Literature

"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.

When Jurassic Park was written, I don't think any scientist seriously thought that genetic material from dinosaurs would ever be recovered. However, that is exactly what was reported in Science a few days ago. The genetic sequences are derived from collagen protein recovered from the fossilised leg bone of a T. rex. The main authors have been publishing for some time about their find of dinosaur soft tissue, and this new paper is the latest step of a remarkable journey of exploration. If amino acid sequences are preserved in other fossilised bones, many new avenues for research will open up.

The bone yielding the collagen used in the research (Source: here)

The paper would have been memorable if that were the only point made by the authors. However, the authors wanted to show that their data could be useful to molecular phylogenetics. They used 21 extant organisms and protein sequence data from an Ice Age mastodon. They used four methods to reconstruct an evolutionary tree. According to the New Scientist report:

"To build the family tree, Asara and colleague Chris Organ compared the T. rex sequence with collagen from other animals. Those with similar collagen sequences were grouped closely together on the tree, while differences in the sequences suggested the animals had long diverged. For the most part, the collagen tree captured relationships palaeontologists and evolutionary biologists had little reason to doubt, including T. rex's kinship to birds and the mastodon's ancestry to elephants."

The relationship between the dinosaur and birds caught the interest of the media. "T. rex confirmed as great granddaddy of all birds" said New Scientist. The Daily Mail had the headline: "Terrifying Tyrannosaurus rex had close links to the humble chicken". One of the more ingenious was the Washington Post: "T. Rex Closer to Gizzards Than Lizards". However, the New Scientist, particularly, over-reached itself with its portrayal of the find. The word "confirmed" is a gross overstatement (see below) and the word "granddaddy" is simply wrong, as birds were contemporaneous with T.rex.

What few have realised is that the T. rex sequence is mainly missing. In their supplementary information, the authors document their data for the dinosaur collagen. It looks like this (where the dashes represent missing data - visible in IE but there is a problem with Firefox. If you are using the latter, copy and paste into a text file to see the data):

----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GATGAPGIAGAPGFPGARGAPGPQGPSGAPGPK---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GVQGPPGPQGPR------------------------------------------------------------------------------------------------------------------------------------------------------------------------GSAGPPGATGFPGAAGR----------------------------------------------------------------------------GVVGLPGQR---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLPGESGAVGPAGPPGSR------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Since molecular phylogenies are somewhat controversial even with full data, it seems completely wild to claim "confirmed" results at this stage of research. Furthermore, surprising outcome was obtained for the green anole (Anolis carolinensis, a lizard). This was expected to be grouped with alligators as a sister taxon. However, the phylogeny reported puts it at the base of the amniotes. This puts it as close to mammals as to alligators. "Such errors are common when working with limited sequences, Asara says." But if the data re T. rex and birds is accepted, why not the Anolis-mammal data? There are indications here that the researchers are letting "generally-agreed relationships" guide their analysis. Even more worrying, they suggest that the phylogeny emerging from their study validates the genuineness of the collagen extracted from the fossil bones. This is dangerously close to a circular argument.

"These results support the endogenous origin of the preserved collagen molecules and confirm the prediction based on morphology that, if biomolecules could be retrieved from a nonavian dinosaur, they would share a higher degree of similarity with birds than with other extant vertebrates."

Some have looked at this analysis and find it too speculative. For example, the Washington Post report has this:

"Pavel Pevzner, director of the Center for Algorithmic and Systems Biology at the University of California at San Diego, said his own research, soon to be published, refutes Asara's work. He said he cannot describe details until they are published, but he was blunt in his response to the new study, which appears in today's issue of the journal Science. The findings are "a joke," Pevzner wrote in an e-mail. "Serious evolutionary biologists will laugh reading this piece.""

Molecular Phylogenetics of Mastodon and Tyrannosaurus rex
Chris L. Organ, Mary H. Schweitzer, Wenxia Zheng, Lisa M. Freimark, Lewis C. Cantley, and John M. Asara
Science 320, 25 April 2008: 499.

