[Taxacom] FW: cladistic analysis for morphological characters -- UPGMA is not cladistics

Richard Jensen rjensen at saintmarys.edu
Wed Nov 14 11:54:32 CST 2012


If you define an explanation, based on careful observation and current 
understanding of evolutionary theory, a story, then there must be no 
causal explanation that you will accept, right? Thus, your suggestion 
that the orang is our closest primate relative is just a story - no 
causality implied.

  I don't choose to define causal that way and I believe we can provide 
causal explanations that are solidly grounded on scientific knowledge 
and theories.

Dick J


On 11/14/2012 12:21 PM, John Grehan wrote:
> 'causal' being another word for a story.
> John Grehan
>
> On Thu, Nov 15, 2012 at 4:02 AM, Richard Jensen 
> <rjensen at saintmarys.edu <mailto:rjensen at saintmarys.edu>> wrote:
>
>     Kirk,
>
>     Don't the branching patterns we see in cladograms (or the nested
>     sets we
>     see in phenograms) imply a cause?  These groups exist for a reason
>     - we
>     have identified characters and examined the distributions of
>     characters
>     to determine if there are patterns.  We could argue that these
>     patterns
>     are just chance consequences of developmental processes, but I would
>     like to believe that these patterns have a causal basis.  Our
>     recognition of, say, Spermatophyta (the seed plants) is based on our
>     understanding that these plants share an evolutionary history
>     reflected
>     in their reproductive (and other) structures.  By examining the fossil
>     record and using the tools of evo-devo, botanists are constructing
>     causal explanations for the patterns we see.
>
>     Dick J
>
>
>     On 11/13/2012 5:30 PM, Kirk Fitzhugh wrote:
>     > Richard,
>     >
>     > I do hope you're referring to my view that a 'tree' sensu a
>     cladogram, not any phenetic contraption, implies a specifiable set
>     of explanatory hypotheses. For that reason, too much emphasis is
>     placed on branching diagrams, when our real interest as scientists
>     is causal understanding. A cladogram is merely a profoundly vague
>     representation of equally vague causal accountings (assuming the
>     name of the game in science is causal understanding).
>     >
>     > Kirk
>     >
>     > --
>     > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>     > 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 <tel:213-763-3233>
>     > FAX: 213-746-2999 <tel:213-746-2999>
>     > e-mail: kfitzhug at nhm.org <mailto:kfitzhug at nhm.org>
>     > http://www.nhm.org/site/research-collections/polychaetous-annelids
>     > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>     >
>     > ________________________________________
>     > From: taxacom-bounces at mailman.nhm.ku.edu
>     <mailto:taxacom-bounces at mailman.nhm.ku.edu>
>     [taxacom-bounces at mailman.nhm.ku.edu
>     <mailto:taxacom-bounces at mailman.nhm.ku.edu>] on behalf of Richard
>     Zander [Richard.Zander at mobot.org <mailto:Richard.Zander at mobot.org>]
>     > Sent: Tuesday, November 13, 2012 10:38 AM
>     > To: Ashley Nicholas; taxacom at mailman.nhm.ku.edu
>     <mailto:taxacom at mailman.nhm.ku.edu>
>     > Subject: Re: [Taxacom] FW: cladistic analysis for morphological
>     characters      -- UPGMA is not cladistics
>     >
>     > Ah, yes, youth should question the decisions of their elders.
>     >
>     >
>     >
>     > Re phenograms and hypotheses, I agree with Fitzhugh, who, on
>     Taxacom,
>     > has doggedly pointed out that a tree is not a causal
>     explanation.  The
>     > neat and well supported cladograms show nesting, which is not a
>     process
>     > in nature (pace birds). The phenograms/cladograms/phylograms need a
>     > process-based explanation. A phenogram is the truth only in that
>     it is a
>     > nested set generated by data selected to generate a nested set. A
>     > phenogram is a phenogram, that's the truth. Basing a
>     classification on a
>     > dendrogram that truly represents the nesting information in the data
>     > means a classification based on truth, but only on a methodological
>     > basis. The causal origin of the nesting shown by the dendrogram
>     may be
>     > serial macroevolutionary transformation at the taxon level, we hope.
>     > Figuring out the latter is difficult. Process-based truth is a
>     rarely
