Science Literature

In February 2012, The Journal of Medical Ethics prepublished electronically an article by two academics from an Australian Centre for Applied Philosophy and Public Ethics. Their paper had the title: "After-birth abortion: why should the baby live?" It developed arguments that many considered to legitimise infanticide for handicapped children. A vigorous debate ensued, with strong criticisms of the paper and its authors. The journal was also criticized for giving a platform to such views, which appeared to add so little to previous cases of advocacy of infanticide. Its editor, Julian Savulescu, contributed this on 28 February 2012:

"As Editor of the Journal, I would like to defend its publication. The arguments presented, in fact, are largely not new and have been presented repeatedly in the academic literature and public fora by the most eminent philosophers and bioethicists in the world, including Peter Singer, Michael Tooley and John Harris in defence of infanticide, which the authors call after-birth abortion. The novel contribution of this paper is not an argument in favour of infanticide - the paper repeats the arguments made famous by Tooley and Singer - but rather their application in consideration of maternal and family interests. The paper also draws attention to the fact that infanticide is practised in the Netherlands."

Consequently, on 2 March 2012, an "open letter" was produced by the authors that was intended to dampen down the flames:

"the article was supposed to be read by other fellow bioethicists who were already familiar with this topic and our arguments. [. . .] We started from the definition of person introduced by Michael Tooley in 1975 and we tried to draw the logical conclusions deriving from this premise. It was meant to be a pure exercise of logic: if X, then Y. We expected that other bioethicists would challenge either the premise or the logical pattern we followed, because this is what happens in academic debates. [. . .] However, we never meant to suggest that after-birth abortion should become legal. This was not made clear enough in the paper. Laws are not just about rational ethical arguments, because there are many practical, emotional, social aspects that are relevant in policy making (such as respecting the plurality of ethical views, people's emotional reactions etc). But we are not policy makers, we are philosophers, and we deal with concepts, not with legal policy."

Moving to the present, the article has now been formally published in an issue of the journal wholly devoted to the debate. Papers are included that present different views on the issues. Professor Udo Schuklenk authored a paper on academic freedom, from the perspective of one who is also an editor of a bioethics journal. In this paper, he expresses concerns about the flak that "academic bioethicists and academic bioethics journals are subjected to by political activists applying pressure from outside of the academy." He identifies two activists that he considers to be abusing academic freedom. The first is Wesley J. Smith, who writes the Human Exceptionalism Blog. The second is Michael Cook, editor of BioEdge. The main complaint appears to be that they are reading articles in academic journals but critiquing them in the public square. Defences of this practice have been made, along with corrections of misinformation, by Wesley J. Smith and by Michael Cook. However, there is also a criticism of the two authors of the controversial academic paper. He does not like their attempt to distinguish a philosophical argument from public policy:

"It is reasonable to demand that those who suggest that this is a purely academic exercise ask themselves why they came up with very practical conclusions—that now somehow they don't mean us (and their many critics) to take very seriously. [. . .] Still, bioethics analyses offering practical conclusions are not theoretical games. Michael Tooley and Peter Singer who have defended similar views for decades can undoubtedly tell many a story about harsh criticism and threats to their persons, but until today - to the best of my knowledge - they have not declared their views a mere thought experiment, undertaken for the sake of it, not really meant to be taken seriously, etc. They do take responsibility for views they hold, and they are right in doing so. Respect for free speech has a flipside, requiring of us to take responsibility for the views that we defend. On what other grounds could we expect our views to be taken seriously. What kind of debate could we reasonably have with discussants who - when cornered - will say 'I didn't really mean it'?" (page 305)

There is therefore some common ground here: it is entirely reasonable to infer that ethical stances lead directly to policy implications. This connection would appear to be clearly implied in the workplace of the two authors: the Centre for Applied Philosophy and Public Ethics. However, there are divergences of view over the issue of academic freedom.

"When all is said and done, this is an academic freedom issue. It has to do with ensuring both that we are able to ask difficult questions, and that we are able to defend conclusions that most people will disagree with. For what it is worth, the infanticide debate is not even a paradigmatic example of the culture wars between the religious and the secularists. Secular bioethicists such as the late Mary Anne Warren have been highly critical of the utilitarian rationale offered in this context. To her birth is a crucial marker event conferring moral standing to the newborn. Academics have always challenged assumptions taken for granted by the mainstream." (pages 305-306)

Academic freedom and academic responsibility go together. We do not have freedom to ignore views that we think are taboo. Anyone discussing issues of abortion and infanticide should take seriously reasons why people affirm the sanctity of life. This requires grappling with issues like mankind being made in the image of God. It is not a case of expecting ethicists to agree with these views, but they need to understand the arguments and engage with them. If they are expunged from academic discourse because these views are "religious", then the result is an imposition on the scope of discussion. This is a denial of academic freedom on upholders of the sanctity of human life who are not allowed to bring such arguments into their academic work. However, the words "sanctity" and "image" are lacking in these papers.

The root problem is that academic ethicists have absorbed a secularised worldview. Over a decade ago, Wesley J. Smith described it in this way:

"Mainstream bioethics reached a consensus long ago that religious values are divisive in a pluralistic society and thus have little place in the formulation of public policy. Those who believe in abortion rights but also hold that all born humans are equally endowed with moral worth, along with those who subscribe to the "do no harm" ethos of the Hippocratic oath, have little impact, since mainstream bioethics rejects Hippocratic medicine as paternalistic and shrugs off equal human moral worth as a relic of the West's religious past."

In this academic ethicists have adopted the philosophical naturalism of academia in general. This turns science into scientism and humans into molecular machines. Everything about humanity has to be portrayed through the reductionist filter of scientism. Our consciousness, our values and our sense of free agency must all be 'explained' via material causation. This straitjacket is illustrated in a recent article (in the Wall Street Journal)on the views of Dr Leon Kass, who has often found himself in a minority among bioethicists when it comes to abortion, euthanasia, embryonic research, cloning and other right-to-life questions.

"Take the concept of human dignity. In a 2008 essay highly critical of Dr. Kass's work on the Bush bioethics council, the Harvard psychologist Steven Pinker questioned the value of dignity as a moral guide. "Dignity is a phenomenon of human perception," Mr. Pinker wrote. "Certain signals in the world trigger an attribution in the perceiver." The perception of human dignity, Mr. Pinker went on, is no different from how "converging lines in a drawing are a cue for the perception of depth." That such an outlook is both blinkered and dangerous, Dr. Kass thinks, should be obvious to anyone who has ever been in love or felt other great emotions. "There's no doubt that the human experience of love," he says, is mirrored by "events that are measurable in the brain. But anybody who has ever fallen in love knows that love is not just an elevated level of some peptide in the hypothalamus.""

Academics adopting the secular materialist worldview will always find themselves demolishing traditional values. They have failed to develop any ethical principles based on secular materialist foundations and they end up as pragmatists, postmodernists or social constructivists. Their conclusions about infanticide are entirely predictable. What is controversial is not that they say such things, but that they are so hostile to philosophical theism appearing in the pages of their academic journals. This is the crunch issue for academic freedom that has yet to be recognised.

After-birth abortion: why should the baby live?
Alberto Giubilini, Francesca Minerva
Journal of Medical Ethics, 2013; 39(5), 261-263 | doi:10.1136/medethics-2011-100411

Abstract: Abortion is largely accepted even for reasons that do not have anything to do with the fetus' health. By showing that (1) both fetuses and newborns do not have the same moral status as actual persons, (2) the fact that both are potential persons is morally irrelevant and (3) adoption is not always in the best interest of actual people, the authors argue that what we call 'after-birth abortion' (killing a newborn) should be permissible in all the cases where abortion is, including cases where the newborn is not disabled.

In defence of academic freedom: bioethics journals under siege
Udo Schuklenk
Journal of Medical Ethics, May 2013, 39(5), 303-306 | doi:10.1136/medethics-2012-100801

Abstract: This article analyses, from a bioethics journal editor's perspective, the threats to academic freedom and freedom of expression that academic bioethicists and academic bioethics journals are subjected to by political activists applying pressure from outside of the academy. I defend bioethicists' academic freedom to reach and defend conclusions many find offensive and 'wrong'. However, I also support the view that academics arguing controversial matters such as, for instance, the moral legitimacy of infanticide should take clear responsibility for the views they defend and should not try to hide behind analytical philosophers' rationales such as wanting to test an argument for the sake of testing an argument. This article proposes that bioethics journals establish higher-quality requirements and more stringent mechanisms of peer review than usual for iconoclastic articles.

See also:

Klinghoffer, D. What Darwin's Enforcers Will Say About Darwin's Doubt: A Prediction (Evolution News & Views, 8 May 2013)

Sixty years have passed since Watson and Crick unveiled the structure of the DNA double helix and tentatively explained how it encodes hereditary information. The Central Dogma of genetics soon followed: that "DNA makes RNA makes protein" makes cells and organisms. Once this "River out of Eden" was flowing, the story of life was deemed to be essentially understood. Genes were considered to provide the blueprint of life and the task of filling in the details had begun. The blueprint motif was prominent in media coverage of the Human Genome project - any who questioned its veracity were regarded as subverting science. But is the consensus position robust? At least one commentator (Philip Ball in Nature) is prepared to say that it is misleading.

