Literature

Explorer 1 was launched by the United States on January 31, 1958. It was the first satellite launched by the United States and it was eminently successful. Apart from validating Wernher von Braun's Jupiter C rocket, the satellite carried a cosmic ray detector designed to measure the radiation environment in Earth orbit. The data produced by this instrument led to the discovery of the Van Allen Radiation belts around the Earth and to major new insights into the way the Earth's magnetic field interacted with charged particles from the sun and beyond. "A permanent new landmark in the heavens, and a hazardous region to be traversed by future spacecraft, the Van Allen belts comprise giant lobes of charged particles trapped by Earth's magnetic field that extend thousands of kilometres into space" (Burrows, 2008). For more on the history of Explorer 1, go here.

Pickering, Van Allen and von Braun holding a model of Explorer 1 (for larger image, go here).

The program manager for Explorer 1 was Dr. Henry L. Richter, Jr. After this success, he continued within the Jet Propulsion Laboratory to oversee the scientific instrumentation for the Ranger, Mariner, and Surveyor Programs. When he left JPL, he continued his career in science and engineering. Two years ago, he published a book with the title: The Universe - A Surprising Cosmological Accident. The summary is as follows:

The universe is where we are, and an examination of it shows remarkable characteristics that allow human life to exist in this place where we live. In particular, the nature of our earth is ideally suited to support life from a wide variety of considerations. Besides human beings, there are all sorts of life forms that are formed the way they are in unique ways, each with its own perfection. What is the chance of this happening by accidental, random events? Come and tour many of these amazing scientific and biological facts and try to imagine how they came about. Accidents of nature? - - Can't be. Are we as people accidents of nature? Unthinkable!

As someone who has spent a life in science, it is interesting to know that Henry Richter finds no incompatibility between his professional work and the recognition of design in the natural world. His career has allowed him to acquire a unique appreciation of the Universe and life on Earth. He finds the "accidents of nature" thesis totally unconvincing. For further comments on Richter's convictions, go here. Design thinking needs to be prominent in the way we think about ourselves and the Cosmos.

A useful way to mark the 50th anniversary of Explorer 1 is to remind ourselves that science is not done in a philosophical vacuum. Whilst many scientists today have adopted philosophical materialism as their metaphysical foundation, the pioneers of science were theists and found ways of integrating their science with a theistic worldview. We are not without examples today of people who have distinguished themselves within the scientific community and have developed a worldview where science and theism are in harmony. Design thinking is a part of this worldview.

The Universe - A Surprising Cosmological Accident
by Henry L. Richter
Xulon Press, September 2006.

Book Description: A book intended to ask fundamental questions pointing out how unique an environment the solar system and earth provides to allow human life to exist - this is no accident!

See also:

Coppedge, D.F. Explorer 1 Chief Discovers Design, Creation-Evolution Headlines, 01/31/2008

Burrows, W.E. Van Allen remembered as belts turn 50, Nature 451, 523 (31 January 2008) | doi:10.1038/451523a

The term "bradytely" has been coined to describe the very slow morphological changes associated with an evolving lineage. One familiar example is the brachiopod Lingula, with living specimens closely matching fossil forms. Another is Limulus, the horseshoe crab. Although the living animals are significantly larger than the fossil forms, they all have the same distinctive body plan.

The North American horseshoe crab, Limulus polyphemus
Image credit: Florida Fish and Wildlife Conservation Commission

It will not be a surprise to be told that there have been numerous research publications on the evolutionary origins of the horseshoe crabs (Family: Limulidae, Class: Xiphosura). It is customary for researchers to identify stem group species and crown group species as they seek to find patterns in the fossil material. This approach has been followed within the class Xiphosura, with a group known as the synziphosurines considered as stem lineage animals living during the Silurian-Carboniferous Periods.
All this work is thrown into the melting-pot by the discovery of Lunataspis aurora, "the oldest horseshoe crab", from Late Ordovician deposits in Canada. This animal is essentially modern in appearance and it predates the synziphosurines. The authors write:

"In most discernible characters, Lunataspis appears to be much closer to certain Late Palaeozoic Paleolimulidae (Xiphosurida) than to any described synziphosurine, and is in fact more limuline in external morphology than many of the bizarre and clearly specialized Carboniferous xiphosurids, such as the Euproopidae. The presence of a presumed horseshoe crab of such modern appearance in Late Ordovician shallow subtidal to intertidal depositional settings has broader potential for constraining other critical stages in euchelicerate phylogeny [. . .]"

The implications of the find are apparent in the short quote above. Organisms thought to be stem group species are either unrelated to the lineage or are specialised, not primitive. This rethinking of the Xiphosura is said by the authors to be "a task well beyond the scope of this brief account". Indeed, but this discovery will fuel much discussion in the future. One wonders whether it will stimulate a rethink about the stem/crown conceptual model of lineage evolution? As an alternative, consider this approach based on stasis rather than darwinian transformation. Organisms can be considered as reservoirs of type-specific biological information at the outset, and their subsequent history can result in various permutations of that biological information (e.g. niche specialisation) or to loss (degenerate forms). This appears to be just as testable as other approaches and, in the case of the limulids, a very nice fit to the data.

The oldest horseshoe crab: a new xiphosurid from Late Ordovician Konservat-Lagerstatten deposits, Manitoba, Canada.
Rudkin, D.M., G.A. Young, and G.S. Nowlan.
Palaeontology, 51(1), 1-9, Jan 2008 | doi: 10.1111/j.1475-4983.2007.00746.x

Abstract: A remarkable new fossil horseshoe crab, Lunataspis aurora gen. et sp. nov., from recently discovered Upper Ordovician (c. 445 Ma) shallow marine Konservat-Lagerstatten deposits in Manitoba (Canada), is characterized by fusion of opisthosomal tergites into two sclerites. A broad mesosoma of six or seven fused segments, followed by a narrow metasoma of three reduced segments, represents an advanced transitional condition in the development of the xiphosurid thoracetron. Lunataspis further possesses a large crescentic prosomal shield bearing lateral compound eyes on weak ophthalmic ridges that flank a low cardiac lobe, and a keeled lanceolate telson. Lunataspis is much older than the proposed 'synziphosurine' stem lineage of Carboniferous and post-Palaeozoic Xiphosurida, yet is strikingly similar to crown group limuline horseshoe crabs, indicating that major features of the distinctive and highly conserved xiphosurid Bauplan evolved considerably earlier in the Palaeozoic than was previously suspected. In addition to establishing a new temporal benchmark for assessing hypotheses of early chelicerate relationships, the discovery of horseshoe crabs in a Late Ordovician marginal marine setting marks the earliest definitive record of this persistent ecological association.

Gerald Joyce wrote of Leslie Orgel, the veteran origin-of-life researcher:

"Although Orgel was a theoretician, he always demanded that theory be subject to rigorous experimental validation. This, he felt, was especially true in the field of the origins of life, where "theories are a dime a dozen and facts are in short supply"."

"If pigs could fly" hypothetical chemistry is thriving in OOL research

These words are dramatically illustrated by Orgel's block-buster of a paper critiquing the metabolic cycle route for the origin of life (OOL), published posthumously in PLoS Biology. Metabolic cycles have been proposed as an alternative (or as a precursor) to the RNA World OOL scenarios. These cycles involve sustained chemical reactions to synthesise biologically interesting molecules. For example: "The proposal that the reverse citric acid cycle operated nonenzymatically on the primitive Earth has been a prominent feature of some scenarios for the origin of life." If advocates have the freedom to argue the case for viable prebiotic chemistry scenarios, there can be no complaint when critics point out their implausibility. Orgel wrote as someone starting out with an open mind and with a commitment to follow the evidence wherever it leads:

"If a complex system of evolvable nonenzymatic cycles that did not depend on residue-by-residue replication could be shown to be feasible, it would mark a breakthrough in origin-of-life studies. What is essential, therefore, is a reasonably detailed description, hopefully supported by experimental evidence, of how an evolvable family of cycles might operate. The scheme should not make unreasonable demands on the efficiency and specificity of the various external and internally generated catalysts that are supposed to be involved. Without such a description, acceptance of the possibility of complex nonenzymatic cyclic organizations that are capable of evolution can only be based on faith, a notoriously dangerous route to scientific progress."

