Science Literature

The phenomenon of convergence has been recognised in external morphology (e.g. the streamlined shape of sharks and porpoises), structural detail (e.g. the camera-like construction of the vertebrate eye and the octopus eye), and in many other functional aspects of organisms (e.g. the echolocation systems used by bats and whales). In textbooks and popular science writing, convergence is often explained in a Darwinian way, invoking the amazing powers of natural selection. However, far from being a curiosity that pops up from time to time, convergence appears to be a pervasive feature of the living world. Championing this perspective is Professor Simon Conway Morris, an evolutionary palaeontologist from Cambridge University, who is actively contributing to debate and constructing an online database of specific examples.

Similarities between different types of animal and plant are examples of convergence (source here)

Triggering this blog is an opinion piece in EMBO Reports, where Conway Morris draws attention to remarkable examples of convergence drawn from the field of molecular biology. Whether we consider systems for sight or sound or smell, the molecules that are crucial for converting stimuli into electrical signals have some fundamental similarities. To enable vision, for example, opsins are employed throughout the animal kingdom.

"[N]ot only do [opsins] belong to the vast family of G-protein-coupled receptors (GPCRs), but it is no accident that, in ears and noses, related transmembrane proteins with the canonical seven helices are also poised to transduce noise and smells into electrical signals and ultimately awareness."

But the main point drawn by Conway Morris relates to the olfactory systems found in insects:

"One component, concentrated in the coeloconic sensilla, is tasked with detecting molecules such as alcohol and ammonia. Here, the machinery depends on the ionotropic glutamate receptors. This appears to be a classic case of co-option because not only are these receptors ancient, they also show fascinating links to synaptic receptors. However, the bulk of the olfactory capacity looks to a series of transmembrane proteins. At first glance, complete with their seven helices spanning the sensory membrane, they look reassuringly like the ever-reliable GPCRs. Except they aren't! Blink twice and then notice that these proteins are back to front so that the amino-terminal is cytoplasmic and the carboxy-terminal extracellular. This is completely opposite to the GPCRs, but surely it represents a trivial difference? On the contrary. Lurking in the insect 'nose' is a ligand-gated cation channel that at first sight looks practically identical to a GPCR but is completely unrelated."

Insects, then, display a "near perfect mimic" in this element of their olfactory systems. For Conway Morris, the interesting corollary is that replaying the tape of life does not lead to something radically different, for the end results are "very much the same". This is the first of the messages to emerge from convergence.

"With respect to the receptor protein, frankly who cares if it is a GPCR or a ligand-gated ion channel protein? They are completely unrelated, but the far more remarkable fact is that, in terms of transduction, the system evidently has no alternative. The molecule must be a seven-helix transmembrane protein; this is the molecule of choice. Evolution meets design: Darwin and Plato embrace."

Setting Darwin alongside Plato is unusual in contemporary science literature. The comment "Evolution meets design" is similarly noteworthy. What is intended here? Darwinian evolution is normally presented as a full explanation of apparent design, so most Darwinists will scratch their heads and question whether Conway Morris really understands Darwinism. An example of this follows later.

Nevertheless, the implication of Darwin embracing Plato is that these two have been apart for too long and the route to achieve reconciliation is via convergence. Darwinists have developed a perspective on evolutionary transformation that looks like a random walk. There is no direction, no goal, no over-riding architecture. The tensions between this approach and the perspective developed by Conway Morris are well expressed in his opening paragraph:

"How best to describe evolution? A drunkard's walk; a shambling billion-year spree punctuated with prat-falls, accompanied by a Beckettian mumbling? Or a sleek greyhound rippling with suppressed energy, racing along the narrow highways of the Darwinian landscape? "Mumble and shuffle" would be the answer of most biologists, but perhaps next time we open our Darwin we should also turn up The Ride of the Valkyries."

So what relevance is Plato for evolutionary biology? Plato's philosophy invoked a transcendent intelligence, and rationality was associated with mind rather than matter. Although chance and necessity have their place in the world, they are part of a bigger picture goverened by the ultimate wisdom. Plato spoke of ideal Forms which represent the essence of what we see around us. The ideal Forms represent reality; the observed objects are transient derivatives. To a critic who stated: "I see particular horses, but not horseness", Plato replied: "That is because you have eyes but no intelligence." This, then, is Plato's contribution to evolutionary biology: convergence points to an essence beyond the particulars. There is a bigger picture that can easily be missed by those who are unaccustomed to contemplating transcendence or who are ideologically opposed to the concept.

It follows that there is no substance to Gould's famous claim that replaying the tape of life would lead to a different set of organic forms. For Conway Morris, replaying the tape of life brings out the same essences - the same ideal Forms. The ubiquity of convergence guarantees it. Even if life were on other planets, it would follow the same patterns:

"Rest assured that on Threga IX - that charming little planet just to the left of Arcturus - eyes will flicker and noses will swivel beneath an alien sun. We can save ourselves all the fuss of an extremely expensive extraterrestrial excursion. In those alien eyes and noses, we can be quite certain that a seven-helix transmembrane protein will be busy telling its owner that the sunset is red and dinner is almost ready."

These issues are highly significant for two reasons. The first concerns the entrenched way Darwinians advance the concepts of randomness, accidents and improbability. At the time of writing, the New Scientist has just published an article on a gene duplication in the hominid lineage that is said to be crucial for understanding human intelligence. The accompanying editorial warms to the idea that humanity's existence is the result of accidental gene duplications. As the excerpt below shows, there is no hint here of Darwin meeting Plato. Instead, this is an example of Darwin slamming the door in Plato's face and insisting that our humanity is all in our genes.

"The more we learn about our evolutionary journey from ape to human, the more astonishing it seems. Around 3.5 million years ago, a gene involved in brain development duplicated itself in one of our ancestors. Around a million years later it did it again. The duplicate genes now play a crucial role in the design of our big, powerful brains. The double duplication joins a handful of other mutations - notably in FOXP2, also known as the "language gene" - that appear to have endowed us with uniquely human traits. It is no exaggeration to say they are the genes that make us human. On one level that is not hugely surprising. The differences between humans and chimps are obviously encoded in DNA, most likely in genes that determine brain architecture. But on another it brings home the sheer improbability of our existence. The essence of humanity largely boils down to a bunch of random mutations, every one of them happening by chance." (Source: We are the improbable ape)

The second reason for saying the issues are significant is because they have educational implications. How are teachers to handle big questions that are actively being discussed in the scientific community? These includes ultimate questions about meaning and purpose, how to understand design in the cosmos, the significance of mankind, the basis of morality and ethics, our experience of consciousness and free agency, and a host of related issues. All of these are receiving attention within scientific disciplines. Focus for a moment on the nature of humanity. Are we improbable accidents of history? Is consciousness explained (in principle) by genetics. It is not difficult to find affirmative responses to these questions coming from scientists. However, any scientists who answers with a "No!" is faced with the charge that they are religiously motivated and that their religious views have no place in the classroom. This has actually happened to Conway Morris. In 2009, he wrote a popular piece in The Guardian, saying things like:

"How to explain mind? Darwin fumbled it. Could he trust his thoughts any more than those of a dog? [. . .] After all, being a product of evolution gives no warrant at all that what we perceive as rationality, and indeed one that science and mathematics employ with almost dizzying success, has as its basis anything more than sheer whimsy. If, however, the universe is actually the product of a rational Mind and evolution is simply the search engine that in leading to sentience and consciousness allows us to discover the fundamental architecture of the universe - a point many mathematicians intuitively sense when they speak of the unreasonable effectiveness of mathematics - then things not only start to make much better sense, but they are also much more interesting. Farewell bleak nihilism; the cold assurances that all is meaningless."

This received several vigorous responses from scientists committed to naturalism (i.e. nature is all there is). One of these was Professor Jerry Coyne, who wrote a blog with the title: Simon Conway Morris becomes a creationist.

"Contra Conway Morris, there are many people who feel that consciousness is "material" in the sense that it arises from purely material causes in a material object: the brain. Understanding how and why consciousness evolved are hard problems, but to throw one's hands up in despair and say, "God made it" is a ludicrous solution. Give biologists another century of work on the brain, for goodness sake! [. . .] Conway Morris is straying from the scientific path here, but he simply can't help himself. He is a committed Christian, and has to find some way to show that the evolution of humans was inevitable."

It is not my purpose here to analyse these comments, but rather to show their relevance to education. At present, we have Coyne's view regarded by legislators and policy-makers as "science" and Conway Morris' view regarded as "religion". The truth is that both Coyne and Conway Morris have developed positions that can be defended as science, and both bring a religious worldview to their science (Coyne's is atheism, Conway Morris' is Christianity). The real problem is that atheistic scientists have gained too much influence, because they have secularised science and turned it into an instrument for promoting their naturalistic philosophy. This leaves them wide open to confirmation bias - all evidences confirm their naturalistic worldview. Education should not be a battle-ground for worldviews. Let the evidences be taught and teachers should be free to help their students examine all hypotheses with intellectual merit that address these evidences. This means a change of direction for many countries, certainly in the US and certainly in the UK. For more from Conway Morris, a short video clip is here. He argues that the world around us shows abundant signs of being structured, and invites us to consider whether we can identify worldviews that are congruent with these evidences.

Molecules of choice?
Simon Conway Morris
EMBO reports, 13, 281 (28 February 2012) | doi:10.1038/embor.2012.21

[First paragraph is quoted above]

Richard Owen is best known for naming the Dinosauria and for opposing Darwin's "On the origin of species". For the former, he is (usually) celebrated, as the name is in common usage around the world. For the latter, he is reviled as a bigot and his stance allowed subsequent generations of evolutionists to tar him as an obscurantist (although conveniently overlooking his scientific arguments). Owen's statue used to have pride of place in London's Natural History Museum (he oversaw the transfer of the natural history collections to the new South Kensington museum in 1881 and he was knighted in 1884). However, in the lead up to the bicentennial celebrations for Charles Darwin, Owen was moved and a marble statue of Darwin was put in his place. Notwithstanding this treatment, the man does not deserve to be shrouded in the mists of history. His achievements were immense, not least of which was his role in the construction of the Natural History Museum. Owen's expertise was in comparative anatomy applied to living and fossil animals, and his status is that of the best known 19th Century naturalist. Today, few know of his contribution to science by the way he approached the numerous contemporary reports of sea-monsters.

