Science Literature

By Robert Deyes
ARN Correspondent

If we look close at cell's own schemes,
precision work, inte-gral teams.
Protein domains that play their role,
so specified, a common goal.
It's hard to think how bits mixed up
like random tea leaves in a cup
could make up schemes of grand design,
so tailor-made, so clocked, so fine.

And so the cells they specialize,
with jobs to do, new tissues rise,
cells work together unified,
communicate both far and wide.
Neuron- impulse forth it sends,
muscle then contracts, leg bends,
lymphocyte- the fort defends,
liver cells the body cleanse.

Cells and tissues form a whole.
Each cell it knows its place, its role.
The body works incessantly.
A stomach, heart, a mind that's free.
From whence did come that thoughtful brain
that takes decisions, loss or gain?
Through inner soul it comes to life,
through stress and strain, through joy and strife.

And creatures learn to live, adapt,
territorial boundaries mapped,
ecosystems grow, divide,
scatter seeds both far and wide.
So who did make such symphony,
so caref'lly planned it seems to be?
Our minds do tell of higher mind,
an earth so purposef'lly designed.

By Robert Deyes

See also:
Biology's Big Bang http://digicoll.library.wisc.edu/cgi-bin/Arts/Arts-idx?type=article&did=ARTS.SBREEDSBURG.I0014&isize=M

Jim, Old Jim http://digicoll.library.wisc.edu/cgi-bin/Arts/Arts-idx?type=article&did=ARTS.SBREEDSBURG.I0015&isize=M

It is well known that the keystone in a stone arch is crucial for the stability of the arch. Indeed, without a good keystone, the arch will collapse. For many years. Theodosius Dobzhansky has been quoted to affirm that evolutionary theory provides the infrastructure that integrates the whole of biology. This is what he said: "Nothing in biology makes sense, except in the light of evolution." Sometimes, the reference to "evolution" relates specifically to Darwinism/neo-Darwinism, and sometimes the reference is to the concept of evolution rather than any particular mechanism. The imminent Bicentennial of the birth of Charles Darwin and the 150th anniversary of his magnum opus is bringing Dobzhansky's words to the fore and applied to Darwin's theory of evolution by natural selection. This is the inference to be drawn from a recent editorial in Scientific American and its accompanying illustration.

Darwinism is said to be a theory that everyone ought to learn (Image source here, Credit Matt Collins)

A major application of this message relates to education. Students need to know about Darwin's theory - indeed, everyone needs to know! The editors conclude:

"One way to celebrate Darwin's birthday is to contemplate how evolutionary studies can achieve broader adoption in secondary and higher education. Natural selection and the complementary idea of how genes, individuals and species change over time should be as much a part of developing critical thinking skills as deductive reasoning and the study of ethics."

It may surprise the Editors of Scientific American, but no one is arguing that natural selection and "how genes, individuals and species change over time" should not be taught. The differences are about how these topics are presented to students and what students are expected to learn. It would have been a welcome contribution to this particular discussion if Glenn Branch and Eugenie Scott had addressed it in their article in Scientific American.

However, instead of engaging with the issues, they devote over three thousand words to a polemic against the supposedly subversive activities of creationists. They bemoan the fact that the Louisiana Science Education Act has become law.

"On its face, the law looks innocuous: it directs the state board of education to "allow and assist teachers, principals, and other school administrators to create and foster an environment within public elementary and secondary schools that promotes critical thinking skills, logical analysis, and open and objective discussion of scientific theories being studied," which includes providing "support and guidance for teachers regarding effective ways to help students understand, analyze, critique, and objectively review scientific theories being studied." What's not to like? Aren't critical thinking, logical analysis, and open and objective discussion exactly what science education aims to promote?
As always in the contentious history of evolution education in the U.S., the devil is in the details. The law explicitly targets evolution, which is unsurprising - for lurking in the background of the law is creationism, the rejection of a scientific explanation of the history of life in favor of a supernatural account involving a personal creator."

They are saying, in effect, that the letter of the law sounds fine, but the letter is a front for creationism, lies and deceit. They do not believe that all teachers will abide by the letter. They expect some to promote unwarranted doubts about evolution:

"Allowing teachers to instil scientifically unwarranted doubts about evolution is clearly beyond the pale. Yet that is what the Louisiana Science Education Act was evidently created, or designed, to do."

This message is one we have heard many times before, and there is no evidence that it has any validity. There are legitimate concerns about the way Darwinism should be explored in the classroom. Many of us think that natural selection is being asked to do far too much - way beyond the empirical evidence that demonstrates what it can do. Many of us think that observed natural variations should not be used to argue the transformation of life from a single cell to the diversity of living things we see today. The objections to Darwinism are scientific, and they need to be fairly addressed in the education of students. These ideas have been explored numerous times in this blog. Here are examples over the past few months: Evolution, Museums and Society, Cichlid fish - another textbook example of evolution in action?, Hairless Dogs as an example of deleterious mutations, A call for an end to Pseudo-Darwinian hype, Adaptations affecting dim-light vision in vertebrates, The formidable problem of assembling the bacterial flagellum.

Of particular concern is the polemical way the arguments are presented. There is no interaction with the scientific issues, but only a desperate attempt to prove the infiltration of creationism into the fabric of science and education. No doubt many are familiar with Of Pandas and People - but do published "analyses" of the book by evolutionists ever get serious with the science? The same can be said of many other resources produced by ID scientists - instead of a scientific discourse, we are fed with unappetising polemic.

Will 2009 be any different? Will ID scientists be allowed to raise scientific questions about the validity of Darwinism? Will anyone suggesting that there are serious issues to consider be hounded as betrayers of science? What about our young people? Will they be allowed to question whether the evidences presented in the classroom are adequate to support the evolutionary theory in the textbook? We all want to promote a healthy scientific mindset, but a refusal to address the issues critically does not bode well for the future.

The Latest Face of Creationism in the Classroom
Glenn Branch and Eugenie C. Scott
Scientific American, December 16, 2008

First para: Professors routinely give advice to students but usually while their charges are still in school. Arthur Landy, a distinguished professor of molecular and cell biology and biochemistry at Brown University, recently decided, however, that he had to remind a former premed student of his that "without evolution, modern biology, including medicine and biotechnology, wouldn't make sense."

Why Everyone Should Learn the Theory of Evolution
The Editors
Scientific American, December, 2008

First para: Charles Darwin did not think of himself as a genius. "I have no great quickness of apprehension or wit which is so remarkable in some clever men ..." he remarked in one passage of his autobiography. Fortunately for the rest of us, he was profoundly wrong in his assessment. So on February 12 the world will mark the bicentennial birthday of a scientist who holds a rightful place alongside Galileo, Copernicus, Newton and Einstein.

Scientists and historians have acquired skills of data analysis which are essential for their professional lives. It is therefore strange to find examples of scholars being satisfied with rather superficial conclusions. A recent case concerns the crimes committed by German scientists during the Nazi era. Most of us ask questions like: 'What perverted the thinking of these scientists?' and 'Why were their peers and their leaders not outraged by the experiments?' However, in a review of a history of the crimes committed in the years 1933-1945 by scientists of the Robert Koch Institute in Berlin, the take-home message is banal:

"What is the bottom line? Do not try to write the history of bad scientists when any of them are still alive. Like [the author of the book], do it only when all of those who were involved are dead."

The long shadow of Darwinism reaches far beyond the domain of science (Image source here, Credit: Noma Bar)

The Nazi leadership in 1933 left the Director of the Institute and six group leaders in place, but required the redundancy of 12 staff because they were Jewish. Thereafter, as staff retired, new appointees were "according to the wishes of the Nazis". Sad to say, nothing more is said in the review about the ideology that was enforced at that time and how it affected the thinking and actions of research scientists.

Claus Schilling was a group leader in 1933. He had been a medical doctor in Africa and was "fascinated by malaria". After retirement, he continued research into finding a vaccine.

"[B]etween 1942 and 1945, he used prisoners from the concentration camp at Dachau in southern Germany for his malaria experiments. Of the 1,200 people he infected with malaria, between 300 and 400 died. Schilling was caught by the Allies and executed in 1946."

Eugen Hagen was a virologist who conducted his infamous experiments in a concentration camp in Alsace. In a letter to his group leader, dated 1943, Hagen wrote:

"I contacted the central office of the SS [the Nazi protective squadron] to receive sufficient human material from worthless lives for our purpose."

Here, at least, is a pointer to the ideology that fostered destructive experimentation with human lives. Some people were regarded as "worthless" and dispensable. Medics, whose life's work involved alleviating suffering and curing diseases, degenerated to murder to further their research ambitions. Even when facing the death sentence, Schilling sought permission "to publish the results of his unethical malaria studies".

However, Muller-Hill does not give us any insights into this thinking in his review. There is no highlighting of ideological issues, no analysis of how these scientists came to view fellow humans as "worthless" and no application to the present day where the ethics of scientific research is firmly on the agenda for discussion. If the book is like the review, opportunities to learn lessons have been lost.

However, I am reluctant to assume that the book passes over the ideological issues so completely. There may be other factors at play here. An article appeared recently in The Daily Telegraph with this by-line: "The Nazis' gruesome experiments became an accepted part of German medical research, according to the author of a new history". The writer is Richard Evans, Regius Professor of Modern History at the University of Cambridge, and his new book is The Third Reich at War. After discussing examples of the abuse of science, he writes:

"What underpinned this behaviour was a widespread belief that some people were less than human, relegated to a lower plane of existence by their inherited degeneracy - or their race."

After this tantalising comment, it is frustrating not to have further analysis of the factors leading to these attitudes. The ideological roots are hidden in this piece; all we see are some aberrant outgrowths of the plant. Yet, the author has done more work on the ideological issues and he does know what factors were at work. Here is a paragraph from an earlier book (The Third Reich in Power, p. 259):

"The real core of Nazi beliefs lay in the faith Hitler proclaimed in his speech of September 1938 in science - a Nazi view of science - as the basis for action. Science demanded the furtherance of the interests not of God but of the human race, and above all the German race and its future in a world ruled by ineluctable laws of Darwinian competition between races and between individuals. This was the sole criterion of morality, overriding the principles of love and compassion that have always formed such an important element in the beliefs of the world's great religions."

The diagnosis is clear. The Nazi's had latched on to the Darwinian theory of evolution by natural selection as a scientific justification of their ascendancy claims. They regarded themselves as representatives of the 'fit' humanity and they considered it a 'law of nature' that the fittest had the right, not just to survive, but also to promote the demise of the less fit. To the Nazi's, it made perfect sense to pursue a policy of extermination for that part of humanity that had nothing to offer their brave new world.

There are lessons here for today. It is important that each scientist thinks about his/her personal ideology and the framework of ethics within which they operate. Unfortunately, there is too much of an ethical vacuum today. People adopt principles for personal or pragmatic reasons. All too often, research ethics gets no deeper than gaining ethical approval from the appropriate ethics committee. Too many scientists are post-modernists when it comes to ethical procedures - all is relative. No one is prepared to move from ethics to morality - to say that anything is right or wrong. For previous blogs on this, go here and here.

This situation leaves the scientific enterprise vulnerable to being corrupted by business interests, funding agencies and ideologically-driven researchers. Many would argue that we are seeing warning signs on a regular basis. Social Darwinism is not dead. It continuously comes back to public debate saying that it has learned from mistakes and that Darwinism must be the only valid interpretive framework for understanding society. A recent presentation of this stance is found in The Economist. This is why the agenda of the ID movement includes opening up debate about the ideological influences in modern thought. This is why it is justified to come back again and again to the corruption of Nazi scientists: they have something important to teach us about the role of ideologies in science and the need for robust foundations for ethical practice.

Crimes in the name of research
Benno Muller-Hill
Nature 456, 575 (4 December 2008) | doi:10.1038/456575a

BOOK REVIEWED - Das Robert Koch-Institut im Nationalsozialismus, by Annette Hinz-Wessels. Kulturverlag Kadmos: 2008. 192 pp. (in German)

First para: The Robert Koch Institute in Berlin was founded in 1891 and conducts research into infectious bacteria and viruses. When it celebrated its centenary, the crimes committed by members of the institute between 1933 and 1945 were apparently not of interest, and were not mentioned. Ten years later, after the Max Planck Society and the DFG, Germany's main research-funding agency, had investigated their own histories, this changed. Scientist Annette Hinz-Wessels has written the first history of the institute, concentrating on the years under National Socialism.

See also:

Evans, R. How Hitler perverted the course of science, Telegraph Online, 02 Dec 2008

Weikart, R. From Darwin to Hitler: Evolutionary Ethics, Eugenics, and Racism in Germany, Palgrave MacMillan, 2004

The past few years has seen a steadily increasing awareness of the phenomenon of antisense transcription, but there has been very little insight into what antisense transcription products actually do. As is well known, DNA provides a template for the transcription of RNA sequences that are then used to make protein products. The distinction between sense and antisense transcription is helpfully made here:

"RNA, which is a single strand of nucleotides, is made by enzymes as an exact base-to-base copy of DNA. Since DNA is double-stranded, only one of these strands, the so-called sense strand, encodes for proteins. In normal DNA transcription, the two strands are split apart, and only the sense strand is copied. The other DNA strand, the "antisense" strand, can also be transcribed into RNA. Antisense transcription is the "reverse" expression of genomic DNA. If the same molecule of DNA is transcribed into antisense RNA, then the transcript has the reverse sequence as the original DNA sequence."

Antisense transcription is not an easy concept to illustrate, but this is how Nature Reviews Genetics did it.

The number of eukaryotic genes that have antisense transcripts seems to be quite high. This finding is stimulating many research projects, three of which have appeared recently in Science. Seila et al. have looked at the factors affecting transcription initiation. The first thing they noted relates to process.

"Transcription of DNA by RNA polymerase II (RNAPII) is an orchestrated process subject to regulation at numerous levels: binding of RNAPII to the promoter, transcription initiation, and elongation. These phases and their transitions require concerted action by many protein complexes and are accompanied by changes in local chromatin structure."

They noted some short (16-30 nucleotide) RNAs near the transcription start site (TSS) of protein-encoding genes. These were given the name TSSa-RNA. They appear to be intimately associated with promoters.

"Based on their direction and position relative to TSSs, we hypothesize that sense and antisense TSSa-RNAs arise from divergent transcription, defined as nonoverlapping transcription initiation events that proceed in opposite directions from the TSS. Divergent transcription is likely a common feature of mammalian TSSs given the presence of TSSa-RNAs in all cell types examined in this study."

There has been considerable uncertainty about whether these short RNAs and the antisense genes have functionality. Not long ago, they would have been lumped in with other "junk" materials and their production would have been regarded as a side-effect within the cell's complex genetic system. This has now changed. Gene regulation is the favoured role for these genetic elements. In a review published a few months ago, Beiter et al. wrote:

"So far, the regulatory potential of gene overlaps has been demonstrated only in a few selected cases of experimentally characterized antisense transcripts. Facing the large-scale antisense transcription observed in eukaryotic genomes, it still remains an open challenge to distinguish transcriptional noise from biological function of gene overlapping patterns."

All three of the new papers in Science develop our understanding of functionality. Seila et al. suggest a possible mechanism giving functionality to the TSSa-RNAs. Core et al. start their abstract with the statement: "RNA polymerases are highly regulated molecular machines." These authors comment on the need for regulation of the elaborate genetic system that can be found in cells: "Transcription of coding and non-coding RNAs by eukaryotic RNA polymerases requires their collaboration with hundreds of transcription factors, to direct and control polymerase recruitment, initiation, elongation and termination." They identify several possible functions for divergent transcription. In addition, He et al. conclude:

"The distribution of antisense transcripts was distinct from that of sense transcripts, was nonrandom across the genome, and differed among cell types. Antisense transcripts thus appear to be a pervasive feature of human cells, suggesting that they are a fundamental component of gene regulation."

Beiter et al. point out that "the mammalian genome contains a large layer of hidden biological information". Antisense transcription has been revealed to be widespread and these new papers are underlining the message that the transcription products have functionality within the "complex interplay between proteins, regulatory RNAs, and chemical and structural alterations of the genome itself". The DNA molecule has an extraordinary depth of information: one strand carries the instructions for the assembly of proteins whereas the other strand of the same DNA gene feeds transcription products into the regulatory system. ID scientists have always been sceptical of the Junk DNA hypothesis and these new findings confirm that the presumption of functionality is highly beneficial for biological science. The keywords are "information" and "systems biology". The systems that we see are exquisitely designed, not cobbled together by an incremental evolutionary process.

Papers discussed:

Divergent Transcription from Active Promoters
Amy C. Seila, J. Mauro Calabrese, Stuart S. Levine, Gene W. Yeo, Peter B. Rahl, Ryan A. Flynn, Richard A. Young, Phillip A. Sharp
Science Express, online 4 December 2008 | DOI: 10.1126/science.1162253

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters
Leighton J. Core, Joshua J. Waterfall, John T. Lis
Science Express, online December 4, 2008 | Science DOI: 10.1126/science.1162228

The Antisense Transcriptomes of Human Cells
Yiping He, Bert Vogelstein, Victor E. Velculescu, Nickolas Papadopoulos, and Kenneth W. Kinzler
Science Express, online December 4 2008; 10.1126/science.1163853

Antisense transcription: A critical look in both directions
T Beiter, E Reich, R Williams, P Simon
Cellular and Molecular Life Sciences, 2008 Sep 15; | doi 10.1007/s00018-008-8381-y

Simulated meteorite impacts have been observed to produce some organic molecules of interest to abiogenesis researchers. A group of Japanese scientists have designed an experiment to see if meteorite impacts could result in "the building blocks of life."

Their experiments validate a theory first proposed by the American astronomer Carl Sagan in the seventies, says Kakegawa. 'He just mentioned this hypothesis in one sentence in a paper, but he didn't do any experiments. Since then, many people have thought meteorites could produce organic molecules, but we are the first to succeed in showing this.'

Some want meteorites to carry life to Earth, whereas others want them to generate the building blocks of life. (Source here. ©iStockphoto.com/thecarlinco)

The authors simulated chondritic meteorites (thought to be the most primitive) impacting the ocean of the early Earth. To do this they created projectiles and fired them into a substrate to compress and shock solid carbon, iron, nickel, water and nitrogen. They report the production of fatty acids, amines and, when ammonia was added, one amino acid (glycine). They suggest that as impacts were frequent in the early Earth, bombardment led to organic molecules accumulating. This is perceived to be relevant to the origin of life.

The Scientific American report emphasized the tentative nature of the research: meteorites "may have helped spawn life" and "Did heat, pressure and carbon from meteorite impacts create biological precursors?" An astrobiologist is said to fear "that theories of life's origin may never move beyond the hypothetical". Astronomer Donald Brownlee found the research interesting but added: "If the body is too large, generated materials are probably destroyed by impact processes." One of the authors of the paper cautioned that the meteorite-impact theory "is not ready to supplant the vaunted Miller-Urey experiment".

Chemistry World quotes Jeffrey Bada, an expert in prebiotic synthesis at the University of California, San Diego, who doesn't think the results are particularly impressive.

'With the exception of methyl amine and acetic and propanic acid, the yields are very, very small,' he says. 'If glycine is indeed made, the amount that would be present in the ocean from one such impact would be about [10 to the power -30] grams per litre - hardly a meaningful concentration.'

From an ID perspective, the word "supplant" is inappropriate for the Miller-Urey experiments because they cannot carry the burden that people want to place on them. The experiments are a dead-end: there is no route for chemical evolution to proceed. There is a fundamental flaw because of the pre-requisite of a reducing atmosphere (which the meteorite impact experiment avoids), because there is no rationale for chirality to emerge from racemic mixtures, and because no progress has been made in resolving the problem of generating biological information. For more on the problems of building life from chemical precursors, go here and here.

It is worth noting a previous study of impact shocks to produce organic molecules (McKay and Borucki, 1996). These authors confirmed that the elemental conposition of shocked material is important. They based their work on cometary gases: methane, hydrogen cyanide and acetylene. Whilst amine groups were produced, productivity was nil with a carbon dioxide rich mixture. It is possibly significant that carbon dioxide was not mentioned along with nitrogen in the new research.

ID scientists interpret the findings of these abiogenesis scenarios as evidence against life having emerged by this route. It is one thing to generate organic molecules but quite another to label them as "precursors of life". Life does not exist without biological information, and until abiogenesis research takes information seriously, it will continue to explore cul-de-sac avenues.

Biomolecule formation by oceanic impacts on early Earth
Yoshihiro Furukawa, Toshimori Sekine, Masahiro Oba, Takeshi Kakegawa & Hiromoto Nakazawa
Nature Geoscience, 2, 62-66 (January 2009)
| doi:10.1038/ngeo383

Abstract: Intense impacts of extraterrestrial objects melted the embryonic Earth, forming an inorganic body with a carbon-dioxide- and nitrogen-rich atmosphere. Certain simple organic molecules have been shown to form under conditions resembling meteorite impacts, although the link between these events and the development of more complex molecules remains unclear. Ordinary chondrites, the most common type of meteorite, contain solid carbon, iron and nickel - elements essential to the formation of organic chemicals. Here we use shock experiments to recreate the conditions surrounding the impact of chondritic meteorites into an early ocean. We used a propellant gun to create a high-velocity impact into a mixture of solid carbon, iron, nickel, water and nitrogen. After the impact, we recovered numerous organic molecules, including fatty acids, amines and an amino acid. We suggest that organic molecules on the early Earth may have arisen from such impact syntheses. As the natural impacts that were frequent on the early Earth are more sustained and reach higher pressures than our experiments, they may have resulted in the synthesis of a greater abundance, variety and complexity of organic compounds.

See also:

Birch, H. Meteorites hitting oceans may have kick-started life, Chemistry World, 08 December 2008

Matson, J. Rock and Roil: Meteorites Hitting Early Earth's Oceans May Have Helped Spawn Life, Scientific American News, 7 December 2008.

McKay, C.P. and W. J. Borucki, W.J., Organic Synthesis in Experimental Impact Shocks, Science, 276, 18 Apr 1996, 390-392.

The advice is this: when you have dug yourself into a hole, stop digging!

Secularism is undermining science, but secularists just keep digging (Source here)

Many who speak for science will say that there is apparent design in the physical universe and, since Darwinian mechanisms are not applicable to non-reproducing matter, there are "only two explanations: a benevolent designer or a multiverse." The multiverse concept has a reproducing cosmos, with an infinity of universes - of which ours is just one where the conditions happen, by accident, to favour the emergence of intelligent life.

Amanda Gefter of New Scientist does not welcome this analysis. Her thoughts were triggered by an article by Tim Folger in Discover (blogged here) which took a strong position on the matter, as is evidenced by the title: "Science's Alternative to an Intelligent Creator: the Multiverse Theory". She was alarmed because the article effectively concedes that there is evidence for intelligent design in the physical universe. She writes that this:

"lends credence to creationists' mistaken claim that the multiverse was invented to serve as science's get-out-of-God-free card. Indeed, Folger's article was immediately referenced on creationist websites, including the Access Research Network, an intelligent-design hub, and Uncommon Descent, the blog of the Seattle-based Discovery Institute's William Dembski."

Gefter's first response is to deny the need for a dichotomy. Actually, this is a valid point at the level of principle. It is good practice in science to work with multiple hypotheses, otherwise testing hypotheses is methodologically weak and the pitfall is to continually validate the favoured hypothesis. This is why educationalists need to be concerned about teaching Darwinism only as the mechanism of evolution, because students emerge thinking that there is no evidence against the theory. Anyway, here is Gefter:

"Pitting the multiverse against religion presents a false dichotomy. Science never boils down to a choice between two alternative explanations. It is always plausible that both are wrong and a third or fourth or fifth will turn out to be correct."

The reason why this is not a good response is that the argument goes much deeper than specific hypotheses. In my earlier blog, I suggested that this was a good case study for the use of Dembski's design filter, with explanatory approaches based on Law, Chance and Design. In the context of the Multiverse, we are not dealing with specific theories, but contrasting paradigms: Law & Chance versus Design. This does lead to a dichotomy, not between science and religion, but between secularist science and theistic science.

Gefter does not realise she is in a hole, so she keeps digging. She wants to break through the dichotomy barrier. She draws on some speculations of some physicists which suggest that observing is a creative force.

"What might a third option look like here? Physicist John Wheeler once offered a suggestion: maybe we should approach cosmic fine-tuning not as a problem but as a clue. Perhaps it is evidence that we somehow endow the universe with certain features by the mere act of observation. It's an idea that Stephen Hawking has been thinking about, too. Hawking advocates what he calls top-down cosmology, in which observers are creating the universe and its entire history right now. If we in some sense create the universe, it is not surprising that the universe is well suited to us.
That's speculative, but at least it's science."

"Speculative"? Yes, certainly.
"At least it's science"? - No, it is science fiction.

These ideas are science fiction because there is no mechanism for observation to affect the fabric of the universe; because no one has suggested a way of testing the hypothesis that "we somehow endow the universe with certain features by the mere act of observation", and because everything we have learned about the universe as a material entity and ourselves as observers goes against the idea that observation affects the object. The only exception involves quantum physics, but no linkage between this scale and that of the universe at large has been made. The next step here is the abandonment of realism, long regarded as a hallmark of the scientific enterprise. If ID scientists are correct in their analysis of contemporary science (i.e. that it is suffering by having to wear the straitjacket of philosophical materialism), then we can make sense of these wild speculations. We can understand them to be driven by the need to force-fit the universe into a conceptual model where design has no place. By contrast, what ID scientists seek is to legitimise design-based explanations within science and to allow the evidence to be evaluated without the need to comply with the secularist worldview.

Why it's not as simple as God vs the multiverse
Amanda Gefter
New Scientist, 4 December 2008

First para: What would you rather believe in, God or the multiverse? It sounds like an instance of cosmic apples and oranges, but increasingly we are being told it's a choice we must make. Take the dialogue earlier this year between Richard Dawkins and physicist Steven Weinberg in Austin, Texas. Discussing the fact that the universe appears fine-tuned for our existence, Weinberg told Dawkins: "If you discovered a really impressive fine-tuning . . . I think you'd really be left with only two explanations: a benevolent designer or a multiverse."

On 11 September 2008, a symposium on the theme "Beyond the Mind-Body Problem: New Paradigms in the Science of Consciousness" was held at the United Nations attended by medical doctors and neuroscientists. The organisers spoke of a search for a more comprehensive perspective on the "self" and the workings of the human mind. The speakers at the conference have been engaged in this search and were ready to consolidate and move on. But in order to develop their thinking, they needed to challenge the prevailing paradigm in neuroscience. "Though much remains to be done, their findings to date have shed a more holistic light on our understanding of the elusive mind-body problem." This holistic view opens up new opportunities for research:

"The symposium will also serve as the occasion for the formal launch of The Human Consciousness Project - a multidisciplinary collaboration of international scientists and physicians who have joined forces to research the nature of consciousness and its relationship with the brain."

Materialist critics say of the new paradigm: "This nasty mind-virus piggybacks on reasonable worries."

The prevailing paradigm in neuroscience is materialism. Everything about the brain is interpreted in terms of physics and chemistry: our sense of free agency, our consciousness, our hopes and our ability to appreciate beauty. Yet this paradigm has only limited results to show for all the effort expended and "scientists have yet to crack the great mystery of how consciousness could emerge from firing neurons". The UN conference set out an agenda for going beyond reductionism. Jeffrey Schwartz warned the delegates that what they were doing would be met with heated opposition, because materialism is deemed by many to be of the essence of science:

"YOU cannot overestimate, how threatened the scientific establishment is by the fact that it now looks like the materialist paradigm is genuinely breaking down. You're gonna hear a lot in the next calendar year about. . . how Darwin's explanation of how human intelligence arose is the only scientific way of doing it. . . I'm asking us as a world community to go out there and tell the scientific establishment, enough is enough! Materialism needs to start fading away and non-materialist causation needs to be understood as part of natural reality."

Sure enough, the event has raised alarm! The New Scientist reported it with the headline: "Creationists declare war over the brain". It has become commonplace for the science media to portray every departure from philosophical naturalism as "creationism" as though that were the ultimate crime for a scientists and no more needs be said. There is evidence that some of the conference speakers have links with the ID Movement, and apparently that is enough to shower derision on them. Since scientists are supposed to be able to grapple with complex issues and think rationally and objectively (rather than emotionally), I do not understand why there is so little outcry against the intolerant attitudes of so many science journalists and writers.

Here are some reactions quoted, described as "the voice of mainstream academia":

Andy Clark, professor of logic and metaphysics at the University of Edinburgh, UK: "This is real and dangerous and coming our way." [. . .] "This is an especially nasty mind-virus because it piggybacks on some otherwise reasonable thoughts and worries."

Patricia Churchland, philosopher of neuroscience at the University of California, San Diego: "it is an argument from ignorance. The fact something isn't currently explained doesn't mean it will never be explained or that we need to completely change not only our neuroscience but our physics."

It is instructive to flag up some of the missing ingredients in this report
1. No interviews with the scientists that were at the symposium are reported. This was noted by Angus Menuge in a letter (unpublished) to New Scientist: "I find it very troubling, that while Amanda Gefter took the trouble of interviewing sources who advocate scientific materialism, she did not interview any critics of that position, instead relying on third-hand reports. This does not seem to reflect journalistic best practice."
2. There was no acknowledgement that ID can lead to new research opportunities. This is perhaps not surprising, because science journalists have been programmed to say that ID closes the door on science. This is bad history, because ID science was the trigger for the time known as the scientific revolution and ever since then ID scientists have consistently demonstrated that ID extends the horizons of scholarly enquiry.
3. There is no acknowledgement that the new paradigm has emerged because of evidence. Materialists cannot allow any evidence to count against their paradigm. They are committed to the principle that all explanations of phenomena have to be formulated by reference to "chance and necessity". Consequently, as in the quote from Churchland above, any hint of evidence against their position is opposed as an argument from ignorance.

Geftner declares that only the materialist perspective is science in her final paragraph. She also throws out the charge that non-materialists are invoking a "God of the gaps" style of argument:

"What can scientists do? They have been criticised for not doing enough to teach the public about evolution. Maybe now they need a big pre-emptive push to engage people with the science of the brain - and help the public appreciate that the brain is no place to invoke the "God of the gaps"."

This "pre-emptive push" seems to be the only response of the materialists! Shout louder! Put more resources into educating the public! Never admit that non-materialist philosophies can lead to fruitful science! Ignore their claims of arguing from evidence and insist that they are using ignorance to invoke the "God of the gaps"!
In a letter of response to New Scientist, Beauregard and Schwartz write:

"We do not question materialist models of the mind-brain complex merely for ideological or political reasons. We want to move beyond them because we have not found them adequate explanations of mind-brain interactions, nor do they point to useful treatment plans. Your writer's attempt to smear scientists who are looking for new directions, while perhaps entertaining, is a poor substitute for thoughtful coverage of a growing area."

Beyond the Mind-Body Problem: New Paradigms in the Science of Consciousness, September 11th 2008, United Nations, New York.

and

Creationists declare war over the brain
Amanda Gefter
New Scientist, 22 October 2008

See also:

Beauregard, M. and Schwartz, J.M. Non-materialist mind, New Scientist, 29 November 2008, page 23.
Go here for the unedited version.

Menuge, A. Unpublished letter to New Scientist, 26 November 2008.

In an informative essay, Janet Browne reflects on three Darwin commemorations: his funeral in Westminster Abbey, the 1909 centennial and the 1959 celebration. Each grasped the "opportunity to push an agenda, and even to adapt the past, so telling us what we like best to hear".

