The ID Update

New information has emerged to show that a prediction of neo-Darwinism has been falsified. Everyone knows that animals adapt to their environments. The surge of interest in climate change has stimulated research into morphological change in Galapagos finches, "Siberian warblers, English sparrows, cuckoos, cowbirds, red-winged blackbirds, and many others." The message coming through is that the sizes and shapes of animals can change quickly in response to environmental constraints. These findings have been used as fundamental evidence to support mainstream thinking about organic evolution. As explained by Prothero et al.:

"The classic neontological model of gradualistic evolution argues that organisms are sensitive to small environmental changes, and readily adapt to such changes through transformations of body size or morphology. Such is the tradition of a century of research on the evolution of fruit flies, lab rats, and many other animals, as well as natural examples like the small-scale adaptations of Galapagos finches to drought and other local environmental stresses."

The Page Museum has over 1 million fossil specimens (source here)

Donald Prothero was a student at the American Museum of Natural History when Niles Eldredge and Stephen Jay Gould proposed the "punctuated equilibrium" hypothesis.

"The "punctuated equilibrium" paper is a masterpiece of writing and incisive thinking, which poses a number of interesting issues. The first part is a general discourse on the philosophy of science, which argues that all scientists are products of their time and culture and tend to see what they expect to see. In this context, Darwin led paleontologists to expect phyletic gradualism, which they vainly tried to document for over a century before the allopatric speciation model came along. Then Eldredge and Gould introduced the details of the allopatric model, described punctuated equilibrium, and give examples from their own research (phacopid trilobites from Eldredge, Bahamian land snails from Gould). [. . .]
Many paleontologists came forward and pointed out that the geological literature was one vast monument to stasis, with relatively few cases where anyone had observed gradual evolution. If species didn't appear suddenly in the fossil record and remain relatively unchanged, then biostratigraphy would never work - and yet almost two centuries of successful biostratigraphic correlations was evidence of just this kind of pattern. As Gould put it, it was the "dirty little secret" hidden in the paleontological closet. Most paleontologists were trained to focus on gradual evolution as the only pattern of interest, and ignored stasis as "not evolutionary change" and therefore uninteresting, to be overlooked or minimized. Once Eldredge and Gould had pointed out that stasis was equally important ("stasis is data" in Gould's words), paleontologists all over the world saw that stasis was the general pattern, and that gradualism was rare - and that is still the consensus 40 years later." (source here)

Prothero went on to study for a PhD, which he completed in 1981. This research developed a familiarity with the abundant and well preserved fossil mammals of the Big Badlands of the High Plains. After careful analysis, it became clear that every mammalian lineage showed stasis. He found that stasis persisted through a time of major climatic change (the Eocene-Oligocene transition). Intrigued, Prothero "began to re-examine the uncritical acceptance of the notion that fossil mammals track environmental changes". He looked at the middle-late Eocene climate upheaval, the Eocene-Oligocene transition, the great expansion of modern grasslands dated at 7.5 million years ago, and the Pleistocene ice ages. The evidence for stasis was impressive. Ice age stasis was recognised, but widely interpreted in terms of animals migrating to where comfortable climates prevailed. This thesis needed more attention.

"I had a bunch of excellent students in my paleontology classes at both Occidental and Caltech, and several wanted to do research with me. I was at a loss over how to supervise so many undergraduates with limited backgrounds, until I realized that we could do a group of related projects practically in our back yard: the Page Museum at La Brea tar pits in Los Angeles. I equipped each one of them with calipers and gave them a measuring protocol, and got them access to the La Brea fossils through the collections managers. Then they each measured a different Ice Age mammal or bird, collecting data on hundreds of bones from all the tar pits with good radiocarbon dates: saber-toothed cats, dire wolves, giant lions, bison, horses, camels, ground sloths, plus the five most common birds: golden and bald eagles, condors, caracaras, and turkeys." (source here)

The studies of individual groups have been published as separate papers, but an overview paper has now appeared. The tarpits allow a sampling of fossil mammals and birds from an interglacial, through a glacial and into the next interglacial. The fauna experienced a major climatic transition and Prothero's goal was to test out the relevance of Bergman's rule (where more cold-adapted species or subspecies tend to have larger body sizes to conserve body heat), and Allen's rule (where more cold-adapted species or subspecies tend to have shorter and more robust limbs and other appendages (such as ears) compared to those of warmer climates). This is what he and his students found:

