Re: Comments on Snoke's approach

From: Pim van Meurs <pimvanmeurs@yahoo.com>
Date: Sat Sep 24 2005 - 12:38:50 EDT

Oops forgot a linl http://www.pandasthumb.org/pt-archives/000306.html

Also in http://www.pandasthumb.org/pt-archives/000335.html, I describe
more in depth neutral networks:

Four properties of the RNA map were derived (scale free networks):

    *

      There are many more sequences than structures.

    *

      There are very few common and many uncommon structures

    *

      The distribution of neutral genotypes (sequences that fold into
      the same structure) is approximately random in sequence space.
      This means that it is possible to define a spherical region with a
      diameter much smaller than the diameter of sequence space which
      contains on the average for every common structure at least one
      sequence that folds into it.

    *

      Existence and connectivity of neutral networks. That is, any
      neutral network is within a close distance of another common
      neutral network.

Schuster et al found that ( “Networks in Molecular Evolution” by PETER
SCHUSTER and PETER F. STADLER)

    Sequences at the intersection of the compatible sets of two neutral
    networks upon the same sequence space were found to be of actual
    interest since they can simultaneously carry the properties of the
    different RNA folds. For example, they can exhibit catalytic
    activities of two ribozymes [43].
    …

    Analogous results were reported for proteins. Computational studies
    predict the existence of neutral networks and shape space covering
    also for polypeptides
    [2, 3]. So far, these predictions are in agreement with
    experiments(see, for example, [36]).

(36) A. D. Keefe and J. W. Szostak
<http://www.hhmi.org/research/investigators/szostak.html>. Functional
proteins from a random-sequence library. Nature, 410:715{718, 2001.

(43) E. A. Schultes and D. P. Bartel. One sequence, two ribozymes:
Implications for the emergence of new ribozyme folds. Science,
289:448{452, 2000.

Schuster et al comment in
http://www.tbi.univie.ac.at/~pks/Presentation/losangeles-03.pdf (
Inverse Folding and Sequence-Structure Maps of Ribonucleic Acids
<http://www.tbi.univie.ac.at/%7Epks/Presentation/losangeles-03.pdf>)

"Simulated populations of replicating and mutating sequences under
selection exhibit many phenomena known from organismal evolution:
neutral drift, punctuated change, plasticity, environmental and genetic
canalization, and the emergence of modularity, see e.g. [13-18].
Laboratory experiments have also generated phenomena consistent with
these patterns [19-21]."

In other words, experiments recover many of the aspects of evolutionary
data.
Received on Sat Sep 24 12:39:12 2005

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