Received: by alpheratz.cpm.aca.mmu.ac.uk id SAA06644 (8.6.9/5.3[ref pg@gmsl.co.uk] for cpm.aca.mmu.ac.uk from fmb-majordomo@mmu.ac.uk); Fri, 19 Jan 2001 18:16:35 GMT From: <Zylogy@aol.com> Message-ID: <c6.102a96b8.2799ddcd@aol.com> Date: Fri, 19 Jan 2001 13:13:33 EST Subject: Re: Phonosemantics and parallels in the genome (and elsewhere) To: memetics@mmu.ac.uk CC: Zylogy@aol.com Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Mailer: AOL 5.0 for Windows sub 129 Sender: fmb-majordomo@mmu.ac.uk Precedence: bulk Reply-To: memetics@mmu.ac.uk
In response to Chris- You got me- I dunno. To borrow terminology from a
moribund ideology- perhap there has always been a "dialectic", and a swing
back and forth. Yin and Yang. Light and Dark. Order and Disorder. Yes and No.
Am I? versus I Am!
Perhaps such a tension is what allows meaningful existance in the first
place. Eternal role playing.
To Derek- I'm fascinated to learn that someone else is interested in this
stuff (been out of the loop for more than 20 years- though I did try to make
a foray while at UCBerkeley about 13 years ago- was rebuffed out of hand by
someone I respected in the genetic code business). Will try to find the
articles.
As for the unclear bits, after figuring out that the periodic table needed
work (oh, about 22 years ago, when I still had dreams of being a protein
chemist), I started playing with other tabularizations- such as the genetic
code and the subatomic particles, to see if anything new could be adduced
from variations in the depictions.
For the genetic code representation, I started looking at the shapes and the
chemical properties of the the amino acid side chains- there did seem to be a
vague correlation with shape, size of the chains as there was with the
solubilites, but the skew was in a different direction. The distribution of
the amino acids in the usual cube re solubility is exceedingly lopsided,
especially in regard to those a.a.'s that have full 4-member columns versus
those that have only 2 (not to mention the 3's and 1's).
So I started to tinker with the ordering- trying to keep the columns parallel
seemed to be one of the mental blocks that automatically popped up. A conceit
from our culture, perhaps. At the same time I'd been interested in trying to
find out if there was a shape/charge code for the immune system (something
that had been bandied about at Berkeley when I was there), so I figured to
look at the DNA itself. The "gas code" as I call it is imperfectly
instantiated, but goes like this: you've got two basic kinds of bases- the
one and two ring (leaving the chemical names out- I don't really care to slap
jargon about). The hydrogen bond between bases from the opposite sides of the
double helix depends on N or O atoms (with intervening hydrogen- thus the
"gas code").
Ideally, what you get is this: in all base pairings, you have one singlet
ring always apposed to a doublet ring. Then, on top of that (if I remember
correctly- my notes have long been buried) you have, for one pair, O and N in
one order, and in the other pair, in a different order (I believe that they
were O,O versus N,N on one and something like N,O versus O,N on the other
pair- can't remember). Anyway, from this "gas code" I started looking for
the "best" graphical representation which captured the order of bases on the
axes of the cube which took it into account.
Not very long after that I got the new cube, which just sort of fell out of
the "gas code" [note here that I said the code was idealized- in DNA one of
the bases is lacking a hydrogen bond where I say it "should" have one for
symmetry's sake- remember this is all theoretical anyway]. The resulting
structure takes the cube and slices it in a way odd to the eyes of folks
brought up on normal cartesian coordinates. Think of a camera tripod. Now
imagine that the apex of that tripod represents one corner of the genetic
code cube, and contains half the cubies, and each leg, starting from the
apex, is 4 cubies long, and 2 by 2 thick. Whats left is another tripod of
exactly the same dimensions, accounting for all the other cubies. The two
apexes are exactly opposite on the cube through its center.
When you do this, each of the three axes of the cube now encode size, shape,
and solubility respectively of the amino acid side chains instead of a random
ordering of bases in the codon. In addition, plus and minus charged species
also end up symmetrically opposed in the cube. Go figure.
A cube so ordered, of course, raises all sorts of questions. What is the
reality, for instance, of the "gas code", and what does it mean? And if such
axial resolution of distinctive "physicochemical" features is real, does it
imply that the code is in some way the natural outcome of selectional forces
that may have occurred on the early earth, perhaps further implying that very
similar codes might be the end product on other worlds (we can eat the
martians!). Recent reports claim that life might have started almost
immediately after the earth was encrusted. Of course fully fledged life might
have just settled in from outside. But I'm getting far off topic.
I like my little reworkings of the standard issue graphical representations.
They seem to be much better distillations of known facts, and push polar
oppositions implicit in the relationships of elements of the matrices
squarely in the face of the observer, something missing from the originals,
constructed with different biases in mind. As for the phonosemantics, and the
diagrammatical iconicity, that's purely my own baby- no one else had gotten
that far with it. I hope to make a decent living off of it.
Jess Tauber
zylogy@aol.com
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