Science Literature

This question has led to some fascinating discussions within the linguistics community and we are indebted to Emma Marris for her recent report which flags up some areas of fundamental disagreement. Representing the mainstream profession are the "historical linguists".

"Historical linguists have been reconstructing languages since the 1780s. Their tool is called the comparative method and it relies on extensive knowledge of the language group at hand, along with a broad grasp of, and intuitive feel for, the ways in which languages change. A linguist might notice that the way a vowel is spoken has shifted in two languages when compared with an ancient one, and infer that the shift happened before the two languages split. This will help to place the split relative to other splits but gives no information about when it happened. Hence the comparative method produces trees, but no dates."

The newcomers are evolutionary biologists working on language histories, using the tools and techniques of molecular phylogenetics. Their approach is to draw an analogy between language evolution and biological evolution: "Like biological species, languages slowly change and sometimes split over time."

"The advent of molecular genetics provided a new depth to the analogy. Just as the four nucleotides of DNA can produce a staggering variety of creatures, the alphabets of the world's languages can generate an infinite number of sentences. These alphabets, the words they make, and the sounds and grammar rules that frame them are passed down from parent to child in a process that, at least superficially, resembles the inheritance of DNA.
Even some complications are the same. Just as species can shade off into a maddening continuum of subspecies, populations and hybrids, languages dissolve into an untidy collection of dialects and intermediate forms. And the rampant borrowing of words between languages resembles, graphically at least, the promiscuous horizontal gene transfer that microbes engage in."

The report portrays the tensions in terms of physics envy, with the old school struggling with the statistics and the new boys bringing quantification to the discipline for the first time.

"It is putting it mildly to say that many historical linguists find the evolutionary biologists working on language histories to be bungling interlopers who have no idea how to handle linguistic data. It is also an understatement to say that some of these interlopers feel that their critics are hidebound traditionalists working on a hopelessly unverifiable system of hunches, received wisdom and personal taste. And that's just the mood between the historical linguists and the newcomers."

The problem for the historical linguists is that the evolutionary modelers appear to have no real feel for the languages they are analyzing. They know that all languages have a deep structure: words, grammar and syntax. Languages are used for communication between intelligent agents about all sorts of things: past, present and future events, concepts and abstract ideas.

"Ultimately, many linguists felt that this type of analysis oversimplified their cherished subject more than they could bear. Linguists love the little details that give a language personality: to them, the identifying sounds or peculiar borrowed words are nuances that tell the tale of a tongue. The new breed brushes over these details in pursuit of generalities, trends and statistical rules."

The problem is that languages are fully teleological, whereas the tools of molecular phylogeny do not acknowledge teleology in genomes. Those tools really grate on those who are experienced in linguistics.

"Why get excited about it when it is still so preliminary?" says Johanna Nichols, a historical linguist at the University of California, Berkeley. "We are not impressed by a computational or mathematical paper per se. We have to see that it blends well with what is known by historical linguistics and really adds to our knowledge. Then we will be excited."

There are many parallels here between this controversy in linguistics and the situation in biology. Not all biologists go along with molecular phylogenetics, as is evident here. These biologists are a diverse group, but they include ID scientists. They point out that if genomes are designed, then it is not a good idea to study them with tools that start with the presumption that there is no design or teleology in nature.

The language barrier
Emma Marris
Nature 453, (21 May 2008) | doi:10.1038/453446a

Extract: A new approach
In the past five to ten years, more and more non-linguists such as Pagel have used the computational tools with which they model evolution to take a crack at languages. And one can see why. Like biological species, languages slowly change and sometimes split over time. Darwin's Galapagos finches evolved either large beaks or small; Latin amor became French amour and Italian amore. Darwin himself noted the 'curious parallel' between the evolution of languages and species in The Descent of Man, and Selection in Relation to Sex.

A Review Of Bobby Henderson's The Gospel Of The Flying Spaghetti Monster
Robert Deyes

Books designed to make a mockery out of key principles that could change the way we view life often make claims not based on evidence but on the author's own personal biases. Sadly Bobby Henderson's The Gospel Of The Flying Spaghetti Monster is no different. For those who have not had the displeasure of reading Henderson's parody, he begins by introducing the reader to his god, the Flying Spaghetti Monster (FSM), and its revering pirates, the so-called Pastafarians, who await a heaven that is filled with beer volcanoes and stripper clubs.

Down on Henderson's imaginary earth, there is plenty of evidence for the FSM- everything from the noodly appearance of DNA to the spaghetti-like structure of the Great Wall Of China stands as testimony to the existence of the pasta god. Reading on one quickly realizes that Henderson is out to make a point (he says so himself)- if there is a place for teaching Intelligent Design (ID) theory in the science classroom of today's public school then there is also a place for teaching about his 'FSMism'. Indeed Henderson argues that since ID theorists claim that evolution is just a theory, so too are other parts of established science such as Newtonian gravity.

To make his point he sets up a farcical scenario in which gravity is simply the manifestation of the FSM pushing on the heads of his human creatures. Over time humans have got taller simply because the FSM, with his limited number of noodly appendages, is unable to keep his pressure on all the heads of the ever-growing human population. None of this is of course meant to be taken seriously. After all, Henderson is just ridiculing ID.

Nevertheless a quick glance through Henderson's book reveals some clear gaps in his understanding of what ID theory does and does not say. For example, Henderson claims that the primary objective of ID theory is to slip the supernatural into science so as to create a 'super-science' the likes of which have not been seen since the middle ages. Accepting the claims of ID in science, Henderson states, is akin to accepting medieval medical practices such as bloodletting into our hospitals.

And yet it is well known that the foundations of the ID movement are built upon scientific evidence that would not have been available to scientists in centuries past (irreducible complexity of molecular systems, the exacting requirements of embryonic development and genetic regulation and the information-rich content of DNA). ID theory has never attempted to slip a supernatural god into the 'gaps' of science but has always used a sound 'cause-and-effect' type approach using what we know about design to infer design in biology.

Henderson hits hard by suggesting that ID proponents have a problem in accepting not only the link between natural selection and antibiotic resistance in bacteria but also the powers of artificial selection in dog breeding (Of course ID can sit quite comfortably with these more limited forms of Darwinian theory). He likewise shows a complete disregard for the issues concerning vestigial organs. While often touted as evidence of a blundering evolutionary process that has not yet fully eliminated organs that have fallen into disuse, what is becoming clear is that many such organs do fulfill important physiological functions. Similarly, recent discoveries in molecular biology have shown that long stretches of so-called 'junk' DNA do indeed play critical roles in the regulation of gene expression.

Later on in the book, Henderson conflates supernatural creation with ID, bringing in the violence of religion, particularly Christianity, as one more reason to do away with any cogent arguments that ID theory might bring to the science 'table'. Henderson not only vilifies the religiously faithful by mocking the power of prayer but also shows that he has never bothered to investigate the scientific underpinnings of the ID movement. After incorrectly associating ID with Young Earth Creationism, he then proceeds to ridicule a God who would deliberately confuse people by creating a universe that is only a few thousand years old and later throwing in evidence that supports a much older creation.