"After six years of work and publication, the conclusion is clear: none of the common Ice Age mammals and birds responded to any of the climate changes at La Brea in the last 35,000 years, even though the region went from dry chaparral to snowy pinon-juniper forests during the peak glacial 20,000 years ago, and then back to the modern chaparral again." (source here)

So Prothero's research has provided solid evidence for stasis and against gradualism in response to environmental change. He is to be commended for following the evidence and not trying to force-fit it into a Darwinian mould. However, he needs to think again about comments like this:

"In four of the biggest climatic-vegetational events of the last 50 million years, the mammals and birds show no noticeable change in response to changing climates. No matter how many presentations I give where I show these data, no one (including myself) has a good explanation yet for such widespread stasis despite the obvious selective pressures of changing climate. Rather than answers, we have more questions - and that's a good thing! Science advances when we discover what we don't know, or we discover that simple answers we'd been following for years no longer work." (source here)
and:
"Such stasis, along with the examples documented from nearly all other Pleistocene mammals and birds, argues that organisms are not as responsive to environmental change as classical neo-Darwinian theory predicts." (Last sentence of the paper)

It is not fair to say that "no one has a good explanation" for the observed stasis. This blog has addressed these issues repeatedly. Stasis is not an oddity in the fossil record - it is pervasive. There are scientists who have concluded there are limits to variation, and that speciation tends to reduce the ability of organisms to respond to their environments. This approach considers that many speciation events result in genetic loss, restricting phenotypic plasticity. This approach has the merit of explaining the observational data - but anyone proposing that there are limits to variation faces a grilling from evolutionists. It's not a case of rejecting their science - it's a case of rejecting their metaphysics.

Size and shape stasis in late Pleistocene mammals and birds from Rancho La Brea during the Last Glacial-Interglacial cycle
Donald R. Prothero, Valerie J. Syverson, Kristina R. Raymond, Meena Madan, Sarah Molina, Ashley Fragomeni, Sylvana DeSantis, Anastasiya Sutyagina, Gina L. Gage
Quaternary Science Reviews, Volume 56, 21 November 2012, Pages 1-10 | http://dx.doi.org/10.1016/j.quascirev.2012.08.015

Abstract: Conventional neo-Darwinian theory views organisms as infinitely sensitive and responsive to their environments, and considers them able to readily change size or shape when they adapt to selective pressures. Yet since 1863 it has been well known that Pleistocene animals and plants do not show much morphological change or speciation in response to the glacial-interglacial climate cycles. We tested this hypothesis with all of the common birds (condors, golden and bald eagles, turkeys, caracaras) and mammals (dire wolves, saber-toothed cats, giant lions, horses, camels, bison, and ground sloths) from Rancho La Brea tar pits in Los Angeles, California, which preserves large samples of many bones from many well-dated pits spanning the 35,000 years of the Last Glacial-Interglacial cycle. Pollen evidence showed the climate changed from chaparral/oaks 35,000 years ago to snowy pinon-juniper forests at the peak glacial 20,000 years ago, then back to the modern chaparral since the glacial-interglacial transition. Based on Bergmann's rule, we would expect peak glacial specimens to have larger body sizes, and based on Allen's rule, peak glacial samples should have shorter and more robust limbs. Yet statistical analysis (ANOVA for parametric samples; Kruskal-Wallis test for non-parametric samples) showed that none of the Pleistocene pit samples is statistically distinct from the rest, indicating complete stasis from 35 ka to 9 ka. The sole exception was the Pit 13 sample of dire wolves (16 ka), which was significantly smaller than the rest, but this did not occur in response to climate change. We also performed a time series analysis of the pit samples. None showed directional change; all were either static or showed a random walk. Thus, the data show that birds and mammals at Rancho La Brea show complete stasis and were unresponsive to the major climate change that occurred at 20 ka, consistent with other studies of Pleistocene animals and plants. Most explanations for such stasis (stabilizing selection, canalization) fail in this setting where climate is changing. One possible explanation is that most large birds and mammals are very broadly adapted and relatively insensitive to changes in their environments, although even the small mammals of the Pleistocene show stasis during climate change, too.