"But I can tell that the usual tidy tale of how 'DNA makes RNA makes protein' is sanitized to the point of distortion. Instead of occasional, muted confessions from genomics boosters and popularizers of evolution that the story has turned out to be a little more complex, there should be a bolder admission - indeed a celebration - of the known unknowns." (page 419)

In 1953, Francis Crick and James Watson described the double helix structure of DNA. (source here)

Numerous discoveries have been "unsettling old assumptions". First, the ENCODE project has put the spotlight on regulation rather than transcription. Not only are genes transcribed (about 1% of the human genome) but so also is at least 80% of the human genome. Numerous regulatory roles have been determined for many of these RNA transcripts, and every week brings more examples of functionality to our attention. Not only do these findings challenge "the old idea that much of the genome is junk", they also show us that we are only beginning to understand the genome's role in the cell.

"According to evolutionary biologist Patrick Phillips at the University of Oregon in Eugene, projects such as ENCODE are showing scientists that they don't really understand how genotypes map to phenotypes, or how exactly evolutionary forces shape any given genome." (page 420)

Second, the field of epigenetics has introduced previously unsuspected constraints, whereby environmental factors influence the phenotype without affecting the genotype.

"For example, epigenetic molecular alterations to DNA, such as the addition of a methyl group, can affect the activity of genes without altering their nucleotide sequences." (page 420)

Third, positional information is not revealed by the documenting of amino acid sequences within the DNS molecule, but this information, when recognised, is significant for development.

"Genes can also be regulated by the spatial organization of the chromosomes, in turn affected by epigenetic markers. Although such effects have long been known, their prevalence may be much greater than previously thought." (page 420)

And there are more evidences to throw into the melting pot. Ball refers to the way gene networks are structured: the genes are the same, but differences in organisation of these networks can result in differences in phenotype. Similarly, changes in regulation could be more significant than changes in the genes themselves. There are big questions about the role of natural selection at the molecular level and it is by no means agreed that natural selection is the dominant driver.

"In short, the current picture of how and where evolution operates, and how this shapes genomes, is something of a mess. That should not be a criticism, but rather a vote of confidence in the healthy, dynamic state of molecular and evolutionary biology." (page 420)

Whilst saying this is not a criticism, there are nevertheless aspects of these developments that should be criticised. Notably, it is necessary to vigorously critique the evolutionary consensus that dominates education and the media. Take education first - and recall how vigorously evolutionists have opposed all attempts to introduce critical, evidence-based thinking about evolutionary theory. They have portrayed this as religiously motivated anti-science lobbying, and have ensured that the consensus positions have prevailed. In this they have betrayed a whole generation of biology students.

"A student referring to textbook discussions of genetics and evolution could be forgiven for thinking that the 'central dogma' devised by Crick and others in the 1960s - in which information flows in a linear, traceable fashion from DNA sequence to messenger RNA to protein, to manifest finally as phenotype - remains the solid foundation of the genomic revolution. In fact, it is beginning to look more like a casualty of it." (page 419)

Furthermore, it is a scandal that the whole spectrum of contemporary thinking in genetics is largely hidden from the broader scientific community. The media provides a welcoming stage for celebrity scientists to pronounce on their outdated views, but dissenters find it hard to present on a science platform. When reading the following quotation, it is worth noting that Prospect magazine has honoured Richard Dawkins as the "world's top thinker" as a result of a recent poll of its readers.

"Barely a whisper of this vibrant debate reaches the public. Take evolutionary biologist Richard Dawkins' description in Prospect magazine last year of the gene as a replicator with "its own unique status as a unit of Darwinian selection". It conjures up the decades-old picture of a little, autonomous stretch of DNA intent on getting itself copied, with no hint that selection operates at all levels of the biological hierarchy, including at the supraorganismal level, or that the very idea of 'gene' has become problematic." (page 420)

Philip Ball does suggest some reasons why there has been a reluctance to acknowledge biological complexity. Whilst not disputing the various points he makes, the analysis is not deep enough. The closest he gets is in the last paragraph:

"When the structure of DNA was first deduced, it seemed to supply the final part of a beautiful puzzle, the solution for which began with Charles Darwin and Gregor Mendel. The simplicity of that picture has proved too alluring." (page 420)

It is not just that simplicity is too alluring; it is that the worldview of the scientists demands simplicity. They are predisposed to look for simplicity and they fall into a trap of confirmation bias. It happened in Darwin's day, when the cell was conceived as a simple building block, and organisms were portrayed as assemblages with varying degrees of complexity (see here). This worldview derives from Deism or Atheism, where everything has to assemble itself: from the cosmos to organisms. The only way that people can imagine this happening is incrementally, deriving complexity from simple building blocks. This is Richard Dawkins explaining the point.

"Darwinian evolution is the only process we know that is ultimately capable of generating anything as complicated as creative intelligences. Once it has done so, of course, those intelligences can create other complex things: works of art and music, advanced technology, computers, the Internet and who knows what in the future? Darwinian evolution may not be the only such generative process in the universe. There may be other "cranes" (Daniel Dennett's term, which he opposes to "skyhooks") that we have not yet discovered or imagined. But, however wonderful and however different from Darwinian evolution those putative cranes may be, they cannot be magic. They will share with Darwinian evolution the facility to raise up complexity, as an emergent property, out of simplicity, while never violating natural law."

Ultimately, then, we have worldview issues to evaluate. Those with a naturalistic mindset interpret all complexity as emergent from natural law with a sprinkling of chance. However, their approach is testable - they require ultimate simplicity and blind (tinkering) processes. Arguably, this approach has been falsified in innumerable areas of science. What we find is ultimate complexity and an extraordinary richness of information. This finding is consistent with, and predicted by, advocates of intelligent design. To move the debate in science forward in a meaningful way, both these avenues of inquiry need to be fully and fairly evaluated.

DNA: Celebrate the unknowns
Philip Ball
Nature, 496, 419-420 (25 April 2013) | doi:10.1038/496419a

On the 60th anniversary of the double helix, we should admit that we don't fully understand how evolution works at the molecular level

See also:

Watson J.D. and Crick F.H.C. Molecular structure of nucleic acids: A structure for deoxyribose nucleic acid. Nature, 1953, 171, 737-738. (also here)

This year marks the centenary of the death of Alfred Russel Wallace, sometimes portrayed as "Darwin's goad". However, as Andrew Berry argues, Wallace should be remembered as a "visionary scientist in his own right, a daring explorer and a passionate socialist". He was awarded the Order of Merit, the highest honour that could be given by the British monarch to a civilian. He has left a -

"- huge scientific legacy, which ranged from discovering natural selection to defining the term species, and from founding the field of evolutionary biogeography to pioneering the study of comparative natural history." (page 162)

The portrait of Wallace is unveiled at the launch of Wallace100 (Source here)

Wallace's first exhibition (four years in the Amazon rainforests) ended in disaster and he narrowly escaped death. As he sailed home in 1852, the ship caught fire and all the specimens he had so carefully collected, including numerous living animals, were lost. Wallace watched the burning wreck from a lifeboat, and it was 10 days before rescuers arrived on the scene. Ever the scientist, he wrote:

"During the night I saw several meteors, and in fact could not be in a better position for observing them, than lying on my back in a small boat in the middle of the Atlantic." (page 163)

Two years later, he was off to the Far East for an 8-year trek. During this time, he established himself as an academic writer and an extremely successful collector, with over 1000 specimens new to science. A landmark paper pointed out that related species tend to be found in the same geographical area.

"Wallace had a prodigious ability to spot patterns in the apparently chaotic (and largely uncatalogued) world of tropical diversity. This is the skill of the true naturalist: to generate a mental database of observed plants and animals that can be referenced when similar forms are encountered elsewhere. It led to his first attempt at biological generalization, a paper he wrote in 1855 while in Sarawak, Borneo: 'On the Law which has Regulated the Introduction of New Species' (often called the Sarawak Law)." (page 163)

Ten years later, Wallace proposed a remarkably modern definition of the species concept:

"In his brilliant 1865 paper on the papilionid butterflies of southeast Asia, he parses variations within and among populations, among subspecies and species, and arrives at this definition: "Species are merely those strongly marked races or local forms which, when in contact, do not intermix, and when inhabiting distinct areas are generally believed to have had a separate origin, and to be incapable of producing a fertile hybrid offspring."
It is emblematic of history's neglect of Wallace that most undergraduates today are taught that the biological species concept was introduced in 1942 by Ernst Mayr." (page 163)

Many students have been introduced to the role played by Wallace in 1858 in triggering a joint presentation alongside Darwin of evolution by natural selection. Suffice to say here that the last word on this has not been written.

However, although Darwin's name is now dominant in evolutionary theory, Wallace is perceived as the Father of historical biogeography. The groundwork was laid in 1857, in a paper about the Aru Islands (off New Guinea). Textbooks today record his discovery of the distinction between Australian fauna and Asian fauna, separated by Wallace's Line.