Orgel set out to answer the question: "Could prebiotic molecules and catalysts plausibly have the attributes that must be assigned to them in order to make the self-organization of the cycles possible?" So thorough is the argumentation, it is difficult to provide a summary in a paragraph or two. The Conclusions section, however, highlights two points very nicely.

First, advocates of metabolic cycles need catalysts for their reactions, but they face the problem that familiar and relevant catalysts are enzymes, which are highly complex structures needing (at least) the RNA World as a prerequisite. So nonenzymatic catalysts have been explored. This is where Orgel puts his finger on the fundamental problem of specificity. Without this, there can be no cycles.

"The most serious challenge to proponents of metabolic cycle theories - the problems presented by the lack of specificity of most nonenzymatic catalysts - has, in general, not been appreciated. If it has, it has been ignored. Theories of the origin of life based on metabolic cycles cannot be justified by the inadequacy of competing theories: they must stand on their own."

Second, there is an embedded tension in all the proposals of hypothetical metabolic cycles leading to replication.

"The prebiotic syntheses that have been investigated experimentally almost always lead to the formation of complex mixtures. Proposed polymer replication schemes are unlikely to succeed except with reasonably pure input monomers. No solution of the origin-of-life problem will be possible until the gap between the two kinds of chemistry is closed."

Orgel's essay contains many other detailed critiques of metabolic cycle research, including numerous valuable comments on methodology (for more about this, go here). Clearly, he thought that there has not been enough testing of hypotheses by empirical work. This prompted his concluding remark:

"However, solutions offered by supporters of geneticist or metabolist scenarios that are dependent on "if pigs could fly" hypothetical chemistry are unlikely to help."

Orgel has bequeathed us a valuable legacy. His essay deserved respect. The main message concerns, not the various detailed critiques, but his commitment to "detailed examination and criticism", his call for claims to be supported "from experimental or theoretical chemistry", and his rejection of the argument that theories can be "justified by the inadequacy of competing theories". Although he was no ally of Intelligent Design, his arguments so closely parallel those of ID scientists that we have to regard his critique as a remarkable example of convergent evolution!

The Implausibility of Metabolic Cycles on the Prebiotic Earth
Leslie E. Orgel
Public Library of Science: Biology, 6(1): e18, Jan 22, 2008, doi:10.1371/journal.pbio.0060018.

First paragraph: Cycles occur widely in all branches of chemistry. The definition of a catalyst as an agent that facilitates the conversion of reactants to products without itself being changed almost guarantees that a catalyst can initiate successive "cycles" of the same reaction. Metabolic cycles are different. Strictly, they are by definition restricted to biochemistry. Like catalytic cycles, they too result in repeated conversions of substrates into products, but they involve much more complex sequences of chemical reactions. As far as I am aware, the formose reaction, which converts formaldehyde to a complicated mixture of products, including various sugars, is the only known nonenzymatic reaction sequence that is at all similar to a metabolic cycle, although the existence of one or two much simpler cycles has been established or made probable in the literature of prebiotic chemistry. The possibility that reactions of hydrogen cyanide (HCN) might form the basis for a complex cyclic organization has been proposed, but there is as yet no experimental evidence to support this proposal.

See also:

Coppedge, D.F. Leslie Orgel's Last Testament: Pigs Don't Fly, and Life Doesn't Just Happen, Creation-Evolution Headlines, 01/26/2008

Joyce, G.F. Obituary: Leslie Orgel (1927-2007), Nature 450, 627 (29 November 2007) | doi:10.1038/450627a

Craig Venter has made a big impact with his announcement of assembling a synthetic version of the Mycoplasma genitalium genome. The work started many years ago when the bacterium with the smallest genome (M. genitalium) was sequenced. The research team then set out to make it artificially.

They "designed fragments of chemically synthesized DNA to build 101 "cassettes" of 5,000 to 7,000 base pairs of genetic code. As a measure to differentiate the synthetic genome versus the native genome, the team created "watermarks" in the synthetic genome. These are short inserted or substituted sequences that encode information not typically found in nature. Other changes the team made to the synthetic genome included disrupting a gene to block infectivity. [. . .] From here, the team devised a five stage assembly process where the cassettes were joined together in subassemblies to make larger and larger pieces that would eventually be combined to build the whole synthetic M. genitalium genome. In the first step, sets of four cassettes were joined to create 25 subassemblies, each about 24,000 base pairs (24kb). These 24kb fragments were cloned into the bacterium Escherichia coli to produce sufficient DNA for the next steps, and for DNA sequence validation. The next step involved combining three 24kb fragments together to create 8 assembled blocks, each about 72,000 base pairs. These 1/8th fragments of the whole genome were again cloned into E. coli for DNA production and DNA sequencing. Step three involved combining two 1/8th fragments together to produce large fragments approximately 144,000 base pairs or 1/4th of the whole genome."

The watermarks have been decoded quickly, as a report in Wired Science reveals. The words are:
VENTERINSTITVTE
CRAIGVENTER
HAMSMITH
CINDIANDCLYDE
GLASSANDCLYDE
The latter three words refer to Venter's colleagues. The reporter commented: "I have to say that I was hoping for something poetic, profound, or clever. [. . .] Instead, we get what we probably should have expected: an advertisement for the Venter Institute."

The quest for artificial life

Large fragments of DNA are very difficult to handle, and this delayed completion. As Philip Ball explains:

"for reasons that the researchers don't yet understand, the final assembly of these quarter-genomes into a single strand didn't run smoothly in the bacterium. So the team transferred them into cells of brewers' yeast to carry out the final steps of the assembly. Smith and his colleagues then extracted the synthetic genomes from the yeast cells, using enzymes to chew up the yeast's own DNA."

The final product has 582,970 base pairs. The assembled genome was again sequenced in order to validate the accuracy of the chemical structure.
By all accounts, this is a remarkable achievement. It has been described as "a technical tour de force" and a "monumental effort". The authors are obviously proud of their success:

"The actual synthesis and assembly of this genome presented a formidable technical challenge. Although chemical synthesis of genes has become routine, the only completely synthetic genomes so far reported have been viral. The largest previously published synthetic DNA that we are aware of is a 32 kb polyketide gene cluster."

Much can be said about the significance of this research. We will limit comments here to address just three points.

1. Whilst the team have successfully assembled the genome, they have had to get some assistance from the humble yeast Saccharomyces cerevisiae. Long strands of DNA were found to be very fragile, and final assembly needed to be done inside yeast cells. Whilst the process is understood to be "transformation-associated recombination", the researchers were not able to do this artificially. It needed the environment of a cell to make it happen. The difficulties of working with DNA strands should promote some appreciation of why intelligent design is so relevant to biology. Those who continue to claim that life assembled as a bottom-up process are not rooting their thinking in the real world.

2. The next phase of research, according to Venter and his team, is to move from the genome to the functioning cell. The new research aim is to discover whether cells can be 'booted up' into action when loaded with this genetic programme. "This is the next step and we are working on it" said Smith (coauthor). Once they can do this, they have the tools to experiment with different genomes: knocking out particular genes and discovering the consequences, and engineering new genes to achieve specific outcomes. Last year, the research team reported a technique for replacing M. genitalium's genome with another taken from a different species, so it might be thought this step is not a major one. However, there are big questions about what is really going on. What is the nature of the interaction between the cell and the genome? Does the cell have information embedded within it that is as important, if not more important, as the digital DNA information? These questions are being asked by people who have not bought into the popular genetic reductionism that has become dominant in this research arena.

3. There are ethical concerns about this research. Listening to Craig Venter today in a radio interview, it was clear he wanted to give reassurances that the scientists really know what they are doing and that unforseen things are not going to happen. The Science Daily report says: "The bioethical group's independent deliberations, published at the same time as the scientific minimal genome research, resulted in a unanimous decision that there were no strong ethical reasons why the work should not continue as long as the scientists involved continued to engage public discussion." Despite all this, some of us remain unconvinced that the researchers really know what they are doing. We are concerned because of the prevalence of genetic reductionism. We are not saying that the researchers are devious people, but they do need to display a more holistic perspective on the workings of living things. They appear to think that if they can control the genome, they control everything. It is this latter view that can lead to dangers being overlooked and safeguards being inadequate.

Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome
Daniel G. Gibson, Gwynedd A. Benders, Cynthia Andrews-Pfannkoch, Evgeniya A. Denisova, Holly Baden-Tillson, Jayshree Zaveri, Timothy B. Stockwell, Anushka Brownley, David W. Thomas, Mikkel A. Algire, Chuck Merryman, Lei Young, Vladimir N. Noskov, John I. Glass, J. Craig Venter, Clyde A. Hutchison III, Hamilton O. Smith
Science Express, January 24, 2008 | DOI: 10.1126/science.1151721

We have synthesized a 582,970 bp Mycoplasma genitalium genome. This synthetic genome, named M. genitalium JCVI-1.0, contains all the genes of wild-type M. genitalium G37 except MG408, which was disrupted by an antibiotic marker to block pathogenicity and to allow for selection. To identify the genome as synthetic, we inserted "watermarks" at intergenic sites known to tolerate transposon insertions. Overlapping "cassettes" of 5 to 7 kb, assembled from chemically synthesized oligonucleotides, were joined by in vitro recombination to produce intermediate assemblies of approximately 24 kb, 72 kb ("1/8 genome"), and 144 kb ("1/4 genome"), which were all cloned as bacterial artificial chromosomes (BACs) in Escherichia coli. Most of these intermediate clones were sequenced, and clones of all four 1/4 genomes with the correct sequence were identified. The complete synthetic genome was assembled by transformation-associated recombination (TAR) cloning in the yeast Saccharomyces cerevisiae, then isolated and sequenced. A clone with the correct sequence was identified. The methods described here will be generally useful for constructing large DNA molecules from chemically synthesized pieces and also from combinations of natural and synthetic DNA segments.

See also:

Ball, P. Genome stitched together by hand, news@nature.com, 24 January 2008, doi:10.1038/news.2008.522

Scientists Create First Synthetic Bacterial Genome - Largest Chemically Defined Structure Synthesized In The Lab, ScienceDaily (January 24, 2008)

Otzi, the Iceman, was discovered in the Tyrolean Alps in 1991. He is thought to have died over 5000 years ago - and he was wearing shoes. Older remains of footwear come mainly from North America, dated to between 6500 and 9000 years ago. Earlier than that, there is a moccasin footprint in France from the Upper Palaeolithic and some cave drawings of men with footwear. Burial sites reveal beads, apparently sewn onto clothing, around the feet of the deceased. These are dated at around 24,000 years ago.

A shoe worn by Otzi, the Iceman

However, many caves identified as Palaeolithic sites have footprints revealing unshod feet. This has led to a widespread view that these people went around barefoot, despite the knowledge that they generally lived in a cold climate.
Foot bones, however, are affected by the footwear we wear, and an interesting avenue of research has been developed by Erik Trinkaus over recent years. He has noted morphological changes in the pedal phalanges of human feet resulting from the presence or absence of footwear. In 2005, he reported that:

"A comparative biomechanical analysis of the proximal pedal phalanges of western Eurasian Middle Paleolithic and middle Upper Paleolithic humans, in the context of those of variably shod recent humans, indicates that supportive footwear was rare in the Middle Paleolithic, but that it became frequent by the middle Upper Paleolithic."

Phalanges of a human foot reveal whether the individual wore shoes habitually

More recent work has compared bones of ancient humans in China with three groups of humans: recent urban Americans, late-prehistoric native Americans and late-prehistoric Inuits . Urban Americans wear shoes habitually, the native Americans went barefoot and the Inuits were hybrids regarding foot-coverings. The Palaeolithic data concerns the Middle Upper Paleolithic modern humans from Sunghir 1 (dated about 27,500 years ago) and even earlier modern humans from Tianyuan 1 (dated about 40,000 years ago). The results are summarized as follows:

"Whether the polar moments of area of the middle phalanges are compared to phalangeal length alone or to phalanx length times body mass, the habitually shod Euroamerican sample has the most gracile phalanges, the habitually barefoot Amerindian sample has the most robust phalanges, and the habitually shod but robust Inuit sample has an intermediate distribution. They are highly significantly different [. . .] for each comparison. The Middle Upper Paleolithic sample clusters largely with the Inuit sample [. . .] These data therefore reinforce the association of footwear with pedal phalangeal gracility in the Middle Upper Paleolithic. To these considerations we can now add the Tianyuan 1 partial skeleton from eastern Asia, which preserves a complete middle pedal phalanx, most likely from ray 2. Its relative pedal phalangeal robusticity, when compared to phalanx length alone, is among the more gracile of the Middle Upper Paleolithic and Puebloan phalanges, moderately gracile for an Inuit, similar to the recent Euroamericans, and completely separate from the late archaic and early modern Middle Paleolithic humans."

In conclusion: "the Tianyuan 1 pedal phalanges should be sufficient to indicate that the pattern of middle toe gracility and its probable association with habitual footwear use predates the emergence of the Middle Upper Paleolithic."

The significance of this research is that the Palaeolithic human communities have suffered from a rather stereotyped image. 'Stone age' people they were, but this does not mean that they lacked human capabilities. As research progresses, more and more features have been identified which close the gap between them and us. The problem is that we have inherited an evolutionary perspective on human origins which leads us to believe that Palaeolithic peoples were transitional between ape-men and modern man. New finds, like evidences of habitual footwear in a human thought to have lived 40,000 years ago, are continually challenging this evolutionary scenario. One day, perhaps, it will be clear that these people were just like us, but living in a harsh and dangerous environment. Then, we'll admire them for what they did achieve.

Anatomical evidence for the antiquity of human footwear: Tianyuan and Sunghir
Erik Trinkaus and Hong Shang
Journal of Archaeological Science, Article in Press

Abstract: Trinkaus [. . .] provided a comparative biomechanical analysis of the proximal pedal phalanges of western Eurasian Middle Paleolithic and Middle Upper Paleolithic humans, in the context of those of variably shod recent humans. The anatomical evidence indicated that supportive footwear was rare in the Middle Paleolithic but became frequent by the Middle Upper Paleolithic. Based on that analysis, additional data are provided for the Middle Upper Paleolithic (~27,500 cal BP) Sunghir 1 and the earlier (~40,000 cal BP) Tianyuan 1 modern humans. Both specimens exhibit relatively gracile middle proximal phalanges in the context of otherwise robust lower limbs. The former specimen reinforces the association of footwear with pedal phalangeal gracility in the Middle Upper Paleolithic. Tianyuan 1 indicates a greater antiquity for the habitual use of footwear than previously inferred, predating the emergence of the Middle Upper Paleolithic.

See also:

Trinkaus, E. Anatomical evidence for the antiquity of human footwear use, Journal of Archaeological Science, 32(10), October 2005, 1515-1526.

"People who need to consult maps, radio traffic reports, or the Global Positioning System to navigate from one city to another should stand in awe of monarch butterflies. They migrate thousands of kilometers to a small winter retreat in Mexico. These intrepid travelers use the sun as a guide, but exactly how has been a mystery. Now researchers demonstrate that monarchs depend on an internal clock to determine their course. [. . .] Without a clock, the sun would prove an unreliable landmark as it moves across the horizon; a clock allows animals to compensate for this apparent motion and maintain a direct course."

So wrote Elizabeth Pennisi in 2003, commenting on a research paper dealing with monarch migration skills. Having established that there is a solar compass and an internal clock, the researchers have been concerned with the genetic components of the clock. This work has appeared recently in PLOS Biology.

The monarch butterfly (Danaus plexippus)

Robinson summarises the genetic clock mechanism that has been elucidated for Drosophila:

"In fruit flies, five proteins are central to the operation of the clock. Clock (Clk) and Cycle (Cyc) bind together to form a transcriptional complex, which drives production of Period (Per) and Timeless (Tim). Per and Tim then link up to repress the production of Clk and Cyc, thus creating a negative-feedback loop controlling the concentrations of Per and Tim - the essence of the clock mechanism. The fifth protein, Cryptochrome (Cry), is light sensitive, and when it absorbs blue light, it disrupts the Per-Tim complex, thereby resetting the periodic oscillations, which keeps the molecular clock and it output rhythms in tune with the ambient light-dark cycle."

It is found that the mouse (thought to be representative of mammals in general) has a modified clock:

"The mammalian clock uses Clk and a Cyc-like protein, but it has no Tim. Instead of a single cryptochrome, it has two, neither of which is light sensitive, but both of which are the major repressors of the mammalian clock feedback loop."

