Science Literature

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.

Hot on the heels of an arthropod with complex compound eyes from the Emu Bay Shale (in Australia) has come an even more dramatic discovery! The same lagerstatten has yielded some fossil eyes, attributed to Anomalocaris, that show just how much 'modernity' can be traced back to the Cambrian fauna.

"The number of ommatidia in the Anomalocaris eyes would almost certainly have greatly exceeded the count based on the exposed surface of the eye alone. [. . .] the total count could be substantially greater than the observed 16,000+ lenses. If this is indeed the case, few living arthropods have as many ommatidia, and these eyes would certainly have functioned with a high degree of acuity. [. . .] Throughout the geological history of Arthropoda, compound eyes have rarely exceeded this size; very large Siluro-Devonian pterygotid eurypterids and some Jurassic thylacocephalans represent some of the rare examples with eyes larger than those of Anomalocaris."

Anomalocaris and its compound eyes (source here)

Inevitably, this raises questions about the way the evolution of compound eyes has been presented in the past. Plots of ommatidia density vs geological time have been used to defend gradualism. However, most of the data was related to trilobites, which are dominated by benthic forms in the Lower Cambrian, diversifying to include nektonic species in the Late Cambrian and subsequent Periods. Now that the eyes of nektonic animals are being discovered and documented, the picture looks rather different. A whole range of eye designs were present during the Early-Middle Cambrian.

"The eyes of Anomalocaris expand the known diversity of visual adaptations in the early Cambrian: low-resolution organs with >100 ommatidia (eodiscoid trilobites), higher-resolution eyes with a distinct bright zone that might have functioned in low light, and very large eyes with a uniformly dense visual field adapted to bright environments."

It should always be remembered that eye complexity means nothing without neuronal processing capability. Light signals have to be transmitted, analysed and decoded as visual images. Modernity in these aspects must be inferred also.

"The very large size of anomalocaridid compound eyes and the visual acuity inferred from the elevated lensnumber and low interommatidial angles suggest that processing of visual information would have required the optic neuropils and brain to be of comparable complexity to crown-group (that is, modern) arthropods. In the crown group, two optic neuropils are reconstructed in the most recent commonancestor, transmitting to a protocerebrum with a median unpaired neuropil, the central body."

Discoveries like this create major challenges for advocates of Darwinian gradualism. Again and again, the source of novelty is pushed earlier into the undocumented past. Gradualism as a working concept is sustained, not by data, but by inference - but the gaps available for gradualist change are ever shrinking!

"Dense, hexagonal packing of ommatidia in compound eyes has been demonstrated to have been unequivocally present in Schinderhannes bartelsi, a Devonian species resolved as the immediate sister group to the arthropod crown group. The eyes of Schinderhannes resemble those of Anomalocaris in being large, stalked, having an ovoid outline of the visual surface, and a highly elevated number of lenses. The finding that Anomalocaris, resolved more basally than Schinderhannes in the arthropod stem group, possesses the same kind of ommatidial packing as in Schinderhannes and crown-group arthropods pushes the origin of compound eyes further down the arthropod stem group. As such, compound eyes evolved earlier than the origin of a hardened tergal exoskeleton and biramous trunk limbs (the latter characters being present in Schinderhannes but not anomalocaridids). We infer that the stalked eyes of all Radiodonta (that is, anomalocaridids) are arthropod-type compound eyes."

The same general analysis applies to all the evolutionary stories that are developed around the fossil record. As in so many research papers, the evolutionary comments are tacked on and are little more than table-talk. The last sentence of the abstract and the last sentence of the paper make the same point: the sophisticated visual system of Anomalocaris would have the consequence of enhancing selection pressures and "probably helped to accelerate the escalatory 'arms race' that began" with the Cambrian fauna.

However, justification of the 'arms race' and the way it is supposed to affect the course of evolution is left to the imagination. As an alternative scenario, consider an ecological perspective. The more we know of Cambrian faunas, the more we are finding evidence of ecosystems adapting to environmental change over time. The changes documented in the fossil record are better explained by reference to ecological concepts combined with the phenomenon of phenotypic plasticity.

Acute vision in the giant Cambrian predatorAnomalocaris and the origin of compound eyes
John R. Paterson, Diego C. Garcia-Bellido, Michael S. Y. Lee, Glenn A. Brock, James B. Jago & Gregory D. Edgecombe
Nature, 480, 237-240 (08 December 2011) | doi:10.1038/nature10689

Until recently, intricate details of the optical design of non-biomineralized arthropod eyes remained elusive in Cambrian Burgess-Shale-type deposits, despite exceptional preservation of soft-part anatomy in such Konservat-Lagerstatten. The structure and development of ommatidia in arthropod compound eyes support a single origin some time before the latest common ancestor of crown-group arthropods, but the appearance of compound eyes in the arthropod stem group has been poorly constrained in the absence of adequate fossils. Here we report 2-3-cm paired eyes from the early Cambrian (approximately 515 million years old) Emu Bay Shale of South Australia, assigned to the Cambrian apex predator Anomalocaris. Their preserved visual surfaces are composed of at least 16,000 hexagonally packed ommatidial lenses (in a single eye), rivalling the most acute compound eyes in modern arthropods. The specimens show two distinct taphonomic modes, preserved as iron oxide (after pyrite) and calcium phosphate, demonstrating that disparate styles of early diagenetic mineralization can replicate the same type of extracellular tissue (that is, cuticle) within a single Burgess-Shale-type deposit. These fossils also provide compelling evidence for the arthropod affinities of anomalocaridids, push the origin of compound eyes deeper down the arthropod stem lineage, and indicate that the compound eye evolved before such features as a hardened exoskeleton. The inferred acuity of the anomalocaridid eye is consistent with other evidence that these animals were highly mobile visual predators in the water column. The existence of large, macrophagous nektonic predators possessing sharp vision - such as Anomalocaris - within the early Cambrian ecosystem probably helped to accelerate the escalatory 'arms race' that began over half a billion years ago

See also:

Marshall, M. First top predator was giant shrimp with amazing eyes, New Scientist (7 December 2011)

The earliest example of a domestic dwelling built from bone has been discovered in the Ukraine. The structure is considered to be 44,000 years old and the builders were Neanderthals. The significance of this is that Neanderthals are supposed to be lacking in creativity and aesthetics, so they are usually portrayed as pragmatists dwelling in caves and rock shelters, largely devoid of characteristics we associate with humanity. Yet again, the evidence base shows the iconic Neanderthal to be a figment of the imagination.