Nature's contribution to the anniversary preparations (Darwin 200 index here)

Darwin's religious views became known through his correspondence. He was content to be known as an agnostic and his view of God, if he did exist, was that he is remote from this world. Christian reaction to Darwinism ranged from "it is atheism" (Charles Hodge) to "God guides the process of evolution" (Asa Gray). Opposition to the technicalities of the theory came from contemporary scientists who were not persuaded that Darwin had a strong case. After Darwin's death, several colleagues in the Royal Society lobbied to have him buried in Westminster Abbey. This was to make a statement about Darwinism and faith and also to turn Darwin into an iconic figure. Browne writes that this was:

"valuable propaganda at a time when relations between science and religion were intensely fraught. The men of the Royal Society used Darwin's funeral as a way to reassure their contemporaries that science was not a threat to moral values, but rather was becoming increasingly important in the modern world."

By 1909, genetics was revealing that much of the variation reported by Darwin was innate and this was stimulating fresh thinking about biological change. "Thus, new forms could emerge de novo, without selective pressure and adaptive success." At the same time, palaeontologists were reporting lineages that "progressed" and this seemed to inject teleology back into biology. Darwinism was becoming sidelined.

"The 1909 commemorations, organised by a small group of naturalists and Darwin family members from the University of Cambridge, provided a way to reassert the primacy of natural selection against other evolutionary rivals."

A much bigger event was the celebration of 1959. This was the platform where the architects of the "modern synthesis" asserted their supremacy.

"The delegates at Chicago did more than celebrate a new union of the biological sciences. They in effect created modern Darwinism by emphatically rejecting any form of Lamarkism [. . .] The delegates also rejected the idea that the fossil record shows signs of directed evolution, and expanded Darwinian thought to cover the evolution of mind and behaviour. During the conference, Julian Huxley, the grandson of Thomas Henry Huxley, gave a secular sermon in the style of his grandfather, and provocatively declared that religious belief was merely a biological feature of evolving mankind."

Browne points out that "much of what we know about Darwin and Darwinism, including his celebrity status, is the result of the 1959 celebration in Chicago." This created the illusion of a consensus among biologists, but the reality is that many have serious doubts about the efficacy of natural selection to do what Darwinism claims for it. Many also doubt that gradualism is the way evolution proceeds. But the consensus means that doubting Darwin becomes a serious academic crime, for which the guilty get expelled from positions of influence and sometimes expelled even from being able to pursue a career in science.

Browne asks: "Will [the 2009] activities have a veiled agenda, as did those of the past?" The answer to this question must be an emphatic yes! If you don't want your mind to be manipulated, you had better develop your critical thinking skills. For more on Darwin as an icon, go here.

Birthdays to remember
Janet Browne
Nature 456, 324-325 (20 November 2008) | doi:10.1038/456324a

Summary: Anniversaries of Charles Darwin's life and work have been used to rewrite and re-energize his theory of natural selection. Janet Browne tracks a century of Darwinian celebrations.

Ever since the 'anthropic principle' entered the language of science, the case for the universe having the hallmarks of design has become progressively stronger. There is a consensus in the thinking of physicists and cosmologists that far exceeds the alleged consensus about anthropogenic global warming, and also the alleged consensus that natural selection is the mechanism for explaining design in living things. Author Tim Folger elevates the principle to "an extraordinary fact" about the universe:

"Its basic properties are uncannily suited for life. Tweak the laws of physics in just about any way and - in this universe, anyway - life as we know it would not exist."

Is our universe one of an infinite series? (Source here)

Folger's article is based on an interview with physicist Andrei Linde, who says: "We have a lot of really, really strange coincidences, and all of these coincidences are such that they make life possible." Many of these are sketched out for the benefit of readers, and Folger comments:

"There are many such examples of the universe's life-friendly properties - so many, in fact, that physicists can't dismiss them all as mere accidents."

If we apply Dembski's design filter approach, we have three avenues to explore: Law, Chance and Design. Law gets very little attention from Folger, despite the intense search for grand Unification Theories (GUT) or Theories of Everything (ToE). The reason is that GUT have not delivered. We cannot explain why the universe is like it is. No progress has been made in showing why the fine-tuning of fundamental constants should be a feature of the physical world. Indeed, the pendulum has swung away from GUT because of the interest in string theory - which has served to underline how extraordinary the evidences of fine-tuning actually are.

"[Polchinski and Bousso]calculated that the basic equations of string theory have an astronomical number of different possible solutions, perhaps as many as [10 to the power 1000]. Each solution represents a unique way to describe the universe."

This brings us straight to the Chance filter, and there is no shortage of people who are prepared to say how infinitesimally small the probability is for our universe to have the properties it does.

Call it a fluke, a mystery, a miracle. Or call it the biggest problem in physics. [. . .]
"If [dark energy] had been any bigger, there would have been enough repulsion from it to overwhelm the gravity that drew the galaxies together, drew the stars together, and drew Earth together," Stanford physicist Leonard Susskind says. "It's one of the greatest mysteries in physics. All we know is that if it were much bigger we wouldn't be here to ask about it."
Nobel laureate Steven Weinberg, a physicist at the University of Texas, agrees. "This is the one fine-tuning that seems to be extreme, far beyond what you could imagine just having to accept as a mere accident," he says.

Scientists who have adopted the metaphysic of secularism and naturalism have no recourse to Design. According to their reasoning, something remarkable must overcome the mindnumbing improbability of our universe. Physicists with this mindset have given birth to the Multiverse Theory. They

"see only one possible explanation: Our universe may be but one of perhaps infinitely many universes in an inconceivably vast multiverse. Most of those universes are barren, but some, like ours, have conditions suitable for life."

Which thought brings us to the third filter of Design. The argument is not based on ignorance but on evidence. We have good reasons to think that a ToE will never be forthcoming - there is no fundamental rationale for thinking that the universe and matter necessarily have the properties we observe. We have good reasons for thinking that Chance is not the answer, because the only way to persist with this explanation is to postulate an infinity of universes with different properties. We have no evidence to suggest that this option is anything more than science fiction. We have excellent reasons for thinking that Design is the answer because, without setting out to look for designed features, scientists have stumbled across them in abundance. Calling these evidences "fine tuning" points to something substantial. Were it not for the metaphysic of secularism, the design inference would be readily embraced.

"I don't think that the multiverse idea destroys the possibility of an intelligent, benevolent creator," Weinberg says. "What it does is remove one of the arguments for it, just as Darwin's theory of evolution made it unnecessary to appeal to a benevolent designer to understand how life developed with such remarkable abilities to survive and breed."
On the other hand, if there is no multiverse, where does that leave physicists? "If there is only one universe," Carr says, "you might have to have a fine-tuner. If you don't want God, you'd better have a multiverse."

Design theory provides the best match with empirical science. If you have any doubts about the pervasive influence of secularisation within contemporary science, this multiverse debate should make the issues clear. Folger's article is very significant for spelling out the thinking of some of the leading figures in the scientific world. For a 2002 comment making the same point, go here. For a recent 2008 comment on these issues, go here.

Science's Alternative to an Intelligent Creator: the Multiverse Theory
Tim Folger
Discover Magazine online, November 10, 2008

First para: A sublime cosmic mystery unfolds on a mild summer afternoon in Palo Alto, California, where I've come to talk with the visionary physicist Andrei Linde. The day seems ordinary enough. Cyclists maneuver through traffic, and orange poppies bloom on dry brown hills near Linde's office on the Stanford University campus. But everything here, right down to the photons lighting the scene after an eight-minute jaunt from the sun, bears witness to an extraordinary fact about the universe: Its basic properties are uncannily suited for life. Tweak the laws of physics in just about any way and - in this universe, anyway - life as we know it would not exist.

In a short article, Bruce MacFadden of the Florida Museum of Natural History suggests that museums can effectively increase public understanding of evolution. Taken at face value, this objective is shared by ID scientists - the main issue relates to content. What is meant by increasing public understanding of evolution? What messages will be communicated to the public? It is clear from MacFadden's article that Darwinism is perceived as capturing the essence of evolution - and this is where the problems start.

Without the connecting lines, would people discern evolutionary links? (Source here)

Apparently, visitors to museums are more likely to "accept evolution" than the general public. Whereas 33% of the US population "rejects the tenets of evolution" but the figure is only 10% for museum visitors. The fuzzy meanings attributed to the word "evolution" make these figures difficult to interpret. For example, ID scientists have no problem accepting that Darwinian mechanisms exist in nature, but typically deny that these mechanisms have anything to do with the origin of phyla, classes, orders and families. Furthermore, there are at least two possible reasons for the survey findings: museums may be doing an effective job of communicating Darwinism already; and, people may be voting with their feet and sceptics may not enjoy visiting museums where an evolutionary story intrudes on the pleasure of seeing the collections.

The understanding of museum visitors was probed in one survey: 95% understood the concept of superposition in geology, 80% were able to recognise that the geological column represents a time line, but only 33% gave the "correct" answer to a question about natural selection.

"[W]ith regard to understanding mechanisms of evolution within a species, a scenario was presented in which successive generations of cheetahs are able to run faster; only one-third of respondents correctly attributed this to natural selection."

The problem with this example is that the natural selection explanation has not emerged from observation but it is inferred from theory: it is another of the "just-so stories" proposed by Darwinists. Cheetah design affects many different aspects of the animal and some of these are likely to be affected by natural selection. However, whether this is the complete story remains an open question. The "natural selection" answer may be the right one, but any confidence in its correctness comes from dogma, not empirical science.

We are given an insight into the thinking of exhibit designers when we read: "The challenge, however, is to find novel interpretive strategies that will attract the public to learn about more challenging concepts such as natural selection". Clearly, the emphasis is not on the collection, but the accompanying message. And in the case of evolution, the public need more exposure to natural selection as a creative force.

ID scientists have their own take on this. We need more and better teaching about evolution. We need to help students recognise what natural selection can and cannot do. This means that empirical studies of natural selection in action are valuable. Visitors to exhibits should be encouraged to develop a critical mind, and to ground thinking on hard data rather than on ideology.

I bounced these ideas off a friend whose career has been in musuem practice. He thought it was worth emphasising the importance of both context and evidence:

"While art and aesthetics are generally regarded as largely self-interpreting, this is not so with natural and human history. The evidence is the same. There may be selectivity in displaying it. But a very high proportion of the message is communicated by a different medium and the effectiveness of that medium is all important. Consider also the implications of displaying a homological series (as with MacFadden's horses) or a comparison of genomes without supplementary interpretation. In exercising their imagination, visitors may be influenced by their particular world-view but without the associated evidence, are unlikely to come to well-founded conclusions."

How should publicly-funded museums construct their exhibits? There is a strong case for requiring the self-appointed Darwinian guardians of science to engage in constructive dialogue with other scholars who do not share their confidence in the conceptual model provided by Darwin. There are some important issues to consider, including:

* Encourage critical thinking vs Provide packaged answers
* Reflect controversies in science vs Promote "consensus" science
* Major on displaying collection vs Major on communicating a story

Many scientists today are honest about the way secularisation has influenced the science community. They regard secularisation as an essential characteristic of science, whereas others of us regard secularisation as an unwelcome intrusion that is ultimately destructive of science. Since public money funds many research programmes and also many museums, and since a large proportion of the public have a theistic worldview, there is an urgent need for a broader-ranging debate over these issues. At present, it looks very much like a one-sided discourse about how the 'public understanding of science' can be aligned closer to that of the secularisers. Is it really the task of museum staff to put visitors right when they point out that the exhibited materials do not justify the accompanying commentary?

"Realizing that evolution is potentially a controversial topic, some institutions such as the Australian Museum communicate an explicit policy statement about the role of evolution as part of their mission. Other institutions, such as the Museum of the Earth in Ithaca, New York, provide training to communicate a consistent policy and content about evolution, as well as prepare docents and staff 'on the floor' on how to respond to controversial questions from visitors."

Evolution, museums and society
Bruce J. MacFadden
Trends in Ecology & Evolution, 23(11), November 2008, 589-591

Abstract: Visitors to natural history museums have an incomplete understanding of evolution. Although they are relatively knowledgeable about fossils and geological time, they have a poor understanding of natural selection. Museums in the 21st century can effectively increase public understanding of evolution through interactive displays, novel content (e.g. genomics), engaging videos and cyberexhibits that communicate to a broad spectrum of society, both within the exhibit halls as well as outside the museum.

Quote from Michael Lynch:

"It has long been clear that much of what we see in biology cannot be explained in terms of natural selection alone, yet we continue to witness an unwarranted proliferation of adaptive stories, in some cases extremely bizarre ones, to explain every aspect of existing and extinct biodiversity. What needs to be accomplished will take more than 12 months. More realistically, it will require the education of a new generation of scientists in the basic principles of evolutionary theory that have emerged since Darwin."

Source: Darwin 200: Great expectations, Nature, 456, 317-318 (20 November 2008) | doi:10.1038/456317a

The biological world is full of remarkable nano-machines, each of which is breathtaking in complexity and elegance. Some are particularly worthy of note because they encapsulate design principles which we can appreciate relatively easily. Such is the case with the circadian clock of the prokaryotic cyanobacterium Synechococcus elongates. An informative review article about this subject has been recently published.

The cyanobacterial circadian clock elements
"The clock is composed of three proteins, KaiA, KaiB and KaiC, that together form a circadian clock. At the beginning of the cycle, KaiA (at the top) stimulates the large KaiC hexamer (center), which then adds phosphate groups to itself. Then, as KaiC fills itself up with phosphates, it binds to KaiB (bottom), which inactivates KaiA and allows the phosphates to be slowly removed. As the number of phosphates drops, KaiB falls off and KaiA can start the cycle again." (Source here)

"Cogs and Gears: The Kai Proteins"
The three Kai proteins make up the cogs and gears of the clock. The core is made of KaiC proteins, which alternate between two states: hypophosphorylated and hyperphosphorylated. The other two proteins promote changes between these states in a highly organised manner, based on reactions at specific sites - known as T432 and S431.

"[T]he KaiC phosphorylation cycle comprises four consecutive steps: (i) T432 phosphorylation, (ii) S431 phosphorylation, (iii) T432 dephosphorylation, and (iv) S431 dephosphorylation. This information provides the framework for a reanalysis of the Kai protein structures, suggesting how the in vitro clock might work."

"Why Biological Time Does Not Run Backward"
Research has identified numerous subtleties in the details of the phosphorylation reactions. These suggest reasons why the cycle only works in one direction.

"Overall, the structural information on the phosphorylation events at the KaiCII subunit interfaces and the inter- and intrasubunit interactions formed by the phosphorylated residues indicates that the number of hydrogen bonds increases as first T432 and subsequently S431 is phosphorylated. This progressive increase in molecular interaction would make the reverse reactions unfavorable, causing a built-in ratcheting mechanism that drives the KaiC oscillator unidirectionally."

"How Does This in Vitro Clockwork Tick?"
The researchers found that the protein assemblage could be made to function outside the cell. They have demonstrated that the circadian oscillations keep to time and provide the cell with a clock that does not get swamped by metabolic noise. Conseqently, even cell division does not disrupt the time-keeping: the daughter cells adopt the same time as the parent.

"The unexpected demonstration that KaiC's phosphorylation status continued to cycle when the three Kai proteins are combined in a test tube and ATP was added to provide energy shows that circadian oscillations are not absolutely dependent upon transcriptional and/or translational feedback."

The authors of the review paper set these fascinating details in an evolutionary context, but it should be pointed out that the research is about the operation of the clock, not its origin. Like so many other studies of this type, the evolutionary comments are a veneer on good science: they do not emerge from the research itself. Here are examples:

"The benefit of a clockwork that is imperturbable even when buffeted by the massive intracellular changes of cell division could have provided an evolutionary driving force for convergent circadian clock mechanisms among diverse organisms.
We now recognize KaiABC as a dynamically oscillating nanomachine that has evolved to precess unidirectionally and robustly."

It has not escaped the attention of ID scientists that this nano-molecular clock is the biological equivalent of Paley's watch. It has cogs and gears, it has a 1-way ratchet, it ticks accurately - and it is integrated into the transcription and translation feedback system of the cell. All this can be found in cyanobacteria that are often portrayed as examples of what "primitive" cells look like. Finding this molecular clock leads to a strong design inference, as is traced out by Rana here.

Structural Insights into a Circadian Oscillator
Carl Hirschie Johnson, Martin Egli, Phoebe L. Stewart.
Science 322, 31 October 2008, 697-701 | DOI: 10.1126/science.1150451

Abstract: An endogenous circadian system in cyanobacteria exerts pervasive control over cellular processes, including global gene expression. Indeed, the entire chromosome undergoes daily cycles of topological changes and compaction. The biochemical machinery underlying a circadian oscillator can be reconstituted in vitro with just three cyanobacterial proteins, KaiA, KaiB, and KaiC. These proteins interact to promote conformational changes and phosphorylation events that determine the phase of the in vitro oscillation. The high-resolution structures of these proteins suggest a ratcheting mechanism by which the KaiABC oscillator ticks unidirectionally. This posttranslational oscillator may interact with transcriptional and translational feedback loops to generate the emergent circadian behavior in vivo. The conjunction of structural, biophysical, and biochemical approaches to this system reveals molecular mechanisms of biological timekeeping.

See also:

Rana, F. A Biochemical Watch found in a Cellular Heath, Reasons to Believe, January 10th, 2008

It has long been recognised that Darwinists love to propose adaptationist stories about the origins of particular traits. Very few of them have the word "spandrel" in their working dictionaries. The Neanderthal nose has been considered as an adaptive structure: there must be a reason why Neanderthals had such big noses.

This gent uses XXL tissues. (Source here)

Some years ago, during a study of Neanderthal skulls, Schwartz and Tattersall identified "two triangular bony projections jutting into the front of the nasal cavity from either side". This was considered significant.

"Jeffrey Laitman, an anatomist at Mount Sinai Medical Center in New York who has been studying Neanderthal anatomy, thinks the bony structures probably helped Neanderthals breathe the cold air of Ice Age Europe. The jutting projections, Laitman suggests, could have provided more surface area on which to lay down mucosal coverings to warm and humidify cold, dry air before it reached the throat and lungs. Previous studies have suggested that the large sinus cavities of Neanderthals served a similar function." (Source here)

So, the argument went, the extra surface area was a more efficient heat transfer mechanism, allowing air to be warmed and humidified more effectively before reaching the lungs. This benefit was of adaptive significance to the Neanderthals, and natural selection ensured that the genetic instructions for making these large noses were passed on to subsequent generations. In a Commentary essay, Laitman et al. (1996) thought they were on to something really important:

"The acquisition and processing of oxygen and its by-products the primary mission of any air-breathing vertebrate. Chewing, walking, reproducing, thinking are all fine, but first one has to breathe. Anthropologists sometimes seem to forget this; evolution never does." [snip]
"[. . .] the overall Neanderthal anatomy suggests a group that relied more heavily upon the nasal rather than the oral route for respiration then do living humans. These specializations were very possibly due to respiratory-related adaptations to their environment. [. . .]"
"Although the exact function(s) of mammalian paranasal sinuses remains unclear, and have indeed become the focus of much recent study, it is likely that in Neanderthals they played at least some part in an air-exchange process, perhaps in warming and humidifying cold and dry air."

Notwithstanding all this, some remained unconvinced about the "respiratory-related adaptations". Callaway writes:

"The Neanderthal nose has been a matter of befuddlement for anthropologists, who point out that modern cold-adapted humans have narrow noses to moisten and warm air as it enters the lung, and reduce water and heat loss during exhalation. Big noses tend to be found in people whose ancestor's evolved in tropical climates, where a large nasal opening helps cool the body."

These scholars regarded the Neanderthal nose as an anomaly. Their preferred explanation was that a big nose goes with a big mouth and a wide jaw. In their view, Neanderthal features were all big, and this was sufficient to explain the facial features.

"To put this theory to the test, [Nathan Holton] and University of Iowa colleague Robert Franciscus, measured facial dimensions in dozens of Neanderthals and humans, ancient and modern. By correlating changes in the size of nose width, the distance between canine teeth, and other features, the researchers could determine whether or not big mouths went with big noses."

The results do not confirm the hypothesis. The researchers "found a slight link between nose and mouth, but not enough to explain Neanderthal noses. However, another measurement - the degree to which the face juts forward - seemed a better match for nose width." This suggests a developmental constraint rather than an adaptation.

Why, then, do Neanderthals have faces that jut further out than humans? "They had them because earlier hominids had them," Houlton says. He laments the tendency of some anthropologists to "atomise the body", and explain each of its part as an exquisite adaptation to an environment.

One additional research finding puts a different light on the adaptationist story noted above: "Fortunately for Neanderthals, their inner noses were narrower than the openings suggest, and therefore well adapted to bone-chilling winters." The moral of this incident seems to be: do not trust adaptationists who "atomise" the body and propose just-so stories for particular elements. Organisms are not collections of discrete elements but should be considered holistically. Evolutionary biologists have drunk too deeply at the well of reductionism.

The paradox of a wide nasal aperture in cold-adapted Neandertals: a causal assessment
Nathan E. Holton and Robert G. Franciscus
Journal of Human Evolution, Article in Press | doi:10.1016/j.jhevol.2008.07.001

Abstract: Neandertals have been characterized as possessing features indicative of cold-climate adaptation largely based on ecogeographical morphological patterning found in recent humans. Interestingly, one character that deviates from this pattern is a relatively wide nasal aperture. The ecogeographical patterning of the nasal aperture in recent humans would predict instead that Neandertals should exhibit reduced nasal breadth dimensions. [. . .] The results of these analyses indicate a weaker association between intercanine breadth and nasal breadth than expected, and that more variation in nasal breadth can be explained through basion-prosthion length rather than anterior palatal breadth dimensions. Moreover, the ontogenetic development of anterior palate breadth does not correspond to the growth trajectory of the breadth of the nose. These results explain the apparent paradox of wide piriform apertures in generally cooler climate-adapted Neandertals without resorting to dentognathic constraints, and provide additional insight into both the adaptive and nonadaptive (i.e., neutral) basis for Neandertal facial evolution.

See also:

Callaway, E. Why did Neanderthals have such big noses?, New Scientist, 27 October 2008

Laitman, J.T., Reidenberg, J.S., Marquez, S. and Gannon, P.J., What the nose knows: new understandings of Neanderthal upper respiratory tract specializations, Proceedings of the National Academy of Sciences, 1996 93(20), 10543-10545.

Schwartz J.H. and Tattersall, I., Significance of some previously unrecognized apomorphies in the nasal region of Homo neanderthalensis, Proceedings of the National Academy of Sciences, 1996 93(20), 10852-10854.

According to Jeffrey L. Bada, marine chemist and origin-of-life researcher, "Stanley Miller was the father of origin-of-life chemistry. And he was the leader in that field for many decades [. . .]. It was the Miller experiment that almost overnight transformed the study of the origin of life into a respectable field of inquiry." From there, it entered the textbooks - and although the academic world moved on in its thinking, the textbooks never ceased to present Miller's findings as a major milestone in the quest for a natural origin of life. This research was analysed by Jonathan Wells in his Icons of Evolution and the textbooks were shown to have selectively reported the research and to have almost completely omitted reference to any of the academic critiques of Miller's work.

New tests on old samples reveal new reaction products but nothing to advance the "life assembled itself" paradigm (Source here)

Miller devoted his research activity to building on his 1953 foundations - but without a lot to show for it.

But Miller's ultimate goal, the creation of a living organism in a test tube, eluded him and other researchers. "Making the amino acids made it seem like the rest of the steps would be very easy," he said in a 1996 interview with Reuters. "It's turned out that it's more difficult than I thought it would be". (Source here)

Miller thought he was looking for the "little trick" that would allow amino acids to self-assemble further, but after a life-time's work might have concluded that a paradigm shift was needed. Other researchers developed the concept of self-assembly, notably Sidney W. Fox - the champion of "microspheres". Whereas Miller needed a wet atmosphere to form amino acids, researchers making proteins (forming peptide bonds between amino acids) needed localities that were dry. Miller himself saw the weaknesses of locating the action near a volcanic vent. It might be dry, but the heat energy would prohibit further self-assembly:

More recently, some scientists - such as German chemist Gunter Wachtershauser - have argued that life was more likely to have originated near submarine vents in chemical processes catalyzed by metals. "I have a very simple response to that," Miller said. "Submarine vents don't make organic compounds; they decompose them," because most of the crucial compounds are unstable at high temperatures." (Source here)

Jeffrey Bada, who was once a student of Miller, inherited Miller's archive of materials produced by his many experiments. With others, Bada used modern, more sensitive equipment to analyse the reaction products. He reports finding many new reaction products at levels too low to be detected by Miller, and particular attention is focused on the volcanic experiments.

"We identified 22 amino acids and five amines in the volcanic experiment, several of which had not been previously identified in Miller's experiments. Vials from the other two experiments were also reanalyzed and found to have a lower diversity of amino acids. The yield of amino acids synthesized in the volcanic experiment is comparable to, and in some cases exceeds, those found in the experiments Miller conducted."

A critique of the findings can be found here and here and a more broadly-based assessment is here.
To be realistic, most people in the academic world have moved on. They are looking elsewhere - in many different directions. This blog has drawn attention to some of the challenges and unsolved problems here and here, notably the total inability of researchers to move beyond chemistry to address the information content of all living things.
Rather than rehearse these arguments again, it might be more effective to draw attention to a recent debate between Richard Dawkins and John Lennox at Oxford's Natural History Museum. Melanie Phillips was there and asked Dawkins some probing questions. Among the responses was this:

"Dawkins told me that, rather than believing in God, he was more receptive to the theory that life on earth had indeed been created by a governing intelligence - but one which had resided on another planet. Leave aside the question of where that extra-terrestrial intelligence had itself come from, is it not remarkable that the arch-apostle of reason finds the concept of God more unlikely as an explanation of the universe than the existence and plenipotentiary power of extra-terrestrial little green men?"

It is now apparent that the hypothesis of "life assembled itself" is bankrupt. Most Origin-of-Life researchers realise this and acknowledge that they are dealing with an indescribably low probability occurrence. Some are prepared to move the problem away from planet Earth to some galactic haven where this improbable event actually occurred - leading eventually to intelligent life and their subsequent seeding of life on Earth. Those who are sympathetic to pangenesis, apparently including Richard Dawkins, at least recognise the problems for abiogenesis theories. I ask - when will this message get a proper place in the textbooks? How long will students be told that important discoveries are just around the corner? Why are students not being fed the truth about what abiogenesis research has actually achieved?

The Miller Volcanic Spark Discharge Experiment
Adam P. Johnson, H. James Cleaves, Jason P. Dworkin, Daniel P. Glavin, Antonio Lazcano, Jeffrey L. Bada
Science 321, 17 October 2008: 404. | DOI: 10.1126/science.1161527

Miller's 1950s experiments used, besides the apparatus known in textbooks, one that generated a hot water mist in the spark flask, simulating a water vapor-rich volcanic eruption. We found the original extracts of this experiment in Miller's material and reanalyzed them. The volcanic apparatus produced a wider variety of amino acids than the classic one. Release of reduced gases in volcanic eruptions accompanied by lightning could have been common on the early Earth. Prebotic compounds synthesized in these environments could have locally accumulated, where they could have undergone further processing [. . .]

See also:

Berardelli, P. Did Volcanoes Spark Life on Earth? ScienceNOW Daily News, 16 October 2008

Pease, R. New spark in classic experiments, BBC News, 16 October 2008

Phillips, M. Is Richard Dawkins still evolving? The Spectator, 23rd October 2008

A web-search on the "father of modern philosophy" reveals the name of the Frenchman Rene Descartes. He was totally opposed to the authority given to Aristotle by his peers. Knowledge is not something handed down by an individual or a group of enlightened thinkers: it has to be justified on its merits.

Descartes is remembered for the way he approached the problem: via doubt. He found reasons for doubting everything, but he realised that he could not doubt his own existence. Je pense, donc je suis has gone down in history as Descartes' way of laying a foundation stone. He went on to develop his ideas about the mind being distinct from the body (Cartesian dualism), the certainty of God's existence, the reality of the external world, and ultimately a unified view of everything. His relentless march of reason captured the imagination of many, and Descartes has been hailed as the champion of rationalism, pre-empting the Enlightenment vision by several generations.

Strange things happened to Descartes' body after his untimely death in Sweden. He was buried in 1650 in a churchyard near to Stockholm. 16 years later, his body was exhumed and conveyed in the darkness of night to the residence of de Terlon, the French ambassador. There, the bones were put in a copper coffin and preparations were made for the long journey to Paris. Before departure, some dismembering of the body took place. This was initiated by the ambassador, who

"had requested the authorities that he might himself be allowed, "religiously", to take possession of Descartes' right index finger, the bone "which had served as an instrument in the immortal writings of the deceased"."

Apparently, several other bones disappeared. "The Swedish family that became the proud owners of Descartes' skull - how, it is not clear - had it lovingly inscribed with Latin verses celebrating its significance as a souvenir of the beginnings of rationality. Successive owners added their own signatures and inscriptions testifying to their own 'faith' in the relic." According to the author of the book under review:

"By the time de Terlon's convoy set off for home, [. . .] fragments of the controversial thinker's earthly remains had already started to be dispersed, as admirers licitly and covertly acquired relics - souvenirs to be treasured and revered, and handed down through the generations."

Celebrating reason by acquiring relics of Descartes (Credit: S. Kambayashi)

Another bout of pilfering took place during the French Revolution.

"As reason replaced faith in the new French Republic, Lenoir rescued the bones of France's greatest rationalist from the church of St Genevieve in Paris [. . .]. Meanwhile, on the eve of the Terror, a French revolutionary committee decreed that the bones should be moved to the Pantheon - the new secular cathedral of the revolution - and a statue erected to Descartes' memory. [. . .]
Once again, the whereabouts of Descartes' bones become shrouded in mystery. It is not even clear that Lenoir's rescued remains were those of the father of rationalism. Nor is it clear what happened to them thereafter. They seem to have gone missing among the carefully documented treasures in Lenoir's museum."

What is to be made of the extraordinary hunger for a piece of Descartes' skeleton? Those who praised this champion of reason might be expected to repudiate superstition and the veneration of relics. There is a paradox here for us to consider. The reviewer and the author appear to have come to the same conclusion:

"For Shorto, his own fascination with this curious piece of narrative history is a mirror for the concerns of each and every one of us, bewildered by modernity and struggling to find meaning and belief in a confusing world. [. . .][His] suggestion is, I think, that we cannot escape from our felt need for faith and devotion, and that, deprived of religious relics we turn to secular forms of worship."

Modern-day atheists frequently present themselves as champions of reason (but never acknowledge that Christians see human rationality as a gift of God). They associate superstition with religion and present themselves as having left that behind. Although they have made enormous strides in creating secular cultures in the Western world, it is noteworthy that superstition, horoscopes and New Age practices are widespread. Rationalism as an agenda does not change mankind's innate "felt need" for something more meaningful. "Secular forms of worship" emerge with remarkable ease. Significantly, it is the Christian community that is far better at resisting superstition than the secularists!

"What Americans Really Believe," a comprehensive new study released by Baylor University yesterday, shows that traditional Christian religion greatly decreases belief in everything from the efficacy of palm readers to the usefulness of astrology. It also shows that the irreligious and the members of more liberal Protestant denominations, far from being resistant to superstition, tend to be much more likely to believe in the paranormal and in pseudoscience than evangelical Christians. (Source here)

Rationalists also make a big mistake when they think of the Deism of Enlightenment scholars as peripheral to their philosophical agenda. Descartes himself is illustrative of this. His foundation is often quoted: "I think, therefore I am", but where does that get us? How do we build on that? It does not take us very far! It was not how Descartes developed his Grand philosophical scheme. Descartes' Deism was needed to give validity to reason and to realism.

