Science Literature

It is not often that naturists complain to the BBC about people wearing clothes in one of their programmes. However, this has happened in the UK recently, after the broadcasting of scenes featuring early humans in the series "Andrew Marr's History of The World". A spokesperson said: "It is astonishing that the BBC, that once proud bastion of journalistic integrity, should be sacrificing its reputation for commercial reasons." According to the Daily Telegraph's report, "The group said that in the Exodus from Africa, Ancient Egypt, the Minoans, the Caribs, the Australian aborigines, and members of a contemporary South American tribe, the costumes were the product of the BBC censors, not history." Instead of contesting the complainants, a representative from BBC Audience Services, said he was sorry about the "compromises in accuracy". Apparently, the corporation felt "obliged" to make compromises in the production of dramatic reconstructions. "You are of course correct in pointing out that, in reality, natives in various scenes in the early part of the series would have been naked," he said. "But in making a series like this we have to take into account the sensitivities of the widest possible world audience." The throwaway phrase "of course" is worthy of critical scrutiny. We need to ask whether these comments accurately represent the findings of science. How much do we actually know about the sartorial habits of prehistoric man?

Bone tools from Cave Bay Cave, Tasmania. "These early tools raise the question of what needles were used for. The Tasmanians found by the first visitors in the 16th and later centuries went virtually naked and are not known to have had needles. It is possible (but unproven) that 22,000 years ago, at the depth of the ice age, they did have some form of clothing which they discarded when the climate warmed after 12,000 years before the present." (source here)

Scientific evidences are really quite modest. We have evidence that Cro-Magnon Man sewed skins together and protected themselves against the cold. Some figurine artefacts suggest clothing. An analysis of the DNA of clothing lice has been used to estimate a date when it originated from head louse ancestors (although this is an indirect avenue of research). An analysis of energy use by Neanderthals in Northern Europe during the mild Eem interglacial period has concluded that they needed well-fitting clothing and footwear to survive (another indirect approach to addressing the issue). We have a situation where there are few constraints for theoretical models. In such cases, presuppositions tend to take over and "just-so" stories tend to be constructed in the name of science (e.g. "how ape-like ancestors lost their body hair£ and "how clothing was first invented"). We need to recognise such explanations as expressions of preconceived ideas about human history and refrain from treating them as scientific conclusions.

One characteristic of research into prehistoric man is that the more we uncover evidence of cultural traits, the more we find the hallmarks of modernity. This is contrary to expectations if evolutionary presuppositions are on the right lines. Some recent papers illustrate this point and are briefly reviewed here.

First, the artistic abilities of Palaeolithic Man.
Several Hungarian researchers have examined prehistoric and modern artwork ranging from cave paintings of cows and elephants to statues and paintings of horses, elephants and other quadrupeds in motion. Their goal was to see how well these artistic depictions matched scientific observations of animal motion. They found that the majority of depictions of these animals walking or trotting had their legs incorrectly positioned, but the prehistoric paintings had the lowest error rates of 46.2%, whereas art prior to 1880 depicted animal motion incorrectly 83.5% of the time. This error rate decreased to 57.9% after 1887. (Source here, commentary here) The cavemen artists were keen observers of the natural world and had the technical and aesthetic skills to portay animals accurately in their paintings.

Second, the ability of Neanderthal Man to self-medicate.
Although Neanderthals have generally been portrayed as hunter/gatherers, their diet has been understood to be primarily carnivorous. However, plant eating was practised and this is where new research has come up with surprises. The researchers examined material entrapped in dental calculus from five Neanderthal individuals from the northern Spain. The abstract has this summary: "Our results provide the first molecular evidence for inhalation of wood-fire smoke and bitumen or oil shale and ingestion of a range of cooked plant foods. We also offer the first evidence for the use of medicinal plants by a Neanderthal individual. The varied use of plants that we have identified suggests that the Neanderthal occupants of El Sidron had a sophisticated knowledge of their natural surroundings which included the ability to select and use certain plants." (Source here) In the discussion, they make it clear that this evidence gives Neanderthals a remarkably modern profile:

"We propose that that the Neanderthal occupants of El Sidron, whose hypothesized, cannibalized remains were discarded at the site, had a sophisticated knowledge of their natural surroundings, and were able to recognize both the nutritional and the medicinal value of certain plants."

Third, Homo heidelbergensis artefacts provide evidence of the use of hafting technology.
It is known that both Neanderthals and early Homo sapiens made spears with hafted stone tips. It is said that this technology becomes relatively common after about 300,000 years ago. The skills for making the spear tips from stone and then attaching them to the shaft are by no means trivial. However, new research has presented "multiple lines of evidence implying that stone points from the site of Kathu Pan 1 in South Africa were hafted to form spears around 500,000 years ago. The points' damaged edges and marks at their base are consistent with the idea that these points were hafted spear tips." (Source here).
The significance of these finds is that the authors must predate those groups of humans that are known to have possessed hafting technology:

"it appears that the common ancestor of Neandertals and Homo sapiens, commonly thought to be Homo heidelbergensis, was the first to develop hafting technology. "It now looks like some of the traits that we associate with modern humans and our nearest relatives can be traced further back in our lineage"."

