Land-based fish helps researchers assess how animals moved to land – and stayed there

Here's Douglas Axe's latest on the subject:

But I’m really not competent myself to comment knowledgably on the current state of such research, so I will grant the possibility, at least in principle, that the search space of functional folded proteins could have been traversed by relatively simple (and mathematically probable) mutational steps in sufficient time to produce those we see today. My sense is that, as the length of proteins increases, the degree of connectedness decreases, and quite rapidly, too.

Petrushka

Axe published the following: Proc. Natl. Acad. Sci. USA Vol. 93, pp. 5590-5594, May 1996 Active barnase variants with completely random hydrophobic cores “ABSTRACT The central structural feature of natural proteins is a tightly packed and highly ordered hydrophobic core. If some measure of exquisite, native-like core packing is necessary for enzymatic function, this would constitute a significant obstacle to the development of novel enzymes, either by design or by natural or experimental evolution. To test the minimum requirements for a core to provide sufficient structural integrity for enzymatic activity, we have produced mutants of the ribonuclease barnase in which 12 of the 13 core residues have together been randomly replaced by hydrophobic alternatives. Using a sensitive biological screen, we find that a strikingly high proportion of these mutants (23%) retain enzymatic activity in vivo. Further substitution at the 13th core position shows that a similar proportion of completely random hydrophobic cores supports enzyme function. Of the active mutants produced, several have no wild-type core residues. These results imply that hydrophobicity is nearly a sufficient criterion for the construction of a functional core and, in conjunction with previous studies, that refinement of a crudely functional core entails more stringent sequence constraints than does the initial attainment of crude core function. Since attainment of crude function is the critical initial step in evolutionary innovation, the relatively scant requirements contributed by the hydrophobic core would greatly reduce the initial hurdle on the evolutionary pathway to novel enzymes. Similarly, experimental development of novel functional proteins might be simplified by limiting core design to mere specification of hydrophobicity and using iterative mutation-selection to optimize core structure.” Petrushka

"Waiting for a beneficial mutation" indicates a huge misunderstanding of evolution. Individuals are already biologically competent. They are not waiting for anything. Some alleles become more frequent in a population due to drift or due to conferring advantage. That's pretty much it. We know by observation of alleles that there are many functionally equivalent or nearly equivalent sequences. Otherwise there would be no genetic diversity. Every individual would be a clone of every other individual. We also know from direct observation of bacterial populations that they manage to thrive despite so-called genetic entropy. We can calculate the average number of mutations per generation and note that populations do not die out from entropy, despite accumulating changes. Petrushka

This reminds me of this cartoon:

Evolution Cartoon - Waiting For That Beneficial Mutation http://www.metacafe.com/watch/4165228/

notes;

When Theory and Experiment Collide — April 16th, 2011 by Douglas Axe Excerpt: Based on our experimental observations and on calculations we made using a published population model [3], we estimated that Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied. http://biologicinstitute.org/2011/04/16/when-theory-and-experiment-collide/ “Mutations are rare phenomena, and a simultaneous change of even two amino acid residues in one protein is totally unlikely. One could think, for instance, that by constantly changing amino acids one by one, it will eventually be possible to change the entire sequence substantially… These minor changes, however, are bound to eventually result in a situation in which the enzyme has ceased to perform its previous function but has not yet begun its ‘new duties’. It is at this point it will be destroyed - along with the organism carrying it.” Maxim D. Frank-Kamenetski, Unraveling DNA, 1997, p. 72. (Professor at Brown U. Center for Advanced Biotechnology and Biomedical Engineering) "a very rough but conservative result is that if all the sequences that define a particular (protein) structure or fold-set where gathered into an area 1 square meter in area, the next island would be tens of millions of light years away." - Kirk Durston Experimental Support for Regarding Functional Classes of Proteins to be Highly Isolated from Each Other: - Michael Behe "From actual experimental results it can easily be calculated that the odds of finding a folded protein are about 1 in 10 to the 65 power (Sauer, MIT).,,, The odds of finding a marked grain of sand in the Sahara Desert three times in a row are about the same as finding one new functional protein structure. Rather than accept the result as a lucky coincidence, most people would be certain that the game had been fixed.” Michael J. Behe, The Weekly Standard, June 7, 1999 http://www.arn.org/docs/behe/mb_smu1992.htm Doug Axe Knows His Work Better Than Steve Matheson Excerpt: Regardless of how the trials are performed, the answer ends up being at least half of the total number of password possibilities, which is the staggering figure of 10^77 (written out as 100, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000). Armed with this calculation, you should be very confident in your skepticism, because a 1 in 10^77 chance of success is, for all practical purposes, no chance of success. My experimentally based estimate of the rarity of functional proteins produced that same figure, making these likewise apparently beyond the reach of chance. http://www.evolutionnews.org/2010/06/doug_axe_knows_his_work_better035561.html Evolution vs. Functional Proteins - Doug Axe - Video http://www.metacafe.com/watch/4018222 Stephen Meyer - Functional Proteins And Information For Body Plans - video http://www.metacafe.com/watch/4050681

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