[Taxacom] Why Taxonomy does NOT matter

Wed Apr 20 11:52:59 CDT 2011

A brief respite between thesis defenses...

I think your statement that DNA homologies are only a measure of overall
similarity is patently ridiculous. I think this MIGHT have been true with
respect to early studies in the 1970's or 1980's, because we had less
background information to work from. But almost all nuclear protein-coding
genes (the main source for most current comprehensive phylogenies, as
opposed to barcoding efforts) align easily without any fancy finagling,
and at this point we can easily check for whether the genes are paralogs
as opposed to orthologs.

The argument of purported homology only meaning similarity could be made
FAR more cogently for most morphological homologies. Molecular
bioinformatics works because these DNA correspondences DO mean something!
I would absolutely LOVE to see the same level of detailed coordination of
morphological data (and there are very bright people working on this via
morphological ontology schemes, MorphBank, MorphoBank, etc.), but it is a
complex, and I think we both agree, ultimately more satisfying, problem to
solve. We can get some really great information from determining true
morphological homologies, but it is more difficult unfortunately than with
DNA data.

You finish with the word "morphogenetics".  DNA homologies are HIGHLY
congruent with actual morphogenetics, just maybe not always with basic
comparative morphology as it is sometimes practiced by taxonomists like
you and me (who, after all, are not usually trying to determine deep
homologies, but instead trying to find diagnostic features for taxa we
wish to treat in a review, revision or monograph). It works for our level
of utility, but we should not pretend that it means more than we
investigated in the first place...