Fourth, evidence of cooking by Homo erectus.
Earlier this year, a team of archaeologists excavated ash of "burnt grass, leaves, brush and bone fragments in sediments 30 metres inside the Wonderwerk Cave in the Northern Cape province". The original occupants of the cave have not been clearly identified, but "the team believes it was probably Homo erectus." The ash has been inspected for signs of being washed into the cave, but the fragments appear to be in situ. This find is not unique - as other ash deposits from horizons associated with H. erectus have suggested fire for cooking. However, the Wonderwerk Cave site is the first where lightning strikes can be ruled out. Previously, many archaeologists doubted that H. erectus could ever use fire for cooking.

So, research continues to challenge the past consensus about cultural evolution. One wonders when this will lead to a new paradigm in palaeoanthropology. But for the present, we have many traditional attitudes claiming to find support from science. The naturist complaints about the lack of nakedness in portrayals of prehistoric man is just one example. So let us look a little closer at the examples they provide: "the Exodus from Africa, Ancient Egypt, the Minoans, the Caribs, the Australian aborigines, and members of a contemporary South American tribe". Of these groups, all are fully modern and had clothed ancestors. Evidences of nakedness go hand in hand with evidences for the loss of other "technologies" by people-groups. Since their migrations were in pre-historical times, there is no information about whether they were clothed or naked when they migrated. What about the "the Exodus from Africa"? This is the "out-of-Africa" theory of the origins of modern man. It is of interest that the clothing lice research has relevance to this issue, because the authors find an association between the origin of modern man and the origin of clothing lice. "Our analysis suggests that the use of clothing likely originated with anatomically modern humans in Africa and reinforces a broad trend of modern human developments in Africa during the Middle to Late Pleistocene." Therefore, a case can be made for the clothing lice departing from Africa along with the humans. Thus, even this example does not support the claims of the naturists.

And earlier in time, can anything be said? The authors of the clothes mite paper write: "Whether archaic hominins used clothing cannot be assessed from these lice and may require the collection of lice from archaic human remains, which is unlikely." Such caution is the nature of science. Nevertheless, we can remind ourselves that advances in knowledge about ancient humans show them to be culturally more advanced than has been predicted by the Darwinian evolutionists. We can have some confidence that this trend will continue and evidences of modernity will continue to be found.

Original literature sources

1. Cavemen Were Better at Depicting Quadruped Walking than Modern Artists: Erroneous Walking Illustrations in the Fine Arts from Prehistory to Today. Gabor Horvath, Etelka Farkas, Ildiko Boncz, Miklos Blaho, Gyorgy Kriska. PLoS ONE, 2012; 7 (12): e49786 | DOI: 10.1371/journal.pone.0049786

2. Neanderthal medics? Evidence for food, cooking, and medicinal plants entrapped in dental calculus. Karen Hardy, Stephen Buckley, Matthew J. Collins, Almudena Estalrrich, Don Brothwell, Les Copeland, Antonio Garcia-Tabernero, Samuel Garcia-Vargas, Marco de la Rasilla, Carles Lalueza-Fox, Rosa Huguet, Markus Bastir, David Santamaria, Marco Madella, Julie Wilson, Angel Fernandez Cortes & Antonio Rosas. Naturwissenschaften, August 2012, Volume 99, Issue 8, pp 617-626 | doi 10.1007/s00114-012-0942-0

3. Evidence for Early Hafted Hunting Technology, Jayne Wilkins, Benjamin J. Schoville, Kyle S. Brown, Michael Chazan, Science, 16 November 2012: Vol. 338, pp. 942-946 | DOI: 10.1126/science.1227608

4. Microstratigraphic evidence of in situ fire in the Acheulean strata of Wonderwerk Cave, Northern Cape province, South Africa, Francesco Berna, Paul Goldberg, Liora Kolska Horwitz, James Brink, Sharon Holt, Marion Bamford, and Michael Chazan, Proceedings of the National Academy of Sciences, 15 May 2012, 109(20), E1215-E1220 | doi:10.1073/pnas.1117620109

5. Origin of Clothing Lice Indicates Early Clothing Use by Anatomically Modern Humans in Africa. M. A. Toups, A. Kitchen, J. E. Light, D. L. Reed. Molecular Biology and Evolution, (January 2011) 28(1), 29-32 | doi: 10.1093/molbev/msq234

Professor Barry Commoner was a prominent cell biologist and became an important leader of the environmental movement. He died on 30 September 2012 aged 95. My introduction to him came whilst browsing the pages of Nature in 1968: an article with the provocative title: "Failure of the Watson-Crick Theory as a Chemical Explanation of Inheritance". This was a fascinating read, and it made me aware of the existence of high profile academics who were prepared to engage with the consensus of the day, providing a spirited assault on orthodoxy. He did not waver in his conviction that there was something seriously wrong with what was known as the "Central Dogma" of molecular biology. But he was too radical for most of his academic colleagues. Commoner found the analysis of Thomas Kuhn helpful: talking across paradigms is difficult because theoretical models are multi-factored. During a visit to the UK in 1971, he was interviewed by Martin Sherwood, who subsequently wrote:

"Barry Commoner is almost a molecular biologist's nightmare. [. . .] His attack on the central dogma has led to "backlash" from the orthodox molecular biologists. None of them has yet accepted his challenge for a public discussion. He has had difficulty in getting his material on the subject published. He likens his problems to those of anyone who, in the terms of Kuhn's theory of the structure of scientific revolutions, is attempting to change the current paradigm, or scientific world picture." (page 103, for more on Kuhn, go here)

Time Magazine cover, February 2, 1970 | Vol.95 No.5 (Source here)

The acme of his challenge came in Harper's Magazine in 2002. The article had the title "Unraveling the DNA Myth" and the tagline was: "The spurious foundation of genetic engineering". The argument could not be ignored, and it aroused the ire of the editor of Nature Genetics. The incredulity expressed in the second paragraph is hard to miss.