The sea serpent spotted by the crew of HMS Daedalus in 1848 (source here)

From the 1830s, Owen kept a special scrapbook containing letters and newspaper reports of sea-serpents and sea-monsters. He was at pains to point out that he did not have an axe to grind on the authenticity of the claims. He wrote to The Times saying: "I am far from insensible to the pleasure of the discovery of a new and rare animal." We should note that sea monsters were regularly spotted by mariners, that newspapers were keen to run stories on reported sightings, and that these stories captured the interest of readers.

Owen's first public comment came in 1848. The crew of HMS Daedalus was near the Cape of Good Hope when they spotted a serpent-like creature pass their ship. It was 30-40 feet long, had a mouthful of jagged teeth, a mane like a horse and it moved through the water at 15 miles per hour. Several officers witnessed the beast and when the warship arrived back in England, the captain supplied The Times with an account and they went to press on 9th October. Owen's response appeared two days later and pointed out that eye-witness accounts without physical evidence need to be treated cautiously. Without a body or body parts, the possibility of misidentification must be considered very real. The public was fascinated by the story and even the Prince Consort became curious. When Owen suggested to him that the sighting was of a large sea lion or seal, the prince described him as a "sea-serpent killer".

The following year, the Duke of Northumberland took possession of the remains of a monster. Owen identified the specimen as a Ribbon Fish.

"Building upon his growing reputation as a deflater of sea monsters, the magazine Punch ran a satirical poem which read in part, 'who killed the sea-serpent? "I", said Professor Owen'" (page 66).

Sightings continued and Owen continued to dismiss the claims that sea-monsters had been discovered. Believers considered the quality of the observers to be definitive; Owen stood by his argument that the failure to find any bones or bodies was more than an absence of evidence - it was evidence of absence. To give greater credibility to the witnesses, those who supported the veracity of sea monsters took recourse to magistrates and lawyers.

"It had become common practice with sea-serpent sightings to hurriedly collect written eyewitness reports of the events preferably before a local magistrate, lawyer or other official government representative. This was thought an acceptable way of proving the veracity of a creature's existence. Reputable witnesses backed up by the imprimatur of law could not possibly be challenged." (page 67).

As might be anticipated, Owen objected to this practice. For him, it was essential for the eye-witness accounts to be supported by physical evidence. His experience told him that eye-witnesses could be wrong. There is a link here with his museum work. Natural history is a discipline based on evidence, and museums are the places to archive evidence of interest to scholars, to educators and the public. Owen was committed to evidence-based science and he found nothing of substance in the "rival expertise of jurisprudence".

It is something of a paradox to find Owen presented here as championing evidence-based science as the antidote for speculation, whereas his critique of Darwinism is usually portrayed as Owen in speculative mode in the face of evidence-based science! No doubt there is a resolution of this paradox that vindicates Owen from inconsistency, but first we shall consider more closely one aspect of the sea-serpent controversy noted above. It is curious to find that magistrates and lawyers were approached to add their authority to eye-witness accounts of sea-serpents.

Today, we might think this a foolish practice because we know instinctively that the skills of magistrates and lawyers are unsuited to underwriting the authenticity of witnesses of sea-monsters. Yet something similar has happened in recent years when US courts have been asked to make judgments about creationism and intelligent design (ID) in science education. At stake is not just state influence over what teachers can and cannot bring before their students, but also the status of the scientific claims of creationism and ID. In particular, the Kitzmiller vs Dover case in 2005 is widely considered to have inflicted a mortal blow to the credibility of ID. The courts are being used by organisations and individuals with a secularising agenda to gain legal authority for their stance and thereby enhance their credibility. Richard Owen would not have been impressed. He would have stressed the importance of evidence-based scholarship. Scientists are supposed to be good at weighing evidences and testing hypotheses. This is where the emphasis should be placed - in education as well as in the laboratory. (for more, go here).

It is this focus on evidence-based science that explains Owen's critique of Darwinism. Despite the claim to have collected a vast array of evidence to support his theory, Darwin was regarded by many of his peers as strong on hypothesis but light on evidence. To treat any critic coming with this perspective as religiously motivated and anti-scientific is to indulge in rhetoric, not scientific discourse. Owen deserved better. There is nothing paradoxical about his cautious approach to sightings of sea-serpents and his critique of Darwin - he was consistently arguing for evidence-based science. Since rhetoric confirmed by legal judgments has become the norm in the US, the recent ruling by Tennessee State to protect teachers who introduce their students to critiques of Darwinism is justified and is to be welcomed.

Richard Owen and the sea-serpent
Brian Regal
Endeavour, Volume 36, Issue 2, June 2012, Pages 65-68 | http://dx.doi.org/10.1016/j.endeavour.2011.12.001

Abstract: The well known naturalist, Richard Owen, had a career long engagement with monstrous creatures. In the 1830s he famously christened large fossil reptiles, Dinosauria. He investigated fossil marine reptiles as well as the giant moa. He also looked into the sea-serpents and sea monsters then drawing wide public attention. He actively collected letters and analyzed correspondence on the topic, consulted with the admiralty on reports of Royal Navy encounters and sightings, and commented in the public press. He concluded that such reports were based upon misidentifications of whales and other large marine mammals, and not run-ins with mythological creatures. His work on the sea-serpent shows that rather than discount the idea out of hand, a number of high profile naturalists were intrigued by monsters and attempted to understand what they were. His work is key to understanding the skepticism over monsters held by modern mainstream science. This skepticism opened the field to later amateur investigators.

See also:

Tyler, D. Remembering Richard Owen as a "non-evolutionary biologist" (ARN Literature Blog, 8 February 2008).

Tyler, D. Evolution, Museums and Society (ARN Literature Blog, 15 November 2008).

Visitors to the Grand Canyon, and especially those who hike to Plateau Point at the end of Bright Angel Trail, will see a major change in rock type when looking into the inner canyon. The steep walls reveal metamorphosed basement rocks, but resting on these are the horizontally-bedded fresher looking Tapeats Sandstones. The linear boundary between them is known as the "Great Unconformity". There are many other unconformities to be found in the Grand Canyon, but this one is by far the most dramatic. It can be traced as far as the eye can see - and beyond. It is found on most continents:

"The Great Unconformity is well exposed in the Grand Canyon, but this geomorphic surface, which records the erosion and weathering of continental crust followed by sediment accumulation, can be traced across Laurentia and globally, including Gondwana, Baltica, Avalonia and Siberia, making it the most widely recognized and distinctive stratigraphic surface in the rock record."

The trail to Plateau Point on the Tapeats Sandstone (above the Great Unconformity) is in the foreground. A cross-section through the rocks, showing the Great Unconformity, can be seen on the other side of the inner gorge. (Source here)

Not only is the unconformity visually striking, but also it occurs at a special horizon in the rock record: above it are fossils of hard-bodied animals - the unconformity marks their first appearance all over the world. So, this feature is much more than a lithological discontinuity: it is also a faunal discontinuity known affectionately as the "Cambrian Explosion". This distinctive feature of the fossil record has engaged the minds of geologists since it was first recognised. The debate has been whether the "explosion" of life forms was an abrupt punctuation of Earth history, or whether the Great Unconformity hides an inferred record of gradual transformation. Geologists in the 19th Century were unduly influenced by James Hutton and Charles Lyell who set out a view of Earth history that involved endless cycles ("we find no vestige of a beginning, - no prospect of an end"). However, as Gould has admirably explained, geological time is more accurately represented by an arrow, the view that was advanced by some of Lyell's contemporaries.

"Lyell and the catastrophists were locked in a fascinating debate of substance about the way of our world, not a wrangle about methodological aspects of uniformity. Their struggle pitted a directional view of history as a vector leading toward cooler climates and more complex life, and fueled by occasional catastrophes, against Lyell's vision of a world in constant motion, but always the same in substance and state, changing bit by bit in a stately dance toward nowhere. This real debate, so lost at our peril in the success of Lyell's rhetoric, was the grandest battle ever fought between the visions of time's arrow and time's cycle." (page 132)

In a recent paper, two geologists have suggested that the processes involved in forming the Great Unconformity provided a trigger for the Cambrian Explosion.

"The magnitude of the unconformity is without rival in the rock record," Gaines says. "When we pieced that together, we realized that its formation must have had profound implications for ocean chemistry at the time when complex life was just proliferating." "We're proposing a triggering mechanism for the Cambrian explosion," says Peters. "Our hypothesis is that biomineralization evolved as a biogeochemical response to an increased influx of continental weathering products during the last stages in the formation of the Great Unconformity." Peters and Gaines looked at data from more than 20,000 rock samples from across North America and found multiple clues, such as unusual mineral deposits with distinct geochemistry, that point to a link between the physical, chemical, and biological effects." (Source here)

The research has examined sediments in North America overlying the Great Unconformity. These are known collectively as the Sauk sequence. The impact of erosion to produce these rocks on seawater chemistry has been assessed comprehensively. The researchers have consider all the major ionic products of weathering and different depositional environments. Carbonate sedimentation is distinctive:

"The signal of enhanced continental crustal weathering is perhaps most conspicuously expressed by precipitation of carbonate sediments, which reached a Phanerozoic peak in shelf burial flux during the Sauk transgression. In Laurentia, the large quantity of Cambrian-Early Ordovician carbonates is known as the 'Great American Bank'. Precipitation of carbonates is an important sink for alkalinity that is derived from chemical weathering." [. . .] "[Their] results are consistent with a recent model of the Cambrian carbon cycle, which demonstrated that unusually large absolute rates of carbon throughput are required to explain global carbon isotopic excursions."

Alongside the carbonate data are analyses of deposits of glauconite, a potassium-, silica-, and iron-rich mineral that is rarely formed today. These findings confirm the same narrative of extensive continental weathering and have led to the proposal of a "trigger" for the Cambrian Explosion.

