Nature September 1 issue

J. Kirk Fitzhugh kfitzhug at NHM.ORG
Fri Sep 9 13:51:42 CDT 2005


Thanks, John. Just a couple of comments on what you say.

There is no reason to consider observations (evidence) in terms of value or
being comparative if the context in which one is dealing with those
observations is explanatory. And, morphological/molecular observations
cannot be regarded as independent research programs unless one is willing
to stipulate that the causal questions associated with each class of
observations are not of the same basic form.  If, on the other hand, our
interest as systematists is to causally account for shared similarities
distributed among members of two or more species, then the causal theory of
choice would be that of descent with modification.  The theory is being
applied to all of these observations, if one is willing to accept that the
nature of the causal questions are the same across those observations, such
that the requirement of total evidence cannot be circumvented.  This is not
an illusion of a solution - it is the only solution given the basic
principle that scientific reasoning should be rational.

To speak of observations as misleading is irrelevant to the inference of
any explanatory hypothesis that is phylogenetic.  To judge the integrity of
observations in terms of our willingness to trust our own perceptions is a
matter to be dealt with prior to explaining those observations.  This is
the criterion that needs to be applied in order to determine whether or not
descent with modification is to be applied to observations across
species.  If descent with modification is the choice, then again, separate
phylogenetic inferences will be irrational.  I would be more concerned
about someone deciding to actively exclude observations without any viable
excuse for why observations of the same properties among members of two or
more species are not to be explained by phylogeny in lieu of other
properties deserving such explanation.

I would not agree that the problem in science is the suppression of
exploration of conflict by editors.  Again, conflict is not the issue, per
the requirement of total evidence.  The problem starts with scientists who
either do not understand or are willing to ignore the requirement of total
evidence and the mechanics of causal inference that is the basis for
phylogenetics.  I do agree with you that there exists a sociological
problem relative to funding agencies and their lack of understanding of the
principles of Science.

Kirk


At 03:56 PM 9/9/2005 -0400, you wrote:
>Kirk,
>
>Thank you for attempting a philosophical solution. I would agree that
>taking the 'total evidence' into consideration is worth pursing IF all
>the evidence was of equal value and directly comparative. In the case of
>the orangutan, when one takes the total evidence into account it is a
>case where patterns of DNA sequence similarities do not match the
>preponderance of uniquely shared morphological characters. If one takes
>the view (as I would) that DNA sequence analysis and morphological
>analysis are each independent research programs, simply combining the
>data would only provide the illusion of a solution. In the case of DNA
>sequence similarities there are good reasons to understand the sequence
>similarity of humans and chimpanzees as phylogenetically misleading
>because of the inability of the current sequence methodology to weed out
>similarities through shared primitive states. Even using outgroups to
>polarize the similarities to build a tree does not solve this problem.
>
>Perhaps to oversimplify, if I were to take 'total evidence' into account
>I would say the world is flat, but I have chosen to selectively accept
>that part of the total evidence that defies common sense experience -
>that the world is round. In the orangutan case it is my opinion
>(obviously not shared by the majority) that the notion that we share
>virtually everything uniquely in common with orangutans and have hominid
>ancestors that do the same thing through a 'mistake' (homoplasy or
>whatever) is more absurd than the possibility that shared primitive
>sequences result in a closer sequence similarity with chimpanzees than
>our real closest relatives.
>
>The real problem for science is not the conflict, but the suppression of
>exploration of the conflict by editors of scientific journals. Perhaps
>it would be too embarrassing to admit that millions of $ may have been
>spent on sequencing the chimpanzee for the wrong reason, or that it
>might be less informative than a far less expensive morphological
>research program (which NSF and other would of course not fund).
>
>John Grehan
>
> > -----Original Message-----
> > From: Taxacom Discussion List [mailto:TAXACOM at LISTSERV.NHM.KU.EDU] On
> > Behalf Of J. Kirk Fitzhugh
> > Sent: Friday, September 09, 2005 2:30 PM
> > To: TAXACOM at LISTSERV.NHM.KU.EDU
> > Subject: Re: [TAXACOM] Nature September 1 issue
> >
> > At 08:34 AM 9/9/2005 -0400, John Grehan wrote:
> > >A solution to the conflicting evidence [regarding relations among
> > >orangutans, chimps, humans] has yet to be resolved. Simply ignoring
>the
> > >problem is not good science.
> >
> > John,
> >
> > The solution for conflicting evidence has been around for a long time.
> > It's
> > called the requirement of total evidence.  Carl Hempel (2001: 114,
> > Science,
> > Explanation, and Rationality) provided a particularly lucid
>description of
> > the solution you seek.  One might then conclude that rationality is
>not a
> > concern of the editors of Nature:
> >
> > 'The general consideration underlying the requirement of total
>evidence is
> > obviously this: If an investigator wishes to decide what credence to
>give
> > to an empirical hypothesis or to what extent to rely on it in planning
>his
> > actions, then rationality demands that he take into account all the
> > relevant evidence available to him; if he were to consider only part
>of
> > that evidence, he might arrive at a much more favorable, or a much
>less
> > favorable, appraisal, but it would surely not be rational for him to
>base
> > his decision on evidence he knew to be selectively biased.  In terms
>of
> > the
> > concept of degree of confirmation, the point might be stated by saying
> > that
> > the degree of confirmation assigned to a hypothesis by the principles
>of
> > inductive logic will represent the rational credibility of the
>hypothesis
> > for a given investigator only if the argument takes into account all
>the
> > relevant evidence available to the investigator' (Hempel 1962, 2001:
>114).
> >
> > Sincerely,
> >
> > Kirk Fitzhugh
> >
> > -----------------------------------------------------
> > 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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