[...]
>BH:==
>> My suspicion is that what you are giving is a physical reason
>> why reversibility would not occur even if it were "possible"
>> according to info-theory.
>
Greg:==
>I think the disagreement we are having is about what the reverse
>transcription is. There is no doubt that the proteing information
>can't be 'put back into' the DNA, because information is lost in
>the decoding. This is uncontroversial, but I do *not* think that
>this means that reverse transcription is *impossible*. (Or even
>that it doesn't happen.) What the information loss tells us is that
>as a matter of fact reverse transcription isn't at all frequent (and
>we can use DNA information to say how infrequent it is). Sadly for
>Lamarck, this turns out to be really, really infrequent. :-) So
>to go back to the dice example, of course the ordered pairs can't be
>reconstructed from the sums, but this is where DNA->protein is different:
>we have a sequence of DNA codons and the proteins they code for. We
>don't have a random process generating DNA codons. If it turned out that
>only 20 or so codons were found in DNA, then even though the alphabet were
>64 letters, we would suspect that reverse transcription were going on.
>Similarly, if we observed that in a list of dice values, only 11 pairs
>occurred, we might expect that reverse translation was going on. That
>is, even though other letters of the alphabet *are* represented in the
>code, some rule in the reverse transcription eliminates them, thus
>driving down the information content of the original code string (once
>it has been decoded and reverse recoded). So the higher information
>content of DNA is proof that reverse transcription doesn't happen (much),
>not proof that there is no possible way to take proteins and reconstruct
>an adequate DNA code for them (which is all that reverse transcription
>demands).
>
>So in some sense, the inability to reconstruct the exact DNA coding
>sequence is irrelevant. If you are a protein what wants to get reverse
>encoded, you don't give a rip if you produce one of the umpteen possible
>DNA codes which would produce you. All you care is that you produce an
>*acceptable* code. (Actually, this brings up an objection to the above:
>if reverse transcription is accompanied by a random process which selects
>codons within the space of possible sequences to code for a protein, then
>all the information in the original DNA sequence can appear in the
>reverse translated one.)
>
Before I forget, your protein that doesn't give a rip reminded me
of Dawkin's selfish gene concept. Would this be a selfish protein?
But this process if it were to occur would seem highly destructive.
Perhaps I'm goofing things up, but I had an intuitive feeling that
the extra storage capacity of DNA might be a mandatory requirement
for evolution to occur.
Now onward. From the above and the subsequent interplay between
yourself, Gene and others I realize that things may be getting beyond
the point where I can make any meaningful comments [this is not
to say I don't often blunder on in such situations anyway :)]
due to my lack of knowledge in molecular biology. In fact, I'm
tempted not to say anything for fear of interfering with the
interesting discussion going on now. Alas, I can't seem to
help myself :-).
I think I'm finally understanding some of the points you've been
trying to make and I think possibly some of our disagreements
are only apparent and stem from some erroneous wording on
my part. So, let me try to re-word some things.
Would it ever be correct to say that information theory prevents
something from happenning? No, information theory is not a
physical entity that it could get down and mingle with molecules
and somehow influence their behavior. [as an experimentalist,
I am under a contractual agreement to say something like this
in any situation where theory encounters the real world ;-) ].
Hopefully, all us realists agree here and apologies to any
mathematicians whom I have offended.
Here I think we come back to a fundamental point, before
we start talking about Shannon entropy of DNA sequences
then we better be darn sure that the genetic information
system satisfies the axioms of information theory. These
axioms are not written on tablets of stone. There may be
systems which convey information in some sense of the
word but don't satisfy these axioms. But, once one is satisfied
that the axioms are satisfied, then all the results of information
theory follow perforce as a result of logic. So, I think what
Yockey was saying is that the central dogma is not something
peculiar to biology. It follows purely from logic (provided the
axioms are satisfied) that it is impossible to transfer information
from lower to higher entropy. Suppose we found a situation
where this happens anyway. This would not imply that the
impossible has occurred or that some mysterious or supernatural
were occurring. What it would imply to me is that one had made
a fundamental mistake and that one or more of the axioms
of information theory doesn't apply. But if one concluded this
then one would have to go full course with it. All talk about
Shannon entropies of DNA in terms of information capacity
become nonsense.
Now I want to return to your comments above. Other than the
parenthetical comment I don't think there is any violation of
information theory principles. Information is not really being passed
to the source, instead, the information capacity of the source is being
degraded until eventually its capacity is the same as that of the
receiver. The parenthitical comment does however seem to go
against the principles of info-theory as the DNA would be receiving
more information than was sent. If I understood Gene correctly,
he was giving some physical reasons for why this doesn't happen.
This reminded me of something Yockey said in the quote I gave
earlier:
===================================
"The irreversibility of the genetic logic operation is
unavoidable for two reasons. First, it is a consequence
of thermodynamic irreversibility that occurs when the
transition function does not have a single value. To allow
reversible operation in the several-to-one mapping case
the computer must record this information in its memory.
The genetic logic system has no such memory." -- Yockey
=====================================
So, what I'm wondering here is whether we should consider
the various things Gene has been saying as the physical
justification for Yockey's statement "The genetic logic system
has no such memory" or am I just clueless (I can't get over
the hurdle of imagining how to receive more information
than was sent, unless there is some memory effect or
information is picked up in transit some how, but if the
latter then where is it stored?)
[...]
Brian Harper
Associate Professor
Applied Mechanics
Ohio State University