"He writes that the certainty of his own existence is the "first principle" of his philosophy. But this just turns out to mean that it is the first certainty that he decided to accept, not that anything else is based upon it. Actually, Descartes infers nothing from his own existence. Instead, he asks how he comes to possess this one certainty, so that he can then find other certainties in the same way. The secret of that certainty is just that it involved "a clear and distinct perception of what I am asserting." Crucially, Descartes then introduces God. He offers several arguments for the existence of God, and, having satisfied himself that there must be a God, he reasons that this God, being good, would not allow His creatures to be seriously deceived, provided that they exercise some restraint and confine their beliefs to what they "clearly and distinctly" perceive to be true. Thus Descartes' system of knowledge depends not on his own existence but on God's." (Source: Gottlieb, 2006)

This becomes crucially important when people present science as a secularised Enlightenment project. The problem is: our senses are being asked to do something that can be justified if we presuppose foundations that cannot be justified by our senses alone: intelligibility, realism, rationality. Descartes and the Enlightenment thinkers needed Deism to do this. Today, it is only the Theist or the Deist who can build a philosophically coherent framework for science. Steve Fuller's comment is very much to the point:

"To be sure, scientific progress is sometimes portrayed as the distinctly human extension of this general evolutionary proclivity. But this is to miss entirely the point of science, which is to do with a unified understanding of all reality, not just the specific bits that permit specific groups reproductive advantage. Science does not make sense unless reality possesses a depth that eludes our normal sensory encounters with the world but can nevertheless be accessed with sufficient application under the right conditions. Thus, science presupposes the intelligibility of reality; that its organisation, whatever its ultimate cause, is tractable to the human mind. Evolutionists have been much quicker to explain religion than science itself, yet it is the latter that should worry them, given the peculiar combination of mental dispositions needed to sustain scientific enquiry." (pages 44-45).

Relics of the modern mind
Lisa Jardine
Nature 455, 863-864 (16 October 2008) | doi:10.1038/455863a

BOOK REVIEWED - Descartes' Bones: A Skeletal History of the Conflict Between Faith and Reason, by Russell Shorto, Doubleday: 2008. 320 pp.

See also:

Fuller, S. Dissent over Descent, Icon Books Ltd., Cambridge, 2008.

Gottlieb, A. Think again, New Yorker, 2006-11-20

It has often been noted that Darwinian mechanisms could not operate prior to the first presumed replicating cell. Without replication, there can be no selection - or can there? This is the conundrum addressed by Nowak and Ohtsuki in their attempt to "formulate a general mathematical theory for the origin of evolution". These authors recognise that the origin of the first replicating cell must have had a sophisticated precursor, because otherwise the jump in complexity would have been too great.

"We have proposed a mathematical theory for studying the origin of evolution. Our aim was to formulate the simplest possible population dynamics that can produce information and complexity. We began with a "binary soup" where activated monomers form random polymers (binary strings) of any length. Selection emerges in prelife, if some sequences grow faster than others. Replication marks the transition from prelife to life, from prevolution to evolution. Prelife allows a continuous origin of life."

A prebiotic chemistry is proposed with activated monomers denoted by 0 or 1 (Source here)

As in all simulations, the model has to involve simplifications. First, the authors propose a primordial soup with monomers as active ingredients. These entities have the potential for generating "unlimited information".

"Let us consider a prebiotic chemistry that produces activated monomers denoted by 0* and 1*. These chemicals can either become deactivated into 0 and 1 or attach to the end of binary strings. We assume, for simplicity, that all sequences grow in one direction. [. . .] Each sequence is produced by a particular lineage that contains all of its precursors. In this way, we can define a prebiotic chemistry that can produce any binary string and thereby generate, in principle, unlimited information and diversity. We call such a system prelife and the associated dynamics prevolution."

It is significant that the authors draw attention to "unlimited information" potential, rather than random sequence generation. But biological information requires much more than a specified bit string! Numerous people have wrestled with the thought that the genetic code needs to be translated if it is to have any biological function. Base sequences are no different from junk if there is no machinery to turn the code into something biologically meaningful - and all the machinery that we are aware of is extraordinarily complex. For more on this, go here. Even allowing that sequences could have emerged containing information in code form, we have not progressed conceptually beyond the typing monkey scenario.

The bit sequences are considered to be formed at a quantifiable speed, and it is also premised that the tempo of decay is quantifiable. "Selection emerges in prelife, if different reactions occur at different rates." In this model, the concept of selection is based on the longevity of sequences that spontaneously form in the soup. This use of the word "selection" is confusing, because there is no sense in which one sequence competes against other sequences and demonstrates fitness in the primordial ecology. The authors claim that the information carriers "compete for resources" but this is not convincing. Resources are relevant to the growth of the sequences, but not to the time before they decay. There is nothing about the longer-lasting sequences that can be related to environmental selection.

"Traditionally, one thinks of natural selection as choosing between different replicators. Natural selection arises if one type reproduces faster than another type, thereby changing the relative abundances of these two types in the population. Natural selection can lead to competitive exclusion or coexistence. In the present theory, however, we encounter natural selection before replication. Different information carriers compete for resources and thereby gain different abundances in the population. Natural selection occurs within prelife and between life and prelife. In our theory, natural selection is not a consequence of replication, but instead natural selection leads to replication. There is "selection for replication" if replicating sequences have a higher abundance than nonreplicating sequences of similar length. We observe that prelife selection is blunt: Typically small differences in growth rates result in small differences in abundance."

There are many more issues of simplification that could be explored. However, enough has been said above to justify the conclusion that this paper does not deserve any more attention until the model is validated. This the authors have avoided doing. They make no attempt to justify their assumptions by reference to current thinking about abiogenesis. They say nothing about the importance of testing the model and validating the findings. This is a great weakness of many research programmes based on simulation, where the authors live in virtual reality and think that because they can model it, there is some substance in their work. One could say exactly the same about simulations of evolution: they may have a use in getting across theoretical concepts but they have no established link with the real world.

The media reporting of this paper suggests hype is in the air. Here is the subtitle from Scientific American: "How did self-replicating molecules come to dominate the early Earth? Using the mathematics of evolutionary dynamics, Martin A. Nowak can explain the change from no life to life". The reader is being invited to conclude that Nowak has answers supported by maths, not that he has an entirely tentative hypothetical model, full of unsubstantialted assumptions. Another example comes from the pen of Roger Highfield. He emphasises the suggestions emerging from the research, as though it provides a foundation on which to build. It would be more realistic to portray the proposed scenario as virtual reality, urgently needing a heavy dose of scientific realism:

"An analysis suggests that the soup of chemicals on the early Earth was naturally evolving towards creating the first life, a discovery that suggests alien life should be common. A mathematical analysis of how simple chemicals crossed the threshold between dead and living suggests that natural selection that gave us the vast diversity of life on the planet, from bacteria to tigers, was at work in the primordial Earth too."

According to Nowak: "Mathematics is the proper language of evolution. I don't know what the 'ultimate understanding' of biology will look like, but one thing is clear: it's all about getting the equations right." Getting the equations right is exactly what this blog is about. The scientific approach is to model real-world systems and test the ability of the model to replicate reality. Nowak's danger is giving the impression he has made a contribution to scientific knowledge without making any attempt to validate his model.

Prevolutionary dynamics and the origin of evolution
Martin A. Nowak and Hisashi Ohtsuki
Proceedings of the National Academy of Sciences, Published online before print September 12, 2008, doi: 10.1073/pnas.0806714105

Abstract: Life is that which replicates and evolves. The origin of life is also the origin of evolution. A fundamental question is when do chemical kinetics become evolutionary dynamics? Here, we formulate a general mathematical theory for the origin of evolution. All known life on earth is based on biological polymers, which act as information carriers and catalysts. Therefore, any theory for the origin of life must address the emergence of such a system. We describe prelife as an alphabet of active monomers that form random polymers. Prelife is a generative system that can produce information. Prevolutionary dynamics have selection and mutation, but no replication. Life marches in with the ability of replication: Polymers act as templates for their own reproduction. Prelife is a scaffold that builds life. Yet, there is competition between life and prelife. There is a phase transition: If the effective replication rate exceeds a critical value, then life outcompetes prelife. Replication is not a prerequisite for selection, but instead, there can be selection for replication. Mutation leads to an error threshold between life and prelife.

See also:

Coppedge, D.F. The Prevolution of Evolution: Life Marches In, Creation-Evolution Headlines, 09/17/2008

Highfield, R. Soup of chemicals on primordial Earth was naturally evolving toward life, The Daily Telegraph, 17/09/2008

Wax, H. Using Math to Explain How Life on Earth Began, Scientific American, October 2008.

Cichlid fish have been called "a crucible for evolution studies". Lake Victoria, in Eastern Africa, contains over 500 species of cichlid fish - all members of the same distinctive family, but differing in numerous details of morphology, behaviour and genetics. Since these species can reasonably be inferred to be linked by common ancestry, they are ideal targets for speciation research. Since many of these fish occupy similar ecological niches within the lake, sympatric speciation mechanisms (not involving geographical isolation) have been considered highly probable.

Speciation - something to shout about? (source here)

The new research focuses on light: colouration and factors affecting vision.

"Water clarity and ambient light vary considerably throughout the lake, and fish of many species range in colour. In shallow parts, blue light is dominant, and the waters are populated by blue males of the species Pundamilia pundamilia. As the water deepens, red light becomes increasingly dominant, and greater numbers of red-coloured males of the species Pundamilia nyererei are seen."

The key finding has been an association between ambient light, the colour of the fish and the genetics of colour vision.

"We found a strong association between the visual gene and fish colour," says Seehausen. "Red fish have the gene that shifts vision towards picking up red light, and the blue fish have visual genes that pick up blue light."

This association, although not surprising, is significant for understanding the ecology of the cichlids. Jenny Boughman, an evolutionary biologist, is quoted as saying: "They show a clear segregation between what the fish see, their colour and where they live." The inference follows that visual sensing plays a significant part in male selection. The authors have not argued a convincing case here:

"But [Boughman] says more work is needed, such as evidence that shows it is the difference in female vision that causes them to pick the differently coloured males. Only that, she argues, would prove that vision is driving the speciation."

Nevertheless, a start has been made: "The group also found that some females with blue-biased vision prefer to mate with blue males, and red-biased females mate with red males [. . .]." But these preferences on the part of some animals falls short of rigorous documentation and the species mechanism is still at the level of hypothesis.

So, what has been achieved? Is this a textbook example of evolution? All the reports of this research emphasise the observations that have been made, and it is correct to say that these observations confirm an association of vision-related parameters. Crucial observations of mating behaviour are in short supply and there are no direct observations of speciation. Yet the Nature summary claims the research provides "clear evidence that speciation can occur through sensory drive without geographical isolation". Nature News is more realistic in its assessment: "The new work is the strongest evidence yet that differences in sensory input - in this case, vision - can give rise to new species."

"The strongest evidence yet" involves a correlation between the visual system, body colour and ecology. Instead of this being used to support a hypothesis of sexual selection based on body colouration, the authors claim to have demonstrated sexual selection in action. This has been picked up by the media as fact: "a fish species in the cichlid family has been observed by scientists in the act of splitting into two distinct species in Lake Victoria" (Source). The cover of Nature proclaims that this is "a textbook example of evolution in action".

Let us suppose that the hypothesis is tested and confirmed, and the "sensory drive speciation" is validated. What are the implications for our understanding of evolution? It means that an ancestral fish population can split into two or more populations on the basis of colour. The daughter populations have differences in sensitivity to light frequencies and differences in body colouration. These may be accompanied by other ecological adaptations. There is no new genetic information - just fine-tuning of existing genetic systems. There is no evidence that these new species lack the potential to interbreed. Indeed, the differences are so slight that hybridisation to produce fertile offspring can be predicted with some confidence.

The claim of "evolution in action" will mean different things to different people. To ID scientists, it means that relatively trivial variations can and do occur in living things. These variations allow organisms to diversify and prosper in new ecological niches as they become accessible. However, these variations have nothing to do with the origin of cichlids, eyes or complex specified information. To most evolutionary biologists, apparently, it means that all the big questions of biological origins can, in principle, be solved. If we can demonstrate speciation in action, then we can rest assured that we also have an explanation of the origins of families, orders, phyla, organs and organelles. Evolutionary biologists can then repeat the mantra that nothing in biology makes sense without evolution.

The punchline: ID scientists are not opposed to the teaching of evolution in schools, but want it taught properly - allowing critical appraisal and the recognition of spin. Let speciation in cichlid fish enter the textbooks, not as a proof of evolution, but as an example of how evidence is brought to bear on current hypotheses of the origin of species.

Speciation through sensory drive in cichlid fish
Ole Seehausen, Yohey Terai, Isabel S. Magalhaes, Karen L. Carleton, Hillary D. J. Mrosso, Ryutaro Miyagi, Inke van der Sluijs, Maria V. Schneider, Martine E. Maan, Hidenori Tachida, Hiroo Imai & Norihiro Okada
Nature 455, 620-626 (2 October 2008) | doi:10.1038/nature07285

Abstract: Theoretically, divergent selection on sensory systems can cause speciation through sensory drive. However, empirical evidence is rare and incomplete. Here we demonstrate sensory drive speciation within island populations of cichlid fish. We identify the ecological and molecular basis of divergent evolution in the cichlid visual system, demonstrate associated divergence in male colouration and female preferences, and show subsequent differentiation at neutral loci, indicating reproductive isolation. Evidence is replicated in several pairs of sympatric populations and species. Variation in the slope of the environmental gradients explains variation in the progress towards speciation: speciation occurs on all but the steepest gradients. This is the most complete demonstration so far of speciation through sensory drive without geographical isolation. Our results also provide a mechanistic explanation for the collapse of cichlid fish species diversity during the anthropogenic eutrophication of Lake Victoria.

See also:

Kirkpatrick, M. & Price, T. Sensory ecology: In sight of speciation, Nature 455, 601-602 (2 October 2008) | doi:10.1038/455601a

Gilbert, N. What you see is how you evolve, Nature News, 1 October 2008 | doi:10.1038/news.2008.1144

One of the more notable fossil finds this year concerns a juvenile gecko lizard, less than an inch long, parts of which were preserved in amber. The researchers have studied a posterior lower limb and foot, and a partial tail. "The discovery has been announced as a new genus and species of gecko, now extinct, and has been named Cretaceogekko. It had a striped pattern that probably served as camouflage."

The tiny foot of Cretaceogekko: a Cretaceous species with modern sophistication. (Image here)

The find is remarkable on two counts. The first is that this specimen nearly doubles the reported age of the oldest known fossil gecko. The previous record was Lower Eocene, but the new find takes us back well into the Age of Dinosaurs. Today, there are about 2000 species of gecko, allocated to nearly 100 genera. There is therefore great natural variability in the group, and it is not surprising that the fossil should be assigned to a new genus. Stasis at the family level is demonstrated: the Gekkonidae have been stable over geological time. This is an observation that needs greater emphasis in education about the history of life on Earth. Evolutionists are so keen to focus on small variations that they miss the big picture, which is that stasis, rather than transformation, characterises the fossil record.

Secondly, the researchers report the presence of "sophisticated adhesive toe pads". The pads on the toes were observed to have "transverse lamellae probably bearing numerous hairlike setae found in many modern geckos".

"The tiny foot of this ancient lizard still shows the tiny "lamellae," or sticky toe hairs, that to this day give modern geckos their unusual ability to cling to surfaces or run across a ceiling. Research programs around the world have tried to mimic this bizarre adhesive capability, with limited success." [For more on recent research, go here].

A good case can be made for gecko setae being irreducibly complex as an aggregated structure. A few setae are useless - there is no significant adhesion. There is no rationale for setae to accumulate on the feet of ancestral geckos, because there is no identifiable functionality unless the assembly is a fully formed. Merely having setae is not enough either, as is clear from the difficulties of producing biomimetic products. If intelligent agency is having a hard time emulating the gecko mechanism for adhesion, it is not unreasonable to ask whether intelligent agency was involved in designing and engineering the real thing. In support of the irreducible complexity argument, it is significant that these toe pads are fully formed in the very oldest specimen known to us. We do not see any transitional structures. This creates an enormous problem for theories of gradual transformation, which must defend a step-by-step route for climbing Mount Improbable. Geckos appear fully formed, and it is the Darwinists that are found contending with the data in order to preserve their theory.

A 100 million year old gecko with sophisticated adhesive toe pads, preserved in amber from Myanmar
E. Nicholas Arnold & George Poinar
Zootaxa, 1847: 62-68 (11 Aug. 2008)

Abstract: A new genus and species of gecko is described from a posterior lower limb and foot, and a partial tail, preserved in Lower Cretaceous amber from Myanmar that is 97-110 My old. It appears to be the oldest unequivocal fossil gecko, predating fragmentary skeletal remains from the Upper Cretaceous and being 43-56 My older than Yanatarogecko from the Lower Eocene, previously the oldest known gecko preserved in amber. It also provides firm evidence that gekkotans and possibly gekkonids were in Asia at this time. The Myanmar specimen shows, that the distinctive foot proportions and sophisticated adhesive mechanism, involving pads on the toes with transverse lamellae probably bearing numerous hairlike setae found in many modern geckos, had already evolved around 100My ago. The specimen is very small, even compared with juveniles of the smallest living geckos. However, the high numbers of lamellae on its toe pads suggest it is from a juvenile of a species with relatively large adult body size.

See also:

Oldest Gecko Fossil Ever Found, Entombed In Amber, ScienceDaily (Sep. 3, 2008)

Tyler, D. Gecko feet set the standard for adhesion, ARN Literature Blog (25 July 2007)

The challenge of working at the nanometre level of detail is one that few people can even comprehend. Despite all the media interest in these new technologies, and despite hearing explanations of the first principles many times, it is still mind-blowing! It is not so surprising, therefore, that people have turned to the natural world, where nano-sized machinery is operating within every cell, and where the variety of mechanisms provides a powerful stimulus for innovation.

"[N]ature illustrates that we are nowhere near the limit of exquisite control over organization; it possesses an extraordinary capacity to assemble complex nanostructures with active and specialized functions. Our ability to precisely position components on the nanometer scale the way nature does, and to do so in a parallel rather than a serial manner, is still limited and is a key goal in nanotechnology and materials science."

Results of some early stage research on DNA nanotechnology.

A review paper has just appeared, looking at the potential of DNA nanotechnology. In the natural world, DNA provides materials for self-assembly and the coordination of the process. Can this be utilised by nanotechnologists working with sequences they have put together. The answer is a resounding yes.

"Of the natural self-assembling molecules, DNA is arguably the most remarkable. A cooperative interplay of hydrogen-bonding, [pi]-stacking, electrostatic, and hydrophobic interactions drives one DNA strand to assemble with its complement into a double helix according to extremely precise base-pairing rules. Additional attributes, such as rigidity on the nanoscale, a diameter of ~2 nm, and a near-infinite number of potential sequences, extend DNA's reach beyond a genetic blueprint for life. DNA is emerging as an attractive tool for nanoscience as well; it is a highly promising template for organizing nanomaterials in a programmable way."

The review is well worth reading and there is little merit in summarising. Researchers have moved from 1D molecules to 2D and 3D structures. A great variety of techniques have been developed, providing a rich toolbox for nano-construction projects. "It is of note that in structural DNA nanotechnology, DNA is used to provide all the parameters for self-assembly: connectivity, structural features, and programmability." Synthetic DNA sequences can be made to fold in predetermined ways.

"Hairpins were incorporated into stapling strands to write words, such as "DNA," and to draw complex objects, such as the outline of the Western Hemisphere. DNA origami will be useful for accessing larger DNA shapes with highly addressable surfaces."

Of particular interest is where this research is heading. There are two major challenges: "the correction of errors that arise in DNA assembly, and the replication and scale-up of DNA nanostructures." Regarding error correction:

"As the complexity of DNA assemblies increases, so will the number of the DNA sequences required to form them. This will necessitate using overlapping, degenerate strands that may assemble into undesirable products. Biological systems have developed a number of elegant strategies to proofread and remove errors during and after assembly. Inspired by these systems, Lu used an approach in which deoxyribozymes (DNAzymes) specifically locate and cleave misassembled structures in gold nanoparticle assemblies. In the presence of the "correct" DNA strands, the DNAzyme is not properly folded and is inactive; however, in the presence of the "incorrect" DNA strands, the DNAzyme is properly folded and proceeds to cleave and remove the errors."

Scaling-up again draws inspiration from biological systems. Throughout the review, "Nature" is portrayed as an agent. Nature does this and Nature does that. When such sophistication is on display, it is difficult to insist on the natural world being a Blind Watchmaker - the product of 'chance and necessity'. This research is crying out for a foundation in design-thinking. Even with our best efforts as intelligent agents, we are just scratching the surface of what we find in living things. Nanotechnology in the natural world reveals exquisite design, not the products of tinkering. It deserves to be credited as the product of intelligent agency!

"Nature builds complexity in a hierarchical way. It progressively increases length scales and relies on a number of noncovalent interactions, including DNA base-pairing, to drive assembly. Supramolecular DNA assembly is a means to weave in principles of hierarchical complexity and new interactions into DNA nanostructures, and opens the door to assembling more diverse functional structures with greater ease."

Assembling Materials with DNA as the Guide
Faisal A. Aldaye, Alison L. Palmer, and Hanadi F. Sleiman
Science 321, 26 September 2008: 1795-1799.

Abstract: DNA's remarkable molecular recognition properties and structural features make it one of the most promising templates to pattern materials with nanoscale precision. The emerging field of DNA nanotechnology strips this molecule from any preconceived biological role and exploits its simple code to generate addressable nanostructures in one, two, and three dimensions. These structures have been used to precisely position proteins, nanoparticles, transition metals, and other functional components into deliberately designed patterns. They can also act as templates for the growth of nanowires, aid in the structural determination of proteins, and provide new platforms for genomics applications. The field of DNA nanotechnology is growing in a number of directions, carrying with it the promise to substantially affect materials science and biology.

When big mistakes are made, time for reflection is well spent. The departure of Professor Michael Reiss from the post of Education Director of the Royal Society counts as a big, big mistake. In an Editorial in Nature, the media are called to account:

"The headlines were damning. [. . .] The reports were wrong. [. . .] Nature was not privy to the conversations between the reporters and editors responsible for this story, so we will leave it to them to consider how such a gross misrepresentation could have happened, and what lessons to draw from it."

A teachable moment - but will anything be learned? (Source here)

The Editorial suggests there are lessons to be learned, but is not prepared to say what those lessons are. However, this is not good enough! Media reporters are not fools, making stories up. They have been encouraged by science leaders to respond to Creationism and Intelligent Design in quite specific ways: lumping them together as the same message, declaring them to be dogma and alien to science, etc. None of this is true, but that's what the science journalists have been groomed to write. So when Michael Reiss comes along saying things that could have been said by a Creationist or an ID advocate, he was treated like an apostate from the community of science.

What about the Royal Society, the public statements of some of its Fellows, and the behind-the-scenes crisis talks? "Nor was Nature privy to the Royal Society's internal deliberations about Reiss, so we will leave it to the officers and fellows of that body to reflect on who has done the most to damage its reputation." Although it is clear that the Editors of Nature are not impressed by the conduct of the Royal Society, they do not suggest any specific lessons to be learned. This is an inadequate response. They could easily have pointed out that Reiss' academic freedom has been overridden by 3 Nobel laureates and others who insisted in his removal. These men cannot be allowed the luxury of saying 'we misunderstood what Reiss was saying' - if they had misunderstood him, they have had ample time to realise their mistake and he ought to be reinstated by now. No, they disagreed profoundly with Reiss' position and they wanted him out. This bigotry matches the vitriol documented against ID advocates in the film Expelled. Antagonism towards anyone who does not conform to the secularist view of science is intense.

The Editors of Nature try to associate Reiss' counsel with that of Eugenie Scott in California:

"Those who argue that allowing discussion of creationism in a science class gives it legitimacy, and that students who ask about it should be firmly directed to take their questions elsewhere, are misguided.
Eugenie Scott, executive director of the National Center for Science Education in Oakland, California, [. . .] points out that in the real world, any such shut-up-and-take-it-elsewhere response from the teacher will inevitably be perceived by the student (and his or her classmates) as a humiliating personal put-down. It will obstruct rather than encourage enquiry and understanding. It will also invite complaints from outraged parents.
What is more, it will squander what experienced educators like to call 'a teachable moment'. All too often, that moment is the one opportunity that a school has to engage resistant students and introduce them to what science has to say."

However, Eugenie Scott does not capture the heart of Reiss' message - which is not based at all on pragmatism. Reiss identifies creationism as a worldview. He identifies ID as a worldview. Within these alternative worldviews, data takes on different meanings. Observed evidences of variation in nature do not count as evidence for macroevolution; homology carries a design message and does not necessarily point to common ancestry; creation-based biology or design-based biology is regarded as testable. To say these approaches to the evidence are "scientifically nonsensical creationist beliefs" goes contrary to the point Reiss has been making. Trying to equate his principled thinking to the pragmatism of Eugenie Scott suggests confusion about these issues. For more on this, go here.

The Michael Reiss incident is a good example of a "teachable moment". There are lessons for science journalists, Royal Society Fellows, and the Editors of Nature. Will this moment be squandered by fudging the issues that have stirred this debate?

Creation and classrooms
Editorial
Nature 455, 431-432 (25 September 2008) | doi:10.1038/455431b

Abstract: Better to confront superstition with science than to disregard the superstitious.

First para: The headlines were damning. "Leading scientist urges teaching of creationism in schools," proclaimed Britain's The Times newspaper on 12 September, echoing the headlines appearing that day in numerous other British media. The stories asserted that Michael Reiss, a biologist and educational researcher, an ordained Anglican minister and (at the time) the education director of the Royal Society, had explicitly advocated that state-school biology classes teach creationism.

It seems that every organisation connected with science has leaders who feel the need to make statements opposing intelligent design and creationism. Whilst most of these get no further than the press release, one has made it to the pages of Genome Biology. The author is Gregory Petsko, President of the American Society for Biochemistry and Molecular Biology (ASBMB ). The first paragraph sets the tone: "the Discovery Institute, that bastion of ignorance, right-wing political ideology, and pseudo-scientific claptrap, the creationist movement has mounted yet another assault on science." The "assault on science" is considered to be partly propaganda and partly legislative. Leaders like Petsko appear to be afflicted with a form of schizophrenia: when writing as scientists, they are rational and moderate; but when confronted by ID or creationism, they erupt in a frenzy of wild assertions.

The search for Frankenstein's monster is ever with us (Source here)

The propaganda charge relates to the film Expelled: No intelligence allowed. It seems to be of little concern to Petsko that the Discovery Institute is not responsible for this film. Knowledge that they have been positive about it is deemed sufficient to incriminate the organisation. Furthermore, Petsko points readers to Richard Dawkins' web site for a "spirited attack on the film" rather than summarising the substance of his charge of propaganda. The really disturbing thing is that there is no sense of outrage that academic freedom has been compromised in the treatment meted out to ID sympathisers. Instead of acknowledging that numerous research scientists have been given a very hard time by evolutionists, the message is implicit that they deserve all they get. Later, Petsko refers to teachers who want to teach creationism in a science class:

"What about the academic freedom argument? If someone wants to teach creationism in a science class, shouldn't they have the right to do so? Certainly - if they want to get fired. Because if they do that they deserve to get fired. It has nothing to do with academic freedom; it's about basic competence."

None of the people documented in Expelled set out to teach creationism. One was an editor of a journal who saw through the peer review process of an ID research paper before publishing it. Others were ID sympathisers whose ambitions to pursue research interests were thwarted by colleagues who insisted "It has nothing to do with academic freedom; it's about basic competence." In the UK, we have just witnessed the removal of Michael Reiss from his position as Education Director of the Royal Society because he did not buy into the dogmatic stance of secularised science demanded by his peers. He is an evolutionist, yet influential scientists deemed him guilty of incompetence. It is good to read some letters supportive of Michael Reiss in today's Independent:

"That a pressure group which appeared to have a limited grasp of the article could pillory a respected science educator to the point of resignation is a lasting disgrace" (Michael Poole),
and
"Michael Reiss is one of the most distinguished science educators we have, [. . .] I am simply surprised that the Royal Society is unable to understand the message that they are conveying to the public, that they are unable to defend and explain the simple argument that their director of education was proposing" (Professor David Waddington).

The second charge brought by Petsko relates to legislation and, in particular, the decision of the Louisiana House of Representatives to approve overwhelmingly a bill supporting academic freedom in teaching controversial issues in science. Possible areas of application were said to be evolutionary theory, the origins of life, global warming and human cloning. The pressure groups promoting evolutionary theory have repeatedly decried the idea that there is any controversy involved. Here is Petsko:

"Let me say this as clearly as possible, so there can be no mistake about what I mean: there is no controversy. Just because a few misguided so-called scientists question the validity of the concept of evolution doesn't mean there is a controversy. [. . .] The fact that some people believe nonsense does not give that nonsense scientific credibility. A challenge to existing scientific principles must be based on evidence, not on belief, and there isn't a shred of evidence to support either creationism or intelligent design. Those ideas belong in a religion or philosophy class, not in a science class."

It is sad to see these words repeated yet again. The Dissent from Darwin list was initiated to put to rest the claim that there was no dissent from Darwin coming from scientists. To call these people a "few misguided so-called scientists" tells us more about Petsko's grasp of the issues than anything else. The problem is that the evolutionary biology pressure groups cannot afford to have any critical scrutiny of their theories, because they know that many of their cherished dogmas are highly vulnerable. They have to insist that any discussion belongs outside science, because the dissenters actually appeal to evidence when they make their arguments! None of this, of course, is saying that we need to teach creationism or intelligent design in schools. The goal in science is to develop skills of critical thinking and reasoning from evidence. For previous posts on these issues, go here, here, here, here and here.

Petsko gave his message the title "It is alive". He likens the perceived threat to "Frankenstein's monster". He writes: "we must all arm ourselves with the one weapon we have that in the end the monster cannot overcome: the truth." There is some hope for a dialogue once it is realised that all those involved in education are committed to truth. ID scientists are not playing games: they are committed to truth - and they see the evidence of intelligent design through their research work. Creationists also are committed to truth. If we can break out of the stereotyped mental images of each other, there is perhaps a constructive way forward.

It is alive
Gregory A Petsko
Genome Biology 2008, 9:106 | doi:10.1186/gb-2008-9-6-106
Reprinted in ASBMB Today, pages 3-4 (August, 2008)

Abstract: We need to familiarize ourselves with the facts of evolution, so that we can mount a spirited defense against creationism and the forces of ignorance.

See also:

Luskin, C. NCSE Promotes Shrill Editorial Suggesting "Students be Forced to Consider the Possibility that There Is No God", Evolution News & Views, 15 September 2008

Professor Michael Reiss is a specialist in science education in the University of London who has been seconded to be the Royal Society's Director of Education. This latter post has been abruptly terminated because remarks made by Reiss were considered to have "led to damage to the Society's reputation". The Royal Society's Press Release is here. The controversy flared up at the same time as Reiss' refereed paper on these issues appeared in Studies in Science Education. We will briefly review aspects of that paper and why Reiss' views were considered outrageous by some senior Fellows of the Royal Society, including three Nobel Laureates.

The most significant aspect of Reiss' paper is the way he handles science. He presents several perspectives of science and considers the educational benefits of getting students to evaluate them.

"One approach that I have found to be of worth in science classes with undergraduates training to be science teachers is, when teaching about the nature of science, to get them to think about the relationship between scientific knowledge and religious knowledge. What seems to work well is to ask students, either on their own or in pairs, to illustrate this by means of a drawing and then for all of us in the class to discuss the various drawings that result. See, for example, the hypothetical representation in Figure 1. A person producing the representation in Figure 1 sees both religious and scientific knowledge as existing but envisages [. . .] no overlap between the two."

An alternative rendering of Reiss' Figure 1: The purported separation of religious knowledge and scientific knowledge (Source here)

This model is, of course, that popularised by Gould in his NOMA approach and often promoted by scientific societies wanting to reassure the public that science offers no threat to religious views. It is, however, not a consensus perception of the science-religion relationship. Reiss goes on to give 2 more figures (not reproduced here).

"However, there are many for whom scientific knowledge and religious knowledge are not distinct. At one end are those who draw religious knowledge as being much smaller than scientific knowledge and wholly or partly contained within it (Figure 2); at the other are those whose worldview is predominantly religious (Figure 3). Understandings of the relationship(s) between science and religion vary greatly, at least in part because of considerable variation in how people conceptualise both science and religion. The visual metaphor in Figures 1, 2 and 3 can be taken too far but it can serve as a useful heuristic device."