The significance of the above is that the monarch butterfly has both of these molecular mechanisms. The authors describe their research findings in this way:

"The circadian clock plays a critical role in monarch butterfly migration by providing the timing component to time-compensated sun compass orientation. Here we characterize a novel molecular clock mechanism in monarchs by focusing on the functions of two CRYPTOCHROME (CRY) proteins. In the monarch clock, CRY1, a Drosophila-like protein, functions as a blue-light photoreceptor for photic entrainment, whereas CRY2, a vertebrate-like protein, functions within the clockwork as the major transcriptional repressor of the self-sustaining feedback loop. An oscillating CRY2-positive neural pathway was also discovered in the monarch brain that may communicate circadian information directly from the circadian clock to the central complex, which is the likely site of the sun compass."

Robinson concludes: "the results in this study suggest that part of the remarkable navigational ability of the butterfly relies on its ability to integrate temporal information from the clock with spatial information from its visual system. This allows the monarch to correct its course as light shifts across the sky over the course of the day." These are fascinating findings. These sophisticated systems are exciting to study and lead to many avenues of further research. At very least, evidence is here in abundance for complex specified information, which is the hallmark of intelligent design.
There are interesting questions too for evolutionists. This quote comes from a report by Faye Flam:

"CRY1 and CRY2 likely started as a single ancestral clock gene, said Adriana Briscoe a biologist at the University of California, Irvine, who was involved with some of the earlier work identifying the two genes. They would have been duplicated by accident in some early life form - probably something that predated the separation of animals from the other kingdoms of life. Over the course of time the two duplicates evolved slightly different functions. The CRY1 gene's proteins respond directly to the blue wavelength of light, while CRY2 uses indirect input from other light-sensing cells, usually located in the eye. Eventually, most organisms lost one form and kept the other."

What we have here is the quest for a plausible story, with some things being likely, other things occurring by accident, and the proposed scenario regarded as probable. We appear to be at the beginning of this particular line of enquiry, so comment is premature. However, the ancestral starting point requires there to have been homologues of both cry1 and cry2, which makes subsequent evolution a form of degeneration. The authors refer to the monarch butterfly having "an ancestral clock in which both cry1 and cry2 are expressed". Evolution by differential gene loss appears to be invoked quite frequently, but it is not the kind of evolutionary change that builds complex specified information.

Cryptochromes Define a Novel Circadian Clock Mechanism in Monarch Butterflies That May Underlie Sun Compass Navigation
Haisun Zhu, Ivo Sauman, Quan Yuan, Amy Casselman, Myai Emery-Le, Patrick Emery, Steven M. Reppert.
PLoS Biology, 8 January 2008, 6(1), e4 doi:10.1371/journal.pbio.0060004

Abstract: The circadian clock plays a vital role in monarch butterfly (Danaus plexippus) migration by providing the timing component of time-compensated sun compass orientation, a process that is important for successful navigation. We therefore evaluated the monarch clockwork by focusing on the functions of a Drosophila-like cryptochrome (cry), designated cry1, and a vertebrate-like cry, designated cry2, that are both expressed in the butterfly and by placing these genes in the context of other relevant clock genes in vivo. [. . .] The results define a novel, CRY-centric clock mechanism in the monarch in which CRY1 likely functions as a blue-light photoreceptor for entrainment, whereas CRY2 functions within the clockwork as the transcriptional repressor of a negative transcriptional feedback loop. Our data further suggest that CRY2 may have a dual role in the monarch butterfly's brain - as a core clock element and as an output that regulates circadian activity in the central complex, the likely site of the sun compass.

See also:

Robinson, R. In Monarchs, Cry2 is King of the Clock, PLoS Biology, January 8, 2008 6(1): e12 doi:10.1371/journal.pbio.0060012

Flam, F. Amazing journey of the monarch butterfly, The Philadelphia Inquirer, 21 January 2008.

Pennisi, E. Monarchs Check Clock to Chart Migration Route, Science, 300, May 23 2003: 1216-1217.

We know from personal experience that moving through a wood thick with undergrowth is a far more daunting task than walking across a grassy field. Imagine what it is like for arthropods!

"When animals, such as spiders and cockroaches, scurry through their natural environment, debris can decrease the probability of a foothold, provide diverse asperities for contact and flow like a fluid causing the animal to slip. Effective mobility over varied terrestrial substrates in the natural world that differ in geometry, compliance and tendency to flow must require a feedback component. Thus, control strategies of legged locomotion in nature cannot be determined without regard to an animal's environment."

What, then, are these control strategies? The first strategy to consider is distributed neural feedback. This requires active sensing by the animals followed by processing of those sensory signals. To do this, the organism must employ an "enormous number and rich variety of motion, contact, length and stress sensors." But it can only operate slowly. "Arthropods can negotiate obstacles, ditches, gaps and uneven surfaces, as well as travel up and along inclines by slow, deliberate stepping." This strategy does not work well when the animal wants to run.

"Highspeed locomotion can be advantageous on irregular terrain because kinetic energy allows the organism to bridge gaps in footholds that slow-moving systems find impassible. Rapid running, however, is a high bandwidth behavior. Delay in neural communication channels reduces synchronization gains, so that an animal's nervous system tends to operate in a decentralized, feedforward manner where coordination is achieved primarily through mechanical coupling and stability through preflexes."

This brings us to the second strategy: distributed mechanical feedback. This is not speeded up neural feedback, but an integration of active and passive neural responses with the kinaesthetic senses of the animal.

"We propose that the control of locomotion on challenging terrain can be simplified during rapid running using distributed mechanical feedback. We demonstrate that animals are effective at traversing challenging terrain at high speeds by distributing the mechanical feedback over limbs moving in appropriate trajectories with components that generate passive responses to leg-surface contact events. Distribution of the mechanical feedback creates effective coupling with environments, and results from the synergistic operation of leg trajectory, leg configuration and attachment mechanism. The control algorithms are in effect embedded in the form of animal itself: control results from the properties of their parts, their morphology and their passive interaction with the environment."

This perspective enables the organisms to understood in new ways:

"arthropods have an impressive array of attachment mechanisms on their feet that can increase a leg's probability of surface contact. Mechanisms include hooks or claws, suckers, glue and friction. Distal tarsal claws have been shown to increase performance on rough, inclined surfaces and during inverted locomotion. Mechanisms in some orientations can require feedback from the nervous system to engage, whereas others operate by passive mechanical feedback to respond to specific mechanical events."

This analysis has inspired research into robot control mechanisms. "The present study tests the hypothesis that distributed mechanical feedback simplifies the control of animal - and robot-surface interactions." The researchers selected substrates that they could define and use in simulation studies. The experimented with spiders, cockcroaches and crabs - multilegged runners. "We verified our results in a physical model, a rapid running, six-legged robot named RHex. We altered leg configuration and attachment mechanism, but not its electronic control strategy."

RHex has extraordinary rough-terrain mobility

This is from their conclusion:

"We found no evidence that these multilegged runners use neural feedback to follow a foreleg's secure foothold or to adjust the location of where their legs contact the substrate. By using the kinetic energy of rapid running to bridge gaps in footholds and distributing mechanical feedback over many legs and locations along the leg, animals can overcome the inherent delays of neural feedback as well the problem of noisy sensors, thereby simplifying control. Use of a physical model, a legged robot, supported our contention because the hexapod was able to traverse low probability foothold terrain better with a broader leg contact area and collapsible spines, but without a single change to its electronic controller. Our discovery of distributed mechanical feedback provided biological inspiration to a robot that can now traverse terrain previously impassable."

It is worth standing back and reflecting on what is happening here. The research team has devoted much time to understanding the control strategies of arthropods and has found that these organisms must be understood in a holistic way. The control system involves distributed neuronal and mechanical feedback mechanisms which are so sophisticated that our best efforts at emulation can only be described as crude. The robot RHex is undoubtedly a product of some highly intelligent research scientists and engineers, but why is it that people baulk at the thought that the multilegged runners they have been studying are also the product of intelligent design?