Henderson continues by making a farce out of the Genesis account and the biblical moral teachings. He selects the wrong targets to support his case against what he sees as the dogmatic approach of the church to science (eg: the execution of Giordano Bruno whose burning at the stake was because of his religious beliefs, not his views on science). He clearly ignores the established fact that it was Christianity that provided the foundation upon which our universe could be understood scientifically. Of course ID theorists have categorically steered clear of equating their designer with the biblical God, using only principles commonly used in other fields of study to infer design in biology.

In The Gospel Of The Flying Spaghetti Monster, Henderson shows his complete lack of appreciation for modern-day challenges to science. To claim as he does that the peer-review process is a water-tight tower of objectivity is to ignore high-profile cases of scientists who have dared challenge established orthodoxy (Stephen Jay Gould's punctuated equilibrium is a case in point). Henderson dismisses the 'irrefutable proof' offered by Michael Behe in support of ID by asserting that Behe's examples of irreducible complexity are as incomprehensible to those outside of mainstream science as Kurt Godel's proof for the existence of God.

Perhaps unbeknown to Henderson is the recognition of Behe's Darwin's Black Box as one of the most accessible reads of contemporary, popular science. Of course one soon gets tired of hearing about the pasta deity and his pirate disciples not to mention Henderson's apparent obsession with noodles. He ends his book with a collection of bogus, fun-poking papers written by scientists who clearly have an ax to grind against ID. Most of these papers are just more fairy-tale imaginings of pirates, noodles and beer volcanoes all of which do little to strengthen Henderson's case. Likewise for Henderson's humor which at times exposes his lack of originality (I was surprised not to see Henderson claiming that 'carbonara' was the essential element of life, that angel hair was a vestige of the FSM's celestial army or that DNA stood for Deity's Noodly Appendages).

While ID clearly has a place in the science classroom, the spaghetti bowl of FSMism should remain in the school canteen. As for Henderson's occasional vulgar language, one can only conclude that he is short of real props to support his case.

A group of stick-like grasshoppers known as the Proscopiidae are widely distributed in Central and South America. They are flightless, mostly wingless (although some genera are equipped with rudimentary wings) and are ecological generalists (in that they feed on several different plant families). Although there are many species, their taxonomy is largely based on the details of unusual male genitalia. Their relationship to other grasshopper superfamilies has not been studied systematically.

An extant proscopiid (Credit: Guilherme Ide)

Until now, the fossil record of the Proscopiidae has been a void. One might have infered a recent origin. However, this is no longer an option because the first known fossils of this group have been found in Early Cretaceous strata (so these insects were around with dinosaurs). The fossils show well-developed wings and several other differences from extant forms. The research paper refers to them as stem-group proscopiids, but it should be remembered that these animals are specialised offshoots from their ancestral forms. The "stem-group" designation merely points to a time when they were less derived (notably, they had not yet lost their wings).

"[I]t is clear that Eoproscopia is less specialised than modern forms in this regard. Nonetheless, Eoproscopia does have the remarkable stick-like body typical of crown-group proscopiids, and it would appear that the family adopted their cryptic mode of life as stick mimics very early in their evolution."

The word "evolution" here deserves to be clarified: the loss of wings is analogous to the loss of vision in cave fish. The scenario is not the evolution of something genuinely novel, but the development of a specialised form from a more generalised ancestor. There is no evidence that this needs more than the reorganisation of existing complexity and also it may be combined with a process of genetic impoverishment.

The most significant aspect of this find is that the fossils are Early Cretaceous. This provides yet another pointer to Punctuated Equilibrium - rapid emergence of the new form followed by stasis (albeit with minor changes). Whereas Darwinism puts the emphasis on the origin of species, Punctuated Equilibrium implies that speciation is not really so important. Extant Proscopiidae comprise 215 species (in 30 genera) but they are all clearly proscopiids. The interesting transformation concerns the origin of the Family, and that happened abruptly and early. Darwinism may be the explanation of the post-Cretaceous story, but it has little relevance to what happened earlier.

THE FIRST FOSSIL PROSCOPIIDAE (INSECTA, ORTHOPTERA, EUMASTACOIDEA) WITH COMMENTS ON THE HISTORICAL BIOGEOGRAPHY AND EVOLUTION OF THE FAMILY
SAM W. HEADS
Palaeontology, 51(2), March 2008 , 499-507 | doi:10.1111/j.1475-4983.2008.00756.x

Abstract: Eoproscopia martilli gen. et sp. nov. is described from the Early Cretaceous (Aptian) Crato Formation Lagerstatte of Ceara State, north-east Brazil. The new taxon is assigned to the extant family Proscopiidae and represents the first occurrence of the group in the fossil record. Eoproscopia is similar to crown group proscopiids in its stick-like habitus, elongate prothorax and absence of the cryptopleuron, but differs in the presence of well-developed wings, the short head with a small, simple fastigium, the prothoracic legs being inserted near the posterior margin of the prothorax, and the absence of spines on the metathoracic tibiae. The discovery of Eoproscopia extends the geological range of the family by approximately 110 myr and confirms the presence of stem-group proscopiids in the Atlantic rift zone of South America during the Early Cretaceous.

See also:

Tyler, D. Stasis in the fossil record of leaf insects, ARN Literature Blog, 14 January 2007.

Box Canyon in Idaho, US, is an amphitheatre-headed canyon that is a classic example of its type. With no obvious flow of water into the canyon, geomorphologists in the past have looked at possible mechanisms of erosion and have come up with groundwater seepage. The idea was that groundwater flows were high enough to weaken the rock and to give loose particles sufficient movement to commence canyon formation. However, recent research has shifted the emphasis from slow erosion processes to something catastrophic.

"We fully expected to find Box Canyon was carved by groundwater, but then all the evidence we found pointed at a megaflood," said Michael Lamb, a geomorphologist at the University of California, Berkeley. [. . .] "The entire canyon seems to have been cut out of the earth by this flood," Lamb said. Although hardened lava, or basalt, is hard, "it's very fractured material. When lava cools, it contracts and cracks just like mud does. All this cracking makes the basalt like a pile of stacked blocks. So while small floods might cause little erosion, a large enough flood can pull these blocks out of place."

High-resolution topographic map of Box Canyon, Idaho. (Image credit: Michael P. Lamb and New Scientist. Larger image.)

What stimulated a rethink about Box Canyon was a critical evaluation of the favoured model:

"But when Lamb and his colleagues looked closer, the sapping hypothesis fell apart. Their calculations indicate that flowing spring water is too feeble by a factor of 22 to move the existing bouldery rubble downstream and make room for more. Moreover, spring water is chemically incapable of eroding the rubble by dissolution. And rock dating showed that erosion of the canyon's head wall ceased 45,000 years ago - further evidence that the present water flow isn't up to the job of cutting a canyon."

