Science Literature

Can there be any student of palaeontology who does not have some awareness of the fossils from the Burgess Shale? With their exquisite preservation, including soft body parts, these animals have provided a window into Middle Cambrian life that has only recently been supplemented by other material. Charles Doolittle Walcott is the person who discovered the most significant fossil site. By 1917, his collection numbered 65,000 fossils. His publications set the scene for subsequent debates about the significance of these animals.

"Walcott's 1909 discovery was not the first, but the best Burgess Shale site. By his collections and publications, Walcott contributed more than anyone, before or since, to drawing back the curtain obscuring our view of the life of the Cambrian world. For this alone, he deserves the glory of this month's centennial celebrations."

The Darwinian model of evolutionary transformation does not explain the explosion of life in Cambrian seas (source here)

My interest in this blog is not the history of the discovery, but the significance these fossils have for palaeontological thinking. Three phases of understanding can be identified.

1. Walcott's interpretations. From today's vantage point, it is easy to underestimate the challenge facing this pioneer. Numerous fossil animals were collected by Walcott that had no identifiable living descendants. Nevertheless, he made every effort to find meaningful links to defend his classification of the organisms. Collins draws attention to a 1911 paper on soft-bodied animals: 4 sea cucumbers, 1 jellyfish and some annelid worms.

"Walcott's identifications did not fare well. Only one of the sea cucumbers is still thought to be a sea cucumber, and the jellyfish is now known to be part of an extraordinary arthropod. Of the 12 annelid worms, only one is still recognized as such. Walcott was on more familiar ground with his publication of arthropods in 1912 but, even here, many of the 8 genera he described are now known to belong to classes different to those which he assigned them."

2. Whittington's reinterpretations. For over 40 years, little work was done on Walcott's collection. Then, in the late 1960s, Harry Whittington and colleagues took up the challenge. They were more ready to recognise "unknown affinities" and acknowledge the weirdness of some Cambrian animals.

"This was the first time that anyone had questioned Walcott's implicit assumption that Cambrian animals belonged to groups alive today. [. . .] None of Walcott's contemporaries, nor indeed the scientists who followed him, questioned Walcott's assumption that the Burgess Shale animals belonged to living animal groups; not until Whittington."

Enter Stephen Jay Gould in 1989 with the publication of Wonderful Life. Apart from retelling the story of the Burgess Shale fauna to a new generation of readers, Gould developed three major arguments, summarised below.

The first pointed out significant human factors affecting the way palaeontological work is done. Walcott was criticised "for 'shoehorning' his animals into known groups, so delaying the true understanding of the Burgess Shale fossils".

Second, Gould claimed to recognise new body plans (phyla) in the "weird wonders" revealed by the Whittington group. This, he claimed, pointed to contingency and chance being dominant factors in the history of life. It did not escape the notice of some that this perspective fitted well into Gould's Marxist/atheist worldview.

Third, Gould wanted to point out the incompatibility between the history of life as revealed by the fossils (the sudden appearance of new body plans) and the theoretical understanding of life's diversity provided by Darwinism (which requires gradualism and incremental branching patterns).

3. Desmond Collins' fieldwork and revised classifications. Starting in 1975, Collins (the author of the Nature essay) led "18 seasons of fieldwork and excavation in the Burgess Shale". Many new localities were found, 3 new faunas, plus "a flood of new specimens" in the period 1983-2000. New forms were described and old forms were re-described.

"Today, we have returned mostly to Walcott's practice of classifying Burgess Shale animals in living animal groups, but the groups are different. There are some extinct classes, such as the Dinicarida, but very few extinct phyla. Five of Gould's weird wonders have been classified, only one in a new phylum."

Collins has provided us with a helpful overview with which as assessment of the issues raised by Gould can be made. We shall look at each of the three arguments in turn.

First, the issue of Walcott's "shoehorning". Collins choice of word is different: he refers to Walcott's "misadventures". Clearly, mistakes were made - but not only by Walcott! It can be argued that Gould himself shoehorned the Burgess Shale data to fit a story that matched his 'contingency' worldview. He wanted to be able to say that if the tape of life were ran again, life's history would look very different.

