[Taxacom] DNA homologies

[Steve Manning]

>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".
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>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..).
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>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.

For what it is worth, I suggest you make clear what you mean by 
"theoretical" throughout the previous paragraph.  That term has enough 
different definitions and interpretations that it can be ambiguous even to 
scientists.  Of course any 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

I think it would be interesting to attempt to learn of paleoclimates in 
which chimpanzees, humans, and orangutans evolved, based on 
paleobiogeography; note differences, and see if any of them correlate with 
morphological or molecular differences, possibly resulting in stronger 
selection for some of those features in one group than another.  For 
example, did the probable available diet of chimps or orangutans differ 
enough that certain oral features became more important for survival in one 
than the other?  Similar analyses could be made concerning the well-known 
other evolutionary processes (genetic drift - were the probable population 
sizes of one group significantly larger than the others?; inbreeding - what 
environments tend to favor this?; evidence of competitors for ecological 
niches that would probably strongly select for certain features) in one or 
the other of humans, chimps, and orangutans (and other groups for that 
matter) with regard to individual features.  I think the unspoken 
assumption, justified or not, usually is that macromorphological features 
are more strongly selected than molecular features -  tending to lower the 
probative value of morphological features compared to DNA evidence when 
they conflict. I think until proteomics is further developed that 
assumption is hard to test. (?)

>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.

Basically true - I think attempting to quantify the probabilities of 
certain events
could help, even if only to force people to examine their assumptions.


>
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>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
>
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>
>
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Dr. Steve Manning
Arkansas State University--Beebe
Mathematics and Science
Professor of Biology
P.O. Box 1000
Beebe, AR  72012
Phone: 501-882-8203
Fax: 501-882-4437