>> The minimum number of amino acid substitutions required before selection operates on a new function is zero...<<
>This is not evolution of a novel function, but cooptation of an existing enzyme for another function...
Exaptation does involve a novel function for the original gene, so whether it constitutes the evolution of a novel function seems to be a semantic rather than scientific question
>> In general, the vast majority of new genes seem to be produced from manipulation of existing genes-mixing and matching parts, duplicating and then modifying, etc....<<
>The origin of a new protein by exon shuffling may also be considered a cooptation of a set of preexisting functionalities. This also applies to duplicates of genes happening to already possess an initial minimal activity of a new kind. In such cases, selection is possible from the start. This is microevolution and does not pose any informational problems.<
Micro and macroevolution are defined in too many different ways for me to be sure what you mean here. Exon shuffling and gene duplication followed by modification both produce novel information, something some intelligent design advocates claim is impossible. I don't think you are trying to support such claims, but I would see the combination of parts from several different genes followed by selection for a new function as a relatively substantial innovation.
>But to assume that ALL functionalities emerged in such a manner, without any non-selectable intermediates, is entirely speculative. How do you know this is "the vast majority" of genes? You yourself concede that the origin of "the first gene" is not dealt with. There are an estimated 1000 different protein folds (each grouping a series of protein families or superfamilies) in the biosphere, considering the globular, water-soluble proteins only (Y.I.Wolf, N.V.Grishin, E.V.Koonin, "Estimating the number of protein folds and families from complete genome data", J.Mol.Biol. 299 (2000), 897-905). Almost by definition, these 1000 folds are not related to each other by exon shuffling and gene duplication. Each one of them had to originate somewhere at least once during the past 3.8 billion years. Thus, it would be more realistic to talk about "the first 1000 genes" whose emergence cannot be accounted for at present. These are the cases I am considering when I talk about a mutation!
al random walk without intermediate selection until a minimal selectable activity happens to be produced. These are cases I consider macroevolutionary steps posing considerable informational problems deserving careful attempts at estimating their probability and at possibly finding more realistic evolutionary scenarios than merely assuming that "it must have happened somehow" through selectable intermediates. You may call these the most elementary cases of Behe's "irreducibly complex systems" - whose non-existence has not yet been made plausible.
<
Obviously, examining every known gene sequence to determine the relative frequency of egene duplication, exon shuffling, and the like is not feasible. However, the general pattern that emerges as one examines a gene, one finds related genes with different functions. If there are 1000 truly novel genes, that is still a lot less than the total number of genes in humans, for example. I did not mean to imply that all functions evolved by duplication and modification of existing genes, but rather that it was extremely common. The example of a pseudogene reactivated, discussed in other posts, would be a case of passing through unselected "random" intermediates before arrving at a useful function.
However, I doubt that no two protein folds can be produced from sequential functional modifications of a gene or genes. Taking another example from Graur and Li, an antifreeze protein in one Antarctic fish is derived from a particular enzyme by deletion of most of the enzyme and internal serial duplication of a 3 amino acid sequence. I do not know the folding pattern of the trypsinogen and the antifreeze protein, but I supect they are rather different.
Dr. David Campbell
"Old Seashells"
Biology Department
Saint Mary's College of Maryland
18952 E. Fisher Road
St. Mary's City, MD 20686-3001 USA
dcampbell@osprey.smcm.edu, 301 862-0372 Fax: 301 862-0996
"Mollusks murmured 'Morning!'. And salmon chanted 'Evening!'."-Frank Muir, Oh My Word!
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