Second, the dramatic explosion of novel body plans in the Cambrian, many of which went nowhere and became extinct. The re-classification of Collins' et al has reduced the number of new phyla to one. This undermines Gould's contingency argument. If the logic of Gould's argument is valid, then the re-evaluation of the data implies that we have no grounds for thinking that re-running the tape of life will lead to the emergence of unfamiliar phyla. Gould drew conclusions relating to humanity:

"Homo sapiens, I fear, is a "thing so small" in a vast universe, a wildly improbable evolutionary event well within the realm of contingency. Make of such a conclusion what you will." (page 291).

Significantly, arguments against contingency have been developed by one of Whittington's colleagues - and one of the characters appearing in Wonderful Life - Simon Conway Morris, Professor of Evolutionary Palaeobiology at the University of Cambridge. These arguments, based partly on the Burgess Shale fossils and partly on the phenomenon of convergence, appear in his book The Crucible of Creation (1998). It should not be necessary to say that a design-orientated understanding of these data is entirely consistent with the approach taken by Conway Morris.

"I hope that by now I have persuaded you that whatever importance is attached to the Burgess Shale, it is not in the operation of either historical contingency or in the fable of re-running the film of the history of life." (page 205)

Thirdly, the challenge to Darwinism because of the Cambrian Explosion of life forms. Although Gould's claims regarding additional phyla are no longer defensible, this particular argument still stands. Darwinism predicts gradualism and increasing diversification (Gould's cone of increasing diversity in Chapter 1). The pattern of diversification and decimation (Gould's inverted cone) is still to be found in the Burgess Shale organisms. The fundamental incompatibility between the evidence and Neodarwinism means that Darwin's theory have very little to offer us as an explanation of the origin of diversity and organic complexity.

"Additional Cambrian material is now coming from the Chengjiang fauna in China (particularly new chordates, the group that includes humans), and the Sirius Passet fauna in Greenland. Along with the Burgess Shale animals, they demonstrate that virtually all animal groups alive today were present in Cambrian seas."

Gould drew conclusions of a theological nature when he argued from science that we live in the realm of contingency and are ourselves the product of contingency. Yet few challenged his philosophy of history. And few pointed out that his advocacy of purposelessness in the Cosmos was incompatible with his promotion of the strict separation of science and religion (as non-overlapping magisteria). Now that the consensus in science has moved on, we can see that Gould's Burgess Shale argument for contingency was flawed and that the opposite conclusion is warranted: that the history of life suggests purpose and meaning in the Cosmos. For more on these issues, please refer to Meyer's paper on the evidences for design apparent in the Cambrian Explosion and also the film Darwin's Dilemma.

Misadventures in the Burgess Shale (Restricted access)
Desmond Collins
Nature 460, 952-953 (20 August 2009) | doi:10.1038/460952a

One hundred years after Charles Doolittle Walcott found a wealth of Cambrian fossils in the Rocky Mountains of British Columbia, Desmond Collins reflects on the bumpy road of their classification.

See also:

Gould, S.J. Wonderful Life, Hutchinson Radius, 1989.

Morris, S.C. The Crucible of Creation, Oxford University Press, 1998.

Recent years have seen significant advances in our knowledge of the biology of extinct placoderm fish. These animals are now regarded as the earliest vertebrates capable of live birth. Embryos have been found inside pregnant fish alongside evidence for the presence of an umbilical cord (go here and here). The latest reported find concerns the male reproductive organ necessary for internal fertilisation.

The females of Incisoscutum ritchiei bore live young following internal fertilisation (source here)

The background to the discovery of the male organ is interesting in its own right. Males have "penis-like pelvic claspers similar to those found in fossil Ptyctodontida (a group of unarmoured placoderms) and in sharks".
The fossil revealing this organ was found in 2001, but the pelvic clasper was labelled as the pelvic girdle. Second author Kate Trinajstic explained

"at the time, we didn't realize that live births were possible. [. . .] [E]arlier this year [. . . we] looked at this specimen with a new set of eyes. As soon as [Per Ahlberg] got it under a high power microscope, we both realised we had found the missing clasper".