Fortified by this scepticism, the researchers looked again at the field evidences. Three features at the canyon head convinced them that surface water once flowed into the canyon and that the timescale for formation was only 35 to 160 days.

"First, three concentric semicircles of boulders within the canyon head appear to be waterfall plunge pools with ~2 m of relief. Second, a small notch (~300 m3) in the center of the headwall rim has linear flutelike abrasion marks, millimeters in width and several centimeters long, that follow the local curvature of the notch, indicating past overspill. The scours appear as divots on the inferred upstream end that gradually fan outward and diminish in relief downstream. Third, this scoured rock extends at least 1 km upstream of the canyon head and delineates flow toward the canyon."

The new mechanism brings a paradigm shift to geomorphological thinking about all box canyons. This includes Mars - which has numerous examples of these structures. This is a potential problem for those who are seeking evidences for past life on Mars. Richard Kerr comments: "If martian canyons were gouged out only by rare floods rather than many millennia of slow seepage, Mars may have lacked the continually warm and wet climate needed for the origin and evolution of life." In other words, the quiet warm pools may not have existed: just raging infernos over very short timescales.

However, the idea that a "continually warm and wet climate [is] needed for the origin and evolution of life" is not a scientific statement. We have no evidence that favours the idea that a warm pool can provide the conditions for the spontaneous formation of life. Indeed, all the evidence we have favours the opposite conclusion: whatever chemicals are in the pool, the outcome will be a state of equilibrium rather than an event of extraordinarily low probability. Despite all the discussion over past years, there is still no apparent appreciation of the central issue of generating biologically meaningful information.

One last thought: the researchers have made their breakthrough after realising that the proposed mechanisms for forming box canyons were inadequate. Then they went out to search for new data that would lead them to more satisfying solutions. This is where many of us are with Darwinism. We do not find the proposed mechanisms convincing and we have looked again at the data to find more satisfying solutions. It has led us to a paradigm shift which, we argue, operates within the realm of science.

Formation of Box Canyon, Idaho, by Megaflood: Implications for Seepage Erosion on Earth and Mars
Michael P. Lamb, William E. Dietrich, Sarah M. Aciego, Donald J. DePaolo, and Michael Manga.
Science 320, 23 May 2008: 1067-1070.

Abstract: Amphitheater-headed canyons have been used as diagnostic indicators of erosion by groundwater seepage, which has important implications for landscape evolution on Earth and astrobiology on Mars. Of perhaps any canyon studied, Box Canyon, Idaho, most strongly meets the proposed morphologic criteria for groundwater sapping because it is incised into a basaltic plain with no drainage network upstream, and approximately 10 cubic meters per second of seepage emanates from its vertical headwall. However, sediment transport constraints, 4He and 14C dates, plunge pools, and scoured rock indicate that a megaflood (greater than 220 cubic meters per second) carved the canyon about 45,000 years ago. These results add to a growing recognition of Quaternary catastrophic flooding in the American northwest, and may imply that similar features on Mars also formed by floods rather than seepage erosion.

See also:

Chandler, D.L. Earth canyon hints at ancient megafloods on Mars, NewScientist.com, 22 May 2008.

Choi, C.Q. Ancient Flash Floods Sculpted Earth, Mars, Space.com,, 22 May 2008.

Kerr, R.A. Martian Canyons by a Trickle or a Gush? ScienceNOW Daily News, 22 May 2008.

A new survey of the way evolution is taught in US public schools reveals that there is "a disconnect between legal rulings, scientific consensus, and classroom education."

"The authors show that the disparity in teaching evolution is not linked to differences in state regulations, but can more likely be attributed to differences of religious belief and education amongst teachers. Less than one-third of high school biology teachers believe that God had no part in evolution, nearly one-half believe God had a hand in evolution, and almost one in six believe that God created humans in their present form within the last 10,000 years."

Differences about the teaching of origins in schools are set to continue

Unfortunately, the authors make the usual mistake of thinking that science (and scientists) cannot be described as being "religiously motivated members of the community". It is extraordinary that caricatures have endured so long without being thrown out as unworthy of serious attention! The point can be illustrated by comparing this quote:
"Evolution - more precisely opposition to it - is profoundly important to fundamentalist Christianity, where it has played a critical role in its early formation as doctrine and as a social movement."
. . . with this edited alternative:
"Evolution - more precisely support for it - is profoundly important to fundamentalist scientism, where it has played a critical role in its early formation as doctrine and as a social movement."
Until opinion-formers in science recognise that evolutionary theory is not ideologically neutral but bristling with philosophical stances and ideological agendas, we cannot move forward in this debate.

Two sorts of teachers are described in the essay. The first are those who need a good input of staff-development:

"This is particularly true of the many teachers who lack a full understanding of evolution, or at least confidence in their knowledge of it. Such a lack of confidence can lead teachers to avoid confrontations with students, parents, and the wider community. They may, for example, not treat evolution as the class's organizing principle, or may avoid effective hands-on activity to teach it, or not ask students to apply natural selection to real life situations."

There is much that suggests a condescending attitude here: teachers are professionals yet this report presents some of them as ill-equipped to teach their specialist subject. Reference to "effective hands-on activity to teach it", or asking students "to apply natural selection to real life situations" are pointers to evidences of variation in nature and the influences of natural selection. But this empirical science is something all creationists and ID advocates will want to teach, encouraging critical thought by students about what the evidence actually means. ID scientists have always argued for better teaching of these topics, not for changing the syllabus so these subjects are not taught.

The second type of teacher are those who are creationists (apparently 16% of those surveyed). These are considered to be unresponsive to the legal judgments and the grand statements about the centrality of evolution made by scientific and professional bodies. These people may be unsuitable as teachers and their staff development will involve "certification" to allow them to continue in teaching:

"Scientists concerned about the quality of evolution instruction might have a bigger impact in the classroom by focusing on the certification standards for high school biology teachers. Our study suggests that requiring all teachers to complete a course in evolutionary biology would have a substantial impact on the emphasis on evolution and its centrality in high school biology courses."

This strategy smacks of a "big brother" intervention: if teachers do not conform, they will be 'processed' and if they persist in their folly they will not be allowed to practice their profession. The documentary Expelled has been treated as anti-science by many (e.g. by the AAAS) - but it is not. The film is documenting cases where academic freedom has been trodden underfoot by institutions and colleagues who consider that anyone with serious questions about the validity of evolutionary theory is unsuited to science. The lack of sensitivity to the disgraceful way good academics have been treated is a scandal, and the rapidity with which the charges are dismissed is also a disgrace. But, if this report is a valid indicator, the situation is not going to end with hounding good academics out of universities. Teachers with views that offend the powers-that-be are next.