"The influx of ions to the oceans also likely posed a challenge to the organisms living there. "Your body has to keep a balance of these ions in order to function properly," Peters explains. "If you have too much of one you have to get rid of it, and one way to get rid of it is to make a mineral."
The fossil record shows that the three major biominerals -- calcium phosphate, now found in bones and teeth; calcium carbonate, in invertebrate shells; and silicon dioxide, in radiolarians -- appeared more or less simultaneously around this time and in a diverse array of distantly related organisms."

Some cautionary words are now worth making. The authors have demonstrated a convincing association of changing seawater chemistry and the first appearance of a great diversity of hard-bodied animals. It is reasonable to propose connections between these observational data. The word "trigger" can be used to describe this association. However, the researchers are proposing more than this. They are claiming that the changing environment drove adaptive change in organisms such that they constructed biominerals: bones and teeth, shells and tests. This additional proposal is unsupported by evidence. Whilst we know that organisms today can extract ions from seawater and make minerals, we do not know that organisms lacking the internal systems to make minerals can adapt to changing environments and somehow develop the necessary internal systems. This is not supported by empirical work today, and any talk of it happening in the past is no more than story-telling. This approach brings the same problems as some other proposed "triggers": the higher levels of oxygenation of seawater and the evolution of eyes.

The "adaption to biomineralization" hypothesis can be tested using the data known to us. By studying the way organisms adapt to environmental change, we can assess the potential for the evolution of systems to build hard body parts. The evidence we have points to extinction rather than adaptive change: natural selection can tweak existing parameters affecting morphology and physiology, but biomineralization requires complex specified information - something that natural selection has not been able to provide. Furthermore, we know something of the life forms living before the Cambrian Explosion, and palaeontologists have found it very difficult to show any direct links between these organisms and the Cambrian animals. In 2007, Adolf Seilacher wrote: "The notion that the majority of Ediacaran fossils do not represent stem groups to modern metazoan phyla is now increasingly accepted." (source here). The Ediacaran fauna is still an enigma. A more viable hypothesis for the proposed "trigger" is that changing seawater chemistry was the reason for most of the Ediacaran species becoming extinct.

In a situation like this, where a convincing correlation has been documented but causation is in great need of critical discussion, there is a strong case for multiple working hypotheses. This is needed to remind researchers and students that proposed causation mechanisms are tentative, if not speculative. Alternatives to that suggested in this paper are urgently required. This blog has advanced an alternative perspective on understanding faunal and floral changes found in the fossil record: the concept of ecological succession constrained by environmental factors. This theme has been discussed here in the context of the Cambrian Explosion, and has appeared in numerous other blogs addressing fossilised animals and plants. The research paper discussed above developed the arguments previously advanced. The implication of pursuing the ecology hypothesis is that the fossil record is not so much a record of evolutionary transformation, but a record of colonisation of Earth environments by the diversity of living things.

Formation of the 'Great Unconformity' as a trigger for the Cambrian explosion
Shanan E. Peters & Robert R. Gaines
Nature, 484, 363-366 (19 April 2012) | doi:10.1038/nature10969

The transition between the Proterozoic and Phanerozoic eons, beginning 542 million years (Myr) ago, is distinguished by the diversification of multicellular animals and by their acquisition of mineralized skeletons during the Cambrian period. Considerable progress has been made in documenting and more precisely correlating biotic patterns in the Neoproterozoic-Cambrian fossil record with geochemical and physical environmental perturbations, but the mechanisms responsible for those perturbations remain uncertain. Here we use new stratigraphic and geochemical data to show that early Palaeozoic marine sediments deposited approximately 540-480 Myr ago record both an expansion in the area of shallow epicontinental seas and anomalous patterns of chemical sedimentation that are indicative of increased oceanic alkalinity and enhanced chemical weathering of continental crust. These geochemical conditions were caused by a protracted period of widespread continental denudation during the Neoproterozoic followed by extensive physical reworking of soil, regolith and basement rock during the first continental-scale marine transgression of the Phanerozoic. The resultant globally occurring stratigraphic surface, which in most regions separates continental crystalline basement rock from much younger Cambrian shallow marine sedimentary deposits, is known as the Great Unconformity. Although Darwin and others have interpreted this widespread hiatus in sedimentation on the continents as a failure of the geologic record, this palaeogeomorphic surface represents a unique physical environmental boundary condition that affected seawater chemistry during a time of profound expansion of shallow marine habitats. Thus, the formation of the Great Unconformity may have been an environmental trigger for the evolution of biomineralization and the 'Cambrian explosion' of ecologic and taxonomic diversity following the Neoproterozoic emergence of animals.

See also:

Evidence for a Geologic Trigger of the Cambrian Explosion, ScienceDaily (18 April 2012)

Luskin, C., Does Lots of Sediment in the Ocean Solve the "Mystery" of the Cambrian Explosion? (Evolution News & Views, 27 April 2012)

Tyler, D. Mapping the appearances of Cambrian animals, (ARN Literature blog, 23 December 2010).

It is 50 years since The Structure of Scientific Revolutions presented a radically different perspective on the way scientists carry out their work. Most readers of this book would have been familiar with the scientific method, which sets out the way science is supposed to work. But the textbook "scientific method" underplays the creative contributions provided by scientists, and Thomas Kuhn knew that the history of science provides abundant evidence showing that human factors deserve a much higher profile in our thinking. Yet he knew his book was iconoclastic:

"Kuhn was not at all confident about how Structure would be received. He had been denied tenure at Harvard University in Cambridge, Massachusetts, a few years before, and he wrote to several correspondents after the book was published that he felt he had stuck his neck "very far out". Within months, however, some people were proclaiming a new era in the understanding of science. One biologist joked that all commentary could now be dated with precision: his own efforts had appeared "in the year 2 B.K.", before Kuhn. A decade later, Kuhn was so inundated with correspondence about the book that he despaired of ever again getting any work done."

Cover for the 3rd edition (source here)

After two decades, "Structure had achieved blockbuster status". Sales were approaching a million copies and numerous foreign-language editions had been published. "The book became the most-cited academic work in all of the humanities and social sciences between 1976 and 1983." This last statistic is the key to understanding its subsequent fortune: the book was like a magnet to sociologists of science because its message was about the human face of science. Although Kuhn started his career as a physicist, he crossed over to the history and philosophy of science. What he had to say was less appealing to the science community.

The keyword for Kuhn was "paradigm". Originally, the word was used to refer to a defining example or pattern or model. Later, it was associated with a theoretical framework for understanding an aspect of the world around us. Kuhn's approach drew on both these meanings and gave them new depths.

"[Kuhn] separated his intended meanings into two clusters. One sense referred to a scientific community's reigning theories and methods. The second meaning, which Kuhn argued was both more original and more important, referred to exemplars or model problems, the worked examples on which students and young scientists cut their teeth. As Kuhn appreciated from his own physics training, scientists learned by immersive apprenticeship; they had to hone what Hungarian chemist and philosopher of science Michael Polanyi had called "tacit knowledge" by working through large collections of exemplars rather than by memorizing explicit rules or theorems. More than most scholars of his era, Kuhn taught historians and philosophers to view science as practice rather than syllogism."

Kuhn analysis was, and continues to be, a big influence on my own thinking. His first contribution was to show that incremental progress in science is only part of the story. It is a major part, and it tends to dominate the thinking of most working scientists. Kuhn explained how anomalies in theory are approached: normal science sees anomalies as problems to be solved incrementally whereas revolutionary science sees anomalies as pointers to another, better way of approaching the evidence and defining the problems. Finding that better way leads to a new conceptual framework and constitutes a scientific revolution.

Having contributed this understanding of revolutions in science, Kuhn also cast light on some of the extraordinary tussles that ensue before and after these revolutions. There are strongly worded disputes; scientists display emotion; people feel affronted! Kuhn explained that people who have developed different paradigms of understanding the evidence find it very difficult to communicate with each other. This is relevant to the mixed reception given to Kuhn's book: for some, it was door into a new appreciation of science, but it offended many operating within the positivist paradigm, as Kuhn made "a break with several key positivist doctrines".

"Most controversial was Kuhn's claim that scientists have no way to compare concepts on either side of a scientific revolution. For example, the idea of 'mass' in the Newtonian paradigm is not the same as in the Einsteinian one, Kuhn argued; each concept draws meaning from separate webs of ideas, practices and results. If scientific concepts are bound up in specific ways of viewing the world, like a person who sees only one aspect of a Gestalt psychologist's duck-rabbit figure, then how is it possible to compare one concept to another? To Kuhn, the concepts were incommensurable: no common measure could be found with which to relate them, because scientists, he argued, always interrogate nature through a given paradigm."

An ambiguous figure in which the brain switches between seeing a rabbit and a duck. (Source here)

These insights are extremely helpful when considering controversial issues in our own day. Take the issue of intelligent design, for example. During the rise of science, scholars worked with paradigms that were able to handle the concept of design in nature - and they found it everywhere. With the secularising influences of the Enlightenment came an acceptance of Deism - so design was admitted only as long as it was pushed to the beginnings of natural history. Later came the rise of materialism and naturalism and the desire to redefine science exclusively in terms of natural causation, and this has led us to the evolutionary world view and the rigid exclusion of intelligent design from science. These paradigm changes were accompanied by a failure to understand scholars with a different paradigm: hence the representation of anyone who upholds intelligent design as an advocate of anti-science and superstition.

The Kuhnian analysis is itself under fire today from people who are deeply influenced by the materialist world view. They cling to positivist emphases with a passion that is looking more and more like religious fervour. However, it is good to read this review in Nature. There are certainly areas of disagreement with Kuhn, but let us not lose sight of his masterful and insightful approach.

"Nevertheless, we may still admire Kuhn's dexterity in broaching challenging ideas with a fascinating mix of examples from psychology, history, philosophy and beyond. We need hardly agree with each of Kuhn's propositions to enjoy - and benefit from - this classic book."

In retrospect: The Structure of Scientific Revolutions
David Kaiser
Nature, 484, 164-166 (12 April 2012) | doi:10.1038/484164a

David Kaiser marks the 50th anniversary of an exemplary account of the cycles of scientific progress.