See also:

Prothero, D.R. Darwin's Legacy, eSkeptic (15 February 2012)

Blog Alert

If you are aware of the combinatorial explosion of folding options for proteins, then this paper deserves your attention. If you are unimpressed by such arguments, then Tompa and Rose (the paper's authors) should provide you with a challenge as they wrestle with the question: "how does a viable cell emerge from the bewildering combinatorial complexity of its molecular components?"

In his blog on this paper, Paul Nelson points out that the paper's arguments bear "strongly on the design debate". Indeed, they represent "so remarkable a challenge to widely held assumptions about (for instance) the origin of cells, that its effect promises to be far-reaching. As in, revolutionary."

For those impressed by the "creation" of a bacterial cell in 2010 (previously discussed here), Tompa and Rose have this to say:

"The inability of the interactome to self-assemble de novo imposes limits on efforts to create artificial cells and organisms, that is, synthetic biology. In particular, the stunning experiment of "creating" a viable bacterial cell by transplanting a synthetic chromosome into a host stripped of its own genetic material has been heralded as the generation of a synthetic cell (although not by the paper's authors). Such an interpretation is a misnomer, rather like stuffing a foreign engine into a Ford and declaring it to be a novel design." (p.2078)

The Humpty-Dumpty Effect: A Revolutionary Paper with Far-Reaching Implications
Paul Nelson
Evolution News & Views, October 23, 2012

The Levinthal paradox of the interactome
Tompa, P. & Rose, G.D.
Protein Science, December 2011, 20(12), 2074-2079 | doi: 10.1002/pro.747

Abstract: The central biological question of the 21st century is: how does a viable cell emerge from the bewildering combinatorial complexity of its molecular components? Here, we estimate the combinatorics of self-assembling the protein constituents of a yeast cell, a number so vast that the functional interactome could only have emerged by iterative hierarchic assembly of its component sub-assemblies. A protein can undergo both reversible denaturation and hierarchic self-assembly spontaneously, but a functioning interactome must expend energy to achieve viability. Consequently, it is implausible that a completely "denatured" cell could be reversibly renatured spontaneously, like a protein. Instead, new cells are generated by the division of pre-existing cells, an unbroken chain of renewal tracking back through contingent conditions and evolving responses to the origin of life on the prebiotic earth. We surmise that this non-deterministic temporal continuum could not be reconstructed de novo under present conditions.

Darwin's solitary illustration of evolutionary branching has left a lasting impression in the minds of readers. From an ancestral form, speciation occurs and the diversity of descendants increases. This can be visualised as a cone of morphological variation, extending from the source. However, the Cambrian Explosion provides empirical evidence against this concept, as a large number of organisms appear abruptly. (For more, see here) Yet it has been tempting for Darwinists to interpret the Cambrian species in terms of a number of cones of increasing diversity that all have their origins deeper in the Precambrian. This was something Stephen Jay Gould attempted to counter by proposing an "inverted cone" model. But there is a need for a third model to be on the table for consideration. For some years, it has been recognised that two groups of animals have very similar disparities in the Cambrian and the Recent. These are the arthropods and the priapulid worms.

"Both are reported to have comparable morphological disparity in the Cambrian and the Recent. This is important for our understanding of the manner in which metazoans radiated, because it implies that Cambrian animals had already explored a variety of 'design' options similar to that realized by their present-day counterparts. [. . .] This challenges the traditional 'cone of increasing diversity' (or, more precisely, it shifts this evolutionary model back in time) in favour of an approximately cylindrical model of bodyplan diversity from the Cambrian to the Recent. It also implies that the magnitude of Cambrian morphological diversity requires some form of explanation: whether in terms of Pre-Cambrian evolution at a small size, the gradual Pre-Cambrian differentiation of internal bodyplans decoupled from the appearance of external (and fossilizable) characters in the Cambrian, or some other mechanism." (p.2057)

Priapulus caudatus (source here)

A recent examination of the available evidence about priapulids and their allies has been undertaken by Matthew Wills and colleagues. Previous analyses appeared in 1998 and 2001, but since then there have been a good number of important fossil finds and two published appraisals of the phylogeny of the group. The authors considered that the time was opportune for a reassessment of the cylindrical model of diversity.

