balance that is needed for cell survival and growth." (Source here)

Pigliucci and Boudry rightly trace the emergence of machine metaphors back to, at least, the Middle Ages, and a rise to prominence with the rise of science in the 17th Century. The well-known analogy made by William Harvey is mentioned: the human heart is a pump. The authors also rightly point out that the scientists of the time gave these metaphors some additional substance, because they considered human designs to be imaging designs of the Creator.

"For Newton and many of his contemporaries, the importance of the mechanical conception of nature was greater than the mere term 'metaphor' would suggest, as the development of mechanistic philosophy was itself largely inspired by religious motivations. As Shanks wrote in his account of the history of the design argument, "the very employment of machine metaphors invited theological speculation"."

The authors turn to David Hume to find arguments foreshadowing the demise of design inferences made by the science community. Hume's (1779) Dialogues concerning natural religion is said to expose "several problems with the central analogy". The key thought is that our experience of design is limited to human artifacts, and it is presumptuous to extrapolate from this and make statements about design in general and God's design in particular.

"Hume realized that, at least in some cases, appearances of intelligent design can be deceptive. [. . .] Although Hume does not deny that we can discern similarities between nature and human artifacts, he warns us that the analogy is also defective in several respects. And if the effects are not sufficiently similar, conclusions about similar causes are premature. [. . .] Aware of the fallibility and imperfections of human reasoning, Hume remains highly skeptical about the design inference and the machine analogy, even though he was not able to provide a satisfactory explanation for the appearance of design in nature."

It has always surprised me that David Hume's arguments are considered weighty. The preceding generations of scholars did have a rationale for thinking that there is a relationship between the Creator's design and human design. This was based on the concept of image-bearing, drawn from the Judeo-Christian worldview of the time. If man is made in the image of God, they reasoned, then we design because God designs, and analogies can be drawn between human design and design in nature. Science became, for Johannes Kepler as for them all, "thinking God's thoughts after him".

The real challenge came when the theistic worldview of the pioneers of science was replaced by the deistic worldview of the Enlightenment scholars and the naturalistic worldview of their heirs. Only then does Hume's argument become coherent - and even then, design inferences can still be made at the level of hypotheses that can be tested and potentially falsified.

However, Pigliucci and Boudry suggest these metaphors and analogies are bad science. This needs to be examined closely. They object to the 'cell as a factory' analogy, the 'genome as blueprint' analogy, the 'bacterial flagellum as rotary motor' analogy, and the 'biochemical processes as digital characters in a machine code' analogy. Significantly, all these examples relate primarily to our understanding of how cells function. The major objections to metaphors, however, are linked to theories of development and the need for a viable theory of evolutionary transformation. This gives the clue to the real argument of this paper: Pigliucci and Boudry want to show that the neodarwinian synthesis and genetic reductionism have failed to deliver answers to the real problems of development and evolution, and the popular 'genome as blueprint' metaphor is inhibiting the critical appraisal of existing theory.

The 'blueprint' metaphor receives extensive discussion. They say that wherever it is used, it is always in the context of molecular biology research, not the organism as a whole. They claim that many biologists are concerned about the "hyper-reductionist approach brought about by the molecular revolution". With new discoveries about gene regulation and epigenetics, the blueprint metaphor is looking increasingly limited in its application.

"[N]ew ways of thinking about development and evolution are building a conceptual vocabulary that increasingly distances itself from the machine-information metaphor. [. . .] An answer that is being explored successfully is the idea that the information that makes development possible is localized and sensitive (as well as reactive) to the conditions of the immediate surroundings. In other words, there is no blueprint for the organism, but rather each cell deploys genetic information and adjusts its status to signals coming from the surrounding cellular environment, as well as from the environment external to the organism itself."

The need to move beyond classical genetics is even more pressing when we turn our attention from development to evolution. At best, neodarwinism is perceived to provide relatively few of the answers needed. The "current frontiers of theoretical evolutionary biology" have moved. Further comments on this are found here and here.

An example from Pigliucci and Boudry follows.

"Eva Jablonka and Marion Lamb have gone in some sense a step further and attempted to formalize a broader view of evolutionary change, which depends on the existence of not one but four mechanisms of inheritance: first, the standard genetic system; second, a panoply of epigenetic heritable effects, based on recently or newly discovered phenomena, such as differential methylation of genes, alterations of chromatin structure, so-called interference RNAs,7 and changes in conformation of proteins (e.g., prions), to mention a few; third, behavioral inheritance, mediated through the ability of some animal species to mimic each other's behavior without having it to be "inscribed" in their genes; and fourth cultural inheritance, which is limited to humans and perhaps a few other species of primates, but which has had an obviously disproportionate effect on the recent history of our planet."

The conclusion of all this is that education and research needs to refocus: away from the molecular revolution which is proving increasingly unproductive.

"The preceding discussion, we argue, shows that the limitations intrinsic in metaphors such as 'genes as blueprints' and the like are not just deleterious for science education - which would be bad enough. They actually misdirect or partially derail thinking about what sort of research programs biologists ought to carry out and how. While there is no question that the "molecular revolution" has been a central and positive development in biology, and indeed in science in general, throughout the second part of the 20th century, it is also becoming increasingly clear that the ultra-reductionist approach inspired and fueled by machine-information metaphors is running out of steam and needs to be replaced with more sophisticated and realistic thinking (a kind of reasonable, or non-greedy reductionism, so to speak). Is it then time to retire metaphors like blueprints and machines, and to seek an alternative way to conceptualize biological organisms, or would it perhaps be better to abandon the use of metaphors in this field altogether?"

Anyone reading the abstract of this paper would think that the "bad science" references relate to ID arguments. However, this is not the focus of their arguments! The authors are actually writing about the failure of the Modern Synthesis to understand both development and the processes of evolutionary transformation. They spend most of their critical discussion on the 'genome as blueprint' metaphor. It may surprise most readers to know that few, if any, ID scholars use the analogy outside the context of protein synthesis within the cell. They do not use this metaphor to suggest that the blueprint comprehends all aspects of reproduction and development. I am familiar with ID scholars questioning genetic-reductionism along the lines followed by Pigliucci and Boudry, and arguing that development needs some information-rich organismally-orientated thinking. Similarly, ID scientists critique the approach of the Modern Synthesis to evolutionary theory in much the same way as Pigliucci and Boudry have done. So there is much common ground here. The main complaint appears to be that ID scientists use metaphors to suggest that natural objects are actually intelligently designed. They are comfortable with the thought that the living world evidences features that bear witness to intelligent agency. They make use of analogies between human designs and natural phenomena because they infer intelligent agency for both categories. However, this has not led to bad science. Allowing that analogies are always partial, there should be no difficulty recognising the immense benefits that have come to science by pursuing this approach. Historical examples are easy to find; some recent examples are here and here and here.

Why Machine-Information Metaphors are Bad for Science and Science Education
Massimo Pigliucci and Maarten Boudry
Science and Education, Online October 2010 | DOI: 10.1007/s11191-010-9267-6

Abstract: Genes are often described by biologists using metaphors derived from computational science: they are thought of as carriers of information, as being the equivalent of "blueprints" for the construction of organisms. Likewise, cells are often characterized as "factories" and organisms themselves become analogous to machines. Accordingly, when the human genome project was initially announced, the promise was that we would soon know how a human being is made, just as we know how to make airplanes and buildings. Importantly, modern proponents of Intelligent Design, the latest version of creationism, have exploited biologists' use of the language of information and blueprints to make their spurious case, based on pseudoscientific concepts such as "irreducible complexity" and on flawed analogies between living cells and mechanical factories. However, the living organism = machine analogy was criticized already by David Hume in his Dialogues Concerning Natural Religion. In line with Hume's criticism, over the past several years a more nuanced and accurate understanding of what genes are and how they operate has emerged, ironically in part from the work of computational scientists who take biology, and in particular developmental biology, more seriously than some biologists seem to do. In this article we connect Hume's original criticism of the living organism = machine analogy with the modern ID movement, and illustrate how the use of misleading and outdated metaphors in science can play into the hands of pseudoscientists. Thus, we argue that dropping the blueprint and similar metaphors will improve both the science of biology and its understanding by the general public.

The earliest macrofossils of plants occur in the Silurian Period of Earth history. However, palynology (the study of plant spores, pollen and particulate organic matter in rocks) has pushed the history of plants back to the Middle Ordovician. Newly reported work has documented spores in strata that are dated 8-12 Ma earlier that the previous record holder. Both the research paper (Rubinstein et al. 2010) and the commentary (Wellman 2010) present the findings within a framework of evolutionary transformation. Press coverage puts it this way:

"As land plants matured, they evolved from liverworts into mosses, and then into plants known as hornworts and lycopods. Then ferns appeared before seed plants, of which there are many species today, finally evolved."

Liverworts are ideally suited for colonising barren ground (source here)

The concept of evolution as a 'maturing' trend is itself loaded with cultural baggage. People read into the concept all sorts of ideas that are not explicit or implied by the theory of evolution they espouse. However, landscapes mature, as do ecosystems. By employing the word in an ecological way, we can, perhaps, escape from always viewing the fossil record through evolution-tinted glasses.

The Ordovician spores are referred to as cryptospores because they have some unusual features. Wellman lists seven reasons why the spores should be associated with bryophytes in general and liverworts in particular. Interestingly, the research team found fossilised spores from five different types of liverwort, which is evidence of diversification:

"Spores of liverworts are very simple and are called cryptospores," Dr Rubinstein told the BBC. "The cryptospores that we describe are the earliest to date." These spores, dating from between 473 and 471 million years ago, come from plants belonging to five different genera - groups of species. "That shows plants had already begun to diversify, meaning they must have colonised land earlier than our dated samples," said Dr Rubinstein.

To appreciate the ecological significance of the discovery, we need to remind ourselves of the inhospitable environments that existed in the Ordovician. What land plants could conceivably have survived, let alone prosper, when faced with such arid terrains?

"Colonization of the land by plants presumably occurred in a step-wise fashion starting during the Early Paleozoic with plants at a bryophyte, most likely liverwort, grade of organization. It resulted in acceleration of weathering processes and in the formation of modern terrestrial environments, including structured soils and complex microbial communities; it also profoundly affected carbon cycling, changed the atmosphere composition and irreversibly altered climates."

In such environments, plants lacking stems and roots have significant advantages. Liverworts were able to colonise the land. The lack of a good soil is no disadvantage to a plant without roots, although they do have structures to anchor them to the ground and to absorb water. Their ability to survive both droughts (desiccation up to 90% of water content) and water-logged periods is an asset. The complex process of photosynthesis allows these plants to gain whet they needed to survive and multiply. "Bryophytes assist in the stabilisation of soil crust by colonising bare ground and rocks, and are essential in nutrient recycling, biomass production, and carbon fixing." (source here)

On ecological grounds, the plants that grew in the Ordovician were ideally suited to initiating the colonisation process. They were not there because they were primitive (because there are plenty of complexities if we look for them) but because they were pioneers in the colonisation process. Furthermore, although there is evidence of diversification, the message we need to take home is one of stasis. Having established diversity, the authors of the research paper are constrained to comment that this same diversity is apparent at higher stratigraphical levels. It would appear that diversification was accompanied by stasis. This is not a story of macroevolutionary transformation, but of variations within a basic type. Today there are over 6,000 liverwort species: there is plenty of evidence for diversification, but all of it is within the Liverwort group.

"The assemblage described here includes five cryptospore genera. Both from morphological and systematic points of view, this Dapingian assemblage is not different from younger cryptospore occurrences, including Aeronian (Early Silurian, c. 439-436 Ma) assemblages. This seems to indicate that the evolutionary rate of the earliest embryophytes was extremely low, or that selective pressures did not act on the morphology of propagules."

Early Middle Ordovician evidence for land plants in Argentina (eastern Gondwana)
C. V. Rubinstein, P. Gerrienne, G. S. De La Puente, R. A. Astini, P. Steemans.
New Phytologist (October 2010) 188(2): 365-369 | doi: 10.1111/j.1469-8137.2010.03433.x

Summary: The advent of embryophytes (land plants) is among the most important evolutionary breakthroughs in Earth history. It irreversibly changed climates and biogeochemical processes on a global scale; it allowed all eukaryotic terrestrial life to evolve and to invade nearly all continental environments. Before this work, the earliest unequivocal embryophyte traces were late Darriwilian (late Middle Ordovician; c. 463-461 million yr ago (Ma)) cryptospores from Saudi Arabia and from the Czech Republic (western Gondwana). Here, we processed Dapingian (early Middle Ordovician, c. 473-471 Ma) palynological samples from Argentina (eastern Gondwana). We discovered a diverse cryptospore assemblage, including naked and envelope-enclosed monads and tetrads, representing five genera. [snip]

See also:

Wellman, C.H. The invasion of the land by plants: when and where? New Phytologist, (October 2010) 188(2): 306-309 | DOI: 10.1111/j.1469-8137.2010.03471.x

Walker, M. Fossils of earliest land plants discovered in Argentina, BBC News, 12 October 2010.

The archetypal image of Neanderthals has been one that reinforced the Darwinian story of human evolution. A Washington Post story puts it like this: "Early study of Neanderthals described them as very hairy, brutish, unable to talk or walk like more-modern humans." Although things have changed slowly, media presentations have continued to create an impression that does not differ much from this description. However, the evidence for their humanity has accumulated rather rapidly in recent years, and the past month has seen two significant additions to the literature. A Wired Science report introduces one of these studies like this:

"For decades, Neanderthal was cultural shorthand for primitive. Our closest non-living relatives were caricatured as lumbering, slope-browed simpletons unable to keep pace with nimble, quick-witted Homo sapiens. However, anthropologists have found evidence in recent years suggesting considerable Neanderthal sophistication, and not only in tool-making and hunting, but in their ability to feel [i.e. to show compassion]."

It is time to wear the t-shirt (Source here)

The first paper is concerned with the role of emotions in social relationships and re-appraises the archaeological record of Neanderthals and other Palaeolithic peoples. A summary is provided by Penny Spikins in an interview with Wired.

"We look in the archaeological record for evidence of individuals who were sick, and not able to care for themselves. We see that in early Homo, and by the time we get to Neanderthals, that kind of record becomes much more extensive. Take the "Old Man of Shanidar". He had had degenerative deformities in the base of his legs, would have had difficulty walking, and had a crushing injury to his cranium, so he was probably blind in his left eye. The bones show those injuries occurred when he was adolescent, and he lived to 40. He was probably looked after for 25 to 30 years, which implies that it wasn't just one person looking after him, but several. Most of our Neanderthal skeletons show some evidence of having been looked after for their injuries. And in the age of Neanderthals, you also start to see evidence of deliberate burials and funerary rites. That means a shared feeling."

The other study is from Julien Riel-Salvatore, who has come to realise that the explanations given to evidences of Neanderthal technology and cultural artefacts is flawed. It has been said that Neanderthals gained 'modern' tools and ornaments through contact with groups of migrating Homo sapiens. The thinking was that Neanderthals could not have done it on their own - they lacked creativity. However, by studying a group of Neanderthals that lived separately from Homo sapiens, the picture changes dramatically.

The findings by anthropologist Julien Riel-Salvatore challenge a half-century of conventional wisdom maintaining that Neanderthals were thick-skulled, primitive 'cavemen' overrun and outcompeted by more advanced modern humans arriving in Europe from Africa. "Basically, I am rehabilitating Neanderthals," said Riel-Salvatore, assistant professor of anthropology at UC Denver. "They were far more resourceful than we have given them credit for."

The research has involved an analysis of Uluzzian archaeological sites throughout southern Italy, and Riel-Salvatore has come to the conclusion that the inhabitants responsible for the artefacts were Neanderthals who developed their own unique blend of "projectile points, ochre, bone tools, ornaments".

Such innovations are not traditionally associated with Neanderthals, strongly suggesting that they evolved independently, possibly due to dramatic changes in climate. More importantly, they emerged in an area geographically separated from modern humans. "My conclusion is that if the Uluzzian is a Neanderthal culture it suggests that contacts with modern humans are not necessary to explain the origin of this new behavior. This stands in contrast to the ideas of the past 50 years that Neanderthals had to be acculturated to humans to come up with this technology," he said. "When we show Neanderthals could innovate on their own it casts them in a new light. It 'humanizes' them if you will."

The picture that is emerging, reinforced and validated by the newly reported research, is that Neanderthals are somewhat different, but nevertheless equal. The evolutionary story is misleading and it needs to be discarded. The comments of Riel-Salvatore are spot on:

"The fact that Neanderthals could adapt to new conditions and innovate shows they are culturally similar to us," he said. "Biologically they are also similar. I believe they were a subspecies of human but not a different species." [. . .] "It is likely that Neanderthals were absorbed by modern humans," he said. "My research suggests that they were a different kind of human, but humans nonetheless. We are more brothers than distant cousins."

A previous blog had the title: Neandertals are part of the human family. Other blogs in this series carried similar messages. Burying the view that Neanderthals were half-wits, Darwinist thinking on the origin of religion, The cognitive skills of Stone Age Man, Images of evolution as secular icons, Walks like a man, talks like a man - is it a man?, and Rethinking Neanderthals. If we are prepared to follow the science, we must move on in our understanding of Neanderthals!

From Homininity to Humanity: Compassion from the Earliest Archaics to Modern Humans
Spikins, P.A.; Rutherford, H.E.; Needham, A.P.
Time and Mind, 3(3), November 2010, pp. 303-325 | DOI: 10.2752/175169610X12754030955977

Abstract: We are increasingly aware of the role of emotions and emotional construction in social relationships. However, despite their significance, there are few constructs or theoretical approaches to the evolution of emotions that can be related to the prehistoric archaeological record. Whilst we frequently discuss how archaic humans might have thought, how they felt might seem to be beyond the realm of academic inquiry. In this paper we aim to open up the debate into the construction of emotion in early prehistory by proposing key stages in the emotional motivation to help others; the feeling of compassion, in human evolution. We review existing literature on compassion and highlight what appear to be particularly significant thresholds in the development of compassion for human social relationships and the evolution of the human mind.

A Niche Construction Perspective on the Middle-Upper Paleolithic Transition in Italy
Julien Riel-Salvatore
Journal of Archaeological Method and Theory, published online 19 August 2010 | DOI 10.1007/s10816-010-9093-9

Abstract: This paper presents an overview of the Middle-Upper Paleolithic transition in Italy in light of recent research on the Uluzzian technocomplex and on the paleoecological context of the transition. Drawing on the realization that human niche construction can be documented in the pre-agricultural archaeological record, niche construction theory is used as a conceptual framework to tie together facets of the behavioral, biological, and ecological dimensions of the transition interval into formal models of their interaction over time and in diverse contexts. Ultimately, this effort shows how foragers of the transitional interval in the Italian peninsula were active agents in shaping their evolutionary history, with consequences of some adaptive systems being felt only much later and directing the forces responsible for the ultimate disappearance of the Mousterian and Uluzzian technocomplexes in favor of the proto-Aurignacian industry, the exact nature of which clearly appears to vary on a regional level.

See also:

Neanderthals more advanced than previously thought, EurekAlert, (September 21, 2010)

Drosophila melanogaster is a model organism for the study of genetics and some laboratory populations have been bred for different life-history traits over the course of 30 years. Professor Michael Rose, of UC Irvine, began breeding flies with accelerated development in 1991 (600 generations ago). Doctoral student Molly Burke compared the experimental flies with a control group on a genome-wide basis. This is significant because it is the first time such a study of a sexually reproducing species has been done. Burke examined specific genes and also obtained "whole-genome resequencing data from Drosophila populations that have undergone 600 generations of laboratory selection for accelerated development." The results are noteworthy on several counts:

"For decades, most researchers have assumed that sexual species evolve the same way single-cell bacteria do: A genetic mutation sweeps through a population and quickly becomes "fixated" on a particular portion of DNA. But the UCI work shows that when sex is involved, it's far more complicated. "This research really upends the dominant paradigm about how species evolve," said ecology and evolutionary biology professor Anthony Long, the primary investigator.

Knowing the genome sequence of Drosophila has opened new avenues of research (Source here)

The researchers were looking for the fixation of positive mutations within the genome and within the whole population. This is referred to using the term "selection sweep". When it occurs, the new mutation at a base pair (a novel single nucleotide polymorphism or SNP) not only experiences replication to be transmitted to the descendants of the organism, but the gene pool of variation is effectively swept clean as the new mutation becomes dominant in the whole population. However, such sweeping was conspicuous by its absence.

"Recent research on evolutionary genetics has focused on classic selective sweeps, which are evolutionary processes involving the fixation of newly arising beneficialmutations. In a recombining region, a selected sweep is expected to reduce heterozygosity at SNPs flanking the selected site. [. . .] Notably, we observe no location in the genome where heterozygosity is reduced to anywhere near zero, and this lack of evidence for a classic sweep is a feature of the data regardless of window size."

The paper considers a range of possible explanations for the evidence obtained. First: "Classic sweeps may be occurring, but have had insufficient time to reach fixation." Second: "selection in these lines may generally act on standing variation, and not new mutations." Third, "selection coefficients associated with newly arising mutations are not static but in fact decrease over time." No conclusion is reached regarding these various options.

"Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles. This is notable because in wild populations we expect the strength of natural selection to be less intense and the environment unlikely to remain constant for ~600 generations. Consequently, the probability of fixation in wild populations should be even lower than its likelihood in these experiments. This suggests that selection does not readily expunge genetic variation in sexual populations, a finding which in turn should motivate efforts to discover why this is seemingly the case."

This empirical work is worth noting on two counts. First, we are here considering a mechanism that is central to Darwinian evolution. Positive natural selection of hereditable variation is the key (we are informed) to understanding how descent with modification occurs. However, the first set of empirical data relating to a sexually reproducing species does not confirm that modification works this way. This is why Long's comment is worth repeating: "This research really upends the dominant paradigm about how species evolve". Many scientists have long suspected that the Darwinian mechanisms are inadequate to account for large-scale transformation - these research findings provide empirical support for such doubts.

The other reason for taking an interest in this research is that the Darwinian paradigm has been widely used in the development of drugs for medical use. Whereas the classical view is that genes have specific functions, the new research supports the growing body of evidence that the norm is for genes to have pleiotropic effects. A novel SNP can then be expected to have not one, but many, effects. This has been underplayed by researchers of a darwinian persuasion.

"Based on that flawed paradigm, Rose noted, drugs have been developed to treat diabetes, heart disease and other maladies, some with serious side effects. He said those side effects probably occur because researchers were targeting single genes, rather than the hundreds of possible gene groups like those Burke found in the flies. Most people don't think of flies as close relatives, but the UCI team said previous research had established that humans and other mammals share 70 percent of the same genes as the tiny, banana-eating insect known as Drosophila melanogaster."

Genome-wide analysis of a long-term evolution experiment with Drosophila
Molly K. Burke, Joseph P. Dunham, Parvin Shahrestani, Kevin R. Thornton, Michael R. Rose and Anthony D. Long.
Nature, 467, 587-590, (30 September 2010) | doi: 10.1038/nature09352 (preprint)

Experimental evolution systems allow the genomic study of adaptation, and so far this has been done primarily in asexual systems with small genomes, such as bacteria and yeast. Here we present whole-genome resequencing data from Drosophila melanogaster populations that have experienced over 600 generations of laboratory selection for accelerated development. Flies in these selected populations develop from egg to adult ~20% faster than flies of ancestral control populations, and have evolved a number of other correlated phenotypes. On the basis of 688,520 intermediate-frequency, high-quality single nucleotide polymorphisms, we identify several dozen genomic regions that show strong allele frequency differentiation between a pooled sample of five replicate populations selected for accelerated development and pooled controls. On the basis of resequencing data from a single replicate population with accelerated development, as well as single nucleotide polymorphism data from individual flies from each replicate population, we infer little allele frequency differentiation between replicate populations within a selection treatment. Signatures of selection are qualitatively different than what has been observed in asexual species; in our sexual populations, adaptation is not associated with 'classic' sweeps whereby newly arising, unconditionally advantageous mutations become fixed. More parsimonious explanations include 'incomplete' sweep models, in which mutations have not had enough time to fix, and 'soft' sweep models, in which selection acts on pre-existing, common genetic variants. We conclude that, at least for life history characters such as development time, unconditionally advantageous alleles rarely arise, are associated with small net fitness gains or cannot fix because selection coefficients change over time.

See also:

Scientists Decode Genomes of Precocious Fruit Flies, ScienceDaily (September 19, 2010)

The Michael Reiss saga should not be quickly forgotten. His enforced resignation as the Royal Society's Director of Education in September 2008 was a blot on the history of the Royal Society (see here and here). Yet, after two years, few changes are apparent: Reiss continues to publish his "worldview" perspective on handling creationism in science education (see here) and Royal Society Fellows have continued to talk about irresolvable conflicts at the science/religion interface. It is encouraging, therefore, to find Sylvia Baker formulating a coherent analysis of the conflict and proposing a research agenda to inform future discussion of the issues.

"The controversy, resulting as it did in such serious consequences, raises many issues and concerns. This article will seek to address three of them. First will be considered the subject of the controversy, the teaching of creationism in science classes, second, the status and influence of such bodies as the Royal Society within the science community of the United Kingdom, and third, the question of to what extent the end result was obtained, not by impartial considerations, but rather by an atheistic agenda."

The Purported "NOMA Model" of Science and Religion (Source here)

Fundamental to the controversy is the question: "Is creationism science?" Both the Royal Society and Professor Reiss have declared that evolution is about science and creationism is about religion. They advocate a sphere sovereignty position, also known as NOMA (Stephen Jay Gould's Non-Overlapping MAgisteria). But Reiss recognises that creationism does not accept this position. Creationists have a different worldview, where it makes perfect sense to invoke intelligent design and to say that God's miraculous activity is a necessary part of any explanation of origins. This clash of worldviews is described by Baker in this way:

"The modern creationist movement itself takes a particular approach to the philosophy of science and the influence of world views on the question of origins, as exemplified by publications such as Nancy Pearcey's major work Total Truth: liberating Christianity from its cultural captivity. Schoolchildren who have been influenced by this approach may well have been taught in their homes and churches or mosques that both creation and evolution are essentially philosophical world-view frameworks that operate at the intersection of religion and science."

NOMA has not fared well under the scrutiny of philosophers. The main advocates today are scientists: mostly, but not exclusively, of an atheist persuasion. Baker quotes Professor Steve Fuller sympathetically:

"All theories with the grand explanatory aspirations of creationism or evolutionism are based on worldviews that people have believed for reasons other than their scientific payoff. [. . .] The problem here is one of practice, not principle. In particular, there is nothing intrinsically un- or anti-scientific about creationist ideas. On the contrary, creationist assumptions, especially when God is understood as an intelligent designer, have deeply informed the history of the science that both theists and atheists continue to promote today."

One of the worst aspects of this controversy is that the critics of Reiss failed to base their arguments on any empirical evidence. Their hostility was philosophical and dogmatic. Reiss, however, was responding to evidence drawn from the classroom. Baker refers to three surveys: one of students being taught in independent and state-maintained schools and two others in Christian schools.

"The three studies, taken together, suggest that creationist beliefs among pupils lead to 'an easing of the human spirit', exactly as Astley first predicted (2005, p. 49) when the educational setting is coherent with the religious basis of the pupil's life but that the opposite is true when the setting is hostile and debate is not permitted. In both settings the pupils had been made aware that a theory of origins exists which eliminates the need for a Creator and which is held by the majority of modern scientists. It seems to be the educational setting, not the creationist beliefs themselves, which is leading to an anguished mental state for thousands of young people."

Returning to the issue of philosophical opposition to Reiss, a survey of members of the US National Academy of Sciences shows that 85% are atheists. One of Reiss's atheist critics said that 90% of Fellows of the Royal Society would agree with the criticisms. This suggests a further research agenda to Baker:

"What exactly do [the nation's scientists] believe on this issue and are their views accurately reflected in the pronouncements of such major bodies as the Royal Society? What are their religious beliefs and how do those beliefs relate to their view of what science is?"

Happily, others are saying similar things whilst coming from a different perspective. A current example is an article by Matthew Reisz with the title The dogma delusion (The Times Higher, 23 September 2010). Based on these considerations, Baker writes:

"it is possible that Michael Reiss was sacrificed on the altar of the god of scientific atheism. Journalist Melanie Phillips has no doubt about the matter:
'Totalitarian atheism has taken another scalp. Michael Reiss has been forced out - for daring to suggest that children should be taught to discuss alternative views and subject them to the scrutiny of empirical reasoning.' "

Though regrettable, the forced resignation of Michael Reiss may yet focus attention on matters of great public concern. What is science? Do the beliefs of scientists influence the way they define science? Is NOMA a tool contrived by people with vested interests to manage the interface between science and religion? Baker summarises the issues thus:

"The controversy has been seen to depend on definitions of science and creationism. At the same time, the question of who has the power to define what science is has been raised, as has the possibility that at root the problem is a clash of ideologies, a battle between atheism and religion carried out in the context of science."