"It is tempting to see echoes between Wallace's serendipitous path through life and his contingent interpretation of natural systems: his most famous biogeographical discovery also had a dose of luck. In 1856, having missed a connection as he tried to make his way to Sulawesi, he spent a couple of months on the islands of Bali and Lombok, and noted drastic differences in the wildlife even though the islands are only some 35 kilometres apart. To the south and east, the Australian fauna dominated; to the north and west, the Asian one. He had identified an ancient biogeographic split across southeast Asia that biologist Thomas Henry Huxley later dubbed 'Wallace's Line'." (page 163)

Wallace the scientist is often contrasted with the "other Wallace" who dabbled in "suffrage and socialism", "spiritualism and phrenology". But Berry cautions against thinking like this. "But Wallace's worldview was far more coherent than is often claimed." (page 164) Differences with Darwin came to the fore regarding human evolution. Whereas Darwin expected evolution by natural selection to transform an ape-like animal into a human, Wallace rejected this scenario. He argued for "some kind of non-material intervention in the genesis of humans". His religious views allowed him to be open to this hypothesis, although his arguments were drawn from scientific observations of different races of humanity.

"The more I see of uncivilized people, the better I think of human nature on the whole, and the essential differences between so-called civilized and savage man seem to disappear." (page 164)

Berry comments:

"[Wallace realised that] many humans have abilities that they never have the opportunity to use. Such a situation, Wallace reasoned, cannot evolve through natural selection alone, which promotes only those traits that are useful. Wallace concluded that human evolution required some divine intervention. This argument shows an excellent appreciation of the mechanics of natural selection [. . . ]" (page 164)

Darwin's reaction reveals his own worldview, which was sometimes deistic and sometimes atheistic - but which never allowed any active role for God in the history of life. Berry puts it this way:

"Darwin was horrified, writing to his friend in 1869: "I hope you have not murdered too completely your own and my child."" (page 164)

Whilst Berry is willing to respect Wallace's integrity in departing from Darwin in this key issue, he does not elaborate on the broader implications of worldview thinking. No mention is made of Wallace's Man's Place in the Universe (1903), which discusses the teleological anthropic principle, or his World of Life (1910), which is devoted to intelligent evolution. Wallace saw himself as a theistic scientist who recognised design and purpose in the natural world. Thus, he is a powerful witness against those who portray intelligent design per se as antiscience. People are free to reach different conclusions, but Wallace should not be dismissed as someone who sacrificed reason and science to satisfy religious scruples. This is a worldview issue and, at this level, both theists and atheists are equally religious in their thinking. We can echo Berry's closing words, with the proviso that in the "etc., etc., etc." are found Wallace's advocacy of intelligent design in the natural world.

"As we remember Wallace 100 years after his death, let us celebrate his remarkable scientific achievements and his willingness to take risks and to advocate passionately for what he believed in. He was, after all, both a scientist, and, in his own assessment, a "Red-hot Radical, Land Nationaliser, Socialist, Anti-Militarist, etc., etc., etc." In short, a whole lot more than Darwin's goad." (page 164)

Alfred Russel Wallace: Evolution's red-hot radical
Andrew Berry
Nature, 496, 162-164 (11 April 2013) | doi:10.1038/496162a

Sidekick status does Alfred Russel Wallace an injustice. He was a visionary scientist in his own right, a daring explorer and a passionate socialist, argues Andrew Berry.

See also:

Flannery, M. Why Darwin Is Remembered More than Wallace, Evolution News& Views (5 March 2013)

Flannery, M. Hijacking Alfred Russel Wallace, Evolution News& Views (24 January 2013)

Tyler, D., Why Alfred Russel Wallace deserves to be remembered, ARN Literature Blog (11 March 2008)

Website: Alfred Russel Wallace

Soft-bodied worms from the Burgess Shale fossil beds in Yoho National Park, British Columbia, Canada have been known form over 100 years. They are known by the name Spartobranchus tenuis and are considered one of the most abundant species in the Walcott Quarry community. However, only recently has a detailed examination of their characteristics been made, leading to the conclusion that they are ancient examples of acorn worms. One member of the research team was Christopher Cameron from the University of Montreal, who studies modern-day acorn worms. Identifying the fossils was not problematic: "Spartobranchus is clearly an acorn worm," he said in an interview. "It's almost like someone took a picture of a modern-day animal - it's absolutely astonishing." These animals are not true worms but belong to a very different phylum: the Hemichordates. The name means "half chordate" indicating that hemichordates share some of the characters associated with chordates. This is relevant to some of the discussion below. Hemichordates comprise three classes: the Enteropneusta or acorn worms; the Pterobranchia - minute colonial tube-dwelling organisms; and the Graptolithina or graptolites. Pterobranchs were already known to be part of the Cambrian Explosion, so the inclusion of acorn worms in this flowering of animals is a significant addition to knowledge. According to Henry Gee in Nature:

"Before this report, the earliest-known fossil enteropneusts were Triassic, between 250 million years and 200 million years old. That Caron et al. extend the fossil record of enteropneusts back to the Cambrian period makes their findings notable, even with no other contribution."

Modern acorn worms live underwater in mud and fine sand (source here)

The find is notable because it reinforces the evidences for stasis in the fossil record. This deserves highlighting because so many think that the fossil record documents Darwinian gradualism - which it stubbornly fails to do. It is notable because it reinforces the phenomenon of the Cambrian Explosion, showing that those who try to fit the evidence into a Darwinian framework are shoehorning data and resistant to the testing of their cherished theory. From the abstract:

"The presence of both enteropneusts and pterobranchs in Middle Cambrian strata, suggests that hemichordates originated at the onset of the Cambrian explosion."

Notwithstanding all this, the commentary on the research has a very strong evolutionary emphasis. Firstly, the fossil acorn worm is presented as an important transitional form.

"According to Dr Cameron and colleagues, Spartobranchus tenuis reveals a crucial evolutionary link between two distinct living groups of animals: enteropneusts and pterobranchs."
"Enteropneusts look very different from pterobranchs in as much as the former are worms, whereas the latter are tiny animals, live in tubes, are colonial and have feeding tentacles," explained Professor Simon Conway Morris from the University of Cambridge, UK, who also worked on the study. [. . .] "By finding enteropneusts in tubes we begin to bridge this evolutionary gap," Dr Morris told BBC Nature. Dr Cameron commented: "It's astonishing how similar Spartobranchus tenuis fossils are to modern acorn worms, except that they also formed fibrous tubes." In many of the fossils, remains of the worms were encased in these tubes, and the team believe they lived in the structures and may have even sealed themselves in a doughnut shape within the tubes. (Source here)

The nature of these tubes is clearly important. Gee refers to "pterobranch-like tubes" and considers this an unambiguous witness to transformation. However, the research paper gives more insight into just how "pterobranch-like" the tubes are. It says that approximately one-quarter of specimens are associated with tubes that have a fibrous composition, and that only one individual is ever associated with a tube. There is no evidence that the worms were attached to the tubes, so they were able to leave them to feed or in response to stress. Apart from the use of the word "fibrous", the only other information on the construction of the tubes is that they are sometimes branched and sometimes show tearing. Whilst the researchers have made a case for an evolutionary link, there seems to be scope for weighing these evidences and considering alternatives.

"Two lines of evidence suggest that the collagenous coenecium of pterobranchs had origins in the organic tubes of S. tenuis. First, the tubes of S. tenuis have a fibrous structure that sometimes shows evidence of tearing. We have no evidence of characteristic growth bands (fuselli), a pterobranch innovation that probably appeared with a reduction in size and the evolution of a shield-shaped secretory organ. Second, the secretory proboscis and cephalic shield are homologous in enteropneust and pterobranchs (both protosoma), and thus the transition from inferred involvement of the proboscis in tube construction by S. tenuis to the secretory role of the cephalic shield is unproblematic. We suggest that in the lineage leading to the Enteropneusta, the tube lining was lost, whereas in pterobranchs it provided a substrate for an astonishing radiation, not least in Palaeozoic planktonic ecosystems."

The scenario these researchers favour is that the common ancestor had a capability for tube construction that was present in the early enteropneusts like S. tenuis but then lost. This means that, if there was a common ancestor, the biological information for tube construction was already present. Descendants either exploited this information (the pterobranchs) or lost it (the enteropneusts). It is worth considering what form of evolutionary change this implies. We have novel biological information in the inferred ancestor, modified information in the pterobranchs, and lost information in the enteropneusts. This does not fit the Neo-Darwinian theoretical model because the relevant biological information already existed in the common ancestor. A much better match to this situation is phenotypic plasticity: where radiations of animals and plants utilize existing biological information in varying combinations and permutations. For more on phenotypic plasticity, go here.

The other evolutionary theme concerns the origin of vertebrates. Henry Gee makes this the headline for his News & Views essay: "The discovery, in 500-million-year-old rocks, of fossil acorn worms that lived in tubes illuminates the debate about whether the ancestor of vertebrates was a mobile worm-like animal or a sessile colony dweller." In this debate, the hemichordates are deemed to be of considerable importance.