The Structure of Scientific Revolutions: 50th Anniversary Edition
Thomas S. Kuhn (with an introduction by Ian Hacking) Univ. Chicago Press: 2012. 264 pp. ISBN: 9780226458113

The quest for the Higgs boson has been headline news in the world's media, perhaps owing more to its nickname (the "God particle") than to public understanding of why it is so significant. What is not in doubt is that this attention is good for physics and good for science. With so much attention given to technology exploitation, it is important to remind ourselves that fundamental science provides the foundations for advances in technology - and we still need blue-sky research. The excitement surrounding the Higgs boson stimulated a reflective essay in Nature from science writer Heidi Ledford. The question she addresses is: "What fundamental discoveries in biology might inspire the same thrill?"

"We put the question to experts in various fields. Biology is no stranger to large, international collaborations with lofty goals, they pointed out - the race to sequence the human genome around the turn of the century had scientists riveted. But most biological quests lack the mathematical precision, focus and binary satisfaction of a yes-or-no answer that characterize the pursuit of the Higgs. "Most of what is important is messy, and not given to a moment when you plant a flag and crack the champagne," says Steven Hyman, a neuroscientist at the Broad Institute in Cambridge, Massachusetts. Nevertheless, our informal survey shows that the field has no shortage of fundamental questions that could fill an anticipatory auditorium. These questions concern where and how life started - and why it ends.""

(Source here)

The topics identified are worthy of further thought: there are serious issues that need to be explored relating to the proposed three fundamental questions. The first of these is concerned with exobiology and where life originated. The search for signs of extraterrestrial life has been a feature of so many space exploration projects. The past year has witnessed sustained interest in the string of media reports about so-called "Earth-like planets" discovered by the Kepler Mission (comment on the first rocky planet is here). This, plus on-going discussion of solar system probes, plus the possibility of discovering unusual life-forms on Earth, has the goal of finding data to inform responses to the first biological Higgs question.

"The search for extraterrestrial life can be described as one way to test "a standard model of biology", says astrobiologist Chris McKay of the NASA Ames Research Center in Moffett Field, California. "It's the model of DNA and amino acids and proteins and a genetic code," he says. "It's the common features of all biology, and the framework through which everything we know about life is based." If life fundamentally different from this standard model - perhaps relying on a wildly different biochemistry - were found on another planet, it would show that there is more than one way to produce a living system, he adds."

The second big question is "how familiar life originated on Earth". It would appear that panspermia is not currently perceived as part of the story, but the quest is "how to synthesize an evolving, replicating system from scratch". We are back to the primordial soup or something very like it (but see here). The RNA World approach is the front-runner in the minds of most researchers. RNA can encode information and catalyse chemical reactions, but researchers are working with the hypothesis that RNA could replicate itself to make possible an evolutionary pathway. Ledford interviewed Gerald Joyce of the Scripps Research Institute in La Jolla, California.

"In 2009, a paper from Joyce's lab reported the development of a system of RNA molecules that undergo self-sustaining Darwinian evolution. But enzymes and a human hand were needed to create the RNA sequences to start off the reaction, Joyce says, and so far his lab has not found conditions that would allow the system to form spontaneously. "We're still a bit challenged," he says. "But the system is running more and more efficiently all the time.""

Over and over again, it has been shown that while particular pathways of chemical evolution (abiogenesis) can be demonstrated in the lab, the reactions always need the equivalent of "enzymes and a human hand" to yield any products of interest. There are hints that these repeated failures to achieve a viable RNA World are leading to a change of direction.

"Some believe that RNA may have had a precursor. Ramanarayanan Krishnamurthy at the Scripps Research Institute, is testing novel polymers of organic chemicals that could have formed in the primordial goo, in search of those that could replicate and evolve. "RNA was not the first living entity," says Bada. "It's too complex. Something preceded RNA, and that's where the interest is right now.""

Turning to the third big question, can ageing be delayed? Higgs-like expansions of this question are: "why do we age; what pathways control it; and what are the consequences if they are switched off?" For many years, the consensus has been that the biological networks that influence ageing are highly complex and that simple interventions would achieve very little. However, Ledford draws attention to work where the mutation of a single gene in a nematode worm was successful in extending the lifespan of the organism, and another single gene mutation in mice that achieved the same outcome. Such discoveries certainly stimulate hype, but the realists in the research community know that a breakthrough is not just around the corner.

"Ageing, however, "is almost the complete inverse of the situation of the Higgs particle", reflects Thomas Kirkwood, a leader in the field at Newcastle University, UK. "Everything that we're learning tells us it's highly unlikely that we'll find a single unitary cause.""

All three of these proposals for a "biological Higgs" reveal tensions between the mind-set of the researchers and the labyrinthine complexities of the real world. The problem for the researchers is that the information-rich systems they are studying cannot be reduced to simple physics and chemistry. Until the significance of information is grasped, these research programmes will continue to flounder - despite valiant attempts to keep them alive by spinning apparent successes. Information must be recognised as a substantial entity for understanding biological systems. It is not satisfactory to invent scenarios about information being produced by natural selection acting on molecular systems - we need testable hypotheses, not story-telling.

When information issues are accepted as crucial to the science of biology, we might propose an amended trio of biological Higgs: what makes one egg turn into a fly and another into a horse? Why are we conscious? Can ageing be delayed?

And biologists should not be too keen to envy physicists - who themselves have a problem of seeking a reductionist "Theory of Everything". The search for the Higgs boson may be too closely linked to thinking that the Standard Model is the last word on the subject. Whatever the outcome, physicists are just beginning to scratch the surface in their analysis of fundamental particles. Remember, gravity is still a mystery!

The biological Higgs
Heidi Ledford
Nature, 483, 528-530, (29 March 2012) | doi:10.1038/483528a

From the opening paragraphs: Biologists may have little cause to envy physicists - they generally enjoy more generous funding, more commercial interest and more popular support. But they could have been forgiven a moment of physics envy last December when, after a week of build-up and speculation, researchers at the Large Hadron Collider (LHC) near Geneva in Switzerland addressed a tense, standing-room-only auditorium. Scientists there had caught the strongest hints yet of the Higgs boson: what some have called the 'God particle' and the final missing piece of the standard model that explains the behaviour of subatomic particles. [. . .] All this led Nature to wonder: what fundamental discoveries in biology might inspire the same thrill? We put the question to experts in various fields.

The DNA code is made up of codons (3-letter words) derived from 64 different arrangements of bases linking the two DNA strands. Yet these 64 combinations code for only 20 amino acids and a stop signal (as set out here). Thus, different codons are able to produce the same amino acid. The phenomenon is described as the genetic code having "redundancy". In the early years of molecular biology, this redundancy was perceived as an evolutionary accident, unworthy of detailed research but fortunate because it meant that any damaging effects of point mutations were cushioned. However, the evidence has been accumulating that "redundancy" is a misleading word.

"Scientists have known about this redundancy for 50 years, but in recent years, as more and more genomes from creatures as diverse as domestic dogs to wild rice have been decoded, scientists have come to appreciate that not all redundant codons are equal. Many organisms have a clear preference for one type of codon over another, even though the end result is the same. This begged the question the new research answered: if redundant codons do the same thing, why would nature prefer one to the other?" (Source here)

The ribosome in action in protein translation, assembling (and then completing) a protein step by step [=algorithmically] based on the sequence of three-letter codons in the mRNA tape and using tRNA's as amino acid "taxis" and position-arm tool-tips, implementing a key part of a von Neumann-type self replicator (Source here)

New research into protein synthesis in bacteria has shone new light on these issues. "A hidden and never before recognized layer of information in the genetic code has been uncovered by a team of scientists" using a technique called ribosome profiling. This tool allows gene activity inside living cells to be monitored, including the speed with which proteins are made.

"Ribosome profiling takes account of gene activity by pilfering from a cell all the molecular machines known as ribosomes. Typical bacterial cells are filled with hundreds of thousands of these ribosomes, and human cells have even more. They play a key role in life by translating genetic messages into proteins. Isolating them and pulling out all their genetic material allows scientists to see what proteins a cell is making and where they are in the process. Weissman and Li were able to use this technique to measure the rate of protein synthesis by looking statistically at all the genes being expressed in a bacterial cell." (Source here)

Ribosomes bind to mRNA strands and produce protein products. To do this, they have to "read" the sequence of bases and translate them into the sequence of amino acids that make up the protein. The starting point is an AUG codon. However, AUG sequences can appear elsewhere along the mRNA strand so a mechanism is needed to establish whether the AUG codon is the starting point or just a part of the coding sequence. Prokaryotes make extensive use of the Shine-Dalgarno sequence (SD sequence) within the mRNA located near the start codon. The SD sequence forms a strong bond with an anti-Shine-Dalgarno sequence in the ribosome. Consequently, once the SD-aSD bond is formed, the ribosome can readily locate the correct starting point for synthesising the protein.

The key point emerging from the new research is that "redundancy" affecting SD sequences were found to affect the rate of translation.

"By measuring the rate of protein production in bacteria, the team discovered that slight genetic alterations could have a dramatic effect. This was true even for seemingly insignificant genetic changes known as "silent mutations," which swap out a single DNA letter without changing the ultimate gene product. To their surprise, the scientists found these changes can slow the protein production process to one-tenth of its normal speed or less. [. . .] [T]he speed change is caused by information contained in what are known as redundant codons - small pieces of DNA that form part of the genetic code. They were called "redundant" because they were previously thought to contain duplicative rather than unique instructions. This new discovery challenges half a century of fundamental assumptions in biology." (Source here)

What has been discovered is that the genetic code not only has information about the sequence of amino acids, but also about the rate at which the translational machinery carries out its work. The information is about process as well as content.

"What the scientists hypothesize is that the pausing exists as part of a regulatory mechanism that ensures proper checks - so that cells don't produce proteins at the wrong time or in the wrong abundance." (Source here)

The implications of this work go far beyond bacteria. Redundancy is the wrong word! What we have here is another level of information that needs to be part of ongoing research. Are these better understood as regulatory variants? Cornelius Hunter has drawn attention to the erroneous presumption of evolutionists:

"For evolutionists this redundancy was just another biological kludge revealing nature's dysteleology. Their natural expectation was that mutations that produced no change in the amino acid sequence - the so-called synonymous mutations - would be worthless and discarded by evolution. The massive change required by evolution would come about by altering the amino acid sequences of proteins, and so the gene comparisons between species would mostly reveal mutations that did produce different amino acids - the so-called nonsynonymous mutations. It was yet another in a long line of failed expectations. In fact gene comparisons between different species [. . .] revealed that non synonymous sites are disproportionately more conserved than synonymous sites, sometimes by as much as an order of magnitude or more." (Source here)

Another blog post has raised questions about the way molecular data has been used to defend common descent. With this new understanding of the functionality of "redundant" codons, the argument must be re-visited.