Creationism in the classroom: a controversy with serious consequences
Sylvia Baker
Research in Education, Volume 83, Number 1, May 2010, pp. 78-88

First para: On 16 September 2008 the Revd Professor Michael Reiss resigned from his position as Director of Education at the Royal Society. The immediate context of his resignation was the furore created by the media in the wake of an address that he had given on Thursday 11 September 2008 in Liverpool, at the annual Festival of Science organised by the British Association for the Advancement of Science. The story seemed to be of universal interest, with several papers next day devoting full-page spreads to it, under large, eye-catching headings. For example, the Times (12 September 2008) headlined with 'Royal Society and the case for creationism: leading scientists at odds with Government over religious education', claiming that the Royal Society was supporting Professor Reiss in his 'heretical' views, while the Guardian's banner headline on the same day was 'Teach creationism, says top scientist'.

Earlier this year, the work of Nir Goldman and colleagues was noted (here). Using sophisticated computer modeling tools, it was concluded that cometary impacts could generate C-N bonded oligomers that subsequently break apart to form a glycine-containing complex. This research has now been published in Nature Chemistry, resulting in a new flurry of discussion about the shock synthesis of life.

Topographic map of the Moon based on measurements from the Lunar Orbiter Laser Altimeter, showing the boundary between Oceanus Procellarum, a smooth, relatively young mare region on the western nearside (upper right), and the older, more heavily cratered highlands (center and lower left). Colors indicate increasing elevation from blue to red. Both Earth and Moon experienced the effects of impactors. (Source here)

It is known from Stanley Miller's experiments that amino acids can be synthesized in a reducing atmosphere. However, the evidence for such an atmosphere has become less convincing with time - and even a neutral atmosphere means the Miller route for generating amino acids is unproductive. Cometary impacts, however, can make this point irrelevant, as is explained by John Timmer here.

"One of the problems facing origin-of-life research is that building complex organic chemicals requires a reducing environment, but the early Earth's atmosphere is now thought to have been weakly oxidizing. None of this matters as the comet hits. A typical shockwave quickly reaches conditions where the simple compounds break down, liberating hydrogen ions. These create local reducing environments no matter what the atmosphere looks like."

We should note the nature of the computing challenge for the research team. They started with a mixture of water, methanol, ammonia, carbon monoxide and carbon dioxide. Then, as explained by Timmer:

"they ran molecular dynamics simulations of what might happen to a typical cometary mixture as a blazing hot shockwave passed through, and was followed by a rapid decompression. These were pretty elaborate calculations, with femtosecond time resolution, and molecular interactions that considered quantum effects. Simply modeling the decompression that followed a shockwave for 50 picoseconds involved about 80,000 CPU hours. They also reran the model to simulate different speeds and angles of impact, which produce different pressure/temperature combinations within the shockwave that passes through the comet."

Somehow, the leap from glycine (and amino acids in general) to life has become instinctive rather than reasoned. Nature carried a short report with the title: "Origins of life: Shock synthesis". The research however reported a route to synthesise glycine, not life! Chemistry World was overconfident in its headline: "Comet shockwaves helped stimulate life on Earth", but more nuanced with the byline: "Comet strikes could have delivered the necessary ingredients and conditions to stimulate life on Earth". The reputation of science journalism is not helped by these headlines: the idea that it is a small step from amino acids to life is fantasy! We have had many decades of serious research by very dedicated people, and this has revealed an enormous gulf between organic molecules and organic life. For more on this, go here.

Timmer's assessment of the research is probably the best that can be said:

"Right now, most scientists think that life originated in an RNA world, where proteins didn't exist, and amino acids simply acted as co-factors for some key chemical reactions. So this doesn't necessarily help us understand how life first got started. It may, however, provide some insight into how life started using amino acids in the first place, starting it on the road towards the production of proteins. If basic amino acids were plentiful, then evolution might have simply worked with what was already around."

Everyone acknowledges that cometary impacts have more potential to destroy life than to promote it, so it is worth drawing attention to the most recent study of the lunar impact craters greater than 20 km. This research drew on data gathered by the Lunar Orbiter Laser Altimeter, an instrument on board the Lunar Reconnaissance Orbiter spacecraft. The researchers explain: "These data provide a view of the global distribution of impact craters without the observational uncertainties that arose from measurement of craters on images of heterogeneous illumination condition and uneven coverage and quality." Their findings validate the hypothesis that there has been an early and a later impactor population inside the asteroid belt. The authors write: "Furthermore, it places the transition between these two populations at about the time of Orientale Basin, the last large multi-ringed basin thought to have formed ~3.8 billion years ago." The significance of this for abiogenesis advocates is that their thinking about the origin of life must be temporally constrained. They cannot reasonably postulate an origin prior to 3.9 Ga. Writing in The Daily Telegraph, Matthew Moore points out:

"Any life which may have existed on Earth 3.9 billion years ago would have been wiped out in a devastating asteroid strike, new analysis of Moon craters indicates." [. . .] "Earth and its satellite were bombarded with large asteroids during the solar system's "turbulent youth", striking new topographical maps show. The impacts would have been powerful enough to evaporate any water on our planet and destroy any early organisms."

Compare this with some reports of photosynthetic life at 3.8 Ga and with the general acceptance of life by 3.5 Ga. Life was on Earth in the Early Archaean. The resultant time constraints undermine all chance-based scenarios of abiogenesis. This leaves us with law-based explanations (which are totally unable to account for biological information) or design-based explanations. The latter option is the direction where science is leading us.

Synthesis of glycine-containing complexes in impacts of comets on early Earth
Nir Goldman, Evan J. Reed, Laurence E. Fried, I.-F. William Kuo & Amitesh Maiti.
Nature Chemistry, (September 2010) | doi:10.1038/nchem.827

Delivery of prebiotic compounds to early Earth from an impacting comet is thought to be an unlikely mechanism for the origins of life because of unfavourable chemical conditions on the planet and the high heat from impact. In contrast, we find that impact-induced shock compression of cometary ices followed by expansion to ambient conditions can produce complexes that resemble the amino acid glycine. Our ab initio molecular dynamics simulations show that shock waves drive the synthesis of transient C-N bonded oligomers at extreme pressures and temperatures. On post impact quenching to lower pressures, the oligomers break apart to form a metastable glycine-containing complex. We show that impact from cometary ice could possibly yield amino acids by a synthetic route independent of the pre-existing atmospheric conditions and materials on the planet.

See also:

Mitchinson, A. Origins of life: Shock synthesis, Nature, 467, 281, (16 September 2010) | doi:10.1038/467281a

Head, J.W. et al., Global Distribution of Large Lunar Craters: Implications for Resurfacing and Impactor Populations, Science, 329, 17 September 2010: 1504-1507 | DOI: 10.1126/science.1195050

The ability of some insects to imitate the leaves and stems of plants has fascinated collectors and researchers alike. Wings, legs and other body parts can all contribute to a very effective disguise, a phenomenon known as mimesis. There has been speculation, of course, about the adaptive origins of the observed characters, but very little data is available on which to build anything robust. The fossil record is meagre. The earliest example before this year has been the Eocene leaf insect Eophyllium, already fully formed and functional (noted here). It conveyed no evidence to support a gradual transformation model. Since living examples of leaf mimesis relate to angiosperm plants, it has been inferred that leaf mimesis is a trait that post-dates the appearance of angiosperms in the Cretaceous.

"Given the phylogenetic placement of these families and genera among their respective orders, such mimicry of angiosperm models likely appeared subsequent to (rather than along with) the radiation of flowering plants. Accordingly, it has been considered that leaf mimesis is a mid-Cretaceous or younger phenomenon."

However, new research changes this perception. The findings concern lacewings - a group not known for exhibiting leaf mimesis. The fossil specimens come from the late Middle Jurassic, which is significant because this was a period of Earth history before angiosperms appeared and before they became dominant. The plants then were gymnosperms and many of them had pinnate leaves.

"Two extraordinary fossil lacewings, Bellinympha filicifolia [. . .] and Bellinympha dancei [. . .] from the Jiulongshan Formation in northeastern China, preserve wings that are dramatically modified to resemble pinnate leaves. These are the earliest evidence of leaf mimesis and predate Eophyllium by nearly 120 million years. Bellinympha demonstrates that lacewings of the late Middle Jurassic (165 million years ago) already had evolved highly specialized mimicry of pinnate leaves as a strategy for avoiding predators such as contemporaneous mammals, pterosaurs, dinosaurs, birds, spiders, and other predacious insects, suggesting a much richer biotic world in the Mesozoic Era."

The fossil lacewings have wings that resemble the feather-like leaves of mesozoic gymnosperm plants (Credit: Natl Acad. Sci. Source here)

These fossils are not the earliest lacewings, which go back to Permian times. The authors suggest similarities with Holozamites and Nilssonia, which are Cycadales, and with leaves of some cycadophytes. The finds are the earliest known witnesses to leaf mimesis.

"The numerous pinna-like markings on the wing membranes are remarkably similar to the pinnate leaves of Mesozoic Cycadales and Bennettitales: the dark posterior median region of the wing resembles the rachis of the leaf, whereas the oblique stripes resemble the pinnae. Among the two species, B. filicifolia has a more obvious pattern of pinnate leaves due to a darker and better-defined coloration, whereas B. dancei has a more pronounced central rachis-like region, with a similar zigzag shape near the apical area, but the oblique pinna-like stripes are less developed. Pinna-like markings on the forewings imitate contemporaneous pinnate leaves of Cycadales and Bennettitales that are frequently found in the Daohugou strata."

The research has the effect of emphasising the early appearance of specialisation in insects, including the association between insects and their environments. There are already indications that ecosystems were far more complex than previously thought (for example, see here). Lacewings have been lacewings since the Permian, and this example of mimesis so early in their history is suggestive both of a plasticity of form and also of a possible loss of this plasticity over geological time.

"These species reveal a unique pattern that seems to have disappeared in modern insects and adds to the growing body of evidence documenting that the evolution of insects was more complex before the radiation of angiosperms. These enigmatic scenarios of interactions between insects and gymnosperms were lost during the course of evolutionary history and show a more rich association of insects and their surrounding environment in past geological epochs than previously has been surmised."

Initial complexity followed by relative stasis characterises this group of insects. The Nature briefing on this research refers to the authors suggesting "that the biotic world of the Mesozoic period was more complex than previously thought". Darwinian gradualism gets no support from this research. Abrupt appearance, early specialisation and complex ecosystems are all confirmed.

Ancient pinnate leaf mimesis among lacewings
Yongjie Wang, Zhiqi Liu, Xin Wang, Chungkun Shih, Yunyun Zhao, Michael S. Engel, and Dong Ren.
Proceedings of the National Academy of Sciences, Published online before print August 30, 2010 | doi: 10.1073/pnas.1006460107

Abstract: Insects have evolved diverse methods of predator avoidance, many of which implicate complex adaptations of their wings (e.g., Phylliidae, Nymphalidae, Notodontidae). Among these, angiosperm leaf mimicry is one of the most dramatic, although the historical origins of such modifications are unclear owing to a dearth of paleontological records. Here, we report evidence of pinnate leaf mimesis in two lacewings (Neuroptera): Bellinympha filicifolia Y. Wang, Ren, Liu & Engel gen. et sp. nov. and Bellinympha dancei Y. Wang, Ren, Shih & Engel, sp. nov., from the Middle Jurassic, representing a 165-million year-old specialization between insects and contemporaneous gymnosperms of the Cycadales or Bennettitales. Furthermore, such lacewings demonstrate a preangiosperm origin for leaf mimesis, revealing a lost evolutionary scenario of interactions between insects and gymnosperms. The current fossil record suggests that this enigmatic lineage became extinct during the Early Cretaceous, apparently closely correlated with the decline of Cycadales and Bennettitales at that time, and perhaps owing to the changing floral environment resulted from the rise of flowering plants.

In 1996, palaeontologist Mike Benton published a fascinating analysis of tetrapod evolutionary data and concluded: "Competitive replacement has probably played a minor role in the history of tetrapods. In an assessment of the origins of 840 families of amphibians, reptiles, birds, and mammals, fewer than 26%, and probably fewer than 13%, were identified as candidate competitive replacements (CCR's)." The alternative mechanism proposed was adaptation into new habitats. This finding was presented in the paper as bringing a different emphasis to our understanding of speciation than was brought by Darwin:

"A classic view in evolution has been that many successful radiations of plant and animal groups in the Past have been mediated by competitive interactions. Newly successful groups are said to have outcompeted and displaced the previously established organisms, and hence to have demonstrated some progressive or advantageous feature. [. . .] The pattern of radiation of tetrapods, and indeed of many other groups, suggests that it is unlikely that competitive replacement was paramount."

The pattern of evolution of the vertebrates, showing the relative importance of the major groups through time. (Source and further details here)

Moving the clock forward to the present, with the benefit of a more comprehensive database, Benton has repeated the study. The authors say: "This is the first numerical study investigating the link between tetrapod taxonomic and ecological diversity on a global scale." The findings vindicate the 1996 study and the primary driver of diversification is said to be expansion into new ecospace. Competitive pressures are considered to be of limited importance because evidence for direct competition was not been forthcoming in the study. The emphasis was all on expansion:

"The data show multiple lines of evidence for the role of expansion as the main driver of tetrapod diversification: (i) tetrapods have only explored a third of habitable modes of life; (ii) tetrapods have occupied an exponentially increasing number of modes; (iii) ecological diversification has been driven at an increasing rate by the different tetrapod classes; (iv) successively dominant tetrapod classes have increased the maximum rate of mode utilization; and (v) Tetrapoda exhibit ecological incumbency, observed by a limit at which mode utilization decreased, except at times of mass extinction."

This interpretation of the data has been widely reported because it presents a significantly different picture than is found in the textbooks. BBC News carried the tagline: "Charles Darwin may have been wrong when he argued that competition was the major driving force of evolution." The report continued:

"He imagined a world in which organisms battled for supremacy and only the fittest survived. But new research identifies the availability of "living space", rather than competition, as being of key importance for evolution. Findings question the old adage of "nature red in tooth and claw". [. . .] This concept challenges the idea that intense competition for resources in overcrowded habitats is the major driving force of evolution. Professor Mike Benton, a co-author on the study, explained that "competition did not play a big role in the overall pattern of evolution"."

In her blog, Sarda Sahney, the PhD student who conducted the study with colleagues, identified the writer of the BBC report as Howard Falcon-Lang (the significance of this is the subject of comment below). She provides a summary of the take-home message of this research:

"[T]he rich biodiversity we see on Earth today has grown out of expansion, not competition. Darwin cited competition among animals, coined 'survival of the fittest', as a driver of evolution in his book, On the Origin of Species; since then competition has been considered key to having grown Earth's biodiversity. But while competition has been observed on a small scale, (eg. between species), there is little evidence of competition guiding large-scale shifts in biodiversity, such as the dominance of mammals and birds over reptiles and amphibians in today's world. Our new research supports the idea that animals diversified by expanding into empty ecological roles rather than by direct competition with each other."

Consequently, the implication of all this is that we need to do some hard thinking about Darwin's primary mechanism of evolutionary transformation: the natural selection of hereditable variations. The evidence from the fossil record does not support this account of origins. Instead, vertebrate radiations are expansive radiations into ecospace. Die-hard Neodarwinians should sit up and take note of this! However, the reactions of some are to protest about misreading the significance of the research reported. A member of NCSE staff, Steven Newton, wrote a strongly worded piece with the title: Darwin Was Not Wrong--New Study Being Distorted. His first target is the BBC report:

"Science fares poorly in the media. [. . .] When scientific topics are reported, they are consistently misunderstood and spiced-up with such sensationalism that the original significance is contorted beyond all recognition. Such misreporting has happened again--this time involving Charles Darwin and evolution.
A recent paper in the journal Biology Letters, "Links between global taxonomic diversity, ecological diversity and the expansion of vertebrates on land," by Sarda Sahney, Michael Benton, and Paul Ferry, has caused quite a stir. The normally-staid BBC wrote of this paper, "Charles Darwin may have been wrong when he argued that competition was the major driving force of evolution.""

The significance of Howard Falcon-Lang being the writer of the BBC report can now be clarified. Falcon-Lang is a professional scientist who has widely published in peer-reviewed literature. He writes as a scientist, not as a journalist picking up a story second-hand. He knows that the public needs to read both accurate and interesting science. Did he misunderstand the paper? According to Newton: "A press release for the paper noted that when examining large-scale changes in biodiversity, the data suggest: 'Animals diversified by expanding into empty ecological roles rather than by direct competition with each other'. This paper does not argue that Darwin's conception of small-scale competition within species is incorrect. It does not argue that new species arising out of accumulating changes is a flawed concept. It does not argue Darwin was wrong." Newton is the one misreading the paper, which sets out to identify factors relevant to biodiversification (the origin of species). It claims that competition between species, whether small-scale or large-scale, is not relevant to understanding the phenomenon. Darwin was not wrong to say that "small-scale competition within species" is a real occurrence - but he was wrong to think this phenomenon helps explain the origin of species!

In a previous blog, it was noted that sometimes it is OK to say Darwin was wrong. No one minds when it is said that Darwin was wrong about the origin of the domestic chicken. But there is tremendous resistance to any questioning of his more serious errors. This new work documents one of these. No one disputes that Darwin correctly documented competition between breeding communities and between different species. However, what is the evidence that this is relevant to the origin of species? This new research presents solid data showing that other factors govern vertebrate radiations on land. The ideas have been around at least since 1996, and it is now high time for Darwinists to cool their rhetoric and take these scientific findings on board.

Links between global taxonomic diversity, ecological diversity and the expansion of vertebrates on land
Sarda Sahney, Michael J. Benton and Paul A. Ferry
Biology Letters, 2010, 23(4) 544-547 | doi: 10.1098/rsbl.2009.1024

Abstract: Tetrapod biodiversity today is great; over the past 400 Myr since vertebrates moved onto land, global tetrapod diversity has risen exponentially, punctuated by losses during major extinctions. There are links between the total global diversity of tetrapods and the diversity of their ecological roles, yet no one fully understands the interplay of these two aspects of biodiversity and a numerical analysis of this relationship has not so far been undertaken. Here we show that the global taxonomic and ecological diversity of tetrapods are closely linked. Throughout geological time, patterns of global diversity of tetrapod families show 97 per cent correlation with ecological modes. Global taxonomic and ecological diversity of this group correlates closely with the dominant classes of tetrapods (amphibians in the Palaeozoic, reptiles in the Mesozoic, birds and mammals in the Cenozoic). These groups have driven ecological diversity by expansion and contraction of occupied ecospace, rather than by direct competition within existing ecospace and each group has used ecospace at a greater rate than their predecessors.

See also:

Benton, M. J. Testing the roles of competition and expansion in tetrapod evolution. Proceedings of the Royal Society B, 1996, 263, 641-646 | doi:10.1098/rspb.1996.0096

Genome sequencing has allowed families of genes to be mapped across the phyla, and it is presumed that the presence of a specific gene in different animal groups signifies a shared common ancestor. Over the years, it has become apparent that many significant genes are widely shared in the animal kingdom, and this blog is concerned with two more cases recently published.

Pax genes are typically linked to eye development, although they have a variety of other functions. Pax-6 is regarded as a master control gene known to turn on eye development in the arthropoda, the mollusca, and the vertebrata. The new work extends the analysis to a jellyfish.

"Here we have isolated three Pax genes (Pax-A, Pax-B, and Pax-E) from Cladonema radiatum, a hydrozoan jellyfish with elaborate eyes. Cladonema Pax-A is strongly expressed in the retina, whereas Pax-B and Pax-E are highly expressed in the manubrium, the feeding and reproductive organ."

A model for the monophyletic evolutionary origin of all animal eyes (Source here)

The significance is found in the phylogenetic analysis. The vertebrata belong to the chordata, which are deuterostomes. Arthropoda are ecdysozoans, whereas mollusca are lophotrochozoans: these groups are considered to have a common ancestry in the protostomes. The deuterostomes and protostomes have bilateral symmetry and so, it was concluded, the Pax gene originated, at least, with bilateral animals. The new research brings jellyfish into the picture, which are cnidarians having radial symmetry. This pushes the ancestry of Pax genes back before the inferred Cnidaria-Bilateria separation - well into the Precambrian. This is why the authors of the research paper claim that eyes did not evolve independently many times, but that the evidence points to "the monophyletic evolutionary origin of all animal eyes". This means that the regulatory gene controlling the development of highly complex vision systems evolved long before the need for advanced vision systems. Hence the authors offer the distinctly un-Darwinian interpretation of evolution before adaptation:

"We then propose that during the early evolution of animals, distinct classes of Pax genes, which may have played redundant roles at that time, were flexibly deployed for eye development in different animal lineages."

A similar argument has been made for a gene called BOULE, which is linked to sperm production in humans. This gene has been found also in mice, chickens, snails and sea urchins where it appears to perform a similar function: it is expressed in the testis. When the gene is deleted in mice, it results in sterility due to a lack of sperm. According to the press release:

"This is the first clear evidence that suggests our ability to produce sperm is very ancient, probably originating at the dawn of animal evolution 600 million years ago," said Eugene Xu, assistant professor of obstetrics and gynecology at Feinberg. "This finding suggests that all animal sperm production likely comes from a common prototype." [. . .] "Our findings also show that humans, despite how complex we are, across the evolutionary lines all the way to flies, which are very simple, still have one fundamental element that's shared," Xu said. "It's really surprising because sperm production gets pounded by natural selection," he said. "It tends to change due to strong selective pressures for sperm-specific genes to evolve. There is extra pressure to be a super male to improve reproductive success. This is the one sex-specific element that didn't change across species. This must be so important that it can't change."

The reality is that these examples are representative of many more cases. The findings are not unusual - they are typical. In a recent interview, molecular biologist John Mattick refers to one of the great surprises of the genome projects, one "that very few people have commented on because of their background assumptions".

"[This] is that both the number and range of protein-coding genes have remained largely the same since the base of the metazoan radiation. Caenorhabditis elegans, which is a worm of only 1,000 cells, has almost precisely the same number of protein-coding genes as a human - about 20,000 is the latest estimate - and most of those genes encode similar functions. So the basic parts set for animal development was established several hundred million years ago. In fact, I understand the sponge genome also encodes most, if not all, of the key protein families that are involved in regulating development. Now C. elegans has only got 1,000 cells - a few muscle cells, a few nerve cells, and a gut. We humans have 30 trillion to 100 trillion cells, and the complexity of our body plan organization - including all of the muscles in the face that reflect the range of human emotions, the different bones and organs, and the brain - is enormous."

The implication of this are many. Since the protein-coding DNA has not changed much, we should consider, at least, whether the non-coding DNA is the key to understanding animal complexity - that part of the genome commonly termed "Junk DNA". Mattick puts it like this:

"Since the protein-coding repertoire (notwithstanding some clade-specific innovations) has remained relatively static, the differences in developmental complexity must be due to an expansion of the accompanying regulatory architecture, which presumably lies outside the protein-coding sequences. Now, interestingly, that problem, I think, has been swept under the intellectual carpet because of the relatively facile and widely accepted assumption, which has not been challenged, nor justified, that the combinatorics of transcription factors provide an explosive number of regulatory possibilities - with enough capacity in the system to program anything from a worm to human. But you certainly need to have a more complex regulatory framework to get to a more complex organism, and the astounding thing is that the only thing that does scale with complexity - because the number of genes does not - is the extent of the non-protein-coding genome."

So, we have immensely complex protein coding systems that are relatively static across the phyla and non-coding DNA sequences that are so complex that most biologists are not yet able to recognise them as carrying biological information. The fundamental problem here is the Darwinian mindset that dominates evolutionary biology: the data is being force-fit into an inappropriate conceptual model. Biologists are, of course, free to develop hypotheses to explain the observations, but when we find "redundant roles" for genes and when there is talk of pre-adaptation - we really do need to question what's going on! Is this a good example of Kuhn's 'normal science' and of 'saving the paradigm'? By contrast, ID biologists find that these genome studies fit well into a design matrix, and that design inferences stimulate numerous avenues for research.

Flexibly deployed Pax genes in eye development at the early evolution of animals demonstrated by studies on a hydrozoan jellyfish
Hiroshi Suga, Patrick Tschopp, Daria F. Graziussi, Michael Stierwald, Volker Schmid, and Walter J. Gehring
Proceedings of the National Academy of Sciences USA, Published online before print July 26, 2010, doi: 10.1073/pnas.1008389107

Abstract: Pax transcription factors are involved in a variety of developmental processes in bilaterians, including eye development, a role typically assigned to Pax-6. Although no true Pax-6 gene has been found in nonbilateral animals, some jellyfish have eyes with complex structures. In the cubozoan jellyfish Tripedalia, Pax-B, an ortholog of vertebrate Pax-2/5/8, had been proposed as a regulator of eye development. Here we have isolated three Pax genes (Pax-A, Pax-B, and Pax-E) from Cladonema radiatum, a hydrozoan jellyfish with elaborate eyes. Cladonema Pax-A is strongly expressed in the retina, whereas Pax-B and Pax-E are highly expressed in the manubrium, the feeding and reproductive organ. [. . .] Phylogenetic analysis indicates that Pax-6, Pax-B, and Pax-A belong to different Pax subfamilies, which diverged at the latest before the Cnidaria-Bilateria separation. We argue that our data, showing the involvement of Pax genes in hydrozoan eye development as in bilaterians, supports the monophyletic evolutionary origin of all animal eyes. We then propose that during the early evolution of animals, distinct classes of Pax genes, which may have played redundant roles at that time, were flexibly deployed for eye development in different animal lineages.

Widespread Presence of Human BOULE Homologs among Animals and Conservation of Their Ancient Reproductive Function
Chirag Shah, Michael J. W. VanGompel, Villian Naeem, Yanmei Chen, Terrance Lee, Nicholas Angeloni, Yin Wang, Eugene Yujun Xu.
PLoS Genetics, July 2010, 6(7): e1001022. doi:10.1371/journal.pgen.1001022

Abstract: Sex-specific traits that lead to the production of dimorphic gametes, sperm in males and eggs in females, are fundamental for sexual reproduction and accordingly widespread among animals. Yet the sex-biased genes that underlie these sex-specific traits are under strong selective pressure, and as a result of adaptive evolution they often become divergent. Indeed out of hundreds of male or female fertility genes identified in diverse organisms, only a very small number of them are implicated specifically in reproduction in more than one lineage. Few genes have exhibited a sex-biased, reproductive-specific requirement beyond a given phylum, raising the question of whether any sex-specific gametogenesis factors could be conserved and whether gametogenesis might have evolved multiple times. Here we describe a metazoan origin of a conserved human reproductive protein, BOULE, and its prevalence from primitive basal metazoans to chordates. We found that BOULE homologs are present in the genomes of representative species of each of the major lineages of metazoans and exhibit reproductive-specific expression in all species examined, with a preponderance of male-biased expression. [. . .] This work demonstrates the conservation of a reproductive protein throughout eumetazoa, its predominant testis-biased expression in diverse bilaterian species, and conservation of a male gametogenic requirement in mice. This shows an ancient gametogenesis requirement for Boule among Bilateria and supports a model of a common origin of spermatogenesis.

Non-coding RNAs and eukaryotic evolution - a personal view
John Mattick
BMC Biology, 2010; 8: 67 | doi: 10.1186/1741-7007-8-67.

In this interview, [John Mattick] explains why he thinks non-coding RNA is fundamental to eukaryotic evolution.

Over the years, samples of amber recovered from numerous sites around the world have been found to contain petrified insects, plants and a variety of other exotic inclusions. Invariably, we get an insight into a past world where the flora and fauna look very modern. A recent discovery has identified mammalian hair in amber, whose original owner was a contemporary of dinosaurs.

The shape and structure of mammal hair has remained unchanged since the Cretaceous (Source here)

The dimensions and topography of the two fossilised hairs were analysed carefully, because the find provides the first opportunity to look at Mesozoic mammal hairs preserved in 3D. The result:

"With such features, the cuticular surface of the Archingeay-Les Nouillers hairs shows a modern aspect, implying that the morphology of hair cuticula has remained unchanged throughout most of mammalian evolution."

The New Scientist report says this is the first time researchers have been able to study the pattern of scales on their surface:

"It turns out that the pattern is identical to that found on modern mammalian hair: rows of overlapping scales stacked on top of each other in an orderly fashion, with each row roughly 2 to 8 micrometres high. This discovery is "wonderful progress", says Zhe-Xi Luo, Curator of Vertebrate Paleontology at the Carnegie Museum of Natural History in Pittsburgh, Pennsylvania. "It shows the microstructure of hairs of mammals have always been the same.""

