Phonosemantics and parallels in the genome (and elsewhere)

Date: Thu Jan 18 2001 - 18:37:42 GMT

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    Subject: Phonosemantics and parallels in the genome (and elsewhere)
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    I hope anyone who'd been following what I was talking about has had time to
    digest it. I'm not a one trick pony, though. Been finding that similar
    overall structural motifs seem to pervade material reality at different
    hierarchical levels of organization.

    For instance, there are different types of language- at one extreme we have
    the isolating/analytical type (isolating meaning that words are strictly
    separated from each other/analytical meaning that each word only contains one
    "thought" unalloyed). Chinese, to a certain extent, is or was like this (with
    historical complications). At the other extreme are fusional/synthetic types
    (like many Native American languages- fusional means words come all as one
    big piece- even to the level of entire sentences as single words/synthetic
    means that each piece in this big word consists of more than one "thought".

    Parallels in genetic structure are the split genes of higher eukaryotes
    (allowing all sorts of mix'n'match, like Chinese) on the one extreme, and the
    overlapping genes of many viruses, where there is NO freedom of movement in
    the form (parallel in the word-sentences of American languages, again no

    Agglutinating languages such as Turkish, Mongolian, Korean, etc., where the
    forms are appositional strings, parallel the appositional gene sequences
    found in bacterial genomes. Functional serialization is found with both the
    language and genome organization, in that A leads to B leads to C, etc.

    Split genes need editing, but the introns so cut out may have housekeeping,
    tallying or even other functions which help compartmentalize the final
    product(s). Interestingly, Chinese and the other analytical/isolating
    languages appear to have historically embedded internal grammatical
    information. This often severely alters the surface form of the ancestrally
    reconstructed word root. My guess is that this is unconsciously snipped out
    (but used to construct the syntax and context), much as are the introns in
    the genes.

    As for the overlapping genes of viruses, one has to wonder how such overlap
    could have evolved, given the structural and functional constraints on the
    operation of the genes and their products. The same questions, of course,
    apply to synthetic, fusional languages- how can the mind "unzip" overlapping
    lexical and grammatical morphemes?

    Things don't happen unless they CAN, so obviously mechanisms must be in place
    at both levels of material reality to "shoehorn" the various parts and pieces
    into place and still allow for the orchestration of effector action on them.
    That of course leads one to suspect that the "standard parts" model is still
    valuable: Phonosemantics on the linguistic level, codon triplets and higher
    structural motifs in the genes (either for such things as hairpins in the
    nucleic acids, or helices and sheets in their products, not to mention such
    extra markings as chemical modification of both- there are grammatical
    parallels in language here as well).

    Long ago I read a paper on the chemical solubility of the side-chains of
    amino acid residues. Apparently the organization of the genetic code is far
    from random, as far as where chemical species are in the matrix, which of
    course depends on the codon sequence. But graphic representation isn't a
    fixed, forever given, and what you see on a page may NOT be the best way to
    represent a structure, though it might seem that way at first glance.

    The genetic code is usually represented graphically by a 64 "cubie" 3-D
    matrix, with each axis representing one of the four possible nucleic acid
    monomers. The convention is to lay out the order of each of these the SAME
    WAY on each axis, much as we would on any Cartesian coordinate system. What
    you get, because of the redundant coding, are full or half columns of most of
    the coded amino acids, and this of course has partial ordering re chemical
    affinity of the residue side chain (i.e. water or oil preferences). But I've
    found that by tinkering with the structure of the representation, to take
    into account the actual hydrogen bonding structure at the double-helix
    base-base interface (which side has N, O, and whether the base is single or
    double-ringed), that a motivated variation in the ordering of each cube axis
    is in order.