"The observation that silent synonymous base-pair substitutions can be of functional relevance to gene expression may undercut an argument made often in support of common descent - that is, the argument that, in genes shared between different taxa, a higher frequency of shared synonymous (assumed to be functionally insignificant) substitutions, than would be predicted under the assumption of neutral evolution, necessarily implies common ancestry." (Source here)

If evolutionary theorists have erred in presuming the variants are meaningless apart from tracing evolutionary lineages, what paradigm could help us move forward? The answer is a paradigm that presumes functionality and keeps searching for functionality within the architecture of living cells. The Design paradigm is capable of doing this - what is needed is less polemic from those who are hostile to design and a greater appreciation that biology as a discipline suffers when design issues are not addressed fairly and openly in scientific discourse.

The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria
Gene-Wei Li, Eugene Oh and Jonathan S. Weissman
Nature, 484, 538-541, (26 April 2012) | doi:10.1038/nature10965

Protein synthesis by ribosomes takes place on a linear substrate but at non-uniform speeds. Transient pausing of ribosomes can affect a variety of co-translational processes, including protein targeting and folding. These pauses are influenced by the sequence of the messenger RNA. Thus, redundancy in the genetic code allows the same protein to be translated at different rates. However, our knowledge of both the position and the mechanism of translational pausing in vivo is highly limited. Here we present a genome-wide analysis of translational pausing in bacteria by ribosome profiling - deep sequencing of ribosome-protected mRNA fragments. This approach enables the high-resolution measurement of ribosome density profiles along most transcripts at unperturbed, endogenous expression levels. Unexpectedly, we found that codons decoded by rare transfer RNAs do not lead to slow translation under nutrient-rich conditions. Instead, Shine-Dalgarno-(SD)-like features within coding sequences cause pervasive translational pausing. Using an orthogonal ribosome possessing an altered anti-SD sequence, we show that pausing is due to hybridization between the mRNA and 16S ribosomal RNA of the translating ribosome. In protein-coding sequences, internal SD sequences are disfavoured, which leads to biased usage, avoiding codons and codon pairs that resemble canonical SD sites. Our results indicate that internal SD-like sequences are a major determinant of translation rates and a global driving force for the coding of bacterial genomes.

See also:

New Layer of Genetic Information Helps Determine How Fast Proteins Are Produced, ScienceDaily (28 March 2012)

A New Study Adds Further Depth to the Information Story, by Jonathan M. (Evolution News & Views, 30 March 2012)

Hunter, C. Here's What That New UCSF Paper Says in Plain English (And Why Evolution Needs Another Do-Over) (Darwin's God, 31 March 2012)

Hunter, C. Here is a Completely Different Way of Doing Science, (Darwin's God, 1st April 2012)

A previous blog on Devonian tetrapods remarked on their aquatic lifestyles and noted their suite of mosaic characters that make discussion of evolutionary trajectories highly speculative. Few fossils from the lower Carboniferous were known, but the diversified forms from the middle and upper Carboniferous were clearly components of terrestrial faunas. So, we find a group of aquatic amphibians in the Upper Devonian and a diversified group of terrestrial amphibians in the middle-upper Carboniferous. The puzzle is the lack of any terrestrial fossil material in the lower Carboniferous, leaving evolutionary palaeontologists little or no data to work with. The absence of evidence has been so noticeable that this part of the record has been labelled Romer's Gap (after the distinguished American palaeontologist from the last Century). In 2006, Ward et al. proposed an explanation for the lack of terrestrial fossils that invoked low concentrations of atmospheric oxygen. This, they surmised, inhibited the evolutionary development of ecosystems on land. Since that paper, more discoveries have been made in Scotland in rocks representing Romer's Gap, and "a wealth of new tetrapod and arthropod fossils" have been recovered. The inference can be made that the Romer's Gap ecosystems were not impoverished but, for various reasons, only recently have palaeontologists discovered the evidence needed to warrant this conclusion.

"Rather than beginning immediately following "Romer's Gap", we can now test the hypothesis that diversification and terrestrialization of tetrapods had been taking place during the 15 or more million years that it represents. Our discoveries and other recent new records from elsewhere certainly suggest that many tetrapod lineages have their origins much earlier than previously appreciated, and their earliest appearances may well be extended back in time as the result of further research."

Five toes found near the Scottish fishing village Burnmouth belong to the new caches of fossils. (Credit: J. Clack, Source here)

It is undoubtedly exciting to have this new data to work with. Inevitably, the question to be answered is how the new fossil data affects our understanding of Devonian and Carboniferous tetrapods. The research paper provides an initial insight and the last sentence quoted above gives the gist of the findings. What follows attempts to highlight evidences documented in the research paper. Readers should be aware that the Tournasian stage is the lowest in the Carboniferous, and above this is the Visean stage. Romer's Gap extends from the base of the Tournasian to the middle part of the Visean.

The first locality to be reported is Burnmouth. Isolated tetrapod remains have been found in several horizons.

"The most significant of these is a small (10 mm across the metapodial series) pentadactylous autopod (identity as manus or pes cannot yet be determined). [. . .] Its morphology strongly suggests that its owner was a terrestrial tetrapod. [. . .] The proportions of the metapodials and preserved phalanges, being elongate and gracile, are most similar to those of the Visean forms Silvanerpeton, Eldeceeon, and Balanerpeton, as well as the Late Carboniferous anthracosaur Gephyrostegus, all of which are usually considered to have been terrestrial."

A few metres higher in the sequence, fossil material has been found that is very similar to Crassigyrinus.

"Crassigyrinus is a large tetrapod previously known only from the late Visean and early Namurian of Scotland. The newly discovered jaw ramus is almost exactly the same size as the known specimens, has almost identical external ornamentation, and differs from the known specimens in only minor details of the internal structure. [. . .] This Burnmouth horizon confirms the presence, by this early date, of large vertebrates whose affinities are with later Carboniferous rather than Devonian forms."

The same Formation outcropping at Burnmouth appears again at Willie's Hole to the south-west. Three distinct horizons have revealed tetrapods and many other fossils. In all, there are "100 samples of large and small semiarticulated tetrapod skeletons and isolated bones". In bed 1, reference is made to a small individual that can be provisionally reconstructed. "Its proportions most closely resemble those of the Visean Silvanerpeton or the Late Carboniferous Gephyrostegus.” Bed 2 has one of the largest specimens, but it cannot be assigned to an existing genus. There are indications that this animal was a mosaic of different characters allowing some similarities with other species to be recognised: "but only further study will elucidate their relationships". Another terapod from this bed had characters "reminiscent of that of a temnospondyl"(an upper Carboniferous group).

"[. . .] only further study could confirm or refute such an assignment. If corroborated, it would represent the earliest member of the group by about 15 million years."

Other sites are mentioned more briefly, but the fossil material does not change the position already noted. The authors are confident that their discoveries reveal Romer's Gap to be a collection failure. Consequently, it is not necessary to postulate low atmospheric oxygen levels to explain the absence of fossils.

"Our new records, combined with those from trackways, suggest that tetrapods appear to have recovered relatively rapidly from the EDME [End-Devonian Mass Extinction] by the mid-Tournaisian. Fish groups had evolved, or reevolved, into new large forms (e.g., rhizodonts, lungfishes). By the mid-Visean, not only had tetrapods appeared that are usually considered terrestrial and the base of the crown group been established, but highly specialized secondarily aquatic forms had also evolved."

The important point to note is that the new finds do not reveal an evolutionary trajectory linking the Devonian forms with the Carboniferous forms. Romer's Gap does not have transitional forms but documents the earlier appearance of five-toed Carboniferous forms. As is so frequently found, new fossil finds do not document evolutionary transitions but extend the range of the more "modern" life forms. This is the pattern recognised by advocates of Punctuated Equilibria, not the pattern predicted by Darwinists. For the researchers, the real work is before them.

"These finds will allow us to put forward refined hypotheses, testable by further finds and analyses. The wealth of material from several different sites and environments will provide the opportunity to investigate the causes and consequences of the EDME. Our initial results suggest that reestablishment of at least some components of the tetrapod fauna was achieved within 10 million years. We have established that pentadactyly arose about 20 million years earlier than previously documented. Studies may now examine the interlinkage of environmental and atmospheric changes to faunal turnover, the timing of ecosystem recovery, the sequence of acquisition of terrestrial characters by tetrapods, resolution of the problems of relationships among early tetrapods (and thus the recalibration of the phylogenetic tree), and the time of appearance of crown group tetrapods, based on the presence, rather than the absence, of fossil data."

The last sentence is worthy of note. However, it is in tension with Figure 6 in their paper, which has a family tree of tetrapods. All the fossil evidence shows discontinuity, but evolutionary linkages are marked (all located within Romer's Gap) that are devoid of supporting data. We are still a long way from a science that majors "on the presence, rather than the absence, of fossil data".

Earliest Carboniferous tetrapod and arthropod faunas from Scotland populate Romer's Gap
Timothy R. Smithson, Stanley P. Wood, John E. A. Marshall, and Jennifer A. Clack.
Proceedings of the National Academy of Sciences, published 5 March 2012 | doi:www.pnas.org/cgi/doi/10.1073/pnas.1117332109

Devonian tetrapods (limbed vertebrates), known from an increasingly large number of localities, have been shown to be mainly aquatic with many primitive features. In contrast, the post-Devonian record is marked by an Early Mississippian temporal gap ranging from the earliest Carboniferous (Tournaisian and early Visean) to the mid-Visean. By the mid-Visean, tetrapods had become effectively terrestrial as attested by the presence of stem amniotes, developed an essentially modern aspect, and given rise to the crown group. Up to now, only two localities have yielded tetrapod specimens from the Tournaisian stage: one in Scotland with a single articulated skeleton and one in Nova Scotia with isolated bones, many of uncertain identity. We announce a series of discoveries of Tournaisian-age localities in Scotland that have yielded a wealth of new tetrapod and arthropod fossils. These include both terrestrial and aquatic forms and new taxa. We conclude that the gap in the fossil record has been an artifact of collection failure.