Why is this find worthy of comment? Many people have been brought up to think that the earlier we go back in the fossil record, the more strange the flora and fauna become. Whilst something can be said in favour of this view, it tends to hide the phenomenon of stasis. We do find animal radiations, diversification and extinction, but accompanying this change are pervasive evidences of continuity. The first mammals are thought to have appeared in the Late Triassic, and the first fossilised animal hair is dated as Late Jurassic (preserved as carbonized filaments). Now we find that the Early Cretaceous hair is essentially modern. It is an example of continuity across the geological Periods. It is an example of stasis. It is also an example of the abrupt appearance of complexity.

Mammals lived through the "Age of the Dinosaurs". As time goes on, it is apparent that the diversity of Mesozoic mammals is greater than used to be thought. An example is Castorocauda, from the Middle Jurassic Jiulongshan Formation of Inner Mongolia. This animal is well-preserved and shows specialisation in the fur:

"Castorocauda is preserved with a pelt (guard hairs and under furs), making it the most primitive-known mammal to be preserved with hairs. Carbonized in the fossil, the short and dense under-furs were to keep water from the skin; the longer guard hairs are preserved as impressions on the fossil slab." (Source here)

Mammals are now recognised to have occupied more varied ecological niches than was previously recognised. Castorocauda had specialized skeletal and soft-tissue features for swimming and teeth for eating fish. It is thought that many were ground-living, and a recent discovery is of mammals living in burrows and being prey to digging dinosaurs:

"Two fossilized burrows were spotted nearby. When compared with other burrows researchers have uncovered over the years, the size and complexity of these newfound ones suggest they belonged to mammals - the smaller burrow to a mouse-sized creature, the larger one to a guinea-pig-sized animal. The fact these fossils are so close together suggests they are evidence of dinosaurs scrabbling down to prey on mammals, the researchers suggested." (Source here)

It was a different world - but much that was present is still found today and a gradualist origin of complexity is not confirmed.

Mammalian hairs in Early Cretaceous amber
Romain Vullo, Vincent Girard, Dany Azar and Didier Neraudeau
Naturwissenschaften, 97(7), July 2010, 383-387 | doi 10.1007/s00114-010-0677-8

Abstract: Two mammalian hairs have been found in association with an empty puparium in a 100-million-year-old amber (Early Cretaceous) from France. Although hair is known to be an ancestral, ubiquitous feature in the crown Mammalia, the structure of Mesozoic hair has never been described. In contrast to fur and hair of some Jurassic and Cretaceous mammals preserved as carbonized filaments, the exceptional preservation of the fossils described here allows for the study of the cuticular structure. Results show the oldest direct evidence of hair with a modern scale pattern. This discovery implies that the morphology of hair cuticula may have remained unchanged throughout most of mammalian evolution. The association of these hairs with a possible fly puparium provides paleoecological information and indicates peculiar taphonomic conditions.

Most of the time, scientific research seeks to build on theoretical foundations that have been carefully constructed by the wider research community, often over many years. If a theoretical framework is found to be robust, it gains widespread assent, with few interested in challenging it. Those who are attracted to the idea that science develops progressively are the least likely to talk about challenges. For them, any change is a minor modification of the theoretical edifice. Thomas Kuhn referred to these theoretical frameworks as 'paradigms', and the progressive refinement of that framework as 'normal science'. Kuhn pointed out that anomalies do not trigger the practitioners of 'normal science' to question the paradigm, but they either treat them as problems waiting to be resolved, or they ignore them altogether. In recent months, I've become aware that this phraseology and understanding of scientific activity is intensely irritating to some scientists. They appear to regard such talk as an invention of outsiders with a subversive agenda. A desire to comment on these issues has stimulated this blog, which is based on a paper authored by Walter Alvarez, an experienced and respected scientist working in the field of geology. He introduces his paper thus:

"Lightman and Gingerich (1992) argued that when a ruling theory is successful in accounting for a wide range of observations, scientists ignore observations that are not explained by the theory. They argued that such "anomalies" are only "retro-recognized" when a modification or replacement of the original theory calls attention to and explains the conflicting observations."

The "ruling theory" has been referred to above as the theoretical framework or paradigm. The quotation points out that anomalies tend to have a very low profile until solutions are found, and then the solutions are publicised widely to hail the success of the paradigm. Earth scientists generally understand paradigms. Many have lived through the Plate Tectonics revolution - which is now the ruling paradigm. Alvarez considers that a major revision of this paradigm is needed, and he points to the relevant anomalies that show all is not well.

"Such an anomaly is present in the plate tectonic theory that has dominated geological thinking for the last 30-40 yr. Plate tectonics sees subduction as able to consume an unlimited amount of dense oceanic lithosphere, but unable to continue after convergence brings two buoyant continental masses together. Buoyancy should terminate the convergence, with a new subduction zone initiated somewhere else, where it can consume oceanic lithosphere. This view persists despite evidence that at least some continental collisions have continued long after the continents first collided."

Within plate tectonic theory, there are two categories of mechanisms for driving the crustal plates: boundary forces ("slab pull" by descending plates and "ridge push" (emanating from centres of crustal generation) and drag forces (frictional forces between mantle convection cells and crustal plates). These concepts are introduced to students very early in their studies, and they have become entrenched. For examples, go here and here. For a more advanced treatment, go here. The relative contributions made by these different forces have been much discussed by scientists developing plate tectonic theory. However, firm conclusions have not been reached. If there is any consensus, it is that boundary forces are more significant than drag forces, and that slab pull is more significant than ridge push. Alvarez has the view that with plates carrying continents, drag forces are of major importance. He discusses three cases where plate movements continued long after two continental masses collided. If boundary forces were dominant, motion would cease very quickly. However, if drag forces were significant, the problems disappear. Alvarez started publishing along these lines in 1982 and claims his recent research confirms the earlier hypothesis.

"More than 25 yr ago the present author proposed that protracted collisions may be driven by traction applied at the base of deep lithospheric roots (Alvarez, 1982), and in two subsequent papers (Alvarez, 1990, 2001) used the term "continental undertow" to refer to this driving mechanism. [. . .] Although the data available at the time were insufficient to test the undertow model, there are now many relevant observations. The last section of this paper shows how the anomaly of protracted collisions can be explained by continental undertow."

It is not my intention in this blog to discuss the wider implications of the Alvarez model. My interest is in the way scientific theory develops, the way anomalies are handled and in the (often hidden) influence of dominant paradigms. What we find here in the earth sciences is frequently encountered in the field of evolutionary biology. There are many anomalies between observed data and theory, but these are typically well-known only to researchers close to both. Anomalies (in the main) do not get published until someone proposes a solution - within the ruling paradigm. In plate tectonic theories, anomalies surround the quest for driving forces able to move crustal plates and build mountains; in evolutionary biology, anomalies are pronounced when it comes to explaining how complex specified information is derived from natural causes. Darwinian mechanisms are useful for explaining antibiotic resistance but not the origin of the immune system. They are OK for changing the dimensions of finch beaks but not for constructing beaks. They have some value in elucidating industrial melanism but not for engineering structural colour in moth wings.

Wonderful music, but is there a composer? (Source here)

Researchers who propose paradigm-changing solutions do not find it easy to get their work past editors and reviewers. Intelligent Design (ID) requires a fundamental change of paradigm in the way we think about causation. Most research relating to origins admits only natural causes (naturalism), whereas ID links complex specified information to intelligent agency. ID researchers consider this is an issue that must be evaluated within science, but there are many who think otherwise! This is why Stephen Meyer's peer-refereed paper led to the removal of Richard Sternberg from the role of editor of the Proceedings of the Biological Society of Washington and the subsequent withdrawal of the paper. Other examples of editors (in other disciplines) in trouble because they were willing to publish papers that challenged the dominant paradigm were given in an earlier blog. Although there is a continuing polemic by ID-denigrators based on the supposed lack of peer-reviewed ID research, the situation is slowly changing. Nevertheless, the most important thing to realise is that the playing-field is not level and there are far too many people defending the dominant paradigm for ideological reasons. Their style of engagement with the issues suggests they are not interested in a scientific debate - their polemics are geared to ensuring naturalism is uncontested and that the worldview of science is materialism. Since doctrinaire philosophical materialists do not constitute a majority within science, it is very important that the present impasse is broken.

Protracted continental collisions argue for continental plates driven by basal traction
Walter Alvarez
Earth and Planetary Science Letters, Volume 296, Issues 3-4, 1 August 2010, Pages 434-442 | doi 10.1016/j.epsl.2010.05.030

Abstract: In plate tectonic theory, collision between two continents should quickly terminate because of continental buoyancy. If convergence is to continue, it should do so at a new subduction zone where oceanic crust can be consumed. The protracted continental collisions in the Alps, Zagros, and Himalayas, which have continued to deform continental crust since the early or middle Cenozoic, are therefore anomalies in standard plate tectonic theory. It is commonly held that plates are driven by slab pull, but this does not account for the continuing Tethyan collisions where the descending slab has detached from the subducting continent. These protracted continental collisions are better explained by horizontal traction of the mantle on the base of deep continental roots, dragging the northern and southern continents together along a Tethyan axis of mantle convergence. "Continental undertow" thus resolves the collision anomaly in plate tectonics.

See also:

Tyler, D. Does Science promote atheism? ARN Literature Blog (23 July 2007)

It is well known that orb-weaving spiders put droplets of adhesive all over their webs to catch prey. Although there have been many attempts to study the nature of these adhesives, it is only recently that experiment designs have allowed the mechanism of adhesion to be analysed properly. Single adhesive droplets have been probed at varying extension rates.

"Here, by directly probing single adhesive droplets used by spiders, we demonstrate the importance of the mechanics of adhesive in dramatically enhancing adhesion. We show that glue drops function as a viscoelastic material instead of as a viscous material and that the elasticity of the principle adhesive in this system, the glycoproteins, increases adhesion by two orders of magnitude in comparison with capillary forces, thus putting to rest the old notion of the adhesive being viscous."

Lower Cretaceous spider's web. "The advanced structure of this fossilized web, along with the type of prey that the web caught, indicates that spiders have been fishing insects from the air for a very long time." (Credit: American Museum of Natural History, source here)

The glycoproteins are cross-linked (either physically or chemically) enabling forces to be transmitted efficiently. At slow speeds, the pull-off forces are low; but at high speeds, the forces rise dramatically. Thus, when an insect first impacts the web, it is moving fast - and the web adhesive produces its largest gripping force. This allows the spider time to subdue the insect - and by then the adhesive forces have reduced in magnitude so that the spider can remove the insect from the web with relative ease. As in all biomimetic studies, these are coveted properties that we wish to emulate:

"This finding should significantly benefit the development of synthetic adhesives for biomedical, orthopedics and wound-healing applications. The understanding of how spiders use this unique glue will allow scientists to develop reversible adhesives that work in the presence of water," says Dhinojwala.

Lee points out that spider adhesive is a smart material, and that we are only beginning to understand its secrets.

"Man-made glues are mono-functional - their material properties are designed to stick one thing to another, and that's it. But in Nature Communications, Sahni et al. report that the 'glue' droplets that coat spiders' webs are multi-functional. Depending on the rate at which they are extended, the droplets act either as a viscous adhesive or as a rubber-like elastic solid." [. . .]
"But in-depth knowledge of the molecular structure of the glue droplets on spiders' webs is lacking. [. . .] A series of studies investigating the molecular content and supramolecular assembly of glue droplets is therefore required."

Whilst this research is a splendid example of empirical science in action (understanding how the natural world operates), the issue of origins is raised in this paper. An evolutionary framework is adopted, not because the research is dependent on that framework, but because papers that refer to design (especially "well-designed" features) apparently need to affirm non-intelligent causation. So, the first paragraph of the paper begins with this:

"Nature has evolved a myriad of well-designed adhesives that assist in locomotion, self-defence and prey capture. Geckos use micron-sized hairs as dry adhesives for locomotion. Mussels secrete specialized proteins to stick under water. Modern orb-weaving spiders use micron-sized glue droplets laid on a pair of viscoelastic axial silk for catching prey."

The exquisite design apparent in spider silk does not just relate to its remarkable strength, but to its ability to manage water and also, as noted in this blog, to the properties of the applied adhesive drops. In all these cases, the designs are not easy to reproduce. Large amounts of research funds are devoted to mimicking the natural products. It is not a trivial exercise! Even with years of intelligent activity by teams of researchers, problems remain unsolved. No explanation of origins that attributes all this complexity to natural causation has succeeded in convincing anyone who has not already adopted the ideology of evolutionary theory. Add to this the evidence that the first spiders appeared abruptly in the fossil record: the Mesothelae appear in the Carboniferous essentially identical to living forms. Furthermore, although appearing in Mesozoic and Cenozoic deposits, other spider families are represented which are also comparable with modern specimens. The evolutionary ancestors of the whole group is unknown (see here). It is a shame that a paper that marks a significant step forward in understanding the complexity of spider web stickiness should be mixed up with assertions about origins that are so lacking in substance.

Viscoelastic solids explain spider web stickiness
Vasav Sahni, Todd A. Blackledge and Ali Dhinojwala
Nature Communications, 1, No.19, 1-4, (17 May 2010) | doi:10.1038/ncomms1019

Abstract: Modern orb-weaving spiders have evolved well-designed adhesives to capture preys. This adhesive is laid on a pair of axial silk fibres as micron-sized glue droplets that are composed of an aqueous coat of salts surrounding nodules made of glycoproteins. In this study, we measure the adhesive forces required to separate a small microscopic probe after bringing it in contact with a single glue droplet. These forces are highly rate-dependent and are two orders of magnitude higher than the capillary forces. The glycoproteins in the glue droplets behave as a viscoelastic solid and the elasticity is critical in enhancing adhesion caused by specific adhesive ligands. These results have important implications in mimicking bioadhesives.

See also:

Lee, H. Intelligent glue, Nature, 465, 298-299 (19 May 2010) doi:10.1038/465298a

Researchers discover spider webs' true 'sticking power', PhysOrg.com (May 17, 2010)

UA researchers discover true sticking power of spider webs (video)

Conspiracies to suppress, manipulate and distort information undoubtedly occur. Society needs to be vigilant to guard against deception. An increasing number of alleged conspiracies are being covered by the media, all reflecting in some way on the integrity of politicians, or business leaders or the scientific enterprise. Conspiracy theorists are skilled in appealing to emotion, phrasing allegations in a provocative way, and promoting their own reconstructions of events so as to capture the imagination of the public. Ted Goertzel's essay on this theme sounded some alarm bells when it provided four recent examples:

"Conspiracy theorists - some of them scientifically trained - have claimed that the HIV virus is not the cause of AIDS, that global warming is a manipulative hoax and that vaccines and genetically modified foods are unsafe."

(Source here)

The problem I have with this is that these cases are all examples of dissent within science, whatever else may be said about associated conspiracy theories. My purpose here is not to align myself with all these dissenters (although in two of the cases I find myself at variance with the apparent consensus), but to defend the legitimacy of dissent within science. It is vital for the health of science that dissenters have the opportunity to probe, to question and to challenge the theoretical framework of the science relevant to their case, and to test all theories by reference to empirical data. The danger I see in Goertzel's analysis is that legitimate dissent is marginalised and treated as the product of conspiracy theory. The consequence is that science is damaged because reasoned arguments of dissenters are re-categorised as "emotional appeals, unsupported allegations and unverified speculations".

In Goertzel's analysis, conspiracy theorising is a rhetorical device employed for a variety of cultural, political and personal reasons. To develop the thesis, he finds it "useful to think of conspiracy theorizing as a 'meme', a cultural invention that passes from one mind to another and survives, or dies out, through natural selection". The effect of this definition of the issues is to exclude the conspiracy theorising meme from scientific discourse: a form of demarcation.

My concern is that Goertzel's four main examples of contemporary conspiracy theorising are, as a consequence, excluded from discussion in the world of science and relegated to political, economic and sociological forums. The first of these examples is the relationship between the HIV virus and AIDS. In 2008, Duesberg and colleagues published a paper incorporating their dissenting views in the journal Medical Hypotheses. So strong was the hostile reaction to this paper that the Editor, who personally carried the responsibility for reviewing manuscripts, was given notice of dismissal by Elsevier (the publisher of the journal) unless the peer review process followed a more conventional format. This ultimatum was resisted by the Editor and the entire Editorial Board. According to ScienceInsider (May 17th 2010), "Bruce Charlton, the editor of the controversial journal Medical Hypotheses, was fired last week by publisher Elsevier for refusing to overhaul the review procedures at the journal. Now, a majority of the 19-member Editorial Advisory Board seems set to quit as well." The intervention reveals a variety of influences that are alien to scientific discourse. Those opposed to the Duesberg message are not addressing his arguments but are engaged in a power-struggle to prevent dissenting views being published. For Professor Charlton's parting words, go here.

Case two is anthropogenic global warming. At least, in this instance, Goertzel recognises that both sides have been alleging conspiracies!

"In the realm of science, the 'climategate' scandal that has dogged the University of East Anglia's Climatic Research Unit (CRU; Norwich, UK) has seen the word conspiracy thrown about on both sides of the argument. Climate change 'sceptics' have accused Professor Phil Jones of conspiring with his collaborators to manipulate climate data and the scientific literature, while supporters of the CRU have pointed out that the hacking of the e-mails and the selective, pejorative quoting of their content was a conspiracy to discredit the scientific evidence for climate disruption."

It is worth noting that the two groups of scientists interpret the data in different ways and both claim that the other side is involved in conspiracy theorising. At very least, this ought to sound alarm bells in the minds of all who value the health of science: the priority is to promote evaluation of the scientific arguments, not to close ranks with the consensus and to treat the dissenters as pariahs who have betrayed their scientific training by bowing to vested interests. Goertzel sides with those who think that some of the scientists have been over-enthusiastic and have made mistakes, but also that the link between global warming and human activities (of burning fossil fuels) is robust.

"Climate science is heavily dependent on complex statistical models based on limited data, so it is not surprising that models based on different assumptions give differing results. In presenting their data, some scientists were apparently too quick to smooth trends into a 'hockey stick' model that fitted with their advocacy concerns. Several different groups of well-qualified specialists have now been over the data carefully, and the result is a less linear 'hockey stick' with a rise in temperature during a 'medieval warm period' and a drop during a 'little ice age'. But the sharp increase in warming in the twentieth century, which is the main point of the analysis, is still there."

This appraisal is not shared by the dissenters, who point to far deeper and more fundamental issues. The most important of these is, in my opinion, the strategy of using peer review and editorial control to reinforce the "consensus" position. This is highlighted by Andrew Montford (The Times Higher, 25 March 2010), who wrote: "Among the most serious allegations to emerge in the wake of the leaked emails is that CRU scientists tried to "nobble" scientific journals that accepted papers from sceptics. There are suggestions in the emails that as many as four different journals may have had their normal procedures interfered with."
It is not difficult to find people who have been adversely affected. Here is a statement from Dr Sonja Boehmer-Christiansen, who was editor of one of the above-mentioned journals. "My interests are purely academic, professional and political. I am interested in the value and misuse of the peer review process. The negative attitudes of the IPCC/CRU people to my often sceptical journal have harmed it." There have been several formal enquiries that have cleared the relevant climate science leaders of unprofessional conduct, but many of us are mystified by these outcomes. The unethical practices revealed in the emails seem to be so blatant. The clearest and most sensible peer-reviewed comment on the debacle, in my opinion, comes from Stanley Trimble, professor of geography at the University of California at Los Angeles.

"Having said that, I must add that Climategate is, in my view, the greatest science scandal in my lifetime. Beyond any scientific implications are the implications of the behavior of the East Anglia scientists and their correspondents - suppressing information, denigrating those who don't agree with them, trying to deny others access to scientific journals, questioning motives, and conniving to disfellow skeptical colleagues. These are the earmarks of zealotry. While maybe not illegal, they are most certainly unethical. Civilized people, much less scientists, just don't do those things - but then, apparently they do."

In similar vein, comments could be made to show that Goertzel's other major examples (vaccines and genetically modified foods) originate as dissent within science and consequently the issues deserve to be addressed within science. Undoubtedly, all these controversies affect public policy, so it is not surprising that politicians, economists and advocacy groups become involved. The desire for consensus should be regarded as a threat to science, because it inhibits the freedom of scientists to debate issues. Yet, this desire for consensus is where Goertzel leads us:

"Decision-makers and the general public are best served when scientists specializing on an issue can reach a reasonable degree of consensus, making clear the limits to their knowledge. If scientists cannot do this, surely it is too much to expect politicians or journalists to do it. But efforts to define a consensus are vulnerable to attacks by conspiracy theorists that portray them as mechanisms for suppressing dissent and debate."

Goertzel's view of science puts emphasis on its progressive nature. One a trend is established, the presumption is made that the science is closing in on reality. Such thinking leads to skepticism about the possibility of scientific revolutions and to minimizing the importance of these revolutions in the history of science.

"Efforts to reach consensus on important questions have been discouraged by the influence of philosophers of science who emphasize conflicting research programmes, paradigm shifts and scientific revolutions. While these events do occur in the history of science, they are exceptional. Most sciences, most of the time, progress with an orderly, gradual accumulation of knowledge that is recognized and accepted by specialists in the field. Opposition rooted in religious or ideological concerns is acceptable as part of the democratic political process, but it need not prevent scientists from reaching a consensus when one is justified."

The problem I find with this is that consensus should not be a goal, but it may be a spin-off resulting from the application of the scientific method. It may be desirable for making public policy, but that should not dictate the way scientists operate. Those of us who warm to Thomas Kuhn's analysis of 'normal science' and 'scientific revolutions' have no problem with progression within a paradigm, but we infer that this points to internal consistency rather than realism.

The design paradigm gets a brief mention in Goertzel's paper - in the context of the "advocacy meme" (there are two sides to every question and each side is entitled to equal time to present its case). "George W. Bush famously suggested that students be taught both evolution and "intelligent design" theories so that they could judge which had the most convincing argument." Significantly, Goertzel refers to the sound-bite of a political leader rather than a scientist. But here too, the issue should not be reduced to the conspiracy theory format. There are scientific issues, as Dr Stephen Meyer has shown, concluding that there are "pedagogical, legal and scientific case for exposing students to the scientific controversies that exist about the key claims of neo-darwinism, including the claim that the selection-mutation mechanism can fully account for the appearance of design in biological systems." These controversies are discussed in the textbook Explore Evolution (2009).

My greatest concern about Goertzel's paper is that the scientists representing the consensus position are viewed through positivist glasses. Consequently, they pursue objective information and analysis; they don't have emotional attachments to their theories; they don't make unsupported allegations about those who might differ from them; they do not indulge in unverified speculations. These are cardboard scientists who do not exist in the real world. Sociologists of science ought to know better. What we need in all these contested areas is a greater willingness to engage with those who differ from us; an openness to challenging our own favoured ideas; and a willingness to follow the evidence wherever it leads.

Conspiracy theories in science
Ted Goertzel
EMBO reports, 11(7), July 2010, 493-499 | doi:10.1038/embor.2010.84

First para: Conspiracy theories are easy to propagate and difficult to refute. Fortunately, until a decade or so ago, few serious conspiracy theories haunted the natural sciences. More recently, however, conspiracy theories have begun to gain ground and, in some cases, have struck a chord with a public already mistrustful of science and government. Conspiracy theorists - some of them scientifically trained - have claimed that the HIV virus is not the cause of AIDS, that global warming is a manipulative hoax and that vaccines and genetically modified foods are unsafe. These claims have already caused serious consequences: misguided public health policies, resistance to energy conservation and alternative energy, and dropping vaccination rates.

Climategate: If The Science Is Solid, Why Stoop?
Stanley W. Trimble
Academic Questions, (March 2010) 23(1): 54-56 | doi 10.1007/s12129-009-9149-z

Preface: I must preface my remarks by saying that I believe that there has indeed been climate warming over the past few decades and I believe that human action may be one of the causes. While Climategate may bring into greater question some of the work underlying climate warming, it decidedly does not disprove it.

See also:

Tyler, D. Scientific Consensus is sleep inducing, ARN literature Blog (9 June 2010)

Our knowledge of the fossil record has changed immensely since 1859, when Darwin felt obliged to explain why his hypothesis of gradualism was not confirmed by the study of fossil successions. His argument was, as is well known, that the fossil record exhibits extreme imperfection. The abrupt appearance of macrofossils at the base of the Cambrian was recognized and Darwin deduced that the evolutionary origins of those animals must have extended well back into the Precambrian.

"One-and-a-half centuries of subsequent research have revealed a vast microscopic fossil record of unicellular protists and bacteria extending, some would argue, as far back as there are sedimentary rocks from which they could be recovered. But although fossils of millimetre- to metre-scale multicellular organisms characterize the 90 million years of the Ediacaran period that precedes the Cambrian, pre-Ediacaran macroscopic fossils are exceedingly rare."

The newly reported fossils from Gabon were laid down in shales (Source here)

Over the years, various attempts have been made to vindicate Darwin's approach. The Ediacaran fauna shows that soft-bodied animals were preserved in the Precambrian, even in coarse sandstone beds, suggesting that fossils are not found because they were not there. In any case, there is no gradualist understanding of the Ediacaran fauna or any gradualist connection with the fossils of the "Cambrian Explosion". Prior to this, there is a unicellular fossil record with very few suggestions of macroscopic fossils. The newly reported finds are from sediments dated at 2.1 billion years old. They are interpreted by the researchers "as highly organized and spatially discrete populations of colonial organisms" with growth patterns "commonly associated with multicellular organization". If correct, this makes them the earliest known multicellular life.

"We have these macrofossils turning up in a world that was purely microbial," says Stefan Bengtson, a palaeozoologist at the Swedish Museum of Natural History in Stockholm and a co-author on the report. "That's a big deal because when you finally get big organisms, it changes the way the biosphere works, as they interact with microbes and each other." (Source here)

If confirmed, this discovery are exciting, although it "raises more questions than it answers". We consider below whether Darwin's expectations are met. However, some cautionary comments are appropriate in the interests of promoting multiple working hypotheses. Donoghue and Antcliffe's News & Views article considers the arguments put forward by the research team and declare:

"The null hypothesis, however, has to be that these remains represent bacterial colonies. Future work must determine whether the sterane signature, a hallmark of eukaryotes, is derived from soluble organics generated within the sediments, or whether they migrated into these sediments from younger rock sequences. [. . .] Although the fossils are macroscopic, they do not seem to represent anything other than the basic type of multicellularity, which occurs earlier in time in the form of stromatolites."

We should recognize that some scholars with expertise in this field are skeptical. R. Ford Denison gives several reasons, including: "A consistent size and shape is another criterion for true multicellularity, met by Volvox, for example. The fossils don't look any more consistent in size and shape than one would expect from bacterial colonies." In a Nature News item, Maxmen draws attention to another:

"Calling the Gabon specimens "pseudo-fossils", palaeontologist Adolf Seilacher at Yale University in New Haven, Connecticut, instead interprets them as aggregations of the mineral pyrite that grew in different shapes depending on the changing state of the surrounding sediment. In 1998, Seilacher reported finding a fossil eukaryote 1.1 billion years old. Referring to that find, he says: "I now firmly believe that my own so-called first animals were pseudo-fossils too.""

But let us allow that these putative fossils represent genuine multicellular organisms. Does it support a Darwinian perspective on evolution? Donoghue and Antcliffe think that it does:

"But within the confines of a very patchy global record of Proterozoic and Archaean rocks, which extend from about 3.8 billion years ago to the beginning of the Cambrian, these remains contribute to a fossil record that belies the dated caricature painted in the Origin. It was Darwin's view that absence of organisms in these early intervals of Earth's history would prove his theory of biological evolution wrong. The discovery and continuing elucidation of the Precambrian fossil record has met Darwin's predictions on the extent and structure of evolutionary history."

The "absence of organisms" problem persists for Darwinism, as the abrupt appearance of animal phyla in the Cambrian Period is not preceded by any evidence of gradual transformation. It is preceded by multicellular organisms in the Ediacaran - but largely unrelated to the Cambrian fauna. It is preceded by unicellular life forms, but there is no convincing Darwinian perspective on these (see here and here). The discovery of an isolated early multicellular organism does nothing to support gradualism, because there is no gradual succession of ancestral or descendant forms. The find should be regarded as enigmatic until further insights into context are obtained.