"Neandertals are stumping for bragging rights as the first builders of mammoth-bone structures, an accomplishment usually attributed to Stone Age people. Humanity's extinct cousins constructed a large, ring-shaped enclosure out of 116 mammoth bones and tusks at least 44,000 years ago in West Asia, say archaeologist Laetitia Demay of the National Museum of Natural History in Paris and her colleagues. The bone edifice, which encircles a 40-square-meter area in which mammoths and other animals were butchered, cooked and eaten, served either to keep out cold winds or as a base for a wooden building." (source here)

Caves are portrayed as dwelling places and burial locations for Homo neanderthalensis. This scene is from Hannover Zoo. (Source here)

Finding a building made of mammoth bones is suggestive of a lifestyle that involved creativity, forward planning, cooperation and language. To build a dwelling is suggestive of them living in one place for extended periods of time. In addition, many of the bones had been decorated with carvings and ochre pigments, revealing an aesthetic sense in Neanderthals. Here is a selection of comments from Laetitia Demay, who led the research:

"It appears that Neanderthals were the oldest known humans who used mammoth bones to build a dwelling structure.
"This mammoth bone structure could be described as the basement of a wooden cover or as a windscreen.
"Neanderthals purposely chose large bones of the largest available mammal, the woolly mammoth, to build a structure.
"The mammoth bones have been deliberately selected - long and flat bones, tusks and connected vertebrae - and were circularly arranged.
"The use of bones as building elements can be appreciated as anticipation of climatic variations. Under a cold climate in an open environment, the lack of wood led humans to use bones to build protections against the wind."

People have been talking about revising our assessment of Neanderthals for some time now, but we still find them portrayed as brutish; still as sub-human; still as making noises to communicate rather than using speech. In a report on the research, Richard Gray says that the new finds "add to the growing view that Neanderthals were in fact quite advanced humans who had their own culture and may have even used language to communicate". Another comment is provided by Simon Underdown, an academic who researches Neanderthals at Oxford Brookes University, who said:

"It's another piece in the newly emerging Neanderthal jigsaw puzzle. Far from being the stupid cavemen of popular image it's becoming increasingly clear the Neanderthals were a highly sophisticated species of human. We can now add shelter building to the list of advanced behaviours that includes burying the dead, spoken language, cooking and wearing jewellery."

What is it that stops us thinking that Neanderthals were humans like us? For more on this, and an answer, go here.

Mammoths used as food and building resources by Neanderthals: Zooarchaeological study applied to layer 4, Molodova I (Ukraine)
Laetitia Demay, Stephane Pean, Marylene Patou-Mathis
Quaternary International, In Press, Available online 26 November 2011

Abstract: Considering Neanderthal subsistence, the use of mammoth resources has been particularly discussed. Apart from procurement for food, the use of mammoth bones as building material has been proposed. The hypothesis was based on the discovery made in Molodova I, Ukraine (Dniester valley). In this large multistratified open-air site, a rich Mousterian layer was excavated. Dated to the Inter-Pleniglacial (MIS 3), it has yielded 40 000 lithic remains associated with ca. 3000 mammal bones, mostly from mammoth. Several areas have been excavated: a pit filled with bones, different areas of activities (butchering, tool production), twenty-five hearths and a circular accumulation made of mammoth bones, described as a dwelling structure set up by Neanderthals. Attested dwelling structures made of mammoth bones are known in Upper Paleolithic sites, from Ukraine and Russia, attributed to the Epigravettian tradition. [. . .] Based on anthropogenic marks, mammoth meat has been eaten. The presence of series of striations and ochre on mammoth bones are associated with a technical or symbolic use. Furthermore, mammoth bones have been deliberately selected (long and flat bones, tusks, connected vertebrae) and circularly arranged. This mammoth bone structure could be described as the basement of a wooden cover or as a wind-screen. The inner presence of fifteen hearths, lithic artifacts and waste of mammal butchery and cooking is characteristic of a domestic area, which was probably the centre of a residential camp recurrently settled. It appears that Neanderthals were the oldest known humans who used mammoth bones to build a dwelling structure.

Most biological students think that adaptive radiations and Darwinism go together, and that the mechanisms of genetic mutation and natural selection explain all the data. However, in most cases, this explanation is assumed and not supported by evidence. It is assumed because of the dominance of neodarwinism in evolutionary biology and because students are very impressed with the "mountains of evidence" claimed to support the consensus. Happily, there are some biologists prepared to step outside the paradigm, and one of them is Austin Hughes from the University of South Carolina. In preparing the ground for his iconoclastic analysis, he writes:

"I will refer to this mechanism as the Neo-Darwinian mechanism; and, following general usage, I will refer to an allele that has been fixed by this process as one that has been fixed by positive Darwinian selection. The Neo-Darwinian mechanism is often assumed by biologists to be the only source of adaptive traits of organisms, to the point where 'adaptive evolution' and 'positive (Darwinian) selection' are treated as interchangeable terms in the literature."

Cichlids are a textbook example of rapid speciation - but not of Darwinian evolution! (For more, go here. Image source here)

Also, by way of preparation, he refers to the significant theoretical and evidential base for neutral evolution (Kimura, 1976). There is a phenomenon known as genetic drift involving neutral or nearly neutral mutations. There are mechanisms for fixing these genetic changes - all invisible to natural selection. These are considered to be more important than we realise, evidenced by the continuing scarcity of advantageous mutations. This was recognised in 1976 and it continues to this day.

"In the ensuing decades, a vast amount of molecular sequence data, including complete genome sequences of many organisms, has become available to test for the evidence of positive selection at the molecular level. However, the number of well-established cases has not increased greatly in comparison with those known in the mid-1970s. It is true that a very large number of papers have been published in recent years purporting to show evidence of positive selection on the basis of various statistical methods. However, the vast majority of these cases cannot be considered well established. [. . .] Moreover, in almost all of the putative cases of positive selection identified by statistical analysis of sequence data alone, the biological basis of the supposed selection and even the phenotypic effects, if any, of the supposedly selected nucleotide substitutions have not been addressed."

Hughes has previously pointed out difficulties in identifying evidence for positive selection, yet there appears to be plenty of evidence for purifying selection (the elimination of deleterious variants).

"The predominance of purifying selection was predicted by Kimura and Ohta (1974), and the fact that their prediction has been proved to be correct is the cornerstone of many routine methods of modern bioinformatics, whereby evolutionary conservation of a sequence element (the consequence of purifying selection) is taken as evidence of that element's functional importance."

So, in view of the meagre evidential support for "the Neo-Darwinian mechanism", Hughes turns his attention to the thought that adaptive phenotypes might arise by alternative routes. This has been considered by a few other authors, but the field is wide open. Consequently, Hughes proposes one such mechanism: the plasticity - relaxation - mutation (PRM) mechanism. He argues that the evidential base for this concept is already in existence in the biological literature.