"In a long essay entitled "Unraveling The DNA Myth", Barry Commoner declares that the fruits of the Human Genome Project, along with other findings of modern genetics, have undermined everything geneticists thought to be true about their subject. Francis Crick's central dogma is dead, and the creaky, DNA-based edifice of genetics and biotechnology is baseless. The central dogma, according to Commoner, assumes that "an organism's genome...should fully account for its characteristic assemblage of inherited traits." He continues, arguing that "The premise, unhappily, is false. Tested between 1990 and 2001 in one of the largest and most highly publicized scientific undertakings of our time, the Human Genome Project, the theory collapsed under the weight of fact. There are far too few human genes to account for the complexity of our inherited traits." What's more, "the downfall of the central dogma...also destroyed the scientific foundation of genetic engineering."" (source here)

Commoner was an activist within the AAAS for many years, so it might be expected that Science Magazine would provide something to mark his passing. A news item appeared on 5 October: "Early Leader of Environmental Movement Dies". This brief note carried the information that Commoner was "known as an often provocative scholar", but there is little indication about what those provocative views were. Subsequently, on 23 November, Michael Egan wrote a letter on "Barry Commoner's Place in History". This majored on the thought that "Commoner's life in science offers a crucial perspective on the development of science and public life through the 20th century." His role as an champion of environmentalism was applauded.

"Commoner's Four Laws of Ecology (everything is connected to everything else, everything must go somewhere, nature knows best, and there is no such thing as a free lunch) are perhaps of more social consequence than scientific, but by the 1970s Commoner was - as TIME magazine rightly observed - a scientist "with a classroom of millions". His life and career constitute a model for science activism and social engagement. He should be remembered for his deep-seated belief in the scientist's social responsibility, his duty to the public, and his unwavering faith in an informed citizenry."

It is noticeable that Commoner's critique of the central dogma gets no mention. A careful analysis would show that his environmentalism and his rejection of the central dogma come from the same source: the conviction that life at every level is best understood as a circular system with a network of interactions. There is a unified approach to all his thinking and it is a mistake to think that the environmentalism is independent of challenges to the central dogma. It is, however, very common for people to selectively report so that the hearers get the message the reporter wants them to hear. Winston Churchill is reputed to have said: "History is written by the victors"; he knew how easy it is to pass on a coloured account of the past. The same problem is found within science - those advancing consensus ideas communicate their perspective on the issues to subsequent generations. In Commoner's case, it appears that we are supposed to remember him for his environmentalism, but his challenging views on molecular biology are either deemed best forgotten, or people have failed to realize the importance of this aspect of his life. This same air-brushing, for example, is found in his Wikipedia entry and in many obituaries.

Needless to say, the issues have not gone away. The approach of consensus scientists is to diminish the significance of the arguments advanced. The stance is always one of - we have known all this for a long time and we find no incompatibility between these data and the consensus theory. Here is the editorial in Nature Genetics again:

"And even if one takes Commoner's broader view of the central dogma, it is hard to see what the fuss is about. The often obscure path from genotype to phenotype is, of course, dependent on the protein-protein interactions that underlie alternative splicing, post-translational modification, gene silencing and epigenetic regulation, in addition to a whole host of environmental factors."

The problem is, of course, one of communication across paradigms. The consensus in molecular biology is that DNA provides a blueprint for life but, according to Commoner, the blueprint is provided by the cell as a whole. This is directly relevant to applications of knowledge: if Commoner is right, genetic therapies via DNA manipulation will always provide disappointments. Similarly, when seeking to understand inherited variations, the linear model of Watson-Crick puts all the emphasis on DNA sequences. However, Commoner's systems perspective requires us to consider biological information flows in the cell considered as a whole.

"Biologists have confronted successively - like a nest of Chinese boxes - levels of complexity ranging from the ecosystem to the internal chemistry of the cell. The last box has now been opened. According to the Watson-Crick theory, it should have contained the single source of all the inherited specificity of living organisms - DNA. It is my view that we now know that the last box is empty and that the inherited specificity of life is derived from nothing less than life itself." (Source here)

There are important issues here that Commoner held in common with many design-orientated scientists. This is not just the critiques of neodarwinian theory and the central dogma, but also the priorities for research and educational programmes. It is important to realize that these different paradigms do lead to agendas for action that have practical implications. It was Commoner's view that the Watson-Crick theory is leading us in the wrong direction. (For more on the central dogma, go here.)