Large colonial organisms with coordinated growth in oxygenated environments 2.1 Gyr ago
Abderrazak El Albani, Stefan Bengtson, Donald E. Canfield, Andrey Bekker, Roberto Macchiarelli, Arnaud Mazurier, Emma U. Hammarlund, Philippe Boulvais, Jean-Jacques Dupuy, Claude Fontaine, Franz T. Fursich, Francois Gauthier-Lafaye, Philippe Janvier, Emmanuelle Javaux, Frantz Ossa Ossa, Anne-Catherine Pierson-Wickmann, Armelle Riboulleau, Paul Sardini, Daniel Vachard, Martin Whitehouse & Alain Meunier
Nature, 466, 100-104, (01 July 2010) | doi: 10.1038/nature09166

First para: The evidence for macroscopic life during the Palaeoproterozoic era (2.5-1.6 Gyr ago) is controversial. Except for the nearly 2-Gyr-old coil-shaped fossil Grypania spiralis, which may have been eukaryotic, evidence for morphological and taxonomic biodiversification of macroorganisms only occurs towards the beginning of the Mesoproterozoic era (1.6-1.0 Gyr). Here we report the discovery of centimetre-sized structures from the 2.1-Gyr-old black shales of the Palaeoproterozoic Francevillian B Formation in Gabon, which we interpret as highly organized and spatially discrete populations of colonial organisms. The structures are up to 12 cm in size and have characteristic shapes, with a simple but distinct ground pattern of flexible sheets and, usually, a permeating radial fabric. Geochemical analyses suggest that the sediments were deposited under an oxygenated water column. Carbon and sulphur isotopic data indicate that the structures were distinct biogenic objects, fossilized by pyritization early in the formation of the rock. The growth patterns deduced from the fossil morphologies suggest that the organisms showed cell-to-cell signalling and coordinated responses, as is commonly associated with multicellular organization. The Gabon fossils, occurring after the 2.45-2.32-Gyr increase in atmospheric oxygen concentration10, may be seen as ancient representatives of multicellular life, which expanded so rapidly 1.5 Gyr later, in the Cambrian explosion.

Origins of multicellularity
Philip C. J. Donoghue & Jonathan B. Antcliffe
Nature, 466, 41-42, (01 July 2010) | doi: 10.1038/466041a

Interpreting truly ancient fossils is an especially tricky business. The conclusion that 2.1-billion-year-old structures from Gabon are the remains of large colonial organisms will get palaeobiologists talking.

See also:

Maxmen, A. Ancient macrofossils unearthed in West Africa, Nature News (30 June 2010) | doi:10.1038/news.2010.323

Although geographically widespread, the genus Pelecanus has only 7 or 8 species extant (depending on the classification system used). A similar number of fossil species have been identified, although the morphological differences are quite small. Until recently, the earliest fossil form was dated as Early Miocene. Newly published work pushed the first appearance back to the Early Oligocene, considered to be about 30 million years old. The point of interest for us is that the fossil, and specifically the beak, is said to be "morphologically identical to modern pelicans".

"All these characteristics of the fossil are identical to those of the species in Pelecanus, the single extant genus in the family. [. . .] Therefore, [the specimen] can be considered a morphologically modern pelican of the genus Pelecanus, but it is not closer to any particular extant species."

"It is so similar to modern pelicans, despite its 30 million years" (image: A. Louchart, source here)

The beak is of particular interest, because it is "highly derived" and unique when compared with all other birds. Since the component parts are both unusual and inter-dependent, convergent evolution is not perceived as a viable hypothesis.

"Thus, the evolution of this advanced feeding apparatus, one of the most distinctive arrangements among birds, had already been achieved by the early Oligocene and its morphology is found unchanged in extant pelicans after ca. 30 million years, which can be considered a stasis of long duration."

The authors set out some thoughts to explain this stasis. The first hypothesis is that the beak is functionally optimal over 30 million years, and there has been no selection for change. The whole family can be considered to occupy an adaptive peak on their sector of the adaptive landscape. Another hypothesis is that flying ability is a constraint on morphological adaptation. However, neither of these options are found satisfying and the authors indicate their preference for keeping an open mind:

"The remarkable stasis in the beak of pelicans remains intriguing, and is probably in need of new explanations."

They are undoubtedly right: the stasis is intriguing and new explanations are needed. What we are seeing here is a particular type of stasis, and it concerns complexity. Much diversification has little or no effect on complexity and examples of diversification therefore have little or no bearing on the origin of complexity. The pelican beak, however, is not just a big beak! There are numerous coordinated elements that have to be present for the beak to function at all. The fossil find is important because the earliest fossil of a pelican exhibits the full functionality of the modern birds. As far as the known fossil record is concerned, complexity was present - before the radiation of the Pelecanidae. Yes, this makes stasis in the pelican beak intriguing and it means that Darwinism has nothing to offer by way of an explanation. New explanations should include the options opened up by intelligent design.

The earliest known pelican reveals 30 million years of evolutionary stasis in beak morphology
Antoine Louchart, Nicolas Tourment and Julie Carrier
Journal of Ornithology, advanced publication June 2010 | DOI: 10.1007/s10336-010-0537-5

Abstract: The feeding apparatus of Paleogene birds is rarely well-preserved. Here, we describe the earliest known pelican (early Oligocene, Luberon, southeastern France), with its almost complete beak. Morphologically identical to modern pelicans, the new fossil already shows several advanced features unique to extant species of the genus Pelecanus. It probably belongs to the lineage ancestral to all or some of these pelican species. This fossil reveals a remarkable evolutionary stasis in the morphology of such an advanced avian feeding apparatus through ca. 30 million years. Several hypotheses are proposed to suggest explanations for such examples of long stases in volant homeothermic vertebrates.

See also:

Hecht, J. Pelican fossil poses evolutionary puzzle, New Scientist (22 June 2010)

Today, there seem to be many vested interests in scientific consensus. Universities and science associations often make use of the concept when explaining the importance of science in society and in making pronouncements on issues of public significance. Consensus is relevant to funding agencies, who focus their awards on science that appears to be building on an existing knowledge base. It is a factor in peer review, for it is much harder to get unorthodox ideas past the journal review processes. It influences the media: who is regarded as an 'expert' and who should not get exposure because of their unorthodox ideas. How refreshing, then, to find the Royal Institute of Philosophy offering some cautionary words in an editorial:

"One of the most striking aspects of Karl Popper's philosophy of science is his insistence that scientific consensus is sleep inducing, intellectually speaking. He did not actually put it quite like that. What he pointed out was that the most successful scientific theory ever devised turned out to be false, even though it had been treated as scientifically practically unquestionable for nigh on two centuries. Popper was thinking of Newton's theory, whose refutation (as Popper saw it) in 1917 was a key moment in his own intellectual life."

Popper "called for a clear demarcation between good science, in which theories are constantly challenged, and what he called "pseudo sciences" which couldn't be tested. His debunking of such ideologies led some to describe him as the "murderer of Freud and Marx". [Some of us think the name of Darwin should be added to this list]." (Source here)

Even more welcome are the two examples selected of modern-day scientific consensus: "critics of the theory of evolution and of the reality of climate change". Although the public has been assured time after time that the "science is settled" on these issues, the guardians of these consensus positions will not be pleased by these cautionary words, nor by the judgment offered that the critiques "are not all or entirely without weight".

"Popper's lesson is little heeded to-day. Critics of the theory of evolution and of the reality of climate change are not so much argued with as vilified, excluded and marginalised in polite scientific and even political circles. It is what one might expect from a very powerful institution, like the medieval Church, but not perhaps from one ostensibly committed to critical rationality and the pursuit of falsification. The criticisms which are made of the theory of evolution and of climate change, as these things are currently and consensually understood, are not all or entirely without weight."

It appears to me that the philosophers are not making a judgment on the science, but on the quality of the debate. There are real issues to discuss - the philosophers can recognise that. Furthermore, they are not impressed by the way the defenders of scientific consensus are treating the critiques: ad hominem arguments, straw man arguments, much handwaving, smokescreens and even a refusal to engage with the real issues. Even saying there should be a proper debate can be dangerous:

"We hope that saying that will not bring a heap of opprobrium on our heads. But even if the criticisms were off the wall, those who take Popper seriously may still occasionally catch a whiff of the falsifying rat behind the painted and perfumed consensus."

A recent example of the lack of real debate can be found in the reception of What Darwin Got Wrong by Jerry Fodor and Massimo Piattelli-Palmarini. Here is Douglas Futuyma in Science (7 May 2010) in a review entitled: "Two critics without a clue".

"Fodor and Piattelli-Palmarini show little familiarity with the vast literature on genetic variation, experimental analyses of natural selection, or other topics on which they philosophically expound. They are blithely agnostic about the causes of evolution and apparently uninterested in fostering any program of research. Because they are prominent in their own fields, some readers may suppose that they are authorities on evolution who have written a profound and important book. They aren't, and it isn't."

Another example is the ID prediction of functionality for Junk DNA, and the establishment Darwinists defence of Junk. An interesting report on some recent exchanges is by Jonathan Wells. This concludes:

"If one overlooks the nastiness, it is clear that there are some interesting issues in this debate. Conceptually, what does it mean to say that a segment of DNA has function? Empirically, what does the evidence show? One might think that professors Matheson, Hunt and Moran would address the conceptual issue calmly, rationally, and collegially. But they don't; instead, they stoop to misrepresentation and ridicule. And one might think that they would address the empirical issue by citing published scientific evidence. But they don't; instead, they simply proclaim themselves the only authorities on the subject."

What we are seeing is a warped science. Instead of championing empiricism and testing of hypotheses, the consensus scientists end up appealing to authority and treating the evidence lightly. They are making the same mistake as the Medieval Church.

Scientific Consensus
Editorial
Philosophy, April 2010, 85(2), 181 | doi: 10.1017/S0031819110000161

[Much of the text of this editorial is cited above]

See also this review by another philosopher:

Midgley, M. What Darwin Got Wrong by Jerry Fodor and Massimo Piattelli Palmarini, The Guardian, 6 February 2010.

It took 20 skilled people working for a decade, and an estimated $40 million of funding, but the outcome is spectacular. It is described as "a defining moment in the history of biology and biotechnology" by Mark Bedau, editor of the journal Artificial Life. The BBC News headline was succinct: 'Artificial life' breakthrough announced by scientists. The Economist declared: "Artificial life, the stuff of dreams and nightmares, has arrived". The research paper claims to have made a synthetic cell, and uses the word "creation" in the title.

"We refer to such a cell controlled by a genome assembled from chemically synthesized pieces of DNA as a "synthetic cell", even though the cytoplasm of the recipient cell is not synthetic. Phenotypic effects of the recipient cytoplasm are diluted with protein turnover and as cells carrying only the transplanted genome replicate. Following transplantation and replication on a plate to form a colony (>30 divisions or >10^9 fold dilution), progeny will not contain any protein molecules that were present in the original recipient cell."

"Interesting creatures will be bubbling out of the Venter Institute's labs" (image source here)

It seems obvious that the research team should be congratulated, but we do need to ask - what exactly is it that they are being congratulated for? In a news article in Science, Pennisi wisely puts the word "synthetic" in quotation marks when referring to the whole organism, but is happy with "synthetic genome" in her title. So let's look at the genome and clarify what was done. The exercise was based on the bacterium with the smallest genome: Mycoplasma mycoides. In the past, the team has published a series of papers on constructing building blocks and assembling them. They have learned how to make changes to the code so they could trace progress. Pennisi summarises as follows:

"The researchers started building their synthetic chromosome by going DNA shopping. They bought from a company more than 1000 1080-base sequences that covered the whole M. mycoides genome; to facilitate their assembly in the correct order, the ends of each sequence had 80 bases that overlapped with its neighbors. So that the assembled genome would be recognizable as synthetic, four of the ordered DNA sequences contained strings of bases that, in code, spell out an e-mail address, the names of many of the people involved in the project, and a few famous quotations. Using yeast to assemble the synthetic DNA in stages, the researchers first stitched together 10,000-base sequences, then 100,000-base sequences, and finally the complete genome."

In view of the complexities experienced, the successful assembly was a magnificent achievement. The researchers then embedded their new genome in the cytoplasm of a recipient cell - the related bacterium Mycoplasma capricolum. Unfortunately, the cell died. It took three months to find the problem. The team systematically replaced stretches of the assembled genome with the natural genome until they identified the cause: a single-base mistake in the synthetic code. The research moved on to check the functioning of the replicating bacterium.

"They sequenced the DNA in this colony, confirming that the bacteria had the synthetic genome, and checked that the microbes were indeed making proteins characteristic of M. mycoides rather than M. capricolum. The colony grew like a typical M. mycoides as well. "We clearly transformed one cell into another," says Venter."

The research has long-term practical goals. Will it be possible to design bacteria that have novel functionalities? Clearly, many are working towards that goal. According to one expert, "One thing is sure, interesting creatures will be bubbling out of the Venter Institute's labs". The authors write:

"This work provides a proof of principle for producing cells based upon genome sequences designed in the computer. DNA sequencing of a cellular genome allows storage of the genetic instructions for life as a digital file. The synthetic genome described in this paper has only limited modifications from the naturally occurring M. mycoides genome. However, the approach we have developed should be applicable to the synthesis and transplantation of more novel genomes as genome design progresses."

One of the greatest concerns we should all have is the idea that because we can copy the processes found in living things, we can engineer those processes. The reality continues to be that we are ignorant of so much that is going on in the cell. The incident with the single-base mistake in the coding is just the tip of the iceberg! The information content of cells is such that we are continually out of our depth in understanding even the most basic functions. A specific concern is the way the research team describe the role of the recipient cell: a vessel that can be reprogrammed by the novel genome. This may be feasible with close relatives, but the danger is that information embedded in the recipient cell may be overlooked. The comments of Mae-Wan Ho are pertinent:

"Clearly the scientists have not created life or the bacterial cell. There is a yawning chasm in the physics and chemistry of the living state that the team hasn't even begun to address, let alone bridge. They did not create the genome that was used to transform the bacteria cell, only copied it from another species of the genus, adding a "water mark" for identification, and no doubt, for staking their claim to the synthetic genome. This synthetic genome was not even made from scratch, but cobbled together from pieces found in a catalogue, and then 'transplanted' into cells of the recipient bacterium species (a close relative of the donor) using an antibiotic to select for cells that have accepted the artificial chromosome and allow them to grow."

In his Muse column, Philip Ball also discusses reasons for caution. If we are going to research life, we must not reduce it to engineering the genome, where "the membranes, the cytoplasm - everything except the genes - are mere peripherals to the hard drive of life, whose algorithmic instructions need only be rejigged to produce new organisms."

"Attempts to make a genuinely 'designed' genome, rather than one based on a naturally evolved bacterium, will remind us how sketchy our understanding is of the rules that govern the crucial interactions among genes and with other elements of living cells. In the post-genomics era, our ideas of where the real business of life resides are shifting again. We are moving away from a linear 'code' and towards something altogether more abstract, emergent and entangled. So in marking yet another deepening appreciation of how life operates, the latest 'synthesis of life' seems likely to repeat the historical template."

Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome
Daniel G. Gibson, John I. Glass, Carole Lartigue, Vladimir N. Noskov, Ray-Yuan Chuang, Mikkel A. Algire, Gwynedd A. Benders, Michael G. Montague, Li Ma, Monzia M. Moodie, Chuck Merryman, Sanjay Vashee, Radha Krishnakumar, Nacyra Assad-Garcia, Cynthia Andrews-Pfannkoch, Evgeniya A. Denisova, Lei Young, Zhi-Qing Qi, Thomas H. Segall-Shapiro, Christopher H. Calvey, Prashanth P. Parmar, Clyde A. Hutchison III, Hamilton O. Smith & J. Craig Venter.
Science Express (May 20, 2010), doi 10.1126/science.1190719

Abstract: We report the design, synthesis, and assembly of the 1.08-Mbp Mycoplasma mycoides JCVI-syn1.0 genome starting from digitized genome sequence information and its transplantation into a Mycoplasma capricolum recipient cell to create new Mycoplasma mycoides cells that are controlled only by the synthetic chromosome. The only DNA in the cells is the designed synthetic DNA sequence, including "watermark" sequences and other designed gene deletions and polymorphisms, and mutations acquired during the building process. The new cells have expected phenotypic properties and are capable of continuous self-replication.

See also:

Ball, P. A synthetic creation story, Nature online 24 May 2010 | doi:10.1038/news.2010.261

Ho, M-W., Synthetic Life? Not By a Long Shot, ISIS Report 24/05/10

Life after the synthetic cell, Nature, 465, 422-424, (27 May 2010) |doi:10.1038/465422a

Pennisi, E. Synthetic Genome Brings New Life to Bacterium, Science 328, 21 May 2010, 958-959.

Wells, J. Has Craig Venter Produced Artificial Life? Evolution News & Views (May 24, 2010)

Kaebnick, G., Is the "Synthetic Cell" about Life? The Scientist, 24(7), July 2010, 27. [need to register for access]

The polar bear (Ursus maritimus) exhibits numerous adaptations to cold environments, fur, foot pads, head shape, exclusively carnivorous diet, heightened sense of smell, etc. Their close relationship to the brown bear (Ursus arctos) has long been recognised. Fertile hybrids are well-documented in captivity and there are rare examples of hybrids in the wild - the most recent being in 2006. Interbreeding, however, has not outweighed other taxonomic criteria, although it has been a factor in moving the polar bear from the genus Thalarctos back to the genus Ursus. "With their distinctly different morphology, metabolism, and social and feeding behaviors, the polar and brown bears are classified as separate species." Interestingly, a cluster of brown bears (known as ABC bears) have been found with close genetic links to polar bears.

"Recent genetic studies have shown that polar bears evolved from within brown bears, and that a genetically unique clade of brown bear populations that live exclusively on the Admiralty, Baranof, and Chichagof (ABC) islands of southeastern Alaska's Alexander Archipelago are more closely related to polar bears than to other brown bears."

The cold and dry conditions where this ancient polar bear jaw and canine were fossilized kept DNA within well preserved. (Credit: O. Wiig/University of Oslo's Natural History Museum, source here)

Speciation, then, has occurred, but when? how? and over what timescale? The opportunity to constrain the answers to these questions has come with the discovery of a jawbone with diagnostic polar bear traits from a site in Norway estimated to be 130-110 ky old. This makes it the most ancient sub-fossil yet to be recovered. Approximately 0.1 g of bone powder was used to generate a "complete, high-quality mt genome" using next-generation sequencing technology.

"The organization and length of the genome is comparable to that of extant bears, showing clear sequence similarity to both ABC bears and modern polar bears."

Using these data, phylogenetic analyses have been performed to probe relationships between the fossil bear (the Poolepynten specimen), modern-day polar bears, ABC bears and the modern brown bear variants.

"The phylogenetic results clearly demonstrate, with high support, the close relationship of the subfossil specimen to modern polar bear. Intriguingly, however, this ancient polar bear, which exhibits a very short branch length, lies almost directly at the branching point between polar bear and the genetically unique clade of ABC brown bears. Thus, both cladistically and anagenetically, this ancient specimen existed very close to the most recent common ancestor of polar bears and brown bears."

It is known that the diet of modern polar bears is dominated by ringed seals and bearded seals. Using the stable isotopes of carbon and nitrogen, it is possible to assess whether animal teeth (modern or sub-fossil) have a marine or a terrestrial signature.

"The stable isotope values for the ancient tooth [. . .] were within the range found from extant polar bear teeth and other tissues and were reflective of marine feeding. Importantly, these isotope values are distinct from those found in Late Pleistocene brown bears, including from the ABC brown bear lineage, as well as present-day coastal Alaskan brown bears. Thus, our results clearly demonstrate that the jaw is from an individual that had a feeding ecology similar to present-day polar bears, at the top of the Arctic marine food chain."

Using a molecular clock approach, the divergence time for the split between ABC bears and polar bears was estimated to be 152 ky. A further estimate was made of the emergence of the crown group of polar bears:

"Even more surprising, the age of the modern polar bear crown group (the clade containing the last common ancestor of all extant members) is estimated to be less than 45 ky, slightly older than the age of the ABC bears, a date that is also found with the expanded dataset of control-region sequence fragments. These estimates suggest a very recent and rapid expansion of modern polar bear populations throughout the Arctic since the Late Pleistocene, perhaps following a climate-related population bottleneck, although data from more modern and Holocene polar bear specimens will be required to establish this."

The authors conclude that speciation was rapid, consistent with the punctuated equilibrium (PE) model proposed to explain persistent patterns in the fossil record.

"The stable isotope data, phylogenetic analysis, and the geological and molecular age estimates of the Poolepynten specimen indicate that ancient polar bears adapted extremely rapidly both morphologically and physiologically to their current and unique ecology within only 10-30 ky following their split from a brown bear precursor and, subsequently, within the course of ~100 ky, spread to the full perimeter of the polar basin. As such, the polar bear is an excellent example of evolutionary opportunism within a widespread mammalian lineage. Moreover, the extreme proximity of the Poolepynten specimen to the polar bear ancestor provides a unique case of a morphologically and molecularly validated fossil link between living mammal species."

This research raises important questions for advocates of Darwinism. The PE model has been interpreted by them as a broad brush perspective. Consequently, the fossil record is considered too coarse to pick out the gradual transformation they insist must have occurred (because gradualism is the 'only way' to build complexity and achieve adaptation). However, this polar bear study shows that the timescales for change are too short to permit a viable gradualist explanation. This research shows the PE framework (of abrupt appearance followed by stasis) is realistic. Evolutionary theory must address issues like this and Darwinists should cease their confident rhetoric about the sufficiency of the mechanisms of mutations and natural selection.

Furthermore, Darwinists should realise that mere evidences of speciation are not the same as evidences for their theory. Polar bears display sophisticated adaptations, and if they are not gradualist phenomena, how can they be explained? If biological information is not acquired gradually, where does it come from? The ID perspective on this draws on numerous indicators of pre-existing information (for example, it is now widely recognised that much genetic information and associated regulative systems preceded the Cambrian Explosion). From this perspective, rapid speciation is possible because pre-existing information can be restructured and re-expressed in novel ways. The scientific challenge is to determine the mechanisms responsible for this type of information-rich speciation.

By contrast, Darwinism explains only information-neutral (finch beaks and peppered moths) or information-degradation (antibiotic resistance) scenarios. For confusing these various types of biological transformations, Darwinism's influence on biology has been unhealthy and scientific progress has been inhibited.

Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear
Charlotte Lindqvist, Stephan C. Schuster, Yazhou Sun, Sandra L. Talbot, Ji Qi, Aakrosh Ratan, Lynn P. Tomsho, Lindsay Kasson, Eve Zeyl, Jon Aars, Webb Miller, Olafur Ingolfsson, Lutz Bachmann and Oystein Wiig.
Proceedings of the National Academies of Science, USA, March 16, 2010 vol. 107 no. 11 5053-5057 | doi: 10.1073/pnas.0914266107

Abstract: The polar bear has become the flagship species in the climate-change discussion. However, little is known about how past climate impacted its evolution and persistence, given an extremely poor fossil record. Although it is undisputed from analyses of mitochondrial (mt) DNA that polar bears constitute a lineage within the genetic diversity of brown bears, timing estimates of their divergence have differed considerably. Using next-generation sequencing technology, we have generated a complete, high-quality mt genome from a stratigraphically validated 130,000- to 110,000-year-old polar bear jawbone. In addition, six mt genomes were generated of extant polar bears from Alaska and brown bears from the Admiralty and Baranof islands of the Alexander Archipelago of southeastern Alaska and Kodiak Island. We show that the phylogenetic position of the ancient polar bear lies almost directly at the branching point between polar bears and brown bears, elucidating a unique morphologically and molecularly documented fossil link between living mammal species. Molecular dating and stable isotope analyses also show that by very early in their evolutionary history, polar bears were already inhabitants of the Artic sea ice and had adapted very rapidly to their current and unique ecology at the top of the Arctic marine food chain. As such, polar bears provide an excellent example of evolutionary opportunism within a widespread mammalian lineage.

See also:

Kaplan, M., Ancient polar-bear fossil yields genome, Nature News, online 1 March 2010 | doi:10.1038/news.2010.99

Tyler, D.J. Unexpected genome complexity in the starlet sea anemone, ARN Literature blog (11 July 2007)

On molecular clocks, go here and here.

It was 15 months ago that Science carried a story about the completion of a rough draft of the Neandertal genome. Palaeogeneticist Svante Paabo of the Max Planck Institute for Evolutionary Anthropology in Leipzig was reported as saying "he can't wait to finish crunching the sequence through their computers". It has been quite a long time coming, as it is more than a decade since Paabo first demonstrated it was possible to analyse Neandertal DNA sequences. Earlier reports suggested that Neandertals were sufficiently distinct from humans for them to be classified as a separate species of Homo. The draft genome has more than 3 billion nucleotides collected from three female Neandertals.

"By comparing this composite Neandertal genome with the complete genomes of five living humans from different parts of the world, the researchers found that both Europeans and Asians share 1% to 4% of their nuclear DNA with Neandertals. But Africans do not. This suggests that early modern humans interbred with Neandertals after moderns left Africa, but before they spread into Asia and Europe. The evidence showing interbreeding is "incontrovertible," says paleoanthropologist John Hawks of the University of Wisconsin, Madison, who was not involved in the work. "There's no other way you can explain this"."

Neanderthals once bred with Homo sapiens. (credit PHOTOLIBRARY, source here)

Genetically, then, Neandertals are not altogether extinct. Paabo is quoted as saying: "They live on in some of us". Therefore, the 'Out-of-Africa' model needs revision, as the migrants interbred to some extent with Neandertals and their genetic signatures spread through the migrant populations. According to Rex Dalton in Nature:

"That revelation is likely to revive the debate about whether or not the two groups are separate species, says anthropologist Fred Smith of Illinois State University in Normal, who has studied Neanderthals in Europe. Smith thinks that they are a subspecies of H. sapiens. Now that the genomes can be compared, it will be possible to investigate the genetic roots of some shared features."

This theme is picked up in the pages of New Scientist, and especially noteworthy is the editorial: "Welcome to the human family, Neanderthals". It calls for Neanderthals to be given a warm reception as truly human relatives.

"Svante Paabo, the pioneer of palaeogenetics, equivocated when a reporter asked whether his genome study suggested Neanderthals are the same species as us: "I would more see them as a form of humans that were a bit more different than people are from each other today, but not that much."
Why so shy? Putting aside the vexing question of what defines a species - which flummoxed even Linnaeus and Darwin - it is hard to see why Neanderthals should now be considered as anything other than Homo sapiens. We know that Neanderthals bred with our ancestors and produced fertile offspring, which is one hallmark of a species. And there is plenty more evidence to support giving them the status of Homo sapiens neanderthalis. Neanderthals shared a common ancestor with modern humans around 500,000 years ago. Its descendants went their separate ways as the Neanderthals adapted to colder climes, but then, at least 50,000 years ago, they resumed relations in the eastern Mediterranean, where the two populations met again. This pattern wouldn't necessarily merit separate species status for most animals, so why for us and Neanderthals?"

There is undoubtedly some journalistic enthusiasm here, because the claimed "hallmark of a species" is not valid: hybridisation is not that unusual between species and sometimes it occurs between genera (within the same family). This in itself is not a decisive argument. However, when we combine genetics, morphology and behaviour, the picture looks much clearer.

"There is, of course, more to the concept of being human than ecology and genetics: we are human because we think, talk, love and believe. It is impossible to know the mental life of a Neanderthal, but there is reason to think that it was not so different from our own. The Neanderthal genome differed little from ours, encoding fewer than 100 changes that would affect the shape of proteins. True, some of these differences occur in genes linked to brain function, but similar variation is found among humans today. Moreover, Neanderthals share with us a version of a gene linked to the evolution of speech, and recent archaeological evidence suggests that their minds were capable of the symbolic representations that underlie language and art. If that's not human, then what is?"

This brings us to why Neandertals have been so misinterpreted over the years. Why has it taken us so long to reject the picture of a brutish, grunting caveman devoid of aesthetics and reason? The Editorial starts with these words: "WE HUMANS like to see ourselves as special, at the very pinnacle of all life. That makes us keen to keep a safe distance between ourselves and related species that threaten our sense of uniqueness. Unfortunately, the evidence can sometimes make that difficult." Is this interpretation valid? Do we like to keep a safe distance between ourselves and anything that threatens our uniqueness? Perhaps we should reflect on on the history of scientific racialism, that portrayed races as occupying different rungs of the evolutionary ladder - was this also to keep a safe distance from races that threatened our uniqueness? Furthermore, is it true that we, the population at large, like to keep this safe distance? Why is it that any reports of animals showing apparent cognitive and creative skills are deemed newsworthy, whereas other studies showing a big divide between humans and animals languish in obscurity? I leave these questions for further thought and reflection.

One thing I have noticed over the years is that people with a design perspective have been far more receptive to the idea that Neandertals were part of the human family. They have been impressed by morphological considerations, but the cultural artifacts of Neandertals have made a big impression. In the early days, these were relatively meager, but more recent years have seen a flowering of reports of Neandertal culture. In this blog, these issues have been explored on several occasions: Burying the view that Neanderthals were half-wits, Darwinist thinking on the origin of religion, The cognitive skills of Stone Age Man, Images of evolution as secular icons, Walks like a man, talks like a man - is it a man?, and Rethinking Neanderthals. There is a pattern here, and it is evident even in the original reception given to Neandertal finds. The Darwinian scientists were looking for intermediates and they found one in Neandertal Man. He was portrayed as an ape-man and used to prop up an evolutionary story of ape-to-man evolution. After it was realised that the original finds were bones from someone deformed by disease, the story did not change much. The icon was too important to lose. Darwinism had created a blind spot for palaeoanthropologists and impaired the progress of science. Those able to make design inferences within science have been ahead of the game, but now the genetic data is published, all have to follow. However, would you believe, the same issue of New Scientist that carried the editorial noted above also had an article with the title: "Neanderthals not the only apes humans bred with". Apes? Really! Outdated traditions do not die when it comes to Darwinism - they just get repackaged!