"Does this considerable expansion of our knowledge influence the conclusions of the original paper? We therefore ask to what extent the findings of the initial study are sensitive to factors such as improvements in taxon sampling, the discovery of new fossils through research time and differences in the characters coded." (p.2057)

We shall pass over the "Materials & Methods" and address the results and their implications. The core conclusions of the earlier assessment of disparity have been confirmed.

"It is not surprising that the discovery and description of new fossil taxa (along with better and more detailed studies of both fossil and extant species) has influenced some generalities and many details of the morphospace analyses. However, the general conclusions drawn from the first such study appear robust to these additions and changes." (p.2070)
"Our results were consistent with previous findings: Cambrian priapulids, archaeopriapulids and palaeoscolecids are only marginally less disparate than their extant counterparts." (p.2071)

After pointing out that some of the newer fossil finds are quite close in appearance to some modern forms, the authors point out the significance for grappling with the Cambrian Explosion. Those who seek to smooth out the phenomenon to make it more compatible with Darwinian gradualism are being led by their theoretical premises and are failing to engage with evidence.

"What implications do these new findings have for our understanding of the Cambrian explosion? Most significantly, indices of morphological disparity (unlike morphological phylogenies) are robust to modest differences in taxon and character sampling, lending our results a new rigour. Hence, the near-extant levels of disparity embodied by the Cambrian worms indicate that their appearance in the fossil record must have been preceded by large amounts of morphological change during their divergence from a presumed common ancestor. Although debates on the time available for this divergence are set to continue, the enormous magnitude of the explosion it represents is clear." (p.2072)

The press release about the paper provided this commentary on the significance of the findings:

"Dr Wills first pioneered a study on existing and extinct priapulids in 1998. Fourteen years on, the team looked at a new and expanded data set of anatomical features to see how knowledge of these worms has been affected by new fossil finds. He explained: "The fossils from the Cambrian period can cause a real headache for evolutionary biologists. Instinct tells us to expect simple organisms evolving over time to become increasingly more complex. However during the Cambrian period there was an apparent explosion of different major groups of animals, all appearing simultaneously in the fossil record. We looked at priapulid worms, which were among the first ever predators. What's remarkable is that they had already evolved into a diverse array of forms -- comparable to the morphological variety of their living cousins -- when we first encounter them in the Cambrian fossil record. It's precisely this apparent explosion of anatomical diversity that vexed Darwin and famously attracted the attention of Harvard biologist Stephen Jay Gould.""

The focus on morphological disparity is a welcome aspect of the research, as it allows discussion of overall trends and allows overlaps between fossil and Recent species. The authors present this as one of the strengths of their approach:

"Unlike the results of cladistic analyses (which are extremely sensitive to the details of taxon and character sampling), the results of disparity analyses are much more robust. The intensity of local clustering and discontinuity with which our morphospaces are occupied increases with research time, thus providing greater insights into the structure of the morphospace. Cambrian and post-Cambrian time bins now display positive clustering of their constituent species. Their nonoverlapping distributions also yield a globally heterogeneous pattern when the data for all species are pooled." (p.2072)

From a design perspective, this research is exemplary in drawing out patterns in the data. For too long, we have been led (via the educational system) to view the fossil record through the coloured glasses of Darwinism. This has led to the shoe-horning of data to fit the theory, with very little attention given to testing the theory against the data. With attention to bauplan (or bodyplan) thinking linked to measures of morphospace, and recognising that organisms rich in biological information have phenotypic plasticity that operates independently of natural selection acting on mutations (see here), we have a workable research paradigm. We can enthusiastically endorse the words of co-author Dr Marcello Ruta:

"Detailed scrutiny of other groups of organisms is needed, in order to decipher the rate at which structural, functional and ecological changes occur and how acquisition of new traits impact on group diversification. Ultimately, combined results from these investigations will offer a solid framework for understanding the very roots of Life's grandeur and the astounding variety of species alive today." (source here)

