Re: Sequence Homology

R. Joel Duff (Virkotto@intrnet.net)
Mon, 15 Dec 1997 09:36:40 -0600 (CST)

>Loren and Others
>
>First, I'm not argueing with the validity of sequence inference. It has a
>place in evolutionary knowlege.
>I was wondering how sequence homology tells us anything if we do not at
>first assume a priori that natural selection has occured or if we dont
>first assume a branched evolutionary scheme. An obvious first question to
>ask is if the assumption upon which the inference is drawn is correct and
>valid. Inference of any kind can be dubious, especially in science
>because of the high stakes the public seems to put on its reliability
>(example: the gay gene.)In additon bias becomes a reality. But this is not
>my question.
>Nucleotide sequence dictates structure and by default function of the
>protein. Cytocrome c in general has the same function in the resus monkey
>and in the human. I would guess that your transporter in general has the
>same function in one species than it does in the next. What I am wondering
>is does sequence homology necessarily tell us where we came from if we do
>not first assume the brancing to occur. It seems to be a bit of a circle
>if we use the homology to prove the branching and then assume branching
>in order to give credance to the homology.
>In addition, I have heard the avid creationist make the argument that God
>can use a #10 bolt wherever one is needed in all related species. God as
>designer uses the parts he as already designed just as the Dodge engineer
>uses the same #10 bolt to hold the intripid or the neon engine to the
>motor mount.( I have recently had troubles with my neon). Although by
>definition this is out of the realm of science,It still is an interesting
>question worthy of comment by some of you prolific responders out there.
>JONT>

Jon,

Here is my short response, I'll try to put together a more explicit example
later. My first reaction is to point out the number of times that one can
reconstruct phylogentic relationships of a particular group with different
genes and get the same result. The independence of data sets supporting
the same thing is powerful evidence I think. Look at the ribosomal DNA for
example. I could list many many mutations in the 19S mitochondrial gene
that all leptosporangiate ferns have in common but are lacking from the
eusporangiate ferns (Botrychium and Ophioglossum). Yet the gene folds up
into an identical secondary structure and so presumably has the same
function in both groups. Yet even within the ferns sequence differences
clearly identify particular fern genera as being more similar to one
another. If it were just this gene that would be one thing but looking at
the 18S nuclear sequences we see the identical pattern resulting in
identical relationships yet in all the groups the functional ribosomal RNA
has the same structure. Why then do two genes show the same pattern. If
this is a matter of a 9,10,11,12 etc.. bolt being used in different
genera/families of ferns and they show a particular pattern of similarities
to one another, why should the bolts of another gene show the same pattern
of similarities to one another. I would also point out that the same
overall relationships may be obtained from protein coding genes such as
rbcL and a spacer sequence, the ITS (Internal Transcribed Spacer).

Thats a pretty fuzzy example. I will try to come up with something a little
more specific. I would be willing to wager that the YECs that use the bolt
example have not sat in front of a computer with 50 sequences and worked on
aligning them to one another. The term bolt seems so defined as if one
bolt equalled one species but the differences between one species though
they may be discreet (one mutation verses another) is not so clear. The
cutoff between sequence variation between a species, genus, and higher
order taxa is not easily made. In addition the bolt idea would NOT explain
why different genes show very differnt levels of varation. One gene may
show no difference withina genus (16S SSU rDNA in the chloroplast) while
another shows many differences between individuals in a species (ITS).
These differnce can be explained by the rates of substitution allowed by
selectional pressures. Why did God make some genes with so many
differences while others have none if in each case they are the same
functionally? Enough rambling for now. Hope that helps some.

jd

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