[Taxacom] DNA homologies

[John Grehan]

A while back I received some useful references to papers on DNA
alignment. I intended to summarize the points I extracted from these
papers for the list for further comment, but like so much of life, there
is never enough time at the right time. I still plan to post some points
I extracted (and I still have some reading to do), but in the meantime I
have already started to incorporate some elements into a paper which
includes some paragraphs on why there is at least valid reason to
consider the possibility that the DNA evidence may be misleading about
the human-chimpanzee relationship in the face of concerted contradiction
from macro-biology. So I have pasted below the current text (please
ignore typos) on the DNA. If anyone has any comments on the validity or
otherwise of my representation of the issue I would be most interested
as it will help me finalize my discussion of the problem - even if we
may need to agree to disagree on some aspects.

 

The current text is as follows:

 

Modern human biology is faced by a classic scientific dilemma - two
seemingly contradictory lines of evidence. Molecular biology shows more
similarity between humans and chimpanzees so this is evidence that they
are our nearest living relatives. Uniquely shared (cladistic) features
from macro-biology show humans are more similar to orangutans so this is
evidence that they our nearest living relatives. Most primate
evolutionists reject the orangutan theory out of hand because it is not
supported by the DNA similarities. Molecular geneticist Maryellen Ruvolo
(ref..) identified the DNA similarities of humans and chimpanzees as
sufficient justification for the millions of US taxpayer dollars spent
on sequencing the chimpanzee genome, and she described the orangutan
theory inconceivable "in this day and age of ample molecular evidence".

 

The orangutan relationship is inconceivable only if there is something
about DNA similarities that necessarily invalidates contradictory
macro-biological evidence. Schwartz (ref) noted that molecular
geneticists initially found that molecular relationships generally
agreed with well established morphological classifications, and they
concluded that DNA can accurately recover evolutionary relationships.
There followed a not so subtle shift to the belief that DNA similarities
are the final proof of evolutionary relationships. This widespread
position appears be derived from the principle that DNA is more similar
within species and more dissimilar between species so the differences
map evolutionary relationships. This correlation between similarity and
relationship fails to recognize that the two concepts are not
necessarily identical. In overall similarity crocodiles are
morphologically most similar to other reptiles while the distribution of
uniquely shared features suggests they are most closely related to birds
(ref..). 

 

The historical relationship between DNA similarity and evolutionary
relationship involves several theoretical layers to identify homologous
character states. Unlike morphological characters, the homologies
between DNA bases of different taxa is a theoretical model rather than
empirical observation since comparisons require matching bases between
different lengths of DNA. This match is accomplished by shuffling the
DNA to produce the best overall match by creating artificial DNA 'gaps'
(ref). Through various optimization criteria molecular biologists try to
get the best compromise between the number of substitutions and the
number of gaps even though there is no empirical equivalence between
gaps and substitutions. The result is a data set representing overall of
DNA rather than uniquely derived character states.  Other theoretical
assumptions include a continuous clock like divergence of DNA, the
retention of primitive sequences in primitive groups for cladistic
analysis despite the clock theory, and random mutations in non-coding
regions that somehow retain a non-random pattern correlated with
speciation.. There may be theoretical explanations as to why these
assumptions can be accepted, but that is the point, the explanations are
theoretical, and any theoretical model is open to question.

 

The often stated claim that DNA and other molecular studies get the same
answer is also problematic. Such studies may 'consistently' support the
chimpanzee relationship while also placing gibbons closer to humans than
orangutans. Even the often cited similarity of human and Africana ape
albumens confounds the chimpanzee theory by showing greater similarity
between humans and gorillas. According to molecular geneticist Jonathan
Marks, it is impossible to rank either genotype or morphology as
inherently superior. He argues that where molecular and morphological
data disagree, both must be re-examined carefully. In practice, this
re-examination has not occurred for the science of human evolution.
Schwartz concluded that the orangutan evidence requires a reassessment
of the theoretical frameworks that govern how and why evolutionists
select and interpret the data the way they do. The DNA similarity
between chimpanzees is often described as "genetic", and yet genetics is
more than just the location of DNA bases. All aspects of biology involve
genetics, and Schwartz suggests the role of developmental genetics must
also be addressed since DNA sequences in different parts of the genome
may be combined together in the formation of novel biological features
that would not be detectable when chopping and matching bases in their
sequential linear positions.

 

 

John Grehan

 

Dr. John R. Grehan

Director of Science and Collections

Buffalo Museum of Science1020 Humboldt Parkway

Buffalo, NY 14211-1193

email: jgrehan at sciencebuff.org

Phone: (716) 896-5200 ext 372

 

Panbiogeography

http://www.sciencebuff.org/biogeography_and_evolutionary_biology.php

Ghost moth research

http://www.sciencebuff.org/systematics_and_evolution_of_hepialdiae.php

Human evolution and the great apes

http://www.sciencebuff.org/human_origin_and_the_great_apes.php