Abstract: We report a molecular phylogeny for a nonavian dinosaur, extending our knowledge of trait evolution within nonavian dinosaurs into the macromolecular level of biological organization. Fragments of collagen [alpha]1(I) and [alpha]2(I) proteins extracted from fossil bones of Tyrannosaurus rex and Mammut americanum (mastodon) were analyzed with a variety of phylogenetic methods. Despite missing sequence data, the mastodon groups with elephant and the T. rex groups with birds, consistent with predictions based on genetic and morphological data for mastodon and on morphological data for T. rex. Our findings suggest that molecular data from long-extinct organisms may have the potential for resolving relationships at critical areas in the vertebrate evolutionary tree that have, so far, been phylogenetically intractable.

See also:

Callaway, E. T. rex confirmed as great granddaddy of all birds, NewScientist.com, 24 April 2008

Weiss, R. T. rex closer to Gizzards Than Lizards, The Washington Post, April 25, 2008; A02

Earlier this year, an interesting survey of first-year science students was conducted in the University of Cape Town, South Africa. A questionnaire was distributed to test their "knowledge and opinions of what they thought about evolution". Then came a course of 16 lectures on evolution, covering "the concept of evolution, the mechanisms of evolution, and dealt with hypotheses to test whether evolution occurred". After the course, the students were re-tesed with the same questions. The authors report that they "discovered no statistically significant change in the views of students before the evolution course and thereafter, for questions that challenged religious ideologies about creation, biodiversity, and intelligent design."

The authors frequently compare their findings with other studies, mainly to point out that the pattern is much the same wherever you go.

"Interestingly, the smallest change in Before/After responses to any question was the response to an ID argument, namely that "Organisms are incredibly well designed. This is proof that they must have been created by God." An impasse on this point mirrors the findings of others around the world."

There is a notable tension in their thinking about the relationship between evolutionary theory and Theism. On the one hand, they say that evolutionary theory does bring challenges:

"[D]espite scientific advances in evolutionary biology, evolution is often seen as contentious and "troubling". This is because evolutionary biology intersects and often challenges religious beliefs and values, which lead to an intellectual and spiritual dilemma. Thus, diplomacy and discussion become key in smoothing the interface between science and society."

On the other hand, towards the end, they fall back on sphere sovereignty (Gould's NOMA approach).

"[T]he biggest challenges evolutionary biology faces is that evolution is often equated with atheism, and students often feel that they need to choose between religious convictions and the credibility of evolution [. . .]. It is therefore important that students recognize that science and faith have separate domains, and that there are many scientists who are theists, and accept evolutionary theory as an explanation of the natural world."

Nevertheless, the authors do not appear to be completely convinced about these separate domains, as the write in their conclusions to say:

"We concur with Demastes et al. (1995) that because evolution often challenges preexisting conceptual ideas, a supportive classroom atmosphere is essential to ensure an understanding of evolution, even if this conflicts with cultural belief systems."

This vascillation between "separate domains" and "challenges [to] preexisting conceptual ideas" is a significant problem for educators. What is needed is an open debate about such matters, where evolutionary biologists interact with others advocating either Intelligent Design or Creationism to explore these issues in depth. The problem we face at present is that the science forums that are organised on this topic select their panels very carefully and dialogue and/or exposure to counter arguments is totally missing.

A further insight emerging from the survey is found in this paragraph:

"We further suggest that because students seem amenable to changing their views when presented with "facts", lecturers should ensure that they give examples of experimental evolutionary studies, and there should be strong emphasis on the scientific method of inquiry. [. . .] It may be equally important to simultaneously focus discussion on what constitutes a scientific theory and an empirical test, thereby equipping learners with the necessary tools and understanding to appreciate where ID fails and evolutionary theory holds from a scientific standpoint."

This is very interesting, because this emphasis on presenting "facts" is exactly in line with ID thinking (although the word "evidence" would probably be used to make the point). ID biologists welcome the opportunity to critically scrutinise the evidence, to find out what Darwinian mechanisms can and cannot do, to discuss the potential contribution of evo-devo to explain the diversification of living things and whether there is a route here to build complexity. We seek more evidence-based teaching, and less flag-waving statements like: "It is well recognized by scientists that evolution is the unifying theme that underlies the biological sciences" (which happens to be the first sentence of the paper). ID advocates are similarly keen to promote dialogue on what "constitutes a scientific theory and an empirical test", and the quotation above shows that this is clearly needed!