"Understanding the origin of vertebrates is fascinating not just because it appeases our self-interest, but because it is inherently difficult. Vertebrates seem to have a qualitatively more complex construction than other animals. This means not only that the origin of distinctive features of vertebrate anatomy, such as the head or the neural crest, are difficult to trace among invertebrates, but also that the evolutionary roots of vertebrates as a whole are hard to fathom. In a paper published on Nature's website today, Caron et al. address a fundamental issue in this regard: whether the ancestor of the deuterostomes (the larger assemblage to which vertebrates belong) was a free-living, worm-like creature or a sessile, perhaps colonial, animal. Their answer, for now, is that it was solitary, worm-like and motile."

Since all the major players in this debate (hemichordates, echinoderms and vertebrates) are all found among the Cambrian Explosion fauna, the fossil record cannot be mapped against the Darwinian gradualist branching model. Instead, we have the primacy of a theoretical paradigm about universal common ancestry that presupposes that ancestral relationships must exist and that uses evolutionary cladism as the tool for interpreting evidences (as in Gee's essay. Also, go here for additional comments). Of course, this debate will continue, but it deserves to be pointed out that Meyer et al. (2006), on the contribution made by intelligent design theory to these important issues, continues to be relevant. One is tempted to add that as fossil discoveries accumulate, the case of intelligent design becomes more and more compelling.

Tubicolous enteropneusts from the Cambrian period
Jean-Bernard Caron, Simon Conway Morris and Christopher B. Cameron
Nature, (Online March 2013) | doi:10.1038/nature12017

Hemichordates are a marine group that, apart from one monospecific pelagic larval form, are represented by the vermiform enteropneusts and minute colonial tube-dwelling pterobranchs. Together with echinoderms, they comprise the clade Ambulacraria. Despite their restricted diversity, hemichordates provide important insights into early deuterostome evolution, notably because of their pharyngeal gill slits. Hemichordate phylogeny has long remained problematic, not least because the nature of any transitional form that might serve to link the anatomically disparate enteropneusts and pterobranchs is conjectural. Hence, inter-relationships have also remained controversial. For example, pterobranchs have sometimes been compared to ancestral echinoderms. Molecular data identify enteropneusts as paraphyletic, and harrimaniids as the sister group of pterobranchs. Recent molecular phylogenies suggest that enteropneusts are probably basal within hemichordates, contrary to previous views, but otherwise provide little guidance as to the nature of the primitive hemichordate. In addition, the hemichordate fossil record is almost entirely restricted to peridermal skeletons of pterobranchs, notably graptolites. Owing to their low preservational potentials, fossil enteropneusts are exceedingly rare, and throw no light on either hemichordate phylogeny or the proposed harrimaniid-pterobranch transition. Here we describe an enteropneust, Spartobranchus tenuis (Walcott, 1911), from the Middle Cambrian-period (Series 3, Stage 5) Burgess Shale. It is remarkably similar to the extant harrimaniids, but differs from all known enteropneusts in that it is associated with a fibrous tube that is sometimes branched. We suggest that this is the precursor of the pterobranch periderm, and supports the hypothesis that pterobranchs are miniaturized and derived from an enteropneust-like worm. It also shows that the periderm was acquired before size reduction and acquisition of feeding tentacles, and that coloniality emerged through aggregation of individuals, perhaps similar to the Cambrian rhabdopleurid Fasciculitubus. The presence of both enteropneusts and pterobranchs in Middle Cambrian strata, suggests that hemichordates originated at the onset of the Cambrian explosion.

See also:

Gee, H. Tubular worms from the Burgess Shale, Nature, (Online March 2013) | doi:10.1038/nature11963

Over recent years, researchers have developed the scenario of fleas feasting on pterosaurs and feathered dinosaurs during the Jurassic Period of Earth history. Fossils of strashilid insects have been suggested to have piercing and sucking mouthparts and hind pincers suitable for attaching to a host's hairs or feathers. Further reading on this interpretation is to be found in Rasnitsyn (1992) and Gao et al. (2012). Other putative flea species have also been found and Poinar's (2012) perspective paper has the title: "the 165-million-year itch" (see also here).
A new interpretation of the strashilids has now been proposed after examining spectacular recent finds from the Daohugou beds, Inner Mongolia. The researchers have concluded that the fossils are the remains of flies, not fleas. They were not ectoparasites living on animals, but highly specialized flies adapted to aquatic environments.

"Although definitive Middle Jurassic ectoparasites (fleas) on vertebrates were reported recently from the Daohugou outcrops, earlier speculation regarding strashilids as terrestrial ectoparasites can be rejected owing to an alternative hypothesis stemming from the discovery of hitherto unknown large membranous wings and females of Strashila, in two cases preserved in copula. Males and females have identical head morphologies but differ strongly in the absence of the hind leg pincers in females, which excludes ectoparasitism on terrestrial vertebrates as these are reinterpreted as sex-related structures for grasping the female rather than a host's integument. In addition, unlike ectoparasitic insect lineages, the body is cylindrical in strashilids, rather than dorsoventrally or laterally flattened." (page 94, Huang et al. 2013)

From Poinar (2012): "(A) Reconstruction of the 150 million year old Jurassic flea-like Strashila incredibilis. Note the incredibly long and powerful hind legs clasping the base of two feathers on a feathered dinosaur and a well-developed proboscis. Strashila may have fed on pterosaurs or feathered dinosaurs. Drawing by the author. (B ) Reconstruction of the Chinese Jurassic pseudoflea, Pseudopulex jurassicus, imagined parasitizing a feathered dinosaur." (Source here)

It is worth noting that our understanding of strashilids has changed as a result of finding well preserved specimens. Previous work was based on meagre fossil evidence and was inherently speculative. It is possible to generalise the lessons that should be learned from this: when fossil evidence is sparse, it is unwise to speculate. Unfortunately, the pressures to publicise finds are substantial and are unlikely to diminish. The media is always looking for stories that create interest, and speculation appears to be preferred above caution.

It is also worth noting that the new interpretation of strashilids locates them in a more familiar context. The researchers note characters that are "virtually identical with those of the recent nematoceran flies", are "comparable in critical details with those of nymphomyiids", and "similar to those of nymphomyiids". "We conclude that the Strashilidae were a highly specialized dipteran clade related to Nymphomyiidae, with an aquatic or amphibious life history." This paragraph summarises the evidence:

"These structures provide evidence that strashilids share several potential apomorphies with modern nymphomyiid flies, including the finer details of the antennae, ocelli, wings, terminalia and legs. Their reduced mouthparts and wings are inefficient for feeding and active flight, respectively, and indicate an ephemeral life history, akin to modern nymphomyiid taxa. Similar to modern nymphomyiids, adult Strashilidae probably mated soon after emergence, shed their wings, crawled beneath the water, mated, and in some cases died in copula, with the superposing male grasping the female below, thereby explaining the discoveries of females grasped by males, and both without their wings." (page 96)

It is not without significance that the initial interpretation of the fossil strashilids considered them to be primitive flea-like insects. There were hints from some characters that made sense in the perspective provided by evolutionary theory. However, what we can now see is a highly specialized insect related to Nymphomyiidae. It is derived rather than primitive. And this specialised insect, similar to modern nymphomyiids, was part of the Jurassic world. Is it possible that the Darwinian mindset colours the interpretations placed on fossilised species? Before this thought is dismissed out of hand, the case of the strashilids serves as a salutary case study to ponder.

Amphibious flies and paedomorphism in the Jurassic period
Diying Huang, Andre Nel, Chenyang Cai, Qibin Lin & Michael S. Engel
Nature, 495, 94-97 (07 March 2013) | doi:10.1038/nature11898

Abstract: The species of the Strashilidae (strashilids) have been the most perplexing of fossil insects from the Jurassic period of Russia and China. They have been widely considered to be ectoparasites of pterosaurs or feathered dinosaurs, based on the putative presence of piercing and sucking mouthparts and hind tibio-basitarsal pincers purportedly used to fix onto the host's hairs or feathers. Both the supposed host and parasite occur in the Daohugou beds from the Middle Jurassic epoch of China (approximately 165 million years ago). Here we analyse the morphology of strashilids from the Daohugou beds, and reach markedly different conclusions; namely that strashilids are highly specialized flies (Diptera) bearing large membranous wings, with substantial sexual dimorphism of the hind legs and abdominal extensions. The idea that they belong to an extinct order is unsupported, and the lineage can be placed within the true flies. In terms of major morphological and inferred behavioural features, strashilids resemble the recent (extant) and relict members of the aquatic fly family Nymphomyiidae. Their ontogeny are distinguished by the persistence in adult males of larval abdominal respiratory gills, representing a unique case of paedomorphism among endopterygote insects. Adult strashilids were probably aquatic or amphibious, shedding their wings after emergence and mating in the water.

People who love the countryside and open places tend to value biodiversity and rich ecosystems. There is a perception that a high species diversity helps to stabilise ecosystems by buffering the effects of environmental change, and in addition create ecosystems with greater functionality. According to MacDougall et al. (2013), "Biodiversity can stabilize ecological systems by functional complementarity, with different species thriving under different conditions." However, scientific underpinning has lagged behind tacit knowledge and we are faced with the growth of monocultures in agricultural husbandry and commercial land use. Nevertheless, the situation is changing, and the benefits of biodiversity are being increasingly recognised. Researchers face the problem of complex patterns of human interventions.