"I examine some predictions of this theory and summarize evidence relating to those predictions. The present hypothesis does not deny that the Neo-Darwinian mechanism operates in certain cases. Rather, based on what we can learn from the known cases of positive selection, I conclude that the phenomenon of positive selection may be of relatively minor importance in phenotypic evolution. Instead, phenotypic plasticity and changes in the direction and nature of purifying selection, combined with the chance fixation of neutral or nearly neutral mutations, are proposed to be the major factors in the evolution of adaptive phenotypes."

Much of the paper provides clarification of the PRM mechanism and justifies the claim that the concept has a track record in the literature. The emerging scenario is that organisms typically have an ability to adapt to environmental inputs in ways that change and fix the phenotype. This is a variability that does not depend on mutations for new genetic information, although mutations may be involved in the fixing of the phenotype. The genomic architecture is already present that supports adaptation in a variety of directions. Influences may come from neutral mutations and genetic drift, and they may involve epigenetic mechanisms. After reviewing a variety of evidences, Hughes concludes:

"The PRM mechanism provides unification to the biological sciences by uniting observations at the genomic level (where purifying selection and genetic drift predominate) with those at the phenotypic level (where adaptive characters are well known). As mentioned above, some known examples are suggestive of the action of the PRM mechanism, but it is not yet known how widespread this mechanism is. However, I would predict that the PRM mechanism is likely to be a major mechanism for the origin of evolved adaptations, and perhaps more common than the Neo-Darwinian mechanism."

Let's look at some of the applications of the PRM concept.
First, a comment on the general picture. Adaptive radiations in the fossil record appear to have been rapid, followed by stasis. This pattern is quite unlike the branching illustration found in On the Origin of Species.

"In some cases, the time frame seems rather short for a Darwinian process to have occurred, and in other cases, the effective population sizes of the species in question are small, suggesting that there is unlikely to have been extensive genetic variation in the population prior to selection. However, none of these factors are problematic if these cases of apparent rapid evolution in fact represent cases of phenotypic plasticity, perhaps in some cases rendered heritable through germline DNA methylation. Thus, rather than the paradoxical observation of Darwinian evolution over ecological time, we may be merely seeing incipient evolution by the PRM mechanism, which is expected to operate over ecological time."

Second, the specific case of cichlid fishes is of interest, because these radiations do not have the luxury of extensive time.

"The PRM mechanism provides a simple explanation of such comparatively recent adaptive radiations as that of the cichlids of the East African Great Lakes. The oldest of these lakes, Lake Victoria, is no more than 200,000 years old, and others are still more recent. The diversity of species in these lakes is problematic for Neo-Darwinism, but is easily explained by the PRM mechanism if prior to the divergence of ecotypes the ancestral species showed a phenotypic plasticity similar to that described in sticklebacks."

Third, consider that classic example of adaptive radiation: the Galapagos finches.

"Perhaps ironically, the PRM mechanism can likewise account readily for the radiation of Darwin's finches in the Galapagos Islands. The natural history of Darwin's finches provides many examples where it is plausible that phenotypic plasticity preceded morphological change; a striking example involves the sharper bill shape of a population of the ground finch Geospiza diffilis that feeds on the blood of boobies."

Fourth, the topic of artificial selection is of interest - not least because Darwin (and modern textbooks) portrayed artificial selection as directly relevant to natural selection, whereas Wallace thought it was irrelevant. There is no doubt that artificial selection produces rapid phenotypic change, but we already know that most of this does not involve mutations.

"The same process [incipient evolution by the PRM mechanism] might also be involved in rapid responses to artificial selection, for instance in accelerated domestication."

The significance of this research for the study of biological variation surely deserves our attention. We are not here considering a theory that claims to explain the concept of common descent from a single cell, but it has the more modest aim of explaining adaptive radiations from ancestral populations. However, the main critique that has been advanced is that the PRM hypothesis "does not explain why the ancestral state should be phenotypically plastic, or why this plasticity should be adaptive in the first place." The critique is not a fair one, because the new theory is proposed to explain observations of biological variation, rather than to explain the origin of all species.

The perspective provided by Hughes is one that is based on both theory and empirical data, and it stands up to testing very well. This model of variation provides an understanding that differs markedly from the Darwinism and the Neo-Darwinism of most textbooks. It is time for evolutionists to cease claiming all examples of variation and adaptation as evidence for Darwinian mechanisms of evolution. This is bad science and it is the perpetuation of a consensus by repetition rather than by hypothesis testing and validation. Hughes concludes thus:
"The hypothesis proposed here has the advantage of explaining the available data regarding adaptive evolution on the levels of genomics, ecology and paleontology, without invoking any mechanisms other than the commonly observed phenomena of phenotypic plasticity, purifying selection, mutation and genetic drift. Although it may represent a new perspective to biologists schooled in Neo-Darwinism, this view of life in its own way is not without 'a certain grandeur.'"

Evolution of adaptive phenotypic traits without positive Darwinian selection
A L Hughes
Heredity, advance online publication 2 November 2011 | doi: 10.1038/hdy.2011.97

Recent evidence suggests the frequent occurrence of a simple non-Darwinian (but non-Lamarckian) model for the evolution of adaptive phenotypic traits, here entitled the plasticity-relaxation-mutation (PRM) mechanism. This mechanism involves ancestral phenotypic plasticity followed by specialization in one alternative environment and thus the permanent expression of one alternative phenotype. Once this specialization occurs, purifying selection on the molecular basis of other phenotypes is relaxed. Finally, mutations that permanently eliminate the pathways leading to alternative phenotypes can be fixed by genetic drift. Although the generality of the PRM mechanism is at present unknown, I discuss evidence for its widespread occurrence, including the prevalence of exaptations in evolution, evidence that phenotypic plasticity has preceded adaptation in a number of taxa and evidence that adaptive traits have resulted from loss of alternative developmental pathways. The PRM mechanism can easily explain cases of explosive adaptive radiation, as well as recently reported cases of apparent adaptive evolution over ecological time.

See also:

Levi, P.J. No Positive Selection, No Darwin: A New Non-Darwinian Mechanism for the Origin of Adaptive Phenotypes, Evolution News & Views (November 14, 2011)

Tyler, D. Rodents evolve - but does the evidence suggest phenotypic plasticity? ARN Literature Blog (18 November 2011)

Tyler, D. A call for an end to Pseudo-Darwinian hype, ARN Literature Blog (11 September 2008)

It is universally claimed that the early Earth had a reducing atmosphere. Models have been proposed for the gases to have accumulated after outgassing of volatiles from volcanism. This reducing atmosphere was originally thought to have been dominant throughout the Precambrian, but signs of oxygenation have pushed it back earlier than the earliest rocks that researchers have discovered. The earlier claims for a reducing atmosphere have other explanations, such as resulting from the action of hydrodynamic fluids. This has put severe constraints on theories of abiogenesis, because the proposed mechanisms typically presuppose a reducing atmosphere. By the earliest Archaean, the atmosphere was at least neutral - so abiogenesis is inferred to have occurred even earlier. But moving back earlier brings us to the Late Heavy Bombardment which is generally deemed to have obliterated all traces of any life that may have been present. So there is a little window in the Hadean that is deemed to have offered a reducing atmosphere free from the destructive bombardment.