A Draft Sequence of the Neandertal Genome
Richard E. Green [et al] and Svante Paabo
Science, 328, 7 May 2010: 710-722 | DOI: 10.1126/science.1188021

Abstract: Neandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe and western Asia before disappearing 30,000 years ago. We present a draft sequence of the Neandertal genome composed of more than 4 billion nucleotides from three individuals. Comparisons of the Neandertal genome to the genomes of five present-day humans from different parts of the world identify a number of genomic regions that may have been affected by positive selection in ancestral modern humans, including genes involved in metabolism and in cognitive and skeletal development. We show that Neandertals shared more genetic variants with present-day humans in Eurasia than with present-day humans in sub-Saharan Africa, suggesting that gene flow from Neandertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.

See also:

Dalton, R., Ancient DNA set to rewrite human history, Nature, 465, 148-149, (12 May 2010) | doi:10.1038/465148a

Editorial, Welcome to the human family, Neanderthals, (New Scientist, 12 May 2010)

Gibbons, A., Close Encounters of the Prehistoric Kind, Science 328, 7 May 2010: 680-684.

A previous blog drew attention to Glial (or Muller) cells that conduct light from the surface of the eye's retina to the photoreceptor cells. These cells provide a low-scattering passage for light from the retinal surface to the photoreceptor cells, thus acting as optical fibres. Their function was reported to "mediate the image transfer through the vertebrate retina with minimal distortion and low loss". New research in this area has increased knowledge of their functionality after constructing a light-guiding model of the retina outside the fovea. As a result, the "retina is revealed as an optimal structure designed for improving the sharpness of images".

Schematic of Muller cells funnelling light (source here)

These specialised cells do this in two ways: filtering out stray light and reducing colour dispersion. Stray light is a form of noise, so that the objects of interest are seen less clearly. It is found that the glial cells improve the signal-to-noise ration as light passes through them.

"The simulations showed that the Muller cells transmit a greater proportion of the former to the rods and cones below, while the latter tends to leak out. This suggests the cells act as light filters, keeping images clear. The researchers also found that light that had leaked out of one Muller cell was unlikely to be taken up by a neighbour, because the surrounding nerve cells help disperse it. What's more, the intrinsic optical properties of Muller cells seemed to be tuned to visible light, leaking wavelengths outside and on the edges of the visible spectrum to a greater extent."

The second mechanism relates to colour vision. "Just as light separates in a prism, the lenses in our eyes separate different colours, causing some frequencies to be out of focus at the retina". However, the glial cells have a diameter that is wider at the surface of the retina than at the cone photoreceptor at its base. The optical fibre structure of these cells brings significant improvements.

"Another notable result is that parafoveal color vision is less affected by chromatic aberrations. The longitudinal chromatic aberration spans the focal spot along the retina, where blue focuses before red. Thus both colors cannot be focused simultaneously on the cones. But with glial light guiding the configuration changes: Regardless of the volume of the focal spot, set by chromatic and monochromatic aberrations, the incidence angles are still within our analysis range of a few degrees. That means that they will still be guided by the same glial cell and lead to the same cone."

According to the report in New Scientist, these findings open up potentially fruitful areas for biomimetic research. "The new understanding of the role of Muller cells might find applications in more successful eye transplants and better camera designs, says Ribak." The human eye, which is already a remarkable example of functional engineering, continues to yield more evidences of exquisite design. All the more surprising, then, that Darwinians are persisting in their view that the eye should be listed among evolution's biggest "mistakes". An Editorial in New Scientist reaffirms the validity of this claim:

"Sure, sending light through Muller cells enhances vision, but that is not an argument for choosing to put the wiring in front of the sensors. It still creates a blind spot, where the nerves dive through the light-sensitive cells on their way to the brain. It would make much more sense to put Muller-like cells in front of the sensors, with the wiring behind. Rather than provide evidence in support of intelligent design, the new work is actually yet another example of evolution's extraordinary ability to create workaround solutions to problems arising from earlier iterations. Kenneth Miller, a biologist at Brown University in Providence, Rhode Island, and an untiring veteran of the creation-evolution wars, calls the Muller cells "a retrofit: a successful and highly functional adaptation made necessary by the original architecture of the retina, but a retrofit". The eye's structure, and the blind spot in particular, bears the unmistakable fingerprints of Darwinian evolution."

What we are seeing here fits what Thomas Kuhn called "normal science" in action. Darwinists never predicted the function performed by Muller cells, but once they were recognised, they are dubbed a "retrofit", with credit given to the amazing powers of mutation and natural selection (without any valid supporting evidence). This strategy is to Darwinism what epicycles were to the Ptolemaic cosmology. Actually, Kenneth Miller is retrofitting glial cells into the Darwinian model of the eye's evolution. He has to do this in order to save the theory in which so much intellectual capital is invested. But like the financial markets of today, crises will ensue. Just as commercial markets could not sustain high levels of debt indefinitely, so also Darwinism: they have borrowed excessively in order to sustain mutation and natural selection as viable mechanisms. When people look for substance, they find peppered moths and bird beaks. When they look carefuly, they find exquisite design - not tinkering evolution. All the Darwinists have left to defend their case is the blind spot - that is all that keeps them from the conclusion of optimal design.

Retinal Glial Cells Enhance Human Vision Acuity
A. M. Labin and E. N. Ribak
Physical Review Letters, 104, 158102 (April 2010) [4 pages] | DOI: 10.1103/PhysRevLett.104.158102

Abstract: We construct a light-guiding model of the retina outside the fovea, in which an array of glial (Muller) cells permeates the depth of the retina down to the photoreceptors. Based on measured refractive indices, we propagate light to obtain a significant increase of the intensity at the photoreceptors. For pupils up to 6 mm width, the coupling between neighboring cells is only a few percent. Low cross talk over the whole visible spectrum also explains the insensitivity to chromatic aberrations of the eye. The retina is revealed as an optimal structure designed for improving the sharpness of images.

See also:

Editorial, The eye was evolution's great invention, New Scientist (6 May 2010)

McAlpine, K. Evolution gave flawed eye better vision, New Scientist (6 May 2010)

John Avise commences his paper with a quotation from Michael Behe affirming that research into the molecular workings of the cell leads unambiguously to the conclusion: "design!". To counter this, Avise presents the human genome as clear evidence for non-sentient design. He thinks that conventional evolutionary mechanisms are perfectly capable of explaining complexity, declaring: "it is not my intent here to repeat the voluminous evidence for how natural selection in conjunction with other nonsentient evolutionary forces can yield complex adaptations". Instead, he suggests that the decision as to whether the design is intelligent or non-sentient can be made by looking at the imperfections and flaws evident in the cell's molecular systems.

"Both a Creator God and natural selection are powerful shaping forces that might be expected to have engineered beautiful functionality and efficiency into complex biological features, such as the human genome. The much greater challenge - for proponents of ID and for scientists alike - is to explain complex biological traits that operate inefficiently or even malfunction overtly. On closer inspection, the human genome itself becomes a prime example of a highly complex trait with serious molecular shortcomings."

"The Hopeless Dawn" by Frank Bramley. Don't look to science for a way to face suffering, pain and loss. (source here)

Avise draws our attention to the large number of genetic mutations that have been discovered (most of which are associated with disease or impairment). The figure of 75,000 different disease-causing mutations is mentioned. It should not be necessary to point out that this is not news to ID scholars (some of whom have a professional interest in providing medical treatments for these conditions). The existence of large numbers of deleterious mutations has been used to argue against the efficacy of Darwinian mechanisms of evolutionary transformation (especially as the comparable list of advantageous mutations is not noted for its length). Nevertheless, the reason why Avise presses this information on us is that he thinks ID scientists have been blind to them as witnesses to 'tinkering' evolutionary mechanisms.

"An apologist for the intelligent designer might be tempted to claim that such deleterious mutations are merely unavoidable glitches or secondary departures from a prototypical human genome that otherwise was designed and engineered to near perfection. As I will briefly describe in the next two sections, however, this excuse would be untenable, because all human genomes are also littered with inherent (endogenous) design flaws."

The first of these sections is concerned with "gratuitous genome complexity". Avise presents an argument based on the phenomenon of "split genes". Protein-coding loci are split into coding regions (exons) and non-coding regions (introns). A vast infrastructure of molecular machinery exists to extract the coding information and splice it all together. This is suggested to add time and metabolic cost to the process of making proteins. But the real punch-line is that there are many mutations associated with both intron/exon borders and the splicing machinery. The disadvantages are said to completely outweigh any advantages emerging from the split gene design. After considering other examples of complexity, Avise concludes:

"Why an intelligent and loving designer would have infused the human genome with so many potential (and often realized) regulatory flaws is open to theological debate. [. . .] From an evolutionary perspective, such genomic flaws are easier to explain. Occasional errors in gene regulation and surveillance are to be expected in any complex contrivance that has been engineered over the eons by the endless tinkering of mindless evolutionary forces: mutation, recombination, genetic drift, and natural selection. Again, the complexity of genomic architecture would seem to be a surer signature of tinkered evolution by natural processes than of direct invention by an omnipotent intelligent agent."

This style of argument is in the tradition adopted by Charles Darwin: theological arguments are used to reject intelligent causation, allowing "mindless evolutionary forces" to win by default. ID advocates have responded to these arguments on numerous occasions: design flaws cannot provide a valid argument against intelligent agency because design can co-exist with flaws. For example, flaws in human designs do not imply that the work is the product of a mindless process (design office manager's comments notwithstanding!). Furthermore, in this case, Avise is confusing his theological objections to an intelligent (and loving) designer with his assertion that the complexity of genomic architecture is a "surer signature of tinkered evolution by natural processes". The latter claim is of relevance to the ID perspective, but Avise has only offered his opinion and he has not demonstrated that tinkering can produce anything like spliceosomes, the associated processing machinery or the operational code.

The second category of evidence is "wasteful design". He refers to duplicons, pseudogenes and the "abundance of mobile elements" (collectively known as junk DNA). The argument is essentially the same as was developed for the first category: since a large number of genetic disorders in humans can be traced to mutations affecting these components of the genome, ID is incoherent. The general conclusion drawn is as follows:

"From scientific evidence gathered during the past century, and especially within recent decades, we now understand that the human genome and the metabolic processes it underwrites are riddled with structural and operational deficiencies ranging from the subtle to the egregious. These genetic defects register not only as deleterious mutational departures from some hypothetical genomic ideal but as universal architectural flaws in the standard genomes themselves. The findings of molecular biology thus offer a gargantuan challenge to notions of ID. They extend the age-old theodicy challenge, traditionally motivated by obvious imperfections at the levels of human morphology and behavior, into the innermost molecular sanctum of our physical being."

This paper certainly reinforces the view that the primary argument against intelligent design is theological. Once the concept of intelligent agency is removed, we can relax in the arms of the pitiless, uncaring, blind forces of nature.

"No longer must we anguish about the interventionist motives of a supreme intelligence that permits gross evil and suffering in the world. No longer need we be tempted to blaspheme an omnipotent Deity by charging Him directly responsible for human frailties and physical shortcomings [. . .]. No longer need we blame a Creator God's direct hand for any of these disturbing empirical facts. Instead, we can put the blame squarely on the agency of insentient natural evolutionary causation."

We need to return to the claim that the human genome exhibits the tinkering characteristics of a blind watchmaker. Avise is saying, in effect, that the genome is chaotically complex and highly vulnerable to degradation. What needs to be said in response to this is that we are just beginning to analyse this complexity. The first casualty resulting from new knowledge is the concept of Junk DNA, which is now linked to all sorts of regulatory functions in the cell. Why were so many molecular biologists confident that 98% of our DNA was functionless? Ultimately, their quest for simplicity at the genomic level made them blind to complexity, and the designation "junk" fitted into their preconceived notions of a wasteful evolutionary process. The pendulum has now swung to where complexity is acknowledged - but they still think of it as an unplanned (nonsentient) complexity. The ID prediction is that the pendulum will swing further and reveal an intelligently organised complexity with numerous regulatory feedback mechanisms in place. In his Nature column, Philip Ball correctly cautions against some of the assumptions made by Avise:

"However [. . .] it is worth pointing out that some of the genomic inefficiencies Avise lists are still imperfectly understood. We should be cautious about writing them off as 'flaws', lest we make the same mistake evident in the labelling as 'junk DNA' genomic material that seems increasingly to play a biological role. There seems little prospect that the genome will ever emerge as a paragon of good engineering, but we shouldn't too quickly derogate that which we do not yet understand."

So, are the findings of molecular biology "a gargantuan challenge to notions of ID"? The answer is a resounding no. ID does not set out to address the theodicy argument but to establish whether intelligent design and purposeful information characterises the natural world. It stands in the empiricist tradition. We are not justified in rejecting the findings just because we find them unpalatable. Further, Avise has not provided a robust defence of tinkering evolutionary processes. If anything, his argument is based on ignorance. As we learn more of the complexity of biological systems (probably using the tools of systems biology), we will become better informed about tinkering vs exquisite design. Every week, new research brings relevant information to our attention: this week it is the deciphering of the splicing code (undermining Avise's view that the cell would be better off without introns and that the protein-coding regions of DNA are chaotic). There are good books that base they arguments on what we do know (books like Darwin's Black Box and Signature in the Cell), and these provide us with strong reasons for reaching the conclusion that the design we see is exquisite.

Footprints of nonsentient design inside the human genome
John C. Avise
Proceedings of the National Academy of Sciences, Published online before print May 5, 2010 | doi: 10.1073/pnas.0914609107

Abstract: Intelligent design (ID) - the latest incarnation of religious creationism - posits that complex biological features did not accrue gradually via natural evolutionary forces but, instead, were crafted ex nihilo by a cognitive agent. Yet, many complex biological traits are gratuitously complicated, function poorly, and debilitate their bearers. Furthermore, such dysfunctional traits abound not only in the phenotypes but inside the genomes of eukaryotic species. Here, I highlight several outlandish features of the human genome that defy notions of ID by a caring cognitive agent. These range from de novo mutational glitches that collectively kill or maim countless individuals (including embryos and fetuses) to pervasive architectural flaws (including pseudogenes, parasitic mobile elements, and needlessly baroque regulatory pathways) that are endogenous in every human genome. Gross imperfection at the molecular level presents a conundrum for the traditional paradigms of natural theology as well as for recent assertions of ID, but it is consistent with the notion of nonsentient contrivance by evolutionary forces. In this important philosophical sense, the science of evolutionary genetics should rightly be viewed as an ally (not an adversary) of mainstream religions because it helps the latter to escape the profound theological enigmas posed by notions of ID.

See also:

Ball, P. What a shoddy piece of work is man, Nature News, 3 May 2010 | doi:10.1038/news.2010.215

There is general agreement that science education has its problems, but much less agreement about what those problems are. A helpful review has appeared in Science and it deserves to be widely discussed. Everyone in the science community is aware that critiques, peer review and reasoned argument are essential to the health of our discipline. Consensus has to be earned by this process of critical examination - which does not stop when theories become widely accepted.

"Critique is not, therefore, some peripheral feature of science, but rather it is core to its practice, and without argument and evaluation, the construction of reliable knowledge would be impossible. Whether it is the theoretician who is developing new models of phenomena or the experimentalist who is proposing new ways of collecting data, all scientists must subject their ideas to the scrutiny of their peers. But what of science education?"

Children learning science: these 7-year-olds were tackling chemistry in 1948 (source here)

The problem with much science education is that often these intellectual skills are not developed in the classroom. Students are taught an authoritative body of facts and theories in a way that encourages submission rather than critical appraisal.

"Science education, in contrast, is notable for the absence of argument. Although instructors and teachers may offer many explanations, these are not arguments. To offer an explanation of a fact is to presume it is true. An argument, in contrast, is an attempt to establish truth and commonly consists of a claim that may be supported by either data, warrants (that relate the data to the claim), backings (the premises of the warrant), or qualifiers (the limits of the claim). Some or all of these elements may be the subject of rebuttals or counter-arguments. [. . .] Consequently, science can appear to its students as a monolith of facts, an authoritative discourse where the discursive exploration of ideas, their implications, and their importance is absent. Students then emerge with naive ideas or misconceptions about the nature of science itself."

This problem is so serious that it deserves to be analysed using worldview concepts. What is our understanding of science? What conceptual model leads to a "monolith of facts" and "an authoritative discourse"? It is a "consensus" perspective of science, where 'teaching the controversy' is excluded because only uncontested science is on the curriculum. However, this version of consensus science is a betrayal of basic principles and is highly vulnerable to being steered by political, ideological or business agendas. Teaching based on this consensus model may lead to students adopting "reasoning strategies with a confirmatory bias rather than using logical criteria". Students come to realise that they are rewarded for reaching the 'right' answers rather than developing transferable critical skills.

"The common explanation of the absence of argument is that it is a product of an overemphasis by teachers, curricula, and textbooks on what we know at the expense of how we know. Deep within our cultural fabric, education is still seen simplistically as a process of transmission where knowledge is presented as a set of unequivocal and uncontested facts and transferred from expert to novice. In this world-view, failure of communication is the exception and success the norm. However, in reality, education is a highly complex act where failure is the norm and success the exception."

This week has also seen a stimulating review in the US Chronicle of Higher Education of "the latest of a now common genre of science patriotism, Nonsense on Stilts: How to Tell Science From Bunk (University of Chicago Press), by Massimo Pigliucci, a philosophy professor at the City University of New York." The reviewer, who is himself a philosophy professor, writes of science warriors who have a view of science that is 'authoritative' and 'true'.

"The problem with polemicists like Pigliucci is that a chasm has opened up between two groups that might loosely be distinguished as "philosophers of science" and "science warriors." Philosophers of science, often operating under the aegis of Thomas Kuhn, recognize that science is a diverse, social enterprise that has changed over time, developed different methodologies in different subsciences, and often advanced by taking putative pseudoscience seriously, as in debunking cold fusion. The science warriors, by contrast, often write as if our science of the moment is isomorphic with knowledge of an objective world in itself - Kant be damned! - and any form of inquiry that doesn't fit the writer's criteria of proper science must be banished as "bunk." Pigliucci, typically, hasn't much sympathy for radical philosophies of science."

So, opportunities for argument and the use of critical thinking skills are urgently needed in science education. This is the take-home message of the paper in Science. For years now, scholars open to the detection of intelligent design as a product of scientific research have sought to contribute to the debate about education. 'Teaching the controversy' has been recommended as good educational practice, providing opportunity to develop arguments and to develop critical thinking skills, only to be met with hostility and rejection. There is no controversy, opponents said, evolutionary theory is robust and has achieved the status of consensus science. Evolutionists want to present their favoured ideas as "unequivocal and uncontested". The reason they get away with such shallow reasoning is that there is a wider, more general malaise within science. This is why the Chronicle review (above) is relevant: there is a vocal group of science warriors who are largely advocates of positivism, secularism and atheism that are using science to promote philosophical naturalism. This is why these issues affect us all. This is a struggle for the freedom to follow the evidence wherever it leads, and to resist those who come to us with deductive claims about the way the world is. It is also a struggle for real education instead of indoctrination by secularists.

Arguing to Learn in Science: The Role of Collaborative, Critical Discourse
Jonathan Osborne
Science, 23 April 2010: Vol. 328, pp. 463-466 | DOI: 10.1126/science.1183944

Abstract: Argument and debate are common in science, yet they are virtually absent from science education. Recent research shows, however, that opportunities for students to engage in collaborative discourse and argumentation offer a means of enhancing student conceptual understanding and students' skills and capabilities with scientific reasoning. As one of the hallmarks of the scientist is critical, rational skepticism, the lack of opportunities to develop the ability to reason and argue scientifically would appear to be a significant weakness in contemporary educational practice. In short, knowing what is wrong matters as much as knowing what is right. This paper presents a summary of the main features of this body of research and discusses its implications for the teaching and learning of science.

Science Warriors' Ego Trips
By Carlin Romano
The Chronicle Review, April 25, 2010

1st paragraph: Standing up for science excites some intellectuals the way beautiful actresses arouse Warren Beatty, or career liberals boil the blood of Glenn Beck and Rush Limbaugh. It's visceral. The thinker of this ilk looks in the mirror and sees Galileo bravely muttering "Eppure si muove!" ("And yet, it moves!") while Vatican guards drag him away. Sometimes the hero in the reflection is Voltaire sticking it to the clerics, or Darwin triumphing against both Church and Church-going wife. A brave champion of beleaguered science in the modern age of pseudoscience, this Ayn Rand protagonist sarcastically derides the benighted irrationalists and glows with a self-anointed superiority. Who wouldn't want to feel that sense of power and rightness?

Edward Wasserman and Mark Blumberg are interested in explaining the origins of novel behaviours. They are aware of several research groups working with animals and give the example of crows that were observed to fashion wires into hooks that were in turn used to gain access to food. The researchers interpreted the crow behaviour using the concepts of creativity and insight. But this is a mistake, argue Wasserman and Blumberg. The crows are learning by trial-and-error, not by forethought.

"Nonetheless, we seem to be in the midst of a resurgence of faith among some scientists that animal behavior can be explained by creativity, insight and other mentalistic concepts. For our part, we remain skeptical about the utility of such groundless explanations. Indeed, we are unconvinced that creativity and insight are proper explanations even for human behavior."

Is design a crumbling iconic concept? (source here)

The authors draw inspiration from The Evolution of Useful Things (1993) by the engineer Henry Petroski. The thesis of the book is that the design maxim "form follows function" does not reflect the history of design, and Petroski argues, instead, that "form follows failure". In other words, humans are inveterate tinkerers and indulge in experimentation; some of these avenues are found to lead somewhere and are valued, whereas others are unsuccessful and are abandoned. This leads to an incremental evolutionary process, analogous to the "survival of the fittest".

"It is through this plodding process that today's designs - typically instantiated in the form of a detailed blueprint - embody all of the hard, painful, but often unacknowledged lessons of the past. Most of us are ignorant of that history, yet we glibly proclaim that the final products were intelligently designed, thereby perpetuating the myth of the creative moment. We then carry that myth forward and attribute each new artifact to individual insight, creativity and genius."

The authors of the article are aware of the way that Darwinist thinking has impacted our culture, not just the science of origins. They suggest that even Charles Darwin and Richard Dawkins were not radical enough to apply these ideas to "that last bastion of designer intelligence, our minds". Why should our minds be exempt from being understood in Darwinian terms?

"What did Dawkins mean when he wrote of things that "really are designed"? In The Blind Watchmaker, he provided a clear answer: "All appearances to the contrary, the only watchmaker in nature is the blind forces of physics. [. . .] A true watchmaker has foresight: He designs his cogs and springs, and plans their interconnections, with a future purpose in his mind's eye" [emphasis added].
Such uncritical acceptance of purpose and foresight in human design may well be unwise. [. . .] By attributing the origins of animals and artifacts to different kinds of designers - one blind, the other intelligent - both Darwin and Dawkins lapse into the same kind of "designer thinking" that ensnared creationists like Paley."

The authors are objecting to "mentalistic explanations of behavior", and "giving human designers too much credit". In their eyes, appealing to "foresight and purpose" indicates a lack of critical thinking. The effect of all this is to bring to the fore the stimulus-response framework of behavioural psychology. This makes learning in animals and humans the result of associations being forming between stimuli and responses. The authors refer to psychologist Edward Thorndike and one of his three laws: the "law of effect" says that responses to a stimulus which are followed by a reward will be reinforced and will become habitual.

"Importantly, this positively Darwinian process exists entirely outside the realm of purpose or foresight. If everything in nature is the result of fixed laws, as Darwin himself proposed, then would he not also have marveled at the explanatory power of the law of effect - which was not discovered until several decades after his death - and its compelling parallels with natural selection?"

The authors have contributed an essay which is in the tradition of explaining human beings completely in terms of physics and chemistry. Distinctive aspects of humanity are ultimately treated as myths: consciousness, creativity, foresight and purpose. Design thinking (they suggest) should be reformulated in Darwinian terms and evolutionists should be freed from disputes over "over where to draw the line between things that really are designed and things that only appear to be designed". Some of my past blogs have considered consciousness, evolutionary psychology, Darwin's thinking about the continuity of mind, and attempts to deconstruct love. These research 'findings' have the basic premises of materialism and rationalism. Their philosophical roots are not determined scientifically (for that is impossible) but are assumed. The researchers' attempts to deconstruct humanity are destructive. Happily, they are also flawed. In the case of creativity and design, the authors point to the role of trial and error and generalize from that. What they do not do is to grapple with concepts like induction, intuition, inspiration and brain-storming. Nobody denies that a process of experimentation follows the emergence of a design concept. Most will question whether that process is best described as "trial and error" because they will expect an intelligent design of experiments rather than tinkering. The flaw is to think that because design prototypes experience (intelligent) selection, the whole process is devoid of purpose and foresight.

The main problem facing our culture is that the materialists have tried to gain a monopoly for their favoured philosophy. They are always claiming that you have to be a materialist to do science. This means that they have an easy ride in the journals and in academic forums. Roll on the day when this straightjacket is removed, and scholars can follow the evidence wherever it leads.

Designing Minds
Edward A. Wasserman and Mark S. Blumberg
American Scientist, May-June 2010, Volume 98, Number 3, Pages 183f | DOI: 10.1511/2010.84.183

First paragraph: The basic argument of intelligent design was famously set forth in the watchmaker analogy of William Paley in 1802: The complexity and functionality of a watch imply a watchmaker; analogously, the complexity and functionality of living things also imply a designer, albeit one vastly more potent than a mere watchmaker. This argument rests on a simple analogy between the design of human artifacts and the design of natural forms. For the analogy to work, we must first accept that we design our inventions with purpose and foresight. On this point, most evolutionists and creationists agree. What distinguishes these two camps is that, when accounting for the origin of living things, proponents of intelligent design summon a divine creator, whereas evolutionists credit natural selection. Thus, evolutionists share with creationists the same understanding of design; they differ only in how they invoke it.

OOL researchers need chemical building blocks with which to work, and amino acids are the most basic pre-biotic molecules. The Miller-Urey route for synthesising these molecules in the primordial Earth gained instant popularity for kicking off a self-assembly process. That mechanism has been eclipsed in recent years, not least because the necessary reducing atmosphere was perceived to be unrealistic by researchers. Consequently, interest in other ways of generating amino acids is high and there has been a steady stream of publications that address the issues. One of these mechanisms is concerned with the chemistry of comet and meteorite collisions with planet Earth.

Organic molecules are found in space, but do they have anything to do with biology? (Image credit Mario Iliev, source here)

A previous blog noted Japanese research simulating chondritic meteorite impacts, producing various organic chemicals including one amino acid (glycine). A US group led by Nir Goldman, based at the Lawrence Livermore National Laboratory, has considered cometary impacts. The initial conditions were chosen to match known compositions: a mixture of water, methanol, ammonia, carbon monoxide and carbon dioxide. The mechanism under investigation is shock compression.

"When a comet strikes a planet, a shock wave travels through it as it comes to a sudden halt. This, Goldman explains, compresses the comet, and the compression wave travels through the comet faster than the speed of sound. As a result, the molecules inside deform and bonds break."

The research makes use of validated theory and extensive simulation modeling. The findings are the result of "around one million computer hours on the powerful Atlas computer cluster at Lawrence Livermore". They chose a side-on impact because a head-on collision was considered likely to destroy rather than fabricate.

"For shock compressions lasting about 20 picoseconds at temperatures up to 4,000 K and pressures about 60 gigapascals, the researchers observed formation of chains of carbon and nitrogen atoms, some parts of which were akin to chains of amino acids. When they modeled an expansion period of 50 picoseconds, the longer chains broke up into smaller components, including a glycine-CO2 complex. The overall mixture is acidic, so the glycine-CO2 complex could react with H3O+ to produce glycine and CO2 in an exothermic reaction, Goldman said."

The implications of the research are more controversial. Do the findings help or constrain speculations about panspermia or the origin of life? The answers appear to be both yes and no.

Yes, those advocates of panspermia that point to amino acids in meteorites or comets as indicating a biotic source or as evidence of a directed or undirected colonization of the galaxy need to rethink their arguments. These organic molecules appear to be products of shock chemistry, UV radiation or some other process yet to be discovered. The mere fact of their existence does not provide any basis for inferring extraterrestrial biology. Although the enantiomeric composition of some of these molecules has been deemed to point to a biotic source, this conclusion may be wrong. Mechanisms for producing left-handed molecules in extraterrestrial environments are being examined (example here). So, this casts doubt on the recent claim of Chandra Wickramasinghe that "it seems likely that interstellar organics in large measure [. . .] derive from biology". Consequently, panspermia needs to be defended on other grounds (For example, go here).