"Human land management is often persistent, by intentional (for example, fire suppression and overfishing) or inadvertent (for example, nitrogen pollution) disturbances that homogenize both resident diversity and environmental conditions. Persistent disturbances obscure diversity-stability relationships because they can affect ecosystem function independently of diversity, as when overgrazing directly decreases production and provides opportunities for invasion. Because persistent disturbances can also drive species loss, false positives may arise between diversity and ecosystem function, in which reductions in diversity and function are correlated but have weak mechanistic connections." (MacDougall et al. (2013), page 86)

"Biodiversity is vital for our survival and is a key measure of the health of our planet." (Source here)

Two studies have been published recently that develop the themes of (1) biodiversity promoting more resilient ecosystems, and (2) biodiversity expanding the functionality of ecosystems. First, we consider the issue of resilience.

The study area is in the Pacific Northwest of North America on grasslands described as oak savannah. Human influence has resulted in a loss of plant diversity but an increased yield of grass production. The grasslands are said to remain "resilient to invasive species and climate fluctuation". The research programme involved the periodic burning of experimental plots followed by recovery. The results show that grasslands "were able to recover from burning only in areas that had a relatively high diversity of native plants". By contrast, the species-poor grasslands were rapidly invaded by tree species with the resulting collapse of the savannah ecosystem.

"Our work demonstrates how persistent human activity can homogenize the structure and function of ecological systems, while simultaneously weakening diversity-related compensatory mechanisms needed to respond to sudden disturbance. These findings are consistent with previously demonstrated connections between diversity and ecosystem function, in which a larger portfolio of functional strategies within a community provides insurance against sudden environmental change. Given that many terrestrial systems possess this signature of compositional homogenization owing to persistent human activity, there may be a similar vulnerability to sudden environmental change that will be only evident after the collapse occurs." (MacDougall et al. (2013), page 88)

The second study was concerned with trees, and particularly with the link between ecosystem diversity and ecosystem services (functions). Again, tacit knowledge has recognised the connections before being able to document them by rigorous research.

"Ecosystems provide a wealth of benefits to human society, and the provision of such ecosystem services depends fundamentally on functions performed by organisms. This has led scientists to enquire how the diversity and composition of communities may regulate ecosystem functions. A large body of evidence has established that species diversity promotes ecosystem functions under experimental conditions. There are, however, many exceptions to the positive diversity-function relationship." (Gamfeldt et al. 2013, page 2)

The need is for research designed to look at multiple functions at a regional scale, leading to a more holistic assessment of an ecosystem. The researchers studied plots in production forests. These were relatively species-poor. The maximum recorded was 10, and only 1.5% of the plots hade more than 5 species. They identified six ecosystem services, including tree biomass production.

"Our results from boreal and temperate production forests show that the relationships between tree species richness and multiple ecosystem services were positive to positively hump-shaped, and that all services attained higher levels with five tree species than with one species. Although the relatively high level of tree biomass production with five compared with one tree species may seem both impressive and surprising, we note that similar effect sizes have been found previously. [. . .] There are, unfortunately, no previous studies on the relationships between tree species richness and the other five services that allow for comparisons with our findings." (Gamfeldt et al. 2013, page 2,3)

The paper has an interesting discussion of trade-offs leading to an explanation as to why diversity should be more prominent in strategic thinking in forestry.

"[O]ur results suggest the importance of tree species mixtures for the continued provisioning of ecosystem services from the 2-billion hectares of forest in the world currently managed as production forests or used for multiple purposes (55% of all forests). [. . .] Although the trade-offs we found imply that it will be difficult to maximize all ecosystem services simultaneously at the stand scale, the positive relationships between tree diversity and individual services suggest that adjacently located monocultures would not optimize the provision of ecosystem services at the landscape scale. Instead, adjacent stands, each with multiple species but in different combinations, might be the best way to provide multiple ecosystem services at the landscape scale." (Gamfeldt et al. 2013, page 4)

Some of the deeper issues relating to diversity are explored further below. Research findings are now complementing tacit knowledge that diversity is beneficial for ecosystems and for agriculture. This means that diversity promotion should be an integral part of the different ways we interact with ecosystems - whether for husbandry or for conservation. In other words, 'diversity by design' should be the way we think about human intervention. We might also reflect on 'diversity by design' without human intervention. This means that if the ecosystems we see around us witness to an intelligent Designer, then 'diversity' is a keyword. If this avenue of thought is valid, the inference can be made that mechanisms will exist for promoting diversity. We may then envisage machinery for engineering ecosystems to match environmental constraints. This leads to a highly dynamic perspective of organisms and one that confronts some very stereotyped popular views about design thinking.

The stereotype was advanced by Charles Darwin in his On the Origin of Species. Darwin claimed that if animals and plants were created, they would not display changes. Belief in a Creator, he argued, leads to a doctrine of fixity of species. So any evidence of variation was used to argue for evolution ("my theory") rather than creation. He wrote (Chapter XIV, Page 458): "Authors of the highest eminence seem to be fully satisfied with the view that each species has been independently created", but nowhere did Darwin support this statement with quotations or references to scholars who upheld the doctrine of the fixity of species. He asserted it, and his readers soaked it all up. It has been endlessly repeated over the years, and is part of school textbooks - so the next generation of students is programmed to think like Darwin. The reality is that the fixity of species was not held by scholars contemporary with Darwin. For example, Darwin should have known that his creationist mentor, Professor John Stevens Henslow, had embarked on a research programme to probe the limits of variation of selected plants (Kohn et al. 2005).

If we start with evidence (that diversity is beneficial) and infer that mechanisms exist for promoting diversity, then we will approach the observational data quite differently from Darwin and the Darwinists. We will recognise mechanisms that deliver diversity (e.g. via recombination of DNA during sexual reproduction). We will find that the genome exhibits plasticity, so that many phenotypes can emerge from the same genotype. Scholars today are developing understanding of phenotypic plasticity - a phenomenon that owes nothing to Darwinism. For more on this topic, go here. For case studies, go here and here.

'Diversity by design' is a rational and reasonable starting point for the study of ecology. Those who set out with this perspective will find that they travel along a different path from the one taken by Darwin, and it leads to quite different conclusions. This is a Kuhnian paradigm shift. Dominant and recessive genes are the tip of the iceberg! Speciation that is rapid, rather than gradual, is an indication of diversity by design. When we find non-random mutations or mutation hot spots, these are pointers to designed mechanisms. Epigenetics has the potential for expanding our understanding of the ways for diversity to develop. The more diversity by design is probed, the more it presents itself as a viable and interesting research paradigm.

Diversity loss with persistent human disturbance increases vulnerability to ecosystem collapse
A. S. MacDougall, K. S. McCann, G. Gellner & R. Turkington
Nature, 494, 86-89 (07 February 2013) | doi:10.1038/nature11869

Long-term and persistent human disturbances have simultaneously altered the stability and diversity of ecological systems, with disturbances directly reducing functional attributes such as invasion resistance, while eliminating the buffering effects of high species diversity. Theory predicts that this combination of environmental change and diversity loss increases the risk of abrupt and potentially irreversible ecosystem collapse, but long-term empirical evidence from natural systems is lacking. Here we demonstrate this relationship in a degraded but species-rich pyrogenic grassland in which the combined effects of fire suppression, invasion and trophic collapse have created a species-poor grassland that is highly productive, resilient to yearly climatic fluctuations, and resistant to invasion, but vulnerable to rapid collapse after the re-introduction of fire. We initially show how human disturbance has created a negative relationship between diversity and function, contrary to theoretical predictions. Fire prevention since the mid-nineteenth century is associated with the loss of plant species but it has stabilized high-yield annual production and invasion resistance, comparable to a managed high-yield low-diversity agricultural system. In managing for fire suppression, however, a hidden vulnerability to sudden environmental change emerges that is explained by the elimination of the buffering effects of high species diversity. With the re-introduction of fire, grasslands only persist in areas with remnant concentrations of native species, in which a range of rare and mostly functionally redundant plants proliferate after burning and prevent extensive invasion including a rapid conversion towards woodland. This research shows how biodiversity can be crucial for ecosystem stability despite appearing functionally insignificant beforehand, a relationship probably applicable to many ecosystems given the globally prevalent combination of intensive long-term land management and species loss.

Higher levels of multiple ecosystem services are found in forests with more tree species
Lars Gamfeldt, Tord Snall, Robert Bagchi, Micael Jonsson, Lena Gustafsson, Petter Kjellander, Maria C. Ruiz-Jaen, Mats Froberg, Johan Stendahl, Christopher D. Philipson, Grzegorz Mikusinski, Erik Andersson, Bertil Westerlund, Henrik Andren, Fredrik Moberg, Jon Moen & Jan Bengtsson.
Nature Communications, January 2013, 4, 1340 | doi:10.1038/ncomms2328

Abstract: Forests are of major importance to human society, contributing several crucial ecosystem services. Biodiversity is suggested to positively influence multiple services but evidence from natural systems at scales relevant to management is scarce. Here, across a scale of 400,000 km2, we report that tree species richness in production forests shows positive to positively hump-shaped relationships with multiple ecosystem services. These include production of tree biomass, soil carbon storage, berry production and game production potential. For example, biomass production was approximately 50% greater with five than with one tree species. In addition, we show positive relationships between tree species richness and proxies for other biodiversity components. Importantly, no single tree species was able to promote all services, and some services were negatively correlated to each other. Management of production forests will therefore benefit from considering multiple tree species to sustain the full range of benefits that the society obtains from forests.

