Friday, July 8, 2016

Local Fitness Landscape Mapped Out for Green Fluorescent Protein

Sharp peaks.

Cornelius Hunter quotes a recent article in Nature about GFP:
We were really surprised when we finally had a chance to look at exactly how the interactions between mutations occur. We also did not expect that almost all the mutations that are only slightly damaging on their own can destroy fluorescence completely when combined together.*

Quasispecies: Trapped in Sequence Space

Edward C. Holmes and Andre´s Moya make some interesting comments in "Is the Quasispecies Concept Relevant to RNA Viruses?" JOURNAL OF VIROLOGY, Vol. 76, No. 1, Jan. 2002, p. 460–462:

Friday, July 1, 2016

Unlimited Variation: The Dark Energy of Biology

Alfred Russel Wallace, the co-discoverer of natural selection, wrote in 1858 that his theory could be summarized as “indefinite departure from the original type.” “Indefinite departure” is in fact the central claim of the theory of evolution by natural selection. But it still hasn’t been observed. Richard Dawkins, Jerry Coyne and others keep trying to bully us into accepting that it is a “fact.” OK. Maybe it is. So give us the evidence. We have to read their books carefully to realize how meager it is. They still haven’t shown us that extrapolation.
Back in 2013 Tom Bethell wrote an interesting piece about the "central claim" of modern evolutionary theory.  As with many interesting articles of this nature, my attention was drawn to it by a caustic review by a renowned ID-hater, in this case the inimitable Jeffrey Shallit

Shallit pedantically quibbles about Bethell's criticism of Charles Darwin.  Darwin stated that there was no reason to suppose any limit to variations of forms, e.g. no reason a fish couldn't become an elephant through a long enough series of minuscule changes, which casts natural selection as Dr. Moreau's scalpel working at a geological pace. This has enormous relevance to the extrapolative nature of evolutionary theory, for it is the justification for what Wallace called (as Bethell points out) "indefinite departure from the original type." By "indefinite" Wallace meant that for practical purposes it can be considered infinite, the limits being so indefinitely far out as to not rule out any connection between the varied forms we see and the simplest cell.

It is this sense of extrapolation that is central to evolutionary theory, more so than either common descent or natural selection

In a particularly Dawkins-esque stroke, Shallit pounds the pulpit:
What we do see is evolution taking place today, and we have the fossil record that shows the changes in the past. You have to be particularly dense or dishonest to deny this.
In other words, we already know that any limits to variation don't matter to macroevolutionary theory, because macroevolution must have occurred.  We have these here fossils, and we know Mr. Darwin's speculations about them must be true because we observe limited variation now.  Accept the extrapolation or be denounced as a "denier"! Shallit and his audience stand ready to punish the deniers by pointing and laughing while simultaneous shaking their fists in furious rage. 

Shallit invokes speciation.  I'm not certain if everyone would agree on his instances of speciation (none of which he offers--it is left as an exercise to the reader), but perhaps he would be surprised to know that even most "Young Earth" creationists believe in some limited form of speciation.  In spite of considering himself an expert on pseudo-science, he doesn't even understand the nature of his favorite "pseudoscientific" bugbear, Young Earth Creationism.  He might also be unaware that even though undirected speciation may be necessary for macroevolution, it is not sufficient to explain macroevolution.  In fact, Cornelius Hunter, who is not a Young Earth creationist, does not deny ultra-fast adaptation or an old age of fossils.  Shallit seems to consider him a run-of-the-mill creationist.  It seems that Shallit does not recognize any significant differences among those he considers "creationists" (which for him includes ID advocates).    

All of this is probably lost on evolutionary materialists who depend on a quasi-Newtonian metaphor in which evolution is moving with a sort of inertia.  This is why Jerry Coyne can liken macroevolution to a train in motion (though it is also an artificially powered and directed machine) and Shallit can compare it to cosmological materials flying apart.  (Although, the hypothetical drive powering the quasi-infinite variation of evolution is, in epistemological status, somewhat reminiscent of poorly understood "dark energy.")  
As natural as a train in motion...  Give this choo-choo
enough time and it just might reach the Galapagos Islands.