See also:

Fossil discoveries fill crucial gap in land animal evolution, by Tamera Jones (Planet Earth Online, 7 March 2012)

Fossil pushes back land-animal debut, by Devin Powell (ScienceNews: Monday, March 5th, 2012)

Tetrapod family tree looks like a bush, by David Tyler (ARN Literature blog, 29 April 2009)

Although fossil plants are well documented from the Silurian Period of Earth history, spores from land plants are known from the preceding Ordovician and Cambrian Periods. However, it is not until the Mid-Devonian that fossil forests appear in the fossil record. The Gilboa Forest from New York State was first described in the 1920s and it became known as the earliest fossil forest. It has the same status today. Only one plant was known from this forest - the Eospermatopteris, or "ancient seed fern" - thought to grow up to 10 metres above the ground. They were not woody, but they had characters that that suggest affinities with tree ferns. The original analysis reinforced the evolutionary assumption that the earliest terrestrial systems were essentially simple. Recent research has changed all this.

"Palaeoecological studies of other Devonian-period sites describe early vegetated terrestrial landscapes partitioned into a 'two-dimensional' suite of patches growing side by side, each composed of closely related plants with similar morphologies and life traits, and adapted to the same environmental conditions. This structure of Devonian landscapes has almost become a dogma in palaeobotany, but Stein and colleagues' report provides the first direct evidence that some early forests contained widely divergent groups of plants." (Meyer-Berthaud & Decombeix, 2012, 41)

New interpretation of the Gilboa fossil forest (source here)

The new findings have been made possible by a dam maintenance project that involved the removal of infill from the original quarry where the fossil forest was found. A 1200 square metre palaeosol surface has been exposed and the locations of stumps of Eospermatopteris trees have been mapped. Two other significant components of the forest have been identified. These are:

"a large rhizomatous plant (one with underground stems growing horizontally) belonging to the extinct aneurophytalean progymnosperms; and a tree with bark similar to that of the lycopsid trees that inhabited [Carboniferous] coal swamps." (Meyer-Berthaud & Decombeix, 2012, 41)

The rhizomatous plant is of great interest because secondary xylem was detected in the rhizomes, but not in the shoots. The researchers considered that the shoots were not bio-mechanically capable of self-support. Also,

"they show that the aneurophytalean subterranean system - consisting mainly of rhizomes up to 15 cm in diameter - comprised a large amount of wood and had significantly more mass than previously estimated." (Meyer-Berthaud & Decombeix, 2012, 41)

The lycopsid-like trees were clearly present, but the fossils were not well preserved. They provide, however, a faunal link with the forests of the Carboniferous Period. Diversity is clearly present in the Devonian forest ecosystems, which were "much more complex than previously thought".

The most significant element of this complexity is the "bifacial vascular cambium" that is found in so-called 'modern' trees today. The term refers to the way the central cambium divides to give off water conducting wood towards the inside and food conducting wood towards the outside (the inner layers of the bark). Although Aneurophylates are already known from other Devonian deposits, this is the time they have been shown to have secondary wood typical of both hardwood and softwood trees. Therefore two important features of 'modern' trees - bifacial cambium and secondary thickening - were present in the Devonian Period.

The evolutionary paradigm is so deeply entrenched that every pointer to complexity steers questions as to how it evolved along Darwinian lines. So, Meyer-Berthaud & Decombeix write: the finding of woody rhizomes "adds credibility to the hypothesis that, in early land plants, wood did not evolve as an adaptation for mechanical support" (p.41). One senses that a just-so story is being developed: one that is based on adaptation and the presumption that Darwinian mechanisms are necessary to establish plausibility. However, it should be asked whether an ecological perspective could provide a way forward, given that the Devonian world was very different from today.

Another finding with a bearing on ecology relates to the youthfulness of the forest: it sprang up rapidly in an environment that was tectonically unstable. Gone is the old idea of a tranquil swamp. The researchers relocate the forest close to a shoreline, and recognise "brutal episodes of seal-level rise" that repeatedly flooded the forest and covered plant life with sediment. They suggest that the sizes of the large trees were constrained by environmental disturbances and that they were potentially fast-growing. The inference is that there was little time for the accumulation of materials to form coal.

"Low-angle cross-bedded sandstones in the Gilboa region containing several Eospermatopteris levels suggest that the site was formed by recurrent, marine-influenced and possibly catastrophic, processes with a relatively high frequency of disturbance." (Stein et al. 2012. 81)

These are fascinating discoveries for anyone interested in the history of life on Earth. Wood provides evidences of modernity in the aneurophytaleans, there is unexpected complexity and Eospermatopteris trees indicate transient environments for growing followed by abrupt destruction of the forest. Further research is needed to establish whether an evolutionary framework is justified in order to understand the findings or whether an ecological framework is sufficient. At very least, we should note that the evolutionary approach has resulted in numerous surprises and significant contradictions to the expectations of researchers.

Surprisingly complex community discovered in the mid-Devonian fossil forest at Gilboa
William E. Stein, Christopher M. Berry, Linda VanAller Hernick & Frank Mannolini
Nature, 483, 78-81 (01 March 2012) | doi:10.1038/nature10819

The origin of trees by the mid-Devonian epoch (398-385 million years ago) signals a major change in terrestrial ecosystems with potential long-term consequences including increased weathering, drop in atmospheric CO2, modified climate, changes in sedimentation patterns and mass extinction. However, little is known about the ecology of early forests or how changes in early terrestrial ecosystems influenced global processes. One of the most famous palaeontological records for this time is the 'oldest fossil forest' at Riverside Quarry, Gilboa, New York, USA, discovered in the 1920s. Hundreds of large Eospermatopteris sandstone casts, now thought to represent the bases of standing cladoxylopsid trees, were recovered from a horizon that was originally interpreted as a muddy swamp. [. . .] Here we describe a 1,200 m2 map showing numerous Eospermatopteris root systems in life position within a mixed-age stand of trees. Unexpectedly, large woody rhizomes with adventitious roots and aerial branch systems identified as aneurophytalean progymnosperms run between, and probably climb into, Eospermatopteris trees. We describe the overall habit for these surprisingly large aneurophytaleans, the earliest fossil group having wood produced by a bifacial vascular cambium. The site also provides evidence for arborescence within lycopsids, extending the North American range for trees in this ecologically critical group. The rooting horizon is a dark grey sandy mudstone showing limited root penetration. Although clearly belonging to a wetland coastal plain environment, the forest was probably limited in duration and subject to periodic disturbance. These observations provide fundamental clarification of the palaeoecology of this mixed-group early forest, with important implications for interpreting coeval assemblage data worldwide.

In the shade of the oldest forest
Brigitte Meyer-Berthaud & Anne-Laure Decombeix
Nature, 483, 41-42 (01 March 2012) | doi:10.1038/483041a

The uncovering of a large soil surface preserved under sediment for 390 million years has exposed plant remains which show that the world's earliest forests were much more complex than previously thought.

See also:

World's Oldest Fossilised Forest Unearthed in NY, William Stein (Binghampton University, 28 February 2012)

Floor of Oldest Fossilized Forest Discovered: 385 Million Years Old, ScienceDaily (Mar. 1, 2012)

The abrupt appearance of Cambrian life forms in the Cambrian Period of Earth history continues to provide us with spectacular evidence of sophistication. New research on fossils recovered from petroleum exploration drill cores assigned to the Deadwood Formation of western Canada documents "a cryptic but significant diversity of Cambrian crustaceans". Previously, palaeontologists have had hints of these animals from the nonmineralised remains of minute organisms (<2mm). The new finds are of disarticulated body parts that are unambiguously crustacean, representing branchiopods, copepods and ostracods. They are part of an assemblage known as SCFs (small carbonaceous fossils). They show many signs of modernity.

"The fresh taphonomic perspective of SCFs provides the only direct evidence for sophisticated particle-handling in larger-bodied Cambrian arthropods. This characteristically crustacean-type ecology at the interface of micro- and macroscopic nutrient cycling has otherwise been loosely inferred from overall body form and the proxy record of phytoplankton diversification. The detailed adaptations described here represent the acme of Cambrian differentiation within appendages, an alternative (and potentially correlative) measure of evolving arthropod complexity to the larger-scale tagmosis that has been the focus of previous studies. In part, the new fossils reinforce a picture of early origination and subsequent conservation in crustacean form and function."

Fossil branchiopod-type limbs from the Middle Cambrian Deadwood Formation. (for detailed explanation and the PNAS source, go to Figure 3 here)

Branchiopod-type mandibles have been recovered that have overall shapes and ornamentation that are "conspicuously similar to those of branchiopod crustaceans". There are "striking similarities" with mandibles of "various extant anostracan branchiopods". These body parts are considered to be "adapted for enhanced food-grinding efficiency". The inference from the size of these parts is that these organisms had a body size of at least 10-15 mm and formed part of a more complex ecosystem than is normally envisaged for the Cambrian:

"The presence in the first and second morphotypes of a moderately sized posterior tooth and an asymmetric "tooth-groove" system points to an ecology of mixed benthic scraping and suspension feeding, as opposed to more exclusive predation or suspension feeding."

Some of the most beautifully preserved body parts are the filter plates of branchiopods that are essentially modern in form. Together with other material, the authors have reconstructed the branchiopod crustacean.

It has "a long series of filtering thoracic appendages, [and] an overall body length of at least several millimeters is likely for the more articulated arrays, although a centimetric body size is suggested by isolated filters constructed from substantially larger setae. A mixed scraping/filtering ecology (rather than a wholly planktic mode of life) is suggested by the juxtaposition of filter plates and saw-toothed armatures."

Copepod-type mandibles have been recovered where there are many "close matches" with living species.

"In particular, the prominent projecting seta is comparable in form and position to the potentially homologous "dorsal seta" (sometimes a pair of setae) found in every major order of nonparasitic copepods [i.e., Calanoida, Cyclopoida, Platycopioida, Misophrioida, Harpacticoida and Mormonilloida."

