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)