[Taxacom] DNA homologies

[J. Kirk Fitzhugh]

John,

In reading your introduction, it is fascinating that in the very first 
sentence you identify the crux of the problem: 'contradictory lines of 
evidence.' Ironically then, you do not follow through with actually 
addressing that problem. This is the classic principle in non-deductive 
reasoning that has been recognized since the 19th century, what Carnap 
called the 'requirement of total evidence.' Sure, we hear this phrase used 
in phylogenetics, but almost always in the incorrect context, such that 
systematists have promoted the mistaken view that one can choose to follow 
or ignore the requirement at their leisure. As scientific endeavors are 
supposed to be grounded in thinking that is as rational as possible, the 
requirement of total evidence immediately precludes the kinds of 
phylogenetic inferences from partitioned data that are so popular. I would 
therefore suggest that much of what you wrote is unnecessary. If one of the 
most basic principles of reasoning is not being followed, then any 
subsequent arguments are just ineffective rhetoric.

I have placed some additional comments in brackets below in your original text.

Thanks,
Kirk
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Modern human biology is faced by a classic scientific dilemma - two 
seemingly contradictory lines of evidence. [therein lies the real dilemma - 
that if two or more lines of evidence lead to contradictory hypotheses, 
then that evidence needs to be taken into consideration together, rather 
than separately.] 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. [the pertinent issue is not that of 'similarity,' 
but rather the causal explanations of shared characters among members of 
two or more species.] Most primate evolutionists reject the orangutan 
theory out of hand because it is not supported by the DNA similarities 
[sic]. 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. [this is a nonsensical claim 
for comparison since it is meaningless to compare phylogenetic hypotheses 
inferred from different sets of data - the separate hypotheses are 
explanatory accounts for their respective data, thus any comparisons of 
such branching diagrams lacks any empirical merit.] 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..). [you would do best to remove all 
mention of similarity, as this is not the issue at hand. We speak of the 
same or different properties among some group of organisms, not similarity.]

The historical relationship between DNA similarity and evolutionary 
relationship involves several theoretical layers to identify homologous 
character states. [the proper term here is 'homologues'] 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 
is a straw man argument. all observation statements are hypothetical in 
form, not to mention theory laden.] 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. [overall, this paragraph is irrelevant to the 
issue at hand, which is the fact that the requirement of total evidence is 
being ignored, wherein the acceptance of any of the phylogenetic hypotheses 
based on partitioned data cannot be rationally accepted.]

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J. Kirk Fitzhugh, Ph.D.
Curator of Polychaetes
Invertebrate Zoology Section
Research & Collections Branch
Los Angeles County Museum of Natural History
900 Exposition Blvd
Los Angeles CA 90007

Phone:   213-763-3233
FAX:       213-746-2999
e-mail:   kfitzhug at nhm.org
http://www.nhm.org/research/annelida/staff.html
http://www.nhm.org/research/annelida/index.html
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