Evolution and Creationism in America's Classrooms: A National Portrait
Michael B. Berkman, Julianna Sandell Pacheco, Eric Plutzer
PLoS Biology, 6(5), 20 May 2008: e124 | doi:10.1371/journal.pbio.0060124

Excerpt: We [report] the first nationally representative survey of teachers concerning the teaching of evolution. The survey permits a statistically valid and current portrait of US science teachers that complements US and international surveys of the general public on evolution and scientific literacy and on evolution in the classroom. Between March 5 and May 1, 2007, 939 teachers participated in the study, either by mail or by completing an identical questionnaire online. Our overall response rate of 48% yielded a sample that may be generalized to the population of all public school teachers who taught a high school-level biology course in the 2006-2007 academic year, with all percentage estimates reported in this essay's tables and figures having a margin of error of no more than 3.2% at the 95% confidence level. [. . .] Our results confirm wide variance in classroom instruction and indicate a clear need to focus not only on state and federal policy decisions, but on the everyday instruction in American classrooms.

See also:

Holmes, B. 16% of US science teachers are creationists, New Scientist.com, 20 May 2008.

Teaching evolution: Legal victories aren't enough, EurekAlert, 19-May-2008.

Molecular phylogenetics has been perceived as the route to reconstructing the details of the Tree of Life (the icon of descent from one common ancestor). In their recent essay on the subject, Lane and Archibald explain that the existence of the Tree has the status of fact and the task for researchers is to fill-in the details.

"A well-resolved and accurate phylogenetic reconstruction of life on Earth is the ultimate goal of systematics."

Most research to clarify eukaryotic relationships assumes they will be resolved as a single tree.

One of the major findings of the past decade has been the identification of six eukaryotic 'supergroups' "erected on the basis of an eclectic mix of morphological and molecular sequence data". Whilst there is widespread agreement that the six groups exist, there has been much debate over the specifics and "the relationships between the supergroups are largely unknown".

The main stumbling block concerns the discovery that the genomes of representatives of these groups show a curious mosaic of genes which are interpreted to have come from quite different sources. The inference has been made that endosymbiosis occurred several times in the past: primary endosymbiosis involved the envelopment and integration of prokaryotic genes and secondary endosymbiosis is used to describe genetic interactions between two eukaryotic cells.

"In the case of secondary endosymbiosis, the plastid acts as a genetic Trojan horse, bringing with it the nucleus of an unrelated eukaryotic endosymbiont whose genes meld with - and can replace - their counterparts in the host nuclear genome. The mixing and matching of eukaryotic genes that occurs in the context of secondary endosymbiosis seriously challenges our ability to accurately infer the evolutionary history of these organisms."

Primary endosymbiosis is perceived as a rare and improbable event, whereas secondary endosymbiosis may have occurred many times. In addition to the Trojan horse analogy, the image of Russian dolls is employed to describe the conceptual model.

"Organisms harboring secondary plastids are thus the biological equivalent of nested Russian dolls - a cyanobacterium encased within a eukaryote, enveloped within a second eukaryote. To further complicate matters, some dinoflagellate algae have replaced their plastid with a 'tertiary' plastid, stolen from other chromalveolates including cryptophytes, diatoms and haptophytes, and even a green algal plastid in a case of serial secondary endosymbiosis. Therefore, although all plastids probably trace back to a single primary endosymbiotic event, they have been propagated throughout eukaryotic diversity multiple times by a similar process."

The methodology, then, is to identify these aberrant flows of genetic information and exclude them from the analysis. This leaves "only the genes that accurately reflect the history of the host cell lineage" for further consideration. The problem is that we do not yet know the magnitude of this task. It is certainly not a straightforward or trivial exercise.

"If the number of 'foreign' eukaryotic genes in the genomes of secondary plastid-containing (or formerly containing) organisms is significant, but difficult to detect, then the evolutionary history of the host organism would be very difficult to resolve, because of the presence of genes with two (or more) evolutionary histories."

Whilst endosymbiosis is widely regarded as the mechanism for introducing foreign genes to organisms, the evidence is primarily circumstantial. This is somewhat reminiscent of Darwinism: the overwhelming evidence for Darwinism is not empirical (for the examples of Darwinian mechanisms in action do not add up to explain the origins of complex specified information, body plans and the higher taxa).

"Despite an overwhelming amount of evidence demonstrating that endosymbiont-derived genes readily establish themselves in the nuclear genome of their host, to our knowledge only a handful of studies have thoroughly investigated bona fide transfers of a eukaryotic gene from a secondary endosymbiont nucleus to a host nucleus."

Where is this research going? Like prokaryotes, the two options envisaged by researchers are (1) with enough data, taxonomic resolution will be possible and (2) the formidable challenges cannot be overcome because some foreign genes cannot be identified as such. But there should be a third option on the table for analysis: (3) polyphyletic origins of the eukaryotes. This will not please the Darwinians, but science should be more concerned with truth than with fitting data into a preconceived model.

The eukaryotic tree of life: endosymbiosis takes its TOL
Christopher E. Lane and John M. Archibald
Trends in Ecology & Evolution, 23(5), May 2008, Pages 268-275

Abstract: Resolving the structure of the eukaryotic tree of life remains one of the most important and challenging tasks facing biologists. The notion of six eukaryotic 'supergroups' has recently gained some acceptance, and several papers in 2007 suggest that resolution of higher taxonomic levels is possible. However, in organisms that acquired photosynthesis via secondary (i.e. eukaryote-eukaryote) endosymbiosis, the host nuclear genome is a mosaic of genes derived from two (or more) nuclei, a fact that is often overlooked in studies attempting to reconstruct the deep evolutionary history of eukaryotes. Accurate identification of gene transfers and replacements involving eukaryotic donor and recipient genomes represents a potentially formidable challenge for the phylogenomics community as more protist genomes are sequenced and concatenated data sets grow.

Darwin provided the underlying concept and Haeckel popularised the metaphor of a tree to represent the organic unity of all living things. Prokaryotes collectively have featured as the lowest form of life, but the relationships between the many different prokaryotic organisms have been very difficult to resolve. There are no embryological or morphological characters to give substance to an evolutionary phylogeny. Consequently, up until the 1960s, "bacteriology had to proceed without an evolutionary framework".

Prokaryotes are described as the most 'simple' life forms on Earth.

The change came with the advent of molecular phylogenetics.

"In the 1960s, Zuckerkandl and Pauling defined the new research area of molecular evolution. Within a decade, Woese and colleagues, using indirect methods of oligonucleotide cataloguing from small-subunit rRNA (SSU rRNA), identified one particularly important split within the prokaryotes: that separating the Archaebacteria from the Eubacteria. The identification of this split meant that there might be a third major category of living things on the planet, as divergent from Eubacteria and Eukaryota as each is from the other. Confirmation of the monophyly of these three potential groups seemed to be found in 1989, when the SSU rRNA tree was rooted using anciently duplicated genes."