ACCEPTING EVOLUTION
Anusuya Chinsamy and Eva Plaganyi
Evolution, 62(1), 2008, 248-254 | doi:10.1111/j.1558-5646.2007.00276.x

Poor public perceptions and understanding of evolution are not unique to the developed and more industrialized nations of the world. International resistance to the science of evolutionary biology appears to be driven by both proponents of intelligent design and perceived incompatibilities between evolution and a diversity of religious faiths. We assessed the success of a first-year evolution course at the University of Cape Town and discovered no statistically significant change in the views of students before the evolution course and thereafter, for questions that challenged religious ideologies about creation, biodiversity, and intelligent design. Given that students only appreciably changed their views when presented with "facts," we suggest that teaching approaches that focus on providing examples of experimental evolutionary studies, and a strong emphasis on the scientific method of inquiry, are likely to achieve greater success. This study also reiterates the importance of engaging with students' prior conceptions, and makes suggestions for improving an understanding and appreciation of evolutionary biology in countries such as South Africa with an inadequate secondary science education system, and a dire lack of public engagement with issues in science.

See also:

Educators guide to dealing with "intelligent design", Internal Memorandum, Ivory Tower University, Department of Natural Sciences, no date.

The malaria parasite continues to plague humanity and the death toll is enormous. Much effort has been devoted to studying its life cycle and all identifiable natural mechanisms giving resistance. The best known trait conferring resistance is sickle cell anaemia: this affects red blood cells so that the malaria parasite (Plasmodium falciparum) does not gain a foothold in the body, but at the same time it adversely affects the functionality of the blood so that the human is regarded as having a genetic disease.

Mosquitoes can transmit malaria

It has been found recently that red blood cells from patients with pyruvate kinase deficiency are resistant to invasion by the malaria parasite. Furthermore, those cells that do succumb to infection are more rapidly cleared by macrophages than are infected cells from control subjects. Kevin Kain, one of the lead researchers on the project is quoted as saying: "Our research shows that people who have an enzyme deficiency or those who carry the gene trait for this deficiency may be protected from severe and fatal malaria." It is hoped that the findings will lead to the design of novel therapies by enhancing the body's protective pathways instead of inundating the body with drugs.

This research brings to mind Michael Behe's analysis of malaria research findings for understanding what Darwinian mechanisms can and cannot do. To explain his conclusions, he rejected the analogy of an arms race (often used by Darwinians to describe the outcome of the struggle for survival). In the struggle against the malaria parasite, we do not see an arms race (with the incremental refinement of weapons). Rather, according to Behe, we see trench warfare. In wartime, a bridge could be blown up to prevent the enemy from crossing; a tree could be felled across a railway track to create disruption. The trench warfare analogy fits malaria well (sickle cell anaemia involves damage to the red blood cells, and in this case, resistance is conferred by pyruvate kinase deficiency). The same lessons are learned from antibiotic resistance, which might arise as a loss of a transporter or the alteration of a ribosome.

Darwinians say that we can obtain new functions by mutation and selection, but the evidence is that loss of function is the explanation for both resistance against malaria and antibiotic resistance.

Pyruvate Kinase Deficiency and Malaria
Kodjo Ayi, Gundula Min-Oo, Lena Serghides, Maryanne Crockett, Melanie Kirby-Allen, Ian Quirt, Philippe Gros, and Kevin C. Kain.
The New England Journal of Medicine, 358(17), April 24 2008, 1805-1810.

SUMMARY: Malaria that is caused by Plasmodium falciparum is a significant global health problem. Genetic characteristics of the host influence the severity of disease and the ultimate outcome of infection, and there is evidence of coevolution of the plasmodium parasite with its host. In humans, pyruvate kinase deficiency is the second most common erythrocyte enzyme disorder. Here, we show that pyruvate kinase deficiency provides protection against infection and replication of P. falciparum in human erythrocytes, raising the possibility that mutant pyruvate kinase alleles may confer a protective advantage against malaria in human populations in areas where the disease is endemic.

See also:

Mutation In Human Gene Helps Protect Against Fatal Malaria, ScienceDaily (Apr. 22, 2008)

According to National Geographic News, a remarkable evolutionary change has occurred in a population of lizards:

"Italian wall lizards introduced to a tiny island off the coast of Croatia are evolving in ways that would normally take millions of years to play out, new research shows. In just a few decades the 5-inch-long (13-centimeter-long) lizards have developed a completely new gut structure, larger heads, and a harder bite, researchers say."

