[Taxacom] Predatory Open Access Publishers

John Grehan calabar.john at gmail.com
Sun Sep 16 08:59:23 CDT 2012


>From my perspective the 'problem' comes from not all characters being
created equal (otherwise the phylogenies would be self evident and there
would be no need for systematics in the first place. I admit I do not know
enough statistics to know what is really probable or not in the greater
scheme of things, but it is apparent that if there are two conflicting
phylogenies proposed from developmental [morphological] genetics and
sequence genetics respectively, then there is no recipe for a solution.

Because developmental genetics often involves only one or two characters
for a particular clade it may seem weak compared to a larger number of
sequence similarities. But that appearance is only based on relative
numbers. The other question is whether the similarities in either case
constitute shared derived conditions. Of course I am in the minority on the
answer.

That aside, it is apparent from biogeography that many molecular results
give informative answers, but even then that does not demonstrate their
necessary veracity in all respects.

John Grehan (the reactionary morphologist)

On Sat, Sep 15, 2012 at 1:06 PM, Richard Zander <Richard.Zander at mobot.org>wrote:

>
> Oooo...steamrollered. Okay, Kirk, Hempel rules in one sense, yet I think
> I am also right.
>
> What seems like equivocation is because we are talking past each other.
> In the sense of a universal logic, well sure anything at all relates in
> some way to everything else. Some few degrees of association with
> Francis Bacon, say.
>
> But modern science uses a probabilistic basis, and does not see a
> problem as a sorites that includes a huge number of variables that can
> be worked out by a Mensa type. Although Francis Bacon may have something
> to do with some systematics problem, we can discount the relevance until
> we see some indication that we need to expand the set of evidence.
>
> We agree, however, I think, in that the set of molecular evidence is way
> too small to help solve a taxonomic problem, and I suggest that
> morphological data helps do this. In Bayesian terms, total evidence is
> reflected in the fact that if morphology says ((AB)C) at 99% confidence
> and molecular evidence says ((AC)B) at 99% confidence, then the Bayes
> formula says no hypothesis has better than 50% confidence. This needs
> explanation, not rejection of the problem. Such as, one can redefine the
> problem as evolution is molecular trait changes, period. This is as bad
> as defining evolution as morphological trait changes, period.
>
>
>
> ____________________________
> Richard H. Zander
> Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299 USA Web
> sites: http://www.mobot.org/plantscience/resbot/ and
> http://www.mobot.org/plantscience/bfna/bfnamenu.htm
> Modern Evolutionary Systematics Web site:
> http://www.mobot.org/plantscience/resbot/21EvSy.htm
> UPS and FedExpr -  MBG, 4344 Shaw Blvd, St. Louis 63110 USA
>
> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu
> [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Kirk Fitzhugh
> Sent: Friday, September 14, 2012 7:26 PM
> To: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] Predatory Open Access Publishers
>
> Only because I prefer following principles that are developed well
> beyond the limits of systematics thinking, such as evidential relevance
> and the total evidence requirement:
>
> "It might seem that... the observation that any particular scientific
> investigation is aimed at solving a specified problem, and that the
> initial selection of data should therefore be limited to facts that are
> relevant to the problem. But this will not do, for the statement of a
> problem does not generally determine what kinds of data are relevant to
> its solution.... The notion of 'relevant' facts acquires a clear meaning
> only when some specific answer to the problem has been suggested,
> however tentatively, in the form of a hypothesis: an observed fact will
> then be favorably or unfavorably relevant to the hypothesis according as
> its occurrence is by implication affirmed or denied by the
> hypothesis.... Generally, then, those data are relevant and need to be
> gathered which can support or disconfirm the contemplated hypothesis and
> which thus provide a basis for testing it." C.G. Hempel, 1966, 'Recent
> problems of induction.'
>
> In the scope of systematics inference, which is abductive, evidential
> relevance is determined by whether or not effects in need of explanation
> need to be accounted for by the same theory or set of theories. If the
> same theory(ies) apply, then explaining each of the effects is relevant
> to each other, for otherwise the opportunity for rationally determining
> (abductive) support would be compromised. For instance, we don't take
> each individual shared character and explain its occurrence to the
> exclusion of all other shared characters. We know that at least some of
> those other characters need to be explained in the same causal context
> (e.g. 'speciation' or population splitting events), such that inferring
> an explanation for one character will be relevant to the others. And
> since shared characters form part of the premises of the inference, they
> are part of the evidential support for the concluded hypothesis. Hence
> the reason the requirement of total evidence matters, and why
> partitioned analyses are irrational, and why cladograms derived from
> partitioned analyses can't be compared.
>
> Kirk
>
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