Distributed mechanical feedback in arthropods and robots simplifies control of rapid running on challenging terrain
J C Spagna, D I Goldman, P-C Lin, D E Koditschek and R J Full
Bioinspiration & Biomimimetics, 2(1) (March 2007) 9-18 | doi 10.1088/1748-3182/2/1/002

Abstract. Terrestrial arthropods negotiate demanding terrain more effectively than any search-and-rescue robot. Slow, precise stepping using distributed neural feedback is one strategy for dealing with challenging terrain. Alternatively, arthropods could simplify control on demanding surfaces by rapid running that uses kinetic energy to bridge gaps between footholds. We demonstrate that this is achieved using distributed mechanical feedback, resulting from passive contacts along legs positioned by pre-programmed trajectories favorable to their attachment mechanisms. We used wire-mesh experimental surfaces to determine how a decrease in foothold probability affects speed and stability. Spiders and insects attained high running speeds on simulated terrain with 90% of the surface contact area removed. Cockroaches maintained high speeds even with their tarsi ablated, by generating horizontally oriented leg trajectories. Spiders with more vertically directed leg placement used leg spines, which resulted in more effective distributed contact by interlocking with asperities during leg extension, but collapsing during flexion, preventing entanglement. Ghost crabs, which naturally lack leg spines, showed increased mobility on wire mesh after the addition of artificial, collapsible spines. A bioinspired robot, RHex, was redesigned to maximize effective distributed leg contact, by changing leg orientation and adding directional spines. These changes improved RHex's agility on challenging surfaces without adding sensors or changing the control system.

See also:

RHex Web site

RHex robot (video)

Feedback on this blog from an engineer working in robotics: "Seeing design in an animal as the result of intelligence tends to make me strive for deeper answers to the technical problems of bio/robomechanics and control, whereas seeing animals as the result of evolution tends to make thinking, in my opinion, much shallower."

Soay sheep live in glorious isolation on the tiny island of St Kilda, off the NW coast of Scotland. They provide interesting case studies for geneticists, ecologists and evolutionary biologists. Their "coat color is either dark brown or light tawny; the two phenotypes have been documented for at least 90 years." Changes in the frequency of these colours has stimulated the new research.

Dark and light coat colour morphs in Soay sheep. (For larger image, click here)

According to the authors, "variation in coat color is controlled by a single autosomal locus at which the dark allele is dominant to the light allele". They explain that the "dark coat color is associated with large size, which is heritable and positively correlated with fitness". Consequently, a reasonable prediction to make would be that the numbers of sheep with darker coats will increase in the population. But this is not happening! Observations show very clearly that "the frequency of dark sheep has decreased". This unexpected finding provides the rationale for further research. The authors do not consider the Soay Sheep case to be unusual. On the contrary, it is one of many examples of predictions not matching the data.

"Evolutionary theory states that directional selection on a heritable trait should result in evolutionary change. Analyses of long-term data sets from wild vertebrate populations reveal directional selection on heritable traits, yet many studies report no microevolutionary change (stasis) or, in some cases, responses in the opposite direction to that predicted."

The problem appears to be that genes affect more than one trait (something that we knew already in principle). The researchers found that the allele that is dominant for dark coat colour is associated not only with large body size (and increased fitness) but also with decreased lifetime. This finding was made possible because of the extensive documentation of the life histories of these wild sheep. The nature of this association is considered to be linkage disequilibrium rather than pleiotropy. Once the linkage became clear, the researchers could say:

"Our results actually imply that the light mutation should be increasing in frequency, although genetic drift will also play a role in determining the allelic frequencies."

A general conclusion can therefore be drawn:

"This study shows that selection acting on simple Mendelian traits in natural populations can have a complex genetic basis. This has implications for the study of microevolutionary change in natural populations, because fitness variation at the level of the genotype may not be evident in an analysis of selection on phenotype. Consequently, phenotypic studies may wrongly conclude that selection is not acting on genomic regions containing the loci underlying focal traits and may be unable to explain the microevolutionary dynamics of trait variation."

These comments are important, because nearly all the Darwinian just-so stories make use of the 'one gene - one trait' concept, which is now outdated. Although their scenarios are presented as plausible and reasonable, failure to address linkage disequilibrium and pleiotropy issues opens the door to faulty presuppositions and flawed logic. Educational programmes need to do more to create awareness of the unscientific nature of these Darwinian speculations.
It is to be welcomed that the authors qualify the word evolution using the prefix "micro". Phillip Johnson led the way in showing how many different meanings there are to the word "evolution", but there has been a marked reluctance for editors, authors and journalists to respond positively. If the term "microevolutionary trend" could be used to refer to the vast majority of textbook examples of "evolution", this would represent a major improvement in communication.

A Localized Negative Genetic Correlation Constrains Microevolution of Coat Color in Wild Sheep
J. Gratten, A. J. Wilson, A. F. McRae, D. Beraldi, P. M. Visscher, J. M. Pemberton, and J. Slate
Science, 319, 18 January 2008: 318-320.

Abstract: The evolutionary changes that occur over a small number of generations in natural populations often run counter to what is expected on the basis of the heritability of traits and the selective forces acting upon them. In Soay sheep, dark coat color is associated with large size, which is heritable and positively correlated with fitness, yet the frequency of dark sheep has decreased. This unexpected microevolutionary trend is explained by genetic linkage between the causal mutation underlying the color polymorphism and quantitative trait loci with antagonistic effects on size and fitness. As a consequence, homozygous dark sheep are large, but have reduced fitness relative to phenotypically indistinguishable dark heterozygotes and light sheep. This result demonstrates the importance of understanding the genetic basis of fitness variation when making predictions about the microevolutionary consequences of selection.

See also:

Images of St Kilda Archipeligo, Hirta and Boreray

When the working draft of the human genome was first published, the best estimate of the number of human genes was 35,000. With further analysis, this number fell to about 25,000 and stimulated a debate about why the number was much smaller than expected. A recent study has led to a further significant drop to 20,500. The researchers had realised that some reported sequences might not be genes after all. The ScienceDaily reports thus:

"To distinguish such misidentified genes from true ones, the research team, led by Clamp and Broad Institute director Eric Lander, developed a method that takes advantage of another hallmark of protein-coding genes: conservation by evolution. The researchers considered genes to be valid if and only if similar sequences could be found in other mammals - namely, mouse and dog. Applying this technique to nearly 22,000 genes in the Ensembl gene catalog, the analysis revealed 1,177 "orphan" DNA sequences. These orphans looked like proteins because of their open reading frames, but were not found in either the mouse or dog genomes."

The researchers write:

"The results above are consistent with the orphans being simply random ORFs, rather than valid human protein-coding genes. However, consistency does not constitute proof. Rather, we must rigorously reject the alternative hypothesis."

Two alternative explanations needed to be tested. The first explanation considered was that the sequences were lost in mouse and dog lineages yet retained in the lineage leading to humans. To explore this, the researchers "compared the orphan sequences to the DNA of two primate cousins, chimpanzees and macaques" and confirmed that they were absent there as well. This was taken as proof that the sequences have not been preserved via the primate lineage.
The other possibility is that the orphan sequences are novel to humans. The researchers write:

"If the orphans represent valid human protein-coding genes, we would have to conclude that the vast majority of the orphans were born after the divergence from chimpanzee. Such a model would require a prodigious rate of gene birth in mammalian lineages and a ferocious rate of gene death erasing the huge number of genes born before the divergence from chimpanzee. We reject such a model as wholly implausible. We thus conclude that the vast majority of orphans are simply randomly occurring ORFs that do not represent protein-coding genes."

The significance of this methodology is the insight it gives to the way evolutionary theory is totally dominant in studies of the human genome. Common ancestry is adopted as the framework for interpretation. The "proof" that the orphans are not novel human protein-coding genes is that this would require a "prodigious rate of gene birth" after the human-chimpanzee split. This proof is justified by the theoretical framework (deduction) rather than by analysis of empirical data. After adopting an evolutionary paradigm, the researchers sift the evidence to show that all the genes fit into a coherent pattern of birth and loss. Those that don't fit are simply deduced to be ORFs.

Erasing genes because they do not fit evolutionary theory

An ID perspective is not impressed by this logic because it exhibits circular reasoning. Consequently, there is a serious flaw in the research methodology. Empirical tests for these sequences being non-coding are complex, but they must involve experimentation to explore whether the genetic sequences are associated with gene products.
Grand comments like "There's no real creativity going on in the mammalian genome" are only valid if the research methodology is robust. Furthermore, 1,177 orphan sequences out of 20,500 genes represents over 5% of the human gene resource. It is worth bearing this figure in mind when the 1% difference figure is quoted for the human/chimpanzee genome.
Finally, this research has stirred not a few ID scientists to predict that functionality will be found for some or all of these putative orphan genes. The situation a variant of the "Junk DNA" story of 10 years ago, where the evolutionary biologists were far too quick to invoke functionlessness on the basis of their theory. Happily for science, the "Junk DNA" theory has been forced to be revised. Some of us are prepared to say that the same thing will happen in the case of human orphan genes.

