To which Glenn replied
>There is also the fact that in sequence space lots and lots of functions
perform the same function. There are 10^94 different sequences which
perform the cytochrome c function. (see Hubert Yockey, Information Theory
and Molecular Biology, p. 59). There are even more sequences, surrounding
these in sequence space, which will perform the function very poorly.
....
....
>So not only are their parallel ways to make the sequences, lots of
sequences will work.
But wait, there's MORE!!!!! ("Surely we are wonderfully made....")
The August 31 issue of Science News described how researchers in South
Carolina and New York made insulin act like relaxin (a hormone that relaxes
the uterus during pregnancy).
They did so by modifying ONLY four amino acids. This eliminated much of the
usual effect of insulin (but not all, raising the speculation of designing
double duty hormonal drugs.)
In summary: "Insulin and relaxin interested the group,...., because THEIR
THREE-DIMENSIONAL STRUCTURES WERE VERY SIMILAR EVEN THOUGH THEIR AMINO ACID
SEQUENCES WEREN'T. They thought it would be fun to see if they could trade
reactivities, she says. It's been more difficult, however, to make relaxin
behave like insulin...". [emphasis is mine]
So the upshot is that the focus on sequences of amino acids as uniquely
coding a unique protein missing the biological point (as Glenn pointed out).
What is biologically important about a protein is factors such as shape,
electrical charge distribution, patterns of water repulsion/attraction, etc.
Consequently, most amino acids in any protein can be replaced by other
amino acids, as long as they have similar properties in these regards.
Consequently, there are 10^94 (give or take a few quintrillion) ways of
making cytochrome c.
Focusing on amino acid sequences (as the Young Earthers do) is sort of like
considering computer software as a long sequence of instructions like "IF
xyz = abc THEN DO; a=a +1; b= c*a^2; END; " etc. Under that logic, any
computer program is a unique combination of googels of possibilities. (and
even more if one considers a program as a string of letters & numbers).
However, modern software design is more modular. We focus on steps like
"SORT fileA, MERGE fileA with fileB by field xyz", and ignore the picyune
code underlying the Sort routine, the Merge routine, etc. There is still
sequences of important & unique low level code between long sequences of
canned routines. Under this logic, a computer program is a unique
combination of only billions of possibilities, many of which have the same
functionality.
Similarly [IT IS MY UNDERSTANDING THAT], biological proteins are
modularized, i.e., made of building blocks that fold together in appropriate
ways. Typically, a protein folds together as "an helical spiral, then a
pleated sheet, then a stretch of 3-4 hydophilic amino acids, etc".
The regular sequence of amino acids that make the pleated sheet of course
must be precise, but it's sort of like an architect specifying a brick
sidewalk in a herring bone pattern. He doesn't have to make a blue print
specifying the location of every brick to the nearest quarter inch.
Other parts are little more than filler: almost any amino acid will work.
Mucking with some parts, however, will transform the entire functionality of
the hormone--as the insulin to relaxin transformation illustrates.
So which came first? Insulin or relaxin? The Chicken or the Egg?
[MY SPECULATION] Given the fact that their amino acid sequences are
dissimilar, the question is irrelevant. It would appear that that they
either arose independently (and converged to a similar shape), or they
derived from a common ancesteral protein, which was gradually transformed by
mutations into differing amino sequences while maintaining the 3-D
structure. Prehaps a biologist could enlighten me on this.
Grace & peace,
Dennis Sweitzer