Ostracod-type mandibles closely resemble those belonging to both ostracod subgroups - the Myodocopa and Podocopa.

"The complexity and form of the gnathal edge appear to be shared in particular with halocyprid myodocopes, some of which express a similar suite of characters including a raised toothed blade with adjacent long setae, an intermediate region with a hook-shaped spine, and a protruding grinding surface."

In their discussion, the researchers draw attention to the important evidences of modernity in the fossil material. It is customary to refer to stem-group and crown-group organisms, with the latter representing life forms that have reached a mature phase of evolutionary development.

"[T]he Deadwood fossils risk being assigned to inappropriately derived positions because of their "modern" appearance but disarticulated condition. Therefore, we conservatively assign them to comparatively inclusive clades, identifying crown groups via a synapomorphy shared with a subset of the crown (. . .) Taken together, our results provide unambiguous evidence for a substantial branching by the Late Cambrian of within-crown (pan)crustacean lineages - a largely cryptic component of the Cambrian "explosion" ."

The distinction between stem-group and crown-group forms draws heavily on the presupposition of evolutionary transformation from simpler "primitive" precursors. However, there are many evidences that are not a comfortable fit within this theoretical framework. The Deadwood assemblage is a case in point. All the groups identified demonstrate modernity of form extending back to the Middle Cambrian. Evidence for stem-group characters does not exist. Sophisticated structures are apparent in the first appearance of these organisms.

"In part, the new fossils reinforce a picture of early origination and subsequent conservation in crustacean form and function."

Interestingly, this research points to an ecological (rather than an evolutionary) theoretical framework for understanding the fossil data. The authors refer to an "unanticipated ecologic turnover". This is from their concluding paragraph:

"At the same time, however, the small carbonaceous record provides evidence for unanticipated ecologic turnover. In the modern oceans, branchiopods are represented by a just a few species of small, secondarily marine cladocerans; larger forms, comparable in size to those of the Deadwood (up to ~15 mm or more) and Mount Cap (~50 mm), are now entirely nonmarine. Furthermore, modern free-living copepods are almost all much smaller than the ~5- to 10-mm (plus) Deadwood taxon. In the modern world, visual predators - especially teleost fish - drive down body size in planktic freshwater crustacean communities and strongly constrain the complex behaviors and distribution patterns of krill, a group that shares with the Cambrian branchiopods the attributes of centimetric body size, marine habitat, and (by convergence) thoracic filtering. Significantly, the Deadwood and Mount Cap fossils reveal a contrasting pattern of crustacean distribution in the comparatively "unescalated" Cambrian biosphere."

The scenario, then, is one of adaptation to changing environments, where organisms are affected by environmental factors (including predation). The adaptations do not result in evolutionary novelties, but to changes in size, lifestyles and ability to thrive in waters of different salinity. These changes are not surprising, given the phenomenon of phenotypic plasticity. If some want to describe this as "evolution", then they should note that they are working with a concept that does not begin to explain the origin of branchiopods, copepods and ostracods.

Exceptionally preserved crustaceans from western Canada reveal a cryptic Cambrian radiation
Thomas H. P. Harvey, Maria I. Velez, and Nicholas J. Butterfield
PNAS, Published online before print January 17, 2012, doi: 10.1073/pnas.1115244109

Abstract: The early history of crustaceans is obscured by strong biases in fossil preservation, but a previously overlooked taphonomic mode yields important complementary insights. Here we describe diverse crustacean appendages of Middle and Late Cambrian age from shallow-marine mudstones of the Deadwood Formation in western Canada. The fossils occur as flattened and fragmentary carbonaceous cuticles but provide a suite of phylogenetic and ecological data by virtue of their detailed preservation. In addition to an unprecedented range of complex, largely articulated filtering limbs, we identify at least four distinct types of mandible. Together, these fossils provide the earliest evidence for crown-group branchiopods and total-group copepods and ostracods, extending the respective ranges of these clades back from the Devonian, Pennsylvanian, and Ordovician. Detailed similarities with living forms demonstrate the early origins and subsequent conservation of various complex food-handling adaptations, including a directional mandibular asymmetry that has persisted through half a billion years of evolution. At the same time, the Deadwood fossils indicate profound secular changes in crustacean ecology in terms of body size and environmental distribution. The earliest radiation of crustaceans is largely cryptic in the fossil record, but "small carbonaceous fossils" reveal organisms of surprisingly modern aspect operating in an unfamiliar biosphere.

See also:

Butterfield, N. J. and Harvey, T. H. P. (2012) Small carbonaceous fossils (SCFs): a new measure of early Paleozoic paleobiology. Geology, 40(1). 71-74.

Feedback comments here.

Professor Stephen Hawking is an emerging champion of New Atheist thinking. In his A brief history of time, he intrigued readers with the comment that the discovery of a Theory of Everything would be to know "the mind of God". It has now become clear that he was using an arresting literary device and, in reality, Hawking denies the existence of God and does not think there is a cosmic mind. In the past, many cosmologists have affirmed Theistic or Deistic beliefs and atheists have been a small minority. But this situation is changing and the New Atheists have welcomed Hawking to their ranks. His track record and iconic status amply counterbalances the influence of cosmologists who believe in God. Dawkins puts it this way:

"Darwin kicked him [God] out of biology, but physics remained more uncertain. Hawking is now administering the coup de grace."

God and Stephen Hawking: Whose Design Is It Anyway? (source here)

Hawking's latest book, co-authored with Leonard Mlodinow, develops his approach to the Big Questions that people have always asked, claiming that he is presenting the findings of "science". Examples of these questions are: "What is the nature of reality? Where did all this come from? Did the universe need a Creator?" He goes on to write that the laws of physics, not the will of God, explain our universe.

"The title, The Grand Design, will suggest for many people the existence of a Grand Designer - but that is actually what the book is designed to deny. Hawking's grand conclusion is: "spontaneous creation is the reason there is something rather than nothing, why the universe exists, why we exist. It is not necessary to invoke God to light the blue touch paper and set the universe going."" (p.16)

In this short book, Professor John Lennox of Oxford University subjects Hawking's book to critical scrutiny and finds the logic very weak. Lennox does not follow the NOMA approach of Gould (Non-Overlapping Magisteria) that compartmentalises science and keeps it entirely separate from matters of faith. Lennox writes as a philosopher of science as well as a scientist and recognises there are philosophical foundations for both science and faith. He seeks to clarify these as well as to point out flaws in Hawking's approach.

"I do hope [. . .] that I have at least managed to communicate to you that the widespread belief that atheism is the default intellectual position is untenable. More than that, I hope that for many of you this investigation of Hawking's atheistic belief system will serve to confirm your faith in God, as it has mine, and that it will encourage you not to be ashamed of bringing God into the public square by joining in the debate yourself." (p.96)

Hawking does not understand Theism at all. He is always portraying God as a "God of the Gaps". In particular, when he presents the laws of physics as providing a rationale for origins, he follows it up by inferring that there is no God. It is a case of: 'If law is the explanation, then God is pushed out of being an explanation'. Theists understand things entirely differently! God is the Creator and Sustainer of all material things and he is the author of all natural laws, whether or not we understand them. Discovering more about "law" can never undermine belief in God but inevitably serves to increase our sense of awe and wonder. Hawking wants us to choose between physical law and personal agency, but these are false alternatives. Lennox uses the example of explaining the jet engine - if we were called to choose between the laws of physics or the aeronautical engineer Frank Whittle, we would consider this absurd! Lennox goes to some length to show that theories and laws cannot be appealed to as though they are creative agents - even though this concept is advanced repeatedly by scientists who seek to explain origins in this way. Hawking has not explained why there is something rather than nothing. He starts with gravity but does not explain how gravity came to exist.

"[Hawking and others like him] fail to see that their science does not answer the question as to why something exists rather than nothing, for the simple reason that their science cannot answer that question. They also fail to see that by assumption it is their atheist world-view, not science as such, that excludes God." (p.39)

Hawking presents the multiverse as the "scientific" explanation of cosmic fine tuning. Instead of reinforcing the "old idea that this grand design is the work of some grand designer", he declares that the answer of modern science is that "our universe seems to be one of many, each with different laws". This approach replaces a special, designed universe with an almost infinite spectrum of universes, in one of which we live. To claim that this is the answer of "modern science" fails to acknowledge that there are many cosmologists who reject multiverse thinking. It also pretends that a theory that is devoid of experimental validation can be labelled "science".

"What is very interesting in all of this is the impression being given to readers of The Grand Design that God is somehow rendered unnecessary by science. Yet when one examines the arguments one can see that the intellectual cost of doing so is impossibly high, since it involves an attempt to get rid of the Creator by conferring creatorial powers on something that is not in itself capable of doing any creating - an abstract theory." (p.52)

Numerous other issues are helpfully addressed by Lennox, but the last to be considered here is rationality. Science is a rational activity, as is also philosophy and theology. Lennox finds a link between all three disciplines:

"One of the fundamental themes of Christianity is that the universe was built according to a rational, intelligent design. Far from belief in God hindering science, it is the motor that drove it." (p.73)

But atheistic science reduces rationality to the firing of neurones. In the words of Francis Crick: "You, your joys and your sorrows, your memories and ambitions, your sense of personal identity and free will, are in fact no more than the behaviour of a vast assembly of nerve cells and their associated molecules." Darwin was similarly perplexed about where his worldview was leading him: "With me, the horrid doubt always arises whether the convictions of man's mind, which has been developed from the mind of the lower animals, are of any value or at all trustworthy." Mechanistic, reductionist science ultimately destroys rationality. Lennox has this comment:

"The very existence of the capacity for rational thought is surely a pointer: not downwards to chance and necessity, but upwards to an intelligent source of that capacity." (p.75)

The same issues arise with other human traits of free agency, altruism, morality and consciousness. Atheistic science is a 'universal acid' that corrodes them all away. Lennox argues that the worldview of atheism has nothing to offer us when grappling with these issues. He points the way to satisfying answers in Christian Theism. Worldview differences are again central for understanding ourselves and our place in the world.

