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

John Grehan calabar.john at gmail.com
Wed Nov 14 14:04:42 CST 2012


My take on "story" is that science generates explanatory stories. Sometimes
these stories are called theories or hypotheses, but they are still
stories, human origins from a common ancestor with the chimp or orangutan
included. As for causality - not sure about that. The theory of gravity is
a story that 'explains' why the apple dropped - that gravity is the cause
of the apple dropping - if I know what I am talking about.

On Wed, Nov 14, 2012 at 9:54 AM, Richard Jensen <rjensen at saintmarys.edu>wrote:

> 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>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
>> > FAX: 213-746-2999
>> > e-mail: kfitzhug at nhm.org
>> > http://www.nhm.org/site/research-collections/polychaetous-annelids
>> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> >
>> > ________________________________________
>> > 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: Tuesday, November 13, 2012 10:38 AM
>> > To: Ashley Nicholas; 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]
>> > Sent: Tuesday, November 13, 2012 12:04 PM
>> > To: Richard Zander; 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]
>> > Sent: 13 November 2012 17:52
>> > To: Ashley Nicholas; 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] On Behalf Of Ashley
>> Nicholas
>> > Sent: Tuesday, November 13, 2012 6:01 AM
>> > To: 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] 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>
>> > 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
>>
>>
>> _______________________________________________
>>
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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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