"Impelled by this belief [of the fundamental importance of the Watson-Crick theory], much of current research on a wide array of biological processes, including virus infection, carcinogenesis, differentiation, memory, and the origins of life, has become a search for evidence that might bring these processes within the scope of the Watson-Crick theory. On similar grounds, the theory has begun to influence profoundly the structure of academic programmes in biology, encouraging emphasis on the supposedly universal biochemical origin of the specificity of biological processes, rather than on the diversity and complexity of the processes themselves. [. . .] If correct, the Watson-Crick theory is indeed of overriding importance to biology; conversely, if incorrect, its negative effects on the science may be equally profound." " (Source here)

Barry Commoner's Place in History
Michael Egan
Science, 23 November 2012: 338, 1028 | DOI: 10.1126/science.338.6110.1028-a

The brief announcement on these pages of Dr. Barry Commoner's passing echoed those of mainstream media outlets, which lauded his work in environmental politics ("Early leader of environmental movement dies," News of the Week, 5 October, p. 23). More important, Commoner's life in science offers a crucial perspective on the development of science and public life through the 20th century.

Wag the dogma
Editorial
Nature Genetics, 30, 343 - 344 (2002) | doi:10.1038/ng0402-343

In a recent News & Views article in Nature Genetics, David Goldstein offered that "The natural world is not famous for making life easy for human geneticists." A fair statement, although most would probably agree that at least the hard-won intellectual foundations of the field are secure. What a surprise, then, to pick up February's issue of Harper's Magazine, and to read that the entire enterprise has been revealed to be a sham.

Failure of the Watson-Crick Theory as a Chemical Explanation of Inheritance
Barry Commoner
Nature, 220, 334-340 (26 October 1968) | doi:10.1038/220334a0

Abstract: In reply to recent criticism Professor Commoner discusses current evidence in support of his conclusion that the Watson-Crick theory is an inadequate explanation of inheritance.

See also:

Commoner, B. Unraveling the DNA Myth, Harper's Magazine, Feb 2002

Sherwood, M., Compassionate Cassandra, New Scientist, 8 April 1971, 102-103.

Although there are currently 3,524 species of mosquito (Family Culicidae), there are relatively few examples of fossil species. The most recently published discovery has increased the total number to 26 species, with the earliest coming from Cretaceous amber (much to the delight of Jurassic Park enthusiasts - as these mosquitos could have sucked the blood of dinosaurs). The new fossils are from the Eocene Epoch and have been named Culiseta kishenehn and Culiseta lemniscata. They were unearthed from the Kishenehn Basin, northwestern Montana, USA. They are not in amber, but are compression fossils - the first to be identified from the genus Culiseta.

Ancient mosquito species, Culiseta kishenehn, is very similar to a species living today that spreads a deadly virus affecting horses. (Source here)

As is so often the case, the fossils can be assigned to modern-day families and genera. Speciation within genera with time means that fossils are less frequently linked with extant species. However, in this example, similarities are apparent:

"they look very similar to some living species of the same genus Culiseta", Harbach explains, "Culiseta kishenehn bears close resemblance to the living North American Culiseta melanura, which is a vector of Eastern and Western equine encephalitis viruses (EEE and WEE)".

The modern mosquito carries viruses that infect the brains of horses, causing paralysis and very often death. However, there were no horses in North America during the Eocene Epoch, so this raises questions about what blood these mosquitos drank. It appears that many living species of Culiseta feed on birds. So, says Harbach, "these ancient mosquitoes probably fed on birds too. [. . .] mosquitoes are basically opportunistic and will feed on other types of animals if their preferred hosts are unavailable."

Inevitably, discoverers of new fossils seek to locate their finds within an evolutionary context. If Culiseta shows stasis, which it does, how does this relate to other fossil mosquitos? The researchers suggest that Culiseta is "primitive" and can be interpreted as a stem group which diversified. Whilst the diversification story may be viable, we do need to be careful about the terms "primitive" and "stem group", because the Culiseta are still alive and well today!

"Extant species of Culiseta exhibit generalized features that indicate the genus is a primitive lineage of subfamily Culicinae. Culiseta may be what paleontologists refer to as a "stem group", a paraphyletic or polyphyletic assemblage of species that share features of extinct taxa."

No doubt some readers want to have more on whether mosquitos fed on dinosaur blood. This is the parting comment in the news story from the Natural History Museum:

"Since some of today's mosquitoes also feed on reptiles, could the more ancient mosquitoes have sucked from a dinosaur? Harbach says it's possible. Evidence suggests mosquitoes evolved in the Jurassic Period [. . .]. Harbach concludes, "If the early ancestral mosquitoes had already evolved to feed on blood, it is conceivable that they may have fed on dinosaurs"."

Two Eocene species of Culiseta (Diptera: Culicidae) from the Kishenehn Formation in Montana
Ralph E. Harbach & Dale Greenwalt
Zootaxa, 3530: 25-34 (2012)

Culiseta kishenehn, sp. n. and Cs. lemniscata, sp. n. (Diptera: Culicidae: Culisetini) are described from compression fossils from the 46 million year old Kishenehn shale deposits in Montana, USA. The new species appear to share features with extant species of subgenera Climacura and Culicella, respectively. The antiquity of Culiseta is examined and previously described Eocene fossil species are discussed. Eoaedes gen. n. and Aetheapnomyia gen. n. are established for Aedes damzeni PodÄ—nas and Ae. hoffeinsorum Szadziewski, two Eocene fossil species in Baltic amber.

See also:

New ancient mosquitoes, could there be blood? Natural History Museum News (19 November 2012)

For more on stasis in the fossil record of insects: harvestmen, splay-footed cricket, lacewing, stick grasshopper, Leaf insect.