Reiss' view is that these different perceptions of science are very important for the teaching of issues where science and religious thinking addresses the same topics. These different models represent different paradigms about the world. Indeed, he uses the word "worldview" in this context. He writes: "The strongest argument, in my view, for teaching anything about religion in a science class, whether at school, college or university, is if it helps students better to understand science." This is a simple point, but Reiss has put his finger on the heart of the matter. There is no one "correct" perception of what science is! If the philosophy of science is steam-rollered into any of the above models, it leads to a breakdown of communication and there is no meaningful debate. Thus, those who have adopted a Figure 1 model (or, like Richard Dawkins, deny that religious knowledge even occupies a separate domain) will always treat religious knowledge as, at best, ascientific. They have no option but to say that design-based or creation-based approaches to origins lie outside science.

"Would one want explicitly to teach about creationism in science lessons? Both the knee-jerk and the considered reaction from most scientists and science educators has been 'no'. Here my interest is not in the legal situation that obtains in any one country [. . .] nor in the undoubted demands that teaching in this area can place on teachers but in whether it would be desirable on educational grounds to teach about creationism in science lessons. Given the preceding paragraph, I would not want any such teaching, were it to occur, to give the impression that creationism and the theory of evolution are equally valid scientifically. They are not (and nor is it appropriate to insist on spending equal amounts of time on evolution and creationism in science lessons).
"However, I do not belong to the camp that argues that creationism is necessarily nonscientific. For all that I have no doubt that the overwhelming majority of those who believe in creationism (and intelligent design theory) do so because of their religious beliefs it is logically possible to hold that evolution (sensu major anatomical, physiological, genetic and biochemical changes in organisms over long periods of time) has not happened."

Although Reiss writes as one satisfied with the validity of evolutionary theory, he recognises that it is possible for people with alternative worldviews to interpret the data differently. The relatively high proportion of young people entering schools and colleges with these alternative worldviews makes it imperative to bring issues of creation and design into science education. In his long paper, Reiss covers many other points than those reviewed here. From his conclusion:

"I have examined here the nature of the issue both in general terms and with reference to particular topics. I have argued that there are good reasons for students being introduced to aspects of the science/religion issue in science lessons. Such teaching is not easy, but done well it can be respectful of students, motivating and fulfilling for them and help them to learn more about the nature and content of science."

Michael Reiss' arguments are modest and rational. Although he is aware that others take a different view, he has set out, in good faith, his reasons for introducing discussions of creation and intelligent design in science education. The Times reports some of the reaction thus:

His resignation comes after a campaign by senior Royal Society Fellows who were angered by Professor Reiss's suggestion that science teachers should treat creationist beliefs "not as a misconception but as a world view". Sir Richard Roberts, who won the Nobel Prize for Medicine in 1993, described such views as outrageous, and organised a letter to the society's president, Lord Rees of Ludlow, demanding that Professor Reiss be sacked. Phil Willis MP, the chairman of the Commons Innovation, Universities, Science and Skills Committee, was due to meet Royal Society officers today to demand an explanation of Professor Reiss's comments."

To his credit, Richard Dawkins was prepared to differ from his colleagues: "To call for his resignation on those grounds, as several Nobel-prize-winning Fellows are now doing, comes a little too close to a witch-hunt for my squeamish taste." The influential Lord Winston was also unable to support the call for Reiss to be sacked:

Reacting to his stepping down, Lord Robert Winston, professor of science and society at Imperial College London, said: "I fear that in this action the Royal Society may have only diminished itself. This is not a good day for the reputation of science or scientists. This individual was arguing that we should engage with and address public misconceptions about science - something that the Royal Society should applaud." (Source: BBC News)

There are many who have dismissed the documentary Expelled as worthless, but its witness to discrimination within the academic world is of great importance. Now we find another casualty - someone who is a supporter of evolution but who dared to step outside the boundaries set by the self-appointed gatekeepers of modern secular science. When will these people be called to account?

Robert Matthews has a powerful conclusion to his blog:

"The motto of Royal Society is 'Nullius in verba' - roughly speaking, take no-one's word for it. Its treatment of Reiss suggests that when it comes to words of dissent, the attitude of the Royal Society is closer to that of a madrassa than a learned body."

Should science educators deal with the science/religion issue?
Michael J. Reiss
Studies in Science Education, 44(2), September 2008, 157 - 186 | DOI: 10.1080/03057260802264214

Abstract: I begin by examining the natures of science and religion before looking at the ways in which they relate to one another. I then look at a number of case studies that centre on the relationships between science and religion, including attempts to find mechanisms for divine action in quantum theory and chaos theory, creationism, genetic engineering and the writings of Richard Dawkins. Finally, I consider some of the pedagogical issues that would need to be considered if the science/religion issue is to be addressed in the classroom. I conclude that there are increasing arguments in favour of science educators teaching about the science/religion issue. The principal reason for this is to help students better to learn science. However, such teaching makes greater demands on science educators than has generally been the case. Certain of these demands are identified and some specific suggestions are made as to how a science educator might deal with the science/religion issue.

See also:

Matthews, R. Royal Society or Rotten Society? (First Post, September 17, 2008)

Reiss, M. Science lessons should tackle creationism and intelligent design, (Guardian Science Blog, September 11 2008)

It is widely recognised that dogs provide a fine example of one species (a domesticated wolf) whose different breeds exhibit very large variations in morphology. Some of these variants have a genetic origin, and the details of one of these traits (hairlessness) have recently been clarified.

"The American Kennel Club lists three breeds of hairless dogs: the Chinese crested; [. . .] the Mexican hairless dog; and the Peruvian Inca Orchid dog. These canines typically live a normal life span, though they lack the full set of 42 teeth common to other adult dogs. Researchers have long known that a dominant gene causes this set of abnormalities, called canine ectodermal dysplasia (CED). That means dogs need only inherit one copy of it to be bald; with this particular gene, two copies are lethal. But the gene itself remained a mystery."

Chinese crested dogs: hairless and coated. Graphic here (Tosso Leeb)

It is a mystery no longer, thanks to some detective work by a team of scientists led by Tosso Leeb, a veterinary geneticist at the University of Bern, Switzerland. According to one writeup, "Because Chinese crested dogs have been inbred for decades, the genomes of any two dogs are nearly identical, and slight variations are very apparent." So the researchers compared the genomes of hairless animals with those of "powderpuffs" - the same breed but with more normal hair.

"The technique, called genomewide association mapping, turned up a suspicious-looking region on chromosome 17. To investigate further, Leeb and his team collected additional DNA samples from a wider array of hairless and coated dogs. In all, they looked at 93 hairless and 49 coated Chinese crested dogs, 39 hairless and six coated Peruvian hairless dogs, and eight Mexican hairless dogs (there is no coated counterpart). Mapping the chromosome 17 sequences revealed an insertion of seven letters, or base pairs, of genetic code in a gene called FOXI3 in all of the hairless dogs. Although the exact function of the FOXI3 gene is unknown, other genes in the FOX family control embryonic development in mammals."

FOXI3 appears to function as a switch, with the mutation knocking out the normal development of parts of the unfortunate animal. "Leeb says the mutation most likely interferes with the genetic instructions for hair and teeth proteins, causing CED in dogs." There is particular interest because of the possible implications for humans:

"As it turns out, the human genome sequence that scientists use as a gold standard for deciphering genetic information contained a mistake in the FOXI3 gene, making it impossible for computer programs to find it. Another human sequence contains the correct information, confirming the existence of FOXI3 in people, as well as in mice and dogs, Leeb says."

Apparently, the team are currently engineering the FOXI3 mutation in mice, to find out more. The expectation is that the mutation will have comparable effects in mice, dogs and humans. One commentator suggested this could be a "starting point for research on new baldness remedies in humans".

So, the nature of this mutation is that it is a degeneration of the genome. There is no new information, but rather a loss leading to decreased functionality. These mutants are kept alive by mankind, whether they be Aztecs who considered them sacred nearly 4000 years ago, or whether they be proud owners who are prepared to pay $1000 for the experience of having one as a pet. Outside these environments, they would soon die. The take-home message is that these dogs are witnesses to the largely negative impact of mutations on living things. Darwinists have a hard task when they set out to convince the world that the rare occasional mutation is responsible for building complexity. We are rather short of any good examples of this.

This poor little rascal knows what it's like to have part of his genome deleted (Source here)

A Mutation in Hairless Dogs Implicates FOXI3 in Ectodermal Development
Cord Drogemuller, Elinor K. Karlsson, Marjo K. Hytonen, Michele Perloski, Gaudenz Dolf, Kirsi Sainio, Hannes Lohi, Kerstin Lindblad-Toh, and Tosso Leeb.
Science 321, 12 September 2008: 1462.

Abstract: Mexican and Peruvian hairless dogs and Chinese crested dogs are characterized by missing hair and teeth, a phenotype termed canine ectodermal dysplasia (CED). CED is inherited as a monogenic autosomal semidominant trait. With genomewide association analysis we mapped the CED mutation to a 102-kilo-base pair interval on chromosome 17. The associated interval contains a previously uncharacterized member of the forkhead box transcription factor family (FOXI3), which is specifically expressed in developing hair and teeth. Mutation analysis revealed a frameshift mutation within the FOXI3 coding sequence in hairless dogs. Thus, we have identified FOXI3 as a regulator of ectodermal development.

See also:

Callaway, E., When being bald and ugly is the lesser of two evils, (New Scientist, 11 September 2008)

Saey, T.H. A 'foxi' gene for dog baldness, (Science News: Thursday, September 11th, 2008)

Zelkowitz, R. How Much Is That Baldie in the Window? (ScienceNOW Daily News, 11 September 2008)

Austin Hughes does not mince his words in describing a "major hindrance to progress" in understanding the evolutionary past. He claims that a major factor has been "confusion regarding the role of positive (Darwinian) selection". This addresses some fundamental issues in evolutionary biology because, for many, any evidence of adaptation is automatically interpreted as natural selection favouring adaptive mutations. But yes, just in case you think Hughes might qualify his charge elsewhere, read on and find that he makes it even more explicit!

"To biologists schooled in Neo-Darwinian thought processes, it is virtually axiomatic that any adaptive change must have been fixed as a result of natural selection. But it is important to remember that reality can be more complicated than simplistic textbook scenarios."

"If you have variation, differential reproduction, and heredity, you will have evolution by natural selection as an outcome. It is as simple as that." (Source here)

The problem is not one that can be easily corrected, because it is endemic. According to Hughes: "Thousands of papers are published every year claiming evidence of adaptive evolution on the basis of computational analyses alone, with no evidence whatsoever regarding the phenotypic effects of allegedly adaptive mutations." The researchers have adopted a mindset which blinds them to alternative approaches to handling the data. The problem relates to codon-based methods of testing for positive selection. We do not need here to go over the theory behind these methods, nor follow how Hughes arrives at the view that there has been an "unwarranted generalization" from one case to all cases. However, we can note this conclusion:

"Yet, despite their shaky foundations, numerous publications have used these methods as the basis for claims of positive selection at the molecular level."

The trigger for the alarm bells sounding is a paper by Yokoyama et al (blogged here). Hughes sees this paper as a model of its kind, establishing the genetic basis for variation and devising tests for positive selection which allow conventional thinking to be scrutinized.

"It is to be hoped that the work of Yokoyama et al. will help put an end to these distressing tendencies. By incorporating experimental evidence regarding the phenotypic effects of reconstructed evolutionary changes, this study sets a new standard for studies of adaptive evolution at the molecular level."

The take-home message is that (bad) theory has dominated empirical analysis for too long in evolutionary biology. It is time to put things in order. We need less reliance on the deductive framework provided by neo-Darwinism, and more attention to empiricism and induction. (For a previous blog related to this, go here). Hughes calls for a new standard in research:

"In recent years the literature of evolutionary biology has been glutted with extravagant claims of positive selection on the basis of computational analyses alone, including both codon-based methods and other questionable methods such as the McDonald-Kreitman test. This vast outpouring of pseudo-Darwinian hype has been genuinely harmful to the credibility of evolutionary biology as a science."

With these thoughts in mind, it may be worth revisiting topics (here, here and here) that have been discussed previously: drawing attention to the way theory dominates the interpretations placed on data, and how researchers are curiously blind to alternative approaches to handling the same data. This is Kuhnian "normal" science. It preserves the paradigm - but at what cost?

The origin of adaptive phenotypes
Hughes, Austin L.
Proceedings of the National Academy of Sciences, 105(36), 13193-13194, September 9, 2008 | doi: 10.1073/pnas.0807440105.

First Paragraph: Sequences of DNA provide documentary evidence of the evolutionary past undreamed of by pioneers such as Darwin and Wallace, but their potential as sources of evolutionary information is still far from being realized. A major hindrance to progress has been confusion regarding the role of positive (Darwinian) selection, i.e., natural selection favoring adaptive mutations. In particular, problems have arisen from the widespread use of certain poorly conceived statistical methods to test for positive selection. Thousands of papers are published every year claiming evidence of adaptive evolution on the basis of computational analyses alone, with no evidence whatsoever regarding the phenotypic effects of allegedly adaptive mutations. But it would be a mistake to dismiss Yokoyama et al.'s study, in this issue of PNAS, of the evolution of visual pigments in vertebrates as more of the same. For, unlike all too many recent papers in the field, this study is solidly grounded in biology.

See also:

Coppedge, D.F. How Not to Prove Positive Selection (Creation-Evolution Headlines, Sept 5, 2008).

An important paper has appeared recently on the way organisms have adapted their vision to dim light. The authors point out that the first vertebrates appearing in the fossil record lived in shallow water, open shelf marine environments. Many animals living in these environments today have rhodopsin molecules with their greatest sensitivity to light of about 500 nm, which matches what we know of spectral intensities at dusk. This, then, becomes the baseline figure for light sensitivity, and the authors have identified other maximum sensitivities ([lambda]max) that are representative of animals from different ecological niches.

"According to their [lambda]maxs and light environments, rhodopsins are classified into four groups: deep-sea (480-485 nm), intermediate (490-495 nm), surface (500-507 nm), and red-shifted (525 nm) rhodopsins."

Rhodopsin, a dim-light photoreceptor (Source here)

A major achievement of the research is the identification of modification to rhodopsins that have contributed to wavelength sensitivity. "[T]he [lambda]maxs of most contemporary rhodopsins can be explained largely by a total of 15 amino acid replacements at 12 sites." The authors could, like many others have done, assume that these 15 amino acid changes are the result of positive (Darwinian) selection. However, they did not make this assumption but set out to test for positive selection using various methods. This is where there were some unexpected findings. The surprises are well expressed by Hughes in a commentary essay:

"In fact, the results showed that the codon-based methods were 100% off target. When Bayesian methods were applied to a set of closely related rhodopsin sequences, eight sites were identified as "positively selected." Yet not one of these sites was among the 12 sites known to be involved in adaptive changes in rhodopsin sensitivity. Moreover, amino acid changes at these sites were shown experimentally to have no effect on [lambda]max and thus almost certainly to lack any adaptive significance."

This is a remarkable finding. Adaptation has occurred, but evidence of positive (Darwinian) selection lacks confirmation. At very least, it demonstrates that the Darwinian mechanism of survival of the fittest is not the key to understanding adaptation of dim-light vision. As we shall see (in a separate blog), Hughes goes much further than that.

It is worth noting that the phenotypic adaptations analysed in this research would be regarded as microevolution by many scientists. We are not considering variations needed to form new functionality, but rather the fine-tuning of existing functionality. As such, these findings are no more supportive of evolutionary biology than they are of ID biology or even Creation-orientated biology. However, since the research demonstrates adaptation without positive selection, is this evidence for neutral evolution? Serious questions about this can be raised because of convergence:

"4 of the 15 critical amino acid replacements occurred multiple times during rhodopsin evolution: [. . .]. Such extensive parallel changes strongly implicate the importance of these and other amino acid replacements at the 12 sites in the functional adaptation of vertebrate dim-light vision." [. . .] "In vertebrate rhodopsins, several amino acid replacements occurred multiple times and, furthermore, the biologically significant [lambda]max shifts occurred on at least 18 separate occasions."

This points us away from stochastic processes towards something more structural. In turn, this raises the question whether mechanisms for variation are designed rather than deterministic or stochastic. But this question cannot even be considered by those who reject design on ideological grounds. Here is yet another example of where design perspectives open up novel aspects of research to explain data that does not fit comfortably into the reigning paradigm.

Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates
Shozo Yokoyama, Takashi Tada, Huan Zhang, and Lyle Britt
Proceedings of the National Academy of Sciences, 105(36), 13480-13485, September 9, 2008 | doi:10.1073/pnas.0802426105.

Vertebrate ancestors appeared in a uniform, shallow water environment, but modern species flourish in highly variable niches. A striking array of phenotypes exhibited by contemporary animals is assumed to have evolved by accumulating a series of selectively advantageous mutations. However, the experimental test of such adaptive events at the molecular level is remarkably difficult. One testable phenotype, dim-light vision, is mediated by rhodopsins. Here, we engineered 11 ancestral rhodopsins and show that those in early ancestors absorbed light maximally ([lambda]max) at 500 nm, from which contemporary rhodopsins with variable [lambda]maxs of 480-525 nm evolved on at least 18 separate occasions. These highly environment-specific adaptations seem to have occurred largely by amino acid replacements at 12 sites, and most of those at the remaining 191 (~94%) sites have undergone neutral evolution. The comparison between these results and those inferred by commonly-used parsimony and Bayesian methods demonstrates that statistical tests of positive selection can be misleading without experimental support and that the molecular basis of spectral tuning in rhodopsins should be elucidated by mutagenesis analyses using ancestral pigments.

See also:

Hughes, A.L. The origin of adaptive phenotypes, Proceedings of the National Academy of Sciences, 105(36), 13193-13194, September 9, 2008 | doi: 10.1073/pnas.0807440105.

Coppedge, D.F. How Not to Prove Positive Selection (Creation-Evolution Headlines, Sept 5, 2008).

The iconic status of the bacterial flagellum for ID is easily justified, even though there are numerous other structures with complexities that are similarly astounding. In view of its potential for applications in nano-machines, the flagellum has been much studied and research shows no signs of abating.

The bacterial flagellum (source here)

Interest is not just in the mechanisms of providing torque and the way this is transmitted to the propeller. The researchers are intensely interested in the assembly of the flagellum. A recent review article declares that the assembly of this structure "poses the formidable problem of coupling temporal gene expression to specific stages of the organelle-assembly process".

"To function properly, each component of the final molecular machine that assembles by protein polymerisation must achieve an accurate size and subunit composition. Coordination of this assembly process is aided by gene regulatory mechanisms that manage the logistics of component production, whereas other mechanisms regulate the timing of the specific subunits that are being exported.
[. . .]
"Many regulatory checkpoint mechanisms of flagellum assembly have been elucidated, and these present a sophisticated strategy for coordinating gene expression to the assembly process."

As a review, this article presents a helpful overview of thinking about the assembly process. ID advocates also affirm assembly via natural processes - the intelligent agency is located in the design of the structure and the orchestration of the assembly process. However, the concluding paragraph of this paper introduces new ideas that are not discussed earlier:

"Finally, it seems that the bacterial flagellum is a structure of great complexity. In an attempt to understand why, it is not necessary to resort to intelligent designers, because surely a designer would have fashioned a simpler structure and gene regulation system. We only need to be reminded that evolution demands that changes occur on the existing structure - no starting from scratch. It is fair to say that we are at long last making a dent in our understanding of how this evolutionary process might have occurred for the reducibly complex bacterial flagellum and the beautiful result it has produced."

What is the argument here? It seems to be that the bacterial flagellum and its gene regulation system is too complex to have been fashioned by an intelligent designer! "Surely", affirm the authors, a designer would have gone for something simpler. Perhaps we should congratulate them for devising a novel argument against ID. Normally, we are caricatured as saying 'things are too complicated to have arisen by natural processes', but this argument suggests that the flagellum is too complicated even to have been the result of intelligent agency!

We could be more sympathetic to this reasoning if the authors could identify that part of the spectrum of complexity where the ID argument is justified. However, what we have here is a 'no-win' situation for ID. Furthermore, the reasoning is based on false premises. ID advocates base their design inferences on the recognition of complex specified information, not on "complexity" per se. The issue is not whether the structure is "of great complexity" but whether it exhibits complex specified information. Researchers need to assess whether the phenomenon under investigation could have arisen by the tinkering process of evolutionary transformation or whether it bears the marks of an exquisitely engineered artefact. Since the authors refer to the bacterial flagellum as "a beautiful result", it is not unreasonable to rule out incremental botching. (For more on this, go here). This suggests the burden of proof here rests on those who defend tinkering rather than intelligent agency.

My final comment here is to ask the question why this paragraph is deemed relevant to the subject matter of the review. It does not emerge from the data or the analysis. The word "surely" is lacking in content, appealing to gut feeling rather than evidence. Like so many academic contributions about structures exhibiting complex specified information, the evolutionary anchor is spin rather than substance. If reasoning like this is deemed acceptable in an academic paper, there should be no question of the legitimacy within science forums of arguing the case for intelligent agency.

Coordinating assembly of a bacterial macromolecular machine
Chevance, F.F.V., and Hughes, K.T.
Nature Reviews Microbiology, 6, 455-465, (June 2008)

The assembly of large and complex organelles, such as the bacterial flagellum, poses the formidable problem of coupling temporal gene expression to specific stages of the organelle-assembly process. The discovery that levels of the bacterial flagellar regulatory protein FlgM are controlled by its secretion from the cell in response to the completion of an intermediate flagellar structure (the hook-basal body) was only the first of several discoveries of unique mechanisms that coordinate flagellar gene expression with assembly. In this Review, we discuss this mechanism, together with others that also coordinate gene regulation and flagellar assembly in Gram-negative bacteria.

See also:

Coppedge, D.F. Cellular Machines Work Like Cameras, Winches and Turboprops, (Creation-Evolution Headlines, 3 September 2008)

Nature's editorial linked to the work of the Templeton Foundation (blogged here) has stimulated a response from two scientists who think that only scientists can make truth claims about the world around us. Adherents of religions, in their view, have no business encroaching into this territory. The authors identify a "fundamental conflict" which "can never be reconciled until all religions cease making claims about the nature of reality".

Who can make claims with integrity about the nature of reality?
(Graphic source here)

In their view, religions should be the subjects of scientific enquiry. This is necessary to deconstruct the socially-constructed nature of religious systems.

"The scientific study of religion is indeed full of big questions that need to be addressed, such as why belief in religion is negatively correlated with an acceptance of evolution. One could consider psychological studies of why humans are superstitious and believe impossible things, and comparative sociological studies of religion using materialist explanations of the rise and fall of the world's belief systems."

Cobb and Coyne are in no doubt about the findings (but for a related blog, go here). They distance themselves from the approach adopted by Nature's Editors:

"The outcome of such work, we predict, will not bring science and religion (or 'spirituality') any closer to one another. You suggest that science may bring about "advances in theological thinking". In reality, the only contribution that science can make to the ideas of religion is atheism."

Three points are worthy of note about this correspondence. The first is the complete absence of any historical perspective. There is no acknowledgement that Science emerged from a Christian culture, and that many of science's fundamental concepts are underpinned by Christian theology. Most of the early scientists were Christians, and regarded scientific work as their calling before God. (For more on this, go here).

The second point is the apparent inability of Cobb and Coyne to distinguish between "religion" and underpinning philosophies. This means that they lapse into yet another tired old polemic to set up "science" against "religion". We expect more discernment and substance from intellectual leaders. These matters are well-documented by Christian philosophers of science and ought to be known to anyone wanting to engage in constructive debate over these issues.

Thirdly, Cobb and Coyne confuse cause and effect when the say: "the only contribution that science can make to the ideas of religion is atheism." From the Enlightenment onwards, there has been a secularising trend in science. This is not inherent to science, but it reflects cultural trends among the intelligentsia. This trend is apparent today in the way atheistic scientists redefine science to suit their own philosophy. They write: "Surely science is about finding material explanations of the world". This definition presupposes that "the world" is entirely material and that it can be explained wholly in terms of natural causes. However, to presuppose this is not to prove the point! To presuppose it actually closes up avenues of enquiry that might conceivably lead to design inferences being made, thereby revealing that any explanation of the real world that does not incorporate intelligent causation must be deficient. In terms of methodology, Cobb and Coyne are undermining the integrity of science - to be open to evidence wherever it leads. What they should be recognising is that atheism emerges from a mutant science that has first presumed atheism.

Atheism could be science's contribution to religion
Matthew Cobb and Jerry Coyne
Nature 454, 253-254 (28 August 2008) | doi:10.1038/4541049d

First paragraph: We were perplexed by your Editorial on the work of the Templeton Foundation ('Templeton's legacy' Nature 454, 253-254; 2008). Surely science is about finding material explanations of the world - explanations that can inspire those spooky feelings of awe, wonder and reverence in the hyper-evolved human brain.

Here's some gripping reading for your summer vacation!

The Darwin Conspiracy by Roy Davies (2008)

This publication marks the 150th anniversary of the joint presentation of Darwin and Wallace of their thinking about evolution by natural selection to the Linnean Society. The book is a blockbuster because it claims that "Darwin perpetuated one of the greatest crimes in the history of science". It concludes that Darwin plagiarised Alfred Russel Wallace, deceived the world about the maturity of his own ideas before 1858, and, to satisfy his personal need for glory, failed to give credit to scholars who influenced his thinking.

It needs someone with remarkable abilities to put together such a radical revision of history. The author's experience is in writing, producing and directing documentaries that challenge popular historical narratives. During the 1980s, he was responsible for a TV programme about Darwin that presented a story that was and is widely accepted:

"Darwin [was] a nervous man who concealed the secret of how species originate for more than twenty years, until he was forced to publish when he realised someone else might get there before him. The programme was called The Devil's Chaplain."

Since that time, Davies has come to reject this account as iconic.

"Today, having researched the Darwin record for myself and having been utterly convinced by what I have learned, I believe [. . .] that the original programme (which went out under my name) left a great deal of new information about Darwin unmentioned. If I had known then what I know now, The Devil's Chaplain would never have been made. What you are about to read is the story leading up to the discovery of the origin of species, which I would eagerly have transmitted in its place."

Being a natural sceptic of conspiracy theories, I read this book cautiously - 'convince me if you can!' By the end, I was persuaded. What impressed me was the way Davies drew on the research of numerous Darwin scholars, showing that although they discovered important aspects of Darwin's life and work, they were unable to package their findings into a coherent whole. The person who came closest was Arnold Brackman, who concluded in 1980 that Darwin did plagiarise Wallace. It is the 'big picture' that Davies provides for the first time, and my title makes reference to the earlier eye-opening research papers.

The first researcher to be discussed in the book is Professor Darlington of Oxford University. He sought an answer to the question "by what thought process had Charles Darwin actually arrived at his ideas about evolution?".

"Darlington pointed out that he could not find, in all the accounts of Darwin's work published up to that time, any suggestion that some original germ in Darwin's mind had led inexorably to the full development and enunciation of this big idea."

Darlington recognised that Darwin's writings bore the marks of rhetoric. For example, "Darwin's unawareness of what his contemporaries were thinking matched his unawareness of what his predecessors had written". This comment is highly significant for what comes later, because Darwin was very concerned about gaining precedence for his own ideas and he consistently referred to "my theory".

The second scholar is the anthropologist Loren Eiseley. He identified a mismatch between the time (October 1838) when Darwin read Thomas Malthus's Essay on Population (which Darwin claimed "Here then I had at last got a theory by which to work. . .") and yet 18 months earlier he was already making notes on the very same ideas? After noting many similarities between the way Edward Blyth reported data in his published articles and the wording in Darwin's notebook about these same phenomena, Eiseley came to the conclusion that Darwin had lifted Blyth's thinking about natural selection - without acknowledgement.

"Eiseley believed, even making some allowance for the accidental use of the same sources, that the effect of his research was cumulative. He argued that these many similarities could not be explained by chance and that Darwin had plundered Blyth's articles for the ideas which underpinned the thinking that led to On the Origin of Species."

Barbara Beddall set out to refute Eiseley's suggestion that Darwin had plagiarised Blyth. She particularly wanted to find the letters between Wallace and Darwin - but found that some were missing. She also found, in the period 1853-8, that other letters to Lyell, to Hooker and to Asa Gray were lost. This, in her opinion, was "very odd". She came to the conclusion that they had been deliberately destroyed to obscure the record of how Darwin formulated his theory. She commented: "Without these letters, a clear idea of the extent of Wallace's influence on Darwin is beyond academic assessment and the full story impossible to gauge". But the jigsaw that Davies has assembled does have a clearer picture so that the significance of the missing letters is not "odd" but part of a pattern.

"The idea that it might have been Darwin himself [who destroyed the letters] seems not to have occurred to her."

Altogether, Davies features the work of nine researchers, with each contributing one or more pieces to the jigsaw. This review cannot do justice to the way the arguments develop. Here is just one more nugget. It concerns another letter of Wallace dated 2 March 1858. We know it was posted at the same time as his momentous letter to Darwin that contained the short paper that was presented at the Linnaean meeting in on 1st July that same year. Darwin claimed the letter reached him on 18 June, the same day that he wrote to Lyell to say that Wallace could not have written a better abstract for Darwin's own work. However, as Davies shows, we now have a complete timeline for the transport of this letter from the Dutch East Indies to its arrival in the UK, and the date-stamped envelope of the other letter posted along with the letter to Darwin. These date stamps show that the letter arrived in the UK on 2 June - on course for delivery to the addressee on the following day. Davies writes: "

The arrival of Wallace's letter on 3 June would have given Darwin more than enough time to digest its contents and make the two lengthy changes to the "natural selection" chapter of his manuscript. It would also have allowed him to claim that Wallace's ideas were replicas of his own."

Most people coming across this for the first time will be incredulous, thinking that Darwin's ideas on evolution by natural selection before this time were well documented. Davies shows that this is erroneous. This is why his 'big picture' is so important: Darwin was like a man groping in the dark. He gathered data, hoping to find a synthesis, but theoretical ideas were elusive. When he came across other people's ideas that helped to make sense of the data, he gathered them as well, treating them as his own. The plagiarism of Wallace was not an isolated incident, but part of a pattern of behaviour.

There are really two conspiracies in this book. Lyell and Hooker played a significant role (not in plagiarising, but in engineering circumstances to favour their gentleman friend).

"The members [of the Linnean Society] agreed that Darwin and Wallace should be acknowledged as co-discoverers of the theory of how species evolve, which would henceforth be known as the Darwin-Wallace theory of evolution. The crucial question of priority was settled by placing Darwin's name before Wallace's. Lyell and Hooker had successfully conspired to hand Charles Darwin the proze he had coveted for more than twenty years."

Alfred Russel Wallace in Singapore in 1862 (Source here)

Wallace emerges as the real hero. He could easily be made a role model for young scientists. Davies refers to him as a "brilliant yet unassuming naturalist who was never to comprehend the full extent of the conspiracy enacted against him".

Clearly, if Davies' argument is correct, the iconic Darwin needs to be dethroned. When this is accomplished, we will be in a better position to reappraise his significance as a scientist. In the meantime, here is a summary paragraph from Davies:
"Charles Darwin was a very secretive man with a driving ambition. He neither praised nor tipped his hat in the direction of Jean-Baptiste Lamark or of his grandfather Erasmus. He never openly acknowledged his debt to Edward Blyth, nor to Patrick Matthew (who had been one of the first to write about the 'natural means of selection', a phrase that Darwin modified and used without attribution). He never acknowledged his debt to Wallace. By the time Eiseley, Gruber, Beddall, McKinney, Brackman and Brooks began reassembling the long-lost pieces of the jigsaw, the myth-making surrounding Darwin's achievement, which had so worried Darlington in 1959, was complete."