>     > obtained commodity in science.
>     >
>     >
>     >
>     > Nesting does not happen in nature (there's a scowling sparrow
>     pecking at
>     > my window). Serial transformations do, according to theory. I
>     don't see
>     > much in the literature about serial macroevolution of taxa, but
>     I do see
>     > lots of "answers" about nesting. The question seems to be
>     missing for
>     > those answers. I suggest it is "What are the serial
>     macroevolutionary
>     > transformations that involve these taxa, and how might such help
>     > classification?"
>     >
>     >
>     >
>     > Probably not affect classical classifications much, since Linnaean
>     > classification uses names to distinguish and to group, but not to
>     > reflect wildly varying theories of evolution, which should be
>     discussed,
>     > not cast in nomenclatural stone.
>     >
>     >
>     >
>     > ____________________________
>     > Richard H. Zander
>     > Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299 USA
>     > Web sites: http://www.mobot.org/plantscience/resbot/
>     > <http://www.mobot.org/plantscience/resbot/>  and
>     > http://www.mobot.org/plantscience/bfna/bfnamenu.htm
>     > <http://www.mobot.org/plantscience/bfna/bfnamenu.htm>
>     > Modern Evolutionary Systematics Web site:
>     > http://www.mobot.org/plantscience/resbot/21EvSy.htm
>     > <http://www.mobot.org/plantscience/resbot/21EvSy.htm>
>     > UPS and FedExpr -  MBG, 4344 Shaw Blvd, St. Louis 63110 USA
>     >
>     > ________________________________
>     >
>     > From: Ashley Nicholas [mailto:Nicholasa at ukzn.ac.za
>     <mailto:Nicholasa at ukzn.ac.za>]
>     > Sent: Tuesday, November 13, 2012 12:04 PM
>     > To: Richard Zander; taxacom at mailman.nhm.ku.edu
>     <mailto:taxacom at mailman.nhm.ku.edu>
>     > Subject: RE: [Taxacom] FW: cladistic analysis for morphological
>     > characters -- UPGMA is not cladistics
>     >
>     >
>     >
>     > I agree. Classifications are hierarchical, cladograms are not.
>     However,
>     > both convey different information and perspectives on
>     biodiversity --
>     > which need not be in conflict.
>     >
>     > Richard, I am interested that you say that phenograms cannot be
>     equated
>     > to a hypothesis -- I hope you are not asserting that they are
>     the truth?
>     > Surely, in the end, all the results of any analyses can be used to
>     > induce hypotheses or can be interpreted as a hypothesis? Or they can
>     > also be discarded as unhelpful or empirically questionable.
>     >
>     > I am not sure what your end paragraph is about. What questions
>     are we
>     > talking about? I think we, as a generation, have a better
>     understanding
>     > and insight into what is happening and what has happened in the past
>     > regarding our universe and the phenomena that manifest within
>     what we
>     > perceive as reality. But, in the end, I still agree with Popper, and
>     > some of his predecessors, that all knowledge has some degree of
>     > uncertainty. Scientific consensus does not make something true.
>     > Newtonian determinism was replaced by Einstein and Relativity. I
>     wonder
>     > how many of our most treasure hypotheses, especially those that are
>     > powerfully predictive, will still be up held by empirical
>     scientists in
>     > 300 years time?
>     >
>     > Ashley
>     > ________________________________________
>     > From: Richard Zander [Richard.Zander at mobot.org
>     <mailto:Richard.Zander at mobot.org>]
>     > Sent: 13 November 2012 17:52
>     > To: Ashley Nicholas; taxacom at mailman.nhm.ku.edu
>     <mailto:taxacom at mailman.nhm.ku.edu>
>     > Subject: RE: [Taxacom] FW: cladistic analysis for morphological
>     > characters -- UPGMA is not cladistics
>     >
>     > The resulting phenogram is not a hypothesis, it is the result of an
>     > analysis of properties of nesting in a data set limited to data
>     > informative of those properties. Evolution is not nesting, but
>     nesting
>     > can be informative if you think about it.
>     >
>     > Phylogenetics leaps from nesting to classification without
>     explaining
>     > the nesting in terms of serial macroevolutionary transformations of
>     > taxa.
>     >
>     > Classification is nesting, evolution is not nesting.
>     >
>     > Hey, I think after years and years we are slowly, slowly