No, speculations about the origin of life are not constrained. This is because there is an unwritten rule that all prerequisites for life count as evidence for abiogenesis. Finding a planet in the habitable zone; detecting the presence of water; recovering amino acids from space - all fuel the appetites of those who think that if life can self-assemble on Earth, it can self-assemble anywhere if conditions permit! Thus, the article from Nature News refers to crashing comets creating the "potential for life" and amino acids are described as "markers of potential life".

However, the finding of science emerging from OOL research is that an availability of traces of amino acids does not suggest that life can emerge via either Law or Chance processes. It is significant that people have become familiar with the 1953 experiments of Stanley Miller, but few ever refer to his subsequent work. He spent his career trying to achieve something more significant than amino acid residues but, although other organic compounds were obtained, he repeatedly faced dead ends. "Making the amino acids made it seem like the rest of the steps would be very easy," he said in a 1996 interview with Reuters. "It's turned out that it's more difficult than I thought it would be. It's a series of little tricks. Once you learn the trick, it's very easy. The problem is learning the trick." Miller never learned the trick.

No self-assembly pathway has ever been identified and the fate of all these molecules appears to be degradation. Few in the field have even begun to grapple with the challenge of producing biologically-meaningful information. Amino acids do not create the potential for life: only intelligence deserves to be described like this.

Production of pre-biotic molecules from extraterrestrial sources
Nir Goldman, Evan J. Reed, Laurence E. Fried, I-Feng William Kuo
ACS National Meeting, San Francisco, March 21-25, 2010, Paper 281.

Abstract: It has been proposed that impacts of extraterrestrial ices on early Earth could have been partially responsible for the creation of amino acids on the planet. We present ab initio molecular dynamics simulations of shock compressed aqueous mixtures representative of astrochemical ices found on dust grains and within other celestial bodies. We discover that high shock velocities drive the synthesis of a number of transient, exotic C-N bonded species at significantly higher pressures and temperatures than previously studied. Upon quenching to lower pressure conditions we observe a simple mechanism for the formation of the alpha amino acid glycine, an important component of protein synthesis. We find that shock compression of astrophysical ices followed by rapid expansion is a viable pathway for amino acid formation on a primitive planet, that can be verified by future experimentation.

Comet crash creates potential for life
Katharine Sanderson
Nature News, 26 March 2010 | doi:10.1038/news.2010.152

Abstract: Striking a glancing blow to a planet could create the perfect conditions in a comet's icy core to create amino acids - molecules that are vital to forming life on Earth.

See also:

Deyes, R. Improbabilists, Inevitabilists and the Astonishing Mystery of Life, ARN blog (2 July 2008)

Kemsley, J. Prebiotic Comet Collision Chemistry, Chemical & Engineering News (24 March 2010)

Tyler, D. Did meteorite impacts help to spawn life? ARN Literature blog (12 December 2008)

There has been a complexity explosion in biology - the fuse was lit in 1953 when the structure of DNA was discovered, but during the past two decades we have witnessed a dramatic expansion of data pointing to unanticipated levels of complexity. The hype surrounding the Human Genome Project suggested it would give us the blueprint of human biology and, as a consequence, would provide answers to our most probing questions.

"Mina Bissell, a cancer researcher at the Lawrence Berkeley National Laboratory in California, says that during the Human Genome Project, she was driven to despair by predictions that all the mysteries would be solved. "Famous people would get up and say, 'We will understand everything after this'," she says. "Biology is complex, and that is part of its beauty.""

Is biological complexity analogous to fractal geometry? (source here)

In the early days of the revolution, the focus was on genes. This was regarded as the key that would unlock the mysteries of the cell. Genes were the providers of biological information, and the rest of the genome (98% of it) was deemed to be Junk DNA. Since this did not code for genes, the inference was made that it should be interpreted as an evolutionary artefact, unworthy of serious study.

"Few predicted, for example, that sequencing the genome would undermine the primacy of genes by unveiling whole new classes of elements - sequences that make RNA or have a regulatory role without coding for proteins. Non-coding DNA is crucial to biology, yet knowing that it is there hasn't made it any easier to understand what it does. "We fooled ourselves into thinking the genome was going to be a transparent blueprint, but it's not," says Mel Greaves, a cell biologist at the Institute of Cancer Research in Sutton, UK."

After the Human Genome Project came the recognition of functionality for some of the non-coding DNA. The ENCODE project (which looked in detail at a portion of the human genome) found that 74-93% of DNA was translated into RNA and performed significant roles in the cell.

"Much non-coding DNA has a regulatory role; small RNAs of different varieties seem to control gene expression at the level of both DNA and RNA transcripts in ways that are still only beginning to become clear. "Just the sheer existence of these exotic regulators suggests that our understanding about the most basic things - such as how a cell turns on and off - is incredibly naive," says Joshua Plotkin, a mathematical biologist at the University of Pennsylvania in Philadelphia."

The level of complexity rose higher and higher as it became apparent that the communication within the cell is not best modelled by signalling pathways but by networks of information flows. The discipline of systems biology was created to make sense of the complexity. The verdict appears to be one of partial success, for even the systems biology approach struggles with the levels of complexity that are found.

"In the heady post-genome years, systems biologists started a long list of projects built on this strategy, attempting to model pieces of biology such as the yeast cell, E. coli, the liver and even the 'virtual human'. So far, all these attempts have run up against the same roadblock: there is no way to gather all the relevant data about each interaction included in the model."

The author of this informative feature article on complexity is Erika Check Hayden. As more and more is known, biology does not conform to the reductionist expectation of ultimate simplicity, but instead it appears ever more complex.

"[A]s sequencing and other new technologies spew forth data, the complexity of biology has seemed to grow by orders of magnitude. Delving into it has been like zooming into a Mandelbrot set - a space that is determined by a simple equation, but that reveals ever more intricate patterns as one peers closer at its boundary."

The Mandelbrot set analogy has some value, but there is a danger to it. As Hayden points out above, the apparent intricacy is actually based on a simple equation. The complexity is in the eye of the beholder. Reductionism is entirely comfortable with the Mandelbrot set. But is biology really like this? The question deserves a much more rigorous analysis. Hayden refers to Davidson's work in developmental biology and his claim to find simplicity and order. However, reductionism is not the only paradigm that incorporates simplicity and order. The concepts of complex specified information and irreducible complexity are entirely compatible with evidences of simplicity and order, yet are not explained by the reductionist approach. The domain surveyed by Hayden is home territory for the intelligent design paradigm. ID brings a perspective on biological information that takes us in a different direction to the Mandelbrot set analogy for biological complexity. The main problem for ID has nothing to do with relevance, but with its incompatibility with a materialist approach to science. But this also is a philosophical issue deserving of the widest possible discussion within the scientific community.

Human genome at ten: Life is complicated
Erika Check Hayden
Nature, 464, 664-667 (31 March 2010) | doi:10.1038/464664a

The more biologists look, the more complexity there seems to be. Erika Check Hayden asks if there's a way to make life simpler.

The Laetoli trackways from Tanzania were first reported in 1979 and immediately attracted attention because they provided evidence of bipedalism. The tracks were preserved in volcanic ash dated at 3.6 million years. Many at the time thought they looked exactly like human footprints, but few of the researchers were willing to adopt this interpretation. The debate has been extensive and inconclusive, but some positive leads have recently been published. Evidence is now available to answer the question: did the makers of the trackways walk like humans or like apes?

"In particular, debates over the origins and evolution of bipedalism revolve around whether early bipeds walked with energetically economical human-like extended limb biomechanics, or with more costly ape-like bent-knee, bent-hip (BKBH) kinematics. If early hominins used a BKBH gait, then we must account for the persistence of an energetically costly form of bipedal walking until the evolution of the genus Homo."

The Laetoli trackways (Credit: John Reader/Photo Researchers Inc., source here)

Research in the US involved human subjects walking with different gaits over damp sandy ground. The BKBH gait changes the way the body weight is carried by the feet and this, in turn, affects footprint morphology. Each footprint was recorded with a 3D scanner and quantitative comparisons were made.

"We compared footprints made by subjects walking with a normal, extended limb gait, and with a bent-knee, bent-hip (BKBH) ape-like gait at their preferred speeds with sand water content of 6-8%. These substrate conditions match those of Laetoli, which are described as similar to damp, fine to medium grained sand. We also examined the effects of increased speed and increased substrate moisture (10-12% water) on footprint morphology. We tested the hypothesis that a BKBH gait alters body weight transfer and produces significantly different footprint morphology than an extended limb gait."

The findings were unambiguous. There are significant differences between true bipedal tracks and BKBH tracks - and the Laetoli data is definitely bipedal.

"The relative toe depths of the Laetoli prints show that, by 3.6 Ma, fully extended limb bipedal gait had evolved. Thus, our results provide the earliest unequivocal evidence of human-like bipedalism in the fossil record."

Meanwhile, research in Belgium has been concerned with the more fundamental question as to whether any useful information can be gained from human-like trackways. The researchers were aware of many variables affecting trackway morphologies: the shape of the foot, the mechanical properties of the foot, its kinematics, its kinetics, and the mechanical properties of the substrate.

"[W]e experimentally generate footprints and quantify a selection of relevant subject-dependent and kinesiological variables that might influence the topology of a footprint, left behind in a granular substrate. Analysis will provide a better insight into the information that can (or cannot) be deduced from footprints."

This is a cautious and critical approach, and justifiably so. Their analyses confirmed the complex nature of footprint generation, and they found no unique variable that "determines" the morphology of a footprint. Mistakes have been made.

"For instance, the "obvious" transfer of weight along the lateral margin of the foot is taken as an argument for well-established bipedalism, but it is also observed in chimpanzees and bonobos, although a medial transfer of pressure along the metatarsal heads is not often evident in apes. When focusing on footprints alone (without detailed knowledge of foot anatomy, as is often the case in paleoanthropology) even the footprints of these apes may be falsely interpreted as made by bipeds with a well-developed longitudinal arch."

Having said this, the research did document cross-correlations between the different kinesiological factors investigated. This is where valid and useful information can be expected to be extracted from fossil trackways. This is the kind of information that was obtained in the US research.

"With these precautions in mind, we argue that different zones of a footprint do contain information on several kinesiological aspects of gait. Future research into footprint formation, soil mechanics and hominin foot morphology and locomotion should further increase insight in the causal relationship between these factors."

So how does this impact our understanding of the Laetoli footprints? It allows us to conclude, with greater confidence than before, that the trackways were generated by bipeds. At very least, the pendulum has swung so that the burden of proof now rests on those who would question the bipedal interpretation. This creates a problem for those who are trying to construct an evolutionary pathway for Homo sapiens - because bipedalism has to occur early in the story. Australopithecus afarensis is the primary candidate for making the tracks, but evidence is accumulating that bipedalism was not a characteristic of this ape (for more, go here). The US researchers acknowledge an uncertainty problem: "While our results show that Laetoli hominins walked with human-like kinematics, we still cannot be sure of which hominin taxon made the footprints." They concentrate their thoughts on adaptation: supposedly driven by the reduced energy requirements of a fully bipedal primate.

"Hypotheses for the origins of bipedalism often focus on selection for energy economy in early hominins. Energetic hypotheses are based on the reduced locomotor costs of humans compared to apes walking with BKBH gaits, and therefore, compared to ape-like pre-hominin ancestors."

This adaptationist approach falls foul of the integrated nature of the changes that are needed for an ape to walk upright. These changes affect the feet bones, the leg length, the pelvis, the way the spine attaches to the pelvis and particularly the skull, the vision system, the balance system, and more. This cannot be a single-factor transformation under selection pressure. The adaptive landscape has a steep-sided mountain separating apes and man - and there is no tunnel through the mountain! The implication is that humans walked at Laetoli, and that the textbook stories of human evolution will have to be re-written.

Laetoli Footprints Preserve Earliest Direct Evidence of Human-Like Bipedal Biomechanics
Raichlen DA, Gordon AD, Harcourt-Smith WEH, Foster AD, Haas WR Jr
PLoS ONE, March 2010, 5(3): e9769. doi:10.1371/journal.pone.0009769

Abstract: Debates over the evolution of hominin bipedalism, a defining human characteristic, revolve around whether early bipeds walked more like humans, with energetically efficient extended hind limbs, or more like apes with flexed hind limbs. The 3.6 million year old hominin footprints at Laetoli, Tanzania represent the earliest direct evidence of hominin bipedalism. Determining the kinematics of Laetoli hominins will allow us to understand whether selection acted to decrease energy costs of bipedalism by 3.6 Ma.
[. . .] These results provide us with the earliest direct evidence of kinematically human-like bipedalism currently known, and show that extended limb bipedalism evolved long before the appearance of the genus Homo. Since extended-limb bipedalism is more energetically economical than ape-like bipedalism, energy expenditure was likely an important selection pressure on hominin bipeds by 3.6 Ma.

Experimentally generated footprints in sand: Analysis and consequences for the interpretation of fossil and forensic footprints
K. D'Aout, L. Meert, B. Van Gheluwe, D. De Clercq, P. Aerts
American Journal of Physical Anthropology, 2010, 141(4), 515-525.

Fossilized footprints contain information about the dynamics of gait, but their interpretation is difficult, as they are the combined result of foot anatomy, gait dynamics, and substrate properties. We explore how footprints are generated in modern humans. Sixteen healthy subjects walked on a solid surface and in a layer of fine-grained sand. In each condition, 3D kinematics of the leg and foot were analyzed for three trials at preferred speed, using an infrared camera system. Additionally, calibrated plantar pressures were recorded. After each trial in sand, the depth of the imprint was measured under specific sites. When walking in sand, subjects showed greater toe clearance during swing and a 7 degrees higher knee yield during stance. Maximal pressure was the most influential factor for footprint depth under the heel. For other foot zones, a combination of factors correlates with imprint depth, with pressure impulse (the pressure-time integral) gaining importance distally, at the metatarsal heads and the hallux. We conclude that footprint topology cannot be related to a single variable, but that different zones of the footprint reflect different aspects of the kinesiology of walking. Therefore, an integrated approach, combining anatomical, kinesiological, and substrate-mechanical insights, is necessary for a correct interpretation.

Scientists with an interest in developing design concepts and principles found in the natural world are not instinctively attracted by exhortations to expel design from Biology. However, developing a coherent academic framework that does justice to the design principles being studied has not attracted the attention it deserves. Consequently, many scholars in this field have absorbed views developed by people with a rather different agenda for design. McIntosh recognises there is a problem here, and sets out to provide an alternative perspective.

"Many have taken the view that design is only an illusion in living systems, arguing that such 'apparent design' and accompanying complexity can be explained by the neo-Darwinian paradigm. [. . .] However, [. . .] the inference to original design and intelligence is a perfectly valid alternative from direct analogy to designs within the man-made world."

An essential aerodynamic surface: barbules in one direction have hooks whereas in the other direction the barbules are ridge-like. (Source here)

After providing an overview of different types of feather, McIntosh develops an argument based on "specified functional complexity". There is a multifunctioning and multi-optimisation in feather construction - characteristics that apply to both modern and to fossil feathers - which is said to be "consistent with the design thesis".

"There are the features which are immediately apparent such as aerodynamic loading and the material construction of rachis and barbs to sustain this. However, there are also more subtle features such as the arrangement of hooks and barbules primarily for keeping the feather together, such that they prevent air from going through them during the downstroke but allowing some air to pass through in the upstroke, thus maximising the efficiency of energy use in wing flap. The keratin itself has an extremely high specific strength, and the shape of the filament cross sections used in rachis construction moves from near circular near the root to a curved and ribbed rectangular shape away from the root for structural efficiency under bending and potentially buckling loads."

Although enough has been said already to associate pennaceous feathers with the concept of irreducible complexity, further aspects of a holistic system emerge with consideration of the uropygial (preening) gland at the base of its spine. Hypotheses about the evolution of these feathers involving unintelligent causation have totally failed to provide credible scenarios.

"The ability to reach this gland is a feat of twisting which a bird performs with ease. However, it raises serious issues concerning the supposed evolution of feathers, since it is necessary for the feather construction (barbule ridge and hook system) to arise concurrently with the preening gland and the ability to manoeuvre the neck a full 180 degrees. None of the fossil evidence shows any evidence of such transitions."

The author elaborates on the crucial importance of functional information and the failure of current evolutionary speculations. The hooks and ridges of barbules are clear examples. These barbules have opposite characteristics: "hooks on one side of the barb and ridges on the other so that adjacent barbs become attached by hooked barbules from one barb attaching themselves to ridged barbules from the next barb. [. . .] It is that vital network of barbules which is necessarily a function of the encoded information (software) in the genes. Functional information is vital to such systems." This leads to a discussion of research into pattern formation, primarily to show that the origin of functional information has not been solved (or even addressed).

"However, correct and enlightening as these models are, it is important to recognise that this is not the same as functional information, where coded instructions are involved, first, in the precise ordered arrangement of nucleotides in DNA, and, secondly, in the multifunctioning construction of items from these codes such as hooked and ridged feather barbules. This is a subject of a separate paper by the author where the argument is made that all living systems have coded machinery which sits on high free energy bonds, all of which have to be in place for the system to work."

The second part of the paper develops the same style of argument for the avian lung: the organ must be considered as an integrated system if it is to be understood as functioning machinery, and a "bottom-up" blind watchmaker approach totally fails to explain the evidence for functional information.

"Science can study the effect on the natural world of systems of pre-existing material, but it cannot preclude the possibility of intelligence extraneous to that very matter and energy being involved in its formation. To say otherwise is effectively wedding science to a narrow philosophical foundation. [. . .] Once one opens the possibility that intelligence is involved, the evidence leads very naturally to the conclusion of design, not by going against the known empirical laws (such as gravity [. . .]), but precisely the reverse. We must keep to the 'nullius in verba' motto of the Royal Society ('on the words of no one'), and not preclude from the outset where the evidence may lead."

This paper provides a helpful contribution to the development of multiple hypotheses in science. It deserves to be widely read and analysed by students of science.

Evidence of design in bird feathers and avian respiration
A. C. McIntosh
International Journal of Design & Nature and Ecodynamics, Vol 4, Issue 2, (2009) 154-169.

This paper explores the evidence for design in living systems. In particular, it considers two of the mechanisms used in bird flight. These include feathers and the remarkable counterflow mass exchanger breathing system used in the avian lung system. Both systems are examples of the principle of specified functional complexity, which occurs throughout nature. There is no known recorded example of this developing experimentally where the precursor information or machinery is not already present in embryonic form. Such design features indicate non-evolutionary features being involved.

Anyone attempting to swat a fly will become aware of its remarkable aerodynamic capabilities. Its speed of response and ability to change direction abruptly far exceed our own powers as pursuers. The flight of insects has received considerable attention from researchers and some recent work was stimulated by the recognition of a gap in knowledge. The scientists realized that the previously-studied flight control system involving vision cannot be the explanation for how flies maintain stability in the face of unpredictable short disturbances.

"Corrective behavior often takes advantage of vision. For fruit flies, however, reaction time to visual stimuli is at least 10 wingbeats, so these insects must employ faster sensory circuits to recover from short time-scale disturbances and instabilities."

To study how fruit flies recover from in-flight disturbances, researchers glued magnetic pins to the insects' backs and zapped them with a magnetic field. This fly has a 1.5 mm pin on its back and is held in place by the tip of a sewing needle. (Credit: Wang, Cohen and Guckenheimer labs, Source here)

The experimental work required the research team to abandon ideas of tethering insects or imposing other restrictions on flight behavior. They needed to observe insects in free-flight.

"To probe this fast control strategy, we devised an experimental method that imposes impulsive mechanical disturbances to flying insects while allowing us to measure relevant aspects of flight behavior. We first glue tiny ferromagnetic pins to fruit flies and image their free flight using three orthogonally oriented high-speed video cameras. When a fly enters the filming volume, an optical trigger detects the insect, initiates recording, and activates a pair of Helmholtz coils that produce a magnetic field. The field and pin are both oriented horizontally, so the resulting torque on the pin reorients the yaw, or heading angle, of the insect. We then use a new motion tracking technique to extract the three-dimensional body and wing motions."

What they observed is that prior to the perturbation (which lasted 5ms, or about one wingbeat period), the wings beat symmetrically. After the magnetic torque was applied, 3 wingbeats were needed for the control system to respond, and then "asymmetries in the wing motions appear for about five wingbeats, indicating the insect is actively generating corrective torque". For small perturbations, the insects correct "nearly perfectly", whereas larger perturbations - although corrected to some extent - lead to permanent changes in heading.

"The accuracy of the recovery indicates that a refined control strategy underlies the response of fruit flies to in-flight perturbations. To reveal this strategy, we construct a physics-based model of the observed behavioral response."

Body motions are detected by the halteres: "small vibrating organs [. . .] that act as gyroscopic sensors. Anatomical, mechanical, and behavioral evidence indicates that the halteres serve as detectors of body angular velocity that quickly trigger muscle action." With this model, the halteres have a nonlinear response consistent with vibratory gyroscopes, so sensor saturation explains "why fruit flies are unable to accurately recover from strong perturbations". The control system design principles are as follows:

"These findings suggest that these insects drive their corrective response using an autostabilizing feedback loop in which the sensed angular velocity serves as the input to the flight controller. [. . .] [T]he velocity is sensed by the halteres, processed by a neural controller, and transmitted by the flight motor into specific wing motions that generate aerodynamic torque."

Halteres are remarkable organs and unique to the Diptera. The research raises questions about other autostabilization techniques found in the natural world and how such systems can be incorporated into flying robots.

"Flight control principles uncovered in this model organism may also apply more broadly, and this work provides a template for future studies aimed at determining if other animals employ flight autostabilization. The control strategies across different animals are likely to share common features, because the physics of body rotation is similar across many animals during flapping-wing flight. Additionally, animals that lack halteres may use functionally equivalent mechanosensory structures such as antennae. Finally, the control architecture of the fruit fly offers a blueprint for stabilization of highly maneuverable flapping-wing flying machines."

These design principles were incorporated by intelligent agents into aeroplanes very early in their history (further information is here). It is now apparent that flying insects got there first! In evolutionary terms, we have here a good example of convergence. Since these control systems represent complex specified information (with the greater complexity found in the insect control system), intelligent agency should be invoked in both cases.

"For fixed-wing machines, the need to overcome instabilities spurred the invention of autostabilizing systems by 1912, only 9 years after the Wright brothers first manually controlled airplane flight. The development of such automatic steering systems also led to the first formal description of proportional-integral-derivative control schemes and advanced gyroscopic sensor technology. The fruit fly's autostabilization response is well-modeled by a simple PD scheme that receives input from gyroscopic halteres, and, like airplanes, uses fine adjustment of wing orientation to generate corrective torques. Roughly 350 million years after insects took flight, man converged to this solution for the problem of flight control and joined animals in the skies."

Discovering the flight autostabilizer of fruit flies by inducing aerial stumbles
Leif Ristroph, Attila J. Bergou, Gunnar Ristroph, Katherine Coumes, Gordon J. Berman, John Guckenheimer, Z. Jane Wang and Itai Cohen.
Proceedings of the National Academy of Sciences, 2010, 107:4820-4824 | doi:10.1073/pnas.1000615107

Abstract: Just as the Wright brothers implemented controls to achieve stable airplane flight, flying insects have evolved behavioral strategies that ensure recovery from flight disturbances. Pioneering studies performed on tethered and dissected insects demonstrate that the sensory, neurological, and musculoskeletal systems play important roles in flight control. Such studies, however, cannot produce an integrative model of insect flight stability because they do not incorporate the interaction of these systems with free-flight aerodynamics. We directly investigate control and stability through the application of torque impulses to freely flying fruit flies (Drosophila melanogaster) and measurement of their behavioral response. High-speed video and a new motion tracking method capture the aerial "stumble", and we discover that flies respond to gentle disturbances by accurately returning to their original orientation. These insects take advantage of a stabilizing aerodynamic influence and active torque generation to recover their heading to within 2 deg in less than 60 ms. To explain this recovery behavior, we form a feedback control model that includes the fly's ability to sense body rotations, process this information, and actuate the wing motions that generate corrective aerodynamic torque. Thus, like early man-made aircraft and modern fighter jets, the fruit fly employs an automatic stabilization scheme that reacts to short time-scale disturbances.

See also:

Tyler, D. Biorobotics casts light on the way insects fly, ARN Literature blog (22 February 2007)

The mollusc, known as the scaly-foot gastropod, has been known for about a decade. It was discovered living in the deep sea near the Kairei Indian hydrothermal vent field on the Central Indian Ridge. The natural environment for the animal is harsh. There are extremes of temperatures, high pressures and high acidity levels that can easily damage shells of calcium carbonate. Brachyuran crabs live in the vicinity and these "are known to compress gastropod mollusc shells between their chela" with loads of up to 60N.

"To understand how the valiant gastropod holds up to these trials, Christine Ortiz of MIT and her colleagues used nanoscale experiments and computer simulations to dig in to the shell's structure. Many other species' shells exhibit what Ortiz calls "mechanical property amplification," in which the whole material is hundreds of times stronger than the sum of its parts."

The scaly-foot gastropod uses a unique trilayered shell to protect itself from hazards. (Image credit: Anders Waren, Swedish Museum of Natural History. Source here)

Most exoskeletal structures are technically known as multilayered composites. The parameters are the layer thicknesses, the nano- and microstructure of each layer, the number of layers, the sequence of layers, etc. Each species appears to have its own resultant profile.

"Design, inspired by nature, of engineering materials with robust and multifunctional mechanical properties [i.e., those which sustain a variety of loading conditions] is a topic of major technological interest in a variety of civilian and defense applications. Here, we identify the design principles of the shell of a gastropod mollusc from a deep-sea hydrothermal vent [order Neomphalina, family Peltospiridae, species Crysomallon squamiferum]. This system has a trilayered structure unlike any other known mollusc or any other known natural armor, with a relatively thick compliant organic layer embedded between two stiffer mineralized layers, an outer iron sulfide-based layer and an inner calcified shell."

The outer layer is about 30 micrometres thick and is mineralised: it contains iron sulphide particles (greigite, Fe2S4). This gastropod is the only metazoan known to employ iron sulphide as a skeletal material. The middle layer is about 150 micrometres thick and is thought to be the periostracum (the template for shell mineralization, providing protection against corrosive and dissolutive marine environments, and also chemical protection from boring organisms). The inner layer is composed of aragonite that is itself layered:

"[It] possesses a gradient layer [. . .] with a typical crossed lamellar layer (CLL) microstructure (approximately 50 [micro]m thick), followed by a relatively thick layer also with a CLL microstructure (approximately 200 [micro]m thick, followed by a thin prismatic layer (PL) on the inner surface of the shell (approximately 1.5 [micro]m thick)."

This structure has been studied empirically and modelled. Simulations were performed to understand how the shell responds to impacts and applied loads. There are too many details to document here.

"It is interesting to see how C. squamiferum has created these additional different protection mechanism compared to other gastropod molluscs by using materials plentiful and specific to the deep-sea hydrothermal vent environment, i.e., vent fluids rich in dissolved sulfides and metals.
The design principles of the trilayered shell of C. squamiferum exhibit many aspects that are different from the highly calcified shells of typical gastropod molluscs or any other natural armor. Each material layer serves distinct and multifunctional roles leading to many advantages."

Design principles have emerged from this research. The authors have found new design features leading to enhanced functional performance. "Each material layer serves distinct and multifunctional roles leading to many advantages". They point out that design principles are extremely important because there are so many variables: "The design space for synthetic multilayered structural composites for protective applications is enormous". The great merit of biological systems is that they provide a chart to steer through this space. However, the authors attribute design in biological systems to an "evolutionary process".

"Biological systems, such as the one described here, greatly reduce the engineering design space since efficient threat-protection design concepts have emerged through the lengthy evolutionary process that fulfill the necessary functions and constraints."

The problem with this evolutionary framework is that it has no empirical validity. We have no warrant for explaining design principles via evolutionary processes. The authors explain that they do not know whether the observed design "represents an advanced functional adaptation as an antipredatory response or an exaptation (i.e., a trait that evolved to serve one function, but subsequently and simultaneously may serve other functions)". This comment is, unfortunately, entirely typical of the culture prevailing in science produced by philosophical materialism. Evolutionists have supreme confidence in their theoretical framework, but do not seem to see the need to constrain theory by reference to empirical data. Observed adaptations do not demonstrate the emergence of design concepts. The only sources of design concepts that we know of are intelligent agents. Replacing the culture of materialism by one that integrates information inputs with physics and chemistry is long overdue.

With this alternative culture, paragraphs like the following take on a new richness of meaning:

"In particular, the efficient natural armor structural system described here sustains both mechanical loading, as well as thermal fluctuations with inherent mechanisms to prevent catastrophic failure. The multimaterial, trilayer design and advantageous curved geometry enables structural stiffening, reduction of radial displacements, penetration resistance, and stability during thermal impulses even with the presence of large mismatches between constituent materials. Trilayered sandwich composite designs have had limited use in military applications, and the concepts reported here could lead to bioinspired improvements and broader applicability and improved performance for human, vehicle, and structural armor."