Blog Alert

In 1988, Richard Lenski (of the University of Michigan) and colleagues founded 12 populations of the bacteria Escherichia coli from the same clone. Since then, the bacterial populations have been studied over thousands of generations to provide data relating to real-time experimental evolution. In 2008, Blount, Borland, and Lenski reported significant developments in the ability of E. Coli to metabolise citrate (see here). This was widely perceived as an evolutionary innovation because normal E. coli is unable to digest citrate in the presence of oxygen (although the bacterium can metabolize citrate in the absence of oxygen). In the intervening years, Blount and the research group have analyzed 29 genomes from different generations to find the mutational events that were involved in the observed changes. The research paper has now been published in the journal Nature, and the Editor's summary is as follows:

"It has been suggested that small evolutionary steps pave the way for more major evolutionary leaps - in a combination of Darwinian gradualism and saltationism - but mechanistic details have been hard to determine from natural history. Rich Lenski and colleagues have now combined full-genome sequencing and 'evolutionary replay' experiments to dissect the multi-step origin of one key innovation - the evolution of aerobic citrate-utilization in an experimental bacterial population - over more than 30,000 generations and two decades. The three-step process they unveil, in which potentiation makes a trait possible, actualization makes it manifest and refinement makes it effective, is likely to be typical of other biological revolutions such as the colonization of land by proto-tetrapods."

Zachary Blount, postdoctoral researcher in MSU's BEACON Center for the Study of Evolution in Action, led a team of researchers in documenting the step-by-step process in which organisms evolve new functions. (Credit: Courtesy of Brian Baer, source here)

The Press Release accompanying the paper suggests that it provides the key to understanding evolutionary innovation: "How Organisms Evolve New Functions: Evolution is as Complicated as 1-2-3". There are three steps, which are described as follows:

"The first stage was potentiation, when the E. coli accumulated at least two mutations that set the stage for later events. The second step, actualization, is when the bacteria first began eating citrate, but only just barely nibbling at it. The final stage, refinement, involved mutations that greatly improved the initially weak function. This allowed the citrate eaters to wolf down their new food source and to become dominant in the population.
"We were particularly excited about the actualization stage," Blount said. "The actual mutation involved is quite complex. It re-arranged part of the bacteria's DNA, making a new regulatory module that had not existed before. This new module causes the production of a protein that allows the bacteria to bring citrate into the cell when oxygen is present. That is a new trick for E. coli." " (Source here)

Probably few readers of these reports are aware that experimental evolution has provided evidence that fails to map well on to neodarwinian theory. Instead of mutations creating novel genes, they are typically degradative and sometimes essentially neutral. This was pointed out by Behe in an academic paper an in a recent blog:

"In a manuscript published a few years ago in the Quarterly Review of Biology (Behe 2010), I discussed laboratory evolution results from the past four decades up to that point, including Lenski's. His laboratory had shown clearly that random mutation and selection improved the bacterium with time, as measured by the number of progeny it could produce in a given time. He demonstrated without doubt that beneficial mutations exist and can spread quickly in a population of organisms. However, once Lenski's lab eventually identified the mutations at the DNA level (a difficult task), many of the beneficial mutations turned out to be, surprisingly, degradative ones. In other words, breaking or deleting some pre-existing genes or genetic regulatory elements so that they no longer worked actually helped the organism under the conditions in which it was grown. Other beneficial mutations altered pre-existing genes or regulatory elements somewhat."

It is of interest, consequently, to know whether a similar situation applies to the citrate-consuming E. coli. In Behe's blog, the reported mutations are considered in the light of his 2010 paper. Here is the comment on Actualisation:

"They divide the mutations conceptually into three categories: 1) potentiation; 2) actualization; and 3) refinement. "Actualization" is the name they give to the mutation that first confers a weak ability to transport citrate into the laboratory E. coli. (It turns out that the bacterium is lacking only a protein to transport citrate into the cell in the presence of oxygen; all other enzymes needed to further metabolize citrate are already present.) The gene for the citrate transporter, citT, that works in the absence of oxygen is directly upstream from the genes for two other proteins that have promoters that are active in the presence of oxygen. A duplication of a segment of this region serendipitously placed the citT gene next to one of these promoters, so the citT gene could then be expressed in the presence of oxygen. Gene duplication is a type of mutation that is known to be fairly common, so this result, although requiring a great deal of careful research to pin down, is unsurprising." "

So, in this case, the gene for citrate transportation and all other enzymes needed to metabolize citrate pre-exist. What is new is the mutation that puts the citT gene next to a suitable promoter. This was achieved via a gene duplication mutation. No new information was created, but the mutation was sufficient to activate this key gene. Blount et al. use the term "amplification mutation" to describe what happened: "Amplification mutations can alter the spatial relationship between structural genes and regulatory elements, potentially causing altered regulation and novel traits." Behe comments also refinement stage as follows:

"Further work showed this was due to multiple duplications of the mutant gene region, up to 3-9 copies. Again, gene duplication is a fairly common process, so again it is unsurprising. In another experiment Lenski and co-workers showed that increasing the concentration of the citrate transporter gene was sufficient in itself to account for the greater ability of E. coli to grow on citrate."