The disparity of priapulid, archaeopriapulid and palaeoscolecid worms in the light of new data
M. A. Wills, S. Gerber, M. Ruta, M. Hughes
Journal of Evolutionary Biology, October 2012, 25(10), 2056-2076 | DOI: 10.1111/j.1420-9101.2012.02586.x

Abstract: Priapulids and their extinct relatives, the archaeopriapulids and palaeoscolecids, are vermiform, carnivorous ecdysozoans with an armoured, extensible proboscis. These worms were an important component of marine communities during the Palaeozoic, but were especially abundant and diverse in the Cambrian. Today, they comprise just seven genera in four families. Priapulids were among the first groups used to test hypotheses concerning the morphological disparity of Cambrian fossils relative to the extant fauna. A previous study sampled at the generic level, concluding that Cambrian genera embodied marginally less morphological diversity than their extant counterparts. Here, we sample predominantly at the species level and include numerous fossils and some extant forms described in the last fifteen years. Empirical morphospaces for priapulids, archaeopriapulids and palaeoscolecids are relatively insensitive to changes in the taxon or character sample: their overall form has altered little, despite the markedly improved sampling. Cambrian and post-Cambrian genera occupy adjacent rather than broadly overlapping regions of these spaces, and Cambrian species still show lower morphological disparity than their post-Cambrian counterparts. Crucially, the significance of this difference has increased with improved taxon sampling over research time. In contrast with empirical morphospaces, the phylogeny of priapulids, archaeopriapulids and palaeoscolecids derived from morphological characters is extremely sensitive to details of taxon sampling and the manner in which characters are weighted. However, the extant Priapulidae and Halicryptidae invariably resolve as sister families, with this entire clade subsequently being sister group to the Maccabeidae. In our most inclusive trees, the extant Tubiluchidae are separated from these other living taxa by a number of small, intervening fossil clades.

See also:

Marine Worms Reveal the Deepest Evolutionary Patterns, ScienceDaily (9 October 2012)

The worm-like molluscs, the Aplacophoria, are not well known to most of us, and they are a difficult group to study because they live in deep waters. Their taxonomy has been somewhat controversial, with little agreement on their relationships with other molluscan groups. However, the consensus has been that they are the "most primordial molluscs to be found on earth". There is an evolutionary story that helps to promote this understanding: the other molluscan groups appeared during the Cambrian Explosion, and they have armour of some kind. It is reasonable to postulate a simpler kind of mollusc that had no armour - which appears to be exactly what we have in the aplacophorians. New research, however, has brought a change of view: these naked molluscs are now considered to have evolved from the ancestral shelled forms.

"A fossil unearthed in Great Britain may end a long-running debate about the mollusks, one of life's most diverse invertebrate groups: Which evolved first, shelled forms like clams and snails, or their shell-less, worm-like relatives? The small new fossil, found in marine rocks along the English-Welsh border, provides the best fossil evidence yet that the simpler worm-like mollusks evolved from their more anatomically complex shelled brethren, rather than the other way around." (Source here)

The reconstructed model of Kulindroplax perissokomos (source here).

The experimental background to this find is worthy of note. Although the fossil was discovered a decade ago, its detailed structure has only been revealed recently - by serial grinding at intervals of 30 micro-metres and recording each step digitally. Then, the images have been processed to reconstruct a 3D model using physical-optical tomography. This has revealed a worm-like body covered by seven protective plates reminiscent of a chiton. The body is that of an aplacophoran, whereas the armour is polyplacophoran. The research paper says it is "the first unambiguous combination of palaeoloricate valves and and aplacaphoran body" (p.960). One of the authors of the research paper refers to it as a "kind of missing link".

"This is a kind of missing link with a worm-like body, bearing a series of shells like those of a chiton or coat-of-mail shell," said Derek E. G. Briggs, director of the Yale Peabody Museum of Natural History and one of the paleontologists who studied the new fossil, Kulindroplax perissokomos.