Book Reviewed:
The Darwin Conspiracy - Origins of a Scientific Crime, by Roy Davies, Golden Square Books. May 2008.

Links:

The Darwin Conspiracy Home page

Tyler, D, Charles Darwin - Icon of Evolution, ARN Literature Blog, 30 June 2008

Tyler, D., Why Alfred Russel Wallace deserves to be remembered,ARN Literature Blog, 11 March 2008

Flannery, M. Science or Monkey Business?: A Review of Roy Davies' The Darwin Conspiracy, Uncommon Descent, 1 August 2008

Update:

Wright, T. Alfred Russel Wallace's Fans Gear Up for a Darwinian Struggle, Wall Street Journal, 20 December 2008)

Scientists are generally committed to realism: the conviction that we are studying a world that is objective rather than subjective and that the external world exists independently of human perception. Whilst this provides a coherent framework for the domains of physics and chemistry, there are major ideological issues to address when we come to scientific analysis of humanity. The phenomenon of consciousness has long been controversial: do we exist as persons or is our sense of consciousness a function of brain cell activity? Similar comments can be made about love, hate, our sense of beauty, and spirituality: are these just chemical reactions? (for more on this, go here)

Is consciousness "a learned repertoire of verbal behaviour"? (source here). What can be said about spirituality?

The realist conviction becomes elusive when we study ourselves! Modern science seems committed to deconstructing humanity so that we are, in essence, physics and chemistry, and our cultural behaviours are either adaptive or socially constructed. This applies to much thinking about spirituality. Evolutionary presuppositions are everywhere to be found. The option that man is a spiritual being is not even on the table for consideration.

"Two schools of thought have dominated the debate. The first views religion as a "by-product" of other evolutionary adaptations such as larger brains. The second sees religion itself as adaptive, arguing that its role in social cohesiveness and other traits may have helped humans survive."

New research by Fincher and Thornhill comes from the second of the schools mentioned above. The thesis is that "religion diversity appears to be tied importantly to infectious disease stress across the globe, and the global pattern is consistent with our model of religion genesis". The mechanism is explained thus:

"Religion marks group members [. . .] and can dissuade people from interacting with those outside the group. In areas with rampant infectious disease, this can be an advantage: No outsiders means no outside pathogens. Isolation can also prevent the exchange of ideas, or religions, in this case. That might lead to the rise of many independent religious systems."

The authors present "an evolutionary history of antagonistic coevolution between parasites and hosts and subsequent religion genesis". The more infectious diseases there are, the more religions spring up. The hypothesis advanced by the authors is that "the more a society disperses and mixes with other groups, the more it risks contracting new diseases - in other words, strangers are bad for your health". The reactions that have appeared so far suggest that people are viewing the hypothesis favourably. However, some concerns are worth highlighting.

The first concern is about causation. What is the cause and what is the effect? How do we know? The authors do not appear to discuss these questions. The areas of high religious diversity are in the tropics, where diseases tend to be more virulent and more numerous. Life in the tropics introduces many challenges that are not faced by those of us living in temperate zones of the Earth. Some analysis of lifestyles in the tropics would appear to be warranted, but this is not supplied by the authors. Philip Ball writes:

"It's an intriguing observation. But as with all correlation studies, cause and effect are hard to untangle. One could equally argue that avoiding contact with other social groups simply prevents the spread of some cultural traits at the expense of others, and so merely preserves an intrinsic diversity that has a tendency to arise anywhere. This, indeed, is the basis of some theoretical models for how cultural exchange and transmission occurs. Where opportunities for interaction are fewer, 'island cultures' are more likely to coexist rather than being consumed by a dominant one."

Secondly, the authors case appears to rest heavily on the thought that religions are closed groups, with social insiders and outsiders. This again is controversial. It is completely alien to the spirit of Christianity, which is to respond to the commission of Christ about reaching out to others. Rachel Zelkowitz writes:

"But Courtney Bender, a sociologist of religion at Columbia University, disagrees [with the hypothesis]. Religions around the planet range from being very open to very closed to outsiders, she says: "You can't just say religions have strong boundaries." Indeed, traditional religious societies often interact with those outside their own group for trade or military alliances, says Richard Sosis, an evolutionary biologist at the University of Connecticut."

A third concern is about the data sources. The study is undertaken at a broad-brush level with source data about religions drawn from Barrett et al's World Christian Encyclopedia. What is absent is a discussion of what constitutes a separate religion (as distinct from a local variant). For example, animism appears not to be a distinctly identifiable religion: it is subsumed by a long list of tribally-based religions. The authors do not discuss taxonomic questions, and whether they are "splitters" or "lumpers". They do not say how they handle the data about the 33,830 denominations within Christianity. They do not say how they distinguish between scattered pockets of religious followers and communities, nor how they handle the questions about the size of religious communities. The World Christian Encyclopedia is based on census data, and there are a whole host of uncertainties associated with self-assessment.

Zelkowitz observes that "the evolution of religion itself is not well-understood." This is the key to understanding studies of this kind. There is a strong presupposition in the minds of many scholars that religion must be an evolved behaviour and that it must be possible to identify the drivers for the rise of religion as a phenomenon. What few will even consider in their research is whether man is a spiritual, as well as a material, being and that the drivers for religious diversity come from mankind's spiritual nature. This position is, historically, part of the Christian worldview and, at very least, it deserves to be tested and scrutinised fairly by academics. It is the secularised mindset of scientists that prevents them considering such radical alternatives, and it is the strength of ID based science that multiple hypotheses can be considered - without making any presumptions about the outcomes of research. For a previous blog related to this topic, go here.

Assortative sociality, limited dispersal, infectious disease and the genesis of the global pattern of religion diversity
Corey L. Fincher and Randy Thornhill
Proceedings of the Royal Society B, First Cite, July 29 2008 | doi 10.1098/rspb.2008.0688

Abstract: Why are religions far more numerous in the tropics compared with the temperate areas? We propose, as an answer, that more religions have emerged and are maintained in the tropics because, through localized coevolutionary races with hosts, infectious diseases select for three anticontagion behaviours: in-group assortative sociality; out-group avoidance; and limited dispersal. These behaviours, in turn, create intergroup boundaries that effectively fractionate, isolate and diversify an original culture leading to the genesis of two or more groups from one. Religion is one aspect of a group's culture that undergoes this process. If this argument is correct then, across the globe, religion diversity should correlate positively with infectious disease diversity, reflecting an evolutionary history of antagonistic coevolution between parasites and hosts and subsequent religion genesis. We present evidence that supports this model: for a global sample of traditional societies, societal range size is reduced in areas with more pathogens compared with areas with few pathogens, and in contemporary countries religion diversity is positively related to two measures of parasite stress.

See also:

Zelkowitz, R., Pathogens And Prayer, ScienceNOW Daily News, 30 July 2008

Ball, P., Is religion good for your health? Nature News, 1 August 2008 | doi:10.1038/news.2008.990

O'Leary, D. Evolutionary psychology: British physicist targets theory-of-the-month on "how religion got started", Mindful Hack, 13 August 2008.

The author of the book under review, Kenneth Miller, and the reviewer, PZ Myers, have both gained something of a reputation for their different ways of defending evolutionary theory. Myers is an outspoken atheist who regularly slates Intelligent Design and Creationism in his blog Pharyngula. Miller affirms both Roman Catholicism and evolutionary theory and has made an impact in legal and educational contexts for celebrating "the power of evolutionary theory to explain our existence".

Theistic Evolution: a dream or a nightmare?

Myers adopts the strategy of conflating ID and Creationism by using the term "intelligent design creationism". However, most informed people, when they read this phrase, realise that polemics has come to the fore. The specific issues mentioned (the status of evolutionary theory, Behe's empirical argument for the inability of genetic mutations to build complexity, Dembski's rationale for making design inferences about structures exhibiting complex specified information) make it clear that Myers is giving Intelligent Design advocates the label "the enemies of science".

Rather than explore Miller's references to ID arguments, Myers merely waves a flag: Miller succeeds in "refuting the errors". But Myers does not even concede that the "errors" are worth refuting: he describes ID arguments as a "political attack on the nature of science". This is again a strategy frequently used by Myers - if ID arguments are political, a scientific response is superfluous.

A major part of the review considers the way Miller analyses the appeal of ID thinking to US minds: "The popularity of creationism in the United States is ascribed to independence and rebelliousness rather than religiosity." The implication is that skepticism about evolutionary theory has nothing to do with science! Myers and Miller are allies in seeking to interpret the ID phenomenon in sociological and religious terms. However, the bond between these two is only skin deep, as Myers finds fault with Miller's theistic view of evolution: "his own religious leanings blind him to conflict between faith and science."

There is one part of the alliance that is suggested to be "rock solid" and this concerns the philosophy of science. Here are the relevant quotes:

Miller - "To the intelligent design movement, the rationalism of the Age of Enlightenment, which gave rise to science as we know it, is the true enemy - science will be first redefined, and then the 'bankrupt ideologies' of scientific rationalism can be overthrown once and for all."
Myers - [They] "aim to revise what science means, discarding rationalism, naturalism, materialism and other Enlightenment values to incorporate the supernatural and loosen the rigour of all sciences."

There is both truth and error here. Historically, both are in error, as it was not rationalism that gave rise to science, but Christian Theism (which upholds rationality but not rationalism). The validity of design inferences within science is the point at issue. ID is entirely rational about making these inferences: conclusions are based on evidence and the assessment of probabilities. Rationalism, on the other hand, blocks design inferences being made about the natural world. Consequently, rationalism can become the enemy of truth. It can be an alien influence in science because it closes up legitimate avenues of enquiry: ruling out options on ideological grounds.

Whilst the allies demonstrate agreement regarding rationalism, the underlying rock is not so solid when it comes to naturalism and materialism. It is Myers who slips in comments about these ideologies. His comments are demonstratably false as naturalism and materialism had no contribution to make during the time known as the Scientific Revolution. The ideological basis of science changed with the centuries: Theism hardened to Deism (in the Enlightenment) and then morphed into Naturalism. It appears that Myers wants to ditch the Theism and the Deism and claim that Naturalism is the essence of science. However, the move to Deism and then to Naturalism has not been in the interests of scientific enterprise. What we are seeing today is science being slowly strangled by these ideologies (for a recent comment on this, go here). In the hands of the ideologues, science has become a tool for promoting and enforcing atheism. Kenneth Miller - with allies like this, who needs enemies!

The creationist controversy
PZ Myers
Nature 454, 581-582 (31 July 2008) | doi:10.1038/454581a

BOOK REVIEWED - Only a Theory: Evolution and the Battle for America's Soul by Kenneth R. Miller, Viking: 2008. 256 pp.

First sentence: The United States has a big problem: although we maintain a strong scientific establishment, competitive with the rest of the world in many fields, we also have some of the most backwards proponents of superstitious nonsense in both our electorate and at the highest levels of politics.

See also:

Plantinga, Alvin. Evolution vs. Naturalism. Why they are like oil and water, (Books and Culture, July/August 2008)

Nobel laureate Paul Nurse writes: "Biology stands at an interesting juncture". The many remarkable advances in our understanding of living organisms are mostly built on molecular biology. However, these are mainly at the building block level. And because we have clarified our thinking about these, we have deceived ourselves into thinking that we understand the bigger picture. "Our past successes have led us to underestimate the complexity of living organisms".

"But comprehensive understanding of many higher-level biological phenomena remains elusive. Even at the level of the cell, phenomena such as general cellular homeostasis and the maintenance of cell integrity, the generation of spatial and temporal order, inter- and intracellular signalling, cell 'memory' and reproduction are not fully understood."

Until we understand their information systems, our knowledge of organisms is of a preliminary nature (image source here)

So, where do we go from here? How should these conceptual weaknesses be addressed? The answer is that we need a much greater understanding of information flows in cells, tissues, the whole organisms and also ecosystems.
"We need to focus more on how information is managed in living systems and how this brings about higher-level biological phenomena. There should be a concerted programme to investigate this, which will require both the development of the appropriate languages to describe information processing in biological systems and the generation of more effective methods to translate biochemical descriptions into the functioning of the logic circuits that underpin biological phenomena."

To give an idea of what this means in practice, Nurse refers to the work of describing and cataloguing the logic circuits that are found in nature:

"I shall call these segments 'logic modules'. One example of such a module is the negative feedback loop, which often operates in a homeostatic manner. Another example is the positive feedback loop, which can generate irreversible switch behaviour from one state to another. Combinations of modules will produce more sophisticated outcomes: for example, reversible toggle switches, timers and oscillators."
[snip]
"The next steps will be to use the databases described above to determine the probability that specific components of the chemical tool-kit are associated with a particular logic module. Finally, the modules will be linked together into a complete circuit, allowing outputs to be predicted so that the functioning of the circuit can be translated into a narrative of information flow to describe how the cellular phenomenon works."

There is a welcome emphasis in this essay. However, it is hard to read it without thinking that the author is underplaying the significance of other initiatives to study the role of information in biological systems. Recognition of logic circuits in cell biology is not novel, and systems biology provides an integrated framework for the study of feedback mechanisms, modular structures, robustness of systems and the phenomenon of redundancy. ID scientists have made numerous contributions in this area, witness this position statement from the Biologic Institute:

"When you realize that living cells store, transmit, and process information, the similarities with human technology are unavoidable. But when you get a glimpse of the remarkable sophistication of the cellular processes - and the almost unbelievably small scale of the molecular systems performing them - you begin to realize that humans are novices when it comes to complex design."

The above comment is significant because Nurse has one very important passage where he explains that biological design differs from human design. Nurse comes from the perspective that there is no intelligence behind biological design:

"We need to take account of the biological origins of the logic circuits and networks that operate in cells. Because natural selection operates on pre-existing living organisms, novelties will initially arise as add-ons to systems already in existence, almost guaranteeing some redundancy. Thus, man-made machines, which are generally intelligently designed, will differ from the logic machines found in life. Living machines are intelligently designed and will often be redundant and overly complex. We should anticipate these differences and be prepared for the additional complexity to be found in the logic circuits that manage information in cells."

In principle, here is a way to test the contrasting perspectives of the Blind Watchmaker hypothesis and the Intelligent Design hypothesis. But Nurse is wrong to think that redundancy is not a feature of intelligently designed systems - a chat with a human system designers will quickly reveal many examples! But there are differences: blind evolutionary mechanisms will display the phenomenon of tinkering, with many dead ends and useless pseudosystems. By contrast, intelligent design will evidence exquisite structures with back-up systems that come into operation if the main system fails. If evolutionists will allow their approach to be tested in this way, it could open the door to some really interesting discussions!

One final point: Nurse knows that his proposed project requires a multidisciplinary input. This is absolutely right. Roll on the day when research groups like this consider themselves seriously deficient if there are not at least two members that are open to the possibility of intelligent design. In view of Nurse's personal journey through life, welcoming ID members to his own team could be a stimulus to see if his "sceptical agnostic" position is robust or worthy of fresh critical scrutiny.

"The groups will need to be multidisciplinary, including information theorists, mathematicians, physicists, chemists and computer scientists working closely with experimental biologists who have good biological intuition and who can communicate with members of the other disciplines. Different workshop groups could interact with each other through digital conversations to share ideas."

Life, logic and information
Paul Nurse
Nature 454, 424-426 (24 July 2008) | doi:10.1038/454424a

Focusing on information flow will help us to understand better how cells and organisms work.

In 2005, Massimo Pigliucci, in a book review for Nature, wrote: "The clamour to revise neo-darwinism is becoming so loud that hopefully most practising evolutionary biologists will begin to pay attention. It has been said that science often makes progress not because people change their minds, but because the old ones die off and the new generation is more open to novel ideas." This clamour has not diminished in succeeding years, and one recent evidence of this was a private meeting in Altenberg, Austria, on 10-13 July 2008. This event was publicised in March by Susan Mazur, and her recent comments on the meeting are linked here.

What lies beyond the Modern Synthesis?

However, this blog is to draw attention to a piece in Science from Elizabeth Pennisi. According to Pigliucci, the attention created by Mazur's write-up "frankly caused me embarrassment". The reasons for this are not altogether clear, because there is no doubt that the Altenberg meeting was designed to address the problems of a failing theory. Scientific advances have revealed blind spots in the neo-darwinian synthesis and it is time for a change.

More than genes pass on information from one generation to the next, for example, and development seems to help shape evolution's course. "Many things need fixing," emphasizes one invited speaker, Eva Jablonka of Tel Aviv University in Israel. "I think that a new evolutionary synthesis is long overdue."

Major advances have been made in developmental biology, but these advances reinforce the idea that "development constrains evolution". Neo-darwinians do not warm to this idea, because they have promoted the concept of the adaptive landscape, where there is innate plasticity and where all barriers to transformation can, in principle, be overcome. Discussions of the limits to variation are alien to their mindset. However, once it is recognised that stasis is as important to consider as variation, and that stasis can be a developmental phenomenon (not just governed by the environment), then there are important scientific issues to consider about the limits of variation. Until now, neo-darwinists have treated such questions as an intrusion of religious ideology into science. The contrasting perspectives are explained by Pennisi thus:

From the modern synthesis perspective, Wagner explains, "the body plan is a historical residue of evolutionary time, the afterglow of the evolutionary process" such that more closely related organisms share more features. The alternative view, he says, is that "body plans have internal inertia," and evolution works around this stability.

Another key area of interest concerns "regulation": this is a new buzzword in biology circles; "yet it's another concept virtually ignored in the modern synthesis". This is important because the mechanisms of neodarwinism have been recognised by the Altenberg group as rather ineffective. This follows from any empirical work on what these mechanisms actually achieve.

Bottom line: "New traits contain very little that is new in the way of functional components, whereas regulatory change is crucial," Kirschner and John Gerhart of the University of California, Berkeley, wrote in a supplement to the 15 May 2007 issue of the Proceedings of the National Academy of Sciences. (For my blog on this paper, go here).

A further gap in neodarwinian thinking is epigenetics. Environmental factors can influence the way genes are turned on and off and this creates a "bewildering increase in the complexity of the entire inheritance system". Although it is not mentioned by Pennissi, epigenetics is of interest to ID scientists because the complexity issues have stimulated design inferences.

Certain environmental conditions, such as diet during gestation, can alter the epigenetic patterns of the resulting offspring, and new traits that result can last for generations, says Jablonka, who has been striving to get recognition for this mode of inheritance for years. [. . .] "It's beginning to be accepted that [epigenetics] may actually have something to contribute to evolution," says Jablonka. She argues that because these chemical modifications change how tightly wound DNA is, they also influence other properties of a genome that are relevant to evolution. The coiling of a DNA strand, she points out, can alter the rate of mutation, the ease by which mobile elements can move around, the duplication of genes, and even how much gene exchange occurs between matching chromosomes.

With all this excitement, it is difficult to avoid being seen as a dull spoil-sport if you are a sceptic. However, Jerry Coyne obliges:

It's a joke, says Jerry Coyne of the University of Chicago in Illinois. "I don't think there's anything that needs fixing."

These discussions are interesting to ID scientists, not just because they are addressing issues that are of direct concern to the development of ID thinking. We do not have to presume common descent, and we may yet find that variation is within limits. We may find that the regulatory aspects of genetics are strong evidences for design. We may find that that epigenetics points to new levels of exquisite complexity that reveal the hallmarks of design. We do not presume the outcomes, so for us it is a genuine exploration. By contrast, the secularised approach to science must trace everything back to a universal common ancestor and must explain design in nature entirely by reference to natural causes.

Modernizing the Modern Synthesis
Elizabeth Pennisi
Science 321, 11 July 2008: 196-197 | DOI: 10.1126/science.321.5886.196

Seventy years ago, evolutionary biologists hammered out the modern synthesis to bring Darwin's ideas in line with current insights into how organisms change through time. Some say it's time for Modern Synthesis 2.0

See also:

Pigliucci1, M. Expanding evolution, Nature 435, 565-566 (2 June 2005)

Mazur, S. Altenberg! The Woodstock of Evolution? (Scoop! 4 March 2008)

Nature carries an editorial today relating to the legacy left by the recently deceased John Templeton. The issue is significant because the Templeton Foundation provides significant grants to a great variety of scientists and awards the largest cash prize annually for research relating to spiritual realities. In a world where many scientists seem to compartmentalise science and spiritual realities in two separate boxes, and where others say that spiritual realities are delusional, the Templeton Prize appears distinctly anomalous. The Editorial says that the journal "shares a degree of suspicion with many in the scientific community at any attempt by religiously driven organizations to fund science. A chief concern is that the influential Templeton Foundation might be seeking to inject religion into the scientific world."

Does Darwin needs rescuing from the atheists?

The editorial is concerned that the funding comes with an agenda: one of advocacy. Instead of being open to the evidence, wherever it leads, there is the suspicion that the researchers may be swayed to deliver results that they know the funding body will welcome. It is recognised that Templeton tried to guard against the dangers. "Templeton himself seemed to have just the opposite in mind. He believed institutional religion to be antiquated, and hoped a dialogue with researchers might bring about advances in theological thinking." However, with his passing, there is a need for vigilance:

"A critical scrutiny of the foundation's scientific influence continues to be warranted, and no scientific organization should accept sums of money so large that its mission could be perceived as being swayed by religious or spiritual considerations."

It would have been better if the editorial had set these thoughts in the context of the general principle: that funding bodies must not be allowed to make their grants conditional on advancing their particular agendas. This principle applies to multi-national corporations, governments and pressure groups. The principle in science is that we follow the evidence wherever it leads. So research should never be to "prove" an outcome that is identified at the outset. There should be sufficient in the research programme to allow favoured options to be falsified. As far as I can see, there is no reason to single out the Templeton Foundation for special treatment because it is not unusual for research funding and advocacy to be linked. This is particularly relevant to origins research which is mostly "normal" science in the Kuhnian sense.

Nevertheless, there are grounds for concern in the UK. Recently, a Templeton funded project called "Rescuing Darwin" was announced. This project sets out to "challenge the belief that respect for Darwin and his theory necessitates atheism". (Source here). The partners in the project are Theos, which describes itself as "The Public Theology Think Tank", and the Faraday Institute at Cambridge University. The project will report next year:

"to coincide with the 200th anniversary of Charles Darwin's birth and the 150th anniversary of the publication of The Origin of Species.
The project will research and analyse the extent and nature of evolutionary and anti-evolutionary opinion in the UK, and its relationship to theism, atheism and agnosticism."

Further information on the project has not been released and there is not enough here yet to know whether research funding is linked to advocacy. However, the provisional title of the project raises concerns: "Rescuing Darwin" is about recovering Darwin from the clutches of atheists and showing that theism and Darwinism can coexist. We can get a fair idea of what this means by looking at a recent popular article written by Denis Alexander, who heads up the Faraday Institute. Alexander says that evolution is established "beyond any reasonable doubt". He claims that evolution, as a biological theory "has no ideological implications". He treats every attempt to apply Darwin's theory outside biology as inappropriate and the domain of sociologists (not scientists):

"From a sociological perspective, the phenomenon looks less mysterious. There is a very familiar process in the history of science whereby interest groups move in to utilise the prestige of scientific theories in support of their particular ideology. Unfortunately the end result is that in the public consciousness the actual meaning of the label given to the theory itself changes, and so 'Theory X' becomes socially transformed into 'Theory Y' with all kinds of philosophical barnacles attached to it. Evolution has suffered particularly badly from this kind of process and has been used in support of virtually every kind of 'ism' imaginable, including socialism, capitalism, racism, eugenics, and atheism. As George Bernard Shaw once remarked, Darwin 'had the luck to please everybody who had an axe to grind'."

It is not my intention to critique this excerpt here, although it certainly can be critiqued. My main concern is to point out the implications for research methodology if this stance is adopted. Anyone familiar with the writings of ID scientists will know that the appeal is to evidence. Design inferences are made on the basis of empirical data. If, however, Darwinism is "beyond any reasonable doubt", then the researcher must interpret opposition to Darwinism as a sociological phenomenon and will never acknowledge that scientific dissent is possible. This, in my opinion, undermines the integrity of the research programme and makes it wide open to the charge of advocacy in the name of science. Alexander and the "Rescuing Darwin" project will have to work very hard to address these concerns if they are to have any credence when they present their findings.

Templeton's legacy
Editorial
Nature 454, 253-254 (17 July 2008) | doi:10.1038/454253b

Abstract: The Templeton Foundation's exploration of science and faith merits tolerance, not outright rejection.

See also:

Alexander, D. Viva la evolution! (Third Way, Vol 31, No 6, 28-31, Summer 2008)

Theos wins major grant to 'rescue' Darwin, (Theos News, 3 June 2008)

Flatfish are unusual vertebrates, in that adults are highly asymmetric. Their young are normal enough, but as they get older, they adopt the behavioural traits of mature organisms and undergo significant developmental changes. In particular, one eye migrates around the skull so that both are located on the upper side of the fish. There has been no evidence for this developmental process in the fossil record - until now. According to the Editor of Nature, "a graphic example of a transitional form [has been] spotted in the fossil record, confirming that the evolution of the specialized flatfish bodyplan was a gradual process."

"The drawings show the most ancient fossil (left) with symmetrical eye sockets. Amphistium and Heteronectes, the reexamined fossil fish, show asymmetrical skulls, but maintain eyes on opposite sides of the head. The other two fish drawings show the asymmetrical eye locations and skull of the most current flatfish species." (Source Science News)

The finds are deemed significant because at least one stage of partially offset eyes has been documented. This is considered to challenge advocates of punctuated equilibrium (who argue for sudden jumps) and also creationists (who are supposed to defend the creation of species in their present form).

Matt Friedman, the author of the research paper, says that the fossils are important because "they help to settle a long-standing evolutionary debate and shed light on the mode and tempo of evolutionary change". Apparently, finding one intermediate stage dated at 47 million years is sufficient to say that the tempo was "gradual" and that it occurred over "over thousands to millions of years". We have no earlier fossils without asymmetry, and fully asymmetric flatfish appear in the fossil record at the same time. At very least, we can say that these data do not justify the word "gradual"!

What about the description of the fossils as "transitional"? Morphologically, there is no questioning their intermediate status. The interesting questions relate to understanding this observation. The morphological changes are developmental: they occur in every flatfish living today. These changes do not involve any genetic change - the genome is the same before and after the development of asymmetry. The important difference is that the new fossils are mature, not young. But surely the first explanatory options to be explored relate to developmental mechanisms. Are there environmental factors leading to the retarded development of these fish? Or are there epigenetic influences which mean that normal development was impaired, and these animals represent stunted growth? Curiously, there is no exploration of these options in the research paper or in the science media.

There are further questions about the proposed genetic interpretation of the fossils as transitional. What was driving change? Janvier recognises the importance of asking this question: "What could have been the selective advantage of this unusual anatomy?" He refers to several possible scenarios that have been proposed. However, a friend commented: "The fact the migration of the eye takes place in living creatures should have alerted people to the fact that there is no (significant) selective disadvantage to having an asymmetrical skull."
Arguments over selection forces by Darwinists will no doubt continue, but the quest is, at best, for a plausible 'just-so' story. The real problem is that empirical work with natural selection does not confirm that it is a strong force capable of doing what Darwinists want it to do. Furthermore, it begs the question whether eye migration is a cause or an effect. In 2006, Schreiber concluded:

"Behavior and skull asymmetries precede metamorphosis, and the development of lateralized behaviors was independent of eye position in larvae treated with thyroid hormone and in symmetrical variants. Therefore, lateralized behavior is not an adaptive response to eye translocation, but rather must result from changing vestibular responses to thyroid hormone."

The most noticeable feature of the research concerns the evolutionary hype that has emerged from the journal Nature and from the science media. We are not witnessing an impartial evaluation of the data, but a construction of an argument to "lay to rest" criticisms of Darwinism and evolutionary transformation. For more on this, see Luskin's comments on the National Geographic coverage of the story.

The evolutionary origin of flatfish asymmetry
Matt Friedman
Nature 454, 209-212 (10 July 2008) | doi:10.1038/nature07108

All adult flatfishes (Pleuronectiformes), including the gastronomically familiar plaice, sole, turbot and halibut, have highly asymmetrical skulls, with both eyes placed on one side of the head. This arrangement, one of the most extraordinary anatomical specializations among vertebrates, arises through migration of one eye during late larval development. Although the transformation of symmetrical larvae into asymmetrical juveniles is well documented, the evolutionary origins of flatfish asymmetry are uncertain because there are no transitional forms linking flatfishes with their symmetrical relatives. The supposed inviability of such intermediates gave pleuronectiforms a prominent role in evolutionary debates, leading to attacks on natural selection and arguments for saltatory change. Here I show that Amphistium and the new genus Heteronectes, both extinct spiny-finned fishes from the Eocene epoch of Europe, are the most primitive pleuronectiforms known. The orbital region of the skull in both taxa is strongly asymmetrical, as in living flatfishes, but these genera retain many primitive characters unknown in extant forms. Most remarkably, orbital migration was incomplete in Amphistium and Heteronectes, with eyes remaining on opposite sides of the head in post-metamorphic individuals. This condition is intermediate between that in living pleuronectiforms and the arrangement found in other fishes. Amphistium and Heteronectes indicate that the evolution of the profound cranial asymmetry of extant flatfishes was gradual in nature.

See also:

Cressey, D. The eyes have it, news@nature.com, 9 July 2008 | doi:10.1038/news.2008.946

Janvier, P., Squint of the fossil flatfish, Nature 454, 169-170 (10 July 2008) | doi:10.1038/454169a

Luskin, C. National Geographic Finds Opportunity to Conflate Intelligent Design with Creationism while Misreporting Fish Fossil (Evolution News & Views, July 10, 2008)

Schreiber, A.M. Asymmetric craniofacial remodeling and lateralized behavior in larval flatfish, Journal of Experimental Biology 209, 610-621, 2006.

Ever since its discovery, the platypus has been known as "one of nature's oddest creatures, seemingly assembled from the spare parts of other animals". It was hoped that the genome sequence would cast light on its evolutionary history, but now that it has been published (in May 2008), the picture is no clearer. The mosaic of reptilian, avian and mammalian features apparent at the macro-level is replicated in its genetic code.

"There is nothing quite as enigmatic as a platypus," says Richard Gibbs, who directs the Human Genome Sequencing Center at Baylor College of Medicine in Houston, Texas. "You have got these reptilian repeat patterns and these more recently evolved milk genes and independent evolution of the venom. It all points to how idiosyncratic evolution is."

This graphic in National Geographic "illustrates the traits that the platypus shares with reptiles, birds, and mammals"

"Idiosyncratic" means 'peculiar to the individual', 'eccentric'. Whilst this is a fair summary of the quirky, unpredictable way evolutionary transformation is supposed to occur, the principles underlying the analysis of genomes is that the past course of evolution can be tracked. Cladistic techniques are supposed to offer the possibility of redrawing the Tree of Life. In this case, the real problem is not "idiosyncratic evolution" but the discovery of an idiosyncratic platypus genome!

There are several highlighted genetic features in the Nature News report.

• The platypus has "genes for the family of milk proteins called caseins, which map together in a cluster that matches that of humans."
• "The platypus shares with other mammals four genes associated with the zona pellucida, a gel-like coating that facilitates fertilization of the egg."
• It "has two matches for ZPAX genes that had previously been found only in birds, amphibians and fish. And it shares with the chicken a gene for a type of egg-yolk protein called a vitellogenin."
• "Male platypuses have spurs on their hind legs that are loaded with a venom so potent it can kill a dog. Like the venom of reptiles, the poison is a cocktail of variations on at least three kinds of peptide."
• "[N]one of the platypus X chromosomes resembles the human, dog or mouse X. [. . .] Instead, the platypus Xs better match the avian Z sex chromosome."
• "microRNAs, which regulate gene expression, [revealed] a mix of reptile and mammal examples. "We have microRNAs that are shared with chickens and not mammals as well as ones that are shared with mammals, but not chickens," Hannon says."

