Science Literature

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)