    And, kabam! When you do this, you end up with a graphic representation which
    not only takes into account the chemical solubilities of the amino acid side
    chains and places them SYMMETRICALLY on the cube (absent from the standard
    rep.), but also accounts for the lengths and end structure of the side chains
    as well (so ring, branch, straight segment, zero)- also laid out
    symmetrically. Wouldn't have worked, on the first try, if there wasn't a
    structural motivation for it. Even the stop, start signals end up
    symmetrically disposed (and though I haven't tried it yet, my guess is that
    even the slight variant codings found in different organisms will follow this
    principle of symmetrical organization). By the way, this might be a
    structural parallel to phonosemantics- which also deals with physical
    properties- just not literally.

    At the next lower level of reality, consider the periodic table of the
    elements- the way it is usually laid out (as if it were a city skyline). Just
    one of the myriad attempts- and the one that got adopted finally. The
    motivation was to keep the quantum number blocks together (s, p, d, f), while
    at the same time maintaining the connectivity of atomic number increase as
    best as possible. People thought the one we see is the best compromise.

    One variant that apparently missed (and lucky for me), drops all attempts to
    try to keep the quantum blocks connected, and creates a third dimension for
    the layout of each block in sequence. A physicist named Ted Turner (a
    different guy) thirty years ago calculated that the binding energy of the
    atomic nucleus wouldn't be able to hold that nucleus together after about
    element 120. And of course the synthetic efforts are stalled just shy of that
    number. Sci Fi is nice, but I doubt they'll get further.

    Interestingly, 120 is also just enough to fill out the s shell. And, bammo!
    another fascinating structural organization becomes apparent: Stopping at
    120, one finds that the s shell is 8 rows deep (2 columns= 2 electrons fill
    the shell), the p shell is 6 rows deep (6 across), the d is 4 deep (10
    across), and the f is 2 deep (14 across).

    Those of you interested in numeral series/sequences will not fail to notice
    that there is method to the madness: counting filled orbitals/electron pairs
    (and not singlets) in columns, and adding to the row depths, you always end
    up with 9. Atomic numerology! The boxes decline as 8, 6, 4, 2 in depth for
    s, p, d, f while the orbitals increase 1, 3, 5, 7.

    Most specialists dealing with quantum chemistry will probably think this is
    trivial. But once you map out the graphic representation as I described
    above, you'll see that interesting things pop out of it. You end up with a
    tetrahedron. And that gives one a new and fun way to represent the table- a
    lot more interesting and easy to remember than the one we use today.
    Secondly, and more importantly, the tetrahedron is ordered. Keeping the boxes
    aligned the same as in the current rep. the left edge is about having too
    many electrons, so the tendency is to ionize to drop them, giving one a
    positive charge on the species. The right edge is about not enough electrons,
    so you get ionization grabbing more, giving a negative charge. No big
    discovery here, but it helps make everything nice and neat.

    Ah, but the top edge is about nuclei which tend to fuse, while the bottom
    edge is for those which tend to fission (with caveats about isotopes, which
    add a fourth dimension I haven't mapped yet). There are tendencies on the
    top edge for elements involved in living processes, and at the bottom those
    inimical to them (though it may be, if you follow the clay-based life-origins
    scenarios, the opposite may have originally been true- same with energy
    sources for them).

    And of course there's the well-known semi-metal diagonal on the p box.
    Others? Who can say. All I know is that the tetrahedral representation lets
    you see all this stuff sticking out nice and symmetrically, just as the
    modified cubic representation of the genetic code does for its domain. Just
    as the geometrical models of phonosemantics do for their level of reality.

    Finally- what about that last other famous tabular set of items- the
    fundamental particles? That can be reordered as well, bringing charge (on the
    y axis of the common representation) into seqence (0/3, 1/3, 2/3, 3/3). The x
    axis (electron, muon, tauon matter) needs work, though. Nature really, really
    likes pairing at the fundamental level (even when higher combinations might
    like odd numbers- but then on the other hand there's spin, but don't get me
    started). I predict that there should be a zero-mass column of matter
    paralleling the others. We never see it, for the same reason that we almost
    never see neutrinos. The stuff would have had no tendency to clump
    gravitationally, even though three of the species in the column would have
    charge. The last member, zero charge, zero mass- would be a lost cause. Cold,
    dark matter?? Anyway, enough for now.

    Jess Tauber

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