Analysis of the potentiation stage is different. Behe finds that degradation is the most likely mechanism for this:

"It turns out that the original E. coli they began with decades ago could not benefit from the gene duplication that brought together a citT gene with an oxygen-tolerant promoter. Before it could benefit, a preliminary mutation had to occur in the bacterium somewhere other than the region containing the citrate-metabolism genes. Exactly what that mutation was, Lenski and coworkers were not able to determine. However, they examined the bacterium for mutations that may contribute to potentiation, and speculated that "A mutation in arcB, which encodes a histidine kinase, is noteworthy because disabling that gene upregulates the tricarboxylic acid cycle." (They tried, but were unable to test this hypothesis.) In other words, the "potentiation" may involve degradation of an unrelated gene."

So, a the whole scenario involves the combination of an initial degradation mutation, making it possible for a gene duplication mutation to position the citrate transporter gene next to a promotor, followed by other gene duplication events to enhance the ability to metabolise citrate. These mechanisms do not go beyond the findings of Behe's 2010 paper - which suggests that whilst mutations can tinker with genetic systems, they cannot build them. There are no grounds here for the claim, made by the Editor of Nature, that the three-stage process documented by Blount et al. "is likely to be typical of other biological revolutions such as the colonization of land by proto-tetrapods". There is a great gulf between genetic tinkering and the engineering of complex functional systems. Neodarwinists (such as Hendrickson & Rainey, referenced below) would do well to reflect on Behe's Edge of Evolution concept and the concluding comment of his blog:

"In retrospect, the most surprising aspect of the oxygen-tolerant citT mutation was that it proved so difficult to achieve. If, before Lenski's work was done, someone had sketched for me a cartoon of the original duplication that produced the metabolic change, I would have assumed that would be sufficient - that a single step could achieve it. The fact that it was considerably more difficult than that goes to show that even skeptics like myself overestimate the power of the Darwinian mechanism."

Genomic analysis of a key innovation in an experimental Escherichia coli population
Zachary D. Blount, Jeffrey E. Barrick, Carla J. Davidson & Richard E. Lenski
Nature, 27 September 2012, 489, 513-518 | doi: 10.1038/nature11514 (pdf here)

Abstract: Evolutionary novelties have been important in the history of life, but their origins are usually difficult to examine in detail. We previously described the evolution of a novel trait, aerobic citrate utilization (Cit+), in an experimental population of Escherichia coli. Here we analyse genome sequences to investigate the history and genetic basis of this trait. At least three distinct clades coexisted for more than 10,000 generations before its emergence. The Cit+ trait originated in one clade by a tandem duplication that captured an aerobically expressed promoter for the expression of a previously silent citrate transporter. The clades varied in their propensity to evolve this novel trait, although genotypes able to do so existed in all three clades, implying that multiple potentiating mutations arose during the population's history. Our findings illustrate the importance of promoter capture and altered gene regulation in mediating the exaptation events that often underlie evolutionary innovations.

How the unicorn got its horn
Heather Hendrickson & Paul B. Rainey
Nature, 489, 504-505 (27 September 2012) | doi:10.1038/nature11487

An experiment studying bacterial populations over thousands of generations shows that a novel trait can evolve through rearrangement and amplification of a few pre-existing genes.

Rose-Colored Glasses: Lenski, Citrate, and BioLogos
Michael Behe
Evolution News & Views (13 November 2012)

See also:

How Organisms Evolve New Functions: Evolution is as Complicated as 1-2-3, ScienceDaily (Sep. 19, 2012)

The Latest From Lenski's Lab, Uncommon Descent (8 October 2012)

Innovation or Renovation? by Ann Gauger, Biologic Institute (24 September 2012)

The Central Dogma has had an enormous impact on the way genetics research has developed over the past 50 years. Basically, the dogma states that DNA genes encode mRNA, and mRNA allows proteins to be constructed, and proteins do all the work needed for cells to function. There is a linear logic here that fits into a view of the genome that is static throughout its life and provides a blueprint for life. This is how Franklin and Vondriska introduce their paper:

"Arguably the greatest postmodern coup for reductionism in biology was the articulation of the central dogma. Not since "humors" were discarded from medical practice and logic and experiment instituted as the cornerstones of physiology (which they remain today) had such a revolutionary idea transformed biology and enabled scientific inquiry. Because of its simplicity, the central dogma has the tantalizing allure of deduction: If one accepts the premises (that DNA encodes mRNA, and mRNA, protein), it seems one cannot deny the conclusions (that genes are the blueprint for life). As a result, the central dogma has guided research into causes of disease and phenotype, as well as constituted the basis for the tools used in the laboratory to interrogate these causes for the past half century."

The classic view of the central dogma of biology (source here)

In their review of these issues, Franklin and Vondriska present a systems biology perspective which makes it clear that the central dogma is deficient in numerous ways and that our understanding of living things needs extensive revision. This is an imperative drawn from scientific research and should not be regarded as just another 'point of view'.

"The past decade, however, has witnessed a rapid accumulation of evidence that challenges the linear logic of the central dogma. Four previously unassailable beliefs about the genome - that it is static throughout the life of the organism; that it is invariant between cell type and individual; that changes occurring in somatic cells cannot be inherited (also known as Lamarckian evolution); and that necessary and sufficient information for cellular function is contained in the gene sequence - have all been called into question in the last few years."

