Re: Orthologs was RS

From: Chris Taylor (
Date: Fri 05 May 2006 - 09:33:30 GMT

  • Next message: Keith Henson: "Re: Orthologs was RS"

    Hi Keith, all.

    The proliferation of omes is something I have to deal with every day in my work and it is a _nonsense_. Fine this guy can argue that we should all be allowed to have fun and it'll all come out in the wash, but that ignores the time and resource ploughed into making something of these spurious labels.

    This laissez-faire view also smacks of the really appalling argument deployed when people rightly moan about the proliferation of journals and the ease with which (mainstream) crap can get printed now without being properly critiqued (and
    _binned_): The argument being that you have to wait 2-5 years to see which papers are still being cited, those being the worthwhile ones. Idiocy. I concede that there isn't much we can do about it right now unfortunately (but the projects I and many others are involved with will start to redress the balance fairly soon).

    There's an interesting editorial by a JPR editor asking for informaticians trying to analyse the results of (mostly) mass spectrometric analyses of proteins to properly define and use
    'assignment' and 'identification' where the former is a statistical likelihood, the latter the result of unequivocal
    (easy Ted) corroboration. Biologists trying to build on the work don't always get the distinction you see. If we can't handle the language we already have (and we'll always struggle because natural language sucks for conveying science) why endorse the coining of even more; subdividing further, balkanising and excluding through lack of knowledge (for example, is there a difference between metabolomics and metabonomics [yes but I don't want to go into it here -- nearly all politics]).

    Incidentally, a while ago we did the etymological backtrack and got to 'chromosome' as the first use we could find of the ome affix; except of course that the affix there isn't ome it is
    _s_ome -- as in soma, because a chromo-some is a staining body
    (first seen through light microscopy). So ome is actually a completely meaningless suffix!

    Even the most clear cut ones (genomics [whatever that is defined as, which varies], proteomics, metabolomics, transcriptomics) are rather dysfunctional in that they artificially construct boundaries that are blurry at best, and which my colleagues and I then have to break down to get our jobs done efficiently. As for things like the 'unknownome', gott und himmel.

    Now despite that rant I'm split on this; as a memeticist of sorts I am delighted to see all this novelty springing from this
    (linguistic) innovation; just like bicycles or butterflies or brands -- innovate, capitalise, make variations on the basic theme to create/discover/fill as many niches as possible blah blah blah. And I do get a good laugh out of some of them. It's all fun in the end, with that hat on.

    However, I simultaneously see it as misleading nonsense that is deployed in an attempt to smear kudos on otherwise mundane work. I don't claim that the work being done is valueless, just that this stupid distraction of delineating and rebranding what is fundamentally just a region of the multidimensional bioscience continuum is confusing to some, wastes space and time and generates ridiculous turf/ownership scraps where someone will invent a new omics just because the one they would have gone for is 'controlled' by a big name they don't like, or simply didn't involve them from the start.

    This is as cringe-making as the physicists with that 'brane thing -- basically it's an attempt to be 'cool' in some weird way, to appear cutting edge and savvy. Let's leave 'cool' to the teen magazines.

    Cheers, Chris.

    Keith Henson wrote:
    > 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
    > 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:
    > 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:

    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)

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