From:    Martin Goldberg
To:      David Rice                             Nov-24-93 17:15:48
Subject: Denton's Follies, #3

 DR> On page 284 he produces a list of protein sequence differences
 DR> between a lamprey and some other species.  It reads (numbers
 DR> are percent):
 DR>
 DR>        lamprey -- carp (fish)          75
 DR>        lamprey -- frog (amphibian)     81
 DR>        lamprey -- chicken (bird)       78
 DR>        lamprey -- kangaroo (marsupial) 76
 DR>        lamprey -- human (placental)    73
 DR> I'll leave it to biologists to comment on other blunders found in
 DR> Denton.


Similarity at the DNA and preotein levels is a good indicator of biological
relatedness.  But lets look a little closer as what is being studied...

The "Wobble" hypothesis says that in each codon (triplette of DNA sequence)
that codes for an amino acid, there is a certain amount of room for
conservative replacements..that is that there are a number of different codons
for the same amino acid.  I don't have the genetic code here but I think that
"CCC" codes for glycine.  Now each codon for an amino acid always starts witht
he same letter, ie. all glycine codons start with "C".  But int he second and
third positions, there is room for replacement or wobble.  substituting some
different bases int he second and third position will also produce a glycine
in the chain.  But what if it does not?  It is well known that amino acids can
have certain semi conservative replacements and still generate active
proteins.  This is nto always true but often it is.  So, looking at a protein
chain, it is not needed to have a large amount of sequence similarity in order
for proteins to be functionally identical.  Why is this?  Because the areas
that are of greatest importance are the so called active sites of proteins.
These include the active sites that bind ligands, do enzymatic catalysis, and
the like.  Adn the normally accoutn for little of the proteins total amino
acid content.

Now don't get me wrong...the primary structure (sequence) of proteins is
important as this contributes tot he tertiary (3-D conformation) of the
protein.  We cannot simnply walk away from it, but to claim that sequence
similarity is the basis of all is not the entire answer.

In my lab, I ma involved in a project that sprang from my isolation of a gene
from a gene library of T. pallidum (syphilis) DNA.  This gene produces a
protein of a molecular weight of about 38k daltons.  About 35% of it is
similar to the MEGL-B protein of another bacterial organism.  We are on the
bverge of showing it perform the smae function....that is, the binding of
maltose.  Yet the protein in it's entirety is not that similar to that of the
E. coli version.  so much for the creationists claims that proteins have to be
similar.