Distinguishing protein-coding and noncoding genes in the human genome
Michele Clamp, Ben Fry, Mike Kamal, Xiaohui Xie, James Cuff, Michael F. Lin, Manolis Kellis, Kerstin Lindblad-Toh, and Eric S. Lander.
Proc. Natl. Acad. Sci. USA. 26 November 2007 | DOI: 10.1073/pnas.0709013104

Abstract: Although the Human Genome Project was completed 4 years ago, the catalog of human protein-coding genes remains a matter of controversy. Current catalogs list a total of ~24,500 putative protein-coding genes. It is broadly suspected that a large fraction of these entries are functionally meaningless ORFs present by chance in RNA transcripts, because they show no evidence of evolutionary conservation with mouse or dog. However, there is currently no scientific justification for excluding ORFs simply because they fail to show evolutionary conservation: the alternative hypothesis is that most of these ORFs are actually valid human genes that reflect gene innovation in the primate lineage or gene loss in the other lineages. Here, we reject this hypothesis by carefully analyzing the nonconserved ORFs - specifically, their properties in other primates. We show that the vast majority of these ORFs are random occurrences. The analysis yields, as a by-product, a major revision of the current human catalogs, cutting the number of protein-coding genes to ~20,500. Specifically, it suggests that nonconserved ORFs should be added to the human gene catalog only if there is clear evidence of an encoded protein. It also provides a principled methodology for evaluating future proposed additions to the human gene catalog. Finally, the results indicate that there has been relatively little true innovation in mammalian protein-coding genes.

See also:

Broad Institute of MIT and Harvard, Human Gene Count Tumbles Again, ScienceDaily (Jan. 15, 2008)

Image source - http://www.broad.mit.edu/news-images/erazegene.jpg
Image credit: Bang Wong, Broad Institute | iStockphoto

Francisco Ayala is the chair of the Committee that has produced the booklet Science, evolution, and creationism published this month by the National Academy of Sciences and the Institute of Medicine. He has contributed the editorial for the current issue of the Proceedings of the National Academy of Sciences, explaining why this publication is deemed so important.
Various high-profile legal battles provide the backdrop for the editorial. The booklet is designed to counter the influence of Creationism and Intelligent Design in state education programmes in the US. The editorial highlights several emphases of the booklet, and these are the briefly noted here.
Ayala traces the "Argument from Design" back to the "English clergyman William Paley". Whilst Paley is rightly associated with design arguments, it is noticeable that design deniers characteristically by-pass the earlier arguments of John Ray, one of the pioneers of botanical science in the 17th Century. Here is a scientist arguing that design is pervasive; intelligent design is there for everyone to see. The neglect of Ray's emphasis (as a scientist) on design is a sad reflection on the way contemporary evolutionists use history.

The section of the Editorial on "Evolution and Natural Selection" follows familiar ground in arguing for the centrality of evolution as an organising principle in biology. Evolutionists have got past finding compelling evidence for the theory, and they now research how the process occurs. "Biological evolution is part of a compelling historical narrative that scientists have constructed over the last few centuries".

"Biological evolution is part of a compelling historical narrative" - Ayala

This section concludes thus:

"Darwin's greatest contribution to science is not that he accumulated evidence demonstrating the evolution of life, but that he discovered natural selection, the process that accounts for the design of organisms and their wonderful adaptations to survive and reproduce in the environments where they live, including wings for flying, legs for running, eyes to see, and kidneys that regulate the composition of the blood."

Although presented as confirmed science, this paragraph is actually highly controversial. Ayala has certainly said things like this before, as is blogged here, but he is out-of-step with many of his peers. At the same conference where he promoted this view of Darwinism, Michael Lynch made this protest:

"the myth that all of evolution can be explained by adaptation continues to be perpetuated by our continued homage to Darwin's treatise in the popular literature. For example, Dawkins' agenda to spread the word on the awesome power of natural selection has been quite successful, but it has come at the expense of reference to any other mechanisms, a view that is in some ways profoundly misleading."

The final section is devoted to the thesis that there is no conflict between the evidence for evolution and belief in God. According to Ayala, "Science and religion concern different aspects of the human experience." This was called the NOMA hypothesis by Stephen Jay Gould, and there is no doubt it has had a long history. But today the majority of leading evolutionary biologists do not hold these views: they are adopting a position of overt atheism. For more on this, go here.
Furthermore. Ayala and his colleagues are defining the terms of the truce between science and religion: religion is exclusively concerned with life's purpose and with values. However, this betrays a gross misunderstanding of Christianity, which, apart from being rooted in history, also makes truth claims outside the boundaries of purpose and values.

The NAS booklet has been critiqued by Casey Luskin of the IDEA Center. This covers numerous points not mentioned here. If anyone is tempted to think the booklet is a product of science, their time would be well spent digesting what Luskin has written. What many of us are concerned about is that a naturalistic world view has been turned into a "compelling historical narrative" and nothing is being allowed to undermine that narrative. But there is a scientific debate about all the elements of the story, and that debate must go ahead even though the establishment gatekeepers are trying to close it down.

Science, evolution, and creationism
Francisco J. Ayala
Proceedings of the National Academy of Sciences, January 8, 2008, 105(1), 3-4 | doi 10.1073/pnas.0711608105

On December 20, 2005, John E. Jones III, federal judge for the Middle District of Pennsylvania, issued a 130-page-long decision (Kitzmiller v. Dover Area School District) declaring that "The overwhelming evidence at trial established that ID [intelligent design] is a religious view, a mere re-labeling of creationism, and not a scientific theory ... ID is not supported by any peer-reviewed research, data, or publications."
In 1984, the National Academy of Sciences (NAS) published Science and Creationism: A View from the National Academy of Sciences. A second edition was published in 1999. A third edition, sufficiently modified to deserve a new title, Science, Evolution, and Creationism, published on January 4, 2008 (1). [snip].

The Facts about Intelligent Design: A Response to the National Academy of Sciences' Science, Evolution, and Creationism
Casey Luskin
The IDEA Center, January 2008

A 1982 poll found that only 9% of Americans believed that humans developed through purely natural evolutionary processes. Two years later, the U.S. National Academy of Sciences (NAS) issued its first Science and Creationism booklet, stating that science and religion occupy "separate and mutually exclusive realms."[1] Public skepticism of evolution remained high - a 1993 poll found that only 11% of Americans believed that humans developed through purely natural evolutionary processes. [snip]

There can be no disputing the fact that languages vary with time. To describe observed changes, researchers frequently use the word "evolution", with the limited meaning of change over time. However, since Darwinism has profoundly affected culture, there is always the temptation to presume that languages increase in complexity with time, and that ancient languages (and the languages of people with an under-developed culture) are primitive. This tendency is apparent in a recent research paper on the subject of words that handle numbers:

"Apart from their efficiency, cognitive tools can also be ordered according to their presumed evolution. Because tools are typically developed in order to improve their efficiency, it is reasonable to assume that numeration systems evolve from being simpler to more sophisticated."

The keywords here are "presumed evolution". The conceptual model for the development of language involves usage, and as people get more sophisticated in their culture, so also does their language. But is this conceptual model correct?

Hunter-gatherers in the Amazon rainforest

The research was stimulated by recent controversies relating to the Piraha people of the Amazonian Basin: their culture is characterized by an extreme focus on immediate experience, so concepts, vocabulary and grammar outside the present are largely lacking. This case created a discussion about how "numerical cognition depends on language", and in turn this has stimulated further research.

"We set out to highlight the cognitive efficiency of some allegedly primitive systems in another part of the world and to show how they may have evolved from abstract to more specific as a result of cultural adaptation."

The authors based their fieldwork in Papua New Guinea. There were particular reasons for this:

"One of the remarkable facts about numeration systems in Polynesian languages is their large extent. Clearly, Polynesians were interested in high numbers and had a need to operate with them."

They looked particularly at languages with more restricted counting sequences and came up with some very interesting findings.

"To sum up, the linguistic analysis reveals that the specific counting systems in Mangareva did not precede an abstract system but were rather derived from it, despite their nonabstract nature. And the cognitive analysis suggests that this was done deliberately and for rational purposes."

In other language groups in the same area, there were local needs to extend the options for counting and handling large numbers.