This provides a striking example of human factors affecting the outworking of the scientific method. We are familiar with the idea of scientists gathering data in order to test hypotheses, but much less aware of the way worldviews and paradigms affect what we see as data and what hypotheses we consider to be worthy of testing. When placoderms were considered "primitive", no one was looking for unborn embryos or for the means to achieve internal fertilisation. This was not a hypothesis entertained by the researchers. Even when they looked at a male clasper, they did not recognise what it was. However, once internal fertilisation and live births became accepted (the new paradigm for placoderm biology), the researchers were alerted to new possible explanations of fossil material. Per Ahlberg is quoted as saying: "It provides a pedigree of nearly 400 million years for the "advanced" and seemingly specialized reproductive biology of modern sharks".

Design thinking is like this. Once one accepts the legitimacy of making design inferences within science, the data looks rather different. With the new paradigm, evidences of design appear to be pervasive. Evolutionary presumptions about the "primitiveness" of so-called stem organisms no longer seem coherent. Complex specified information diagnostic of design can be found everywhere we look.

Pelvic claspers confirm chondrichthyan-like internal fertilization in arthrodires
Per Ahlberg, Kate Trinajstic, Zerina Johanson & John Long
Nature 460, 888-889 (13 August 2009) | doi:10.1038/nature08176

Recent finds demonstrate that internal fertilization and viviparity (live birth) were more widespread in the Placodermi, an extinct group of armoured fishes, than was previously realized. Placoderms represent the sister group of the crown group jawed vertebrates (Gnathostomata), making their mode(s) of reproduction potentially informative about primitive gnathostome conditions. An ossified pelvic fin basipterygium discovered in the arthrodire Incisoscutum ritchiei was hypothesized to be identical in males and females, with males presumed to have an additional cartilaginous element or series forming a clasper. Here we report the discovery of a completely ossified pelvic clasper in Incisoscutum ritchiei (WAM 03.3.28) which shows that this interpretation was incorrect: the basipterygium described previously is in fact unique to females. The male clasper is a slender rod attached to a square basal plate that articulates directly with the pelvis. It carries a small cap of dermal bone covered in denticles and small hooks that may be homologous with the much larger dermal component of the ptyctodont clasper.

See also:

Abstractions, Nature 460, 780 (13 August 2009) | doi:10.1038/7257780b

Sharks: Missing Piece Of Fossil Puzzle Found, ScienceDaily (July 14, 2009)

Water striders are found all over the world, moving effortlessly over the surfaces of ponds, lakes and rivers. Fossil Gerridae and Hydrometridae date back to the Upper Paleocene and fossil Veliidae and Mesoveliidae have been discovered in Lower Cretaceous rocks. This implies an origin in the Middle Cretaceous or earlier followed by relative stasis. The insects belong to the Infra order Gerromorpha and all have piercing and sucking mouth parts. Although there is remarkable diversity of leg lengths and shapes, the group is distinguished by the relative lengths of their mid and hind legs. "The mid-legs are disproportionately long and function as oars, whereas the hind-legs are shorter and function as rudders."

A water strider showing its long mid-legs (source here)

The researchers were aware that the "Hox gene Ultrabithorax (Ubx) is known to play multiple roles in defining specific morphological differences among the segments along the anteriorposterior body axis in arthropods, including appendage size, shape, and function". Consequently, testing the role of Ubx became an objective of their research: does this gene affect the leg dimensions of these insects?

Of the three pairs of legs, the front legs are designated L1, the mid-legs L2 and the hind-legs are L3. In the presumed ancestor, the ground plan is L3>L2>L1. The Gerromorpha have L2>L3>L1. The changes are associated with adaptation: locomotion on water surfaces. The research involved mapping early stage development and identifying events where Ubx is expressed.

