Re: How are genes counted in Human Genome Project?
- From: "John Edser" <edser@xxxxxxxxxxxxxx>
- Date: Sat, 14 Oct 2006 13:41:50 -0400 (EDT)
"IRR" iotarhorho@xxxxxxxxxxxxxxxxx wrote:-
JE:-SYNTHETIC
To be CORRECT any segment that is deemed "one gene" has to code for one
polypeptide and NOT one protein. Almost all proteins are complex
combinations of MORE than just one polypeptide which means that at the
very
least MORE than one gene is almost always required to code for ONE
protein.
In biological terms, the enormous difference between a polypeptide and a
protein (which remains glossed over within gene centric theory only
because
it is inconvenient) places genetic epistasis at the forefront of
genetics and not on just the backburner where it has been languishingever
since Fisher et al.
This is in part correct, but is also part incorrect or else easily
misinterpreted:
-A single gene most certainly can encode a single protein, which may or
may
not be a subunit in a protein complex.
JE:-
Polypeptides and proteins only differ in SIZE, i.e. they differ in degree
and not in kind. IOW, they remain CHEMICALLY the same TYPE. Therefore, all
proteins must consist of at least one polypeptide (no exceptions).
Empirically, the vast majority of proteins "in vivo" consist of MORE than
just the one polypeptide (of course this does not apply to "in vitro"
proteins which however only represent biochemical SIMPLIFIED MODELS of
proteins. Indeed, I do not know of a single "in vivo" protein which
consists of just one polypeptide. Perhaps you could enlighten us and provide
an example?
This is what I am saying: IF a DNA/RNA sequence codes for AT LEAST ONE
polypeptide THEN that sequence can be counted as "one gene" within the rules
of gene centric SYNTHETIC genetics. IOW, No matter how large or how
essential a chunk of DNA/RNA happens to be for life to continue, if it DOES
NOT code for at least ONE POLYPEPTIDE then it is NOT defined to be a gene so
it cannot be counted. Quite obviously, I do NOT agree that this is rational.
IOW I disagree with the current SYNTHETIC definition of what can be validly
counted as "one gene".
It is still correct to refer to
individual subunits as proteins, at least in the vernacular of biochemists
I've interacted with.
JE:-
It depends on their length which only an arbitrary measure. In general a
single coding gene only codes for a limited in length peptide and normally
one body protein is a combination of more one of these polypeptides.
-All proteins are polypeptides, but of course many polypeptides are not
proteins (e.g. gramicidin).
JE:-
OK
http://en.wikipedia.org/wiki/Gramicidin
"Gramicidin is a heterogeneous mixture of six antibiotic compounds divided
into three categories: Gramicidin A, Gramicidin B and C, all of which are
obtained from the soil bacterial species Bacillus brevis and called
collectively Gramicidin D. Gramicidin D are linear pentadecapeptides, that
is, they are long protein chains made up of 15 amino acids. This is in
contrast to Gramicidin S which is a cyclic peptide chain."
A chain or a circle of just "15 amino acids" constitutes a polypeptide and
not a protein because it is so small.
However I don't know of any gene whose
product
is a polypeptide but not a protein (but would be quite interested if
anyone
knows an example!)
JE:-
Almost every "in vivo" protein is constructed from more than just one tiny
polypeptide chain. IOW, almost every _natural occurring protein_ is
_necessarily_ coded for by MORE than what is defined within gene centric
SYNTHETIC genetics to be MINIMALLY "one gene".
THEREFORE 1: using gene centric synthetic genetics own assumptions (NOT my
assumptions) almost all body proteins are epistatically coded.
THEREFORE 2: almost all body genes must have an epistatic fitness even if
you just ignore the salient fact that Jim mentioned: all "in vivo" proteins
interact, i.e. more exactly, remain fitness dependent on other proteins
within the same body.
YET: (amazingly) epistatic gene fitnesses are deleted from gene centric
models where these models are routinely applied _uncorrected_ to nature as
valid theories of nature in-their-own-right, e.g. Hamilton's Rule.
snip<
Regards,
John Edser
Independent Researcher
edser@xxxxxxxxxxxxxx
.
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