Thursday, December 14, 2006
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.
...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.
Continued at "Intelligent Design: The God Lab"
*See the New York Times article "In Explaining Life's Complexity, Darwinists and Doubters Clash" (Page 2):
..."If we've defined science such that it cannot get to the true answer, we've got a pretty lame definition of science," said Douglas D. Axe, a molecular biologist and the director of research at the Biologic Institute, a new research center in Seattle that looks at the organization of biological systems, including intelligent design issues. Dr. Axe said he had received "significant" financing from the Discovery Institute, but he declined to give any other details about the institute or its financing...
**1) "Extreme functional sensitivity to conservative amino acid changes on enzyme exteriors" Journal of Molecular Biology, vol 301, p 585.
Mutagenesis studies and alignments of homologous sequences have demonstrated that protein function typically is compatible with a variety of amino-acid residues at most exterior non-active-site positions. These observations have led to the current view that functional constraints on sequence are minimal at these positions. Here, it is shown that this inference assumes that the set of acceptable residues at each position is independent of the overall sequence context. Two approaches are used to test this assumption. First, highly conservative replacements of exterior residues, none of which would cause significant functional disruption alone, are combined until roughly one in five have been changed. This is found to cause complete loss of function in vivo for two unrelated monomeric enzymes: barnase (a bacterial RNase) and TEM-1 beta-lactamase. Second, a set of hybrid sequences is constructed from the 50 %-identical TEM-1 and Proteus mirabilis beta-lactamases. These hybrids match the TEM-1 sequence except for a region at the C-terminal end, where they are random composites of the two parents. All of these hybrids are biologically inactive. In both experiments, complete loss of activity demonstrates the importance of sequence context in determining whether substitutions are functionally acceptable. Contrary to the prevalent view, then, enzyme function places severe constraints on residue identities at positions showing evolutionary variability, and at exterior non-active-site positions, in particular. Homologues sharing less than about two-thirds sequence identity should probably be viewed as distinct designs with their own sets of optimising features.
2) "Estimating the prevalence of protein sequences adopting functional enzyme folds." Journal of Molecular Biology 2004 Aug 27;341(5):1295-315.
Proteins employ a wide variety of folds to perform their biological functions. How are these folds first acquired? An important step toward answering this is to obtain an estimate of the overall prevalence of sequences adopting functional folds. Since tertiary structure is needed for a typical enzyme active site to form, one way to obtain this estimate is to measure the prevalence of sequences supporting a working active site. Although the immense number of sequence combinations makes wholly random sampling unfeasible, two key simplifications may provide a solution. First, given the importance of hydrophobic interactions to protein folding, it seems likely that the sample space can be restricted to sequences carrying the hydropathic signature of a known fold. Second, because folds are stabilized by the cooperative action of many local interactions distributed throughout the structure, the overall problem of fold stabilization may be viewed reasonably as a collection of coupled local problems. This enables the difficulty of the whole problem to be assessed by assessing the difficulty of several smaller problems. Using these simplifications, the difficulty of specifying a working beta-lactamase domain is assessed here. An alignment of homologous domain sequences is used to deduce the pattern of hydropathic constraints along chains that form the domain fold. Starting with a weakly functional sequence carrying this signature, clusters of ten side-chains within the fold are replaced randomly, within the boundaries of the signature, and tested for function. The prevalence of low-level function in four such experiments indicates that roughly one in 10(64) signature-consistent sequences forms a working domain. Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10(77), adding to the body of evidence that functional folds require highly extraordinary sequences.