"For decades, scientists believed that the atmosphere of early Earth was highly reduced, meaning that oxygen was greatly limited. Such oxygen-poor conditions would have resulted in an atmosphere filled with noxious methane, carbon monoxide, hydrogen sulfide, and ammonia. To date, there remain widely held theories and studies of how life on Earth may have been built out of this deadly atmosphere cocktail." (Source here)

Artist's impression of the Hadean Earth (source here)

The evidence for a Hadean reducing atmosphere has been entirely theoretical. It does not rest on empirical evidence because there has been so little to work with. However, a new study of zircon crystals has reported some fascinating results that allow speculation about the Hadean black box to be replaced by empirical evidence. Zircons have been identified that carry signatures identifying them with the Hadean - and zircons are remarkably stable once formed. Using zircons dated to almost 4.4 Ga, the researchers have analysed their redox state (a measure of the degree of oxygenation of the mineral). This gives a handle on the type of gases that would have been outgassed by the magmas, and so, according to these models of Earth history, the type of atmosphere that would have been formed.

"Unlike other materials that are destroyed over time by erosion and subduction, certain zircons are nearly as old as Earth itself. As such, zircons can literally tell the entire history of the planet - if you know the right questions to ask. The scientists sought to determine the oxidation levels of the magmas that formed these ancient zircons to quantify, for the first time ever, how oxidized were the gases being released early in Earth's history. Understanding the level of oxidation could spell the difference between nasty swamp gas and the mixture of water vapor and carbon dioxide we are currently so accustomed to, according to study lead author Dustin Trail, a postdoctoral researcher in the Center for Astrobiology. "By determining the oxidation state of the magmas that created zircon, we could then determine the types of gases that would eventually make their way into the atmosphere," said Trail." (Source here)

It is important to realise what was predicted by prevailing theories: the redox state of the magmas with which the zircons were associated was expected to be strongly reducing. This prediction is a necessary part of the Earth having a reducing atmosphere in the Hadean. The research findings did not confirm the prediction. Here is the comment of the authors of a News & Views commentary in Nature:

"[In] this issue, Trail et al. report their analysis of the sole mineral survivors of the Hadean, zircon samples more than 4 billion years old. Their findings allowed them to determine the 'fugacity' of oxygen in Hadean magmatic melts, a quantity that acts as a measure of magmatic redox conditions. Unexpectedly, the zircons record oxygen fugacities identical to those in the present-day mantle, leading the authors to conclude that Hadean volcanic gases were as highly oxidized as those emitted today."

To keep the reducing atmosphere theoretical approach, the timescales must again shrink. The window is now less that 150 Ma - right at the beginning of Earth history - preceding the Late Heavy Bombardment. If life appeared so early, it must have been pulverised before the Archaean provided an environment stable enough for single-celled organisms to survive.

"Their findings extend the mantle's oxidized realm to almost 4.4 billion years ago. Although somewhat tenuous, this is the first direct evidence of the redox state of the earliest Earth. If the zircons analysed by the authors are representative of the Hadean eon, this result shrinks the duration of the reduced era of Earth's mantle to less than 150 million years. It also increases the lag time between the oxidation of the mantle and the subsequent oxidation of the atmosphere [. . .]." (source here)

The authors are well aware of the implications of their research. We need to discard theories that require a reducing atmosphere on Earth - if interest in these theories is to be perpetuated, then locations should be sought outside the Earth.

"The calibrations reveal an atmosphere with an oxidation state closer to present-day conditions. The findings provide an important starting point for future research on the origins of life on Earth. [. . .] Despite being the atmosphere that life currently breathes, lives, and thrives on, our current oxidized atmosphere is not currently understood to be a great starting point for life. Methane and its oxygen-poor counterparts have much more biologic potential to jump from inorganic compounds to life-supporting amino acids and DNA. As such, Watson thinks the discovery of his group may reinvigorate theories that perhaps those building blocks for life were not created on Earth, but delivered from elsewhere in the galaxy." (Source here)

There are two points worth making here. The first concerns the importance of empirical evidence in developing theory. The problem for any historical science is that it is relatively easy for speculation to become dominant because testing hypotheses by reference to empirical data is often a challenge. Abiogenesis is a case in point. The reducing atmosphere scenario and the mechanisms for turning simple chemicals into self-replicating cells have received theoretical development that has gone far beyond the evidential base. So confident have researchers become that they have created the delusion that it is unscientific to even challenge the consensus! Yet they have had to retreat before the evidence. The Archaean atmosphere was realised not to be reducing, so the theorists retreated to the Hadean where data is almost non-existent. They could just about live there - until this week! Now, they must revise their theories to make it all happen in the first 150 Ma of Earth history (and somehow miraculously survive bombardment) or move it "elsewhere in the galaxy". If you are aware of "god of the gaps" reasoning, this case seems to fit the pattern pretty well - the argument is from theory unsupported by evidence and there is a progressive retreat in response to evidence to a place where the theory looks untenable.

The second point is that science has not demonstrated self-correction as it is supposed to do. Evidence has been around for 30 years that the Earth's early atmosphere was not reducing. Jonathan Wells has summarised the research evidence against the reducing atmosphere in Icons of Evolution (2000). He refers to geologists who declared the concept to be mere "dogma" in 1982. Yet the reducing atmosphere has persisted in textbooks, the media, and in the research community to this day! The new research findings bring a renewed challenge to the science community: it is time to revise the textbooks and to follow the evidence wherever it leads.