Jim

> Well of course it is my position that the evolutionary homologies of DNA
> are less the 'truth' than often asserted. There is nothing empirical to
> demonstrate that DNA homologies (which are often created through
> alignment or clustering rather than empirical observation) represent
> anything more than a measure of overall similarity since there is no
> prior removal of primitive retentions. I agree that the issue is not
> about morphology vs molecules since the two are connected, but I do have
> a problem about how molecules are assumed to give certain kinds of
> information as a falsifier of morphogenetics.
>
> John Grehan
>
> -----Original Message-----
> From: jwhitfie at life.illinois.edu [mailto:jwhitfie at life.illinois.edu]
> Sent: Wednesday, April 20, 2011 9:51 AM
> To: John Grehan
> Cc: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] Why Taxonomy does NOT matter
>
> A brief set of comments before I have to disengage for other end-of-term
> work commitments...
>
> DNA analysis might very well replace "morphogenetic analysis" in terms
> of
> PHYLOGENY as more data and analytical insights accumulate. It has way
> more
> individual points of data, and also is (in many but admittedly not ALL
> cases) FAR more easy to find true evolutionary homologies within
> (despite
> some missives on this listserve, mainly by scientists who don't mainly
> deal with molecular data). Morphological traits can have quite complex
> genetic and developmental underpinnings, and almost all of the best work
> on morphological homology I have read in recent years comes from the
> evo-devo community. In my admittedly biased view this is way more
> interesting than basic molecular evolution, but IN NO WAY easier to
> interpret in terms of homology and evolution.
>
> DNA analysis is of course NOT likely to replace comparative morphology
> anytime soon in terms of field taxonomic diagnostics, and at the other
> end
> of the spectrum, functional morphology.  I regard these other uses of
> comparative morphology as EVERY BIT as important for biology as
> phylogeny.
> Armed with a well-supported phylogeny and some strong field natural
> history, some REALLY interesting evolutionary functional insights can be
> pursued. In my view the problem has really never been molecules versus
> morphology, but other problems:
>
> 1) the recent devaluation of basic descriptive taxonomy and functional
> morphology (vs. phylogenetic "analysis") as potential careers. Not to
> mention the fact that field natural historians get basically zippo in
> terms of credit! What is the deal here?  Do we really think we know that
> much about the world around us? Give me a break!
>
> 2) the battle between science as an evidence-based enterprise versus an
> authority-based enterprise. Didn't Descartes already fight this battle
> centuries ago? Jesus, do we have to do it again? Reminds me of the Pogo
> quotation: " We have met the enemy, and they are us"!
>
> OK, outta here for now...
>
> JIm
>
>
>
>
>
>
>
>
>> An integrative spirit if fine if there is a basis for doing so. I can
> see barcoding being ok as a short cut for identification for entities
> that have already been sorted out, but as a replacement it gets more
> problematic. I get the impression that barcoding is seen as a
>> replacement, and that's where I see a problem. The comparable issue is
> over whether DNA sequence analysis should replace morphogenetic analysis
> as is widely believed.
>> John Grehan
>> -----Original Message-----
>> From: taxacom-bounces at mailman.nhm.ku.edu
>> [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of
>> jwhitfie at life.illinois.edu
>> Sent: Wednesday, April 20, 2011 8:54 AM
>> To: Andrew Mitchell
>> Cc: 'taxacom at mailman.nhm.ku.edu'
>> Subject: Re: [Taxacom] Why Taxonomy does NOT matter
>> I agree totally at one level, but one has to agree that some of the
> barcoders have a very naive view of the taxonomic enterprise. Getting on
> the same team is good!  I hope we can move towards good science too,
> though...
>> Jim
>> P. S.  I have gotten involved with at least some of the core
> barcoders,
> and find that they absolutely LOVE it when we have more kinds of data to
> wrap into the analysis and interpretation. I have to say SOME
>> traditionally based taxonomists do not have the same openness to new
> types
>> of evidence. They seem more interested in preserving their own
> "expert"
> status.  As a traditionally based taxonomist and supposed "expert"
> myself,
>> I find this unfortunate. We can all learn from new, and real, data,
> but is
>> has to be in an integrative spirit. No? What is the alternative?
>>> Hi All,
>>> I think the real reason that astronomers can get huge grants and
> taxonomists can't is that taxonomists/systematists are such a
>> fractious
>>> bunch they just can't help but shoot themselves in the foot by
>> protesting
>>> vociferously against any emerging large initiatives. A case in point
>> is
>>> barcoding. The concept has caught the public's imagination and could
>> bring
>>> megabucks to taxonomy, but instead of seeing the possibilities,
>> getting
>>> involved and working together to integrate and improve this fledgling
> system many taxonomists would rather fire shots from the sidelines.
>> Have
>>> you ever seen a documentary on TV where say radioastronomers slam
> gamma-ray astronomers as having no understanding of their
>> subdiscipline?
>>> Of course not! They would rather work together to build the
>> multi-billion
>>> dollar SKA that they can all use.
>>> Now that I'm sticking my neck out I may as well add that funding
>> models
>>> which favour "innovation" over all else are partly to blame. This is
>> why
>>> we have so many different initiatives digitising taxonomy
> (checklists,
> species pages & images, the heritage literature) with limited
>>> interactivity - each successive proposal must demonstrate that it is
>> doing
>>> something "innovative", i.e. different from existing projects.
>>> OK, my flame guards are up so fire away!
>>> Andrew
>>> Andrew Mitchell
>>> Integrative Systematist
>>> Entomology
>>> Australian Museum
>>> 6 College Street Sydney NSW 2010 Australia
>>> t 61 2 9320 6346   f 61 2 9320 6042
>>> www.australianmuseum.net.au
>>
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>> --
>> James B. Whitfield
>> Department of Entomology
>> 320 Morrill Hall
>> 505 S. Goodwin Avenue
>> University of Illinois
>> Urbana, IL 61801
>> http://www.life.illinois.edu/whitfield
>> _______________________________________________
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>
> --
> James B. Whitfield
> Department of Entomology
> 320 Morrill Hall
> 505 S. Goodwin Avenue
> University of Illinois
> Urbana, IL 61801
> http://www.life.illinois.edu/whitfield
>
>
>
>
>
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-- 
James B. Whitfield
Department of Entomology
320 Morrill Hall
505 S. Goodwin Avenue
University of Illinois
Urbana, IL 61801
http://www.life.illinois.edu/whitfield