Monday, July 11, 2005

New Scientist reaction 1

From "A sceptic's guide to intelligent design", New Scientist 9/7/05(Bob Holmes and James Randerson)
But these calculations [of how improbable it is that proteins could arise by chance] are logically flawed because they focus on a single, specified outcome, says Kenneth Miller ... It is like equating the odds of drawing a particular two-pair hand - say a pair of red queens, a pair of black 10s and the ace of clubs. "By demanding a particular outcome, as opposed to a functional outcome, you stack the odds," Miller says. What these calculations fail to recognise is that many different protein sequences can be functional. It is not uncommon for proteins in different species to vary by 80 to 90 per cent, yet still perform the same function.

Firstly, let's note that the odds of a particular sequence of amino acids arising varies geometrically with the length of the sequence. So if 10 amino acids need to be specified, the improbability is 1 in 20^10 - that is, 1 in 10^13. If 100 amino acids need to be specified, the improbability is 1 in 20^100 - that is, 1 in 10^130. For the sake of argument, let's assume that this represents one typical protein. This number - 1 in 10^130 - is pretty much at the limit of the "probabilistic resources" of the universe - in other words, in the entire history of the universe, if all matter were dedicated to randomly producing amino acid sequences all the time, you might stand a reasonable chance of coming up with one fully specified 100 aa residue protein.

That much isn't contested. What is disputed by ID opponents is that this 100 amino acid protein needs to be fully specified. The improbability is irrelevant, opponents of ID argue, because a less specified protein would still be functional, and natural selection provides a basis for improving its functionality. "Therefore evolution is true." (see below)

However, how specified does a sequence of amino acids need to be to provide some functionality? The authors mention that proteins in different species might vary by 80 to 90 per cent and yet still perform the same function. Let's say that our 100 aa residue protein only needs to be 15% specified: this represents an improbability of 1 in 10^19. Where do first attempts at searching for new functionality come from? And do cells really have the energy resources and the informational resources to experiment with new amino acid sequences to search for particular functionality? These questions are fundamental to the debate about whether random mutation and natural selection might work as a basis for evolution.

Most papers which talk about the appearance of new functionality in organisms show the co-option of already present complex proteins. But the question isn't addressed as to where these predecessors might have arisen from. You can't keep on moving the problem back - at some stage, proteins with specific functionality have to appear from somewhere (even if the level of specification only amounts to improbabilities of between 1 in 10^20 and 1 in 10^50).

Is 10 to 20 per cent a typical level of specification for proteins to start to express functionality? Or is this the most generous estimate? The similarity in Cytochrome C (conveniently, a protein that is around 100 aa residues in length) between humans and yeast, discussed in an article here,
is 64%. If cytochrome C has to be 36% specified to have the required functionality, this still represents an improbability of 1 in 10^46. Obviously, this is a lot less improbable than 1 in 10^130 - but if the entire mass of the earth were randomly generated proteins of typically 1000 proton molecular weight, only 1 in 10 would correspond to this reduced specification of cytochrome c.

(I think!)

If it doesn't need to be 36% specified to have the required functionality, then how specified does it need to be? Convincing answers to questions like this would do a great deal to bolster the credibility of darwinian challenges to ID - but they don't arise.

This argument against ID is not sound. It is a vague hand-waving argument, which when examined closely fails to offer any detail or insight into how evolution might solve probabilistic problems.