Despite the claims that the new data provides more "evidence for its place in the ancestral line of animal evolution", the evolutionary story is distinctly fuzzy. Identifying a reasonable lineage was deemed impossible in the case of the reptilian venom: this is regarded by the researchers as having an independent origin. "The similarity in venom is an example of convergent evolution between the two tetrapods."

These traits, and others, are considered in an article on the Truth in Science website here. The various evidences are weighed and it is concluded that evolutionary theory does not deliver a coherent story. Indeed, it is far worse than this: the platypus genome is truly idiosyncratic! The essay concludes:

"Thus the platypus will remain a significant misfit in any Darwinian scheme. Is it from a sauropsid lineage which includes reptiles and birds? Is it from a synapsid lineage which supposedly led to the emergence of the mammals? Or is it derived independently from some unknown ancestral amniote? Or could it be that the Darwinian hypothesis, cladistic analysis or any other classification system for that matter is just far too restrictive? Without doubt, there are mammal-like reptiles as there are reptile-like mammals. The platypus is a Darwinian cautionary tale. Is it a bird or is it a plain . . . old platypus?"

Genome analysis of the platypus reveals unique signatures of evolution
Wesley C. Warren, et al.
Nature 453, 175-183 (8 May 2008) | doi:10.1038/nature06936

Abstract: We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation.

See also:

Brown, S. Top billing for platypus at end of evolution tree, Nature, 453, 7 May 2008, 138-9 | doi:10.1038/453138a

A draft sequence of the platypus genome reveals reptilian and mammalian elements and provides more evidence for its place in the ancestral line of animal evolution. The platypus (Ornithorhynchus anatinus) is endemic to Australia and one of nature's oddest creatures, seemingly assembled from the spare parts of other animals. The semi-aquatic monotreme is a venomous, duck-billed mammal that lays eggs, nurses its young and occupies a lonely twig at the end of a sparse branch of the vertebrate evolutionary tree. Now, the structure of its genome has revealed new clues to how mammals evolved. [snip]

Platypus: a Darwinian Cautionary Tale (Truth in Science, 7 July 2008)

Contemporary presentations of evolutionary theory seem always to incorporate cladograms, sometimes at the species level and sometimes relating groups of organisms. Cladistics is being used to chart the course of evolutionary history. Yet, since it was first developed as a methodology for phylogenetics, it has routinely attracted the critical attention of philosophers of science. Some years ago, Colin Patterson brought these debates to a head when he championed transformed cladism to free cladistics from the charge of circular reasoning. One of the famous controversies about this is discussed here. However, although the unransformed version of cladistics continues to be widely used, the problems remain.

"All life on Earth is united by evolutionary history; we are all evolutionary cousins - twigs on the tree of life. Phylogenetic systematics is the formal name for the field within biology that reconstructs evolutionary history and studies the patterns of relationships among organisms." (source here)

Lars Vogt has contributed a thoughtful analysis of contemporary thinking in a paper entitled: "The unfalsifiability of cladograms and its consequences". Crucial background theory comes from the philosopher Karl Popper:

"As Popperian falsificationism takes in such a central role within the respective theoretical discussions I will take in the Popperian point of view throughout this paper. [. . .] I will infer and discuss the consequences of consistently applying falsificationism to phylogenetics. Therefore, this paper represents a thought-experiment: let's assume Popperian falsificationism is really the only reasonable and justifiable way to do empirical research - What would this imply for phylogenetics?"

The paper is technically demanding and there's not a lot to be gained by trying to digest it to a paragraph or two here. But we do need to note the conclusion:

"Consequently, sensu Popper's demarcation criterion of falsifiability, seeking phylogenetic trees does not represent a scientific endeavour and cladograms represent no scientific but metaphysical hypotheses."

Putting this in more popular language, cladists have adopted a variety of rationales to justify giving weight and credence to their evolutionary trees, but these rationales do not survive critical scrutiny if the test is Popper's demarcation criterion for science.

This disquieting outcome leads Vogt to point to a resolution that makes a distinction between empirical and historical science and limits Popper's criterion to the former:

"All the conclusions presented here rest on the premise that Popperian falsificationism is the only valid scientific theoretical approach. This is highly questionable and might turn out to be wrong, especially with respect to historical sciences - and phylogenetics represents a historical science. The reason for my doubts refers to the fact that it is in principle impossible to predict future observations to test historical hypotheses, which represents the initial idea of Popper's hypothetico-deductive setting - to test necessary predictions against future observations. This rationale is obviously designed for sciences that use experiments in which they control a set of critical conditions in order to generate the deductively predicted necessary effect in order to test a universal causal hypothesis. Perhaps it is time that phylogeneticists develop their own philosophy, a philosophy of phylogenetics that meets the specific requirements of our scientific field, instead of trying to apply a philosophy like Popper's falsificationism that has been developed for experimental sciences such as physics, which is seeking universal laws and regularities instead of the reconstruction of particular historical events."

Crucial to Vogt's point is the distinction between "experimental science" and "historical science". Many scholars involved in the Origins debate have been arguing for some time that there are significant methodological differences between physics and chemistry (empirical sciences) and historical geology and evolutionary biology (historical sciences). It has been noted on numerous occasions that many evolutionists like to champion empirical science and then claim, using Popper's criterion) that the thinking of their opponents is unjustifiable. Consequently, Vogt's contribution makes a really interesting contribution to debate, because he demonstrates in a compelling way that evolutionary biologists face the same charge of adopting unfalsifiable methodologies. He shows that the cladistic approach rests on metaphysical foundations and the outputs of the method are heavily dependent on the assumptions input by the researchers.

Anyone familiar with origins debates will realise that cladistics is a special case of a general principle. So-called proofs of evolutionary transformation are only convincing to those who presuppose common ancestry. The debates within evolutionary circles are always about specifics: the broader issues are not debated because they have an axiomatic status. So, evolutionary theorists do not have the mental tools that would allow them to disprove common ancestry, or whether design inferences are warranted. Consequently, it is not unreasonable to conclude, from the perspective of empirical science, that proposed evolutionary scenarios represent not "scientific but metaphysical hypotheses".

The unfalsifiability of cladograms and its consequences
L. Vogt
Cladistics, 24(1), February 2008, 62-73 | doi 10.1111/j.1096-0031.2007.00169.x

Abstract: Popper's falsificationism provides the normative reference system in recent discussions regarding theory and methodology of systematics. According to Popper, the falsifiability of a hypothesis represents a necessary precondition for its corroborability. It is shown that cladograms, independent of "strict", "methodological" or "sophisticated" falsification, are not falsifiable in principle. No present observation is prohibited by any tree hypothesis and, thus, no Popperian test of cladograms exists. It is shown that the congruence test, which is commonly said to represent a Popperian test of cladograms, instead tests sets of apomorphy hypotheses. Three different strategies that have been proposed to circumvent this problem are discussed and refuted: (1) referring to Popper's convention to renounce ad hoc maneuvers; (2) referring to Popper's treatment of probability hypotheses; and (3) decoupling corroboration from falsification. As a consequence, within a Popperian framework the unfalsifiability of cladograms implies that cladograms cannot explain any present day observation and, thus, represent metaphysical hypotheses.
However, Popper's falsificationism has been criticized and questioned by many philosophers before and it seems to be about time that phylogeneticists develop their own philosophy of phylogenetics that meets their specific requirements of a historical science that is not seeking for universal laws and regularities, but instead reconstructing particular historical events.

Discussions of ID and related topics are often characterised by the word 'polarised'. Stereotyped thinking is widespread and there is often a lack of any real engagement with the issues. It is a pleasure, therefore, to find a thoughtful contribution that stands back from the confrontational stance.

"As a philosopher of science, I am mainly interested in the arguments. At the end of the day, do we need an explanation for the fine-tuning of the cosmos? If so, what is the best explanation? Likewise for the origin of life on Earth and its evolution over time; what are the competing explanations and how do we assess them? These are questions that can be discussed at a scholarly level. The purpose of this essay is to push that discussion along just a bit."

"Surrounded by sophists, we are left without a Socrates" - Jeffrey Koperski

Koperski considers four arguments against ID, two of which are flawed and deserve to be refuted. The other two have some value for meaningful discourse. These arguments are highlighted below, together with Koperski's evaluation of them. The additional thoughts are mine.

The first flawed argument concerns the way ID is regarded as a Trojan horse, "sneaking good old-fashioned creation science past the censors". This is the message conveyed by the label "Intelligent Design Creationism". Koperski's evaluation is clear enough:

"In my view, labeling those who doubt the efficacy of genetic mutation and natural selection "creationists" is a rhetorical strategy, what some logic texts call "stereotyping". Cable television provides ready exemplars for both the creationist stereotype and its cousin, the fundamentalist. Critics try to shape the debate by connecting ID to these templates. If successful, little work needs to be done. The labels tell us who represents the side of rationality over and against the side of ignorance. Having sorted us and them, what they actually say matters little, whoever they happen to be. We must recognize that although this is a common argumentative strategy in talk radio and presidential politics, it is not itself a logical critique. Placing the black hat on one's opponent is no substitute for an argument."

The second flawed argument is that "ID posits a nonphysical intelligence, it violates MN [methodological naturalism] and is therefore not science". This argument essentially defines the problem away. It is as though ID can be dismissed on philosophical grounds without considering any other arguments. Here is Koperski again:

"The bottom line is this: The future use or suspension of MN depends on what is discovered. If the best explanation for some new phenomenon is design, even supernatural design, it would still count as a scientific explanation. It borders on academic incompetence to pretend that science has strict boundaries and then gerrymander those boundaries to keep out the riffraff. Philosophers of science in particular should know better."

In this section, Koperski deals with the charge that ID is a science-stopper:

"Let us consider an objection. Some argue that design explanations would hamper the progress of science. Because "God did it" is potentially an answer to any Why question, allowing design back into biology is a science stopper. If divine fiat is an acceptable explanation, why push on with difficult and expensive research? [. . .] I think this is a plausible objection. If one already has an answer to a question, why search for another? The only thing I ask is that we hold this claim up against the history of science in order to test it. [. . .] As far as I can tell, "God did it" is simply not an answer that theists reach for whenever research bogs down."

Significantly, both of these flawed arguments played a significant role in the Kitzmiller v. Dover 2005 trial. Judge Jones would do well to read what Koperski has to say about this. His words are sufficient to show that the legal judgment was flawed.

"We have examined two bad arguments used against ID. Both are rhetorically effective, persuading teachers and judges alike, and I fully expect to see them in the future. My appeal to those in the academy is this: Let us not use bad arguments as a means to an end."

So, we move on to consider two grounds for properly criticising ID. Allowing that it can contribute to science, is ID demonstrating good science? Some ID science focuses on the problems for evolutionary theory, and neo-Darwinism in particular. These contributions point out examples of irreducible complexity and complex specified information. Without going into details, Koperski considers the responses that have been made to these arguments sufficient to show that neo-Darwinism is still alive and well. "In other words, there are many soft anomalies in the literature but no hard ones."

"The second kind of ID science includes research that fits nicely within a design framework, even though the researchers themselves do not support ID. For example, ID proponents often speak favorably of research showing that so-called junk DNA actually is functional. The idea is that one should expect more purpose in biological structures than would be expected from a Darwinian point of view. The nanotechnology approach to microscopic systems is also considered very ID-friendly. The reason scientists find such utility in thinking of biological systems as machines is because, in some sense, that is what they are. The conceptual link with human artifacts is not merely a metaphor. These kinds of ID-related science are well and good, as far as they go. What critics rightly clamor for, however, is peer-reviewed research in which design has more than a mere heuristic role."

Certainly, both these aspects of ID science feature in this blog and many other ID writings. Basically, we are ready to accept Koperski's challenge and engage further on these matters - but we do ask that this be conducted within the science community. The evidence to date is that science journals and science conferences are willing to discuss these issues as long as ID advocates are excluded from having a voice. This is not an acceptable way to conduct this debate. Furthermore, Koperski is too willing to accept the peer-review argument. All the evidence to date is that editors publishing an overt ID paper are deemed to have failed in their duty to the science community and are therefore incompetent. Koperski writes: "Some think of ID primarily as a weapon in the culture wars. Anti-design bias in the academy is part of the backlash. Had ID consistently emphasized research over public exposure, the atmosphere of the debate would be different today." But this argument presupposes that the culture war is an ID invention! If there really is a culture war, no amount of ID research will satisfy the critics! For more on this, go here.

The second "good" argument against ID is that it is more radical than necessary. Koperski refers to the conservatism of science and the preference for incremental change.

"Even if orthodox neo-Darwinism collapses, design obviously is not the only alternative. More important, the rivals are more conservative vis a vis the reigning theory. They do not challenge MN. In fact, very little would have to be added to textbook evolutionary theory if one or more of these is accepted. If any one of them is capable of resolving the problems posed by complex structures and macroevolution, ID is a more radical solution than is needed. In short, if scientific conservatism is a defensible, normative principle of theory change, it undermines the acceptability of ID."

The problem with this analysis is that it has no sense of history. The pioneers of science were ID advocates. Science was born and nurtured with the legitimacy of making design inferences. The trends over the centuries have been towards secularisation and achieving this in biology was Darwin's achievement. This is why the secularists are so keen to make Darwin's bicentennial a success. The issue is not conservatism, but metaphysics. For some of us, the issue is one of science reconnecting with its roots.

Two Bad Ways to Attack Intelligent Design and Two Good Ones
Jeffrey Koperski
Zygon, 43 (2), June 2008, pages 433-449

Abstract: Four arguments are examined in order to assess the state of the Intelligent Design debate. First, critics continually cite the fact that ID proponents have religious motivations. When used as criticism of ID arguments, this is an obvious ad hominem. Nonetheless, philosophers and scientists alike continue to wield such arguments for their rhetorical value. Second, in his expert testimony in the Dover trial, philosopher Robert Pennock used repudiated claims in order to brand ID as a kind of pseudoscience. His arguments hinge on the nature of methodological naturalism as a metatheoretic shaping principle. We examine the use of such principles in science and the history of science. Special attention is given to the demarcation problem. Third, the scientific merits of ID are examined. Critics rightly demand more than promissory notes for ID to move beyond the fringe. Fourth, although methodological naturalism gets a lot of attention, there is another shaping principle to contend with, namely, conservatism. Science, like most disciplines, tends to change in an incremental rather than revolutionary manner. When ID is compared to other non- or quasi-Darwinian proposals, it appears to be a more radical solution than is needed in the face of the anomalies.

The buildup for the 2009 bicentennial of Darwin's birth suggests that there is more here than celebrating the life of this Victorian gentleman scientist. An essay in Nature, marking the 150th anniversary of the short paper Alfred Russel Wallace sent to Darwin unveiling his thoughts on evolution by natural selection, gives some clues about the wider agenda for Darwin's acclaim.

Do we see the real Darwin? or do we get an image constructed by his heirs? (Source here)

Darwin communicated the striking convergence between his own thinking and that of Wallace in a letter to Charles Lyell on 18 June 1858. Lyell and Hooker urged a joint publication of the theory, so the article by Wallace and another from Darwin was read at a meeting of the Linnean Society on 1st July. At the time, it was not perceived as a landmark event in science. Neither Darwin or Wallace was present and their papers made little impact.

Thomas Bell, president of the Linnean Society, guaranteed himself an unfortunate footnote in the history books by writing in his annual review of 1858: "The year which has passed has not, indeed, been marked by any of those striking discoveries which at once revolutionize, so to speak, the department of science on which they bear".

The convergence can be attributed to intelligent design. Both men were thinking along the same lines and proposed essentially the same mechanism to explain evolutionary transformation. They were not alone as pioneers. In 1831, the plant breeder Patrick Matthew had proposed essentially the same theory in the appendix of a book on arboriculture - but he did not develop his ideas further.

"Exploring Wallace's role in the evolutionary story reveals a host of other figures who also deserve to be heard. over the past twenty years, the Darwinian revolution has been shown to be neither a revolution as commonly understood nor solely due to Darwin. Many people proposed developmental schemes, some as famous as Jean-Baptiste Lamark and Herbert Spencer, others relatively unknown but just as interesting. To remember Wallace is therefore to recognise that "evolution was in the air", and prompts one to wonder how Darwin's name rose so smoothly to the top."

Berry and Browne (the authors of the essay) refer to several factors explaining why Darwin became so dominant. The first concerns the honour placed on those who advance science: "precedence is everything; posterity ignores the second place". This is not particularly convincing, as Matthew has a justifiable claim for precedence, and both Darwin and Wallace agreed with joint publication of their ideas in 1858. Secondly, "major changes in scientific theory are not just about the formulation of new ideas, but also depend on circulation and discussion." Whilst there is no doubt that Darwin's work did trigger discussion, we should note that many of the responses were critical. His proposals were not received as the key to unlock the mystery of life, but many felt that his theory, where it could be tested, was not confirmed by the evidence. Thirdly, the authors point to Wallace's contribution to his own eclipse by adopting the term Darwinism and undermining his credibility as a scientist by becoming "a spiritualist". I have referred to these aspects of Wallace in a previous blog.

If we take Wallace on his own merits, he had many commendable strengths. "In fact, he was a superb scientist, whose contributions to many aspects of evolutionary biology and biogeography remain influential. His conduct in the evolution business is exemplary." So why was he eclipsed by Darwin? This comment deserves further thought:

"[T]he making of a new theory rarely occurs in isolation. Rather, it depends on the support of colleagues, social networks and interactions within the scientific community, as well as the power of the theory itself."

The key to understand this situation is that Darwinism is not just a scientific theory. Those who think this (and I am referring primarily to theistic evolutionists) appear to be blind to this analysis of history. Darwinism succeeded because it fitted into the next phase of Enlightenment rationalism. Up until Darwin, Enlightenment science was content to coexist with a modified Deism, where God was the First Cause and then left Creation to run as a giant machine apart from occasional interventions of destruction and recreation. Darwin's approach allowed these interventions to be excluded and God was restricted to acting as the First Cause and science became autonomous. Of course, there were a growing number of science leaders, including Darwin, who were prepared to contemplate agnosticism about God and wanted to promote the secularisation of science. Wallace was not part of this ideological shift, so he remained an outsider. Darwin was a prominent node in the network of Victorian science, and it suited his colleagues for him to be the front-man for their ideological revolution.

Why are these things important? It is because there continue to be many who think that ID advocates have invented the concept of a culture war. They think that Darwinism should always be considered as a "pure" scientific theory. The flaw with this is that it never was and it cannot today be defended purely on science grounds. There have always been significant doubts as to what variations (mutations) and natural selection can accomplish. However, to acknowledge this should not be isolated from the ideology underpinning Darwinism - which is where the real drivers are in these debates. That is why Wallace, with his teleological world-view, did not find a place in the emerging secularised scientific culture.

The other beetle-hunter
Andrew Berry and Janet Browne
Nature 453, 1188-1190 (26 June 2008) | doi:10.1038/4531188a

Abstract: Thanks to a fateful letter, the theory of evolution by natural selection was unveiled 150 years ago this week. Andrew Berry and Janet Browne celebrate the letter's writer, Alfred Russel Wallace.

There are many species of bacteria with two modes of life: one is motile with swimming propelled by rotating flagella, and the other is sessile as part of a biofilm. What happens when they change from free swimming mode to attached mode?

"Two things typically happen next. Cells stop expressing genes that encode components of the flagellum, and they secrete a sticky matrix of polysaccharides that holds them together on the surface. Once at a surface, swimming may be a hindrance rather than a help, and an inverse relationship between swimming and attachment has been seen in many diverse species. However, the molecular details underlying this arrest in motility have not been fleshed out. Are flagella ejected or dismantled? If not, do they keep rotating until they are jammed by the newly formed matrix?"

A nanotechnology clutch disengages the flagellum's tail from the engine that powers its rotation (source here)

It turns out that neither of these possibilities apply. Recent research by Blair et al. has shown that there is an "off-switch for rotation". This device utilises a special protein, EpsE.

"To determine whether EpsE acts as a brake that locks the motor, or a clutch that leaves the rotor freely spinning, Blair et al. tethered bacteria to a substrate by their filaments and observed rotation of the cell bodies around single flagellar motors. Under the influence of EpsE, cells stopped spinning but continued to undergo free rotational Brownian motion, indicating a clutch mechanism."

This finding has been a surprise:

It had been thought that bacteria slowed down by switching off the genes that make flagella, says Richard Berry, a physicist at the University of Oxford, UK, who studies molecular motors.
"This is a completely unknown thing," he says. "The previous wisdom was that flagella would spin for ever."

With hindsight, the clutch mechanism makes a lot of sense:

"The direct inhibition of motor rotation by EpsE represents a newly discovered control mechanism for bacterial swimming. Bacterial flagella are large protein complexes that require about 40 to 50 genes to assemble. Thus, the most obvious advantage of the EpsE mechanism over transcriptional control of flagellar genes is speed. In B. subtilis, only one protein, EpsE, needs to be expressed to stop the motor. Presumably, this is important if cells are to stay put in the early stages of biofilm formation. However, the advantages of a clutch over a brake mechanism are not so clear. Perhaps free rotation of flagella - or, alternatively, reduced motility during the transition to the EpsE-inhibited state - is important for the formation of well-structured biofilms. Or maybe a clutch is simply easier to make than a brake."

The researchers contrast the strategy of turning off flagellum synthesis with the clutch alternative, and supply one additional consideration - the possible need for reactivation of the flagellar motor:

"The flagellum is an elaborate, durable, energetically expensive, molecular machine and simply turning off de novo flagellum synthesis does not necessarily arrest motility. Once flagellar gene expression is inactivated, multiple rounds of cell division may be required to segregate preexisting flagella to extinction in daughter cells. In contrast, the clutch requires the synthesis of only a single protein to inhibit motility. Furthermore, if biofilm formation is prematurely aborted, flagella once disabled by the clutch might be reactivated, allowing cells to bypass fresh investment in flagellar synthesis. Whereas flagellum expression and assembly are complex and slow, clutch control is simple, rapid, and potentially reversible."

The clutch "solution" is therefore a neat, effective and potentially reversible mechanism. The authors describe it as "simple", which is OK if the meaning is that just one component is needed to disengage the flagellar motor. However, this conceptual simplicity in no way conflicts with understanding this system in terms of complex specified information. The researchers have identified a gene epsE responsible for making the EpsE protein which engages with the critical protein transmitting torque to the flagellum and removing the link to the source of power. The measure of complexity is in the unique shape of the EpsE protein and its ability to engage with the torque-transmitting protein so that power is no longer transmitted. The team is now "looking for a protein that disengages the clutch and reconnects the motor". This would help to disaggregate biofilms and could lead to significant medical applications. One measure of "simplicity" is the ease of finding such a protein. My prediction is that the researchers will not be using the word "simple" to describe this phase of the research. The science community is well aware that nanotechnology successes are achieved only by the application of sophisticated science and intelligent engineering design.

A Molecular Clutch Disables Flagella in the Bacillus subtilis Biofilm
Kris M. Blair, Linda Turner, Jared T. Winkelman, Howard C. Berg, and Daniel B. Kearns
Science 320, 20 June 2008: 1636-1638.

Abstract: Biofilms are multicellular aggregates of sessile bacteria encased by an extracellular matrix and are important medically as a source of drug-resistant microbes. In Bacillus subtilis, we found that an operon required for biofilm matrix biosynthesis also encoded an inhibitor of motility, EpsE. EpsE arrested flagellar rotation in a manner similar to that of a clutch, by disengaging motor force-generating elements in cells embedded in the biofilm matrix. The clutch is a simple, rapid, and potentially reversible form of motility control.

See also:

Berry R.M. and Armitage, J.P., How Bacteria Change Gear, Science 320, 20 June 2008: 1599-1600.

Whitfield, J. Bacterial engines have their own clutch, news@nature.com, 19 June 2008 | doi:10.1038/news.2008.903

The instinctive reaction of most people to this question is "Of course not! Without critical thinking, science is dead!" So when one of the leading science journals carries a report on the Louisiana bill promoting the development of "critical thinking skills" describing it as an "attack [. . .] on the teaching of evolution and mainstream scientific thought on global warming and other topics" - it is time to reflect on the reasons why.

One of the many caricatures of "academic freedom" initiatives (Source here)

The report puts great weight on the scientific consensus about evolution. It refers to "mainstream scientific thought", the "overwhelming support from our science teacher members", and to "agreed-upon standards". The implication is that all talk of "critical thinking" to challenge the consensus must be motivated by factors outside science. Consequently, we read comments like: "Science educators say the new wording is intended simply to circumvent rulings by U.S. courts that creationism and intelligent design are unconstitutional religious intrusions into a public school science curriculum."

This dismissive perception fails to acknowledge the intense debates and fundamental differences about evolution that exist within the scientific community (for a current example, go here). Can any issue relating to evolutionary theory be found that is free from controversy? I cannot think of one. The emphasis on 'consensus', with the implication that dissent comes from outside science, is actually alien to the spirit if science. It can (and should) be argued that this emphasis is a threat to the health and vigour of all disciplines of science. Sociologists of science have come to recognise that the 'consensus' argument is part of a struggle for power and influence. In his recent book, Professor Steve Fuller suggests that "public professions of faith in evolution by scientists are best interpreted as simply marking solidarity with the reigning orthodoxy" (p.32). He refers to one of the major recent 'consensus' statements on evolution:

"The first case is the InterAcademy Panel of 67 national academies of science, which in June 2006 issued a joint statement calling for the promotion of evolutionary theory in schools against an alleged worldwide creationist threat. Yet, the statement failed to identify any specific evolutionary mechanisms for mandatory instruction, resorting instead to an anodyne characterisation of evolution as somehow responsible for the diversity of life on Earth, and an easy dismissal of young-Earth creationism. One suspects that to manufacture the appearance of widespread scientific consensus, the statement's drafters were forced to edit out any specifically Darwinian references, especially to natural selection, that might prove divisive to some of the signatories." (p.32-33)

The inclusion of Global Warming issue is very interesting. This is another topic where 'the scientific consensus' has been thrust down the throats of the public, political leaders and funding bodies. The issue, of course, is not primarily about global warming per se, but whether the human activity of burning fossil fuels (and releasing extra carbon dioxide) has had a significant influence on atmospheric temperatures. (For a useful overview of issues, go here). It will be a surprise to many that there is a significant community of dissenting scientists who feel that the consensus is contrived and are very concerned about the pressures they face to conform. They vigorously object to the ad hominem claim that their dissent is sponsored by oil companies. Their responses in the media reveal titles and counter-arguments that have much common ground with the experiences of ID scientists. There is a general problem here for the science community to address: consensus arguments are being constructed which are undermining scholarly activity by treating dissent as anti-science and driven by vested interests. It appears to me that the real problem is with the champions of consensus, for they are selectively reporting the science issues and have an agenda that includes power, influence and access to research funds.

The consensus arguments about evolution are somewhat more complex than this. Why is it that "academic freedom" issues and the promotion of "critical thinking skills" are linked so easily to "creationism and intelligent design"? Those who do this are either advocates of philosophical materialism ('matter is all there is' so living things must be explained by material processes only and any dissent about this must be religious) or people who have adopted sphere sovereignty in their thinking about science. This is Gould's NOMA thesis, which requires an absolute line to be drawn between science/facts and religion/values. Anything to do with design (they say) is located within the religion/values sphere and is completely outside science. By embracing one of these philosophical stances, the opponents of the Louisiana bill have driven into a cul-de-sac which results in their flat, stereotyped responses. They are unable to conceive that their might be any philosophy of science other than their own, and they cannot recognise scientific arguments against evolution even when they are spelled out. As evidence of this, the cover of Explore Evolution is reproduced in the Science report with the comment "Political science?" Sad! It looks as though the author would benefit from education that develops "critical thinking skills".

This graphic is given the title: "Political Science?" in Science

Louisiana Opens School Door for Opponents of Evolution
Fayana Richards
Science 320, 20 June 2008: 1572.

A bill passed overwhelmingly by the Louisiana state legislature and expected to become law as early as next week marks the latest attack in the United States on the teaching of evolution and mainstream scientific thought on global warming and other topics.

See also:

Fuller, S. Dissent over Descent, Icon Books Ltd, Cambridge, 2008 (Chapter 1).

Crowther, R. Explore Evolution Textbook Featured in Science Magazine, Evolution News & Views, 22 June 2008

Crowther, R. Victory in Louisiana: Governor Jindal Signs Historic Science Education Act On Evolution and Education, Evolution News & Views, 27 June 2008

West, J.G. Louisiana Confounds the Science Thought Police (National Review Online, July 08, 2008)

Robert Deyes
ARN Correspondent

If Darwin was right then we would be just sophisticated monkeys, there would be no right or wrong, just 'make-em-up' ethics and there would be no God. This was the assessment of one local of Kanawha County in West Virginia as journalist Lee Strobel arrived to capture the story of Anti-Darwinian protests in 1974. Strobel at the time was a self-confessed atheist, believing that much of what the anti-Darwinian movement was promulgating reflected nothing more than blind ignorance. He considered the biblical creation story as simply fictitious, surpassed and discredited as it was by the knowledge gleaned by modern science. That year, as the protests against the teaching of Darwin in West Virginia's schools heated up, Strobel found himself alienated by the residents of a town that had already banished several hundred different textbooks from school circulation- books that, according to the local school board, taught the "wrong kind of ethic". In all truth Strobel was very much a convert of the scientific story of evolution, convinced as he was by the 'facts' and apparently clear-cut examples in support of evolutionary theory. As Strobel saw things, the random and undirected nature of Darwinism could not be reconciled with the purposeful nature of the biblical account. The very least that could be said was that, if Darwinism were as unshakable as its proponents claimed, God would not be needed for life to emerge. The Case For A Creator is an account of Strobel's journey to test the veracity of the apparent 'facts' of evolution and the materialistic world view- a journey that takes him across the United States as he interviews several key experts in various fields of science.

The first stop over for Strobel is with Jonathan Wells- a Berkeley graduate whose outspoken criticism of some of the icons of evolution is well known. During the interview Wells dismantles the evidences that Strobel had himself learnt as a graduate by showing how much of what we supposedly know about evolution is unsupported by the evidence. It is now widely accepted for example that Stanley Miller's laboratory experiments showing how amino acids could be generated under reducing atmospheric conditions did not accurately mimic the environment of the early earth. And yet today these experiments continue to feature prominently in biology text books as does Darwin's tree of life. As Wells points out, rather than revealing an unbroken chain of intermediates linking all of life to a few early forms as Darwin's tree required, the fossil record shows a sudden 'explosion' of life approximately 550 million years ago during which most of the major animal taxa appeared in a five million year time frame without any preceding intermediates. Equally troubling is the finding that embryologist Ernst Haeckel modified his now famous drawings of vertebrate embryos so that they would fit within preconceived ideas of an evolutionary continuum. Wells' criticism of the disjunction that exists between apparently homologous structures in vertebrates- that is, those structures that are considered to reveal common ancestry- and the genes responsible for their formation, different as they are in different animal species, shows just how much of what we know today contradicts the basic tenets of Darwinism.

During Strobel's journey, philosopher Stephen Meyer makes his case for an intelligently-designed universe on the grounds that the information-rich instruction code of DNA that comprises life directly parallels information-rich code that we know has been generated by intelligent agents. Meyer asserts how it is the irreducibly complexity of many of the 'machines' of the cellular world, with their requirement for all their components to be present before their function can be achieved, that most clearly defies the expectations of the Darwinian framework. As Meyer argues, since natural selection can only begin to select systems that have reached a minimal level of functionality and since this functionality is only attained when all the components of these systems are present, their initial assembly must have been directed by some guiding process. That is, they must have been intelligently designed. Biochemistry Professor Michael Behe, also on Strobel's long list of visits, was the initial proponent of irreducible complexity in biology. Behe has provided several examples of irreducibly complex biological systems notably the blood clotting cascade, the structure of the bacterial flagellum and the makeup of tiny hairs called cilia citing them as evidence for an intelligently-designed biological world.