There are two other fossils that hint at affinities between these two groups. Considered as a whole, the authors consider that we have good evidence for the "flexibility and disparity of the palaeoloricate bauplan" (p.95). Their cladistic analysis suggests that these two groups come together in a natural clade: the Aculifera. This is perceived as a sister group to the Conchifera. The emerging phylogenetic analysis may signal an "end to a long-running debate about the mollusks" (source here). The authorts also point out that their work is complementary to some other studies involving molecular evidence (such as that of Kokot, et al. cited below):

"The recovery of Aculifera and Conchifera in all variants of our analysis demonstrates the strong support that fossil data bow offer for the Aculifera hypothesis, paralleling recent molecular evidence favouring this topology." (p.96)

One implication of this study is that the aplacophorans are not the "most primordial molluscs to be found on earth". No longer should they be thought of as appearing on Earth during the Cambrian explosion. These animals are derived, having shed their armour. The Press Release puts it this way: the new fossil "provides the best fossil evidence yet that the simpler worm-like mollusks evolved from their more anatomically complex shelled brethren, rather than the other way around." The research paper concludes:

"Aplacophorans were primitively shelled molluscs; the few living forms represent the survivors of a diverse valve-bearing Palaeozoic clade." (p.96)

The research points us to the value of using the bauplan paradigm in our scientific work. The Darwinist mindset tends to lose sight of the higher taxonomic categories, and its adherents focus on the origin of new species by natural selection acting on natural variations. New biological information is said to be generated by this species-level process. However, bauplan thinking is far more open to flexibility and disparity arising from existing biological information by permutation and combination. This creates a major issue for cladism to address: how do we assess whether characters are primitive or derived? This study gives us a practical example: a character everyone once thought was primitive has turned out to be derived. If most species are permutations within their bauplan, then the weight given to natural selection acting on natural variations is greatly overplayed.

Furthermore, if bauplan thinking is given due weight, the quest for evolutionary linkages is an agenda for finding false positives. Diversification is unlikely to be linear, but fractal, depending on environmental factors. Classic examples of relevant Darwinist misinterpretation are the alleged horse lineage, the mammal-like reptiles, and hominids. Palaeontologists have been much more aware of the "bushy" nature of diversification trends than evolutionary biologists!

The description of "missing link" should also be considered in the light of bauplan thinking. The new fossil has pointed to a common ancestry for the aplacophorans and the polyplacophorans. These are united in the Aculifera, a natural clade. The newly described fossil is a "link" between the two groups, and it has previously been "missing". In this sense, the significance of a missing link is to unite biological groups with a common bauplan. This is quite different from the Darwinian use of the term, whereby a fossil organism marks a key transition in an evolutionary lineage. The two usages of the phrase should not be confused.

A Silurian armoured aplacophoran and implications for molluscan phylogeny
Mark D. Sutton, Derek E. G. Briggs, David J. Siveter, Derek J. Siveter & Julia D. Sigwart
Nature, 490, 94-97 (04 October 2012) | doi:10.1038/nature11328

The Mollusca is one of the most diverse, important and well-studied invertebrate phyla; however, relationships among major molluscan taxa have long been a subject of controversy. In particular, the position of the shell-less vermiform Aplacophora and its relationship to the better-known Polyplacophora (chitons) have been problematic: Aplacophora has been treated as a paraphyletic or monophyletic group at the base of the Mollusca, proximate to other derived clades such as Cephalopoda, or as sister group to the Polyplacophora, forming the clade Aculifera. Resolution of this debate is required to allow the evolutionary origins of Mollusca to be reconstructed with confidence. Recent fossil finds support the Aculifera hypothesis, demonstrating that the Palaeozoic-era palaeoloricate 'chitons' included taxa combining certain polyplacophoran and aplacophoran characteristics. However, fossils combining an unambiguously aplacophoran-like body with chiton-like valves have remained elusive. Here we describe such a fossil, Kulindroplax perissokomos gen. et sp. nov., from the Herefordshire Lagerstatte (about 425 million years BP), a Silurian deposit preserving a marine biota in unusual three-dimensional detail. The specimen is reconstructed three-dimensionally through physical-optical tomography. Phylogenetic analysis indicates that this and many other palaeoloricate chitons are crown-group aplacophorans.

See also:

Which Came First, Shells or No Shells? Ancient Mollusk Tells a Contrary Story
ScienceDaily (Oct. 3, 2012)

Kocot, K.M. et al. Phylogenomics reveals deep molluscan relationships, Nature, 477, 452-456 (22 September 2011) | doi:10.1038/nature10382