[...deleted]
>In algorithmic information theory we would consider practically the
>same problem except that we would flip the same coin 10 times in
>row (rather than 10 coins simultaneously), recording the sequence
>of heads and tails as we go. This would be more directly
>applicable to say a protein since it is not only the number of
>occurances of the various amino acids that is important but the
>specific sequence in which they occur.
Or we could flip them all simultaneously and then write down the results
going from L to R to obtain a sequence. ;-) However, the light bulbs just
came on in my mind; the key is the distinction is in macrostates the results
are summed up into two totals where as in algorithmic information theory the
sequence is important. You're right, complexity is another whole ball game
from thermodynamics. I didn't fully appreciate that until just now. Thanks!
>For a protein we could imagine
>rolling a die with 20 faces (is this the right number of aas?)
[rest deleted...]
You are right in that there are 20 amino acids. However, each amino acid
has *2* isomers which are identical in chemical composition, but mirror
images of each other--like your left and right hands. (This is one of those
quirkly little things only a chemist would think of. :-) The punch line is
that biological proteins use only one of these isomers. If the wrong-handed
isomer gets in the chain, it usually screws up the alpha helices/beta
sheets, altering the 3-d structure and messing up its function. Obviously,
some spots are more sensitive to substitution than others, but still, too
many wrong-handed AA'a are bad news. However, the isomers are identical
except for handedness--they have the same stabilities and therefore equal
populations in the primordial organic soup. Thus, in order for a successful
protein to emerge, a string of nearly all one-handed AA's must be assembled
from an equal mixture of left handed and right handed molecules. Which,
using the coin flipping analogy, is equivalent to all heads or all tails (a
highly improbable ordered macrostate of affairs). Sorry I didn't explain
that I was talking about the left handed/right handed isomer composition and
the AA sequencing in my orginal post. By the way, the same thing holds for
a DNA/RNA sequence--each nucleotide has two mirror isomers also.
Conclusion: It seems that the abiogenesis of biomolecules is both
thermodynamically improbable AND complex. :-) I'm looking forward to this
post you keep teasing us with.
__________________________________________________________
"Looking back, there's a thread of love and grace
Connecting each line and space I've known" -David Meece
==========================================================
Eddie Gene Olmstead, Jr. Chemistry Department
Asst. Professor of Chemistry Gordon College
Email: olmstead@gordonc.edu 255 Grapevine Road
Phone: (508) 927-2300 Ext. 4393 Wenham, MA 01984