"Our results show that Ubx establishes the appendage ground plan in water striders through elongating L2, and through multiple functions that establish the identity of the third thoracic segment, including the shortening of L3. In other insects that present the common L3>L2>L1 appendage ground plan such as O. fasciatus and Acheta domesticus, Ubx is expressed in L3 only and functions to elongate its size. Therefore in the novel L2>L3>L1 ground plan of water striders, Ubx has evolved a new expression domain but maintained its ancestral elongating function in L2, whereas in L3, Ubx has maintained its ancestral expression domain but evolved a new shortening function."

In an accompanying press release, Professor Locke Rowe expresses surprise that the one gene had two opposite functions. At the present stage of the research, there is no insight yet into the way this gene operates and why it is different from other insect ground plans.

"To our surprise, we discovered that Ultrabithorax performs opposite functions in different limbs. It lengthens the mid-legs but shortens the hind-legs to establish this unusual body plan that allows water striders to glide on the water surface."

So far, so good. This is all interesting stuff. But then the focus shifts from development (involving empirical studies) to evolution (which goes into the realm of history). The press release continues:

"Determining how these major evolutionary changes happen is a central goal of evolutionary biology, explained Rowe. "Many have marveled at the ability of water striders to walk on water, and we are excited to have discovered the gene that has affected this evolutionary change." "

This research can be understood in terms of the evo-devo approach: small genetic changes affecting early development can achieve significant evolutionary transformations in adult organisms. Let us suppose that the authors are right in thinking that the "evolution of a novel appendage ground plan in water striders is driven by changes in the Hox gene Ultrabithorax". The novelty is in the relative lengths of the mid and hind legs. This is not a new organ and there appears to be no change in the complexity of the specified information.

We need to be realistic in our assessment of what has been achieved. In a blog, Cornelius Hunter writes about this research: "Incredibly, evolutionists were quick to add their gratuitous, scientifically meaningless, interpretation of the findings. [. . .] How cogent. This would be like entering an automobile manufacturing plant, finding the robot that installs the doors, and claiming to have discovered how the doors evolved." There are likely to be many other characteristics of water striders that need to be in place before there is a functioning organism. Perhaps these need to be analysed in some detail before getting too excited by the Ubx story.

Evolution of a Novel Appendage Ground Plan in Water Striders Is Driven by Changes in the Hox Gene Ultrabithorax
Abderrahman Khila, Ehab Abouheif, Locke Rowe
PLoS Genetics, 5(7): e1000583, 2009 | DOI: 10.1371/journal.pgen.1000583

Abstract: Water striders, a group of semi-aquatic bugs adapted to life on the water surface, have evolved mid-legs (L2) that are long relative to their hind-legs (L3). This novel appendage ground plan is a derived feature among insects, where L2 function as oars and L3 as rudders. The Hox gene Ultrabithorax (Ubx) is known to increase appendage size in a variety of insects. Using gene expression and RNAi analysis, we discovered that Ubx is expressed in both L2 and L3, but Ubx functions to elongate L2 and to shorten L3 in the water strider Gerris buenoi. Therefore, within hemimetabolous insects, Ubx has evolved a new expression domain but maintained its ancestral elongating function in L2, whereas Ubx has maintained its ancestral expression domain but evolved a new shortening function in L3. These changes in Ubx expression and function may have been a key event in the evolution of the distinct appendage ground plan in water striders.

See also:

Luke, K. U of T scientists identify gene that enables water striders to glide across water, University of Texas Press Release (August 13, 2009)

The general public is led to think that Charles Darwin magnificently solved the problems associated with the emergence of biological complexity. Many opinion-formers write confidently about the revolution triggered by the publication of "On the origin of species" in 1859. These people have developed a 'consensus' position which they use to convince scientific societies, policy makers, funding agencies and educationalists that any dilution of Darwinism is a retrograde step, ushering in a dark age for science. What will they make - and what will we make - of an essay in Nature Physics that talks about breaking with "many of the presuppositions of traditional evolutionary thinking" and highlights its message with these words:

"A coming revolution may go so far as to unseat Darwinian evolution as the key explanatory process in biology."