The experiment started in 1971, when 5 adult pairs of Podarcis sicula were introduced to the tiny island of Pod Mrcaru. Then came the Croatian War of Independence which lasted until the mid-1990s. Tourism did not start again, however, until about 2004, and this is when researchers returned to the island to see what had happened in the intervening years.

"Lizards Evolve "Overnight" on Island" says National Geographic News (to enlarge, click here)

What had happened to the introduced species? What impact had this had on the native lizards? "What they found, however, was shocking." No trace was found of the lizard species Podarcis milisellensis, which had previously inhabited the island. The introduced species were everywhere, at higher densities than their homeland. Furthermore, they had developed an appetite for eating plant food (34% in the Spring and 61% in the summer) whereas plant consumption in the source population was low (4%-7%). Their social structure was different and the lizards no longer defended territories.

Detailed analysis revealed three apparently related morphological changes: "head morphology, bite strength, and digestive tract structure". They appear to be adaptive, as all are related to the increased diet of plant materials.

"Physically, however, the lizards were not built to digest a vegetarian diet. Researchers found that the lizards developed cecal valves - muscles between the large and small intestine - that slowed down food digestion in fermenting chambers, which allowed their bodies to process the vegetation's cellulose into volatile fatty acids. "They evolved an expanded gut to allow them to process these leaves," Irschick said, adding it was something that had not been documented before. "This was a brand-new structure.""

In the paper, the authors note that <1% of all currently known species of squamates have cecal valves, and that: "These valves are similar in overall appearance and structure to those found in herbivorous lacertid, agamid, and iguanid lizards and are not found in other populations of P. sicula or in P. melisellensis." Herbivory explains why cecal valves are useful to these lizards. Also, "along with the ability to digest plants came the ability to bite harder, powered by a head that had grown longer and wider." All these changes came in a 36 year time window.

So, the question must be asked: how are we to understand the observations? The harder bite and the larger head are two aspects of the same phenomenon. Observations like this can be related to trends observed in artificial selection and they are not surprising. We have no reason to think that natural selection acting on natural variations over 30 generations cannot deliver this outcome.

The cecal valve finding is, however, dramatic. This is the finding that drew the comment that the animals "are evolving in ways that would normally take millions of years to play out". There can be no rationale for a Darwinian mechanism here - involving incremental assembly of the cecal valve. There is no time for this, even if a gradualist route could be found. No, the relevant genetic information must be present in the ancestors and epigenetic factors can be inferred to have activated the relevant mechanisms to make the structure. This research is revealing that organisms have a capacity for variability that goes significantly beyond their current phenotype. This implication has not escaped the attention of creationist biologists, who find this research a vindication of their view that animal radiations are rapid and the expression of innate variability embedded in the genome. It would be an interesting and educational activity for students to evaluate this theoretical model alongside others - although we can already be confident that Darwinism would not fare well in the exercise.

Rapid large-scale evolutionary divergence in morphology and performance associated with exploitation of a different dietary resource
Anthony Herrel, Katleen Huyghe, Bieke Vanhooydonck, Thierry Backeljau, Karin Breugelmans, Irena Grbac, Raoul Van Damme, and Duncan J. Irschick
Proceedings of the National Academy of Sciences, 25 March 2008 105: 4792-4795 | doi 10.1073/pnas.0711998105

Abstract: Although rapid adaptive changes in morphology on ecological time scales are now well documented in natural populations, the effects of such changes on whole-organism performance capacity and the consequences on ecological dynamics at the population level are often unclear. Here we show how lizards have rapidly evolved differences in head morphology, bite strength, and digestive tract structure after experimental introduction into a novel environment. Despite the short time scale (~36 years) since this introduction, these changes in morphology and performance parallel those typically documented among species and even families of lizards in both the type and extent of their specialization. Moreover, these changes have occurred side-by-side with dramatic changes in population density and social structure, providing a compelling example of how the invasion of a novel habitat can evolutionarily drive multiple aspects of the phenotype.

See also:

Johnson, K., Lizards Rapidly Evolve After Introduction to Island National Geographic News (April 21, 2008)

Lizards Undergo Rapid Evolution After Introduction To A New Home, ScienceDaily (Apr. 18, 2008)

The first known lungless frog has been found in the Indonesian region of Borneo. It lives in fast-flowing water and breathes entirely through its skin.