This work provided a boost to evolutionary perspectives of prokaryotes. Since the breakthrough came with SSU rRNA, this was perceived as "the ultimate molecular chronometer".

"Optimism concerning the existence of a single unifying tree of life was at its peak; the SSU rRNA tree was crowned as the "universal tree of life," and was used to devise a new (three-domain-based) phylogenetic classification of life. The legacy of this work is that today there are more than 400 000 SSU rRNA sequences in the public sequence repositories, the vast majority of which have been sequenced for phylogenetic purposes."

With the advent of more data, this evolutionary picture has become blurred and confused. "Phylogenies inferred from alternative markers were often found to be incongruent with the topology of the SSU rRNA tree." "It became less clear why the SSU rRNA should have been preferred over other markers to derive the universal tree of life." Optimism was replaced by pessimism: "a gene that could be considered a universal chronometer that has kept track of the clonal history of cellular life since its origin is thus unlikely to exist."

ID advocates have repeatedly argued that design inferences are not based on ignorance, but on knowledge. Compare that argument with this:

"The new uncertainty at the end of the last century was different from that of half a century before. Prior to the molecular era, the absence of data caused uncertainty. With the arrival of complete genomes, uncertainty was not anymore caused by lack of data. Instead, now the very existence of the universal tree of life was on trial."
[. . .]
"Evidence accumulating during the 1990s and the earliest years of the new millennium seemed to suggest that there was no tree of life, [. . .]."

The key mechanism that was proposed as an explanation of the data was horizontal gene transfer (HGT). But this mechanism undermined the method for recovering a phylogeny from genetic signals. "Even if a prokaryotic tree exists, its most basal nodes might not be recoverable because of phylogenetic signal erosion, HGT, ortholog misidentification or a combination of all three."

"The minimal assumption for the existence of a prokaryotic tree is the existence of a core set of non-transferable (i.e. vertically inherited) genes, but evidence suggests that such a core set of genes cannot exist."
[. . .]
"In the next 10 years, as an ever-increasing number of genomes will become available, we might see either the rebirth of the tree of life hypothesis or its ultimate downfall. It is still too early to say in which direction the evidence will swing."

Unfortunately, there are only two options being considered by most of the researchers. The first is that further work will eventually find a way around these problems and a robust Tree of Life for prokaryotes will emerge. The second is the genetic annealing model proposed by Carl Woese, with HGT as initially dominant in single-celled communities - replacing the tree metaphor with a network. But there is a third option: that we are discovering evidences for the polyphyletic origin of prokaryotes. What we would like is to have this option on the table for academic discussion. The presumption that everything has evolved from an original self-replicating cell needs to be tested, not accepted as the unchallenged default.

The prokaryotic tree of life: past, present . . . and future?
James O. McInerney, James A. Cotton and Davide Pisani
Trends in Ecology & Evolution, 23(5), May 2008, Pages 276-281.

Abstract: No accepted phylogenetic scheme for prokaryotes emerged until the late 1970s. Prior to that, it was assumed that there was a phylogenetic tree uniting all prokaryotes, but no suitable data were available for its construction. For 20 years, through the 1980s and 1990s, rRNA phylogenies were the gold standard. However, beginning in the last decade, findings from genomic data have challenged this new consensus. Gene trees can conflict greatly, and strains of the same species can differ enormously in genome content. Horizontal gene transfer is now known to be a significant influence on genome evolution. The next decade is likely to resolve whether or not we retain the centuries-old metaphor of the tree for all of life.

"At the request of the Swiss government, an ethics panel has weighed in on the "dignity" of plants and opined that the arbitrary killing of flora is morally wrong. This is no hoax. The concept of what could be called "plant rights" is being seriously debated." The initiative derives from a sincerely held conviction that the word "dignity" should be associated with all life forms. The Swiss Federal Constitution, which has triggered this study, is itself a product of a collective social conscience and a Federal Ethics Committee was given the task of articulating what the concept of "dignity" means in the context of plants.

Should convictions about the dignity of plants affect the way we cut and cook asparagus? (source: go here)

How did the working group proceed? What ethical principles did they identify? The participants were not of one mind on the issues: "Even within the ECNH, the intuitions relating to the extent and justification of moral responsibilities towards plants were highly heterogeneous." They sought to capture this diversity of opinion:

"So if we are trying to put the idea of the dignity of living beings into concrete terms for plants, we must first show which basic ethical positions permit the consideration of plants for their own sake. This discussion was structured by means of a decision tree."

Much of the report (12 pages) is devoted to documenting the different perspectives contributed by working group members. It is worth highlighting the absence of appeal to scientific method. Furthermore, there was no lead to any alternative source of knowledge. Theocentrism was defined as: "The basis for this position is the idea of a God who is creator, and therefore the creative ground of all living organisms. What counts for its own sake is God. All organisms count because of their relationship to God." However, the report also says: "No member takes the theocentric position." The emphasis in the report is on capturing what the "dignity of plants" meant to the assembled experts and then suggesting what this might mean for contemporary society. This approach bears all the hallmarks of relativised socially-constructed knowledge. This is a post-modern response to the problem of defining the dignity of plants.

Previous blogs (here and here) have identified postmodernism as a response to the materialist worldview. Despite numerous books and articles, a framework for ethics supported by the scientific method has not emerged. It is possible to find examples of almost any practice in the world of nature, so if the natural world gives us 'norms', then anything goes! The philosophy of naturalism has two faces when it comes to ethics. The first option is to adopt sphere sovereignty (Gould's NOMA) and push ethics out of the arena of public knowledge. This leads straight to postmodernism for every academic discipline other than science (although if you are not a scientist, science also is viewed through postmodern glasses). The other option is to find an ethic within science - usually informed by evolutionary theory. This allows advocates of that ethic to speak with a semblance of authority, but the reality is that their schemes are no more evidence-based than adaptationist just-so stories.

The reaction of the Nature report about plant dignity was to express bewilderment and to publicise the opinion of one scientist that "things will start to become clearer when legal challenges to specific research projects come to court, and case law becomes established." One is inclined to comment: what else can be done if ethics are socially constructed?

ID is not a worldview, although advocates do seek to sensitise people to the worldviews that are prevailing in academia. ID does not come with a blueprint for explaining the dignity of plants. However, since the ID community has concluded that there are innumerable evidences for design in living things, and since design implies purpose and meaning, then ID provides a context for thinking that an objective environmental ethic actually exists. Consequently, seeking out this ethical knowledge is an activity worthy of scholars everywhere.

The dignity of living beings with regard to plants
Moral consideration of plants for their own sake
Ariane Willemsen (Editor)
Federal Ethics Committee on Non-Human Biotechnology (ECNH), April 2008.

