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dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: June 14 2012,16:09   

http://informatics.indiana.edu/rocha......ee.html

For those of us who are incredibly bored with the output of retired veterinarian David Abel, here is a link to an article that is partially a source for his word salad.

"Physicodynamics", "epistemic cut", etc.

The interesting thing is that Pattee's conclusion is exactly the opposite of Abel's.

Quote
13. Real-life conditions for bridging the epistemic cut
Finally, I will summarize some of the physical requirements for successfully bridging the epistemic cut. In effect we are answering von Neumann's "most intriguing, exciting, and important question of why the molecules . . . are the sort of things they are." First is the search problem. It was a problem for Darwin, and with the discovery of the DNA helix and the code that precisely maps base sequences to protein sequences the search problem appeared worse. By assuming that molecular details are significant one sees a base sequence space that is hopelessly large for any detailed search. But while this assumption is correct for the symbolic side of the cut we now know that the assumption is wrong for the function on the other side of the cut. Bridging the epistemic cuts implies executing classifications of physical details, and the quality of the classifications determine the quality of function. We know that protein sequences are functionally highly redundant and that many amino acid replacements do not significantly alter the function. We also know that many base sequence aliases can construct proteins with essentially the same shape. Also, simplified models of RNA secondary folding suggest that the search is not like looking for a specific needle in an infinite haystack, but looking for any needle in a haystack full of needles that are uniformly distributed (e.g., Schuster, 1994). There is also evidence that the search is far more efficient than classical blind variation. Artificial genetic algorithms have shown unexpected success in finding acceptable solutions for many types of search problems that appear logically or algorithmically intractable.

The second requirement is for reliable self-replication. This is a complex adaptive balancing act between conflicting requirements at many levels. On the one hand, complete reliability would not allow any search, variation, or evolution at all. On the other hand, too little reliability will produce extinction by an error catastrophe. At the folding level where the degeneracy of base sequences is partially removed, there must be a balance between a stable energy landscape to allow rapid folding and permanence, and the complex conformational degeneracies necessary for flexible specific binding and rapid catalysis. The folding process is uniquely complex in many ways. It is a transformation across all three spatial dimensions, over temporal scales covering many orders of magnitude, and involving strong bonds and many weaker forces in coherent highly nonlinear interactions. The complexity of any detailed quantum mechanical description of such non-integrable constraints means that such folding problems can only be treated statistically. Even formulating a microscopic description appears intractable. It is not even obvious that a linear sequence of several hundred amino acids, or any such heteropolymer, should fold reliably into a specific globular shape. That such flexible globules should be able to perform high-speed, highly specific catalysis is even less obvious. Yet we know this is the case, and we usually take these incredible functions for granted (e.g., Frauenfelder and Wolynes, 1994).

The last requirement I mentioned was how smoothly variations in the genetic sequences can produce adaptation in functions. Here again there must be a balance between conflicting requirements. Rapid folding and stability of a protein requires steep energy landscapes, while optimization of function requires fine tuning of the folded shape of the protein by small changes in genetic sequences. This requires a relatively smooth energy landscape. Balancing these requirements is eased by large enough molecules so that major folding conditions are buffered from local fine-tuning changes in sequences (e.g., Conrad, 1990). The degree to which these and other requirements are met by natural selection on the one hand and by non-selective ordering principles on the other will only be decided by empirical study of the molecular details.


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Iím referring to evolution, not changes in allele frequencies. - Cornelius Hunter
Iím not an evolutionist, Iím a change in allele frequentist! - Nakashima

  
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