"As the researchers were doing initial dissections of the frogs as they caught them in the field, they were surprised to discover these amphibians lacked lungs. "At first I did not believe that the frogs had no lungs, but then, we just kept on seeing the evidence pile up. I was flabbergasted," Bickford said."

Barbourula kalimantanensis (Photo: David Bickford, Current Biology. Larger image here.)

Although the words "evolution" and "evolutionary history" are noticeable in the paper and media reports, it is worth reminding ourselves that lunglessness involves the loss of a complex organ. The find reveals degenerative change, rather like blindness in cave fish. Such traits are all derived features, indicative of extreme specialisation.

"Of all tetrapods (animals with four limbs), lunglessness is only known to occur in amphibians. There are many lungless salamanders and a single species of caecilian, a limbless amphibian resembling an earthworm, known to science. Nevertheless, Bickford said, the complete loss of lungs is a particularly rare evolutionary event that has probably only occurred three times. The discovery of lunglessness in a secretive Bornean frog supports the idea that lungs are a malleable trait in amphibians, which represent the evolutionary sister group to all other tetrapods, according to the researchers."

As a general rule, as knowledge develops, so does the language we use. Researchers find it necessary to define their terminology and even invent new words to ensure clarity. Significantly, this has not happened with one particular word in evolutionary biology. There are numerous meanings of the word "evolution" and yet its usage within the research community is much the same as usage by the man in the street. Sometimes it refers to allele changes in a population (e.g. the peppered moth), sometimes to the development of barriers to breeding (e.g. ring species), and there are several other usages that reach deeper into Darwin's "Tree of Life" concept. In addition, there is the philosophical meaning of the word: drawing together gradualism, materialism and the rejection of ultimate purpose. Many years ago, Phillip Johnson drew attention to this problem in his lectures and books, but the evolutionary community seems to prefer retaining the E-word with a fuzzy meaning.

These thoughts are relevant to the lungless frog because this is not an example illustrating the evolution of complexity, but the reverse. It is also relevant because, for research to progress, it is important to clarify mechanisms. The tendency within evolutionary biology is to explore a variety of mechanisms but to fall back on Darwinism when the going gets tough. Darwinism is the baseline that is deemed secure (especially as 2009 approaches). The problem is that Darwinism can explain only minor changes and extrapolation of observed small variations to explain major transitions has never been justified scientifically. Fuzzy meanings to "Evolution" are inhibitors: they do nothing to move research forward.

To develop an analogy, this frog has some similarities with evolutionary biology research. As long as there is plenty of aerated water, the research team has a sense that progress is being made. However, when the water becomes stagnant (as it often does!), the team finds it cannot breathe properly. The tools they are using do not deliver convincing answers. What is needed is a breath of fresh air - and this can be provided by people who are prepared to look outside the philosophical naturalism of their peers and recognise pervasive design features in the natural world. By grappling with design in living things, the capabilities and limitations of each proposed mechanism can be explored without it being force-fitted into a particular paradigm.

A lungless frog discovered on Borneo
David Bickford, Djoko Iskandar, and Anggraini Barlian
Current Biology, online 17 April 2008, 18(9), | doi 10.1016/j.cub.2008.03.010

Summary: The evolution of lunglessness in tetrapods (amphibians, reptiles, birds, and mammals) is an exceedingly rare event. So far lunglessness is known to occur only in amphibians, in particular two families of salamanders [1, 2] and a single species of caecilian [3]. Here, we report the first case of complete lunglessness in a frog, Barbourula kalimantanensis, from the Indonesian portion of Borneo. Previously only known from two specimens [4, 5], a recent expedition to central Kalimantan on Borneo rediscovered two new populations of this enigmatic aquatic frog. This allowed for a more comprehensive assessment of the species' ecology and anatomy that led to the discovery of its lack of lungs. Loss of lungs in Amphibia is most likely due to their evolutionary history at the interface between aquatic and terrestrial habitats and their ancient ability to respire through the skin [5].

See also:

First Lungless Frog Discovered, ScienceDaily (Apr. 8, 2008)

Choi, C.Q. Bizarre Frog Has No Lungs, Livescience (7 April 2008)