Blog Alert

A frequently heard phrase in discussions of the science of origins is "evidence-based". It is important that scientists affirm that their work has to do with evidence and that it is different from speculation. This blog is concerned with the evidence base for evolutionary innovation via gene duplication. The press release for the paper under consideration claims that the researchers have come up with answers, but it also contains a significant acknowledgement that, in the past, there have been significant unanswered questions about this topic:

"An important unanswered question in Darwin's theory of evolution is how new characteristics seem to appear out of nowhere. Such innovations appear to contradict the principle of gradual change, in which existing characteristics slowly evolve into another form. Yet we know that many "inventions" took place during the evolution of life."

"These results provide answers to an argument frequently used by opponents of the theory of evolution: the chance of the occurrence of a new characteristic - a functional new segment of DNA - from scratch is similar to the chance of a modern jumbo jet assembling spontaneously from a few pieces of scrap metal." (Sources - text and graphic)

The scientists consider that they have succeeded in rebuilding the DNA and proteins of prehistoric yeast cells. This is what they say:

Steven Maere: "We used sequence reconstruction algorithms to predict the DNA sequence of ancestral genes from dozens of present-day DNA sequences. This enabled us to rebuild the corresponding ancestral proteins."
Karin Voordeckers: "We searched very specifically for how the yeast adapted to break down various sources of sugar. We found that the primal gene that codes for the protein for the digestion of maltose - a sugar in grain - was copied a number of times during evolution. The DNA of some copies changed slightly, resulting in new proteins that could break down different sugars. By modeling these changes in the corresponding proteins, we now understand how just a few changes in the DNA can lead to the development of new activity in the corresponding proteins"
The scientists think that this type of duplication of the DNA often forms the basis of the emergence of apparently "new" proteins. In other words: the jumbo jet is gradually built from a copy of an existing airplane.

In a blog on the research, Doug Axe finds that the paper does not explain the origin of anything new. He suggests that the authors have used the word "Innovation" in their title in an "innovative" way!

"They clearly want to say that they've shown how a bunch of brand new enzyme activities can evolve from an ancestral enzyme that lacks them. I understand their passion. That's what I'd want to say if I wanted Darwinism to be true. And, truth be told, science papers do allow authors to cast their results in their own terms. But they also press them to state the facts plainly, and in this case here's the plain statement:
"The preduplication [i.e., ancestral] ancMalS enzyme was multifunctional and already contained the different activities found in the postduplication [i.e., evolved] enzymes, albeit at a lower level."
So, all we have here is a demonstration of what we already knew -- that evolution can adjust somewhat the relative preferences enzymes show for the molecules they already work on. Those aren't new activities, though, and this isn't a new result either."

Axe is reminding us that the evidence base says "complexity comes from complexity", which should be regarded as the finding of science. Those who seek to build complexity gradually from simple precursors are still presuming the answers rather than discovering them. The words quoted above: "Yet we know that many "inventions" took place during the evolution of life" is stating a 'given' of evolutionary theory and is unwilling to even consider that the evidence points elsewhere.

Reconstruction of Ancestral Metabolic Enzymes Reveals Molecular Mechanisms Underlying Evolutionary Innovation through Gene Duplication
Karin Voordeckers, Chris A. Brown, Kevin Vanneste, Elisa van der Zande, Arnout Voet, Steven Maere, Kevin J. Verstrepen
PLoS Biology, 10(12): e1001446 | doi:10.1371/journal.pbio.1001446

Abstract: Gene duplications are believed to facilitate evolutionary innovation. However, the mechanisms shaping the fate of duplicated genes remain heavily debated because the molecular processes and evolutionary forces involved are difficult to reconstruct. Here, we study a large family of fungal glucosidase genes that underwent several duplication events. We reconstruct all key ancestral enzymes and show that the very first preduplication enzyme was primarily active on maltose-like substrates, with trace activity for isomaltose-like sugars. Structural analysis and activity measurements on resurrected and present-day enzymes suggest that both activities cannot be fully optimized in a single enzyme. However, gene duplications repeatedly spawned daughter genes in which mutations optimized either isomaltase or maltase activity. Interestingly, similar shifts in enzyme activity were reached multiple times via different evolutionary routes. Together, our results provide a detailed picture of the molecular mechanisms that drove divergence of these duplicated enzymes and show that whereas the classic models of dosage, sub-, and neofunctionalization are helpful to conceptualize the implications of gene duplication, the three mechanisms co-occur and intertwine.

Blog:

Belgian Waffle by Douglas Axe (Biologic Institute, 17 January 2013)

It is often said that the timescales for evolution are too long to allow speciation to be studied experimentally. Consequently, researchers look to the fossil record to provide the evidence base. However, this also has its limitations. With fossils, molecular analyses are not possible because soft tissues decay rapidly. Furthermore, the drivers of speciation are often a matter of speculation. Nevertheless, by selecting a depositional environment that provides a sequence of stratigraphical horizons that allow analysis of environmental factors, some informative studies are possible.

"Long-lived lakes are virtually predetermined for these studies, because of their duration and relative stability, being therefore often called 'islands of evolution'. Many studies have proven this fact repeatedly, including the papers on the impressive morphological developments in the Middle Miocene Lake Steinheim planorbids, the Neogene Aegean freshwater gastropods, or the Recent Lake Tanganyika gastropods." (page 117)

Geographical setting of Lake Pannon (source here)

The research considered in this blog has gathered data from Lake Pannon. In the past, this covered parts of eastern Austria, Hungary, Slovakia, Croatia, Serbia, and western Romania. At its maximum, it covered 290,000 km2; it lasted from the Late Miocene to the Early Pliocene. A stratigraphy has been developed and its diverse fauna logged. The research paper considers the changing fortunes of the gastropod genus Melanopsis over successive stages of the lake's chronological development.

"The aim of this paper is to document and discuss the phenotypic evolution in a single evolutionary lineage by modern morphometric analysis. The investigated geological interval of c. 1.6 Ma provides an excellent opportunity to study alternating modes of evolution in the fossil record, including stasis, the proposed adaptive radiation, and the final extinction of one of the emerging branches. The integration of a comprehensive set of palaeoenvironmental data taken from the literature provides the necessary link between the observed phenotypic evolution and underlying parameters, potentially allowing evaluation of the taxonomic status of the phenotypes." (pages 117-118)

"Recent Melanopsis praemorsa (Linnaeus, 1758) is a generalist, living in a great variety of habitats. These include rivers, ponds, springs, shallow lakes with inundated marshes, mud and gravel shores of estuaries, irrigation canals, and oases. It tolerates high temperatures and brackish conditions. This species feeds variably on algae, detritus and carrion." (image source here)

The authors are very cautious about affirming that any particular phenotype is a species. They are aware that taxonomists have tended to declare a novel phenotype to be a species rather too easily. This is relevant to Melanopsis, and all the phenotypes observed have been given specific names by researchers. Those appearing in this study are: Melanopsis impressa, M. pseudonarzolina, M. coaequat, M. fossilis, M. rugosa, M. handmanniana and M. vindobonensis. All are illustrated in Figure 2 in the research paper.

"Moreover, the authors act on the a priori assumptions of the distinctiveness of species within a lineage. To retain objectivity, we refrained from any predefined species/subspecies delimitations, many of which were proposed in earlier studies, and refer to the different morphologies as phenotypes." (page 117)

Morphometric analysis of gastropod shells has many challenges. The authors explain their approach, which is based on defining the curves (or outlines) that make up the shape. This gave a quantitative dimension to the observed phenotypic changes that correlated well with the descriptive morphological work of taxonomists. Environmental interpretations draw on prior research:

"Both the samples used for the morphological analysis as well as the major part of the isotope samples studied by Harzhauser et al. (2007) originate from a geographically small area at the western margin of Lake Pannon. Based on the previously published isotope data a rather detailed model of palaeoenvironmental change is available for the time interval and area studied. This model is used to correlate changes observed in gastropod morphology with palaeoclimate shifts." (p.120)

The scenario that emerges has three phases.

Phase 1. Fluvio-deltaic but arid environment. The molluscs lived in flowing water and tended to be small and slender (i.e. the streamlined shape matched these conditions). This situation was stable and stasis is reported.

Phase 2. Humid climate with increased precipitation. The lake level rose and water flows became slow and sluggish. Stabilising selection for the streamlined morphology ceased, and the molluscs experienced a radiation of phenotypes. Several different morphologies emerged, finding their niche somewhere in the lake.

Phase 3. Climatic instability. The environment fluctuated, with variable river discharges, lake level changes, lake stratification with periodic eutrophic conditions involving algal blooms. The impact was felt primarily by shallow water animals such as Melanopsis. Gastropod phenotypes reduced during this phase until only one phenotype was left: a small form that is inferred to have coped with the range of environmental stresses experienced. There is some evidence that this morphology is adapted to higher water energies.

The authors are careful to avoid claiming too much. They are aware that they are unable to identify the mode of speciation. The term "adaptive radiation" is one they use tentatively.