The dynamics of interacting populations of viruses and bacteria (Source here)

The essay is a contribution to cross-disciplinary thinking. It starts with an awareness of collective phenomena in modern physics. Thinking has moved away from reductionism and is adopting a holistic interactionism. The new focus is:

"- on the fundamentals of phase transitions and other ordering phenomena in condensed-matter systems, on pattern formation out of equilibrium, and on the rich cooperative dynamics of granular and glassy systems, polymers and other forms of 'soft matter', or charge carriers in high-temperature superconductors and other exotic materials."

The writer, Mark Buchanan, sees a parallel between physics and biology. The tools of physics and engineering are already being used to understand interacting networks within biological systems:

"It now seems clear that biology may also have a second act linked to the widespread importance of collective phenomena. The explosion of genetic and proteomic data, of course, has ushered in the era of systems biology, as biologists have come to recognize the need to gain a more holistic understanding of the functioning of organisms."

However, it is horizontal gene transfer that is perceived to be ushering in the overthrow of Darwinism. This is because all the mechanisms that are being seriously discussed to account for the data invoke environmental influences/drivers. Buchanan argues that the phenomenon can be regarded as confirmed, even though our understanding of mechanisms is in its infancy.

"The clear impact of horizontal gene transfer on bacterial evolution has been established only fairly recently using large-scale genome sequencing, and in the context of a small number of bacteria. Biologists have only begun exploring the various environmental factors that promote or limit horizontal gene transfer, and know almost nothing of how this mechanism of genetic sharing influences the overall logic of the evolutionary process itself."

Why does this take us beyond Darwinism? It is because the mechanisms of Darwinian evolution are inherently reductionistic, with individual life forms struggling for survival in competition with other individuals. Within Darwinian theory, the environment acts as a filter, allowing the fit to live on. Horizontal gene transfer (HGT) moves us away from individuals and towards breeding populations, and the environment becomes a driver of genetic change rather than a passive filter. The tree of life now looks like an unstructured bush (for more, see here).

"[T]he apparent ubiquity of horizontal gene transfer implies that microorganisms have an impressive capacity to actively alter their genomes in response to environmental stresses or opportunities, and this capability is intimately linked to their involvement in a larger community in which the diversity of genetic material resides. Consequently, [. . .] the basic concept of an organism as an isolated biological entity with a unique genetic make-up makes little sense in the bacterial world, as the genetic repertoire of an entire population, as well as foreign species, is available to any individual within it."

Talk of unseating Darwinian evolution has not gone down well with some. Larry Moran quotes some of Buchanan's visionary words and declares: "This kind of hyperbole is not helpful. Shame on Nature Physics for publishing it." However, we could do with more substance in arguments against this essay. Darwinism is inherently reductionistic and it can devise ways of framing HGT to fit into its own mental models. But what it cannot easily do is adopt the holistic perspectives that are emerging everywhere. This is why some of us find a framework of design to be compelling. Design provides a coherent context for systems biology, for biomimetics, and for many other contemporary areas of research. Furthermore, although our understanding of HGT is imperfect and in its infancy, design thinking provides a warrant for inferring the origin of genes capable of being transferred, and for understanding the roles played by HGT in populations.

Collectivist revolution in evolution
Mark Buchanan
Nature Physics, 5(8), (August 2009), 531-531 | doi:10.1038/nphys1352 (Text here)

Last few sentences: The conjecture is that horizontal gene transfer was indeed required for the present genetic code to take the form it has, and that the emergence of life most likely went through a series of stages, with the early stage more Lamarckian in character, and only the latter stages becoming more Darwinian.
Exploring that point in greater detail will be a task for a new kind of biology, one that breaks with many of the presuppositions of traditional evolutionary thinking, and explores the potential for rich and surprising dynamics in a collective setting. It will almost surely benefit from the ideas and experience of physics, which has already experienced its own collectivist revolution.