Thank you to Rob Willox for sending this in.

Reposted from New Scientist:
http://www.newscientist.com/article.ns?id=mg19225824.000

PAY a visit to the Biologic Institute and you are liable to get a chilly reception. "We only see people with appointments," states the man who finally responds to my persistent knocks. Then he slams the door on me.

I am standing on the ground floor of an office building in Redmond, Washington, the Seattle suburb best known as home town to Microsoft. What I'm trying to find out is whether the 1-year-old institute is the new face of another industry that has sprung up in the area - the one that has set out to try to prove evolution is wrong.

This is my second attempt to engage in person with scientists at Biologic. At the institute's other facility in nearby Fremont, researchers work at benches lined with fume hoods, incubators and microscopes - a typical scene in this up-and-coming biotech hub. Most of them there proved just as reluctant to speak with a New Scientist reporter.

The reticence cloaks an unorthodox agenda. "We are the first ones doing what we might call lab science in intelligent design," says George Weber, the only one of Biologic's four directors who would speak openly with me. "The objective is to challenge the scientific community on naturalism." Weber is not a scientist but a retired professor of business and administration at the Presbyterian Whitworth College in Spokane, Washington. He heads the Spokane chapter of Reasonstobelieve.org, a Christian organisation that seeks to challenge Darwinism.

The anti-evolution movement's latest response to Darwin is intelligent design (ID). Its fundamental premise is that certain features of living organisms are too complex to have evolved without the direct intervention of an intelligent designer. In ID literature that designer remains cautiously anonymous, but for many proponents he corresponds closely with the God of the Christian Bible. Over the past few years the movement's media-savvy public face has been the Seattle-based Discovery Institute, which has championed intelligent design, claiming it to be a legitimate scientific theory, and supported its key architects. It was Discovery that provided the funding to get the Biologic Institute up and running.

Last week I learned that following his communication with New Scientist, Weber has left the board of the Biologic Institute. Douglas Axe, the lab's senior researcher and spokesman, told me in an email that Weber "was found to have seriously misunderstood the purpose of Biologic and to have misrepresented it". Axe's portrayal of the Biologic Institute's purpose excludes religious connotation. He says that the lab's main objective "is to show that the design perspective can lead to better science", although he allows that the Biologic Institute will "contribute substantially to the scientific case for intelligent design".

This science-first message suggests that the developing anti-evolution movement in the US has moved on to a new stage - one in which opponents of evolutionary biology, trained as research scientists, take to the lab in search of the creator's handiwork. In light of recent events, it also makes sense as a public relations strategy.

ID was dealt a significant blow when parents in the Dover school district of Pennsylvania successfully challenged the right of school board officials to introduce pro-ID material into high school biology classrooms. In December 2005, US federal court judge John Jones ruled that it was unconstitutional to teach ID in public schools because it would violate the separation of church and state as laid out in the First Amendment (New Scientist, 7 January, p 8).

In addition to its religious undertones, ID had not "been the subject of testing and research", Jones stated, nor had it "generated peer-reviewed publications", and so had no business in science classes. Wary of losing similar court cases, at least four state education boards subsequently rejected or removed ID-friendly language from their high-school curricula, or are expected do so when newly elected members take office next year.

These developments underscored ID's most serious weakness. "The criticism that has been levelled against them most frequently is that they talk about science but they don't do science," says Richard Olmstead, a biologist at the University of Washington in Seattle who has spoken out against the teaching of ID in science classes.

Research agenda

The message is clear. If ID supporters can bolster their case by citing more experimental research, another judge at some future date might conclude that ID does qualify as science, and is therefore a legitimate topic for discussion in American science classrooms. This is precisely the kind of scientific respectability that research at the Biologic Institute is attempting to provide. "We need all the input we can get in the sciences," Weber told me. "What we are doing is necessary to move ID along."

Axe appears to be one of the prime movers in this latest version of the anti-evolution enterprise. In a Discovery Institute strategy paper that was leaked on the internet in 1999, Axe is identified as heading up a molecular biology programme that has the aim of undercutting the scientific basis for evolution. At that time he was funded by the Discovery Institute and working as a postdoctoral fellow at the Centre for Protein Engineering, a research centre in Cambridge, UK, funded by the Medical Research Council, under the supervision of protein specialist Alan Fersht of the University of Cambridge.

Fersht says he did not at first know about the Discovery Institute's support for ID. "People do work in labs on external funding. Basically he [Axe] had a fellowship from what I thought was a bona fide research institute," he says. When another researcher in his lab pointed to the Discovery Institute's agenda and suggested that Axe be asked to leave, Fersht refused. "I have always been fairly easy-going about people working in the lab. I said I was not going to throw him out. What he was doing was asking legitimate questions about how a protein folded."

In 2000 Axe published a paper about protein mutations (Journal of Molecular Biology, vol 301, p 585). The paper itself makes no mention of ID, but William Dembski, a philosopher and senior fellow at the Discovery Institute, cites it as peer-reviewed evidence for ID (see "Building a case").

By 2002 it was becoming clear that Axe and Fersht were in dispute with each other over the implications of work going on in Fersht's lab. At the time Fersht was preparing to publish a retraction of a paper in which he and three colleagues had claimed to have caused one enzyme to evolve the functionality of another (Nature, vol 403, p 617). Axe interpreted the fact that problems had surfaced with the result as evidence that there were problems with the theory of evolution. "I described to Alan preliminary results of mine that seemed to challenge the ability of spontaneous mutations to produce proteins with fundamentally new structures, and I suggested that the struggling projects under his direction might actually be pointing to the same conclusion," Axe told me in an email. Fersht disagreed with the suggestion. The problem result "didn't show anything of the sort", he says. "It showed there were inadequacies in our knowledge."

