[Taxacom] Predatory Open Access Publishers

Richard Zander Richard.Zander at mobot.org
Sun Sep 16 13:45:21 CDT 2012


Oh, I was testing for knowledge of popular culture. Everybody is
supposed to be a few degrees of association from Kevin Bacon. Apparently
you are a scholar, Kirk, and ignore popular culture. Probably you also
read books instead of watching the latest videos or 400 TV channels!

Taxacom: Regarding Kirk's comments on total evidence, I have this awful
feeling that Kirk is right, but I don't understand him. 

I agree (with that which Kirk is probably saying or would have said were
he to couch it in short English words rather than in Hempelish, and
maybe give some examples) that a nested diagram does not explain, for
instance, serial macroevolutionary transformations of taxa. 

Phylogenetics cannot estimate monophyly because a surviving taxon in
morphological evolutionary stasis (strong stabilizing selection) may
have generated many daughter species, genera or even families. Monophyly
starts where the progenitor taxon starts, and that can be sometimes
estimated by non-phylogenetically informative inferences but certainly
not by a cladogram. 

Phylogenetics cannot estimate monophyly. Did I say that? I'll make a
macro for it.


____________________________
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: Kirk Fitzhugh [mailto:kfitzhugh at nhm.org] 
Sent: Sunday, September 16, 2012 1:11 PM
To: Richard Zander; taxacom at mailman.nhm.ku.edu
Subject: RE: [Taxacom] Predatory Open Access Publishers

Francis Bacon? What in the world does Bacon have to do with any of this?
As for probabilism, lets remember that we're all involved with
non-deductive reasoning, so by implication our hypotheses are not
certain. Once again, identifying that we're doing what is routinely done
in all sciences - seeking causal understanding - then our discussions
are simply bouncing around in abductive space.

Your last paragraph refers to solving a 'taxonomic problem.' What is
that problem other than to provide causal accountings for observations?
Bayes won't help you here, except in speaking of our background
knowledge we include in our abductive inferences. It's all really
simple: If one class of effects in need of explanation have positive or
negative support consequences on the explanation of another class of
effects, then there is a relevance relation. Where this is most apparent
is when we attempt to explain both sets of effects by way of the same
sorts of causal conditions, as in those causal conditions (profoundly
vague as they are) implied by those branching diagrams called
cladograms. As I have said before, there is no epistemic basis for
comparing cladograms explaining different sets of observations.

Kirk

________________________________________
From: taxacom-bounces at mailman.nhm.ku.edu
[taxacom-bounces at mailman.nhm.ku.edu] on behalf of Richard Zander
[Richard.Zander at mobot.org]
Sent: Saturday, September 15, 2012 10:06 AM
To: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] Predatory Open Access Publishers

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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