[Paleopsych] FW: RE: [pcp-discuss:] The likely Meta-System Transition in molecular evolution

Sat Nov 27 18:48:50 UTC 2004

>From: "Shann Turnbull" <sturnbull at mba1963.hbs.edu>
>Reply-To: pcp-discuss at lanl.gov
>To: <pcp-discuss at lanl.gov>
>CC: <vturchin at bellatlantic.net>
>Subject: RE: [pcp-discuss:] The likely Meta-System Transition in molecular 
>evolution
>Date: Sat, 27 Nov 2004 17:45:44 +1100
>
>I also found the Mattick article exciting, but not being a biologist is was
>not because that it challenged our thinking about the role of DNA but
>because it indicated how the strategies found in nature for building 
>complex
>self-reproducing organisations might provide guidance on how to design
>complex social organisations and perhaps even a "global brain".
>
>It showed the need for an interdisciplinary approach to progress insights
>into all the disciplines involved.
>
>Regards
>
>Shann
>
>Shann Turnbull PhD http://www.aprim.net/associates/turnbull.htm
>Principal, International Institute for Self-governance
>PO Box 266 Woollahra, Sydney, Australia 1350
>Ph+612 9328 7466 Mobile 0418 222 378, Papers at:
>http://ssrn.com/author=26239
>
>
>-----Original Message-----
>From: owner-pcp-discuss at maillist.lanl.gov
>[mailto:owner-pcp-discuss at maillist.lanl.gov] On Behalf Of Cliff Joslyn
>Sent: Saturday, 27 November 2004 4:28 PM
>To: pcp-discuss at lanl.gov
>Cc: vturchin at bellatlantic.net
>Subject: [pcp-discuss:] The likely Meta-System Transition in molecular
>evolution
>
>I would like to draw everyone's attention to:
>
>Mattick, John: (2004) ``The Hidden Genetic Program of Complex
>Organisms'', Scientific American, v. 291:4, pp. 60-67
>
>See also his technical papers:
>
>"The evolution of controlled multitasked gene networks: The role of
>introns and other noncoding RNAs in the development of complex
>organisms", Mattick, JS; Gagen, MJ Source: Molecular Biology and
>Evolution; September, 2001; v.18, no.9, p.1611-1630
>
>"Challenging the dogma: The hidden layer of non-protein-coding RNAs in
>complex organisms."  Mattick, JS Source: BioEssays; October 2003;
>v.25, no.10, p.930-939
>
>"RNA regulation: a new genetics?"  Mattick, JS Source: NATURE REVIEWS
>GENETICS; APR 2004; v.5, no.4, p.316-323
>
>I saw Mattick give a technical plenary at the 2003 Intelligence
>Systems for Molecular Biology (ISMB 03, one of the two premier
>bioinformatics conferences), and was really blown away. The Scientific
>American article is a superb semi-technical distillation of his
>work. He has a revolutionary, but simple and elegant, thesis, highly
>coherent with the principles of evolutionary cybernetics, and most
>importantly, highly likely to be TRUE, about molecular evolution. It
>puts so much of what I know about biological systems in context, while
>answering many current mysteries, and really opens up the kind of
>explanatory paradigm we've been lacking for so long, but is so
>obviously suggested by a cybernetic perspective.
>
>In brief, consider these facts:
>
>*) Most genomes are characterized by a VERY high degree (> 98%) of
>genomic sequence which are not genes, that is, does not code for
>protein. This includes introns and so-called "intergenic space".
>
>*) However, recent evidence indicates that much of this genome is
>actually expressed as RNA, and moreover, good chunks of it are
>identical among evolutionarily distinct orgnanisms. This is a property
>called "conservation", which indicates that it's functionally
>significant for survival. And moreover, portions of non-coding DNA are
>MORE highly conserved than proteins.
>
>*) This is NOT true in prokaryotes (bacteria lacking nuclei), but is
>in eukaryotes. Prokaryotes were the only life on earth for 2.5 B
>years. But a few hundred million years after the emergence of
>eukaryotes also saw the origin of metazoans (multi-cellular
>organisms), all of which are eukaryotes.