First para: The Federal Constitution has three forms of protection for plants: the protection of biodiversity, species protection, and the duty to take the dignity of living beings into consideration when handling plants. The constitutional term 'living beings' encompasses animals, plants and other organisms. At legislative level, the Gene Technology Act limits the scope of the term to animals and plants. Previous discussion within constitutional law relates the term Wurde der Kreatur ('dignity of living beings') to the value of the individual organism for its own sake.

See also:

Smith, W.J. The Silent Scream of the Asparagus, The Weekly Standard, 12 May 2008, Volume 13, Issue 33

Abbott, A. Swiss 'dignity' law is threat to plant biology, Nature, 452, 23 April 2008, 919 | doi:10.1038/452919a

Several US States are considering academic freedom bills to protect teachers and students from charges of being ideologically motivated if they encourage critical evaluation of origins theories. For example, the text before the Missouri House is:

"teachers shall be permitted to help students understand, analyze, critique, and review in an objective manner the scientific strengths and scientific weaknesses of theories of biological and chemical evolution."

Such bills are justified because Darwinists recognise that their theory is being threatened and they have an evangelical zeal for protecting it from being undermined. The need for critical appraisal is demonstrated every time someone claims an example of natural selection as evidence for "evolution" - whether the phenomenon is antibiotic resistance or morphological change in lizards. Not surprisingly, many educators want to be able to discuss the evidence freely: what it demonstrates and what it does not demonstrate. Yet Darwinists are so sensitive about their theory that they portray critical scrutiny as subversive to science. They claim that framing the issue in terms of academic freedom is a cloak for teaching creationism.

Educators need to be able to discuss the cracks in Darwinism without fear of their professionalism being questioned.

The film Expelled! has crystallised thinking for many. Sad to say, dissent over the fundamentals appears not to be an option if you want to stay within the science community. There are too many cases of good scientists who have been excluded because they dared question the 'unquestionable'. These scientists have been treated shabbily by some colleagues who have openly declared that they are unfit to teach or practise science. Their academic freedom is being denied.

Unfortunately, the latest issue of Science perpetuates these problems. Yudhijit Bhattacharjee starts with the comment:

"If creationism is a mutating virus, as many educators believe, then its latest guise is legislation to protect "academic freedom." Politicians in five U.S. states are pushing bills to enable educators to teach alternatives to evolution by protecting their "right" to discuss with students the idea of intelligent design (ID)."

Clearly, the intent in this article is to suggest that "academic freedom" is a cloak for injecting religion into the classroom. The presenter of Expelled!, Ben Stein, is said to have "helped intelligent design proponents in their efforts to dethrone Darwin". Not a word here about the reality of intolerance within the scientific community. There is no recognition that many scientists have scientific concerns about the way evolutionary theory is taught. How can science be healthy when issues like this cannot be openly explored!

The same issue of Science has two letters commenting on a palaeontologist's journey from young-earth creationism to acceptance of evolution (published in a previous issue). The first illustrates the intolerance documented in Expelled!:

"Science magazine is not the place to give even a hint of respectability to those who would deny the fundamental fact of evolution. There is too much at stake, for our children and our society, to give any credence to those promoting unscientific nonsense (creationism or intelligent design) and justifying irrational beliefs under the guise of religion."

The second letter comes from an advocate of Gould's NOMA approach to science and faith issues:

"We within the scientific community must continue to present the demonstrable evidence from the physical realm and clearly express how that evidence supports our current interpretations. This effort is not served well at all by dogmatic pronouncements such as "Evolution is fact," even if such statements are accurate. Furthermore, for members of the scientific community to make theological statements in the name of science is philosophically illegitimate, and destructive in our truth-seeking efforts."

This correspondent objects to evolutionists claiming, for example, that Darwinism has made it possible to be an intellectually fulfilled atheist. Nevertheless, he wants to appear humble by not being dogmatic about "Evolution is a fact" even though he thinks it is. The missing contribution of this letter is the recognition that the "scientific community" includes ID advocates and also creationists. Were he to acknowledge this, he might usefully suggest that a dialogue within science over these issues is much needed. However, on present showing, this would result in himself being ostracised because he would be making it easier for the opposition to get a hearing.

Faced with such intransigence from the leaders of the scientific community, there should be no surprise when the public shows disquiet about science itself. But this would be in no-one's interest - for the real argument is not with science, but with ideologically-minded scientists who are trying to use science as a tool to further their own agendas. This point is important, because there are a growing number of young people who are alarmed at what they see in the scientific community: a dogmatism about a materialistic worldview that is equated with science. Some are being turned away. This is one message that champions of the 'public understanding of science' appear to have totally missed!

States Push Academic Freedom Bills
Yudhijit Bhattacharjee
Science 320, 9 May 2008: 731.

See also:

Missouri House of Representatives' Committee on Elementary and Secondary Education bill.

Stevens, C.W. Evolution and Faith: Empathy Is Misplaced, Science, 320, 9 May 2008, 745 | DOI: 10.1126/science.320.5877.745b

Whipple, A. Evolution and Faith: Empathy Is Crucial, Science, 320, 9 May 2008, 745 | DOI: 10.1126/science.320.5877.745c

Connor, K. It May Be 2008 at Home, But in the Academy It's 1984, Townhall.com, Sunday, May 11, 2008

Just when you thought there was little innovative thinking about the origin of religion, along comes an anthropologist to prove you wrong! My initial reaction on reading Maurice Bloch's new paper was to think: "How refreshing!" At last, here is someone who can see the emptiness of evolutionary explanations for the origin of religion. Here is a taster of his objections to this particular genre of evolutionary story-telling:

"The third problem with such theories is that they explain religion as a product of core knowledge or modular capacities, such as naive physics, number, naive biology and naive psychology, all of which, with the possible exception of the last, we share with all our anthropoid relatives. Such a proposal is therefore unconvincing simply because no other animal than humans manifests any behaviour that is remotely like what is usually called religion."

Furthermore, when the academic world and the media latch on to any hint of similarity between apes and humans, it is almost a relief to find someone recognising that there are major discontinuities. Contrast this write-up of Ape Genius with Bloch:

"Chimpanzees do not have anything which remotely resembles the many and varied phenomena that have been labelled religion in anthropology. Indeed, this was probably also true of early sapiens. But, more importantly, there is also something else that chimpanzees, and probably early sapiens, do not have. This is social roles or social groups, understood in one particular sense of the word social."

There is a twist to Lennon's song (and to Dawkins' polemic) - you can't both imagine and do away with religion! (For larger image, go here)

There are two key words in Bloch's paper: transactional and transcendental. Transactional behaviour relates to the moulding of roles and groups by "a process of continual manipulation, assertions and defeats". This is found in chimpanzee social organisation and it is found also among humans. Transcendental behaviour, however, consists of essentialized roles and groups. "Essentialized roles exist separately from the individual who holds them. Rights and duties apply to the role and not to the individual." Bloch has a striking illustration of this from the life of a Malagasy village elder known to him for a long time.

