[Taxacom] DNA homologies

Thu Sep 28 15:16:13 CDT 2006

Kirk,

You have some very interesting comments and assertions which I think
illustrate why the orangutan theory can provide a very useful focus for
systematic issues - if they theory can be acknowledged to exist.

Over the years I have seen a number of assertions of what one "has to
do". I can well understand that the requirements of total evidence may
be considered by supporters as the rational thing to do and I respect
that some hold to that view. Mine is different in that respect and it
may even be a minority point of view. Combining DNA and macro-biological
characters may provide total evidence if the characters are of the same
kind. Most systematists may believe that to be the case. I am not so
sure.

Anyway, that aside, your comments are helpful and I will rephrase some
parts (not that this will necessarily result in conformity to your
perspective). I can be a bit dense at times so please explain the [sic]
after DNA similarities - what would you suggest the wording should be?

Interesting about comparison of molecular and macro-biological data
being nonsensical since that would seem to be what one is doing when
combining data. Either way, it is what the early molecular systematists
did to successfully argue that molecular characters are phylogenetically
informative and no one seemed to challenge them on that.

I would think similarity is all about the distribution of same or
different properties. At least I do not see at this time sufficient
reason not to use the term so I will stick to it for now.

Homologues - ok, I'm happy to use that term.

I'll try to rephrase on the theoretical vs empirical part to see if I
can get something more precise. As Pierre has also pointed out,
everything is theoretical. But there is a difference in methodological
operation - or at least that is what I perceive. The DNA base homologues
are derived from an algorithm (whether by hand or computer) that matches
bases together that are not matched just by putting the DNA strands
together. This process is not used in morphology - although Pierre
raises the interesting question of whether matching homologues where the
morphology is missing bits is the same thing or not. So I will try to do
justice to my intentions, although it seems like it could open Pandora's
box to an unpredictable degree.

Perhaps you are right about total evidence, but this is not what
molecular geneticists and almost all primate systematists believe. They
believe that DNA similarities (or whatever) cannot be challenged, that
they stand in their own right as the last word on evolutionary
relationships between humans and great apes.

I expect my response is going to be no more satisfactory to you than to
Pierre. This is something I will have to live with. Since I hold some
minority views on evolution it is inevitable that I am in the wrong if
popularity is the measure of scientific validity. I have already come
across the question of 'total evidence' in biogeography where I have
been criticized for taking Croizat's uncompromising (but integrated)
view. But thank you for the VERY helpful feedback. It is appreciated!

John Grehan

> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
> bounces at mailman.nhm.ku.edu] On Behalf Of J. Kirk Fitzhugh
> Sent: Thursday, September 28, 2006 2:38 PM
> To: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] DNA homologies
> 
> 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
> ---------------------------------------------------
> 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.]
> 
> -----------------------------------------------------
> 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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