>
>*) Nonetheless, prokaryotes have on the same order of magnitude of
>number of genes as eukaryotes. The riddle that organismal size and
>complexity (however measured, a different discussion) does not
>correlate to the number of genes present is well noted, especially in
>the wake of the genomic revolution.
>
>*) BUT, total genome size, and in particular the RATIO of non-coding
>to coding genome DOES more or less correlate with complexity.
>
>*) Finally, we note that the standard hypothesis for explaining
>regulatory organization of sufficient complexity to generate metazoans
>is that it is somehow embedded in the combinatorics of protein
>interaction, that is, proteins acting on each other to form regulatory
>networks. This is despite the fact that to a first approximation,
>regulatory complexity must grow non-linearally with the number of
>"components" controlled, on the order of the quadratic (to handle
>pairs of proteins). And indeed, in PROKARYOTES the number of genes
>increases with the square of organism size, up to a limit where the
>number of regulatory genes is predicted to exceed the number of
>functional genes, and the plateaus.
>
>The conclusion is inescapable: there was a major evolutionary step at
>2.5 B years where an RNA-mediated network for the regulation of
>protein function, encoded in "non-coding" DNA (introns and
>intergenic space), arose, which resulted in the possibility of complex
>organisms, including eukaryotes and especially the morphological
>development of, and cell differentiation within, metazoans. Mattick
>uses the metaphor of genes as simply the "parts list" (a description
>of the individual TYPES of "lego blocks"), and the rest as the
>instructions for putting them together (how many blocks of which type
>to use where and when in morphological development).
>
>The argument is so strong and so reasonable, and simply MUST be
>accepted prima facie: "The implications of this rule are
>staggering. We may have totally misunderstood the nature of the
>genomic programming and the basis of variations in traits among
>individuals and species." (Mattick, the Sci Am paper).
>
>There's much more to this argument, including some fascinating
>observations about further GENETIC specialty of primates, and even
>humans. And while I've seen one of Mattick's technical talks, and read
>the Sci Am piece, I have not studied his papers. Nor am I anything
>like an expert in this area. My good colleagues here at LANL who are
>molecular biologists say "yes, he's made a splash, but let's go slow".
>And of course revolutionary ideas require the strongest evidence, and
>Mattick is suggesting nothing other than a major revision to, if not
>an obliteration of, the Central Dogma:
>
>"We may be witnessing such a turning point in our understanding of
>genetic information. The central dogma of molecular biology for the
>past half a century and more has stated that genetic information
>encoded in DNA is transcribed as intermediary molecules of RNA, which
>are in turn translated into the amino acid sequences that make up
>proteins. The prevailing assumption, embodied in the credo 'one gene,
>one protein', has been that genes are generally synonymous with
>proteins. A corollary has been that proteins, in addition to their
>structural and enzymatic roles in cells, must be the primary agents
>for regulating the expression, or activation, of genes."  (Mattick,
>the Sci Am paper).
>
>But fortunately, I'm not a biologist, and so I can without hesitancy
>say the following to this group of people interested in (and some
>dedicated to) Turchin's Meta-System Transition (MST) theory.
>
>Turchin's original evolutionary system begins with multi-cellular
>organisms, and we have speculated for some time about extending the
>ideas to earlier evolutionary times. The route is now open with the
>origin of the control of genetic expression. In the MST schema, this
>is "X is the control of genetic expression", and I don't really know
>what X is, something like "protein mechanisms" or "protein
>interaction". But the other hallmarks of am MST are there, in the
>possible divergence and specialization of the components being
>controlled.
>-----
>O---------------------------------------------------------------------------
> >
>| Cliff Joslyn, Research Team Leader (Cybernetician at Large)
>| Knowledge Systems & Computational Biology; Computer & Computational
>Science
>| Los Alamos National Laboratory, Mail Stop B265, Los Alamos NM 87545 USA
>| joslyn at lanl.gov     http://www.c3.lanl.gov/~joslyn     (505) 667-9096
>V All the world is biscuit-shaped. . .
>
>========================================
>Posting to pcp-discuss at lanl.gov from Cliff Joslyn <joslyn at lanl.gov>
>
>
>========================================
>Posting to pcp-discuss at lanl.gov from "Shann Turnbull" 
><sturnbull at mba1963.hbs.edu>