"The crucial difference between the Christian view and Hawking's view is that Christians do not believe that this universe is a closed system of cause and effect. They believe that it is open to the causal activity of its Creator God." (p.88)

The book certainly deserves to receive the "Award of Merit" in the "2012 Christianity Today Book Awards".

Book reviewed:
God and Stephen Hawking
John C. Lennox
Lion Hudson plc, Oxford. 2011.
ISBN 978 0 7459 5549 0

In the year 2000, an international conference considered the question "What is life?" Every participant was asked to draft a definition, and every speaker was required to address the central question. According to David Abel, who was one of the speakers, no two definitions of life were the same. This finding replicated that obtained by Rizotti who, in 1996, published a book with the title Defining Life. Abel considers that definitions can be grouped into two subsets: one of which perceives life as an essentially physicochemical phenomenon, and the other has an emphasis on coded information superimposed on material systems (developing Hubert Yockey's seminal ideas).

"Yockey was among the first to realize the linear digital nature of genetic control. Many others have appreciated that life was somehow different, but could not put their finger on exactly what this difference is. Ernst Mayr argued that physics and chemistry do not explain life. Monod and Bohr argued the same. Bohr pointed out, "Life is consistent with, but undecidable from physics and chemistry." Kuppers agreed." (p.107)

Hurricane Ivan over the Gulf Coast: ordered but not self-organised (source here)

Abel's review paper argues that life manifests characteristics that cannot be explained by physicodynamics alone, whether the focus falls on chance or on necessity (natural law). This is because biological information governing life processes and organisation is essentially nonphysical.

"The most fundamental distinction is the ability of "life" to exercise formal (nonphysical) organizational and pragmatic control over its otherwise physical interactions (e.g., chemical reactions, molecular associations, electrostatic attractions/repulsions; hydrophilic/hydrophobic tendencies, phase transitions; quantum uncertainty and "information entanglement"). The formal controls are attributable specifically to Prescriptive Information (PI) and its carefully regulated algorithmic processing. More than anything else, the ability to organize, regulate and holistically manage physicodynamics into a formal meta-metabolic scheme that values and pursues staying alive is what defines the uniqueness of life." (p.108)

Some have thought that the genetics of the simplest living prokaryote provides insight into the question "What is life?" Mycoplasma genitalium has a 580-kilo-base-pair genome containing 470 genes. However, sequencing is just the first step towards understanding this free-living cell. Research has revealed unsuspected complexities in the regulation of these genes.

"The number of interacting, formally integrated layers and dimensions of life's Prescriptive Information (PI), even in the simplest known free-living organisms, is mind-boggling." (p. 108-9)

Rather than persevere with the challenge of trying to define life, Abel suggests that it is more realistic and productive to identify the distinguishing characteristic of life. Nine of these are listed. In the main, they relate to familiar characteristics: possession of a membrane, reproduction, metabolism, etc., but expressed using words that identify the biological information requirements.

"All free-living classes of archaea, eubacteria, and eukaryotes meet all nine of the above criteria. Eliminate any one of the above nine requirements, and it remains to be demonstrated whether that system could remain "alive". RNA strands, DNA strands, prions, viroids, and viruses are not free-living organisms. They fail to meet many of the above well-recognized characteristics of independent "life"." (p.109)

Having established this baseline, Abel identifies a number of issues arising from these distinctives that warrant further discussion. However, in every case, Abel counsels caution, because there have been far too many cases of scholars defending pet theories by the selective use of evidences, rather than building theory on well-grounded empirical foundations. "Science must constantly guard itself against Kuhnian paradigm ruts". First, the concept of complexity is in need of urgent clarification. Many scholars appear unable to get beyond the Shannon approach to quantification.

"The place to begin understanding the phenomenon of linear digital prescription is a study of the three different types of sequence complexity. Biologically functional linear complexity lies in the subset of Functional Sequence Complexity (FSC), not Ordered Sequence Complexity (OSC) or Random Sequence Complexity (RSC). Functional Sequence Complexity (FSC) is a linear string of monomers or composite units that collectively perform some nontrivial function. Empirical evidence of the purely spontaneous formation of such strings, especially when more than 10 loci are involved, is sorely lacking. [. . .] FSC is a succession of algorithmic selections leading to function. Selection, specification, or signification of certain "choices" in FSC sequences results only from nonrandom selection. These selections at successive decision nodes cannot be forced by deterministic cause-and-effect necessity. If they were, nearly all decision-node selections would be the same. They would be highly ordered (OSC). Moreover, the selections cannot be random (RSC). No sophisticated program has ever been observed to be written by successive coin flips where heads is "1" and tails is "0"." (p.112)

This leads us to the concept of functional information. Abel distinguishes between two subsets: descriptive (DI) and prescriptive (PI). He refers to a Mercedes automobile to clarify the distinction. DI tells us about the component parts of the car and how they operate together in a harmonious way. PI tells us how to engineer and build that Mercedes.

"Unfortunately, many semantic information theorists make the mistake of thinking of functional information solely in terms of human epistemology, and specifically description (DI). This in effect limits the meaning of "function". DI provides valued common-sense knowledge to human beings about the way things already are. Being can be described to provide one form of function. [. . . ] The term "functional information" as used in peer-reviewed naturalistic biological literature by Nobel laureate Jack Szostak et al. in 2003 can be a completely inadequate descriptor of the "how to" information - the instructions - required to organize and program sophisticated utility. Potential formal function must be prescribed in advance by Prescriptive Information (PI) via decision node programming, not just described after the fact. As its name implies, PI specifically conceives and prescribes utility." (p.114)

Whereas some consider digital information to be crucial for understanding biological evolution via Darwinian mechanisms, Abel is unimpressed. Random mutations are incapable of constructing PI, with or without natural section.

"Life crosses The Cybernetic Cut across a one-way CS (Configurable Switch) Bridge. This bridge traverses a great ravine. On one side is found all those phenomena that can be explained by physicodynamics alone. On the other side are those phenomena than can be explained only by selection for potential (not-yet-existing) function. Traffic across this bridge flows only from the nonphysical world of formalism into the physical world through the instantiation of purposeful choices. Such instantiation requires arbitrary (dynamically inert) physical configurable switch-settings and selections of physical symbol vehicles in a material symbol system." (p.116)

Some have sought an explanation of PI using the concept of self-organisation. They suggest that if snowflakes form exquisite patterns naturally, why not life? The answer is very simple. Abel points out that there is confusion here between self-ordering phenomena and self-organisation. He distinguishes two types of self-ordering phenomena: sustained and dissipative. Sustained structures include crystals and snowflakes, and dissipative structures emerge from chaos, like the vortex that forms as water runs out of a bathtub, or the order observed in a hurricane. But neither of these types of self-ordering deliver organisation. At this point, Abel's clarification of the characteristics of life sets a benchmark to guide our analysis.

"Self-ordering events occur spontaneously daily. But, they do not involve decision nodes or dynamically-inert, purposeful, configurable switch settings. No logic gates need to be programmed with self-ordering phenomena. Self-ordering events involve no steering toward algorithmic success or "computational halting". Self-ordering phenomena are purely physicodynamic and incapable of organizational attempts. Laws and fractals are both compression algorithms containing minimal complexity and information. Inanimate physicodynamics cannot exercise purposeful choices or pursue potential function. No model of undirected evolution pursues the goal of future utility." (p.120)

Even the word "system" is widely used without thinking rigorously about what a system actually is. When Abel uses the term, he is referring to a "sustained functional system" that is organised rather than ordered. As an example, consider what is intended when people talk about a weather system:

"It is merely a physicodynamic interface of wind, temperature and atmospheric pressure differential. A weather front may involve phase changes and manifest self-ordering (e.g., a hurricane); but it is not organized. It manifests no choice contingency, no purposes or goals, no accomplishment of function or utility. Weather fronts have no formal components, no computational achievements, no algorithmic optimization, and no intended purpose."(p.118-9)

Throughout the review paper, Abel draws attention to the relevance of philosophy for analysing the various approaches that have been made to answer questions about life. He points to the inadequacy of physicalism or materialism to grapple with data relating to Prescriptive Information. A different paradigm is needed which is more appropriate for engaging with the different characteristics of life.

"Materialistic presuppositional commitments are causing us to turn our backs on a rapidly growing empirical biological reality that hollers into our deaf ears, "Materialism is dead!" We will never understand life under the purely metaphysical imperative, "Physicodynamics is all there is, ever was, or ever will be". Professional philosophers of science rightly respond, "SEZ WHO?" How was that pontification scientifically determined? The scientific method itself cannot be reduced to mass and energy. Neither can language, translation, coding and decoding, mathematics, logic theory, programming, symbol systems, the integration of circuits, computation, categorizations, results tabulation, the drawing and discussion of conclusions. The prevailing Kuhnian paradigm rut of philosophic physicalism is obstructing scientific progress, biology in particular. There is more to life than chemistry. All known life is cybernetic. Control is choice-contingent and formal, not physicodynamic." (p.125)

This paper is necessary reading for all who have an interest in abiogenesis research!

Is Life Unique?
David L. Abel
Life, 2012, 2(1), 106-134 | doi:10.3390/life2010106

Abstract: Is life physicochemically unique? No. Is life unique? Yes. Life manifests innumerable formalisms that cannot be generated or explained by physicodynamics alone. Life pursues thousands of biofunctional goals, not the least of which is staying alive. Neither physicodynamics, nor evolution, pursue goals. Life is largely directed by linear digital programming and by the Prescriptive Information (PI) instantiated particularly into physicodynamically indeterminate nucleotide sequencing. Epigenomic controls only compound the sophistication of these formalisms. Life employs representationalism through the use of symbol systems. Life manifests autonomy, homeostasis far from equilibrium in the harshest of environments, positive and negative feedback mechanisms, prevention and correction of its own errors, and organization of its components into Sustained Functional Systems (SFS). Chance and necessity - heat agitation and the cause-and-effect determinism of nature's orderliness - cannot spawn formalisms such as mathematics, language, symbol systems, coding, decoding, logic, organization (not to be confused with mere self-ordering), integration of circuits, computational success, and the pursuit of functionality. All of these characteristics of life are formal, not physical.