The oxidation state of Hadean magmas and implications for early Earth's atmosphere
Dustin Trail, E. Bruce Watson & Nicholas D. Tailby
Nature, 480, 79-82, (01 December 2011) | doi:10.1038/nature10655

Magmatic outgassing of volatiles from Earth's interior probably played a critical part in determining the composition of the earliest atmosphere, more than 4,000 million years (Myr) ago. Given an elemental inventory of hydrogen, carbon, nitrogen, oxygen and sulphur, the identity of molecular species in gaseous volcanic emanations depends critically on the pressure (fugacity) of oxygen. Reduced melts having oxygen fugacities close to that defined by the iron-wustite buffer would yield volatile species such as CH4, H2, H2S, NH3 and CO, whereas melts close to the fayalite-magnetite-quartz buffer would be similar to present-day conditions and would be dominated by H2O, CO2, SO2 and N2. Direct constraints on the oxidation state of terrestrial magmas before 3,850 Myr before present (that is, the Hadean eon) are tenuous because the rock record is sparse or absent. Samples from this earliest period of Earth's history are limited to igneous detrital zircons that pre-date the known rock record, with ages approaching ~4,400 Myr. Here we report a redox-sensitive calibration to determine the oxidation state of Hadean magmatic melts that is based on the incorporation of cerium into zircon crystals. We find that the melts have average oxygen fugacities that are consistent with an oxidation state defined by the fayalite-magnetite-quartz buffer, similar to present-day conditions. Moreover, selected Hadean zircons (having chemical characteristics consistent with crystallization specifically from mantle-derived melts) suggest oxygen fugacities similar to those of Archaean and present-day mantle-derived lavas as early as ~4,350 Myr before present. These results suggest that outgassing of Earth's interior later than ~200 Myr into the history of Solar System formation would not have resulted in a reducing atmosphere.

Redox state of early magmas
Bruno Scaillet & Fabrice Gaillard
Nature, 480, 48-49 (01 December 2011) | doi:10.1038/480048a

A study of cerium in zircon minerals has allowed an assessment of the redox conditions that prevailed when Earth's earliest magmas formed. The results suggest that the mantle became oxidized sooner than had been thought.

See also:

Setting the Stage for Life: Scientists Make Key Discovery About the Atmosphere of Early Earth, ScienceDaily (30 November 2011)

Earlier this year, the UK government's chief scientist, John Beddington, delivered a speech in which he urged his audience of 300 government scientists to be "grossly intolerant" of "pernicious" and "fatuous" "pseudoscience". Clearly, Beddington was outraged by people claiming to speak in the name of science but who are promoting views that he regarded as dangerously erroneous. This broadside resulted in two contributions to the correspondence column of Nature. The first was by Professor Andy Stirling, who last year contributed a science policy commentary to Nature. Stirling was not comfortable with the issues highlighted by Beddington as pseudoscience.

"In this he included: scepticism of genetic modification technology; "illegitimate" advocacy of environmental precaution in response to unknowns; and suggestions that science is subject to morality. This approach is a rejection not just of irrational denial but of entirely reasonable social scepticism concerning science itself. [. . .] Open publication, peer review, experimentation and critical respect for evidence help promote reasoned argument. But rational scepticism is as important outside as inside the social practices of science. Hence the motto of Britain's Royal Society, 'Nullius in verba': take nothing solely on authority - even from scientists."

Does the "weight of consensus" trump "rational scepticism"? (image here)

The other correspondence was written by Professor Brian Wynne, who was also alarmed by the use of the term "pseudoscience" to describe those who were challenging government science on certain policy issues. Wynne also contributed to the pages of Nature last year when he reviewed a book that documented ways in which scientific uncertainty has been manipulated to undermine evidence that supported regulation. The review was not altogether favourable. Wynne explains that the book is incomplete: "it does not examine other areas, such as genetically modified organisms, in which grounds for doubt have been downplayed rather than amplified by powerful players to the same deregulatory ends". He would like to see discussion of "how science can be led to overreach itself in arbitrating public facts, meanings and norms". Regarding the Beddington speech, Wynne writes:

"However, none of the growing range of public issues involving important scientific questions can be reduced, as Beddington did, simply to "science" or "pseudoscience". [. . .] What policy advisers anoint as 'science' for intended public authority always embodies unstated policy-related commitments, including presumptions over the defining questions. Such social questions in public science should be recognized and debated openly. Scientific knowledge should inform public issues, not define them."

The following week, Beddington replied. "Andy Stirling and Brian Wynne call respectively for a democratic approach to scepticism and for recognition that scientific evidence often forms only part of complex decisions. I agree with them on both counts". When pressed, scientists will agree on principles, but it is not unusual for substantial differences to persist in their analysis of the issues. This is where the attainment of a "consensus" status is important, for this sways the decisions of policy makers.

"Of course it is true that advancement is attained through criticism, scepticism and debate. But my point was that there can sometimes be a thin line between healthy scepticism and a cynical approach that ignores or distorts inconvenient evidence. Where significant consensus exists on an issue, this has not always been made obvious; also, tokenistic opposing views can be presented in a way that exaggerates their support. Clearly, the role of scientific evidence in decision-making must be considered in the wider political and social context. However, I make no apology for demanding that the fundamental evidence and weight of consensus in such cases is set out in a proper and fair way."

Unfortunately, the matter of "consensus science" was not discussed further, but it is obviously a key issue for policy makers and science advisors. The drive to achieve a "consensus" often becomes a social and political battle, rather than the healthy convergence of thinking within the science community. The way things have developed makes "consensus" a problem for the science community, because dissenting voices are sidelined and debate is squashed (for more, go here).

Consensus science has become a big issue for all concerned with Origins. For many, the debate is over - the consensus has spoken. Some will say: there is no controversy. They regularly ask: where are the peer-reviewed papers supporting your views? These attitudes spill over into the arena for policy-making in education. Words like "pernicious" and "fatuous" and "pseudoscience" are commonplace. But what we are witnessing is the same fundamental problem: an uncompromising rejection of rational scepticism on these issues reinforced by personal worldviews that allow no deviation from the philosophy of naturalism.

This year has seen some high profile cases of bigotry and intolerance in the world of science. The science community in general appears to be in a state of denial about these cases of blatant trampling on academic freedom and liberty of conscience. The first of these cases relates to the astronomer Martin Gaskell who was the leading candidate for the founding director of a new observatory at the University of Kentucky. Although there is evidence that he was judged the best candidate, he was turned down because of his Christian beliefs and willingness to use the word "creation" in discussions. Although he explained he is a theistic evolutionist, this was not enough to turn away suspicions that his scientific judgment could be swayed by irrational factors. In January of this year, the university authorities agreed an out-of-court settlement to avoid the charge of religious discrimination being considered. For further comment see here. This did not stop some scientists thinking that Gaskell should have been turned down because of his Christianity. For an example, see Richard Dawkins' comments here.

A second example concerns the mathematician Granville Sewell, whose paper "A Second Look at the Second Law" was accepted by Applied Mathematics Letters in January 2011. However, as a result of fierce protests from people who cannot bear to see ID scholars publish in refereed journals, the paper was withdrawn at the last moment by the editor. After some exchanges, the journal apologised to Dr Sewell and provided some financial compensation. For further comments on this case, go here and here.

