niiicholas
Posts: 319
Joined: May 2002
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Hi,
While reading this interview with Phil Johnson, leader of the ID movement:
Berkeley’s Radical
An Interview with Phillip E. Johnson
...I was struck by this section:
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You have said there is no natural explanation for the rise of genetic information. How important is that question in the debate?
PJ: The Wedge of Truth is all about those issues. The scientific key is, "No natural processes create genetic information." As soon as we get that out, there’s only one way the debate can go because Darwinists aren’t going to come up with a mechanism. They’ll start out talking about the peppered moth, and when that self-destructs, then they’ll say, "Oh, self-organizing systems, or the fourth law of thermodynamics," and other nonsense, which is just covering up ignorance.
Genetic information is the issue, but it isn’t the final issue. After you make that breakthrough, then you see other ways in which the theory is questionable. Darwinists will say, "Oh, well, maybe the mechanism has some problems, but the "fact of evolution"—common ancestry—is not in question. We distinguish the fact of evolution from the mechanism of evolution."
But that’s a bogus distinction because the "fact"—common ancestry—incorporates the mechanism. It’s just a matter of "now you see it, now you don’t." They are saying the mechanism by which a father and mother give birth to children is the same mechanism by which our "bacterial ancestors" gave birth to human beings. They say it’s all a process of natural reproduction and naturally occurring variation in the offspring.
Biologists affiliated with the Intelligent Design movement nail down the distinction by showing that DNA mutations do not create evolution in any significant sense. Instead, they make birth defects, so the whole thing is false from the get-go. There is no way you can establish that a bacterium is the parent of a complex animal. There is no mechanism to make the change, no historical or fossil evidence that such a change ever occurred, and there’s no way to duplicate the process in a lab.
Once you get that in the debate, then we will be poised for a metaphysical and intellectual reversal that is every bit as profound as the one with Copernicus. People will say, "My gosh, we’ve been completely misled by this fundamental truth of the creation story of our culture. We can no longer understand the world that way."
How do you change the way people regard the authority of science? Get them to think of it as a much more limited thing. Science is very reliable when scientists stick to the kinds of things that can be tested by refutable experiments, but much of what they tell us is outside that. When they have to fake the mechanisms, it becomes a very dubious philosophy. That raises the question of why so many very brilliant people were misled for so long and did such a good job of rationalizing these things.
When the mechanism of Darwinism becomes discredited, it’s like a train that’s been turned around. You can say, "Well, that’s interesting, but the train is still in the same place. The world, Yale, Berkeley, are still there. The New York Times is still telling us what to think. So why isn’t everything different?" Well, it is different, but you can’t see it yet. The train is turned in the opposite direction. It’s going to start out very slowly, but it’s moving on the logical tracks towards something very different, and when we get there, our great-great-grand-children will see how different things are.
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Note that the "scientific key" to the whole ID argument (according to Johnson) is this: "No natural processes create genetic information."
This strikes me as easily and trivially refutable by numerous examples. Anything that starts with genetic information amount X, and ends up with genetic information amount X+Y, should qualify. The classic case would be X=information in a genome before a gene duplicates & diverges under selection, and X+Y being the information in the genome after this has occurred.
Another less-often considered example should be (IMO) when a mutation (let's say "beneficial to at least part of the population" to avoid the obvious objection) arises in a *population*. Here,
X=information in the genomes of a population
Y=information in the beneficial mutation
I realize that "information" has no single definition in biology, one could also argue that "new information" would arise through novel combinations of alleles, etc. For the purposes of this thread, I suggest the following working definition:
Genetic information=functional DNA that encodes useful/beneficial proteins or regulatory sequences
...as this is what the IDers mean by "genetic information" (except of course when they are challenged on the topic, wherein they promptly begin the obfuscation and goal-post moving, rather like eternally elusive creationist definition of "kind").
