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Author
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Topic: John R. Bracht: Inventions, Algorithms, and Biological Design
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Janitor@MIT
Member
Member # 125
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posted 17. July 2002 12:58
I appreciate your response, brief though it is, Francis. I appreciate the fact that the participants here generally are thoughtful and reflective, and there are little of the reflexive, defensive, and formulaic responses that tend to plague the introduction of questions, challenges, new ideas, and new perspectives. (Could I be any more ingratiating? Sheesh!) As an aside, while I was doing some research on two subjects that have come up here I noticed a recurrent theme: “Surprise.” I thought I would compile a list of the research papers in which I had seen that term used recently (all published in the last four years).
Point well taken, eland, but what I’m suggesting, more forcefully, is that EC (as a model or simulation of biological evolution), tied to the traditional popgen model, is antiquated. The assumptions of the canonical model are fundamentally flawed. Its not a question of a more or less accurate approximation—it isn’t even in the ballpark!
Both design and evolution are searches for solutions in complex problem spaces. Recently many researchers have strongly suggested a structure to the “living space” that contrasts significantly with Sewall Wright’s classical “fitness landscape,” that has been so profoundly influential over Neo-Darwinism and its in silico progeny: E.g., see Barbel, M., R. Stadler, P.F. Stadler, G.P. Wagner, & W.F. Fontana. 2001. The topology of the possible: Formal spaces underlying patterns of evolutionary change. PDF online.
“[En bloc] Genomic rearrangements short-circuit the simple metric generated by one point mutations, usually underlying the intuition of evolution on landscapes… Thus, although fitness landscapes have a meaning for small scale adjustments associated to fine-tuning of binding constants, it is an unjustified concept for evolutionary changes on the scale of speciation events (Bornholdt, S. & K. Sneppen. 2000. “Robustness as an Evolutionary Principle,” Proc. R. Soc. London B 267: 2281-2286. arXiv:cond-mat/0003333 20 Mar 2000).”
Nimwegen, E. v., James P. Crutchfield, & Martijn Huynen, “Neutral evolution and mutational robustness,” PNAS 96: 9716-9720, August 1999, “Here we develop a model [Based on Eigen’s quasi-species model.] for the evolution of populations on neutral networks and show analytically that, for biologically relevant population sizes and mutation rates, a population’s distribution over a neutral network is determined solely by the network’s topology… independent of evolutionary parameters—such as mutation rate, selection advantage, and population size [given population size-mutation rate product >>1]…” And references therein, especially Huynen, et al (1996).
This also relates to a subject that James Barham and I have briefly discussed in the “Robustness” topic, where some background is referred to:
“A small world topology may therefore have a significant impact on the behavior of dynamical systems. How do they effect the search problem (Toby Walsh, “Search in a Small World,” PDF online.)?” See also Chen, H., et al, “Formal Models of Heavy-Tailed Behavior in Combinatorial Search,” and references therein (PDF online.); Gomes, C.P., et al, “Boosting Combinatorial Search Through Randomization,” (PDF online.); and (Very interesting!) Jon Kleinberg, “The Small-World Phenomenon: An Algorithmic Perspective,” HTML online.
IMHO, these developments represent a fundamental theoretical reorientation.
Erratum: Ernst Mayr was incorrectly paraphrased above: “It is important to clear up first some misconceptions still held by a few, not familiar with modern genetics: 1) Evolution is not primarily a genetic event [Highlighting my error.]… it is selection that induces evolutionary change (1963. Animal Species and Evolution. Belknap Press. NY. p. 613)…” ( LOL James Barham is no doubt wearily familiar with the logical error in this statement, which Darwin himself vainly attempted to circumvent.) Pace Mayr I do think that evolution is “primarily a genetic event,” and I think the direction research is taking us (if it can be characterized as a “direction”) is decidedly more “friendly” to the opinion often expressed here, that there is indeed something intrinsically “intelligent” to the design-evolution of life. (Not exactly topical; just a “parting shot” at the last surviving member of the Columbian Cabal. LOL)
I apologize, Mr. Moderator, for “stretching the rules” here; there’s not much “original content,” but hopefully it contributes to John Bracht’s thesis.
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Moderator
Administrator
Member # 1
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posted 17. July 2002 13:42
Janitor,
I think your post leads the discussion in a positive direction. I'm generally pretty lenient about posting references to articles and quoting external sources as long as they are put in context and are used to clarify an idea or further an argument by the poster.
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Frances
Member
Member # 169
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posted 18. July 2002 13:45
Janitor,
Thanks so much for your links and references. I found a wealth of information to wade through once I deal with the failing hard disk on my machine.
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