Protection mechanisms of the iron-plated armor of a deep-sea hydrothermal vent gastropod
Haimin Yao, Ming Dao, Timothy Imholt, Jamie Huang, Kevin Wheeler, Alejandro Bonilla, Subra Suresh, and Christine Ortiz
Proceedings of the National Academy of Sciences, January 19, 2010, vol. 107, no. 3, 987-992 | doi:10.1073/pnas.0912988107

Abstract: Biological exoskeletons, in particular those with unusually robust and multifunctional properties, hold enormous potential for the development of improved load-bearing and protective engineering materials. Here, we report new materials and mechanical design principles of the iron-plated multilayered structure of the natural armor of Crysomallon squamiferum, a recently discovered gastropod mollusc from the Kairei Indian hydrothermal vent field, which is unlike any other known natural or synthetic engineered armor. We have determined through nanoscale experiments and computational simulations of a predatory attack that the specific combination of different materials, microstructures, interfacial geometries, gradation, and layering are advantageous for penetration resistance, energy dissipation, mitigation of fracture and crack arrest, reduction of back deflections, and resistance to bending and tensile loads. The structure-property-performance relationships described are expected to be of technological interest for a variety of civilian and defense applications.

See also:

Grossman, L. Snail In Shining Armor, Science News, February 13th, 2010; Vol.177 #4 (p. 13)

Spider silk has been an active area for biomimetics research for several years. Spinoff companies have been launched in anticipation of commercial gains. However, despite the enthusiasm and commitment of research staff, the prizes are still elusive. Whilst the main goal is to produce fibres that are as strong and as flexible as spider silk, there are other aspects of the natural material that have attracted the interest of researchers. One of these concerns the ability of webs to be a site for dew collection.

"When Lei Jiang first observed the phenomenon, he was intrigued. "How does that happen?" he wondered. After all, he says, "if you took a human hair, water would not stick to it like that". His initial curiosity led to an almost five-year-long study. The findings could have implications for the design of materials for water collection and for the efficiency of chemical reactions."

Spider silk manipulates water with skill (source here)

Not only do webs attract dew, the droplets are able to hang stably on the silk fibres. This suggests the presence of a microstructural mechanism. All polymeric fibres have a microstructure and spider silk is no exception. SEM images reveal a series of amorphous regions (called puffs) and crystalline regions (called joints). The nanofibrils are highly hydrophilic: enhancing wettability and favourable for condensing dew. The puffs have a very open structure and are semi-transparent in images. However, when water starts to condense, the puffs shrink - first to "opaque bumps" and then to "spindle-knots". As they shrink, tiny water droplets coalesce to form larger drops with movement from joints to spindle-knots.

"Further work revealed that movement of the droplets towards the knots is directed by two forces acting together: the force generated by a gradient of surface energy on the fibrils and the one produced by the spindle shape of the knots. "This is quite different from other reported surfaces, on which drops are driven just by individual forces," says Jiang."

These findings are stimulating human invention. The research paper reports success with nylon filaments that are coated with a hydrophilic material that dries in tiny knots similar to those found in spider silk. The goal now is to produce something of commercial value.

"These observations clearly show that our artificial spider silk not only mimics the structure of wet-rebuilt spider silk but also its directional water collection capability. We therefore anticipate that the design principles uncovered and implemented in this study will aid the development of functional fibres for use in water collection and in liquid aerosols filtering in manufacturing processes."

Why does the spider produce a web with dew-gathering potential? "The researchers are unsure of why the spider has evolved to possess this ability. "It could be for its drinking activities, or it could be to refresh the web structure to make it stronger and stickier for prey," Jiang told physicsworld.com." Magdalena Helmer wrote a short News & Views piece on "Dew catchers", saying: "spiders don't need to look for water because the silk fibres that they spin are highly efficient at collecting it from moist air". However, direct evidence of functionality is lacking. There is considerable scepticism that spiders make any use of dew-gathering.

"But Fritz Vollrath, who studies spider silk at Oxford University in the UK, disagrees with Jiang's theory. He thinks spider silk has to be dry to function. 'If I am correct, then the authors are studying an artefact, which is still interesting, although it has no biological function,' says Vollrath. [. . .] Brent Opell, a spider expert at Virginia Tech in Virginia, US, is equally cautious about the results, although he says the experimental work is sound. 'The implication that [capture] threads have evolved to harvest moisture is not the view of most arachnologists,' he says."

Is there an ID perspective on this? Wherever researchers recognise "design principles" in the natural world, the answer is, of course, 'yes'. The presumption with ID is that design features imply functionality, whether or not we know the details. Dew gathering is a unique and remarkable feature of spider silk simply because other fibres do not display such behaviour. The authors comment:

"We observed such directional water collection behaviour only with wetted silk fibres (that is, wet-rebuilt silk) from the cribellate spider Uloborus walckenaerius; in contrast, silkworm silk and nylon fibres with a uniform structure did not exhibit the directional water collection phenomenon."

Whether evolutionists can explain 'how the spider came to gather dew' is more uncertain. Even with functionality identified, perfecting this highly engineered system makes it most reasonable to infer intelligent, rather than natural, causation.

Directional water collection on wetted spider silk
Yongmei Zheng, Hao Bai, Zhongbing Huang, Xuelin Tian, Fu-Qiang Nie, Yong Zhao, Jin Zhai & Lei Jiang
Nature, 463, 640-643 (4 February 2010) | doi:10.1038/nature08729

First paragraph: Many biological surfaces in both the plant and animal kingdom possess unusual structural features at the micro- and nanometre-scale that control their interaction with water and hence wettability. An intriguing example is provided by desert beetles, which use micrometre-sized patterns of hydrophobic and hydrophilic regions on their backs to capture water from humid air. As anyone who has admired spider webs adorned with dew drops will appreciate, spider silk is also capable of efficiently collecting water from air. Here we show that the water-collecting ability of the capture silk of the cribellate spider Uloborus walckenaerius is the result of a unique fibre structure that forms after wetting, with the 'wet-rebuilt' fibres characterized by periodic spindle-knots made of random nanofibrils and separated by joints made of aligned nanofibrils. These structural features result in a surface energy gradient between the spindle-knots and the joints and also in a difference in Laplace pressure, with both factors acting together to achieve continuous condensation and directional collection of water drops around spindle-knots. Submillimetre-sized liquid drops have been driven by surface energy gradients or a difference in Laplace pressure, but until now neither force on its own has been used to overcome the larger hysteresis effects that make the movement of micrometre-sized drops more difficult. By tapping into both driving forces, spider silk achieves this task. Inspired by this finding, we designed artificial fibres that mimic the structural features of silk and exhibit its directional water-collecting ability.

Making the paper: Lei Jiang
Nature, 463, 586 (4 February 2010) | doi:10.1038/7281586a

Abstract: Spider silk structure holds secret to catching water as well as flies.

See also:

Birch, H. How spider silk soaks up water, Chemistry World (3 February 2010)

Dacey, J. Spider web inspires fibres for industry, physicsworld.com (3 February 2010)

Helmer, M. Dew catchers, Nature, 463, 618 (4 February 2010) | doi:10.1038/463618a

Two research psychologists have contributed an Opinion paper based on the empirical finding "that individuals presented with unfamiliar moral dilemmas show no difference in their responses if they have a religious background or not". The data used was obtained from an online web questionnaire which is open to any volunteer participants (including myself). Findings are reported elsewhere and in their Opinion paper the authors provide only a summary:

"These studies, carried out using the web-based Moral Sense Test (http://moral.wjh.harvard.edu/), recruit thousands of male and female subjects, with educational levels that range from elementary school to graduate degrees, with political affiliations that range from liberal to conservative, and religious backgrounds that range from devout to atheist. In each of these studies, subjects read and judged the moral permissibility of an action on a 7pt-Likert scale [. . .]. Each scenario presented a contrast between a harmful action and a significant benefit in terms of lives saved."

Moral dilemmas come in all shapes and sizes (source here)

The hypothetical scenarios in the test present dilemmas where actions that are evidently harmful to human life considered in isolation result in significant benefits to other humans (whose lives are saved). The generalized results are as follows:

"More specifically, in dozens of dilemmas, and with thousands of subjects, the pattern of moral judgments delivered by subjects with a religious background do not differ from those who are atheists, and even in cases where we find statistically significant differences, the effect sizes are trivial."

This conclusion is the anchor-point for the author's wide-ranging discussion of the origin of morality and, as indicated in their title, the origin of religion. In evaluating their paper, we need to consider whether their empirical starting point is robust enough to carry such far-reaching conclusions.

Some caution is needed in the way "religious background" is understood. There is no systematic probing of the concept in the web-based questionnaire. Participants have to select a label that best fits their current religion, the religion of their upbringing, and locate themselves on the spectrum of "not-at-all" religious to "very" religious. This is all pretty superficial and subjective, given the diversity of religious experience around the world. There is no attempt to use Likert scales to assess the degree to which respondents understood God to be a creator, transcendent, immanent, able to answer prayer or, even more relevant, the reference point for our sense of right and wrong. Consequently, the term "religious" is 1-dimensional and almost devoid of content. Yet, the authors place considerable weight on their analysis of responses gathered.

More caution is needed when we read in the above quote about "trivial" effect sizes. In another study the authors mention, radical altruism was the focus of interest: does religious background affect thinking about whether to sacrifice ones own life "in order to save the lives of a greater number of anonymous others". Significant differences were found. But these could be predicted, say the authors, "given the fact that many religions praise martyrdom". They go on to offer this analysis:

"[A]lthough there are significant evolutionary pressures against such acts of radical altruism, religious pressures might lead people to offer this judgment because they believe it is the morally appropriate answer. What religion can do, and what political and legal institutions can do as well, is alter local and highly specific cases. And yet, they appear to have no influence at all on the intuitive system that operates more generally, and for unfamiliar cases."

These comments about the need for caution are intended to show that the authors have a very inadequate view of the concept of "religion". To them, the various religions can all be lumped together and there are no distinctions worth making. They do not see the need to explain why they think that radical altruism can somehow be linked to the praise of martyrdom. Even when differences are discernable between the moral judgments of the religious and those of atheists, they are considered trivial apparently because there are (untested) evolutionary explanations of why the religious are so minded. All this raises questions about the adopted methodology and the analysis of the authors.

Before making further comments on the arguments built on the empirical findings, it is useful to note some comments by Philip Ball, writing a column for Nature. He draws attention to the conceptual framework underpinning the research: "By taking it as a given that religion is an evolved social behaviour rather than a matter of divine revelation, [the authors' paper] tacitly adopts an atheistic framework." Ball is absolutely right, and we can add the thought that tacit atheism is a pervasive problem in many areas of scholarly activity. Given their presuppositions, no one should expect the authors to reach a conclusion that challenges atheism. However, this does not mean such conclusions cannot be drawn by others who approach the same data with a different conceptual framework.

The first thesis developed in the paper is that "moral intuitions operate independently of religious background" and are therefore not explained by religion. The authors develop an analogy with linguistics, where the concept of innate ability for language acquisition is widely held, and this innate ability is independent of the cultural background. Ball describes this thesis in this way:

"The paper [ . . ] challenges the assertion commonly made in defence of religion: that it inculcates a moral awareness. If we follow the authors' line of thinking, religious people are no more likely to be moral than atheists."

Whenever there is only one hypothesis on the table, there should be concern! Scholars should be cultivating multiple working hypotheses and looking for ways of testing them. To show the significance of an alternative conceptual framework, consider a perspective that understands mankind as made in the image of its Designer. Innate abilities are imparted by this Designer: we speak because the Designer speaks; we have a moral awareness because the Designer is the reference point for what is right and what is wrong. These innate abilities affect all people - whether they are atheists or religious, whether they are pantheists or theists, whether they are male or female, young or old. This is a hypothesis that explains the data and scholars who "tacitly adopt[] an atheistic framework" are excluding this alternative purely on ideological grounds.

The second thesis is concerned with the origin of religion. The authors think their work on moral intuitions leads naturally to the hypothesis that religion is a by-product of pre-existing capabilities.

"Specifically, recent work in moral psychology supports the view that religion evolved as a cognitive by-product of pre-existing capacities that evolved for non-religious functions."
[. . .]
"Religion is a set of ideas that survives in cultural transmission because it effectively parasitizes other evolved cognitive structures."
[. . .]
"Here again, religion stands on the shoulders of cognitive giants, psychological mechanisms that evolved for solving more general problems of social interactions in large, genetically unrelated groups."

For the purposes of this blog, we shall defer comment and let Philip Ball speak: "Whether it [i.e. the research] 'explains' religion is another matter."

"It's debatable, however, whether these moral tests are probing religion or culture as a moral-forming agency, because non-believers in a predominantly religious culture are likely to acquire the moral predispositions of the majority. Western culture, say, has long been shaped by Christian morality. [. . .] But to uncover religion's roots, is morality necessarily the best place to look? It seems hard to credit the idea that the immense cultural investment in religion was made merely to strengthen and fine-tune existing neural circuits related to morality. [. . .] Yet attempting to explain the origins of such a rich cultural phenomenon as religion is doomed to some extent to be a thankless task. For to 'explain' Chartres Cathedral or Bach's Mass in B Minor in terms of non-kin cooperation is obviously to have explained nothing."

The origins of religion: evolved adaptation or by-product?
Ilkka Pyysiainen and Marc Hauser
Trends in Cognitive Sciences, 14(3), 104-109, March 2010 | doi:10.1016/j.tics.2009.12.007

Abstract: Considerable debate has surrounded the question of the origins and evolution of religion. One proposal views religion as an adaptation for cooperation, whereas an alternative proposal views religion as a by-product of evolved, non-religious, cognitive functions. We critically evaluate each approach, explore the link between religion and morality in particular, and argue that recent empirical work in moral psychology provides stronger support for the by-product approach. Specifically, despite differences in religious background, individuals show no difference in the pattern of their moral judgments for unfamiliar moral scenarios. These findings suggest that religion evolved from pre-existing cognitive functions, but that it may then have been subject to selection, creating an adaptively designed system for solving the problem of cooperation.

Morals don't come from God
Philip Ball
Nature, 8 February 2010 | doi:10.1038/news.2010.55

Abstract: The finding that religion scarcely influences moral intuition undermines the idea that a godless society will be immoral, says Philip Ball. Whether it 'explains' religion is another matter.

See also:

Morality Research Sheds Light on the Origins of Religion, ScienceDaily (9 February 2010)

Hunter, C. Important New Paper on Evolutionary Explanation, Darwin's God (8 February 2010)

It is well known that Darwin speculated on what might happen in "some warm little pond" (previously discussed here). But it was not until 1929 that J.B.S. Haldane developed a testable hypothesis involving a "prebiotic broth, or primordial soup". He proposed that organic compounds were made when methane, ammonia and water reacted as a result of energy supplied by ultraviolet radiation. The reaction products were suggested to have accumulated in a "hot dilute soup" in the primeval earth. In this scenario, further reactions led to macromolecules, protocells and then life.

"Backed up by Stanley Miller's (1953) inorganic synthesis of organic molecules in the laboratory, it seemed to generations of scientists that Haldane's narrative was basically right, and all that was left was to sort out the details."

It is time to move on from this unproductive research (source here)

Miller's experiments became an icon of naturalistic evolution and entered the textbooks with very little critical analysis of the findings. Even recently, Miller's work was acclaimed in the journal Science. Happily, there are opportunities to get beyond the hype but, as Jonathan Wells showed in his Icons of Evolution, these contributions rarely get beyond the technical literature. William Martin and colleagues have presented a strong case for retiring the primordial soup concept from active service. It has reached the grand old age of 81 and, as a hypothesis, it has not been confirmed. Normally, when hypotheses are tested and found wanting, they are discarded - but we are now overdue for this to happen with the primordial soup. It is "well past its sell-by date".

Two reasons are provided in the paper. The first is that a soup of organic chemicals will be in thermodynamic equilibrium. The reaction products are already present and there is no obvious source of energy to drive polymerisation or any other significant change. "Ionizing UV radiation inherently destroys as much as it creates."

"[T]he homogeneous soup has no internal free energy that would allow them to react further. Life is not just about replication; it is also a coupling of chemical reactions - exergonic ones that release energy and endergonic ones that utilise it, preventing the dissipation of energy as heat. It is commonplace to say that life requires energy, but the conception of a primordial soup fails to recognise or incorporate the importance of energy flux. On the congruence principle, what life needed was not some harsh and problematic source of energy like UV radiation (or lightning), but a continuous and replenishing source of chemical energy."

The second reason concerns fermentation as the primordial mechanism of energy generation in a world without oxygen. Haldane promoted this idea, and De Duve supported it as the mechanism for sustaining anaerobic life. "If there can be said to be a textbook view, this is it."

"But there are profound difficulties - both chemical and biological - in viewing fermentation as primitive rather than derived. Fermentation is chemically a disproportionation - not a simple redox reaction, in which electrons are stripped from a donor and passed onto an acceptor, driven by strong thermodynamics. In contrast with respiration, the amount of energy released by fermentation is tiny, reflecting its lack of thermodynamic driving force. To tap such an insignificant source of energy requires more rather than less sophistication, and indeed about 12 enzymes are needed to catalyse a complex succession of steps in glycolytic-type fermentations based around the Embden-Meyerhoff pathway. These enzymes are proteins encoded by genes, which would have had to evolve as a functional unit without any other source of energy in the primordial oceans - close to an impossibility in an RNA world, let alone the only way to evolve one."

The authors go on to defend their view that fermentation is a sophisticated, rather than a primordial, derivation. This brings them to the crunch question:

"But if there was no soup, and no energy from UV radiation or fermentation, then where was the energy that powered the emergence of life?"

They go on to propose alkaline hydrothermal vents as the primordial source of energy for life. They develop their idea that the origin of life can be considered distintly from the origin of replication. They support Russell et al's (1993) proposal that chemiosmosis is "an inherent property of life, one inherited from the very place and space where it arose". Their paper is exploratory, not plotting out any details of what the Last Universal Common Ancestor (LUCA) looked like, but considering how chemiosmosis might have worked in the setting of alkaline hydrothermal vents. Further discussion of this is needed, of course, but this blog is to draw attention to the challenge these authors present to OOL researchers generally and to textbook authors/educators.

"It is time to cast off the shackles of fermentation in some primordial soup as 'life without oxygen' - an idea that dates back to a time before anybody had any understanding of how ATP is made - and to embrace the most revolutionary idea in biology since Darwin as the key not only to the bioenergetics of all life on Earth today, but to its very origin.(80) Thus it seems to us likely that LUCA grew on the H2/CO2 couple, and that she was naturally chemiosmotic."

How did LUCA make a living? Chemiosmosis in the origin of life
Nick Lane, John F. Allen, William Martin
Bioessays, 32(4), 271-280, April 2010 | DOI: 10.1002/bies.200900131

Despite thermodynamic, bioenergetic and phylogenetic failings, the 81-year-old concept of primordial soup remains central to mainstream thinking on the origin of life. But soup is homogeneous in pH and redox potential, and so has no capacity for energy coupling by chemiosmosis. Thermodynamic constraints make chemiosmosis strictly necessary for carbon and energy metabolism in all free-living chemotrophs, and presumably the first free-living cells too. Proton gradients form naturally at alkaline hydrothermal vents and are viewed as central to the origin of life. Here we consider how the earliest cells might have harnessed a geochemically created proton-motive force and then learned to make their own, a transition that was necessary for their escape from the vents. Synthesis of ATP by chemiosmosis today involves generation of an ion gradient by means of vectorial electron transfer from a donor to an acceptor. We argue that the first donor was hydrogen and the first acceptor CO2.

See also:

New Research Rejects 80-Year Theory of 'Primordial Soup' as the Origin of Life, ScienceDaily (3 February 2010)

Warren, D. Back to the beginning, The Ottawa Citizen (6 February 2010)

Two years ago, "the most primitive bat known" was reported in Nature. It was not primitive in its wings and body, but "the morphology of the ear region suggests that it could not echolocate, making it a possible intermediate link between bats and their non-flying, non-echolocating mammalian ancestors". At the time, the find was suggested to settle the question as to which came first: flight or echolocation? The answer was a definite flight first.

"The problem of understanding bat evolution dates back at least to Charles Darwin, who in The Origin of Species enumerated a list of difficulties he saw with the theory of evolution by natural selection. The example often discussed is the origin of the eye. But Darwin also mentioned the vexed issue of how bats had arisen from terrestrial ancestors." Speakman 2008).

Onychonycteris finneyi was featured on the cover of Nature in February 2008 (Source here)

This assessment of the fossil must now be reappraised. New work on modern-day bats has revealed another mechanism of echolocation. One of the authors described the work thus:

"We borrowed 35 specimens from the Royal Ontario Museum in Toronto and performed micro-computed tomography on them. This imaging technique allowed us to see the fine details of the bats' ear and throat regions: the larynges, stylohyals and tympanic bones. Previous work had relied on dissecting these bones, a challenge in animals as small as bats. We found that the fusion or connection of two bone structures - the stylohyal bone in a bat's throat and the tympanic bone in the ear region of its skull - was a feature of all laryngeally echolocating bat species we studied."

This finding is new and unexpected. It means that previous conclusions need to be reappraised. This is exactly what is happening with the "most primitive fossil bat".

"The relatively small cochleae and lack of paddle-like expansions on the cranial tips of the stylohyal bones have been interpreted as evidence that O. finneyi lacked laryngeal echolocation, which supports the hypothesis that flight evolved before echolocation. However, we find that articulation between the stylohyal and tympanic bones is a better predictor of laryngeal echolocation ability than the shape of the stylohyal bone, at least among extant bats. If the stylohyal bones articulated with the tympanic bones in O. finneyi, then we propose that this species had the capacity for laryngeal echolocation. Our results thus reopen basic questions about the timing of the appearance of echolocation and flight in the evolution of bats."

There are several lessons to be learned here - and one of these is to always be prepared to hold judgment on the word "primitive" - even if it is said to be the "most primitive"!

A bony connection signals laryngeal echolocation in bats
Nina Veselka, David D. McErlain, David W. Holdsworth, Judith L. Eger, Rethy K. Chhem, Matthew J. Mason, Kirsty L. Brain, Paul A. Faure & M. Brock Fenton
Nature 463, 939-942 (18 February 2010) | doi:10.1038/nature08737

Echolocation is usually associated with bats. Many echolocating bats produce signals in the larynx, but a few species produce tongue clicks. Here, studies show that in all bats that use larynx-generated clicks, the stylohyal bone is connected to the tympanic bone. Study of the stylohyal and tympanic bones of a primitive fossil bat indicates that this species may have been able to echolocate, despite previous evidence to the contrary, raising the question of when and how echolocation evolved in bats.

Last year, a workshop was hosted by the International Society of Protistologists at their North American Section Meeting. The workshop was given the title "Horizontal Gene Transfer and Phylogenetic Evolution Debunk Intelligent Design". Some of the presentations have recently been published, and one of these is the focus of attention here. One does not get beyond the first paragraph before finding that the authors regard Neodarwinism as robust and that all challengers have abandoned science:

"Despite the overwhelming body of evidence that supports the basic tenets of evolution (i.e. common descent of organisms with different forms being the result of natural selection acting upon naturally occurring variation), there is a large proportion of the American population that does not accept the validity of what is perhaps the most rigorously tested scientific hypothesis in history."

The "six" kingdom taxonomic scheme (Image from Purves et al., source here)

The second paragraph points the finger at Dr Michael Behe and his influential books Darwin's Black Box and The Edge of Evolution. Although the paper covers much ground, it is one of Behe's arguments that engage their attention.

"In his book "The Edge of Evolution: The Search for the Limits of Darwinism" Behe (2007) draws heavily upon the example of drug resistance in the malarial parasite Plasmodium falciparum as one biochemical pathway that is supposedly too complex to have arisen through natural evolutionary processes. According to Behe (2007), the odds that mutations required to impart chloroquine resistance in Plasmodium could arise naturally are so impossibly long that they lie beyond what he considers "The Edge of Evolution".

Anyone who has read Behe's book and understands his analysis would be alerted at this point to a wearying straw man argument. If you are going to critique someone, you ought to, at least, be able to paraphrase their arguments correctly. One wonders why the workshop participants did not put the authors right. In addition, one wonders why the referees did not point out the need for correction. But further, one wonders why the journal editor did not invite peer review from an ID microbiologist. Certainly, the peer review system failed on this occasion. Happily, the internet does allow misinformation to be corrected, and Behe has posted comments which show that the authors, instead of "dispelling the myths of Intelligent Design" are actually promoting myths about Intelligent Design. Here are Behe's concluding words:

"To recap, several years after The Edge of Evolution was published a scientific society held a workshop to demonstrate the book's errors. Yet they couldn't even get the book's argument straight, and the experimental work they cited against my argument is not even pertinent to it. Apparently the design argument drives some scientists so much to distraction that they lose their normally robust powers of reasoning."

Clearly, there is more to be said about the underlying issues. In the abstract of the paper, ID advocates are said to have the goal of "challenging the philosophy of scientific materialism". This is a good place to start an analysis of the issues: because scientific materialism needs to be challenged. Science has no basis for concluding that matter is all there is and that all causation is natural. Those who claim this are importing an ideology that was absent in the early days of science (when the pioneers were theistic scientists, who were quite comfortable with the thought that the natural world is designed). People with different ideologies look at the same data in different ways, and protagonists who do not recognise this are spreading more heat than light. My fear is that instead of discarding this paper as based on false premises, blind crusaders for philosophical materialism will hail it as "excellent article" and will add it to their list of peer reviewed publications showing that the ID approach is bankrupt.

Using Protistan Examples to Dispel the Myths of Intelligent Design
Mark A. Farmer and Andrea Habura
Journal of Eukaryotic Microbiology, 57(1), 2010, 3-10 | doi 10.1111/j.1550-7408.2009.00460.x

ABSTRACT: In recent years the teaching of the religiously based philosophy of intelligent design (ID) has been proposed as an alternative to modern evolutionary theory. Advocates of ID are largely motivated by their opposition to naturalistic explanations of biological diversity, in accordance with their goal of challenging the philosophy of scientific materialism. Intelligent design has been embraced by a wide variety of creationists who promote highly questionable claims that purport to show the inadequacy of evolutionary theory, which they consider to be a threat to a theistic worldview. We find that examples from protistan biology are well suited for providing evidence of many key evolutionary concepts, and have often been misrepresented or roundly ignored by ID advocates. These include examples of adaptations and radiations that are said to be statistically impossible, as well as examples of speciation both in the laboratory and as documented in the fossil record. Because many biologists may not be familiar with the richness of the protist evolution dataset or with ID-based criticisms of evolution, we provide examples of current ID arguments and specific protistan counter-examples.

Misusing Protistan Examples to Propagate Myths about Intelligent Design
Michael J. Behe
Uncommon Descent, 15 February 2010

Introductory sentences: The Journal of Eukaryotic Microbiology recently published several papers from a workshop sponsored by the International Society of Protistologists entitled "Horizontal Gene Transfer and Phylogenetic Evolution Debunk Intelligent Design." So here we have a respected scientific society, presumably planning a workshop months in advance, and finally laying out their considered case for why intelligent design fails. As you might imagine, I was most anxious to read about it. Unfortunately, rather than scholarly papers, the manuscripts read like press releases from the National Center for (Darwinian) Science Education.

Much to the dismay of the BADs (Birds Are Dinosaurs), there is a group of scientists who are in denial of the thesis that theropod dinosaurs evolved into birds. Furthermore, this BAND of scholars (Birds Are Not Dinosaurs) have published in the esteemed PNAS and not in some obscure low-ranked journal. The research was concerned with the dromaeosaurid Microraptor gui, which was first described in 2002 and has flight feathers on all four limbs. The research team modelled M. gui flight and concluded that gliding was its forte.

"We suggest that Microraptor was an adept glider and would have had little difficulty gliding from tree trunk to tree trunk or climbing trees, but would have been very awkward and vulnerable on the ground. The primary feathers on the tarsometatarsus (foot) of the hindwing of M. gui were too long in relation to the limb bones to have allowed the hindwing to fold compactly as does the modern bird wing. Just as colugos and sloths have their limbs encumbered by patagia, the hindwing feathers on Microraptor would severely hamper any terrestrial locomotion."

John Ruben draws attention to an image drawn in 1915 by naturalist William Beebe. It suggests a hypothetical view of what early birds may have looked like, gliding down from trees - and it bears a striking similarity to a fossil discovered in 2003 that is raising new doubts about whether birds descended from ground-dwelling theropod dinosaurs (Source here)

In an accompanying commentary, John Ruben reviewed the history of the controversy over the origins of bird flight. Much to the disapproval of the BADs, Ruben presents those skeptical of the cursorial, ground-upwards hypothesis as scholars who have championed reasoning from evidence. The new research, Ruben suggests, favours gliding, arboreal proto-birds. But he also suggests that some more radical thinking may be warranted:

"So, is the answer, after all, a hybrid of the two old theories, i.e., avian origins from an arboreal, gliding theropod dinosaur? Perhaps, but then this is paleobiology - very recent data suggest that many clearly cursorial theropods previously thought to have been feathered may not have been so and that dromaeosaurs, the group that birds are assumed to have been derived from, may not even have been dinosaurs. What pops up next is anyone's guess."