So, let's use this thread to accumulate examples of natural processes increasing "genetic information" in the above-described sense. Other things that might be relevant, e.g. studies of the increase of Shannon information in selective algorithms, could also be posted, just note the form of information as relevant.
nic
PS: I'll start off with one of my favorite examples:
Sdic, sperm dynein intermediate chain, a new gene which evolved over the past few million years by the duplication, fusion, and modification of two genes that are now on each side of Sdic on the chromosome.
Here is a brief introduction from Ian Musgrave:
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My second favorite example is the Sdic gene, where the annexin and dynenin intermediate chain genes were duplicated in tandem, then the intervening sequences deleted to form a single new gene, (the Sperm specific dynenin intermediate chain gene Sdic). The good thing about this example is that a previously non-coding part of the sequence became the protein coding sequence, and the protein coding sequence has a non-coding role.
Capy P. (1998 Dec 10). Evolutionary biology. A plastic genome [news; comment] Nature, 396, 522-3.
Nurminsky DI, Nurminskaya MV, De Aguiar D, and Hartl DL. (1998 Dec 10). Selective sweep of a newly evolved sperm-specific gene in Drosophila [see comments] Nature, 396, 572-5.
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Here is the Nurminsky et al. 1998 article:
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pubmed link
Nature 1998 Dec 10;396(6711):572-5
Selective sweep of a newly evolved sperm-specific gene in Drosophila.
Nurminsky DI, Nurminskaya MV, De Aguiar D, Hartl DL.
Harvard University, Department of Organismic & Evolutionary Biology, Cambridge, Massachusetts 02138, USA.
The pattern of genetic variation across the genome of Drosophila melanogaster is consistent with the occurrence of frequent 'selective sweeps', in which new favourable mutations become incorporated into the species so quickly that linked alleles can 'hitchhike' and also become fixed. Because of the hitchhiking of linked genes, it is generally difficult to identify the target of any putative selective sweep. Here, however, we identify a new gene in D. melanogaster that codes for a sperm-specific axonemal dynein subunit. The gene has a new testes-specific promoter derived from a protein-coding region in a gene encoding the cell-adhesion protein annexin X (AnnX), and it contains a new protein-coding exon derived from an intron in a gene encoding a cytoplasmic dynein intermediate chain (Cdic). The new transcription unit, designated Sdic (for sperm-specific dynein intermediate chain), has been duplicated about tenfold in a tandem array. Consistent with the selective sweep of this gene, the level of genetic polymorphism near Sdic is unusually low. The discovery of this gene supports other results that point to the rapid molecular evolution of male reproductive functions.
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Since then, this article has been published:
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Pubmed link
Nurminsky D, Aguiar DD, Bustamante CD, Hartl DL.
Chromosomal effects of rapid gene evolution in Drosophila melanogaster.
Science. 2001 Jan 5;291(5501):128-30.
Rapid adaptive fixation of a new favorable mutation is expected to affect neighboring genes along the chromosome. Evolutionary theory predicts that the chromosomal region would show a reduced level of genetic variation and an excess of rare alleles. We have confirmed these predictions in a region of the X chromosome of Drosophila melanogaster that contains a newly evolved gene for a component of the sperm axoneme. In D. simulans, where the novel gene does not exist, the pattern of genetic variation is consistent with selection against recurrent deleterious mutations. These findings imply that the pattern of genetic variation along a chromosome may be useful for inferring its evolutionary history and for revealing regions in which recent adaptive fixations have taken place.
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This article is a good review of the general topic of the evolution of new genes:
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pubmed link
Curr Opin Genet Dev 2001 Dec;11(6):673-80
Evolution of novel genes.
Long M.
Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago Illinois 60637, USA. mlong@midway.uchicago.edu
Much progress in understanding the evolution of new genes has been accomplished in the past few years. Molecular mechanisms such as illegitimate recombination and LINE element mediated 3' transduction underlying exon shuffling, a major process for generating new genes, are better understood. The identification of young genes in invertebrates and vertebrates has revealed a significant role of adaptive evolution acting on initially rudimentary gene structures created as if by evolutionary tinkers. New genes in humans and our primate relatives add a new component to the understanding of genetic divergence between humans and non-humans.
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Have fun,
nic
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