[Taxacom] Methodological plurality [was cladistic analysis for morphological characters -- UPGMA is not cladistics]

Richard Jensen rjensen at saintmarys.edu
Tue Nov 20 10:55:39 CST 2012


Hi Ashley,

I don't believe it will be possible, at least in the short term, to 
reach agreement on a single method.  That day may come, but I see it as 
a long-way off.

I do believe there is something worthwhile in looking for agreement 
among methods (and, as a committe member, I would disappointed if the 
candidate had not done that!).  If one uses a variety of methods on the 
same data set, or the same method on different data sets, one can look 
for consensus.  If a particular "clade" or "nested set" keeps showing 
up, then one might begin to believe that there is an underlying signal 
reflecting something interesting.  Of course, we would still have to 
agree on a consensus method, but a strong signal should still be 
identifiable.Cheers,

Dick J


On 11/20/2012 11:05 AM, Ashley Nicholas wrote:
> "Congruence or conflict across methods tells us little or nothing about clade support."
>
> I agree with this statement and many of the others given below. However, this discussion has left me feeling somewhat unsettled and very conflicted. Say we use just one method, as advocated, what do we have in the end? A tree that may have good clade support but which hangs unconnected to anything else but itself. Surely this end result will eventually have to be tested or retested? As pointed out, the chances are there will not be congruence when it is retested with a different method -- which means the result needs to be treated as highly uncertain from the start. The only way this uncertain tree can be tested is if it is tested using the same method. What is the solution to this dilemma? It would seem we only have two choices. Either systematists agree to use only one method and abandon all others. Or we explore the question/problem more widely with as many methods as possible and see what insight (if any) we gain from this. Albeit bearing in mind the flaws to this plural
>   ist approach and the fact we are not comparing apples with apples (in a methodological sense).
>
> I would hesitate to abandon congruence and consilience because of the rich rewards it has already given us in terms of understanding our universe. E.g. Newton's connection of failing objects on earth and planets going around the sun actually being linked by the same cause. Which brings me to the comment: "If two people that view the same world (the data) differently, come to the same result they could just as well both be wrong or both be right." But isn't this why as scientists we test and explore further? In the case of Newton the movement of Mercury eventually falsified his hypothesis of gravity and lead the way to relativity.
>
> I am not a molecular systematist (my postgrads are co-supervised by someone more qualified) but I am now wondering what advice I should give them as we have tended to use a pluralist approach in the past. Will the examiners of PhD theses be happy with students using only one analytical method?
>
> Thanks for this interesting thread and the insights provided. I have really gained a lot from this discussion. Even if it has left me feeling conflicted.
>
> Ashley
>
> -----Original Message-----
> Kip, I will have to steal this for thesis defenses:
>
> "agreement of 5-7 different methods. Good feeling is the same as statistical support, right?"
>
> Dan
>
> On Sat, Nov 17, 2012 at 3:27 PM, Kipling (Kip) Will <kipwill at berkeley.edu>wrote:
>
>> On 11/15/2012 7:51 AM, Ashley Nicholas wrote:
>>> I guess they do this to assess if there is any congruence in the
>>> results
>> of all three analytical methods?
>>
>> On 11/17/2012 6:42 AM, Dan Lahr wrote:
>>> More interestingly though, you raise an issue that has always
>>> bothered
>> me:
>>> people using multiple reconstructions methods.  I'll start by saying
>>> I do not have a strong stance nor the answers to this question.
>>>
>>> In principle, it seems philosophically incoherent
>>
>> This is a point that triggers my peeve response. The incoherence Dan
>> refers to being the root of my discomfort. Different methods have
>> unique, but partially overlapping, ontological and epistemological
>> starting points and so their congruence cannot be considered to mean
>> much of anything at all. And yet, many (most?) publications throw the
>> "big three" (ML, Pars, Bayes) at every data set, almost never
>> explaining why or what it means, usually then one is picked (with
>> little explanation why that one) and the rest ignored. I have
>> facetiously suggested to people that if they add UPGMA and NJ that
>> they might feel even more warm and fuzzy (or Poy, traditional
>> Hennigian, SWAG, etc.), given agreement of 5-7 different methods. Good
>> feeling is the same as statistical support, right?
>>
>> Congruence or conflict across methods tells us little or nothing about
>> clade support.
>>
>> 1. These are not independent data being run using the different
>> methods so this fails to be support through consilience. If two people
>> that view the same world (the data) differently, come to the same
>> result they could just as well both be wrong or both be right. That
>> agreement (or
>> lack) tells us little about the result, perhaps more about the methods.
>> Using Pars for morphology and, for example, ML for DNA sequence data,
>> may be a situation where one can invoke consilience, but I doubt that
>> is to be preferred over a combined analysis.
>>
>> 2. If one cast all methods to be a form of one particular method (e.g.
>> parsimony is just one model of likelihood) and thinks of using the
>> different methods as a "sensitivity" analysis, then it is a very poor
>> sensitivity analysis indeed. We have many much better ways to explore
>> sensitivity of results across parameter space.
>>
>> 3. If congruence is thought of as a measure of support, even as a
>> vague, number-free tingly feeling, and if we want to maximize that
>> congruence, then this is maximized where all methods converge, which
>> would probably can be achieved by using model parameters in ML, etc, to fit parsimony.
>> Of course that would be a silly thing to do, unless you really believe
>> congruence across methods means something. I don't see statisticians
>> using multiple different tests and then implying or claiming that
>> since those three test all (or say 2 out of 3) had significant
>> p=values the result is "more significant" (increased "truthiness"?).
>>
>> It is legitimate to do a comparison of methods for its own sake, they
>> each have properties worth exploring, but that is rarely what is
>> published. One may wish to specifically test certain assumptions,
>> again that is valid, but when there is no explanation for the
>> methodological plurality, or a simple statement that implies support,
>> e.g. "ML and Pars gave basically the save topology" and nothing more,
>> it seems a waste of time. If its phylogeny, topology or evolution
>> along branches one is after, then pick the appropriate method, justify
>> it and understand its limitations.
>>
>> Echoing this-
>>
>> On 11/17/2012 6:42 AM, Dan Lahr wrote:
>>> you should choose a strategy and stick with it, many of the
>>> different
>> analytical methods are logically incompatible.
>>
>>
>> yep, Dan is right.
>>
>> kip
>> --
>>
>> Contact info:
>>
>> Kipling W. Will
>> Associate Professor/Insect Systematist Associate Director,Essig Museum
>> of Entomology
>>
>> send specimens to:
>> Essig Museum of Entomology
>> 1101 Valley Life Sciences Building, #4780 University of California,
>> Berkeley Berkeley, CA 94720-4780
>>
>> letter mail to:
>> 130 Mulford Hall
>> ESPM Dept.- Organisms & Environment Div.
>> University of California
>> Berkeley, California 94720
>>
>> fax 510-643-5438
>>
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>
>
> --
> ___________________
> Daniel J. G. Lahr, PhD
> Dept of Zoology, Univ. of Sao Paulo, Brazil _______________________________________________
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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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