Posted by Casey Luskin has to be a bit of an embarrassment to the IDists…at least, he would be, if the IDists had anyone competent with whom to compare him. I tore down a previous example of Luskin’s incompetence at genetics, and now he’s gone and done it again. He complains about an article by Richard Dawkins that explains how gene duplication and divergence are processes that lead to the evolution of new information in the genome. Luskin, who I suspect has never taken a single biology class in his life, thinks he can rebut the story. He fails miserably in everything except revealing his own ignorance.
It’s quite a long-winded piece of blithering nonsense, so I’m going to focus on just three objections.
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First, Luskin tries to trivialize gene duplication, a strategy that Michael Egnor also followed.
Yet during the actual gene-duplication process, a pre-existing gene is merely copied, and nothing truly new is generated. As Michael Egnor said in response to PZ Myers: “[G]ene duplication is, presumably, not to be taken too seriously. If you count copies as new information, you must have a hard time with plagiarism in your classes. All that the miscreant students would have to say is ‘It’s just like gene duplication. Plagiarism is new information- you said so on your blog!’”
This isn’t right, on many levels. Copying a pre-existing gene does create new information … but it’s just a small amount. Luskin can’t be serious in considering this a weakness: evolutionary biology would predict only small changes at any one time. If a process produced a massive increase in the information content of the genome in a biologically functional way (that is, not just the production of random noise), then we’d have to say that you’ve found evidence for Intelligent Design. A succession of small genetic changes is what we expect from evolution and genetics, and that’s what we see.
The plagiarism problem Egnor invents is nonsense. The primary problem with plagiarism in the classroom is that it is unethical, and represents the appropriation of ideas from another source without acknowledgment. If a student were to quote a source wholesale while providing full attribution, it would not be considered plagiarism…although the student would be failed for failing to demonstrate any understanding of the material or providing any significant new insight. We expect our students to demonstrate intelligence, after all; duplication is not a product of intelligence.
And again, whoosh, this will fly over their heads: the processes we describe in evolutionary genetics exhibit incremental increases in information in the absence of intelligent input — contrary to the expectations of the IDists.
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It wouldn’t be a creationist article without a quote-mine, and Luskin obliges. You’d think they’d learn, someday … whenever I see somebody at the Discovery Institute quote something from the scientific literature, I know to immediately check the source, and I am never disappointed. They always mangle it. Here’s Luskin in action:
A recent study in Nature admitted, “Gene duplication and loss is a powerful source of functional innovation. However, the general principles that govern this process are still largely unknown.” (Ilan Wapinski, Avi Pfeffer, Nir Friedman & Aviv Regev, “Natural history and evolutionary principles of gene duplication in fungi,” Nature, Vol. 449:54-61 (September 6, 2007).) Yet the crucial question that must be answered by the gene duplication mechanism is, exactly how does the duplicate copy acquire an entirely new function?
Oh, dear. That sounds like an awful admission, doesn’t it? Would you be surprised to learn that it’s very much like the infamous quote from Darwin, where he admits that the evolution of something as complex as the eye seems absurd, but then goes on to explain how it happened? That’s exactly the case here. Luskin has pulled out the first two sentences of the abstract, where the authors set up the problem they are about to address, and throws away the rest of the work where they go into detail on the evolutionary histories of orthologues in fungal genomes. Here’s the full abstract.
Gene duplication and loss is a powerful source of functional innovation. However, the general principles that govern this process are still largely unknown. With the growing number of sequenced genomes, it is now possible to examine these events in a comprehensive and unbiased manner. Here, we develop a procedure that resolves the evolutionary history of all genes in a large group of species. We apply our procedure to seventeen fungal genomes to create a genome-wide catalogue of gene trees that determine precise orthology and paralogy relations across these species. We show that gene duplication and loss is highly constrained by the functional properties and interacting partners of genes. In particular, stress-related genes exhibit many duplications and losses, whereas growth-related genes show selection against such changes. Whole-genome duplication circumvents this constraint and relaxes the dichotomy, resulting in an expanded functional scope of gene duplication. By characterizing the functional fate of duplicate genes we show that duplicated genes rarely diverge with respect to biochemical function, but typically diverge with respect to regulatory control. Surprisingly, paralogous modules of genes rarely arise, even after whole-genome duplication. Rather, gene duplication may drive the modularization of functional networks through specialization, thereby disentangling cellular systems.
Tsk, tsk. It’s an interesting paper that documents the details of a number of cases of gene duplication and divergence, and Luskin ignores it all (I suspect because he lacks the competence to understand it) to imply the paper is about our failure to understand the processes. I just mentioned that my primary concerns with student work are that they demonstrate good citation ethics and that they show understanding; Luskin has just failed on both counts. He has misrepresented the sense of a paper and he has shown that he doesn’t understand the work. A student who turned in that kind of shoddy effort to me would get an immediate “F”.
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Finally, Luskin shows that not only does he fail to understand the duplication part, but he hasn’t got much of a grip on the divergence part, either. He invents a silly challenge of his own.
So here is my “Information Challenge”: For the sake of the argument, I will grant that every stage of the evolutionary pathway I requested above will survive, and thus I’ll give natural selection every possible benefit of the doubt. What I need is a step-by-step mutation account of how one sentence evolved into the other wherein the sentence remains functional – i.e., it has comprehensible English meaning – at all stages of its evolution. In short, I request to see how:
“METHINKSDAWKINSDOTHPROTESTTOOMUCH”
can evolve into:
“BUTIMSUREDAWKINSBELIEVESHEISRIGHT”
by changing the first sentence one letter at a time, and having it always retain some comprehensible English meaning along each small step of its evolution. This seems like a reasonable request, as it is not highly different from what Darwinists are telling me can happen in nature.
No, it has some significant differences. The genetic code is degenerate — there are many synonyms in the ‘language’. Much, but not all, of a protein is going to be tolerant to a fairly wide range of amino acid substitutions. That means that in this analogy, the simulation ought to tolerate a great many misspellings, and that many of the words ought to be dispensable as far as generating meaning. In addition, evolution isn’t trying to drive one amino acid sequence to another specific amino acid sequence; selection is only going to work for retention of general functionality. English has too much specificity to work in this analogy. If he said he had a text string with a lot of gibberish containing the words “DAWKINS” and “PROTEST”, and he wanted to see a step by step series of shifts that turned it into a string with some other gibberish that conserved “DAWKINS” and evolved the word “RIGHT”, and that slight misspellings in the intermediates were acceptable, he’d probably declare the exercise trivial and too easy — but that’s exactly what happens in the evolution of proteins. It’s not pre-specified, it’s fault-tolerant to a degree, and it’s not that big a deal.
And furthermore, we already have the real thing. Not an analogy, not a guess, but a “step-by-step mutation account” of how one functional protein evolved into another protein with a different function, by a process of gene duplication and divergence. He might try reading Ian Musgrave’s summary of the evolution of the cortisol and aldosterone receptors. It’s cool stuff, it describes exactly what he demands in a real protein, and the degree of detail goes right down to the order of single amino acid changes. It’s perfect.
Of course, we also know exactly how the IDists react when scientists do provide explanations in terms of tiny incremental changes. Suddenly, the details become “piddling”, and they ignore them. I expect Luskin will do the same.
Pathetic in his ignorance, appalling in his dishonesty, and disgraceful in his unwarranted arrogance … that’s Casey Luskin. It’s really a mark of the growing desperation of the Discovery Institute that they are constantly dragging out this pipsqueak lawyer to lecture the public on biology.
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