"By now, he is old, physically weak and a little bit senile. He has difficulty in recognizing people. He spends most of his days in a foetal position wrapped up in a blanket. Yet he is treated with continual deference, consideration, respect and even fear. Whenever there is a ritual to be performed, he has to be put in charge so that he can bless the participants. When he is treated with great respect he is being behaved to, and he accordingly behaves towards others as a transcendental elder. This does not mean, however, that he is not also within the transactional social system. While as a transcendental elder he is little different to what he was when he was in his prime several years ago, as a transactional player he has lost out completely in the machiavellian game of influence, and nobody takes much note of him anymore or of his opinions since in the continual power play of daily life he has become insignificant."

By comparison, chimpanzee sociality is purely transactional. "[T]he transcendental social does not exist among the chimpanzees." The human sense of the transcendental is presented as the key to understanding religion.

"The transcendental network can with no problem include the dead, ancestors and gods as well as living role holders and members of essentialized groups. Ancestors and gods are compatible with living elders or members of nations because all are equally mysterious invisible, in other words transcendental."

Given the sense of transcendence, religion is not something extra, needing an explanation in its own right, but it is an expression of a central human characteristic, deeply affecting many other cultural behaviours. Those who present religion as a superstition, a delusion or a virus of the mind are making a category mistake. Richard Dawkins and his unhappy band of atheist zealots are out of their depth when they indulge in their polemics. They are missing something of fundamental importance to being human.

Given this sense of transcendence, religion is not a phenomenon that needs to be explained. "Once we realize this omnipresence of the imaginary in the everyday, nothing special is left to explain concerning religion." But it is necessary to explain our sense of transcendence. Where does this come from?

"What needs to be explained is the much more general question, how it is that we can act so much of the time towards visible people in terms of their invisible halo. The tool for this fundamental operation is the capacity for imagination. It is while searching for neurological evidence for the development of this capacity and of its social implications that we, in passing, will account for religious-like phenomena."

It is at this point that Bloch seems to restrict the nature of the enquiry. Is this investigation bounded by the dictates of naturalism, or can avenues of enquiry related to design be explored? If the sense of transcendence is really something special, why rule out lines of enquiry that take us beyond materialism? We are here touching on the related issue of consciousness: is that a matter of neuronal activity only? Science may not be able to answer all our questions, but there is absolutely no reason (apart from insisting on a dogma) for denying the right to ask them in academia.

Why religion is nothing special but is central
Maurice Bloch
Philosophical Transactions of the Royal Society B, Firstcite, 21 February 2008 | DOI:10.1098/rstb.2008.0007

Abstract: It is proposed that explaining religion in evolutionary terms is a misleading enterprise because religion is an indissoluble part of a unique aspect of human social organization. Theoretical and empirical research should focus on what differentiates human sociality from that of other primates, i.e. the fact that members of society often act towards each other in terms of essentialized roles and groups. These have a phenomenological existence that is not based on everyday empirical monitoring but on imagined statuses and communities, such as clans or nations. The neurological basis for this type of social, which includes religion, will therefore depend on the development of imagination. It is suggested that such a development of imagination occurred at about the time of the Upper Palaeolithic 'revolution'.

Coghlan, A. Religion a figment of human imagination, NewScientist.com (28 April 2008)

This is a case study of Paranthropus boisei, an ape-like animal that is regarded by evolutionists as a member of the human family tree. It is "known popularly as the "Nutcracker Man" because it has the biggest, flattest cheek teeth and the thickest enamel of any known hominin." Inevitably, these teeth have stimulated discussion about the animal's diet.

"Since the first specimen was reported by Mary and Louis Leakey in 1959, scientists have believed that P. boisei fed on nuts and seeds or roots and tubers found on the savannas throughout eastern Africa because the teeth, cranium and mandible appear to be built for chewing and crunching hard objects."

Paranthropus boisei (Source)

The research has involved a microwear texture analysis of the molars of seven specimens of P. boisei. This utilised sophisticated microscopy techniques to map patterns of pits and scratches on the surface of the teeth.

"The researchers looked at complexity and directionality of wear textures in the teeth they examined. Since food interacts with teeth, it leaves behind telltale signs that can be measured. Hard, brittle foods like nuts and seeds tend to lead to more complex tooth profiles, while tough foods like leaves lead to more parallel scratches, which corresponds with directionality.
They compared the dental microwear profiles of P. boisei to the microwear profiles of modern-day primates that eat different types of diets - grey-cheeked mangabeys and brown capuchins, which eat mostly soft items but fall back on hard nuts or palm fronds, and the mantled howling monkey and silvered leaf monkey, which eat mostly leaves and other tough foods."

The results were surprising.

"The P. boisei teeth had light wear, suggesting that none of the individuals ate extremely hard or tough foods in the days leading up to death. It's a pattern more consistent with modern-day fruit-eating animals than with most modern-day primates. "It looks more like they were eating Jell-o," Ungar said."

So, teeth that look as though they are an adaptation to eating hard foods show a microwear texture that suggests they bit into soft fruit. This is a paradox that can be illustrated today by the gorilla - and there are some important implications.

"If you give a gorilla a choice of eating a sugary fruit or a leaf, it will take the fruit every time," Ungar said. "But if you look at a gorilla's skull, its sharp teeth are adapted to consuming tough leaves. They don't eat the leaves unless they have to."
This finding represents a fundamental shift in the way researchers look at the diets of these hominins. "This challenges the fundamental assumptions of why such specializations occur in nature," Ungar said. "It shows that animals can develop an extreme degree of specialization without the specialized object becoming a preferred resource."

These findings provide another nail in the coffin of adaptationism. There is a tendency in the evolutionary literature to provide a "Just-So" story for every trait. Even though Darwinists know this approach lacks rigour, they show total commitment to finding plausible accounts for the origins of every feature they see. However, it is now becoming apparent that some specialisations are vestigial and have lost touch with their roots. This gives even more of a free hand to adaptationist storytelling/speculation.

Furthermore, the implications are even more significant for Darwinists. If the mechanisms of variation and natural selection forged the original adaptation, why are these mechanisms apparently powerless to bring about further transformation with continuing environmental change? Why was P. boisei left with over-engineered dentition when the animal ate the equivalent of Jell-o? Why do gorillas have teeth that are out of character with their diet? The "adaptive landscape" concept invokes morphological continuity for adaptive change, but these findings suggest that adaptation may not always be a reversible or multi-way process. Some trajectories of adaptation may lead an organism into a cul-de-sac from which it cannot retreat. This leads to a model of genetic impoverishment by specialisation and speciation that explains a significant body of data. It is a useful model to explain some aspects of extinction. But it is not a model that Darwinists have embraced, because it does not fit comfortably with their adaptive landscape model, nor with their extrapolation of microevolutionary change to macroevolution.

