> >
> >I will challenge one thing you have said, that is your and yockey's use of
> >the probability numbers for the total number of cytochrome c's that are
> >possible. There will always be the need to exceed the data in this area,
> >but the number you use for the number of unique functional cytochrome c
> >molecules (10^93) is off by a factor of 10^90 at present. There is no
> >assurance that a substitution of aa1 in molecule "x" will allow that
> >substitution in molecule "y". Since the functional and structural
behavior
> > if cytochrome c is determined by a *combination* of amino acids, each
> >*potential* new combination would have to be tested (in a ilving system in
> >which it occurs) before it could be included in the sample. It is glib
and
> >naive to assert that any amino acid found at a specific site in the
> >cytochrome c molecule validates that amino acid for that site with all
> >other valid amino acids at other sites. This is an assumption tha Yockey
> >wrongly makes in developing his statistic.
>
> That is not what Yockey is doing. He is not using ANY amino acid at a given
> site. If he did, then the total number of functional molecules would be
> the equivalent of the total possible combinations. WHat Yockey is doing is
> substituting hydrophylic for hydrophylic and hydrophobic for hydrophobic
> etc. He also utilizes the fact that numerous other species have differences
> at a given site and their cytochromes work just fine. THis observational
> data also vastly increases the number of possible functional sequences that
> perform cytochrome c's function.
Belial to Satan: "Is it my imagination, or is there a cold draft blowing
through Hell today?"
Satan to Belial: "Kevin O'Brien and Art Chadwick actually agree on
something."
Lilith to Satan: "That explains the frost on the windows."
Yes, I must admit, horrifying though it may be, but I find I must agree with
Art on this one.
Glenn, Art's point was not that Yockey used any amino acid at a given site,
but that Yockey cannot justify his rather liberal assumption regarding the
variation he permits at most of his sites. From reading his book, it seems
to me that the only question Yockey asked was what amino acids could be
substituted at any particular site to give a functional protein. The problem
with this question is that it assumes all sites are independent from each
other, that the amino acid you put in one site has no influence over the
amino acid that can go into any other site except the two to four closest to
the first site. In other words, at say site 45, Yockey only cared about what
amino acids could go into site 45 that would be compatible with the amino
acids at sites 44 and 46; he didn't seem to care whether the amino acid at
site 45 would be compatable with the amino acid at site 16 or at site 98.
Yet that could make all the difference in the world. The choice of amino
acid to go into a particular site is determined by its immediate environment,
but this environment is not limited to the amino acids on either side of the
site. In a folded protein chain, amino acids from farther away on the chain
can in fact be part of that environment, thus helping to determine what amino
acid could go there.
The point is that Yockey cannot assume that, just because sites are more than
a few amino acids apart, they can be treated as if they would not interact
with each other. It is because ALL the amino acids in a protein chain
interact with each other to some degree either directly or indirectly that
you must test *combinations* of amino acid substitutions before you can go to
the lengths that Yockey has gone. In essense what Yockey is ignoring in his
analysis is that it is a *specific sequence* of amino acids that has
cytochrome c activity, not a mixture of amino acids.
Until Yockey's alternative sequences are tested, we cannot know the extent to
which he may be triumphantly right or horribly wrong, but at the present,
based soley on the fact that the assumptions behind his analysis violate
known laws of protein chemistry, I consider it to be flawed, useless and
misleading.
Kevin L. O'Brien