Wednesday, September 6, 2006

Pseudo Explanations

More along with what I would expect from Scientific American, we find yet another blatant demonstration of what caused Philip Johnson to become “Darwin's Nemesis.” Though someone like Fuz Rana or Michael Behe could better address the gaping holes in the scientific community’s flawed assumptions about pseudogenes, it amazes me that even a former Marine like me can spot the inanity in the lengths to which some naturalists will go to account for them.

Long written off as the dead relics of eons of evolutionary mutation, the writers allow that:
“recent evidence of activity among pseudogenes, and their potential resurrection, suggests some are not entirely dead after all.”
Like the poor guy in the wooden cart (from “Monty Python & The Holy Grail” – sorry) who has the audacity to claim “he’s not dead yet,” evolutionary biologists would love to club those rascally pseudogenes over the head. But they just won’t go away. This is not a startling new revelation. Intelligent Design theorists have predicted it. When “Darwin’s Black Box” was published 10 years ago, Michael Behe quoted biologist Ken Miller’s assertion that:
“The theory of intelligent design, cannot explain the presence of non-functional pseudogenes unless it is willing to allow that the designer made serious errors, wasting millions of bases of DNA on a blueprint full of junk and scribbles. Evolution, in contrast, can easily explain them as nothing more than failed experiments in a random process of gene duplication that persist in the genome as evolutionary remnants.”
Not so fast Mr. Miller. At the time, Behe responded to Miller by citing three shortcomings with his claim:

1) Because the use of a structure has not yet been discovered, it does not follow that none exists. Miller’s appeal is to a naturalistic explanation that assumes what it should be trying to prove – a kind of a naturalism of the gaps.

2) Even if the pseudogenes have no function, that fact provides no explanation for how they arose in the first place. The simple reproduction of a pseudogene requires more than a dozen sophisticated proteins to separate, align, copy, reconfigure and reinsert nucleotides back into the DNA. Evolution provides no explanation for how such a process could have come to be.

3) Implicitly required in Miller’s claim is an assumption that Intelligent Design proposes that these pseudogenes arose in the recent past. But Intelligent Design makes no such claim. The fact that a complex system shows evidence of being designed is completely devoid of any claim about when this might have taken place.

Behe went on to speculate about potential uses for pseudogenes:
“includ[ing] bonding to active hemoglobin genes during DNA replication in order to stabilize the DNA; guiding DNA recombination events; and aligning protein factors relative to the active genes.”
Back to the article ... Ten years after “Black Box” was published, the authors have found that pseudogenes are found in great numbers across the genomes of many life forms. A comparison of these reveals …
“a puzzling phenomenon [in that] … a few pseudogenes appear to be better preserved than one would expect if their sequences were drifting neutrally … more than half the heavily transcribed sequences [in the genome] map to regions outside of known genes. What is more, a number of those transcriptionally active intergenic areas overlap with pseudogenes, suggesting that pseudogenes may have life left in them.”
They go on to describe the possibility …
“that pseudogenes play some ongoing part in regulating the activity of functional genes.”
That Mr. Behe may seem to be getting the last laugh where pseudogenes are concerned is satisfying. But what is more relevant is the irony embedded in the naturalistic “explanation” for Behe’s apparently successful prediction. The authors find it …
“hard to imagine that these pseudogenes had the specific role they now perform when they first arose. Instead their activity may be the result of selection preserving happy accidents or of nature having figured out an efficient way to reuse the broken parts of genes by converting them to regulatory elements … pseudogenes may be considered not only as dead genes but also as potentially unborn genes: a resource tucked away in our genetic closet to be drawn on in changing circumstancesIt is already clear that a whole genome is less like a static library of information than an active computer operating system for a living thing.”
These are pretty lofty claims for the irrational, random, unguided, non-teleological process naturalistic scientists call Darwinian Evolution. Inanimate, irrational, unguided processes do not encode, preserve, access and maintain informational libraries or “figure out” more efficient ways of doing things. The information-laden, intelligent-action-suggesting language used to describe the characteristics of these entities formerly known as the “evolutionary road kill” is pretty astounding. I welcome it and look forward to hearing more. For if these are the kinds of explanations we will be asked to choke down in order to keep the naturalistic paradigm alive, its funeral can’t be too far away.

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