Dental Microwear and Diet of the Plio-Pleistocene Hominin Paranthropus boisei
Peter S. Ungar, Frederick E. Grine, Mark F. Teaford.
PLoS ONE 3(4) 30 April 2008: e2044 | doi:10.1371/journal.pone.0002044

Abstract: The Plio-Pleistocene hominin Paranthropus boisei had enormous, flat, thickly enameled cheek teeth, a robust cranium and mandible, and inferred massive, powerful chewing muscles. This specialized morphology, which earned P. boisei the nickname "Nutcracker Man", suggests that this hominin could have consumed very mechanically challenging foods. It has been recently argued, however, that specialized hominin morphology may indicate adaptations for the consumption of occasional fallback foods rather than preferred resources. Dental microwear offers a potential means by which to test this hypothesis in that it reflects actual use rather than genetic adaptation. High microwear surface texture complexity and anisotropy in extant primates can be associated with the consumption of exceptionally hard and tough foods respectively. Here we present the first quantitative analysis of dental microwear for P. boisei. Seven specimens examined preserved unobscured antemortem molar microwear. These all show relatively low complexity and anisotropy values. This suggests that none of the individuals consumed especially hard or tough foods in the days before they died. The apparent discrepancy between microwear and functional anatomy is consistent with the idea that P. boisei presents a hominin example of Liem's Paradox, wherein a highly derived morphology need not reflect a specialized diet.

See also:

New Findings Challenge Conventional Ideas On Evolution Of Human Diet, Natural Selection, ScienceDaily (Apr. 30, 2008)

Andrew Moore is manager of the Science & Society Programme at the European Molecular Biology Organization and he has some strong views on the way evolutionary theory is taught within Europe. In a Commentary article in Nature, he is insistent that "Science teaching must evolve". This is (possibly) a welcome emphasis, because ID advocates have been saying something similar for a long time. In this context, the word "evolve" does not mean undirected, unsupervised change, but the intelligent engineering of the curriculum and the way it is taught.

A resource for teachers not mentioned by Moore (For more, go here)

There is common ground with Andrew Moore about some of the faults of present practices.

"[M]ost schools across Europe still teach phylogeny based on comparative anatomy, embryology and physiology. This works fairly well, but to preserve it as the paradigm to describe evolution in the face of a more robust approach is like continuing to describe the universe and matter in terms of newtonian mechanics, neglecting relativity and quantum mechanics. In fact, it is worse, because newtonian mechanics is sound and consistent within certain frames of reference. Phylogeny based on similarity of form is fundamentally unsound because of the adaptation and convergent evolution witnessed in nature."

Clearly, Moore finds serious limitations in traditional approaches to taxonomy. There are too many ambiguities for this to be handled within school science classes, and it is certainly possible for students to question the outcomes in ways that would not show evolutionary theory in a favourable light. The result, says Moore, is that "they leave school without fully understanding how well supported evolutionary theory is. Worse still, the understanding they have - based on the fossil record - is easy prey to specious arguments from anti-science movements." So, instead, Moore wants a strong emphasis on molecular phylogeny:

"Molecular phylogenetics is routine science. In the early 1960s researchers were already comparing gene sequences to infer evolutionary relatedness. Early work included the comparison of haemoglobin sequences between horses, pigs, cattle and rabbits, and between various primates."
and:
"It is, however, worth asking how teachers will deal with the material. The theoretical basis of molecular phylogenetics should be simple to grasp. A useful, albeit imperfect, analogy is the tracing of modern European languages back to archaic language groups by studying 'mutations' in spelling and pronunciation. [. . .] But equipping teachers with modern tools is rather left to chance, and many have trouble with ideas such as the molecular clock - a basic concept in molecular evolution."

This heavy emphasis on molecular phylogenetics does not do justice to the different assessments by scientists of this particular methodology of handling data. An important contribution to this legitimate debate was blogged here: Undermining the assumed hegemony of molecular systematics. Another blog drew attention to the problems of using molecular data to assess time intervals: Molecular clocks tell the wrong time!

The point is that these are legitimate debates within science. The implication of Moore's essay is that the molecular data is free of the ambiguities of "comparative anatomy, embryology and physiology" and the "fossil record". But this is simply erroneous.

Another problem area for origins teaching where there is (possible) agreement concerns Origin of Life research. Moore realises that this is not Darwinism and that it is highly speculative. He writes in a way that is reminiscent of an ID scientist with concerns about the way this subject is taught:

"Speculations on the chemical origins of life are almost universally covered in school curricula under 'Evolution', despite the questionable relevance of the topic for evolution, and its rather uncertain scientific basis. At most it represents an opportunity to discuss the principles of disagreement and competing ideas in science. But it is far from sound evolutionary theory."

Is there a way forward? Moore sees some light on the horizon.

"A developer of first-class teaching resources in molecular biology, the National Centre for Biotechnology Education (NCBE) in Reading, UK, will soon make a significant contribution for molecular evolution. [. . .] the NCBE is preparing "A birthday present from Mr Darwin": a teaching resource on modern concepts in evolution, to be circulated to UK schools and hosted on a freely accessible webpage. One of the 12 exercises, for example, involves studying the melanocortin-1 receptor (McR1) gene sequences from paleontological finds to deduce the probable coat colour of woolly mammoths."

In passing, it is worth noting that ID scientists would put the emphasis on molecular biology and its implications for variation in living things (rather than molecular evolution). However, the puzzle in the quote above is that the "probable coat colour of woolly mammoths" completely by-passes anything linked to Darwin's theory. The genetics of body hair colouration is common ground for ID and evolutionary biologists.

Let's go to the final paragraph:

"There is something more serious at stake: the erosion of public trust in Darwin's original theory of evolution by natural selection in the face of 'alternative theories' from the Intelligent Design movement. An article in Science recently demonstrated a moderate correlation between knowledge of genetics and acceptance of the theory of evolution among members of the general public. No less than before, evolutionary theory needs to be buttressed by all the good science it can get, and there is no better place to start than in school."

Oh dear! Where is the emphasis on finding truth? Where is the desire to explore the issues and follow the evidence wherever it leads? Implicit in this article is the recognition that the traditional defences of Darwinism are not as rigorous or persuasive as Darwinists would like them to be. Instead of teaching evidence for and against the theory and developing critical skills in students, the counsel is one of burying old arguments and closing ranks behind molecular phylogenetics to buttress up Darwin's explanation of the origin of species. Is this what education is really about?

Science teaching must evolve
Andrew Moore
Nature 453, 31-32 (1 May 2008) | doi:10.1038/453031a

Abstract: Evolutionary theory, study and knowledge moved on dramatically in the latter half of the twentieth century, but school teaching, curricula and teacher training are still in the primeval soup era

See also:

Tyler, D. Suggestions for improving the teaching of evolutionary biology, ARN Literature Blog, 25 April 2008.