In March 2002, Axe left Fersht's lab to work as a visiting scientist at the structural biology unit of the Babraham Institute, also in Cambridge. His work there, again funded by the Discovery Institute, led to the publication of a second paper in 2004 (Journal of Molecular Biology, vol 341, p 1295) that was again cited by ID proponents as evidence in its favour.

Since 2004 Axe has resurfaced in Washington state, where he has set up shop at the Biologic Institute, a short drive away from the Discovery Institute. Weber told me that Biologic was a "branch of Discovery". Both Axe and Discovery spokesperson Rob Crowther insist that it is a "separate entity".

Biologic's staff consists of at least three researchers, including Ann Gauger, who like Axe signed a petition titled "a statement of dissent against Darwin's theory of evolution" that was organised by the Discovery Institute in September 2005. In 1985 Gauger published a paper on cell adhesion in fruit flies (Nature, vol 313, p 395) while completing a PhD from the University of Washington, and then went on to publish more papers as a postdoctoral fellow at Harvard University. Her former supervisor, Larry Goldstein, now at the University of California, San Diego, expressed surprise when he learned of her association with the anti-evolution movement.

Gauger would not speak to New Scientist about her work. According to Axe, the projects currently under way at Biologic include "examining the origin of metabolic pathways in bacteria, the evolution of gene order in bacteria, and the evolution of protein folds".

Certainly the topics Axe mentions are of interest to science, says Kenneth Miller, a cell biologist at Brown University in Providence, Rhode Island, who testified as an expert witness for the pro-evolution side at the Dover trial. Miller adds that they might be of particular interest to people intent on undermining evolution if, like Axe's earlier work on protein folding, they can be used to highlight structures and functions whose origins and evolution are not well understood.

In addition to protein and cell biology, Biologic is pursuing a programme in computational biology which draws on the expertise of another of its researchers, Brendan Dixon, a former software developer at Microsoft. According to Axe, "On the computational side, we are nearing completion of a system for exploring the evolution of artificial genes that are considerably more life-like than has been the case previously."

Dixon also declined to speak with New Scientist, but there are reasons why the computational arena might be of interest to the anti-evolution movement. Starting in 2001, Robert Pennock at Michigan State University in East Lansing and colleagues wrote a computer program that behaves like a self-replicating organism able to mutate unpredictably and evolve (Nature, vol 423, p 139). The experiment demonstrates how natural selection and random mutation give rise to increasingly complex organisms.

For anti-evolutionists, this was a discouraging result. "That one really got to them," says Barbara Forrest, a philosopher at Southeastern Louisiana University in Hammond who studies the anti-evolution movement. It would not be surprising if Biologic wanted to challenge the impact of Pennock's work by finding a counter-example in which a computer simulation fails to produce complexity by random mutation alone. Such a counter-example, once published, would be available for citation by proponents of ID. Even if the citations do not appear in peer-reviewed literature, says Forrest, they could still have an influence on politicians and school board officials, who might not be sensitive to this distinction.

Miller agrees that work of this kind would help anti-evolutionists politically. "If Axe can produce a few more papers in good journals they will be able to cite a growing body of evidence favouring ID," he says.

However, Steve Fuller, a sociologist at the University of Warwick, UK, who testified in favour of ID in the Dover trial, believes the Biologic Institute's activities could help break down barriers between religious people and scientists. "Regardless of whether the science cuts any ice against evolution, one of the virtues is that it could provide a kind of model for how religiously motivated people can go into the lab."

Ronald Numbers, a historian at the University of Wisconsin, Madison, who has studied creationism, views it in a different light. The lab's existence will help sustain support within the anti-evolution community, he says. "It will be good for the troops if leaders in the ID movement can claim: 'We're not just talking theory. We have labs, we have real scientists working on this.'"

Building a case

While researching protein structure at various institutes in the UK, Douglas Axe, now at the Biologic Institute in Redmond, Washington, published two peer-reviewed papers that are cited by anti-evolutionists as evidence that intelligent design is backed by serious science.

"Extreme functional sensitivity to conservative amino acid changes on enzyme exteriors" Journal of Molecular Biology, vol 301, p 585.

What it reports Inducing multiple mutations in a bacterial enzyme causes it to lose its ability to perform its role as an antibiotic disabler.

How ID proponents use it Because such mutations destroy "the possibility of any functioning" in the enzyme, it could not have arisen via "Darwinian pathways" (William Dembski, from Debating Design: From Darwin to DNA, Cambridge University Press, p 327).

What scientists say Major modifications can be made to proteins without destroying function. Also, making many mutations at once is different to gradual evolution, where dud mutations get weeded out.

"Estimating the prevalence of protein sequences adopting functional enzyme folds" Journal of Molecular Biology, vol 341, p 1295.


What it reports Calculates the probability that a random sequence of amino acids will result in the folded shape that a protein needs to function as an enzyme.

How ID proponents use it The probability of creating a functioning protein fold "at random" is very low, making "appeals to chance absurd, even granting the duration of the entire universe" (Stephen Meyer, Proceedings of the Biological Society of Washington, vol 117, p 213).

What scientists say the vast majority of protein folds probably evolved via alteration of other smaller functional amino acid chains.
From issue 2582 of New Scientist magazine, 16 December 2006, page 8-11