"Nevertheless, the correlation between the phenotypic changes and the environmental alterations strongly argues for ecologically driven natural selection. Consequently, the strong phenotypic divergence is thought to reflect reproductive isolation. The argument for directional selection is corroborated by the fact that both shape and size traits show massive changes within the interval of the proposed adaptive radiation. Hunt (2007) suggested body size to be a more common subject to directional selection than shape traits." (p.124)

So, what has this research achieved? A sequence of morphological changes has been identified and a correlation has been made with palaeoenvironmental data. The authors suggest that an adaptive radiation occurred when the climate became more humid, with higher precipitation and higher lake levels. They note that stratigraphic resolution was coarse, so that conclusions were unable to be drawn as to whether speciation was gradual or punctuated.

It should be said that the clearest examples of adaptation are in phases 1 and 3, where the phenotypes can be regarded as tuned to environmental factors. Phase 2 is more a case of lifting constraints, so that a wider range of morphologies were viable. Whether or not they are adaptive does not yet appear to be established. We have a radiation, but it may be a case of populating the larger ecospace.

The authors see their work as contributing to a greater understanding of how morphological changes are related to evolutionary mechanisms. It is worth pointing out that the data does not take us very far in this direction. The morphologies can be described as examples of micro-evolutionary change. The Melanopsis gastropods are all members of the same genus. Whilst morphologies change, there are no evolutionary novelties. Indeed, there is no evidence here for anything more than multiple phenotypes emerging from the same genotype. The situation fits well with the concept of phenotypic plasticity (discussed here and here). A relevant comment comes from Luskin, pointing out the implications of the research of Austin Hughes:

"This leads to the question: How, then, do new traits arise? Rather than relying on positive selection, Hughes claims that one prevalent mechanism in producing new traits is the relaxation of purifying selection -- i.e. random genetic drift. But genetic drift, of course, is essentially a random process where mutations not only arise without respect to the needs of the organism, but also are preserved (or lost) without regard for the needs of the organism. In other words, it would have no reason to build complex traits."

There is nothing here to support the thesis that macroevolution is but the extrapolation of microevolution. Indeed, the argument can be made that the observed phenotypes in Melanopsis occur within limits: constrained by the Melanopsis genotype. There may be no requirement for new genetic information to produce the range of observed phenotypes. If this is the case, far too much emphasis is being placed on speciation. The real question for evolutionary biologists relate to the origin of novelty, of body plans, and ultimately of biological information.

Phenotypic evolution in a fossil gastropod species lineage: Evidence for adaptive radiation?
Thomas A. Neubauer, Mathias Harzhauser, Andreas Kroh
Palaeogeography, Palaeoclimatology, Palaeoecology, 370, 15 January 2013, 117-126.

Abstract: Detecting speciation in the fossil record is a particularly challenging matter. Palaeontologists are usually confronted with poor preservation and limited knowledge on the palaeoenvironment. Even in the contrary case of adequate preservation and information, the linkage of pattern to process is often obscured by insufficient temporal resolution. Consequently, reliable documentations of speciation in fossils with discussions on underlying mechanisms are rare. Here we present a well-resolved pattern of morphological evolution in a fossil species lineage of the gastropod Melanopsis in the long-lived Lake Pannon. These developments are related to environmental changes, documented by isotope and stratigraphical data. After a long period of stasis, the ancestral species experiences a phenotypic change expressed as shift and expansion of the morphospace. The appearance of several new phenotypes along with changes in the environment is interpreted as adaptive radiation. Lake-level high stands affect distribution and availability of habitats and, as a result of varied functional demands on shell geometry, the distribution of phenotypes. The ongoing divergence of the morphospace into two branches argues for increasing reproductive isolation, consistent with the model of ecological speciation. In the latest phase, however, progressively unstable conditions restrict availability of niches, allowing survival of one branch only.

In 1998, Xiao, Zhang & Knoll dazzled the palaeontological world with spectacular fossil embryos from Doushantuo, China. To find soft-bodied embryos is noteworthy in its own right, but these embryos were from the late Precambrian (the early part of the Ediacaran Period) and were identified as belonging to animals. The search for animal signatures before the Cambrian (when there was an explosion of animal life) has been intense - for Darwin predicted that they would one day be discovered and their absence presented him with a dilemma. Multicellular ediacaran fossils have been found, but their affinities with cambrian animals has been controversial. For example, one of the most widely cited examples (Charnia interpreted as a sea pen) did not stand up to critical scrutiny (Antcliffe and Brasier, 2007). Consequently, to find animal embryos in the early Ediacaran was deemed to be worth heralding. Stephen Jay Gould put pen to paper straight away, saying that "Fossils of tiny embryos 570 million years old may well be the greatest paleontological discovery of our time." More recently, Butterfield (2011) put it like this:

"Ever since Darwin there has been a disturbing void, both paleontological and psychological, at the base of the Phanerozoic eon. If his theory of gradualistic evolution be true, then surely the pre-Phanerozoic oceans must have swarmed with living animals - despite their conspicuous absence from the early fossil record. Thus, the 1998 report of fossilized animal embryos in the early Ediacaran Doushantuo Formation of South China was met with almost palpable relief."

The Doushantuo embryos made an enormous impact (source here)

However, several researchers have found the "animal" interpretation unconvincing. The fossilised characters regarded as diagnostic of animals have been found in other types of organism. Other features that have been observed are not "animal" at all. The first major challenge came in 2007, when Bailey et al. documented similarities with a modern giant sulphur-oxidising bacteria going by the name Thiomargarita. However, there were still problems: this interpretation explained some, but not all, of the data. What was needed was more fundamental research in order to evaluate alternative hypotheses. The two most significant avenues of research have been: to probe the inner structure of the embryos using Synchrotron X-ray tomographic microscopy; and reappraising, using experimental taphonomy, what realistically can be preserved of biological tissue and how this can be distinguished from diagenetic mineralisation.

Hagadorn et al. (2006) used X-ray computed tomography and reported internal cellular structures that were suggested to be "fossilized nuclei, spindle bundles, or other organelles". This boosted the "animal" interpretation, but it was also consistent with the giant sulphur bacteria hypothesis.

Then came a bombshell. Huldtgren et al. (2011) showed internal features incompatible with multicellular metazoan embryos, instead, there was a good fit with the embryos belonging to protists, and the observations are of structures producing "propagules for dispersion".

In parallel with this research, an experimental taphonomy study was published by Cunningham et al. (2012). This tested the hypothesis that the embryos should be identified as giant sulphur bacteria. Distinct differences were found between the experimentally preserved and the fossilised forms. The authors concluded that the hypothesis is falsified. Kaplan's News report in Nature had this to say:

"Of the 450 fossils scanned, 14 were found to contain structures that look like nuclei. In one of these specimens, three of the eight structures even have the elongated or dumb-bell shape of modern nuclei about to replicate. This hints that the organism died during cellular division. "We were enthralled to find nuclear division preserved by fossilization. It confirmed that the fossil organisms were not bacteria, but we soon realized that they were not like animals either, as animal nuclei tend to lose their contours during cell division, and these nuclei did not," says Bengtson."

The expertise developed in this experimental approach to fossilisation has developed the knowledge base for distinguishing between preserved biological material and diagenetic mineralisation. This has allowed a more general evaluation of extant fossil material. One casualty has been Vernanimalcula guizhouena, also from the Doushantuo Formation, which has been interpreted as the earliest bilaterian animal. Now, the diagnostic animal features are regarded as the products of diagenesis (Bengtson et al., 2012).

This blog has been stimulated by a lecture on the Doushantuo microfossils by Dr John Cunningham of the University of Bristol and co-author of several of the research papers cited above. The lecture was very useful to me for putting into context the various contributions that have been made since 1998, and it made me think that its content should be more widely known. The lecture abstract gave the conclusion that "there is currently no convincing evidence for advanced animals with bilateral symmetry in the Doushantuo biota". This particular quest for animals preceding the Cambrian Explosion has drawn a blank. Needless to say, Darwin's dilemma remains in full force.

Links to the literature cited are provided above. The two most recent research papers are as follows:

Experimental taphonomy of giant sulphur bacteria: implications for the interpretation of the embryo-like Ediacaran Doushantuo fossils
J. A. Cunningham, C.-W. Thomas, S. Bengtson, F. Marone, M. Stampanoni, F. R. Turner, J. V. Bailey, R. A. Raff, E. C. Raff and P. C. J. Donoghue.
Proc. R. Soc. B, 7 May 2012, 279, 1857-1864 | doi: 10.1098/rspb.2011.2064

Abstract: The Ediacaran Doushantuo biota has yielded fossils interpreted as eukaryotic organisms, either animal embryos or eukaryotes basal or distantly related to Metazoa. However, the fossils have been interpreted alternatively as giant sulphur bacteria similar to the extant Thiomargarita. To test this hypothesis, living and decayed Thiomargarita were compared with Doushantuo fossils and experimental taphonomic pathways were compared with modern embryos. In the fossils, as in eukaryotic cells, subcellular structures are distributed throughout cell volume; in Thiomargarita, a central vacuole encompasses approximately 98 per cent cell volume. Key features of the fossils, including putative lipid vesicles and nuclei, complex envelope ornament, and ornate outer vesicles are incompatible with living and decay morphologies observed in Thiomargarita. Microbial taphonomy of Thiomargarita also differed from that of embryos. Embryo tissues can be consumed and replaced by bacteria, forming a replica composed of a three-dimensional biofilm, a stable fabric for potential fossilization. Vacuolated Thiomargarita cells collapse easily and do not provide an internal substrate for bacteria. The findings do not support the hypothesis that giant sulphur bacteria are an appropriate interpretative model for the embryo-like Doushantuo fossils. However, sulphur bacteria may have mediated fossil mineralization and may provide a potential bacterial analogue for other macroscopic Precambrian remains.