"Both lines of development started from the same regularly decimal and abstract numeration system inherited from Proto-Oceanic and therefore speak against a linear evolution of numerical cognition. Numeration systems do not always evolve from simple to more complex and from specific to abstract systems."

This research leads to numerous interesting avenues of thought, but here we will focus on the presuppositions scholars bring to their work. In particular, we should note that the presupposition of 'simple to sophisticated' is misleading in linguistics. There are no primitive languages to research! (for a podcast on this, go here). Languages are complex, and there is no evidence that they ever were anything other than complex. Darwinistic influences are entirely responsible for the concept of a primitive language - not evidence. We do have evidence for complex languages becoming simpler and for complex languages becoming more complex (as is reported in this paper), but the starting point is always complexity. Theories of language based on the gradual emergence of complexity are theory-driven and deserve careful scrutiny, particularly when scholars justify their model with the words: "it is reasonable to assume".

The Limits of Counting: Numerical Cognition between Evolution and Culture
Sieghard Beller and Andrea Bender
Science, 319, 11 January 2008: 213-215.

Abstract: Number words that, in principle, allow all kinds of objects to be counted ad infinitum are one basic requirement for complex numerical cognition. Accordingly, short or object-specific counting sequences in a language are often regarded as earlier steps in the evolution from premathematical conceptions to greater abstraction. We present some instances from Melanesia and Polynesia, whose short or object-specific sequences originated from the same extensive and abstract sequence. Furthermore, the object-specific sequences can be shown to be cognitively advantageous for calculations without notation because they use larger counting units, thereby abbreviating higher numbers, enhancing the counting process, and extending the limits of counting. These results expand our knowledge both regarding numerical cognition and regarding the evolution of numeration systems.

Podcast: There are no primitive languages (22 minutes, May 26 2006)

Bower, B. The Piraha challenge: an Amazonian tribe takes grammar to a strange place, Science News, Dec 10, 2005

In a past editorial in Science, the case was made for "recognizing evolution as a basic science for medicine". The authors say that "evolution is the vibrant foundation for all biology [. . .] but its full potential for use in medicine has yet to be realized". A historical perspective, however, shows that design inferences have played an important role in medicine. Many medical advances have involved the use of reverse engineering. Medics have been great pragmatists, using engineering principles to understand anatomy, biochemistry and physiology before finding ways to address medical conditions.

Da Vinci's Vitruvian Man

An interesting case of a "guiding principle" for medical research has recently appeared. The report gives this summary of the work:

"The researchers removed all the cells from a dead rat heart, leaving the valves and outer structure as scaffolding for new heart cells injected from newborn rats. Within two weeks, the cells formed a new beating heart that conducted electrical impulses and pumped a small amount of blood.
With modifications, scientists should be able to grow a human heart by taking stem cells from a patient's bone marrow and placing them in a cadaver heart that has been prepared as a scaffold, Dr. Taylor said in a telephone interview from her laboratory in Minneapolis. The early success "opens the door to this notion that you can make any organ: kidney, liver, lung, pancreas - you name it and we hope we can make it," she said."

The details need not concern us here. The take-home message concerns the guiding principle of the laboratory. Instead of forcing cells to behave in ways determined by experimenters, the philosophy is to go with the flow and get the cells to do things naturally.

"Dr. Doris A. Taylor, the head of the team that created the rat heart, said she followed a guiding principle of her laboratory: "give nature the tools, and get out of the way."
"We just took nature's own building blocks to build a new organ," Dr. Taylor said of her team's report in the journal Nature Medicine."

The methodology is neatly compatible with design principles: by working with cells and allowing them to do what they are designed to do, results follow.

Perfusion-decellularized matrix: using nature's platform to engineer a bioartificial heart
Harald C Ott, Thomas S Matthiesen, Saik-Kia Goh, Lauren D Black, Stefan M Kren, Theoden I Netoff and Doris A Taylor
Nature Medicine, Published online: 13 January 2008; | doi:10.1038/nm1684

About 3,000 individuals in the United States are awaiting a donor heart; worldwide, 22 million individuals are living with heart failure. A bioartificial heart is a theoretical alternative to transplantation or mechanical left ventricular support. Generating a bioartificial heart requires engineering of cardiac architecture, appropriate cellular constituents and pump function. We decellularized hearts by coronary perfusion with detergents, preserved the underlying extracellular matrix, and produced an acellular, perfusable vascular architecture, competent acellular valves and intact chamber geometry. To mimic cardiac cell composition, we reseeded these constructs with cardiac or endothelial cells. To establish function, we maintained eight constructs for up to 28 d by coronary perfusion in a bioreactor that simulated cardiac physiology. By day 4, we observed macroscopic contractions. By day 8, under physiological load and electrical stimulation, constructs could generate pump function (equivalent to about 2% of adult or 25% of 16-week fetal heart function) in a modified working heart preparation.

See also:
Altman, L.K. Team Creates Rat Heart Using Cells of Baby Rats,
The New York Times, Monday, January 14, 2008

Although the BAD group (Birds Are Dinosaurs) are in the ascendancy, the small BAND (Birds Are Not Dinosaurs) of dissidents has many reasons to think that currently it has the better arguments. The latest broadside has come from Professor Lingham-Soliar, who has spent a lot of time researching the processes of decay of modern-day organisms in order to better understand partial decay of fossilised animals.

Psittacosaurus without the fuzz

The latest research concerns the skin of the dinosaur Psittacosaurus, a bipedal, plant-eating, ceratopsian dinosaur. This fossil material provides "a deep cross section through the dermis, which includes multiple layers of collagenous fibres in excess of 25, among the highest recorded in vertebrates, with a further 15 more layers (poorly preserved) estimated for the entire height of the section." This is a remarkable find and, as the author writes, it gives us an "unprecedented understanding of the dinosaur skin". The animal was very well protected by this covering:

"These fibre layers comprise regularly disposed fibres arranged in left- and right-handed geodesic helices, matching the pattern at the surface and reasonably inferred for the entire section. As noted from the studies on modern-day animals, this fibre structure plays a critical part in the stresses and strains the skin may be subjected to and is ideally suited to providing support and protection."

Now, Psittacosaurus was a ceratopsian dinosaur "occupying a phylogenetic position far removed from theropod dinosaurs and bird origins". Nevertheless, some have suggested that the bristle-like structures adorning the tail of Psittacosaurus were prototype feathers. Lingham-Soliar considers it significant that no traces of protofeathers could be found in the skin. The structures interpreted by others as protofeathers are actually post-mortem collagen degeneration features. Also, he makes a link between this fossil and the therapods:

"How would the dermis of a theropod dinosaur compare structurally with that of Psittacosaurus? Notwithstanding probable differences in thickness, it is reasonable to think that there would not have been fundamental differences in structure between the dermis of a theropod and that of a non-theropod dinosaur in so far as protection and support are concerned."

A report in The Daily Telegraph quotes the author at some length.

"Scientists must really now choose - belief in the nebulous idea of protofeathers or the reality of collagen, the dominant protein in vertebrates. I am convinced from the nonsense spouted by many of the people who denounce collagen in favour of protofeathers that they have never actually seen collagen in its natural or decomposing state."
[snip]
"What is highly significant in the present study are the masses of collagen fibres found - over 40 dermal layers seen for the first time in a fossil animal, which shows how vitally important collagen was in providing support and protection of the enclosed body mass of dinosaurs per se. It is hardly surprising that the Chinese dinosaurs, as they decomposed, exposed quantities of these structures."

This new work is not an isolated finding, but it builds on a substantial body of published research (e.g. Feduccia et al. 2005) showing that the popular theropod dinosaur to bird transformation really is a BAD theory.

A unique cross section through the skin of the dinosaur Psittacosaurus from China showing a complex fibre architecture
Theagarten Lingham-Soliar
Proceedings of the Royal Society B, FirstCite Early Online Publishing; DOI: 10.1098/rspb.2007.1342.

Abstract: This paper reports on a unique preservation of soft tissues in the ventrolateral region of the plant-eating dinosaur Psittacosaurus from the Jehol biota of China. The preservation is of a deep cross section through the dermis, which includes multiple layers of collagenous fibres in excess of 25, among the highest recorded in vertebrates, with a further 15 more layers (poorly preserved) estimated for the entire height of the section. Also, for the first time in a dinosaur two fibre layers parallel to the skin surface are preserved deep within the dermis at the base of the cross section. These fibre layers comprise regularly disposed fibres arranged in left- and right-handed geodesic helices, matching the pattern at the surface and reasonably inferred for the entire section. As noted from the studies on modern-day animals, this fibre structure plays a critical part in the stresses and strains the skin may be subjected to and is ideally suited to providing support and protection. Psittacosaurus gives a remarkable, unprecedented understanding of the dinosaur skin.

