Orthologs was RS

From: Keith Henson (hkhenson@rogers.com)
Date: Thu 04 May 2006 - 19:22:21 GMT

  • Next message: Douglas Brooker: "Re: RS"

    At 07:26 AM 5/4/2006 -0700, Richard wrote:
    >Kate wrote:

    snip

    > You can reconstruct it for yourself by
    >listening, but that isn't the same thing as replication.>>
    >
    >Sure it is. In fact, memes evolve to more stable forms precisely because of
    >people's ability to reinvent information and fill in gaps.
    >
    >Richard Brodie
    >www.memecentral.com

    Recently put up Evolutionary Psychology, Memes and the Origin of War on Kuro5hin (pronounced "corrosion") for lack a place to get it reviewed. Now it may be that not having a PhD simply makes it impossible to get a paper reviewed. Another fact is that places that will consider such a mixed list of subjects may just not be out there.

    In the process for looking for a journal that might consider future papers, I searched for "evolutionary psychology" on BioMed Central, a net repository of many journals. There were only two links.

    I also tried "meme" and got too many hits because it is used as the name for a software package. "Memes" gave 5 hits, one of them being here:

    http://genomebiology.com/2001/2/4/comment/1005

    I found it interesting, particularly this:

    "A meme is a resilient unit of cultural inheritance, a definition that includes the more conventional notions of 'concept', 'idea' or 'theory' but is much broader."

    With which I have no fault. Will quote a big chunk of it for your amusement
    (a number of line breaks added to improve readability).

    Keith Henson
    *************************

    An apology for orthologs - or brave new memes Eugene V Koonin

    snip

    So what's the issue with all these new terms (or "exapted" ones, to use a favorite term of Stephen Jay Gould's to indicate something pre-existing that has been recruited for a new function)?

    Or, for a good measure, with all the mushrooming '-omes' - transcriptome, proteome, metabolome, and even phylome, a really fresh one that has been introduced to designate the complete set of phylogenetic trees for the genes from a given genome (Sicheritz-Ponten T, Andersson SG: Nucleic Acids Res 2001, 29:545-552)? Is the world a better place because of them?

    Actually, for what it's worth, I think it is. These are not just words, after all: they are new memes for the science of a new age. The meme, of course, is itself a quintessential neologism, a brilliant (in my opinion) invention Richard Dawkins first introduced in his 1976 book The Selfish Gene. A meme is a resilient unit of cultural inheritance, a definition that includes the more conventional notions of 'concept', 'idea' or 'theory' but is much broader.

    The 'ortholog meme', for example, encapsulates a whole panoply of diverse concepts beyond the strict definition: the existence of discrete gene histories that can be traced back to the last universal common ancestor, at least in principle; a broad distribution of evolutionary rates, as a result of which some orthologs are highly conserved whereas the similarity between others is barely detectable; as a synthesis of the previous two notions, the primacy of the actual historical relationship, once revealed, over the quantitative criterion of similarity, in establishing orthology and predicting function; the possibility of one-to-many and many-to-many orthologous relationships as a result of terminal duplications; the genuine difficulties encountered by the concept of orthology because of the fluidity of protein-domain architectures, particularly in multicellular eukaryotes... and more.

    Expounding it all would require a dissertation, some parts of which would be vague or controversial - but the simple term ortholog conveys all these notions, and that is why it seems to be a (relatively) successful meme.

    Now, by talking about a 'successful' meme, we have hit on something important. Memes, like genes, evolve through an interplay of mutation and selection (as described, in fascinating detail, by Daniel Dennett in his 1995 book Darwin's Dangerous Idea: Evolution and the Meanings of Life).

    This is why it doesn't make sense to worry too much about the proliferation of terms: those that correspond to good, fit memes will survive and prosper, while the rest will die out or will lead a marginal existence. This is how new scientific paradigms are born - as collections of new memes, at first haphazard, and then, after selection does its job, coherent.

    Those old enough to remember the early, heroic days of molecular biology
    (see also Horace Judson's fascinating 1996 book The Eighth Day of Creation: Makers of the Revolution in Biology) will recall the wild bloom of various
    '-ons'.

    Some, like codon and operon, designate truly important memes and are now all over the place; others have respectable but modest lives, like replicon or regulon; yet others have been more or less marginalized, like cistron
    (which remains respectable in poly- and mono-cistronic forms); and some became extinct, for example, recon (used to mean a unit of recombination). Similar fates will, of course, befall the '-omes' that propagate in these early days of genome science.

    Personally, I have little doubt that proteome and transcriptome are here to stay; I am a little less confident about metabolome and phylome, although I quite like the latter. My main point, however, is a tribute to meme selection: the fittest will survive!

    ***********************

    =============================================================== This was distributed via the memetics list associated with the Journal of Memetics - Evolutionary Models of Information Transmission For information about the journal and the list (e.g. unsubscribing) see: http://www.cpm.mmu.ac.uk/jom-emit

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