>     converging on
>     > agreeing what the question is for all those answers in the
>     literature.
>     >
>     > ____________________________
>     > 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>
>     > [mailto:taxacom-bounces at mailman.nhm.ku.edu
>     <mailto:taxacom-bounces at mailman.nhm.ku.edu>] On Behalf Of Ashley
>     Nicholas
>     > Sent: Tuesday, November 13, 2012 6:01 AM
>     > To: taxacom at mailman.nhm.ku.edu <mailto:taxacom at mailman.nhm.ku.edu>
>     > Subject: [Taxacom] FW: cladistic analysis for morphological
>     characters
>     > -- UPGMA is not cladistics
>     >
>     > John you are right,
>     >
>     > UPGMA is a phenetics method and is not eplicitly evolutionary.
>     It only
>     > measures similarity, and similarity is not always a good
>     indicator of
>     > descent from a common ancestor. This is especially true in flowering
>     > plants where convergent evolution/homoplasy is rife.
>     >
>     > Analogous (rather than homologous) base pair sequences are
>     probably less
>     > common than in morphology -- so maybe molecular systematists can get
>     > away with approximating it to an evolutionary tree. However, in
>     the end
>     > it is not an explicit evolutionary tree -- and this needs to be
>     > acknowledged rather than ignored (which is what usually happens).
>     > However, no matter what, the resulting phenogram is a
>     hypothesis. This
>     > hypothesis is as valid as any other hypothesis (until falsified)
>     -- and
>     > probably carries some interesting insightes and may generate some
>     > interesting questions for further explorations.
>     >
>     > The text books say a minum of 60 characters is needed but I
>     would think
>     > the number of characters needed would depend on the size of the
>     group
>     > being analysed. Some statistician has probably established this??
>     >
>     > Regards
>     > Ashley
>     >
>     > -----Original Message-----
>     > From: taxacom-bounces at mailman.nhm.ku.edu
>     <mailto:taxacom-bounces at mailman.nhm.ku.edu>
>     > [mailto:taxacom-bounces at mailman.nhm.ku.edu
>     <mailto:taxacom-bounces at mailman.nhm.ku.edu>] On Behalf Of John Grehan
>     > Sent: 10 November 2012 17:08
>     > To: Sami Rabei
>     > Cc: TAXACOM
>     > Subject: Re: [Taxacom] cladistic analysis for morphological
>     characters
>     >
>     > In my opinion its ok to make a cladistic analysis for any number of
>     > characters. It just depends where those characters are clustered
>     within
>     > the group analyzed as to the result. I suspect that unless the
>     > characters are dispersed throughout the 44 species, there will
>     be some
>     > clades that have some measure of good support, others that do
>     not, and
>     > others that whose relationships are unresolved.
>     >
>     > I'm a bit out of touch with all methods, but I recall UPGMA is a
>     > phenetic method?
>     >
>     > John Grehan
>     >
>     > On Sat, Nov 10, 2012 at 6:45 AM, Sami Rabei
>     <samirabei at mans.edu.eg <mailto:samirabei at mans.edu.eg>>
>     > wrote:
>     >
>     >> Dear All
>     >>
>     >> I have 81 morphological characters for 44 species. it is right
>     to make
>     >> a cladistic analysis for them. If it is ok which program I can use
>     >> it.On the other hand I did UPGMA .
>     >>
>     >> Many Thanks in advance
>     >>
>     >> All the best.
>     >>
>     >> Sami Rabei
>     >>
>     >> http://mansoura.academia.edu/SamiRabei
>     >>
>     >> ----------------------------------
>     >> With my Best Wishes
>     >> Sami Hussein Rabei, Ph.D.
>     >> Botany Department
>     >> Faculty of Science,
>     >> Damietta University
>     >> New Damietta , Post Box 34517
>     >> Damietta
>     >> Egypt .
>     >>
>     >> Tel. Mobile: 002 0127 3601618
>     >> Tel. Work: 002 057 2403981
>     >> Tel. Home: 002 057 2403108
>     >> Fax: 002 057 2403868
>     >>
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>     --
>     Richard J. Jensen, Professor
>     Department of Biology
>     Saint Mary's College
>     Notre Dame, IN 46556
>     Tel: 574-284-4674 <tel:574-284-4674>
>
>
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-- 
Richard J. Jensen, Professor
Department of Biology
Saint Mary's College
Notre Dame, IN 46556
Tel: 574-284-4674




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