A third case concerns a group of geologists participating in annual meetings of the American Geophysical Union and the Geological Society of America. They have given lectures, presented posters, and even led a field trip. The reason why this has generated much heat is that the group members are Young Earth Creationists. They have chosen to participate in professional activities rather than stand outside like exiles from the geological community. The reactions of mainstream geologists have been mixed. A plea to keep these people out of the meetings appeared in EOS, the magazine of the AGU. The YEC geologists were described as "the enemies of science" and the call was for the professional societies to "enforce objective acceptance guidelines" based on "high scientific merit" (with YEC geology defined as being "devoid of scientific merit"). For a blustering report by someone who was at this Fall's meeting, go here. Steven Newton wrote, in New Scientist, that Creationist "infiltration" of scientific conferences seems outrageous, but banning them would do more harm than good. One wonders whether this counsel will prevail or whether those baying for strenuous efforts to keep them out will be successful.

The most recent case to note is that of David Coppedge who worked at NASA's Jet Propulsion Lab (JPL) as a system administrator. His employer first demoted and then terminated his employment. Apparently, Coppedge's "crime" was to share pro-intelligent design videos with coworkers. He was first forbidden to talk with colleagues about these issues, which he complied with. However, he was then terminated for "pushing religion". For more on this, go here. A legal action is under way because California's Fair Employment and Housing Act forbids employers from taking adverse action against an employee because of the employee's religious expression or affiliation. Since NASA is publicly funded, US citizens are able to influence this situation - for advice, go here and here.

These four recent cases show that all in not well in the science community. The entrenched attitudes captured in the film "Expelled" are still with us. Intolerance, bigotry and posturing is found not only in origins issues, but in many other areas of science. There are many indications that we need to lay again some foundations for science, because instead of following the evidence wherever it leads, far too many scholars are protecting their own patch and portraying as pseudoscience anything that does not fit into their personal agenda.

Intolerance: retain healthy scepticism, by Andy Stirling
Nature, 471, 305 (17 March 2011) | doi:10.1038/471305a

Intolerance: science informs, not defines, by Brian Wynne
Nature, 471, 305 (17 March 2011) | doi:10.1038/471305b

Intolerance: UK chief scientist responds, by John Beddington
Nature, 471, 448, (24 March 2011) | doi:10.1038/471448d

Whose foot in the door? by Paul S. Braterman and John W. Geissman
EOS, Transactions of the American Geophysical Union, 92(18), 153 (3 May 2011)

It is well known that rodents "evolve" fast. Archaeologists have used fossil vole remains as a means of dating because the different morphologies and species link to different time zones: this is the "vole clock". So pervasive are these changes, it has become a matter of note when stasis is observed! A case in point is the birch mouse (genus Sicista). A "living fossil" at the generic level has been found in Inner Mongolia by Yuri Kimura, a doctoral student. It has been identified by its fossilised teeth - the only part of the animal still accessible for study. The teeth can be read like a book, with the cusps, valleys and ridges providing a signature by which the animal is known.

"The new fossils of Sicista primus from the Early Miocene age are also now the earliest known record of Sicista, the birch mouse genus that comprises 13 modern and 7 fossil species, said Kimura. As a result, Sicista now boasts the most ancient ancestry of the 326 genera in the largest rodent suborder to which it belongs, Myomorpha. The suborder includes laboratory mice and rats. "The birch mouse is a rare case of a small mammal genus persisting from the Early Miocene without significant morphological changes," Kimura said in reporting the findings."

Paleontologist Yuri Kimura, Southern Methodist University in Dallas, identified a new species of birch mice, Sicista primus, from 17 tiny teeth. A single molar is about the size of half a grain of rice. The teeth, however, are distinctive among the various genera of rodents known as Dipodidae. Cusps, valleys, ridges and other distinguishing characteristics on the surface of the teeth are identifiable through a microscope. (Credit: Yuri Kimura/Southern Methodist University, source here.)

As far as chronology is concerned, the new fossil is said to be 17 million years old. Previous to this, the earliest fossil of Sicista was considered to be about 9 million years old. Whilst these figures are small compared with those obtained for the coelacanth, or the horse shoe crab, or the Wollemi Pine, they are large for rodents.

"[The observed diversity within this] rodent genus is not unusual, but the long record of the genus Sicista, first recognized at ~17 Ma, is unusual. The discovery of Early Miocene S. primus reveals that Sicista is fundamental to understanding how a long-lived genus persisted among substantially fast-evolving rodent groups."

The above comment concludes the paper, and there is no discussion of how the observation of stasis contributes to a better understanding of stasis. The last sentence says little more than "The fact is fundamental to understanding the fact". Darwinians commonly present everything in terms of adaptive evolution and refer to 'stabilising selection' or to a 'lack of change in the environment'. Whilst this can pass as a reasonable hypothesis with the coelacanth and some other cases, it does not sound at all convincing when the stasis is the exception (as is the case with rodents) rather than an isolated case. This is where multiple working hypotheses are particularly valuable, so that we can weigh alternatives rather than trying to fit everything into a Darwinian framework.

One avenue to explore is whether the rodent radiations could be the result of generating different permutations from the same genetic material. This can occur because the genotype can be expressed in different ways, arising from the phenomenon of phenotypic plasticity. Various triggers, such as from the environment, may be invoked to explain the changes in phenotype followed by the persistence of a specific phenotype for a period of time. A recent analysis of this approach is by Hughes (2011) who points out that phenotypic plasticity provides a ready explanation for abrupt changes in morphology (that cannot be attributed to the gradualistic mechanisms of Darwinism).

"Widespread occurrence of the PRM mechanism [plasticity-relaxation-mutation] would easily explain recently reported cases of apparent phenotypic evolution over ecological time. In most such cases, there has been no genetic evidence demonstrating the operation of the classic Neo-Darwinian mechanism of allelic replacement. In some cases, the time frame seems rather short for a Darwinian process to have occurred, and in other cases, the effective population sizes of the species in question are small, suggesting that there is unlikely to have been extensive genetic variation in the population prior to selection. However, none of these factors are problematic if these cases of apparent rapid evolution in fact represent cases of phenotypic plasticity, perhaps in some cases rendered heritable through germline DNA methylation. Thus, rather than the paradoxical observation of Darwinian evolution over ecological time, we may be merely seeing incipient evolution by the PRM mechanism, which is expected to operate over ecological time."

It is worth saying that Hughes considers that the adaptive evolution mechanism to be poorly supported by data, and he is unimpressed by recent statistical analyses claiming to demonstrate positive adaptation. His non-Darwinian mechanism provides a ready explanation for rapid changes in morphology and he uses as examples adaptive radiations of the cichlid fishes in Africa, and the diversification seen in Darwin's finches in the Galapagos.