Undoubtedly, the trigger for change has been the discovery of extraordinary complexity in cellular processes as revealed by systems biology research. It is now necessary to refer to networks of interactions when explaining any aspect of cellular function. And the very existence of these networks defies the central dogma:

"However, these studies have yet to reveal an invariant relationship between structure and function. There is no code that can account for how the hierarchical structure of DNA and proteins establishes the complex genomic regulatory programs that exist in distinct differentiated cells, as there is to explain, for example, how DNA encodes RNA and RNA, protein."

Systems biology has stimulated thought about the complexity of interacting entities and processes. There is an enormous difference between a DNA gene coding for a protein, and the formation and orchestration of the infrastructure of the whole cell. Those who grasp the nettle by posing questions about cellular processes realise that we do not have the answers. Some form of organising principle must be invoked - transcending the genetic code for making proteins. The central dogma is not central enough - for the really important questions are never asked by its advocates!

"The presence of such properties suggests emergent control in the formation of the network in addition to emergent control of its function once formed. How can this emergence be measured rather than just observed? An enigma in biology is how a cell with (at least) thousands of proteins can reproducibly form and behave in the same manner without central control."

Research findings that point to the inadequacies of the central dogma are summarised in a Table and discussed in the text. It is not the purpose of this blog to precis this part of the paper, but the key issues for consideration are evident in these words by the authors:

"[W]e identify 5 ways in which "-omics" technologies are changing basic and clinical research and contributing to a revisiting of the central dogma: First, by deemphasizing the unidirectional flow of information (i.e, DNA to RNA to protein); second, by placing an emphasis on modules of genes/proteins/molecules rather than individual factors; third, by enabling the discovery and quantification of emergent properties present at different scales of information; fourth, by revealing the role of networks in biological function; and fifth, by allowing for new dimensionality in the analysis of all biological molecules."

The key point being made here is that a change in thinking about molecular biology is urgently needed. There is a tendency for people to say that the central dogma is still valid, but it needs supplementing and enhancing. This would be a mistake. The consequence of treating this as incremental learning is that fundamental questions are neglected and science suffers. Arguably, science is already suffering. The meagre results emerging from medical genetics appears to be a consequence of researchers adopting the central dogma paradigm; and there are serious concerns about the whole of GM food research because the science shows no signs of being informed by any systems thinking. Incremental learning and tweaking of the central dogma can be ruled out because the five observations discussed in the review paper demonstrate outcomes that are not predicted by the central dogma, and in some cases actually falsify the central dogma.

This conclusion has important implications for the debate about design in nature. What can be said about the organising principles within the cell? Should intelligence be invoked, or is causation naturalistic? The authors refer to an "unknown process" - which at very least implies that there is a scientific debate to be had. However, note this concluding paragraph of the paper:

"The greatest present challenge for biology is the limit of reductionism. The term systems biology itself underscores our linguistic circumscription of this problem. A system, no matter how complex, is a defined entity; it is a human creation. We conceptualize an evolvable central information unit that describes (and orchestrates) the piecewise assembly of the machine that is a cell. We conceptualize watches, even if we shun the watchmaker."

The authors are saying that by using a systems biology approach, we need to invoke the concept of a central information unit that orchestrates cellular processes. In other words, the cell looks designed and there are analogies with human creations. But they also suggest that we may choose to shun the designer. Some of us want to see the day when shunning the designer of cells is perceived to be as incoherent and as irrational as shunning the designer of a watch.

Genomes, Proteomes, and the Central Dogma
Sarah Franklin and Thomas M. Vondriska
Circulation: Cardiovascular Genetics, October 2011; 4: 576 | DOI: 10.1161/CIRCGENETICS.110.957795

Abstract: Systems biology, with its associated technologies of proteomics, genomics, and metabolomics, is driving the evolution of our understanding of cardiovascular physiology. Rather than studying individual molecules or even single reactions, a systems approach allows integration of orthogonal data sets from distinct tiers of biological data, including gene, RNA, protein, metabolite, and other component networks. Together these networks give rise to emergent properties of cellular function, and it is their reprogramming that causes disease. We present 5 observations regarding how systems biology is guiding a revisiting of the central dogma: (1) It deemphasizes the unidirectional flow of information from genes to proteins; (2) it reveals the role of modules of molecules as opposed to individual proteins acting in isolation; (3) it enables discovery of novel emergent properties; (4) it demonstrates the importance of networks in biology; and (5) it adds new dimensionality to the study of biological systems.

See also:

Tyler, D. Beyond Genes and the Central Dogma, ARN Literature Blog (14 September 2007).

Words convey meaning, and the word pseudogene conveys the sense of a gene that is a sham, that is spurious, that is phoney. It is a word that is widely used in the literature on genetics, where pseudogenes are regarded as defunct relatives of functional genes. The dominant reason for studying them is because they "provide a record of how the genomic DNA has been changed without [. . .] evolutionary pressure and can be used as a model for determining the underlying rates of nucleotide substitution, insertion and deletion in the greater genome" (Source here). Recent research has challenged this assessment of these genetic elements and the textbooks need to be revised comprehensively. Nearly everything that has been widely accepted about pseudogenes has been proven false.

