[Taxacom] Predatory Open Access Publishers

Kirk Fitzhugh kfitzhugh at nhm.org
Fri Sep 14 19:26:17 CDT 2012

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.


On 9/14/2012 2:49 PM, Richard Zander wrote:
> I see "total evidence" as the need to explain all relevant facts, facts
> being well-documented observations.
> This means first you get rid of facts that are not relevant. In
> evolution this means descent with modification of the particular taxon
> you are studying. Then you explain all relevant evidence in some
> inclusive theory, OR explain in some reasonable way why you can't. For
> instance, suppose you get observations of some process that are one
> "red" observation and 20 "green" observations. You can't just throw out
> the "red." You can't just throw out the "red" because it is rare or
> inconvenient. If "red" was generated by a different aspect of the
> process you are analyzing, then this is an explanation.
> If morphological analysis says "red" and molecular analysis says "green"
> with a ton of more data then you have to explain why morphological
> analysis says "red." "Red" is a fact and a probability distribution does
> not explain 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: taxacom-bounces at mailman.nhm.ku.edu
> [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of John Grehan
> Sent: Thursday, September 13, 2012 5:45 PM
> To: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] Predatory Open Access Publishers
> Of course, in the general sense that one should consider all evidence
> before making one's choices about what evidence to use.
> John Grehan
> On Thu, Sep 13, 2012 at 6:13 PM, Kirk Fitzhugh <kfitzhugh at nhm.org>
> wrote:
>> John,
>> I am referring to the requirement as recognized in all fields of
>> science. I'm sure you've read the basic literature on the subject that
>> exists beyond the vacuum of systematics. If not, may I direct you to
>> these two papers as primers:
>> Fitzhugh, K. 2006. The 'requirement of total evidence' and its role in
>> phylogenetic systematics. Biology & Philosophy 21: 309--351.
>> Fitzhugh, K. 2012. The limits of understanding in biological
>> systematics. Zootaxa 3435: 40--67.
>> Kirk
>> On 9/13/2012 2:27 PM, John Grehan wrote:
>>> When it comes to the requirement of 'total evidence' being a 'basic
>> tenet'
>>> I would have to say that the demand for combining molecular and
>>> morphological evidence can be more of a total fraud than a tenet.
> Since
>>> Kirk did not specify what he meant by total evidence I do not
> attribute
>> the
>>> molecular sequence/morphology combination to his label, but I would
>>> certainly point out that the idea of combining the evidence is not
>>> automatically a basic tenet other than by those who so believe.
>>> John Grehan
>>> On Thu, Sep 13, 2012 at 12:46 PM, Kirk Fitzhugh <kfitzhugh at nhm.org>
>> wrote:
>>>> I'm reminded of what Stephen Stearns says in a Yale University
> article,
>>>> 'Some Modest Advice for Graduate Students
>>>> <http://www.eeb.yale.edu/stearns/advice.htm>:' "The pressure to
> publish
>>>> has corroded the quality of journals and the quality of
> intellectual
>>>> life." Perhaps rather than complaining about 'predatory' journals,
> we
>>>> need to change research standards. Stop thinking that the number of
>>>> publications per year or journal impact factor are reasonable
> indicators
>>>> of the quality of one's research. As one fluent in philosophy of
>>>> science, I'm astounded at the poor quality of systematics research
> that
>>>> regularly gets published in 'high end' journals. We continue to
> have a
>>>> community that does not understand some of the most basic tenets of
>>>> science, e.g. the nature of inference, the requirement of total
>>>> evidence, or mechanics of hypothesis testing.
>>>> Kirk
>>>> On 9/13/2012 8:24 AM, Sergio Vargas wrote:
>>>>> Dear taxacomers:
>>>>> A colleague gently send a link to a Nature editorial on Open
> Access
>>>>> publishing. In case you are interested please find the link(s)
> below.
>>>>> I know the topic has been raised before in the list. I think this
> will
>>>>> be especially important in taxonomy now that e-only publication is
>>>>> possible.
>>>>> Predatory publishers are corrupting open access:
> http://www.nature.com/news/predatory-publishers-are-corrupting-open-acce
> ss-1.11385
>>>>> (A) List of predatory open access publishers:
>>>>> http://scholarlyoa.com/publishers/
>>>>> cheers
>>>>> sergio
>>>> --
>>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>>> J. Kirk Fitzhugh, Ph.D.
>>>> Curator of Polychaetes
>>>> Invertebrate Zoology Section
>>>> Research & Collections Branch
>>>> Natural History Museum of Los Angeles County
>>>> 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/site/research-collections/polychaetous-annelids
>>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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