Matti Pitkänen (matpitka@pcu.helsinki.fi)
Sun, 5 Dec 1999 07:38:15 +0200
Hi All,
have been thinking about the realization of the genetic
code and slept not too much. I am in confusiastic state
of mind but cannot resist the temptation to write.
It seems that manysheeted DNA provides an elegant solution
to the mystery how genetic programs are organized.
The problem of junk DNA disappears and precise
quantitative predictions about the general structure
of genetic program hierarchy follow.
1. Also genetic programs are modular.
The first thing the programmer learns is to modularize.
Also genetic programs must have modular structure. Gene codes
protein catalyzing second gene to catylyze protein to.... to catalyze
building block protein. Gene can be characterize by
its level in subprogram hierarchy.
2. Hierarchical structure of genetic programs
and manysheeted DNA.
Manysheeted DNA allows to realize genetic subprogram hierarchy.
Subprograms correspond to p-adic spacetime sheets and subprogram
hierarchy corresponds to the hierarchy of p-adic spacetime
sheets. Number of levels in subprogram hierarchy can
be deduced from the size of organism.
Number of levels in program hierarchy is the number
of p-adic length scales between atomic length scale
and body size. The larger the organism, the larger the
number of program levels. This gives one important
testable characteristic of species and would be valuable
guide in attempts to understand how genetic code functions.
One can identify the hierarchical level of gene by looking
how many genes it activates before building block protein
is coded.
Examples:
a) Viruses should have 4 hierarchy
levels. k=139, 149,151, 157. Lipid layers,
cell membrane. Genes coding proteins coding genes coding
proteins coding building block proteins.
b) Bacteria should have 5 levels. k=139,149,151,157,163.
c) Fruit fly should have 12 levels since its size is below
L(197)= about 1.6 cm.
d) Animals with size between L(199)=about 16 cm
and L(211)=about 10 m have 15 hierarchy levels. Note the
large gap after L(199). We belong to this level.
The difference between chimpanzees and us is
presumably mostly due to the different top level
programs implying different sizes for body and brain
modules.
e) The next level corresponds to the level of dinosauri
and whales having sixteen levels. The next level is
L(223) and corresponds to size of 640 m.
Does not seem to be realizable in the near future!
3. Could genes code also topologically quantized em field
characterizing organism?
Revolutions in evolution mean generation of a new
main program level and previous main program becomes
subprogram. This means also increase of the size of the organism.
This would suggest that dinosauri where more advanced than
us! Could this be the case.
One could of course ask whether the visible size
of organism really determines the number of program
levels. Could it be that DNA programs also electromagnetic
structure around the organism. Topologically quantized
electromagnetic field, the "aura", characterizing the organism?
Whether this is the case, can be tested sooner or later
by deciphering the number of the program levels in the genome of
human!
4. Connection with proteins.
Gene coding protein catalyzing second gene to code of a
second protein coding protein catalyzing third gene to ....
are submodules. Process starts from largest spacetime sheet having
# contacts with gene and proceeds gradually to atomic
length scale. Body, organ, cell, organelle,..
Gene can be characterized by the p-adic k_G characterizing
the largest spacetime sheet to which it has # contacts.
Presumably also proteins can be classified by the
the number k_P characterizing the largest spacetime
sheet to which protein has # contacts.
Presumably the k_P <k_G if G codes P activating
in turn some lower level gene.
It seems that *DNA sequences with same chemical structure*
could correspond to different genetic programs since
also the manysheeted structure associated with DNA
affects its functioning. Same is true
for proteins. The catalytic powers of protein depend
on the distribution of its # contacts!
5. Junk DNA as unused program modules.
Large text processing programs contain large number of modules
not used by average user. In the similar manner
organisms contain some common basic repertoare of
programs at lower level. Otherwise it could occur
that existing higher level program would call nonexisting
subprogram. Genome is like collection of programs gradually
increasing when new programs constructed from basic modules
are added.
Individual of a given species does not use all its submodules.
This is probably the case for higher level modules.
Interesting question is whether junk DNA is different for the
individuals of a species.
Second interesting question is how universal the basic modules
are. I learned for a week or two ago that all animals seem
to have same basic genes. It might be that the collection of
basic programs distinguishes between animals, plants, fungi
etc.
The basic programs associated with bacteria should
be common to animals and plants: they indeed are: mitocondria
having their own bacteria like DNA! Also viruses are present
in their own manner: is their sole function to
help in finding bugs in genetic programs?
Note that something like 10 percent of DNA corresponds
to basic program modules.
6. Tests
The identification the levels of
various genes in program hierarchy would mean
a tremendous boost in the understanding
of genetic code. Also medical applications are obvious.
7. Why chromosomes?
The first thing to come into mind is that chromosomes
correspond to submodules. This cannot be the case.
Dog has 39 chromosomes and Homo Sapines has 23!
Number Nc of chromosomes measures the ability of
species to produces different variations. 2^Nc is the number
of possible combinations of chromoses in sexual breeding.
There are indeed very many different looking dogs
hanging around!
8. Genes and Memes
For years ago I proposed a model for DNA-protein as a material
realization of formal system and deduced the basic numbers
of genetic code from a model for abstraction process.
[See the chapter "Quantum model for intelligent systems"
of "TGD inspired theory of consciousness..." at
http://www.physics.helsinki.fi/~matpitka/cbook.html ]
It seems that this model might make sense! Genes are
material realizations of cognitive spacetime sheets representing
ideas, memes. This material realization of memes
is like documentation. Without documentatation
ideas come and go and are forgotten. When coded into bones
and flesh memes can survive.
The ongoing process of computerization seems to be a completely
new kind of trick for memes to document themselves and occurring
at the level of electromagnetic Mother Gaia! Perhaps
the p-adic length scale involved is comparable to Earth's
size! Could these programs running in our
machines and generating ELF frequency em fields be much more than
we believe them to be! Fascinating!
Best,
Matti Pitkanen
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