A vast body of data is accumulating outside of the realm of biology in support of the design inference and many scientists are now realizing how uniquely fit for the existence of life our own earth appears to be. We now know that not only is our earth ideally positioned in our solar system so as to meet the survival needs of animals and plants but that it is also very well placed for humans to make important scientific discoveries about our cosmos. Strobel's interview with philosopher Jay Richards and astronomer Guillermo Gonzalez provides a catalog of such 'biocentricities'. Everything from the protective influence of the larger planets in our solar system to the consistent warmth and energy from our sun, from the effect of the moon on the tilt of the earth's axis to the overall mass of the earth, from the influence of the earth's own internal heat on the earth's environment to the orbit of our solar system within the strict confines of a 'habitability zone' around our galaxy draws us to the inevitable conclusion that ours is in every sense a unique world, designed as it is for our own enjoyment. As Strobel's discussions with physicist Robin Collins make all too clear, the physical characteristics of the elements that make up matter throughout the cosmos fall precisely within the narrow range of values that are permissible if life is to exist. The magnitude of the gravitational force, the size of the cosmological constant in Einstein's equations of general relativity, the difference in size between the protons and neutrons of atomic nuclei and the size of the strong and weak atomic forces that hold atoms together are so exactly placed in this permissible range that we can only conclude that an intelligence has been at work in the design of our cosmos. Theologian William Lane Craig likewise presents his arguments for a single, finely-tuned and controlled cosmic origin approximately 14 billion years ago from which our universe has subsequently expanded.

One of Strobel's final interviews is with philosopher J.P Moreland to discuss the subject of human and animal consciousness. While many contend that consciousness in humans is nothing more than the by-product of accumulating brain power, others such as Moreland conclude that it reveals something much deeper. Indeed observations on human behavior point to what psychologists call 'dualism'- a state in which consciousness and the mind exist separate from the rest of the brain. Our awareness of our selves- own thoughts, our own emotions, our desires and our own decisions- points to an entity one might call the 'soul' that exists outside of the electrical firings of the brain mass inside our heads. This 'inner and private mind' of man, asserts philosopher Alvin Platinga, is that one part of man that appears inaccessible to a naturalistic explanation. What we know about the mind of man, Moreland argues, directly agrees with the Christian world view of an omnipresent God who exists everywhere and manifests his presence in humanity through the soul. In the end Strobel's case also leads him to the identification of the God of Christianity as the designer whose works have fashioned all that we see around us. But metaphysical assertions aside, the scientific evidence that Strobel accumulates in his book provide a strong case against the purely naturalistic assertions of modern day Darwinism. Indeed one can only imagine how things would have turned out for the inhabitants of Kanawha County and the rest of West Virginia if they had been aware of this evidence back in 1974. They would have had a case to defend that was based on a very compelling scientific story.

After cellulose, lignin is a major constituent of plant material, comprising 25-33% of the dry mass and imparting mechanical strength and conducting water. There are three major types of lignin, depending on the monomers involved in the formation of this material. "Lignins are derived mainly from the phenylpropanoid monomers p-coumaryl, coniferyl, and sinapyl alcohol, which give rise to p-hydroxyphenyl, guaiacyl, and syringyl subunits when incorporated into the lignin polymer." These different types are significant for the research being considered here. "Generally, ferns and gymnosperms deposit lignins that are derived primarily from guaiacyl monomers together with a small proportion of p-hydroxyphenyl units, whereas angiosperm lignins are guaiacyl/syringyl copolymers that also can contain some p-hydroxyphenyl monomers." Since angiosperms appear in the Late Cretaceous, and the other types of vascular plant are found from the Silurian, some have thought that syringyl lignin is a late arrival in the evolutionary story of plants.

Selaginella moellendorffii (Source here)

The plant studied is a lycophyte - Selaginella moellendorffii - popularly known as spike moss. It can be considered a living fossil, and is described by the researchers as "a relict of an ancient vascular plant lineage". Its genome has been sequenced and it is the subject of numerous studies relating to lycophytes.

In their discussion, the researchers summarise their findings in this way:

"The distribution of syringyl lignin in the plant kingdom suggested two possible models for the evolution of F5H [an essential component in the formation of syringyl lignin]. First, the enzyme could have arisen early in plant evolution, was lost in ferns and gymnosperms, but was not lost in angiosperms or Selaginella. Alternatively, F5H could have evolved independently in lycophyte and angiosperm lineages after they had diverged. Our results suggest that the second model is correct and that F5H from Selaginella is functionally equivalent to, but phylogenetically independent from, angiosperm F5Hs. This conclusion is further supported by the observation that syringyl lignin derivatives are not detected in extant members of the Lycopodiaceae and have not been found in fossils of the extinct lycophyte Sigillaria ovata (order Lepidodendrales)."

The press release for the research paper summarises the achievement in these words:

"Biologists have discovered that a fundamental building block in the cells of flowering plants evolved independently, yet almost identically, on a separate branch of the evolutionary tree - in an ancient plant group called lycophytes that originated at least 420 million years ago. Researchers believe that flowering plants evolved from gymnosperms, the group that includes conifers, ginkgos and related plants. This group split from lycophytes hundreds of millions of years before flowering plants appeared. The building block, called syringyl lignin, is a critical part of the plants' scaffolding and water-transport systems. It apparently emerged separately in the two plant groups, much like flight arose separately in both bats and birds."

The conclusion, that this complex material "evolved independently" deserves careful scrutiny. We are dealing here with some very complex chemistry that does not exist in isolation from other aspects of the plant. The idea that almost identical innovations occurred independently may be the best of the explanations considered above, but there is at least one other option that needs to be considered: and that emerges from a design inference. Complex chemistry like this does not just happen: it suggests the presence of intelligence. This is confirmed by the potential this research offers for engineering plants for easier lignin breakdown in the manufacture of biofuels:

"Findings from studies such as this really have implications regarding the potential for designing plants to better make use of cellulose in cell walls," said Gerald Berkowitz [. . .] "Different forms of lignin are present in crop plant cell walls; engineering plants to express specifically syringyl lignin could allow for easier break down of cellulose. Overcoming this obstacle is an important next step for advancing second generation biofuel production."

These researchers are proposing to use their expertise in biotechnology and design engineering to bring about changes to plants that bear comparison with changes evolutionists attribute to mindless tinkering processes. This particular plant provides a remarkable example of convergence that argues against contingency in evolution and for intelligent agency in the way plant materials are constructed.

Independent origins of syringyl lignin in vascular plants
Jing-Ke Weng, Xu Li, Jake Stout, and Clint Chapple
Proceedings of the National Academy of Sciences USA, June 3, 2008, vol. 105, no. 22, 7887-7892.

Lycophytes arose in the early Silurian (~400 Mya) and represent a major lineage of vascular plants that has evolved in parallel with the ferns, gymnosperms, and angiosperms. A hallmark of vascular plants is the presence of the phenolic lignin heteropolymer in xylem and other sclerified cell types. Although syringyl lignin is often considered to be restricted in angiosperms, it has been detected in lycophytes as well. Here we report the characterization of a cytochrome P450-dependent monooxygenase from the lycophyte Selaginella moellendorffii. Gene expression data, cross-species complementation experiments, and in vitro enzyme assays indicate that this P450 is a ferulic acid/coniferaldehyde/coniferyl alcohol 5-hydroxylase (F5H), and is capable of diverting guaiacyl-substituted intermediates into syringyl lignin biosynthesis. Phylogenetic analysis indicates that the Selaginella F5H represents a new family of plant P450s and suggests that it has evolved independently of angiosperm F5Hs.

See also:

Fundamental Building Block In Flowering Plants Evolved Independently, Yet Almost Identically In Ancient Plants, ScienceDaily (May 28, 2008)

In 1969, a large meteorite fell to the ground about 100 miles north of Melbourne, Australia. It broke apart before impact, and the science community has been left with numerous fragments. It is a carbonaceous chondrite, which is commonly thought to be closest in composition to the source materials that formed the terrestrial planets. There has been extensive research into the organic contents of this meteorite, and some of this has concerned contamination. There are some evidences for contamination and some evidences supporting an extraterrestrial origin for the organic molecules. The latest research claims that there are "extraterrestrial nucleobases in the Murchison meteorite".

The Murchison Meteorite continues to attract interest from scientists and the media (source here)

What has been found? The researchers report "many biologically relevant organic molecules" and highlight uracil and xanthine for attention. These are the nucleobases referred to in the title of their paper. They are described as "precursors to the molecules that make up DNA and RNA". Uracil is used to store information contained in RNA, and xanthine is a metabolic intermediate in the breakdown of purine nucleotides (which only works in conjunction with suitable enzymes). What they are not are "genetic material" (as announced by the Imperial College Press Release and repeated by several other forums: ScienceDaily, PhysOrg.com, popsci.com).

Having reported the presence of these molecules, the authors go on to speculate about their significance. Since these molecules represent primordial material, they can be inferred to have been transported to the Earth's surface in the Hadean Period of Earth history. They "may have played a key role in life's origin." Their presence allows a more critical appraisal of theories about the endogenous production of amino acids (which no longer look viable as a source of these building blocks).

"Our data advance proposals that life's raw materials were delivered to the early Earth and other planetary bodies by exogenous sources, including carbonaceous meteorites. In contrast, the endogenous synthesis of prebiotic organic compounds may have been constrained by the conditions on the young Earth, perhaps most importantly by the oxidation state of the atmosphere. For example, only low yields of amino acids were produced under non-reducing conditions in the Miller-Urey-type experiment. Yet, whatever the inventory of endogenous organic compounds on the ancient Earth, it would have been augmented by extraterrestrial material. It is estimated that these sources delivered ~10^9 kg of carbon per year to the Earth during the heavy bombardment phase 4.5-3.9 billion years ago."

The researchers are very excited about their find and its potential for helping theories of abiogenesis:

"We believe early life may have adopted nucleobases from meteoritic fragments for use in genetic coding which enabled them to pass on their successful features to subsequent generations." (Zita Martins)
"Because meteorites represent left over materials from the formation of the solar system, the key components for life - including nucleobases - could be widespread in the cosmos. As more and more of life's raw materials are discovered in objects from space, the possibility of life springing forth wherever the right chemistry is present becomes more likely." (Mark Sephton)

This message is echoed in the media reports. For example, popsci.com says: "If the basic ingredients are zipping around throughout the cosmos, the likelihood of life taking shape wherever the chemistry is right is most certainly increased." Comments like this do not provide a service to anyone, for they confuse rather than clarify. The same point applies to the search for liquid water on other astronomical bodies - as though finding water is the key to life springing forth wherever the right chemistry is present. Research has shown over and over again that life does not self-assemble. Put all the ingredients of life together in a soup and you do not get life! Those who present the issue as one for chemists to solve are seriously astray. It is crucially important to focus on biological information and where it comes from. Law and chance do not deliver. Abiogenesis research that considers only these options has confirmed repeatedly that life does not emerge from a chemistry set. What is needed is a reorientation to the role of information, and for this, we need design perspectives in science.

"In my opinion, there is no basis in known chemistry for the belief that long sequences of reactions can organize spontaneously - and every reason to believe that they cannot. The problem of achieving sufficient specificity, whether in aqueous solution or on the surface of a mineral, is so severe that the chance of closing a cycle of reactions as complex as the reverse citric acid cycle, for example, is negligible." Orgel, Leslie, (Dec 1998) "The origin of life - a review of facts and speculations," Trends in Biochemical Sciences, 23: 491-495.

Extraterrestrial nucleobases in the Murchison meteorite
Zita Martins, Oliver Botta, Marilyn L. Fogel, Mark A. Sephton, Daniel P. Glavin, Jonathan S. Watson, Jason P. Dworkin, Alan W. Schwartz and Pascale Ehrenfreund
Earth and Planetary Science Letters, 270(1-2), 15 June 2008, 130-136

Abstract: Carbon-rich meteorites, carbonaceous chondrites, contain many biologically relevant organic molecules and delivered prebiotic material to the young Earth. We present compound-specific carbon isotope data indicating that measured purine and pyrimidine compounds are indigenous components of the Murchison meteorite. Carbon isotope ratios for uracil and xanthine of [delta]13C [. . .] indicate a non-terrestrial origin for these compounds. These new results demonstrate that organic compounds, which are components of the genetic code in modern biochemistry, were already present in the early solar system and may have played a key role in life's origin.

Robert Deyes
ARN Correspondent

Historically the field of evolutionary biology has been plagued with a fundamental move to fit or adapt scientific data into the picture of organic continuity that Darwin painted in The Origin Of Species (Ref 1). So strong has been this move that on occasions scientific objectivity has been lost and replaced by, what could only be described as a 'force of fit' to ensure that the validity of Darwinian theory was maintained (Ref 1). The unity of form observed during embryonic development was according to Darwin indicative of "the progenitor [. . .] of all the members of the same great class" (Ref 2, p. 600). Darwin's conviction over the importance of the embryological picture to his theory was made plainly clear in his autobiography where he wrote that,

"hardly any point gave me so much satisfaction when I was at work on The Origin, as the explanation of the wide difference in many classes between the embryo and the adult animal, and of the close resemblance of the embryos within each class" (Ref 3, p.125)

Darwin was not an embryologist and so relied very heavily on the viewpoints of his contemporaries. One of these was Professor Ernst Haeckel who, famous for his comparative drawings of embryos including those of fish and amphibians, brought seemingly strong confirmatory evidence to the Darwinian thesis. Darwin had a high regard for Haeckel's perspective and saw Haeckel's study of embryonic characters as "a great beginning" that showed us "how classification will in the future be treated" (Ref 2, p. 579). And yet Haeckel was overzealous and in making his embryo drawings, depicted a number of important details incorrectly (Ref 4). As Michael Richardson and his colleagues pointed out in a letter to Science, significant variations in embryonic size and form were missed (Ref 4). What Haeckel's inaccuracies demonstrated was a zeal to make the data 'fit' the theory. After all, these inaccuracies tended towards supporting the idea of a common progenitor rather than negating it. Richardson and his colleagues revealed the degree of 'supportive approximation' that Haeckel employed in his drawings when they published photographic evidence of progressive stages of development amongst different vertebrate species (Ref 4). Their results showed that, while there was a close correlation between embryonic developmental sequences between humans and other mammals, there was a very weak correlation between humans and other classes of vertebrates. (For Richardson's photos, go here).

Today Haeckel is remembered for his biogenetic law in which he proposed that "ontogeny recapitulated phylogeny" (Ref 5, p. 353). Haeckel theorized that animals climbed up their own family tree during embryonic development and as such presented us with a vision of how things had once been. Armed with his inaccurate representations of embryonic development and the convincing arguments of his biogenetic law, Haeckel created the phylogenist's 'dream' (Ref 6, pp. 246-247). However, by the beginning of the twentieth century, the shine of recapitulation had lost its luster. Gould recounts the disappointment that ensued with a quote from E.B Wilson's description of the "exact" experimental method:

It is a ground of reproach to morphologists that their science should be burdened with such a mass of phylogenetic speculations and hypotheses, many of them mutually exclusive, in the absence of any well-defined standard of value by which to estimate their relative probability. The truth is that the search [. . .] has too often led to a wild speculation unworthy of the name of science; and it would be small wonder if the modern student, especially after a training in the methods of more exact sciences, should regard the whole phylogenetic aspect of morphology as a kind of speculative pedantry unworthy of serious attention." (Ref 6, p. 247)

Paleontologists David Raup and Steven Stanley were equally emphatic about the inaccuracies of Haeckel's claims:

"During the eighteenth and early nineteenth centuries, many students of Mesozoic ammonites attempted to apply Haeckel's recapitulation theory to all ammonite species, believing that the course of ammonite evolution could thus be read from ontogenetic changes in shell ornamentation and suture patterns. In 1901, Pavlow invalidated the strict recapitulation concept by showing that in certain Jurassic lineages of ammonites new evolutionary features arose in the early stages of ontogeny; not until later in the evolutionary history of their respective lineages were these changes retained in the adult stages [. . .] ontogenetic development of the new features was retarded, relative to time of reproductive maturation." (Ref 7, p.275)

In other words, changes in the adult form arose after changes in the embryo, not before. It could no longer be convincingly argued that ontogenetic changes were a reflection of some evolutionary past. In light of such findings, it is paradoxical that prominent zoologists such as Richard Dawkins still maintain the importance of the so called 'embryological continuum'. Dawkins wrote, for example, that science, "can point out that the (embryological) continuum that seamlessly joins a non-sentient foetus to a sentient adult is analogous to the (evolutionary) continuum that joins humans to other species" (Ref 8, p.34). Likewise science writer David Quammen emphasized the classical Darwinian perception of the embryo not only as "the animal in its less modified state" but also the embryo as revealing, "the structure of its progenitor" (Ref 9, p. 13). Obviously, Dawkins and Quammen are at odds with the alternative, more persuasive assessment that was built on empirical evidence.

"The assumption that ancestral reminiscences could always be distinguished from recent embryonic adaptations had not been sustained. Too many stages were missing, too many others discombobulated. The application of Haeckel's law produced endless, unresolvable, fruitless argument, not an unambiguous tree of life." (Ref 6, p. 246)

These findings are in themselves preliminary indicators that the different classes of vertebrate are discontinuous. The data does not fit Darwin's premise of a few common progenitors from which all of life had originated.

REFERENCES

1. Gareth Nelson (1998), Colin Patterson (1933-98): Paleontologist-reformer of the fossil record, Nature, Volume 394 p626

2. Charles Darwin (1859), The Origin of Species By Means of Natural Selection Or The Preservation of Favored Races In the Struggle For Survival, Modern Library Paperbacks Edition (1998), New York

3. Charles Darwin, The autobiography of Charles Darwin, Copyright held by Nora Barlow in 1958, W.W. Norton and Company Inc, New York

4. Michael K. Richardson, James Hanken, Lynne Selwood, Glenda M. Wright, Robert J. Richards, Claude Pieau, Albert Raynaud (1998), Haeckel, Embryos, and Evolution, Science Vol 280 p293

5. Stephen Jay Gould (2002), The Structure of Evolutionary Theory, Belknap Press of Harvard University Press, Cambridge, Massachusetts

6. Stephen Jay Gould (1992), The Panda's Thumb- More Reflections In Natural History W.W Norton and Company, New York

7. David Raup and Steven Stanley (1971), Principles of Paleontology, W. H. Freeman and Company, San Francisco

8. Richard Dawkins (2003), A Devil's Chaplain, Published by Weidenfeld and Nicolson, London

9. David Quammen (2004), Was Darwin Wrong? National Geographic Magazine, November 2004 pp4-31

Robert Deyes

In his book The Crucible of Creation Conway Morris brought the Cambrian era of the earth's history to life with a pseudo-real journey into the past (Ref 1, pp. 63-115). Formidable amongst the examples of animals that he discussed was the Anomalocaris - a creature that David Gee would describe as, "a fearsome-looking metre-long predator" with "a circular mouth like a kitchen garbage-disposal unit" (Ref 2) What we also learn from the Cambrian explosion is that many of the animals that made their first appearance during that sudden moment of time would continue to exist for millions of years later albeit in different forms and in varying degrees of ecological 'domination' (Ref 3). The hand of a film director moving actors around the stage of life's theater is the picture that emerges. As paleontologist Niles Eldredge emphasized it is difficult to get away from the idea that someone was at the root of this theatrical jiggering:

"There really is something strange about the Cambrian. It is very much as if [. . .] life got going and somehow, somewhere, someone decided that it wasn't quite right. But rather than starting all over again, a simple, radical, reorganization was effected: new players were recruited, to be sure, and old ones dropped, but there was also a matter of emphasis - an expanded role for some, a diminished role for others - all rather reminiscent of cabinet changes at the beginning of a second presidential term" (Ref 3 p83)

The Cambrian Explosion is in tension with the fossil data (Source here)

Eldredge described the Cambrian explosion as a global event in which, "very suddenly, and at about the same horizon the world over, life showed up in the rocks with a bang" (Ref 3. p24). Gregory Wray, Russell Doolittle and colleagues dismissed the suddenness of this event presupposing a much earlier, unrecorded divergence of animal life (Ref 4,5). Interestingly this sudden appearance was not confined solely to invertebrate phyla. In 1999 a team from the Northwest University in China found fossil specimens in the Chinese Chengjiang region that suggested that vertebrates had also experienced a sudden origin in the lower Cambrian (Ref 6). It was the sudden appearance of so many animal phyla or body plans in a period of only several million years that led Stephen Meyer and his colleagues to infer that a concurrent quantum leap must have occurred in the molecular and cellular components of these organisms (Ref 7, pp. 31-37). These observations led Stephen Meyer and colleagues to the conclusion that intelligent design, rather than natural, undirected processes, provided the best causal explanation for the origin of the Cambrian fauna (Ref 7). Likewise the subsequent maintenance of phyletic disparity from the Cambrian to the present day constituted a phenomenon that, based on what we know from our everyday experiences, implied intelligent causation (Ref 7). Concluding their arguments Meyer and colleagues wrote:

"As a result of this observed "stasis" and the absence of "directional change," the morphological disparity or isolation between distinct animal body plans has remained un-bridged. Moreover [. . .] developmental mechanisms constrain the degree to which organisms may vary without deleterious consequences. Intelligent design also helps to explain these phenomena. Human experience suggests that designed objects have a functional integrity that makes the modification of some parts of their basic architecture difficult or even impossible" (Ref 7, p39).

We only have to look at modern forms of technology to realize just how right such an assessment is. Many cases can be cited where technology exhibits the same functional form now as it did at its inception. The car is a classical example of this. While having changed in detail over the last 100 years (introduction of automatic gear shifts, aerodynamic shaping, turbo engines, etc.), the car exhibits the same functional form that it always has (axles, wheels, drive shafts and chassis) (Refs 7, 8). Conversely there are examples of technological form that exhibit a marked discontinuity. The CD ROM, for example, represents a functional unit that does not directly follow on from the technology employed in the earlier LP record. In short, LPs and the CD ROM demonstrate a functional and structural disparity that parallels that which we see in the Cambrian fauna. Our technological world is rife with such examples of systems that mirror the maintenance of functional integrity that we see in biology (Refs 7, 8).

The maintenance of the basic Cambrian body plans throughout their subsequent history is best demonstrated through what Meyer and colleagues call 'the inverted cone of diversity' (Refs 7, 8). To understand what we mean by this, consider the basis of the Darwinian model of natural selection - a model that predicts the gradual increase in diversity from a few common ancestors at the beginning of the evolutionary process. This model is precisely the reverse of what we see in reality since, as already demonstrated, the Cambrian displays phyletic-level disparity preceding species-level diversity (Refs 7, 8). This inverted cone is once again precisely what we see in the blueprints or prototypes of everyday technological designs. Such prototypes are conceived first and only then are parts assembled, changes made and slight modifications executed. The Cambrian reproduces this order of construction very well- animals are first materially instantiated in their disparate, phyletic groups forming the fundamental body plans upon which subsequent modifications are made (Refs 7,8). The Cambrian explosion thus represents the epitome of what the modern Intelligent Design (ID) movement is all about.

References
1. Simon Conway Morris (1998), The Crucible of Creation; The Burgess Shale And The Rise Of Animals, 1st Ed, Oxford University Press

2. David Gee (1999), Relics: Squashy fossil in the bag, Nature Science Update

3. Niles Eldredge (1987), Life Pulse: Episodes From The Story of The Fossil Record, Facts On File Publications, New York

4. Gregory Wray, Jeffrey Levinton and Leo. H. Shapiro (1996), Molecular Evidence for Deep Precambrian Divergences Among Metazoan Phyla, Science Vol 274 pp 568-573

5. Russell F. Doolittle, Da-Fei Feng, Simon Tsang, Glen Cho, Elizabeth Little (1996), Determining Divergence Times of the Major Kingdoms of Living Organisms with a Protein Clock, Science Vol 271 pp 470-477

6. D-G. Shu, H-L. Luo, S. Conway Morris, X-L. Zhang, S-X. Hu, L. Chen, J. Han, M. Zhu, Y. Li and L-Z. Chen (1999), Lower Cambrian vertebrates from south China, Nature 402, 42 – 46

7. Stephen Meyer, Paul Nelson and Paul Chien (2001) The Cambrian Explosion: Biology's Big Bang, http://www.discovery.org/articleFiles/PDFs/Cambrian.pdf

8. Stephen Meyer (2004), The Origin of Biological Information and the Higher Taxonomic Categories, Proceedings of the Biological Society of Washington, Volume 117, pp. 213-239

The most trenchant and effective critiques of evolutionary biology have tended to come from scholars who are themselves advocates of evolutionary biology. Two books have appeared in recent years, both reviewed by Johan Bolhuis in the pages of Science. "In the end", says Bolhuis, "the two books are complementary, and together they constitute a formidable critique of evolutionary psychology." The theory of evolution is

"generally considered one of the most important intellectual achievements of the modern age. It therefore seems logical to extend the theory to cognition, as Darwin himself did in The Descent of Man when he considered human characteristics such as morality or emotions to have been evolved. Evolutionary psychology aims to do just that: applying evolutionary theory to the human mind. Specifically, it proposes that the mind consists of cognitive modules that evolved in response to selection pressures faced by our Stone Age ancestors. The approach has a wide popular appeal, perhaps because it often addresses such exciting topics as human desire, sex, and passion."

The archetypal evolutionary psychology perspective of human nature (Image source here)

The first book is Adapting Minds by David J. Buller. Since this was published in 2005, comment here will be brief.

Buller eventually concludes that the paradigm is not particularly well founded theoretically. One of its key claims is that "our modern skulls house stone-age minds" - that the human mind has not evolved significantly since the Pleistocene. Buller offers overwhelming evidence for the contrary conclusion. As he puts it, "There is no reason to think that contemporary humans are, like Fred and Wilma Flintstone, just Pleistocene hunter-gatherers struggling to survive and reproduce in evolutionarily novel suburban habitats."

The review offers a specific example, drawn from Buller's own analysis of child abuse data in the US.

"Buller devotes three chapters to the paradigm's interpretations of mate preferences, marriage and infidelity, and parenthood. In one, he focuses on Martin Daly and Margo Wilson's evidence for what they have called "discriminative parental solicitude." They provided data suggesting that children are much more likely to suffer abuse from stepparents than from their biological parents. Their findings are consistent with an evolutionary interpretation whereby parental investment is directed at increasing the chances of survival of one's own genes. Buller argues that Daly and Wilson's analysis is influenced by a reporting bias. He and Elliott Smith have analyzed a large dataset on child abuse in the United States, and they conclude that the evidence does not support the evolutionary psychology hypothesis."

The second book, by Robert C. Richardson, has the provocative title: Evolutionary Psychology as Maladapted Psychology. Despite this, Bolhuis writes: "The merit of his critique is that it is not polemic in the way those of some of his fellow critics (such as Jerry Fodor or Stephen Jay Gould) have been." The approach is to consider the methodology of evolutionary psychology: "he criticizes mainly the methods used by evolutionary psychologists".

"Richardson evaluates in some detail whether particular human cognitive traits, such as language or human reasoning, can be seen as adaptations. He concludes that although it should be possible to find evidence to support such claims, evolutionary psychologists have generally failed to do so. [. . .] The main problem with evolutionary psychology is that it usually does not consider alternative explanations but takes the assumption of adaptation through natural selection as given."

This point is very important. A characteristic of Kuhn's "normal science" is that people work within the paradigm. They are typically blind to alternatives that can only be considered rigorously by moving outside the paradigm. Evolutionary psychologists have given priority to dogma by emphasising adaptation and presuming an evolutionary trajectory. But this approach leads to force-fitting data to theory and because the dogma reigns supreme, the system cannot be falsified.

A major problem is that critical data is typically lacking. Theory reigns unconstrained by data! Often, it is very difficult to contest the conclusions of the evolutionary psychologists. Thus far, the onus of proof has tended to rest on the sceptics, but this is methodologically very weak. It allows theory to dominate with the guise of empirical science.

"At various places in Evolutionary Psychology as Maladaptive Psychology, Richardson concludes that we simply lack the historical evidence for a reconstruction of the evolution of human cognition. For human language, an "explanation" favored by evolutionary psychology is that it evolved for use in complex social groups, that is, there was a functional demand for language. Richardson rightly suggests that paleontologists are unlikely to unearth the evidence that can inform us about the social structure of our ancestral communities."

Bolhuis reveals something of his own concern when elaborating on this point:

The study of evolution is concerned with a historical reconstruction of traits. It does not, and cannot, address the mechanisms that are involved in the human brain. Those fall within the domains of neuroscience and cognitive psychology. In that sense, evolutionary psychology will never succeed, because it attempts to explain mechanisms by appealing to the history of these mechanisms. To use the author's words, "We might as well explain the structure of orchids in terms of their beauty." In this excellent book, Richardson shows very clearly that attempts at reconstruction of our cognitive history amount to little more than "speculation disguised as results."

Piling On the Selection Pressure
Johan J. Bolhuis
Science 320, 6 June 2008: 1293 | DOI: 10.1126/science.1157403

A review of Evolutionary Psychology as Maladapted Psychology by Robert C. Richardson, MIT Press, Cambridge, MA, 2007. 225 pp. ISBN 9780262182607.

We're Not Fred or Wilma
Johan J. Bolhuis
Science 309, 29 July 2005: 706 | DOI: 10.1126/science.1115209

A review of Adapting Minds by David J. Buller, MIT Press, Cambridge, MA, 2005. 564 pp. ISBN 0-262-02579-5.

Robert Deyes

Astronomer and mathematician Chandra Wickramasinghe, has been a notable figure in the ongoing scientific debates on evolution, promulgating the unlikelihood that natural selection could explain the origin of something as complicated as the cell [1]. Wickramasinghe is better known for his conviction that life is a "cosmic phenomenon" - that it is through cosmic dust that life has been seeded on earth [1]. Yet he is also known for his criticism of what he calls Darwinist indoctrination as witnessed in his appearance at the 1981 Creation Science trial in Arkansas. In his testimony he severely attacked Darwinian theory on the basis that the accumulation of mutations upon which natural selection supposedly acted would, if anything, lead to the gradual degradation and not accumulation of the genetic information that we see in organisms today [1]. He thus relegated Darwinian Theory to its more conservative form in which, "the processes of mutation and natural selection can only produce very minor effects in life as a kind of fine tuning of the whole evolutionary process" [1].

The low probabilities of obtaining functional enzymes in a primordial soup rule out explanations appealing to law and chance (image source here)

Wickramasinghe argued that gaps in the fossil record as well as the absence of transitional forms linking up the different phyletic groupings of fossils make the broader application of Darwinism across biology untenable [1]. Nevertheless, what really convinced Wickramasinghe of the insufficiency of Darwinism was that specific enzymes are needed within the cell for life to even exist. According to Wickramasinghe, if one were to envisage the random assembly of all these enzymes from some concoction of amino acids in a hypothetical primordial soup, the odds of obtaining these enzymes with the specific functions they have in the cell would be a staggeringly low 1 in 10exp40,000. As he subsequently concluded, "the number of shufflings needed to find life exceeds by many powers of 10 the number of all the atoms in the entire observable Universe". [1]

The above observations themselves provide a source of awe and contravene the rather dismissive trivialization often used to oppose the inference of design- that the very fact that we are here to look back on the history of the universe is testimony that this very small probability must have been fulfilled without recourse to a designer's 'hand'. In reviewing Harold Morowitz work, for example, physicist and Nobel laureate Murray Gell-Mann defined prebiotic evolution as a 'gateway event' in which the synthesis of nucleotides permitted genomes to simply, "come into existence" [2]. But the inference that big things like genomes come out of small changes like the synthesis of nucleotides carries with it a complete lack of causal specificity [3]. We have no naturalistic causal chain that takes us from a primordial soup to a living cell. From the origin of the bacterial cell to the advent of the first single-celled eukaryotes and the eventual evolution of higher animals, we find crevasse-size gaps and discontinuities that do not lend themselves easily to simple 'gateway event'-type explanations. True, there is a clearly observable increase in the level of complexity throughout our natural history and certainly we observe the emergence of higher levels of organization in the 'aggrandizement' of human societies and animal communities. Nevertheless, while theorists such as Stuart Kauffman believe that chemicals can arrange themselves into stable cycles 'for free', without any purpose or forethought [4], design theorists see the complexity of living form as a hallmark of an intelligence behind the design. I would concur.