The Science Daily report points to these more fundamental divergences of view:

The weight of the evidence is now suggesting that not only did birds not descend from dinosaurs, Ruben said, but that some species now believed to be dinosaurs may have descended from birds.
"We're finally breaking out of the conventional wisdom of the last 20 years, which insisted that birds evolved from dinosaurs and that the debate is all over and done with," Ruben said. "This issue isn't resolved at all. There are just too many inconsistencies with the idea that birds had dinosaur ancestors, and this newest study adds to that."

Breaking out of the conventional wisdom? Yes - we need some more of that!

Paleobiology and the origins of avian flight
John Ruben
Proceedings of the National Academy of Sciences, published online before print February 9, 2010 | doi:10.1073/pnas.0915099107

First sentence: Interpreting the paleobiology of long extinct taxa, pesky new fossils, and reinterpretations of well-known fossils, sharply at odds with conventional wisdom never seem to cease popping up.

Model tests of gliding with different hindwing configurations in the four-winged dromaeosaurid Microraptor gui
David E. Alexander, Enpu Gong, Larry D. Martin, David A. Burnham, and Amanda R. Falk
Proceedings of the National Academy of Sciences, Published online before print January 25, 2010 | doi: 10.1073/pnas.0911852107

Abstract: Fossils of the remarkable dromaeosaurid Microraptor gui and relatives clearly show well-developed flight feathers on the hind limbs as well as the front limbs. No modern vertebrate has hind limbs functioning as independent, fully developed wings; so, lacking a living example, little agreement exists on the functional morphology or likely flight configuration of the hindwing. Using a detailed reconstruction based on the actual skeleton of one individual, cast in the round, we developed light-weight, three-dimensional physical models and performed glide tests with anatomically reasonable hindwing configurations. Models were tested with hindwings abducted and extended laterally, as well as with a previously described biplane configuration. [. . .] Although the biplane model glided almost as well as the other models, it was structurally deficient and required an unlikely weight distribution (very heavy head) for stable gliding. Our model with laterally abducted hindwings represents a biologically and aerodynamically reasonable configuration for this four-winged gliding animal. M. gui's feathered hindwings, although effective for gliding, would have seriously hampered terrestrial locomotion.

See also:

Bird-from-Dinosaur Theory of Evolution Challenged: Was It the Other Way Around?, ScienceDaily (Feb. 10, 2010)

Deyes, R. B.A.R.B: Birds Are Really.....Birds!, ARN Literature Blog (25 June 2009)

Tyler, D. Did birds fly in the Late Triassic? ARN Literature Blog (16 June 2009)

Professor Steve Fuller is known as a prolific author whose analysis of the scientific enterprise is iconoclastic. He was famously involved as a defense witness in the Kitzmiller v. Dover Area School District (2005) trial, for which he has received a great deal of flak. The essay cited below provides an explanation of his involvement and a challenge for other qualified people to ensure that their voices are heard.

"I believe that tenured historians, philosophers, and sociologists of science - when presented with the opportunity - have a professional obligation to get involved in public controversies over what should count as science. I stress 'tenured' because the involved academics need to be materially protected from the consequences of their involvement, given the amount of misrepresentation and abuse that is likely to follow, whatever position they take."

Why are so few willing to follow this advice? (Source here)

Those who want to read specific comments on the trial should read the essay. My interest here is in the broader issue of what science studies brings to the discussion of origins. Fuller is dissatisfied with the limited scope of the discourse to date because the dominant voices have functioned as "underlaborer[s] to science". He points out "two types of public exemplars" that have been associated with science studies:

"On the one hand, there is the Michael Ruse figure who supplies a historical and philosophical hinterland to the dominant scientific paradigm so as to complement its purely empirical success with a broader cultural and conceptual grounding that will appeal to those unfamiliar with the technical science. On the other hand, there is the Robert Pennock figure, more typical of the younger generation, who outright collaborates with established scientists in their research, providing a running legitimizing narrative in co-authored articles published in technical and popular forums. In both cases, the science studies scholar functions as an underlaborer to science, as opposed to a true metascientist."

Science studies need to rise above partisanship and develop robust contributions to knowledge that do not need the endorsement of the 'scientific consensus' to justify their validity.

"A metascientist evaluates science from a standpoint that does not presuppose the legitimacy of the dominant paradigm. He or she starts by asking why we pursue science in the first place - the question of ends - and then turns to consider the extent to which the normal pursuit of science satisfies those ends. This is the role I have tried to exemplify. [. . .] The approach is 'constructivist' without being 'relativist' in the way these two terms are normally understood in epistemology."

These social epistemological principles are then applied to the origins controversy. Fuller is interested in this debate because it presents so many important and interesting issues needing rational discussion. However, Fuller finds that far too much bigotry has been expressed and has concluded that something needs to be done to raise the level of debate.

"In terms of the evolution-creation controversy, the bottom line for me, then, is not to satisfy the wishes of particular communities by allowing creationism to be taught, but to avoid the opportunity costs to everyone if creationism is not allowed to be taught."

These opportunity costs are worthy of elaboration. Fuller identifies several of these. The first draws attention to the history of science and the fact that many scientists have done good work motivated by the presupposition that the natural world is the handiwork of an Intelligent Designer. Those who say that toleration of ID will be the death of science and the beginning of a new dark age are in denial of history.

"Here I have in mind the overwhelmingly positive role that belief in an intelligent designer has played in motivating religious people to enter and stick with scientific careers, which have resulted in findings that command the assent of even those who lack faith."

The second opportunity cost is academic freedom. Fuller has already made it clear that he thinks tenured academics should be taking the lead in challenging the dominant paradigm. It is simply too risky for others to stick their heads above the parapet - they are easy targets and they get hurt. They are treated as guilty by association and their ideas are deemed unworthy of any further consideration.

"When we start to judge ideas rather than texts, intentions rather than practices, we become complicit in the erosion of academic freedom. Perhaps the most widely publicized recent case to cross that line was the forced resignation of Michael Reiss as director of science education for the Royal Society. Reiss had the temerity to suggest that science teachers should take seriously - albeit critically - creationist queries raised by their students. Reiss, who also holds a chair at the University of London's Institute of Education, based this judgment on his own research on science pedagogy. It is worth noting that he did not propose that teachers should themselves introduce the creationist ideas - yet the Royal Society deemed he still had to go."

The third opportunity cost is concerned with the quality of debate. Academics are supposed to use their minds when defending a position or critiquing others. However, the origins issue reveals people ruled by emotions, prejudices and ideologies.

"The pervasive anti-Christian bigotry surrounding the evolution-creation debate has had other knock-on effects on the conduct of intellectual discourse. It becomes an excuse to lower the tone in both academic and public discussions. Anyone prepared to defend any form of creationism should expect enormous negative attention in the blogosphere, ranging from occasional derision to outright invitations to trash the defender. At first I believed that my own intervention would clarify misunderstandings but it only seemed to intensify them, not least because I addressed my opponents in the spirit they addressed me. They were not prepared to entertain the idea that it was they and not I who misunderstood."

These three opportunity costs deserve the serious attention of all who are engaged in the controversy. However, the dominant response has been to ignore these points and persist in old patterns of thinking and tired polemics. Some have expressed their frustration with Fuller for his bad judgment. One of these is Michael Lynch, Professor of Science & Technology Studies at Cornell University, who has published several articles condemning Fuller's role as an expert witness in the Dover trial. One of these was in the same journal Spontaneous Generations that carried the essay under consideration here, to which Fuller has recently responded. He pointed out that his "game" is not for short-term gain but for long-term success.

"In that context, I undertake a risky performance in the spirit of a living experiment, the results of which should prove instructive not only to myself but also to others who in the future are similarly well-positioned to bring science studies to bear on public policy. The only mistake would be for others not to repeat the experiment."

Fuller is prepared to criticize Ruse and Pennock for being "traitors to their training" and guilty of "intellectual treason". He is prepared to say that Barbara Forrest's tactic has been to shift the argument from evaluation of ideas to the "intentions of those promoting them", thereby following in the footsteps of John Dewey who used this approach to earn a reputation as "one of the foremost Red-baiters in the US philosophical establishment in the 1940s and '50s". These charges are not ad hominems but are based on analysis of their arguments. The issues are far too important to allow room for complacency - academic freedoms are being eroded, young scientists are fearful of expressing any positive views on design, parental responsibilities for the education of their children are being eroded (with charges of "child abuse" being thrown around), and much more. But Fuller is also prepared to press upon tenured academics the obligation he thinks they have to use their positions of relative security to contribute to public controversies about the nature of science. There is an urgency about the situation. The least that can be said is that Fuller is a trail blazer. No one can criticize him for not acting out what he is encouraging others to do.

Science Studies Goes Public: A Report on an Ongoing Performance
Steve Fuller
Spontaneous Generations, 2(1), (2008), 11-21

First para: I believe that tenured historians, philosophers, and sociologists of science - when presented with the opportunity - have a professional obligation to get involved in public controversies over what should count as science. I stress 'tenured' because the involved academics need to be materially protected from the consequences of their involvement, given the amount of misrepresentation and abuse that is likely to follow, whatever position they take. Indeed, the institution of academic tenure justifies itself most clearly in such heat-seeking situations, where one may appear to offer a reasoned defense for views that many consider indefensible. To be sure, the opportunities for involvement will vary in kind and number, but I believe that we are obliged to embrace them. In the specific case of 'demarcation' questions of what counts as science, the people who possess the sort of general and comparative knowledge most relevant for adducing this matter are historians, philosophers, and sociologists of science - not professional scientists unschooled in these areas.

Response to Lynch
Steve Fuller
Spontaneous Generations, 3(1), (2009), 220-222.

See also:

Lynch, M. Going Public: A Cautionary Tale, Spontaneous Generations, 3(1), (2009), 212-219.

Tyler, D. A "teachable moment" regarding the departure of Michael Reiss, ARN Literature blog (25 September 2008)

Tyler, D. Michael Reiss and the science-religion issue, ARN Literature blog (17 September 2008)

Over the years, there has been much interest in the design of running shoes, with product designers building in protection against impacts and other perceived hazards. However, continuing reports of repetitive strain injuries warrant further research and product re-design. The topic has come to the surface recently with a comparison of the forces experienced by feet of habitually shod versus habitually barefoot runners. It emerges that barefoot runners make contact with the ground in a way that avoids impact-related discomfort and injury.

On the left, a habitually shod Kenyan who is heel-striking; on the right, a Kenyan who has never worn shoes and who is forefoot striking in the way most barefoot runners land. Below are representative force traces (in units of body weight) showing how the two styles of running differ in the force generated when the foot collides with the ground. The barefoot runner lands with no collisional force. (Image: Daniel E. Lieberman, Source here)

As a matter of observation, most habitually shod runners first contact the ground with their heel. This is referred to as heel-striking or rear-foot strike. Modern running shoes have been designed to reduce the impact forces with the help of additional cushioning at the heel. Barefoot runners first contact the ground with the front part of their feet and bend their ankles more as they run. This is referred to as fore-foot or mid-foot strike. This mode of running results in reduced collision forces and enhanced comfort.

"People who don't wear shoes when they run have an astonishingly different strike," says Daniel E. Lieberman, professor of human evolutionary biology at Harvard University and co-author of a paper appearing this week in the journal Nature. "By landing on the middle or front of the foot, barefoot runners have almost no impact collision, much less than most shod runners generate when they heel-strike. Most people today think barefoot running is dangerous and hurts, but actually you can run barefoot on the world's hardest surfaces without the slightest discomfort and pain. All you need is a few calluses to avoid roughing up the skin of the foot. Further, it might be less injurious than the way some people run in shoes."

Since this is a topic where there are numerous agents with commercial interests, the authors of the research paper have felt the need to issue a disclaimer that their reported work is essentially empirical in nature.

"Please note that we present no data on how people should run, whether shoes cause some injuries, or whether barefoot running causes other kinds of injuries. We believe there is a strong need for controlled, prospective studies on these problems." (Source here)

However, the authors go well beyond the empirical data in their analysis when they ground their work in a framework of evolutionary biology. This is also the starting point for Jungers' commentary on the research: "A commitment to walking and running on two legs distinguishes humans from apes, and has long been the defining adaptation of the hominins - the lineages that include both humans and our extinct relatives. This form of locomotion (bipedalism) has been around for millions of years, and we have been unshod for more than 99% of that time." The view, therefore, is that the context for understanding running is that it has evolved as an adaptation under the influence of natural selection.

"Our feet were made in part for running," Lieberman says. But as he and his co-authors write in Nature: "Humans have engaged in endurance running for millions of years, but the modern running shoe was not invented until the 1970s. For most of human evolutionary history, runners were either barefoot or wore minimal footwear such as sandals or moccasins with smaller heels and little cushioning."

There is another perspective on this, which is that of design. Design advocates will affirm: 'Our feet were designed in part for running'. Humans live in many different environments, and the design issues are affected by the need to walk, jump, climb, carry and run in these different environments. A sensitivity to design means that we need to understand how our feet work best in different conditions, so it follows that runners should adopt a biomechanical and physiological approach to developing good running habits. Runners should train to develop the full potential of the design features of their bodies. An evolutionary story of how ape-like animals developed bipedalism is simply a veneer overlying the empirical data.

Foot strike patterns and collision forces in habitually barefoot versus shod runners
Daniel E. Lieberman, Madhusudhan Venkadesan, William A. Werbel, Adam I. Daoud, Susan D'Andrea, Irene S. Davis, Robert Ojiambo Mang'Eni & Yannis Pitsiladis
Nature 463, 531-535 (28 January 2010) | doi:10.1038/nature08723

First para: Humans have engaged in endurance running for millions of years, but the modern running shoe was not invented until the 1970s. For most of human evolutionary history, runners were either barefoot or wore minimal footwear such as sandals or moccasins with smaller heels and little cushioning relative to modern running shoes. We wondered how runners coped with the impact caused by the foot colliding with the ground before the invention of the modern shoe. Here we show that habitually barefoot endurance runners often land on the fore-foot (fore-foot strike) before bringing down the heel, but they sometimes land with a flat foot (mid-foot strike) or, less often, on the heel (rear-foot strike). In contrast, habitually shod runners mostly rear-foot strike, facilitated by the elevated and cushioned heel of the modern running shoe. Kinematic and kinetic analyses show that even on hard surfaces, barefoot runners who fore-foot strike generate smaller collision forces than shod rear-foot strikers. This difference results primarily from a more plantarflexed foot at landing and more ankle compliance during impact, decreasing the effective mass of the body that collides with the ground. Fore-foot- and mid-foot-strike gaits were probably more common when humans ran barefoot or in minimal shoes, and may protect the feet and lower limbs from some of the impact-related injuries now experienced by a high percentage of runners.

See also:

The Barefoot Professor: by Nature Video

Jungers, W.L., Barefoot running strikes back, Nature 463, 433-434 (28 January 2010) | doi:10.1038/463433a

Tyler, D. The human body is built for running, ARN Literature blog (29 October 2009)

The first species to have its genome decoded by 'next-generation-sequencing' (NGS) machines is the giant panda (Ailuropoda melanoleuca). The individual animal was known previously to the world as the mascot of the 2008 Beijing Olympic Games. Scientists have been excited by the report because the NGS approach is significantly cheaper and faster than other methods. It is not the purpose of this blog to assess the robustness of the method, but it is important to be aware that the reported sequence utilizes previously determined genomes as a reference platform: dog and human genomes in this case.

"Using evidence-based gene prediction, the human and dog genes [. . .] were projected onto the panda genome, and the gene loci were defined by using both sequence similarity and whole-genome synteny information."

The iconic giant panda's genetic makeup reveals degradation (Source here)

The estimated size of the giant panda genome is said to be 2.40 Gb (compared with 2.45 Gb for the dog genome and 3.0 Gb for humans) making up about 21,000 genes (similar to humans). "Overall, we found that the quality of the predicted panda genes was comparable to that of other well-annotated mammalian genes." Although the panda eats only bamboo leaves, genes associated with carnivory are present in the panda:

"Of interest, our analysis of genes potentially involved in the evolution of the panda's reliance on bamboo in its diet showed that the panda seems to have maintained the genetic requirements for being purely carnivorous even though its diet is primarily herbivorous."

There was no trace of genes that encode enzymes for digesting cellulose, raising questions about how the panda can possibly survive on bamboo. The hypothesis proposed is that the bamboo diet "may instead be more dependent on its gut microbiome". Confirmation of this will require further work. A related dietary factor concerns the sense of taste. The authors refer to the five components of taste: sweetness, saltiness, sourness, bitterness and umami. The giant panda has lost the capability of sensing umami, which means that meat has become unappetizing.

"Umami is sensed through the T1R family. In the panda genome, T1R2 and T1R3 are in an intact form, but T1R1 has become a pseudogene - we found that [. . .] two panda T1R1 exons contain transcript errors."
"Two frameshift mutations occurred in the third and sixth exons of the panda T1R1 gene. The third exon contained a 2-bp ('GG') insertion; the sixth exon contained a 4-bp ('GTGT') deletion."

A possible genetic factor affecting the giant panda's low fecundity rate was identified. Nearly all of the mammalian reproduction genes were mapped, and "a putative pseudo follicle-stimulating hormone (FSH) [beta]-subunit gene (giant panda-FSHB2)" was noted. The authors comment:

"At this stage, whether the pseudo FSHB2 gene contributes to the reproduction features of the giant panda remains to be determined."

Some have considered whether the panda genome helps resolve the animal's taxonomic status. Although most place the panda in the bear family (Ursidae), a case has been made that it belongs elsewhere - in the raccoon family (Ailuridae). Since we do not have the genomes for any of these possible relatives, there is little more that can be said on the matter. However, even if other genomes were sequenced, does the "genome" tell us much about what makes a bear differ from a raccoon or a dog or a human? The genome can be described as the repository of housekeeping genes; it provides the materials needed for the organism to function - but something much more than this is needed to inform taxonomy. The ENCODE project (along with many others) has revealed rich functionality in the non-coding DNA (alias 'junk DNA'). Consequently, it is probable that the gene sequencers are just scratching at the surface of genetic information.

If the giant panda is correctly assigned to the Ursidae, the new research contributes significantly to the way we understand the speciation of this animal. Before genome sequencing, we could say that it has diversified significantly from ancestral Ursidae stock. It has a reduced number of chromosomes, 42, whereas most bears have 74. It has a wholly vegetarian diet and it has a modified sesamoid bone which it uses to strip bamboo leaves from stems. The panda genome findings provide the background for understanding herbivory: the panda still retains the genes for carnivory but mutations have destroyed the taste trigger for it to eat meat. Although the panda cannot make enzymes for digesting plant food, communities of gut microbes are the most likely explanation of its continuing survival. The reproduction problems experienced by giant pandas may also be linked to a mutation affecting follicle stimulation.

The overall picture is one of speciation/diversification linked to genetic degradation. Natural selection, which has often been portrayed as all-powerful and capable of building exquisitely complex structures, has failed to provide the giant panda with any enzymes for digesting plant food. We do not know whether the modified sesamoid bone is an evolutionary innovation, a part of the degradation story or information neutral. The News & Views essay that accompanies the research paper calls the panda China's "national treasure" - and so it is. However, from the perspective of genetics, the giant panda is not in a healthy state. Whatever else may be relevant, this case has strong affinities with speciation by gene pool reduction. From the perspective of Darwinism, the giant panda genome testifies to the failure of Darwinian mechanisms to overcome problems caused by mutations. From the perspective of design, we have a story of how a superbly designed carnivore has managed to survive the effects of genetic degradation. From a conservation perspective, without human intervention, the chances of long-term survival are slender.

There is also the finding that Jingjing's genome has a high degree of genetic diversity, but she is unlikely to be representative of the panda population taken as a whole. It is more prudent to assume that the relatively isolated panda enclaves harbour problems of inbreeding and that Jingjing is an example of the benefits of breeding across enclaves - further supporting the case for human intervention.

The sequence and de novo assembly of the giant panda genome
Li, R. et al.
Nature 463, 311-317 (21 January 2010) | doi:10.1038/nature08696

Abstract: Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes.

See also:

Worley, K.C. and Gibbs, R.A. Decoding a national treasure, Nature 463, 303-304 (21 January 2010) | doi:10.1038/463303a

Qiu, J., Genome reveals panda's carnivorous side, 13 December 2009, Nature News | doi:10.1038/news.2009.1141

The claim that Rubisco is poorly designed or unintelligently designed was appearing in textbooks in the 1990s. The idea has been picked up recently in a News & Views piece by John Ellis. He writes that Rubisco "is a relic of a bygone age" and his essay has the title: "Tackling unintelligent design".

"Rubisco is the most important enyzme on the planet - virtually all the organic carbon in the biosphere derives ultimately from the carbon dioxide that this enzyme fixes from the atmosphere. But Rubisco is also one of the most inefficient enzymes on the planet. It evolved when the atmospheric composition was different from that of today, and its failure to adapt significantly to the modern atmosphere limits agricultural productivity."

RuBisCO has an active site (binding pocket) that binds ribulose-1,5-bisphosphate (RuBP) and catalyzes the reaction between RuBP and CO2 or O2. In the figure, the two large RuBisCO subunits (blue and cyan) sandwich an RuBP molecule (orange) in the active site. The site is gated by the C-terminus (yellow), lysine 128 (purple), and loop 6 (green), which undergo periodic conformational changes that open or close the site. Reactants enter and products escape while it is in an open state, and carbon-fixation reactions occur during the closed state. (Image credit: Paul Crozier, Sandia National Labs. Source here)

Over the past decade, the pendulum has swung away from the idea that Rubisco is unintelligent design. Its achievements are remarkable, as Griffiths (2006) explains:

"It is curious that Rubisco should fix CO2 at all, as there is 25 times more O2 than CO2 in solution at 25 degC, and a 500-fold difference between them in gaseous form. Yet only 25% of reactions are oxygenase events at this temperature, and carbon intermediates 'lost' to the carbon fixation reactions by oxygenase action are metabolized and partly recovered by the so-called photorespiratory pathway. Catalysis begins with activation of Rubisco by the enzyme Rubisco activase, when first CO2 and then a magnesium ion bind to the active site. The substrate, ribulose bisphosphate, then reacts with these to form an enediol intermediate, which engages with either another CO2 or an O2 molecule, either of which must diffuse down a solvent channel to reach the active site."

The analysis of Tcherkez et al. (2006) was significant for showing that Rubisco does not bear the marks of Darwinian tinkering and that research to genetic modify the enzyme to gain agricultural benefits can be expected to deliver only "modest improvements" in its efficiency of operation.

"Further, [our hypothesis] raises the possibility that, despite appearing sluggish and confused, most Rubiscos may be near-optimally adapted to their different gaseous and thermal environments. If so, genetic manipulation can be expected to achieve only modest improvements in the efficiency of Rubisco and plant growth. Such improvement would be limited to the magnitude of the scatter apparent in the correlations (Fig. 3), if the scatter represents incomplete optimization (see above). [. . .] Such adaptation in response to the changing atmosphere and temperature appears to have been instrumental in enabling the expansion of the biosphere to its current size."

Design theorists have drawn attention to three additional considerations:
1. A single-factor analysis of Rubisco is inadequate. The parameters considered to conclude the enzyme is poorly designed and inefficient are very limited. We should note that our perceptions of intelligent design are typically subjective, and most claims for poor design do not stand up to the test of time - further research leads to a greater appreciation of design (a good example being mammalian eye design). Furthermore, unintelligent design of architectures we deem sub-optimal should not be regarded as the only possible hypothesis. Multiple factors are likely to be relevant as chemosynthetic carbon fixation also makes use of Rubisco. It is employed by organisms living at hydrothermal vents and cold hydrocarbon seeps.
2. Photorespiration, the consumption of oxygen to produce a sugar that ultimately forms carbon dioxide during a series of reactions, may not be a mark of inefficiency, but the process may be useful to the plant. The null hypothesis for Design theorists is that processes have functionality. This hypothesis is not without some support: the process of photosynthesis is not just to capture CO2 and release oxygen because nitrate assimilation in plant shoots depends on photorespiration, as Rachmilevitch et al (2004) have shown.
3. Ecological considerations should be included in the analysis. If design is relevant to understanding the way plants work, we should consider not only the benefits to the organism (which limits the horizon for those with a Darwinian perspective) but also the biosphere as a whole. Rubisco's ability to capture CO2 increases with increasing CO2 content in the atmosphere, so its efficiency rises in a CO2-rich atmosphere. However, increasing oxygen levels in the atmosphere will reduce Rubisco's ability to capture carbon. So a negative feedback mechanism exists to regulate the relative concentrations of oxygen and carbon dioxide in the atmosphere. This is another example of design affecting the Earth's ecology - for more on this, go here.

Ellis was commenting on a paper by Liu et al. that reports on work to produce a Rubisco in vitro. In order to do this, the authors required two chaperone proteins, ATP and addition of 18 protein subunits (taken from a cyanobacterial Rubisco) to be introduced in the correct sequence to get yields of the enzyme. It is hoped that this procedure can be used to produce mutated versions that can be screened for improved effectiveness. It's all very interesting, but the biggest mystery is why people who expend so much intellectual energy on improving this remarkable molecule can live with the thought that "Rubisco is a superb example of unintelligent design for the modern world". Maybe research funds would be better spent exploring avenues identified using the presumption that this enzyme is optimally designed.

Tackling unintelligent design
R. John Ellis
Nature 463, 164-165 (14 January 2010) | doi:10.1038/463164a [restricted link]

Abstract: The key enzyme in photosynthesis, Rubisco, is a relic of a bygone age. The ability to assemble Rubisco in the test tube offers the prospect of genetically manipulating the enzyme to make it fit for the modern world.

Coupled chaperone action in folding and assembly of hexadecameric Rubisco
Cuimin Liu, Anna L. Young, Amanda Starling-Windhof, Andreas Bracher, Sandra Saschenbrecker, Bharathi Vasudeva Rao, Karnam Vasudeva Rao, Otto Berninghausen, Thorsten Mielke, F. Ulrich Hartl, Roland Beckmann & Manajit Hayer-Hartl.
Nature 463, 197-202 (14 January 2010) | doi:10.1038/nature08651 [restricted link]

Abstract: Form I Rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase), a complex of eight large (RbcL) and eight small (RbcS) subunits, catalyses the fixation of atmospheric CO2 in photosynthesis. The limited catalytic efficiency of Rubisco has sparked extensive efforts to re-engineer the enzyme with the goal of enhancing agricultural productivity. To facilitate such efforts we analysed the formation of cyanobacterial form I Rubisco by in vitro reconstitution and cryo-electron microscopy. We show that RbcL subunit folding by the GroEL/GroES chaperonin is tightly coupled with assembly mediated by the chaperone RbcX2. RbcL monomers remain partially unstable and retain high affinity for GroEL until captured by RbcX2. As revealed by the structure of a RbcL8-(RbcX2)8 assembly intermediate, RbcX2 acts as a molecular staple in stabilizing the RbcL subunits as dimers and facilitates RbcL8 core assembly. Finally, addition of RbcS results in RbcX2 release and holoenzyme formation. Specific assembly chaperones may be required more generally in the formation of complex oligomeric structures when folding is closely coupled to assembly.

See also:

Griffiths, H., Designs on Rubisco, Nature 441, 940-941 (22 June 2006) | doi:10.1038/441940a [restricted link]

Rachmilevitch, S., Cousins, A.B., Bloom, A.J., 2004. Nitrate Assimilation in plant shoots depends on photorespiration. Proceedings of the National Academy of Sciences USA, 101(31), 11506-11510 | doi: 10.1073/pnas.0404388101 [abstract]

Tcherkez, G.G.B., Farquhar, G.D. and Andrews, T.J., Despite slow catalysis and confused substrate specificity, all ribulose bisphosphate carboxylases may be nearly perfectly optimized, Proceedings of the National Academy of Sciences USA, May 9, 2006, 103(19), 7246-7251 | doi: 10.1073/pnas.0600605103 [abstract]

"It seems we have all been guilty of defaming Neanderthal man" declared a recent Editorial in The Guardian. This comment was triggered by a report documenting evidence for the use of pigments and decorative shells by Neanderthals. This is claimed to have occurred many years before any direct contact with modern humans, thereby undermining any thought that the artefacts did not really represent Neanderthal culture. Personal adornment, using a variety of colours, implies an aesthetic sense and an appreciation of symbolism. Since Neanderthals have often been presented as lacking these "modern" traits, the new research demands a reappraisal.

This decorative shell likely adorned the neck of a Neanderthal (Image credit Joao Zilhao, Source here)

It may be helpful to describe the findings by reference to a design methodology.