Peter: >But natural selection can only test a functional feature already present to some minimal degree. If we consider the entire historical developmental path of a functionality (e.g. an enzyme), including all of the functional information contained in it, its specific activity must have started sometime with a minimal amount of activity just sufficient to make it selectable. And before that? This is the interesting part of its history, because without selection, we can estimate a probability of random emergence. Afterwards, normal darwinian evolution sets in, and I see no way of estimating probabilities. There may be many other critical points in the evolution of a new function, but this is certainly the first one of them - and it is habitually ignored by evolutionary biologists.<
Me (new) Mutated versions of a functional gene may retain the initial function under some circumstances but change under other conditions. The classic example of this is temperature sensitivity in mutations. A change in temperature may directly affect the protein configuration, or it may induce heat shock, causing chaperone proteins to be put into use for controlling heat damage and thus freeing the formerly chaperoned proteins to assume new configurations. Several detrimental examples are known experimentally. However, Carter et al. (1998, J. Paleont. 72:991-1010) suggested that a low-temperature sensitive mutation in a protein involved in bivalve shell structure could have mediated changes from aragonite to calcite. This was based on the paleontological pattern rather than genetic work.
Peter >The only reason I brought it up at all is because natural selection is the only natural source of biological information we know of. <
Me (new) I would think mutation is the source of information and selection tests the usefulness of the information in a given context.
Peter >What I call a truly novel gene is one whose function has never before existed in the entire biosphere, no matter what led to the last step which originated the first minimal amount of the new activity. If it is a mixing of old genes, the new gene may display a combination of the old functions (whose novelty is a matter of definition, but these cases need not concern us here), or possibly (but very unlikely) something entirely new, while the old functions no longer exist (perhaps due to clipping). For a reasonable discussion of such a possibility, we should have actual examples where this happened.<
Me (new) How specifically do you define function? The only way I can think of to ensure that a gene function has never before appeared in the biosphere is to look at genes interacting with novel artificial compounds (resistance to DDT, for example). It seems more feasible and equally relevant to look at genes that clearly show innovation in a given organism. The antifreeze gene in the Antarctic toothfish, derived from trypsinogen, is both structurally and functionally novel (Chen et al. 1997. PNAS USA 94:3811-3816). Perhaps a similar antifreeze gene evolved in some organism during one of the Precambrian or Paleozoic ice ages, but that does not seem to distract from the novelty of this innovation.
Peter >This is the reason why I concentrate on folds (i.e. sequences without any recognizable homology), rather than families.<
Me (new) Different folds may have recognizable homology at some other level. For example, there are two aminoacyl-tRNA synthetase families. The proteins show no similarity across families. However, the DNA sequences are similar if you turn one of them around in the opposite direction (Rodin and Ohno, 1995, Orig. Life Evol. Biosphere 25:565-589). Most of the antifreeze gene mentioned above is poly-Thr-Ala-Ala, which is unlikely to fold in the same way as the original protein, although the first exon is retained largely intact. These codons are derived largely from intronic nucleotides in the original gene, also involving a frame shift for those parts derived from previously exonic nucletides. Thus, what was non-functional DNA in the ancestral gene is now functional.
Me (old) >>>> The example of a pseudogene reactivated, discussed in other posts, would be a case of passing through unselected "random" intermediates before arriving at a useful function.<<<<
Peter (old)>>>Do you know of any case where such a path via unselected intermediates has been documented in a real biological system, not just stated as a general hypothesis?<<<
Me (new) Actually, that was a specific example rather than a general idea. Gene duplication was promptly followed by one copy becoming a pseudogene in the ancestor of true ruminants (Pecora). True deer, giraffes, antelopes, sheep, and early-diverging bovids all have a pseudogene. However, partial gene conversion in the common ancestor of certain bovids (cattle, Cape buffalo, and water buffalo) corrected three major mutations in the pseudogene, allowing it to resume a function similar to that of the ancestral gene but in a different part of the body. Most of the gene is still homologous to the pseudogene. This is certainly not a particularly novel function, but it does show functionality after a period of unselected mutation.
Tim >>Interestingly, this system arose in much the way that one would expect an IC system to evolve: indirectly, through steps of selection under conditions that were not the same as where the system finally emerged.<<
Peter>If this should turn out to be the case, it would not constitute an IC system, as each mutation can be selected by itself and the intermediate is viable.<
Me (new) This hinges on the definition of IC [irreducibly complex]. If it is defined strictly as a multipart system that cannot function when incomplete and cannot evolve through intermediate steps, then the system would not be IC. However, the system does pass some of the criteria proposed as proof that a system is IC. It is a multipart system that does not function without all its parts, and the partial systems are not favored by selection. Thus, it might be more accurate to say that this example shows certain popular criteria for IC are inadequate.
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!
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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