"The hypothesis proposed here has the advantage of explaining the available data regarding adaptive evolution on the levels of genomics, ecology and paleontology, without invoking any mechanisms other than the commonly observed phenomena of phenotypic plasticity, purifying selection, mutation and genetic drift. Although it may represent a new perspective to biologists schooled in Neo-Darwinism, this view of life in its own way is not without 'a certain grandeur'."

Kimura is correct that Sicista primus can help us understand better the nature of rapid adaptive radiations. But this is only likely to be realised if scholars are prepared to move out of the comfort zone of neo-Darwinism to test their hypotheses with empirical data.

The earliest record of birch mice from the Early Miocene Nei Mongol, China
Yuri Kimura
Naturwissenschaften, (2011) 98:87-95 | DOI 10.1007/s00114-010-0744-1

Abstract: The earliest species of birch mouse, Sicista primus sp. nov., was recovered from the 17-Ma-old (Early Miocene) Gashunyinadege locality, central Nei Mongol, China. It is ~9 Ma older than the previous first appearance datum of Sicista in Eurasia. This study indicates that North American Macrognathomys is a synonym of Eurasian Sicista, having 12 shared dental characters. As a result, the biogeography of dipodids indicates that Asian Sicista dispersed to North America as opposed to the hypothesis that Sicista originated from the North American clade. Sicista is one of the few extant rodent genera that originated as early as the Early Miocene.

See also:

No Positive Selection, No Darwin: A New Non-Darwinian Mechanism for the Origin of Adaptive Phenotypes, by P.J. Levi (Evolution News & Views, November 14, 2011)

Evolution of adaptive phenotypic traits without positive Darwinian selection, by A L Hughes, Heredity advance online publication, 2 November 2011 | doi: 10.1038/hdy.2011.97

Birch Mouse Ancestor Discovered in Inner Mongolia Is New Species of Rare 'Living Fossil', ScienceDaily (May 25, 2011)

In a cave in a fringing reef, at a depth of 35m, off the Ngemelis Island, Republic of Palau, an amazing fish was discovered in March 2009. Not only was this fish new to science, but the more it was studied, the more unusual it appeared to be.

"Despite some early questions about its affinities, preliminary phylogenetic analysis based on whole mitogenome sequences and numerous osteological features confidently placed this fish within the true eels. Additional morphological and molecular analyses demonstrate that in some features it is more primitive than Recent eels, and in others, even more primitive than the oldest known fossil eels, suggesting that it represents a 'living fossil' without a known fossil record. [. . .] Here, we describe a new family, genus and species for this enigmatic eel. We demonstrate, based on convincing evidence from morphology and whole mitochondrial genomes, that this genus is the most primitive living member of the Anguilliformes, and we accordingly assign it to a new family."

Protanguilla palau alive (Source here). For a video of the fish, go here.

Eels are grouped together in the Order Anguilliformes. There are 19 families, 146 genera and 819 species. One family has the freshwater species, and the others are all marine. These 19 families are fairly well defined, but numerous groupings (at the sub-order level) have been proposed (indicating that the inter-relationships are debatable). Additionally, there are a number of eel species represented only as fossils. These have some differences from modern forms which can be understood within a framework of diversification and adaptation.

"Anguilliforms first appeared as fossils in the Cretaceous about 100 million years ago (Ma) and have lost their pelvic fins, and their dorsal, anal and caudal fins have become confluent. Many eels are adapted for occupying small spaces or burrowing, but they occur in diverse habitats, ranging from benthic shallow-water to deep-shelf, slope and abyssal plain, open-water, meso- and bathypelagic realms."

The research team has carried out a very thorough analysis of similarities and differences between Recent eels (excluding Protanguilla), Protanguilla, and the earliest fossil eels (from the Cretaceous). They wanted to provide an input into the unresolved debate about which Recent eels have the most primitive morphologies. They considered all the characters discussed by previous researchers and have added some additional characters that they deemed relevant. The first outcome was to identify 15 characters that are shared by all eels, whether living or fossilised. These are considered synapomorphic for the order. Then, the authors present their analysis of differences within the order. The summary is as follows:

"The preponderance of morphological evidence indicates that Protanguilla is an anguilliform eel that diverged very early in the evolution of the Anguilliformes and is morphologically more primitive than all living eels. It shares at least 15 characters diagnostic of both Cretaceous and Recent taxa of the order, and seven derived characters of Recent eels lacking in the Cretaceous forms. Most notably, Protanguilla differs from all Recent eels in having a premaxilla, metapterygoid, free symplectic and uppermost two hypurals free from one another, all primitive features that also characterize Cretaceous eels, and is more primitive than the latter in having a fully developed set of gill rakers, fewer than 90 vertebrae and a pterosphenoid that forms part of the posterior margin of the orbit."

Various options are possible with the molecular data, but the authors major on one tree that is a close match to the morphological evidence. There are ways of estimating divergence times using the molecular data, and the authors come up with a figure of 220 Ma for Protanguilla - predating significantly the earliest fossil eels. This is the reason they identify the living animal as a "living fossil" - it is deduced to represent a form that preceded all known fossil eels.

"Its long, independent evolutionary history (estimated to date back to the early Mesozoic era), its retention of primitive morphological features, and its apparently restricted distribution warrant its recognition as a "living fossil" and have generated a level of excitement reminiscent of the discovery of another living fossil fish, the coelacanth, in the late 1930's." (Source here)

There are at least three reasons why this interpretation of Protanguilla is premature.
1. I know of no other case where an animal is declared to be a "living fossil" when it is completely unknown as a fossil. Its evolutionary history has been deduced. In this sense, the find is quite different from the coelacanth, which has a significant fossil record.
2. The analysis of characters is essentially an analysis of three groups of eels: Recent, Protanguilla, and the Cretaceous fossils. There are puzzles as well as patterns. John McCosker, chair of Aquatic Biology at the California Academy of Sciences, commented that: "The analysis they have performed using morphology and genetics is brilliant and invites as many questions about eel evolution as it solves."
The analysis has been underpinned by the presupposition of evolutionary transformation, but it is important to articulate the unresolved issues with this approach.
3. There appears to be no interest in exploring any alternative perspectives on diversification. All is presented in terms of evolutionary transformation. There is no sign of a "multiple working hypotheses" approach. Are other avenues even available to explore? This blog is not the place to do this, but John McCosker may help us to identify at least one alternative. He explains that much of the adaptation and diversification story is characterised by the loss of body parts:

"Eels, to most amateur naturalists, aren't even thought of as fish," McCosker said. "They are, in fact, an excellent case of evolution involving the loss of body parts rather than their exaggeration, and in discovering the basal lineage of true eels, the authors have helped to trace the process of eel evolution further back in its ancestry."

