Re: Human/chimp similarity measures

Cliff Lundberg (cliff@noe.com)
Wed, 06 Oct 1999 10:34:33 -0700

Huxter4441@aol.com wrote:

> The first three techniques are based upon small-scale
> sampling, which Stephen cites as a difficulty. DNA
> hybridization, though, is based upon large-scale sampling,
> involving much longer stretches of DNA than are referenced by
> any of the other techniques. DNA hybridization provides a
> comparison without reference to whether the sequence being
> analyzed is composed of coding regions, non-coding regions,
> or a mixture of the two.

Can someone provide more detail on how this works? It seems to me that
if one doesn't use *all* the DNA in the nuclei, that comparisons will be
inevitably skewed by the sampling of different regions. And the measurement
of heat required seems too crude a technique to resolve the matters in
question.

>A basic description of DNA hybridization can be found at
><http://www.science.lander.edu/rsfox/111syst.html>.
I excerpt from this reference:
>DNA from two organisms of interest is removed and heated to cause the 2
strands to
>separate into complementary strands. The single stranded DNA from the two
species is
>mixed and allowed to cool so that double stranded DNA will reform. The new
double strands
>are hybrids. That is they are composed of one strand from each species. How
tightly the two
>strands bond to each other is a measure of how similar their nucleotide
sequences are. if
>they are perfect complements, with no different nucleotides, they will bond
perfectly at all
>base pairs for the entire length. if they differ they will not find partners
for all their bases. The
>more different they are, the poorer the match and the looser the bonding. The
hybrid
>molecules can be heated to cause them to separate again. The amount of heat
needed to
>separate them is proportional to the tightness of the bonding between them. If
the
>nucleotide sequences are identical then more heat will be required. The more
different they
>are, the less the heat that will be needed.

> Of course, skeptics can point to the position of Dr. Marks on
> the original DNA hybridization work. See
> <http://socrates.berkeley.edu/~jonmarks/biblio.html>.

Again, excerpting from the citation:
>Informally, the work has largely been exorcised from the primary literature,
and there are
>hardly any people even using the technique any more, since it appears capable
of solving
>phylogenetic questions only when considerable liberties are taken with the
data analysis.
>(With such liberties in data analysis, after all, any technique will work!)
Powell himself
>quietly abandoned it a few years ago.

--
Cliff Lundberg  ~  San Francisco  ~  cliff@noe.com