[1]Details of Chandra Wickramasinghe's testimony at the 1981 Arkansas Evolution/Creation trial can be found at http://www.panspermia.org/chandra.htm

[2] Murray Gell-Mann (1994), The Quark and the Jaguar, Adventures in the simple and the complex. W.H. Freeman and Company, New York p.240

[3] William Dembski (2002), No Free Lunch: Why Specified Complexity Cannot Be Purchased Without Intelligence, Rowman & Littlefield Publishers, Inc, Lanham, Maryland pp 239-246

[4] Stuart Kauffman (2000), Investigations, Oxford University Press, New York

Copyright(c), 2008, Robert Deyes

According to the authors of the paper, research has uncovered "the evolution of a key innovation"; the New Scientist report refers to "a major evolutionary innovation" and "a rare and complex new trait"; The Scientist calls it a "big evolutionary jump". They are referring to the "ability to metabolise citrate, a [. . .] nutrient in their culture medium that E. coli normally cannot use."

Escherichia coli (source here)

The experimental work involved keeping 12 strains of the bacterium E. coli in a medium where there was glucose for them to metabolise, but also a plentiful supply of citrate. "Examining E. coli cultures that his lab has maintained since 1988, Lenski found that one population of the bacterium had evolved the ability to metabolize citrate - an unprecedented trait - after more than 30,000 generations, or approximately 15 years." Using samples preserved from earlier stages of this extended experiment, the research team established that one of the 12 populations gained a hidden mutation after about 20,000 generations. Only this population later developed the ability to metabolise citate. Thus, it can be inferred that "this evolutionary novelty grew from the accumulation of unpredictable, chance events."

"It's a very elegant demonstration that major changes may depend on accretion of minor changes before hand," said Albert Bennett, a University of California, Irvine evolutionary physiologist who gave Lenski feedback on the study before it was published in PNAS. "What's really demonstrated here is that the way has to be paved before hand."

This research is being hailed as a vindication of evolutionary theory against the sceptics:

"Lenski's experiment is also yet another poke in the eye for anti-evolutionists, notes Jerry Coyne, an evolutionary biologist at the University of Chicago. "The thing I like most is it says you can get these complex traits evolving by a combination of unlikely events," he says. "That's just what creationists say can't happen."

There are several observation that should be made before reaching general conclusions. The first relates to the machinery needed to metabolise citrate. The system to do this is already largely in place, but one enzyme is lacking. This is the comment from Mike Behe:

"Now, wild E. coli already has a number of enzymes that normally use citrate and can digest it (it's not some exotic chemical the bacterium has never seen before). However, the wild bacterium lacks an enzyme called a "citrate permease" which can transport citrate from outside the cell through the cell's membrane into its interior. So all the bacterium needed to do to use citrate was to find a way to get it into the cell. The rest of the machinery for its metabolism was already there. As Lenski put it, "The only known barrier to aerobic growth on citrate is its inability to transport citrate under oxic conditions."

Consequently, it is at least worth asking the question whether the E.coli bacterium had, in the past, lost the ability to metabolise citrate and what we are now seeing is a restoration of that damaged system. If this were the case, we should not be talking about "a major evolutionary innovation" but rather about the way complex systems can be impaired by mutations.

As yet, it is not known what mutations were involved. But clearly, if there were two, and if the first was needed before the second could complete the job, the experiments demonstrate how difficult it is to achieve orchestrated changes. This was exactly the point of Behe's study of ways of achieving resistance to malaria. In his words:

"I think the results fit a lot more easily into the viewpoint of The Edge of Evolution. One of the major points of the book was that if only one mutation is needed to confer some ability, then Darwinian evolution has little problem finding it. But if more than one is needed, the probability of getting all the right ones grows exponentially worse. "If two mutations have to occur before there is a net beneficial effect - if an intermediate state is harmful, or less fit than the starting state - then there is already a big evolutionary problem." And what if more than two are needed? The task quickly gets out of reach of random mutation."

So, far from this research being "another poke in the eye for anti-evolutionists", it demonstrates a major problem for those evolutionists who want to claim Darwinism can achieve major transformations. These mutations are not only rare, they are also useless without the pre-existence of a biochemical system that can turn the products of mutation into something beneficial. Behe writes:

"If the development of many of the features of the cell required multiple mutations during the course of evolution, then the cell is beyond Darwinian explanation. I show in The Edge of Evolution that it is very reasonable to conclude they did."

Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli
Zachary D. Blount, Christina Z. Borland, and Richard E. Lenski
Proc. Natl. Acad. Sci. USA, 10.1073/pnas.0803151105

Abstract: The role of historical contingency in evolution has been much debated, but rarely tested. Twelve initially identical populations of Escherichia coli were founded in 1988 to investigate this issue. They have since evolved in a glucose-limited medium that also contains citrate, which E. coli cannot use as a carbon source under oxic conditions. No population evolved the capacity to exploit citrate for >30,000 generations, although each population tested billions of mutations. A citrate-using (Cit+) variant finally evolved in one population by 31,500 generations, causing an increase in population size and diversity. The long-delayed and unique evolution of this function might indicate the involvement of some extremely rare mutation. Alternately, it may involve an ordinary mutation, but one whose physical occurrence or phenotypic expression is contingent on prior mutations in that population. We tested these hypotheses in experiments that "replayed" evolution from different points in that population's history. We observed no Cit+ mutants among 8.4 x 1012 ancestral cells, nor among 9 x 1012 cells from 60 clones sampled in the first 15,000 generations. However, we observed a significantly greater tendency for later clones to evolve Cit+, indicating that some potentiating mutation arose by 20,000 generations. This potentiating change increased the mutation rate to Cit+ but did not cause generalized hypermutability. Thus, the evolution of this phenotype was contingent on the particular history of that population. More generally, we suggest that historical contingency is especially important when it facilitates the evolution of key innovations that are not easily evolved by gradual, cumulative selection.

See also:

Behe, M. Multiple mutations needed for E. coli, Amazon Blog, 6 June 2008

Grant, B. Evolution loves history, The Scientist Newsblog, 2 June 2008

Holmes, B. Bacteria make major evolutionary shift in the lab, New Scientist, 09 June 2008

Robert Deyes

The molecular basis of sight is as complex as it is beautiful with interactions between proteins called transducins, phosphodiesterases, ion channels and pumps converting the original photon of light that reaches the eye into a signal that the brain can process (Ref 1). Studies have also revealed an added luxury of sight - self-repair and self-correction of optical aberration (Ref 2). A team of scientists at Cornell heading the study showed how, through neuronal feedback loops linking the eye to the brain, the brain could compensate for at least three different types of visual aberration - a finding that lead the head of the study, Cornell University professor Howard Howland to conclude that, "visual acuity is a result of various component parts 'wanting' to see better [. . .] able to sense aberrations and to change shape and function" (Ref 2). It thus seems rather paradoxical that some should come to the conclusion that complex organs such as the eye are, "not the work of some great composer but of an insensible drudge - an instrument, like all others, built by a tinkerer" (Ref 3).

A variety of feedback mechanisms mean that we see better than we might expect (graphic source here)

Why is it that prominent Darwinists such as Richard Dawkins reject purposeful design in the biological realm even though such a realm, by their own admission, exhibits design and provides every indication having been designed (Ref 4)? A look at Darwin's own reasons for rejecting design provides an important clue. According to Dawkins, Darwin's loss of faith in a purposeful designer came partly from his observation of the 'degoutant' in the natural world (Ref 4). Considering the digger wasp as a prime illustration of the macabre habits of nature, Dawkins recounts how these creatures lay their eggs within the bodies of other insects upon which the emergent larvae consequently feed (Ref 4). The female digger wasps guide their stings so precisely into their prey that their victims become irreversibly paralyzed but do not die (Ref 4). This scenario, according to Dawkins, is the best evidence that nature is not cruel but only pitilessly indifferent to the well being of its members (Ref 4). In Darwin's eyes, it was difficult to admit that an omnipotent and beneficent God could design something so savage and unappealing (Ref 4). Unfortunately for Darwin, in this instance he allowed his judgment to be clouded by his own subjective expectations of what the Judeo-Christian Creator would and would not do. In reference to the Ichneumonidae, distant cousins of the killer wasps, for example, he wrote,

"I cannot persuade myself that a beneficent and omnipotent God would have designedly created the Ichneumonidae with the express intention of their feeding within the living bodies of caterpillars." (Ref 5)

In the process of setting such an expectation, Darwin had unreasonably closed the door on design. Dawkins similarly concluded that the apparent roundabout and seemingly wasteful way through which the recurrent laryngeal nerve loops through the human body presented a perfect illustration of the limitation of evolutionary perfection and evidence for non-design (Ref 6). After all, no one in their right mind would have made a contraption so inefficient and imperfect (Ref 6). Inefficient and imperfect in whose eyes and why is this relevant?

An inference that a system is not designed simply because its design is not how we would expect it to be is not an inference based on scientific evidence but rather on personal bias. Clearly we have much to learn from nature if we are to reap the benefits of automated, self-correcting systems such as the eye; clearly we have a lot to learn from the designer whose systems we can identify throughout our natural world.

References

1. Michael J Behe (1996) Darwin's Black Box-The Biochemical Challenges to Evolution, 1st Edition, Simon and Schuster, New York; pp. 18-22
2. Better than Hubble, human eye can self-correct some optical faults.
3. Cornelius Hunter (2001) Darwin's God, Evolution and the Problem of Evil, Brazos Press, Grand Rapids, Michigan, p. 83
4. Richard Dawkins (1996), God's Utility Function, Phoenix, Orion Books Ltd, London
5. David Hull (1991), The God of the Galapagos, Nature, Volume 352, pp 485-486
6. Richard Dawkins (2003) A Devil's Chaplain, Weidenfeld and Nicolson London, UK, p.192

Copyright (c), Robert Deyes, 2007

Although parrots are familiar birds today, they are very sparsely represented in the fossil record. This means thinking is largely unconstrained by data. The discovery of two fossil parrots from the Lower Eocene of Denmark has made a significant change to this situation. The new fossils are considered to predate the previous 'oldest parrot' by 40 million years.

Jardine's Parrot (Source: here)

Of the two fossil birds, one is considered a member of the "stem group" and the other (Mopsitta tanta) a representative of "crown group" species. The implication is that stem and crown species co-existed.

"Mopsitta tanta is in many respects, more similar to Recent Psittaciformes than to any other Palaeogene psittaciform. Although it is not absolutely certain on the basis of preserved features (humeral morphology cannot be entirely diagnostic at this level), it is highly likely that Mopsitta tanta is a member of Psittacidae, therefore providing further support to the hypothesis of an early Eocene (or earlier) radiation of Psittaciformes; it is likely that representatives of crown-group Psittaciformes such as Mopsitta, existed in the Early Eocene alongside their stem-group counterparts Pseudasturidae and Quercypsittacidae."

The main focus of this blog concerns the rapidity of the radiation. Although Darwinists like to emphasise gradualism, with a slow pathway linking stem and crown species, here they are found together almost at the beginning of the Tertiary (which is the earliest many palaeontologists would put them). It's another reminder that speciation is not Darwinian, and the mechanisms that explain faunal radiations are currently unknown.

As a postscript, it is worth revisiting Thomas Stidham's 1998 report of a parrot jawbone from the Cretaceous. This raised many eyebrows because it was so early. The consensus seems to be that it was misidentified. "Dyke and Mayr (1999) considered it to be of uncertain taxonomic affinity because of the fragmentary nature of the material and the possibility that it could be from any number of other taxa, such as a caenagnathid-like theropod dinosaur". Whilst caution is justified, there is a possibility that judgments have been influenced by the low credibility of finding a Cretaceous parrot. With the confirmed presence of modern parrots in the Lower Eocene, credibility should no longer be an issue.

Two new parrots (psittaciformes) from the Lower Eocene Fur Formation of Denmark
DAVID M. WATERHOUSE, BENT E. K. LINDOW, NIKITA V. ZELENKOV, GARETH J. DYKE.
Palaeontology, 51(3), May 2008, 575-582 | doi:10.1111/j.1475-4983.2008.00777.x

Abstract: Two new fossil psittaciform birds from the Lower Eocene 'Mo Clay' (Fur Formation) of Denmark (c. 54 Ma) are described. An unnamed specimen is assigned to the extinct avian family of stem-group parrots, Pseudasturidae (genus and species incertae sedis), while a second (Mopsitta tanta gen. et sp. nov.) is the largest fossil parrot yet known. Both specimens are the first fossil records of these birds from Denmark. Although the phylogenetic position of Mopsitta is unclear (it is classified as family incertae sedis), this form is phylogenetically closer to Recent Pstittacidae than to other known Palaeogene psittaciforms and may, therefore, represent the oldest known crown-group parrot.

A lower jaw from a Cretaceous parrot
Thomas A. Stidham
Nature 396, 29-30 (5 November 1998) | doi:10.1038/23841

All known Cretaceous bird fossils representing modern higher taxa are from the aquatic groups Anseriformes, Gaviiformes, Procellariiformes and Charadriiformes. Here I describe a toothless avian dentary symphysis (fused jawbone) from the latest Cretaceous of Wyoming, United States. This symphysis appears to represent the oldest known parrot and is, to my knowledge, the first known fossil of a 'terrestrial' modern bird group from the Cretaceous. The existence of this fossil supports the hypothesis, based on molecular divergence data, that most or all of the major modern bird groups were present in the Cretaceous.

The problem for colour vision can be summarised thus: "The focal length of a simple lens varies as a function of the wavelength of light. Short wavelengths (blue) are focused at shorter distances from the lens, whereas long wavelengths (red) are focused at longer distances from the lens. This longitudinal chromatic aberration (LCA) leads to chromatic blur that degrades image quality." Commercial lenses that are corrected for LCA make use of components made from materials with different refractive indices.

"The biological solution to LCA is the multifocal lens. Such a lens has several distinct zones that focus monochromatic light of a particular wavelength at different distances. Since the refractive power of the multifocal lens is also a function of the wavelength of light, each of the zones of different focal length for monochromatic light focuses a different band of wavelengths on the same plane in the retina. A sharp colour image is created on the background of defocused light. This solution seems at first sight to be inferior to the technical solution, but has the important advantage that the optical system is considerably smaller, which is of energetic benefit to the animal."

The biological solution is utilised in a wide range of animals. "The success of this optical design is reflected in the multifocal systems present in a variety of amphibians, reptiles and mammals (including primates). The evolutionary origins of this lens design, however, are unknown." The research team has set out to cast light on the antiquity of the multifocal lens. Their methodology is very interesting. The key to understanding it is "stasis". Once originated, body plans show little deviation. Similarly, complex structures having come into existence do not change significantly. Genes are conserved rather than modified. As Gould so forcibly argued: "stasis is data" and this principle appears to underpin this research. As we shall note, adopting this principle does not lead to findings that favour Darwinian gradualism.

The southern hemisphere lamprey, Geotria australis, showing its well-developed eye (Source: go here).

The researchers have chosen to work with lampreys, which are extant jawless fish. Recognisable lampreys are also found as fossils in Cambrian rocks, predating bony fish. The argument is: if multifocal optics are found in lampreys, this establishes the design as an early innovation, predating the cartilaginous fish (chondrichthyes) and the bony fish (osteichthyes). Conversely, if multifocal optics are not found, the innovation comes later. Genetic information relevant to this investigation concerns the presence of photopigments, and evidence was known to suggest there was value in an analysis of lamprey colour vision.

"The southern hemisphere lamprey Geotria australis possesses five photopigments [. . .]. At least three of the five visual pigments [. . .] are orthologous to the visual pigments in jawed vertebrates. Although rod opsin-like opsin type A (RhA) and type B (RhB ) of lampreys share similarities with the rod opsin (Rh1) and Rh1-like cone opsin (Rh2) of jawed vertebrates, respectively, the functional identity of the receptors housing these visual pigments remains elusive. It has, however, been suggested that all five photoreceptors in G. australis have close affinities to those of cones in gnathostomes."

The findings relate to all lamprey species studied, selected to be representative of the group:

"All four species of lamprey were found to have multifocal lenses, optically similar to those of bony fishes."
"This is the first study to show that the eyes of lampreys (Agnatha), extant representatives of the earliest vertebrates, possess multifocal lenses and therefore the optical apparatus for well-focused colour vision."

The implications are (1) that colour vision via multifocal optics is a Cambrian-Recent phenomenon; and (2) that multifocal optics is suggestive of a monophyletic origin.

"The presence of multifocal lenses in the eyes of lampreys confirms the early origins of colour vision in vertebrates, and suggests that other aquatic vertebrates and tetrapods have retained this optical feature, the latter despite the transition from an aquatic environment to a terrestrial habitat, where the cornea comes into play as an additional refractive element."
"The presence of multifocal lenses in representatives of all vertebrate classes studied thus far and their absence in cephalopods suggests a monophyletic origin for this lens design. Convergent evolution in so many vertebrate lineages is unlikely."

This should give Richard Dawkins (and others who think that eyes evolved easily) something to think about. Allowing an evolutionary perspective on the data, multifocal optics evolved once and then has been passed on to descendants with very little change. The same data permits a design perspective, as there is no hint here how such complexity evolved rapidly.

"The presence of at least four visual pigments [. . .] in the last common ancestor of jawed and jawless vertebrates suggests that the earliest vertebrates were able to sample a rich spectral light environment and enjoy the many advantages of colour vision. Our findings suggest that the eyes of these ancient animals were capable of forming well-focused colour images."

Early evolution of multifocal optics for well-focused colour vision in vertebrates
O. S. E. Gustafsson, S. P. Collin and R. H. H. Kroger
Journal of Experimental Biology 211, 1559-1564 (2008) | doi: 10.1242/jeb.016048

Jawless fishes (Agnatha; lampreys and hagfishes) most closely resemble the earliest stage in vertebrate evolution and lamprey-like animals already existed in the Lower Cambrian [about 540 million years ago (MYA)]. Agnathans are thought to have separated from the main vertebrate lineage at least 500 MYA. Hagfishes have primitive eyes, but the eyes of adult lampreys are well-developed. The southern hemisphere lamprey, Geotria australis, possesses five types of opsin genes, three of which are clearly orthologous to the opsin genes of jawed vertebrates. This suggests that the last common ancestor of all vertebrate lineages possessed a complex colour vision system. In the eyes of many bony fishes and tetrapods, well-focused colour images are created by multifocal crystalline lenses that compensate for longitudinal chromatic aberration. To trace the evolutionary origins of multifocal lenses, we studied the optical properties of the lenses in four species of lamprey (Geotria australis, Mordacia praecox, Lampetra fluviatilis and Petromyzon marinus), with representatives from all three of the extant lamprey families. Multifocal lenses are present in all lampreys studied. This suggests that the ability to create well-focused colour images with multifocal optical systems also evolved very early.

Robert Deyes

Switches, rheostats, electrical circuits and complex feedback loops that regulate household devices as well as national power grids are things that we have become so accustomed to in our own lives that we generally take them for granted. That is, until they break down. We saw this on a massive scale in the summer of 2003 when New York and other US and Canadian cities were brought to a stand still as power blackouts swept the east coast. A New Scientist report at the time claimed a total of 50 million people were affected (Ref 1). Needless to say, it took several days to bring things back to normal. The economic impact of the catastrophe cost the American and Canadian governments billions of dollars (Ref 1).

Switches turn genes on and off in the cell

Incredibly, regulated circuits and switches also exist inside the microscopic world turning genes on at the precise moments that their products are required and shutting them off when those same products become unnecessary, superfluous or even detrimental. In a fascinating study headed by a group at the Wistar Institute in Philadelphia it has now become clear that histones - proteins that are involved in packing DNA into individual chromosomes - play a fundamental role in regulating which genes are turned on and off in the cell (Ref 2). It appears that small molecular groups attached onto these histone proteins can serve as on/off switches that modulate which genes are on or off at any given moment. These molecular groups become attached to the histones as a result of multi-component machines that turn on genes. Karl Henry's group at the Wistar has revealed the functionality of one of these multi-component machines called the SAGA complex that attaches a molecular group called ubiquitin onto one of the Histones (Ref 2). What is surprising about the SAGA complex is that the removal of the ubiquitin molecular group from the Histones does not turn genes off. Rather it seems that both the addition and subsequent removal of ubiquitin, both by the SAGA complex, provide an essential sequence for turning genes on (Ref 2). This finding places an extra level of complexity to the previously held view that genes could be turned on or off through simple on/off switches. Now it appears that such switches operate through a specified order of molecular changes. In the case of SAGA, the correct order is absolutely critical if genes are going to be turned on correctly.

So it is that we learn that the 'conversion' of the genetic instruction into protein through the initial step of transcription involves more than polymerases - the reading molecules that chug along the DNA and generate RNA. It is a carefully planned, well-orchestrated series of events involving molecular switches. We see a complexity that intuitively does not seem to be accessible to unguided assembly. As mathematician David Berlinski quipped, "wherever the biologist looks, there is complexity beyond complexity, the entanglement of things ramifying downward from the organism to the cell" (Ref 3).

What caused the east coast electricity blackout? According to the New Scientist report there were two crucial pieces of software that failed on that frightful day (Ref 1). As alarm systems failed, more lines shut down and voltages fluctuated, the entire network spun out of control with the inevitable consequence of a massive power shut down. America suffered its worst power cut in recent memory because the correct order of processes and procedures so essential for the smooth running of an electricity grid had not been met. What happened on that horrific day during the heat of the summer sun was due to operator failure and could have been easily prevented. The New Scientist report mentions, for example, that one engineer left for lunch when a critical maneuver needed to be carried out (Ref 2). It is profoundly ironic that one of America's worst power failures should occur at precisely the moment that intelligent agency left the scene. As with man-made designs, evidence points to an intelligence behind the precision functioning of the cellular world.

References

1. Celeste Biever (2003) 'Preventable' failures caused US power blackout, New Scientist, 20th November, 2003

2. Karl W. Henry, Anastasia Wyce, Wan-Sheng Lo, Laura J. Duggan, N.C.Tolga Emre, Cheng-Fu Kao, Lorraine Pillus, Ali Shilatifard, Mary Ann Osley, Shelley L. Berger (2003) Transcriptional activation via sequential histone H2B ubiquitylation and deubiquitylation mediated by SAGA-associated Ubp8, Genes & Development Vol 17 pp2648-2663

3. David Berlinski (1996), The Deniable Darwin, http://www.discovery.org (see 'Articles by Center Fellows')

The "Age of Fishes" was in the Devonian Period of Earth history, when placoderm fishes became the dominant group of vertebrates. Largely on the basis of their place low down in the Tree of Life, placoderms have been regarded as "early primitive fish" which were slow and dull. We now need to question the validity of this perspective and whether it owes more to evolutionary presuppositions than to evidence.

Masterpricis attenboroughi is revealed as viviparous

The great majority of modern fish indulge in spawning: females lay large numbers of eggs and males fertilise those eggs after they have left the mothers' bodies. The process appears inefficient because few of the eggs grow to mature adults. However, in the absence of predators (such as after an environmental crisis), it is a great way for populations to expand rapidly.

Some fish, like sharks and rays, fertilise internally. Some are ovoviviparous, whereby the eggs remain in the body cavity of the female for protection, but the mother does not provide the embryos with nutrients. The rest are viviparous, giving both food and protection before they are born. Palaeontologists had "suspected that some placoderms fertilised internally". This is because "The males of a sub-group of placoderms , called ptyctodontids, have clasper-like appendages dangling from their pelvic fins - these are reminiscent of the claspers of modern sharks that are used to inseminate females." How far were these placoderms like the sharks and rays? The new fossil finds show that at least some placoderms were viviparous.

"With the discovery of the embryos we can now be sure that at least some placoderms gave birth to live young" says Per Ahlberg at Uppsala University in Sweden.
[. . .]
"Our ongoing investigations suggest that viviparity is more widespread than previously thought in early placoderms," says Long [at Museum Victoria in Melbourne, Australia].

From an evolutionary perspective, these placoderms "had a remarkably advanced reproductive biology". The reproductive system for internal fertilisation and viviparity is far more complex that the system for spawning. Yet the complex system appears in the placoderms, which represent the first flowering of vertebrate life in the fossil record.

For a long time, trilobite eyes served as an icon of complexity in the Cambrian. As time passes, this has been supplemented by many evidences of advanced morphologies (for examples, go here and here). Analysis of the genomes of so-called "primitive" organisms has revealed genes that are also found in more sophisticated animals. This new research reveals viviparity in some placoderm fish. How much more evidence do we need to show that Darwinian gradualism is in tension with the data?

Looking for patterns of oviparous, ovoviviparous and viviparous animals allows some generalisations. Mammals (with the exception of monotremes) are viviparous and there are a few cases of vivipary in reptiles, fish and insects. But when the focus changes to look at the details, and when the interpretive framework is the Tree of Life, then there are many difficulties. In a comment on the Nature news item, David Bump draws attention to the problems the authors have identified:

"...the complex behavioural, morphological, and physiological mechanisms required for successful copulation and internal fertilisation in chondrichthyans (Hamlett & Koob 1999) must have evolved independently and non-reversibly 12 times in teleosts..." It also claims that "Live bearing evolved from egg laying independently in all classes of vertebrates except birds, and also in many invertebrate clades." That's a lot of independent, sudden appearances of a complex reproductive strategy. It must take a lot of faith to believe in all that being the result of purely natural evolutionary processes, which haven't yet been shown to be capable of producing such changes.

This is a fair comment. We need a different paradigm - one that is not embarrassed by the riches of biological information found in supposedly primitive life-forms.

Live birth in the Devonian period
John A. Long, Kate Trinajstic, Gavin C. Young & Tim Senden
Nature 453, 650-652 (29 May 2008) | doi:10.1038/nature06966

The extinct placoderm fishes were the dominant group of vertebrates throughout the Middle Palaeozoic era1, yet controversy about their relationships within the gnathostomes (jawed vertebrates) is partly due to different interpretations of their reproductive biology. Here we document the oldest record of a live-bearing vertebrate in a new ptyctodontid placoderm, Materpiscis attenboroughi gen. et sp. nov., from the Late Devonian Gogo Formation of Australia (approximately 380 million years ago). The new specimen, remarkably preserved in three dimensions, contains a single, intra-uterine embryo connected by a permineralized umbilical cord. An amorphous crystalline mass near the umbilical cord possibly represents the recrystallized yolk sac. Another ptyctodont from the Gogo Formation, Austroptyctodus gardineri, also shows three small embryos inside it in the same position. Ptyctodontids have already provided the oldest definite evidence for vertebrate copulation, and the new specimens confirm that some placoderms had a remarkably advanced reproductive biology, comparable to that of some modern sharks and rays. The new discovery points to internal fertilization and viviparity in vertebrates as originating earliest within placoderms.

See also:

Dennis, C., The oldest pregnant mum, Nature 453, 575 (28 May 2008) | doi:10.1038/453575a

Morelle, R. Fossil reveals oldest live birth, BBC News, 28 May 2008

Mother fish, Museum Victoria News, 29 May, 2008 (with two video clips)

Robert Deyes

Real life compounds and real life experiments were the themes of a Nature Biotechnology article about a biologically-based machine that could play Tic Tac Toe (In the UK, the game of Naughts and Crosses) against human players. A Nature review of the paper told of a machine that could make 'decisions' that would not only allow it to win but win every time (Ref 1). Tic Tac Toe is of course a very simple game to play the idea being that the first to generate a row of either three crosses or 'zeros' on a nine-square grid wins the game. This new version of the game on the other hand was different and involved a rather contrived set of operational rules. Designed by Milan Stojanovic and Darko Stefanovic the machine was made up of nine individual square holes or wells, rather like a waffle, each containing a special concoction of biological enzymes. Play would begin when the human player added magnesium to each well of the waffle, triggering off a series of reactions in the process (Ref 1,2). The machine would then 'make' its first move, always from the center square of the nine-square waffle visible through special enzymatic reactions that caused the well to change colour. The player would be forced to then make their first move in the top left most square and, in the process, add a special piece of DNA to all of the wells (Ref 1,2). Thus every well was 'informed' of the player's first move. And so it went on, each time the human player being obligated to add special pieces of DNA to each of the remaining wells. The most that the human player could ever hope for was a draw (Ref 2). Nevertheless, it seemed from Stojanovic's and Stefanovic's design plan that complex biological 'machines' could be designed to make decisions based on inputs fed into it by human agents. Artificial Life had apparently made a move out of the computer-based simulation.

In another sense, Stojanovic's and Stefanovic's game was altogether very disappointing for those keen to demonstrate a simple route for generating complex feedback networks. After all, this biological machine had no powers to gain from experience and improve its strategy. Moreover, unlike the human players, Stojanovic's and Stefanovic's game did not display any ability to self-organize thought processes into winning strategies or chemicals into closed sets of catalytic reactions. It simply did what it had been instructed to do and all this within a very constraining set of conditions. The inventory list of components that Stojanovic and Stefanovic had used, for example, had been carefully selected for what was conceptually a very simple game. Each hole of the nine-welled waffle contained carefully designed DNA enzymes with YES, AND and NOT gates rather like the electrical circuit boards used in high school physics classes. The conditions within each hole of the nine-well waffle were carefully tweaked and fine-tuned to ensure that the reactions would work. The authors themselves reported how their initial attempts at playing the game resulted in, "further empirical improvements" to ensure that the machine worked (Ref 2). Indeed this biological machine never lost because it implemented the perfect strategy. In all fairness, Stojanovic and Stefanovic never designed their machine to learn from experience. Nevertheless they were successful at demonstrating just how difficult it is to design a biological machine that could carry out even the simplest of tasks - hardly what one would hope for those arguing for the natural emergence of complex biological systems.

The same sort of bleak findings have been reported in other studies designed to harness the practical benefits of bacteria. Drew Endy, a biologist at MIT, is a pioneer in making novel bacterial strains that might one day become bioproducers of disease targeting drugs (Ref 3). Yet for Endy and other biologists, the results of genetic engineering have been disappointing and frustrating to say the least primarily because of the time needed to engineer bacteria to do even the simplest of tasks (Ref 3). Endy has taken on the challenge of designing a library of genetic parts, or 'biobricks', that can be inserted into bacteria to achieve certain basic functions. Endy's work might one day soon provide an accessory shop of sorts where researchers can customize their bacteria rather like automobile aficionados might customize their car. Yet the problem with customizing bacteria in this way is that, over relatively short periods of time, the genetically engineered parts mutate and become non-functional. As Ron Weissman of Princeton reported,

"Replication is far from perfect. We've built circuits and seen them mutate in half the cells within five hours. The larger the circuit is, the faster it tends to mutate" (Ref 3).

As science writer Wayt Gibbs reminds us, scientists are coming to terms with the relative difficulty of engineering even the shortest stretches of DNA to achieve even the most basic of functions (Ref 3). Many of the products of these short pieces of DNA have proved to be toxic to the cells requiring careful tweaking and trimming before being successfully introduced into bacteria. In other words, biological entities such as bacteria do not lend themselves easily to even the smallest of changes in their molecular composition. They require precision-directed design if such viable changes in their molecular constitution are to be made.

References

1. The Nature Review of the paper written by Stojanovic and Stefanovic was published by Helen Pearson in Nature on the 21st of August, 2003 and can be found at http://www.nature.com/nsu/030818/030818-9.html

2. Milan N Stojanovic and Darko Stefanovic (2003), A deoxyribozyme-based molecular automaton, Nature Biotechnology, Volume 21 Number 9 pp 1069 - 1074.

3. W. Wayt Gibbs (2004) Synthetic Life, Scientific American, Volume 290 (5) pp 74-81.

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