See also:

Feduccia, A., Lingham-Soliar , T. and Hinchliffe, J.R. Do feathered dinosaurs exist? Testing the hypothesis on neontological and paleontological evidence, Journal of Morphology, November 2005, 266(2): 125-66.

Highfield, R. Bald truth about dinosaur feathers, The Daily Telegraph: 09/01/2008

The Editors of Nature give three cheers for the newly published NAS booklet that defends evolutionary theory against ID and Creationism.

Spreading the word - the NAS booklet

In their opinion, the document demonstrates:

"it is possible to summarize the reasons why evolution is in effect as much a scientific fact as the existence of atoms or the orbiting of Earth round the Sun, even though there are plenty of refinements to be explored."

Not only is evolution a fact, they say, "Evolution is of profound importance to modern biology and medicine." Consequently, it behoves everyone to promote evolution!

"Accordingly, anyone who has the ability to explain the evidence behind this fact to their students, their friends and relatives should be given the ammunition to do so. Between now and the 200th anniversary of Charles Darwin's birth on 12 February 2009, every science academy and society with a stake in the credibility of evolution should summarize evidence for it on their website and take every opportunity to promote it."

Here are just a few constructive responses to this missionary fervour.

1. It is important to distinguish between empirical science and historical science. One involves the repeatability of controlled experimentation; the other adopts the 'smoking gun' methodology appropriate for unique past events. The distinction is important, because all parties in these debates about evolution share a commitment to empirical data. The differences emerge when we move from present-day processes to reconstruct the past. This is why claims that evolution is just as much a "fact" as "the existence of atoms or the orbiting of Earth round the Sun" are philosophically defective.

2. The Editorial and the NAS booklet perpetuate the polarised 'science vs religion' template for the debate. Both overlook the fact that much of the evidence for "evolution" is perfectly compatible with ID or creationist thinking. The debate is about what these evidences actually mean. The debate is a scientific one, yet the Editorial and the NAS booklet imply that science is only being advanced by the evolution side.

3. It is not true that evolution is of profound importance to modern biology and medicine. Biological research, in the main, proceeds using design principles: the presumption of functionality, etc. The 2005 survey by Professor Philip Skell refutes the Editorial's claim:

"Darwinian evolution, whatever its other virtues, does not provide a fruitful heuristic in experimental biology. This becomes especially clear when we compare it with a heuristic framework such as the atomic model, which opens up structural chemistry and leads to advances in the synthesis of a multitude of new molecules of practical benefit.
None of this demonstrates that Darwinism is false. It does, however, mean that the claim that it is the cornerstone of modern experimental biology will be met with quiet skepticism from a growing number of scientists in fields where theories actually do serve as cornerstones for tangible breakthroughs."

Similarly with medicine. Traditional medicine is based on the premise that the human body is designed in an intelligent way. Attempts to launch "Darwinian medicine" are a recent phenomenon.

4. The exhortation to promote the theory of evolution misses the pulse of the debate. What is needed is engagement with the science and the underpinning philosophical issues. It is not a case of shouting louder, but of interacting in a meaningful way. Resistance to dialogue is a conspicuous feature of our age, but dialogue is what we need to do justice to these challenges to evolutionary theory.

Spread the word (Editorial)
Nature 451, 108 (10 January 2008) | doi:10.1038/451108b

Abstract : Evolution is a scientific fact, and every organization whose research depends on it should explain why.

See also:

Holden, C. Evolution: Read All About It! ScienceNOW Daily News, 4 January 2008.

Skell, P.S., Why do we invoke Darwin? The Scientist, Aug. 29, 2005, 19(16), 10.

Critique of NAS Report on Evolution - Part 1. Hail Darwin! by Cornelius Hunter, ID Report, ARN, 10 January 2008

Critique of NAS Report on Evolution -- Part 2. The Facts about Intelligent Design, ID Report, ARN, 13 January 2008

In a letter to a friend, Charles Darwin described the abrupt appearance of the flowering plants in the fossil record as "an abominable mystery". This endearing phrase has continued to be used up to the present day, although many hopefuls have been applauded in the media for having solved the mystery.

Fossil and modern maple leaves

A very helpful review of the recent research in this area is provided by Frohlich and Chase. They report that many new discoveries have sharpened thinking on the early diversity of the angiosperms. Theories that once held sway among researchers have been discarded:

"The 'anthophyte theory', the dominant concept of the 1980s and 1990s, has been eclipsed; Gnetales, previously thought to be closest to the angiosperms, are related instead to other extant gymnosperms, probably most closely to conifers."

Major new areas for research relate to molecular data, and many new ideas have been proposed. There is optimism about a solution:

"Formulation of detailed, testable theories combined with study of fossils and genes has the power to dispel the mystery surrounding the origin of both flowers and angiosperms."

One of the biggest problems is that the fossil plant material shows only crown-group specimens.

"There are no studied fossils clearly representing stem-group angiosperms, that is, of plants related to extant angiosperms but attached below the basal node of extant angiosperms in the tree. Such fossils might provide spectacular direct evidence of morphological change along this unknown stretch of evolutionary history."

A few years ago, there was great excitement when one transitional form was found, but this died down when a more convincing analysis was made.

"Archaefructus, originally thought to be a stem-group angiosperm of Jurassic age, is not; it has been re-dated as mid-Early Cretaceous, and its reproductive unit has been reinterpreted as an inflorescence, not a flower."

Archaefructus liaoningensis

Has the mystery been dispelled? The title of the review says it all: "the origin of angiosperms is still a great mystery". The authors expect that "evo-devo" concepts will lead to solutions:

"The appearance in the past decade of theories of flower origin, stimulated by developmental genetic data from modern plants, marks a major shift in attempts to solve Darwin's "abominable mystery". By building a model of the common aspects of floral developmental controls and comparing these with common elements of gymnosperm systems, we can build a picture of the genetic architecture underpinning floral structure in primitive angiosperms and test theories of how floral systems could have arisen."

What we have here is yet another example of abrupt appearance: an angiosperm explosion. It is "abominable" to Darwinists because of their commitment to gradualism. Their theory is in tension with the fossil record - and they have to hold this scientific data lightly by saying it is seriously imperfect. Notwithstanding all this, the reviewers retain a foot firmly in the Darwinian camp with this parting comment:

"a palaeobotanical deus ex machina is possible at any time if a fossil is discovered that illustrates intermediate steps in the evolution of critical angiosperm attributes, such as the carpel with its included ovules or the angiosperm stamen with its specialized structure."

After a dozen years of progress the origin of angiosperms is still a great mystery
Michael W. Frohlich and Mark W. Chase
Nature 450, 1184-1189 (20 December 2007) | doi:10.1038/nature06393

Here we discuss recent advances surrounding the origin of angiosperms. Putatively primitive characters are now much better understood because of a vastly improved understanding of angiosperm phylogenetics, and recent discoveries of fossil flowers have provided an increasingly detailed picture of early diversity in the angiosperms. The 'anthophyte theory', the dominant concept of the 1980s and 1990s, has been eclipsed; Gnetales, previously thought to be closest to the angiosperms, are related instead to other extant gymnosperms, probably most closely to conifers. Finally, new theories of flower origins have been proposed based on gene function, duplication and loss, as well as on morphology. Further studies of genetic mechanisms that control reproductive development in seed plants provide a most promising avenue for further research, including tests of these recent theories. Identification of fossils with morphologies that convincingly place them close to angiosperms could still revolutionize understanding of angiosperm origins.

Quote: "The rapid development as far as we can judge of all the higher plants within recent geological times is an abominable mystery."
Darwin, C.R., Letter to J.D. Hooker, July 22nd 1879, in Darwin F. and Seward A.C., eds., More Letters of Charles Darwin: A Record of His Work in a Series of Hitherto Unpublished Papers, John Murray: London, 1903, Vol. II, pp.20-21.

Prior to the dramatic appearance of the Cambrian hard-bodied fauna, the only multicellular fossils to be found belong to the Ediacaran assemblage of soft-bodied marin