"Pseudogenes were long considered as junk genomic DNA: present in the genome but non-coding and without function. However, discoveries in the ancient protist T. brucei, as well as in some metazoan, indicate that pseudogene regulation is widespread in eukaryotes. Accordingly, the moniker "pseudogene" has been challenged. Interestingly, in addition to eukaryotes, pseudogenes have also been reported from bacteria, although their function remains unknown. [. . .] Once pseudogene functions are shown to occur in all sorts of organisms, including eukaryotes and prokaryotes, the concept of pseudogene will need to be substantially modified." (p.30-31)

Comparing genomes of related organisms has been likened to reading alternative history novels, but there really is no reason why there should not also be consideration of alternative design scenarios. (source here)

In an informative review paper, Wen et al. (2012) document recent findings that warrant a radical revision of the pseudogene concept. The first line of evidence concerns conservation. We should note first that "pseudogenes are pervasive, and usually abundant, in all eukaryotic organisms." (p.27) We are not addressing a trivial aspect of genetics! Conserved pseudogenes do not fit the above claim that they "provide a record of how the genomic DNA has been changed without [. . .] evolutionary pressure."

"[C]omparative analysis of processed pseudogenes in the mouse and human genomes has surprisingly demonstrated that 60% of the processed pseudogenes are conserved in both mammalian species. The high abundance and conservation of the pseudogenes in a variety of species indicate that selective pressures preserve these genetic elements, and suggest that they may indeed perform important biological functions." (p.27)

The second line of evidence is that many examples of functionality have been documented.

"Evidence of expression of pseudogenes has been demonstrated not only in animals but also in plants, such as Arabidopsis (2-5%) and rice (2-3%). The issue arises, if pseudogenes are dysfunctional, why are they so highly expressed? Two possibilities may explain it. One possible explanation is that these pseudogenes are only incidental by-products in the transcription events of other genes, because they are under the effect of the same promoters. An alternative explanation, which we are more inclined to accept, is that the pseudogene transcripts are in fact functional but not random products. More and more accumulating examples support this alternative explanation." (p.28)

Three distinct types of functionality have been documented. These are: natural antisense suppression, RNA interference and gene competitors. Antisense suppression was first proposed in 1986 and first documented in 1992. The regulatory potential of the pseudogene was established. More cases followed, demonstrating that it was not an isolated instance. "These results suggested that antisense binding is an important pseudogene modulation pathway." (p.28.

The RNA interference (RNAi) pathway has been found in many eukaryotes, the first being reported in 2008. The pseudogene is involved in the production of small interference RNAs or microRNAs. The authors write:

"Recently, we established a library of small RNAs (<30 nt) from the bloodstream forms of Trypanosoma brucei by high through-put sequencing, and identified a large fraction of small RNAs derived from the pseudogenes by pairing with complementary transcripts. Ensuing experimental results proved that these pseudogene-derived siRNAs suppressed the expression of their homological protein-coding genes by RNAi. This discovery in an ancient protist, as well as similar discoveries in mouse and plants, indicates that pseudogene-RNAi regulation must have evolved early and thus be widely spread among eukaryotes." (p.28)

Regarding gene competitors, the authors explain that pseudogenes have been shown to act as endogenous competitive RNAs to their cognate genes. "Pseudogenes can perform not only as decoys of stabling/decaying factors but also as small inhibitors." (p.28) An example is cited that has a bearing on our understanding of some cancers.

There is also a fourth category of pseudogene activity: they actually do code for an active product, but researchers have difficulty detecting this using conventional methodologies. This is because the coding only takes place in special circumstances (such as within a cancerous cell).

"Results from the [proteomic mass spectrometry] analysis in mouse has disclosed nine processed pseudogenes that display unique peptide sequences suggesting that they are translated into proteins. Altogether, these results indicate that the discovery of pseudogene functions depends on the skills and methodologies used. Many expressed pseudogenes remain to be annotated. We believe that more and more functional pseudogenes will be discovered as novel biological technologies are developed in the future." (p.31)

This review paper explains that we are just beginning to understand the role pseudogenes play in cells. It seems utterly foolish for people to carry on writing about pseudogenes as though none of this research has taken place. With hindsight it appears obvious that we ought to have presumed functionality and not allowed ourselves to be led by a blind dogma that assigns a "junk" status based on a presumed evolutionary history. Those people who persist in using pseudogenes as an argument against design in living things are only showing their ignorance of contemporary research and betraying the fundamental principles of science.

Pseudogenes are not pseudo any more
Yan-Zi Wen, Ling-Ling Zheng, Liang-Hu Qu, Francisco J Ayala and Zhao-Rong Lun
RNA Biology, Volume 9, Issue 1, January 2012, Pages 27 - 32.
http://dx.doi.org/10.4161/rna.9.1.18277

Abstract: Recent significant progress toward understanding the function of pseudogenes in protozoa (Trypanosoma brucei), metazoa (mouse) and plants, make it pertinent to provide a brief overview on what has been learned about this fascinating subject. We discuss the regulatory mechanisms of pseudogenes at the post-transcriptional level and advance new ideas toward understanding the evolution of these, sometimes called "garbage genes" or "junk DNA", seeking to stimulate the interest of scientists and additional research on the subject. We hope this point-of-view can be helpful to scientists working or seeking to work on these and related issues.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

See also:

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

Blog Alert

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

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

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

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

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

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

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

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

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

Priapulus caudatus (source here)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

See also:

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

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

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

The reconstructed model of Kulindroplax perissokomos (source here).

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

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

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

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

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

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

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

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

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

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

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

See also:

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

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