A merciful death for the "earliest bilaterian," Vernanimalcula
Stefan Bengtson, John A. Cunningham, Chongyu Yin, and Philip C.J. Donoghue.
Evolution & Development, 14(5), 421-427 (Sept/Oct 2012) | DOI: 10.1111/j.1525-142X.2012.00562.x [pdf here]

Summary: Fossils described as Vernanimalcula guizhouena, from the nearly 600 million-year-old Doushantuo Formation in South China, have been interpreted as the remains of bilaterian animals. As such they would represent the oldest putative record of bilaterian animals in Earth history, and they have been invoked in debate over this formative episode of early animal evolution. However, this interpretation is fallacious. We review the evidential basis of the biological interpretation of Vernanimalcula, concluding that the structures key to animal identity are effects of mineralization that do not represent biological tissues, and, furthermore, that it is not possible to derive its anatomical reconstruction on the basis of the available evidence. There is no evidential basis for interpreting Vernanimalcula as an animal, let alone a bilaterian. The conclusions of evolutionary studies that have relied upon the bilaterian interpretation of Vernanimalcula must be called into question.

The discovery of soft-bodied fossils located at the top of Precambrian sedimentary sequences was a landmark for palaeontology. Prior to finding these forms, there was nothing between single-celled fossils and the sophisticated animals in Lower Cambrian rocks. There was a 'gap' in the fossil record that was a dilemma for Charles Darwin when he discussed the matter in On the Origin of Species. (6th ed., p.286): "To the question why we do not find rich fossiliferous deposits belonging to these assumed earliest periods prior to the Cambrian system, I can give no satisfactory answer." Unfortunately, whilst these soft-bodied organisms are now widely known, they do not provide a transition to the animals of the Lower Cambrian. There are few (if any) connections that can be made across the Precambrian/Cambrian boundary. There is still uncertainty as to what these life forms actually are and where they fit into the larger picture. Three scenarios have been proposed in recent years: early ancestors of marine invertebrate phyla, giant marine protists, and lichenized fungi. It is the third of these options that has been boosted in newly reported work by Gregory Retallack.

Life on land in the Ediacaran? Dickinsonia: fossil marine worms or land-living lichen? (Source here).

The Ediacaran fossils have been widely regarded as a marine fauna. The rocks are associated with a variety of depositional environments, but all are marine. A relevant example is the type section for these fossils: the Ediacaran Member of the Rawnsley Quartzite, north of Adelaide, Australia. The following description of Selden and Nudds (2004) summarises the literature, and it illustrates the radical nature of reinterpreting the enclosed fossils as terrestrial.

"The Ediacaran Member consists of a series of siltstones and sandstones which represent pelagic to inter-tidal conditions. The implication is that there was a continental edge delivering sediment into deep water, at times by means of turbidite flows and occasionally as a delta which shallowed the water to sub- and inter-tidal levels. Some storm horizons can be seen. It is at these shallow levels, around the storm wave base, that the fossils occur." (Evolution of Fossil Ecosystems, page 12)

In 1994, Retallack formally proposed that some Ediacaran fossils should be identified as lichens. He has recently worked on the type section of Ediacaran strata and has published a reinterpretation: they are concluded to be non-marine (lagoonal-aeolian) with palaeosols (Retallack, 2012). On these surfaces, he maintains, lichens grew. It is not my purpose here to discuss these evidences, but it is worth drawing attention to Paul Knauth's News & Views contribution to Nature, where he encourages an openness to these controversial views:

"As is usual in sedimentology, observations can be construed in alternative ways, and interpretations for these strata have historically covered the gamut of geological possibilities - from lacustrine to lagoonal, coastal and open marine. It is appropriate that interpretations change or are superseded with the arrival of new observations, and that is why this publication is fascinating and timely and should be considered seriously. Although Retallack's ideas are at odds with the accepted dogma, these do not need to be mutually exclusive."

At very least, Retallack deserves to be taken seriously. He has made a strong case, addressing both sedimentological and palaeontological aspects. His ideas have developed over a 20 year period and, arguably, the hypotheses he has developed have been tested and upheld. Knauth is willing to approach these radical ideas with an open mind. His concluding words are to be applauded:

"So I say, until the forensic evidence for Ediacaran habitats becomes strongly compelling one way or the other, let multiple hypotheses thrive!"

The major interest to us in this blog is the question: what are the implications if Retallack is correct? First, the relationship of the Ediacaran life forms to the animals of the Cambrian Explosion will need to be reappraised. There is no way that land-based lichens could be ancestors of animals. This point is, naturally enough, brought out in media reports and other commentaries. We need only add that Darwin's dilemma is reinforced.

"This would mean that at least some Ediacarans lived on land, under the sky, perhaps in the manner of lichens, or microbial colonies that form soil crusts. The Ediacarans, then, would be the now-not-so-rare (and not at all mythical) creatures that first colonized the land - not just in puddles, but in soils indicative of a dry, cold desert. This is as far away as imaginable from the oceanic idyll that many have assumed for Ediacaran organisms, and have reconstructed as such in a million coffee-table books." (Editorial in Nature)
"This discovery has implications for the tree of life, because it removes Ediacaran fossils from the ancestry of animals," said Retallack, professor of geological sciences and co-director of paleontological collections at the UO's Museum of Natural and Cultural History. (ScienceDaily report)

Second, we should note the difficulties encountered by geologists in interpreting the depositional environment of the Ediacaran Member. Although there are many useful principles to guide interpretations, geologists also bring presuppositions and conceptual models that influence what they see and what they consider significant. The problem with the Precambrian is that it is not familiar territory. The rocks represent a history of the Earth that is not representative of the present day. Yet, uniformitarianism is a favoured dogma in the Earth sciences, and this is a problem because it restricts the range of options for interpretation. Retallack's review and evaluation of alternative interpretations is valuable, as is also his analysis of evidences supporting palaeosols in the Ediacaran Member.

Third, the colonisation of Earth by living things needs further consideration. The presently favoured scheme for interpreting Earth history is characterised by evolutionary transformation. All stories of Life on Earth appear to have evolution as the integrating theme. This always brings questions about ancestor/descendant relationships (as we have noted for the Ediacaran life forms). But does it have to be like this? An alternative perspective, discussed on numerous occasions in this blog, is a scheme based on colonisation. As a rough guide, the principle is that wherever conditions enable viable ecosystems, life forms appear to occupy those environments. The Ediacaran may be a good example: with the development of palaeosols in otherwise barren land, colonisation by lichen-like organisms took place. For other examples, follow this link.

Ediacaran life on land
Gregory J. Retallack
Nature, 493, 89-92, (03 January 2013) | doi:10.1038/nature11777

Ediacaran (635-542  million years ago) fossils have been regarded as early animal ancestors of the Cambrian evolutionary explosion of marine invertebrate phyla, as giant marine protists and as lichenized fungi. Recent documentation of palaeosols in the Ediacara Member of the Rawnsley Quartzite of South Australia confirms past interpretations of lagoonal-aeolian deposition based on synsedimentary ferruginization and loessic texture. Further evidence for palaeosols comes from non-marine facies, dilation cracks, soil nodules, sand crystals, stable isotopic data and mass balance geochemistry. Here I show that the uppermost surfaces of the palaeosols have a variety of fossils in growth position, including Charniodiscus, Dickinsonia, Hallidaya, Parvancorina, Phyllozoon, Praecambridium, Rugoconites, Tribrachidium and 'old-elephant skin' (ichnogenus Rivularites). These fossils were preserved as ferruginous impressions, like plant fossils, and biological soil crusts of Phanerozoic eon sandy palaeosols. Sand crystals after gypsum and nodules of carbonate are shallow within the palaeosols, even after correcting for burial compaction. Periglacial involutions and modest geochemical differentiation of the palaeosols are evidence of a dry, cold temperate Ediacaran palaeoclimate in South Australia. This new interpretation of some Ediacaran fossils as large sessile organisms of cool, dry soils, is compatible with observations that Ediacaran fossils were similar in appearance and preservation to lichens and other microbial colonies of biological soil crusts, rather than marine animals1, or protists.

Palaeontology: Fossils come in to land
Shuhai Xiao & L. Paul Knauth
Nature, 493, (3 January 2013) 28-29 | doi:10.1038/nature11765

Fossils found in rocks of the Ediacaran period in Australia have been previously characterized as early marine organisms. But a report suggests that these rocks are fossilized soils. So did some of these Ediacaran organisms in fact live on land, like lichens? A palaeontologist and a geologist weigh up the evidence.