An important example, relevant to the "living fossil" interpretation of Protanguilla, is the full set of bony toothed "rakers", in the gill arches. These are said to be a common feature in most bony fishes, but they are lacking in both fossil and living eels. This is taken as evidence supporting the transitional status of the new eel. However, are there other ways of analysing these data? Can characters be related to adaptations and lifestyle? Does the presence or absence of one trait have a bearing on the presence or absence of another? Is the general loss of body parts an indication of degeneration rather than evolution? We are growing in appreciation of the mosaic structure of many animal forms, and are questioning whether morphologies can carry the load necessary to support evolutionary explanations. It would be interesting to revisit eel morphology with this model of mosaic body forms and see whether the diversification story looks more like a bush than a tree. If it does, the take-home message may not be evolution, but variations based on different permutations of the same biological information.

A 'living fossil' eel (Anguilliformes: Protanguillidae, fam. nov.) from an undersea cave in Palau
G. David Johnson, Hitoshi Ida, Jiro Sakaue, Tetsuya Sado, Takashi Asahida, and Masaki Miya
Proceedings of the Royal Society B, Published online before print August 17, 2011, doi:10.1098/rspb.2011.1289

Abstract: We report the discovery of an enigmatic, small eel-like fish from a 35 m-deep fringing-reef cave in the western Pacific Ocean Republic of Palau that exhibits an unusual suite of morphological characters. Many of these uniquely characterize the Recent members of the 19 families comprising the elopomorph order Anguilliformes, the true eels. Others are found among anguilliforms only in the Cretaceous fossils, and still others are primitive with respect to both Recent and fossil eels. Thus, morphological evidence explicitly places it as the most basal lineage (i.e. the sister group of extant anguilliforms). Phylogenetic analysis and divergence time estimation based on whole mitogenome sequences from various actinopterygians, including representatives of all eel families, demonstrate that this fish represents one of the most basal, independent lineages of the true eels, with a long evolutionary history comparable to that of the entire Anguilliformes (approx. 200 Myr). Such a long, independent evolutionary history dating back to the early Mesozoic and a retention of primitive morphological features (e.g. the presence of a premaxilla, metapterygoid, free symplectic, gill rakers, pseudobranch and distinct caudal fin rays) warrant recognition of this species as a 'living fossil' of the true eels, herein described as Protanguilla palau genus et species nov. in the new family Protanguillidae.

See also:

Most Primitive Living Eel Discovered: Creating a New Species, Genus and Family of Animal, ScienceDaily (17 August 2011)

Viegas, J. 'Living Fossil' Retains Dinosaur-Era Look, (Discovery News, Tue Aug 16, 2011)

Entomologists interested in the Coleoptera (beetles) may find themselves struggling with an information overload because there are said to be about 350,000 species alive today. A previous blog drew attention to Darwinian approaches to explaining these large numbers, and to an evidence-based explanation that is not Darwinian. The presumption seems to have been that speciation has occurred so readily that the life-time of an individual species is short. This has affected studies of Pleistocene sub-fossil specimens, in that the finds were assumed to represent extinct species:

"Originally, the remains from the Pleistocene peat-bog or asphalt deposits were assigned to extinct species by historical authors, supporting the idea of a high evolutionary rate induced by the climate changes during the Pleistocene."

General view of the modern Helophorus sibiricus and its newly discovered Early Miocene fossil counterpart. The close-ups show the species-specific granulation of the pronotum in both the recent specimen (top) and the fossil (bottom), one of the characteristics that allowed a reliable identification of the fossil. (Source here. Credit: Martin Fikacek)

With further research, similarities with modern species were recognised and the previous "finding" was completely overturned!

"Later, more detailed studies of sub-fossil specimens sometimes based even on the study of their well-preserved genitalia revealed that the majority of Pleistocene sub-fossil beetles belong to recent species and resulted in the Pleistocene evolutionary stasis paradigm."

The stasis paradigm has not been applied to pre-Pleistocene specimens. This is largely because the information needed to assign a fossil to a modern species is largely lacking in these fossils - so it is assumed (again) that the finds represent extinct species.

"A large missing piece for the acceptance of long-living insects as a general phenomenon and for understanding the reasons for survival of the particular species is the scarcity of the fossils of such species. The reasons seem to be rather straightforward - the majority of the fossils bear too few details to allow a detailed comparison with living species, whose taxonomy is often based on the shape of male genitalia and other details."

Consequently, the recent find of an early Miocene beetle that can be assigned to an extant species was unexpected. The ScienceDaily report notes: "A study of an Early Miocene fossil from southern Siberia [. . .] led to the surprising find that the fossil belongs to a species of aquatic beetles which is still alive today and widely distributed in Eurasia." We should note that the age assigned to this fossil is 16-23 million years, but the average duration of an insect species (let alone a beetle species) is considered to be much shorter.

"The Siberian fossil provides new data for the long-lasting debate among scientists about the average duration of an insect species. It was originally estimated to be ca. 2-3 million years based on the available fossil record, but slowly accumulating data begin to show that such an estimate is an oversimplification of the problem."

Oversimplification is a problem, but it is not solved by the token concession that acknowledges there are a few long-lived species. The root problems are the assumptions that scholars bring to the study of fossil beetles. Just as reconsideration of the Pleistocene beetles led to the recognition of stasis, coleopterists need to be open to stasis being a pervasive feature of the fossil record. Although diversification has occurred readily in the past, in general speciation is followed by stasis. This is not the Darwinian paradigm! Sad to say, this is point in the argument where we struggle to get a meaningful response from Darwinists. There is plenty of scope for discussion of these issues - for more on this and the relevance to intelligent design, go here.

A long-living species of the hydrophiloid beetles: Helophorus sibiricus from the early Miocene deposits of Kartashevo (Siberia, Russia)
Martin Fikacek, Alexander Prokin, Robert Angus.
ZooKeys, 2011; 130 (0): 239 | DOI: 10.3897/zookeys.130.1378

Abstract: The recent hydrophiloid species Helophorus (Gephelophorus) sibiricus (Motschulsky, 1860) is recorded from the early Miocene deposits of Kartashevo assigned to the Ombinsk Formation. A detailed comparison with recent specimens allowed a confident identification of the fossil specimen, which is therefore the oldest record of a recent species for the Hydrophiloidea. The paleodistribution as well as recent distribution of the species is summarized, and the relevance of the fossil is discussed. In addition, the complex geological settings of the Kartashevo area are briefly summarized.

See also:

Living Species of Aquatic Beetle Found in 20-Million-Year-Old Sediments, ScienceDaily (Oct. 6, 2011)