[Taxacom] molecular systematics again. Was Why Taxonomy does NOT matter

Wed Apr 20 12:55:35 CDT 2011

-----Original Message-----
From: jwhitfie at life.illinois.edu [mailto:jwhitfie at life.illinois.edu] 
Sent: Wednesday, April 20, 2011 1:38 PM
To: John Grehan
Cc: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] molecular systematics again. Was Why Taxonomy
does NOT matter

"Sorry, John, but you simply fill up days and days of Taxacom entries
with
scientifically ignorant rants about how people are distorting primate
relationships."

What is an ignorant rant is all a matter of perspective. No doubt that
is what 'they' said about Darwin too. (and not I'm not comparing myself
to Darwin, just that just because the accusation can be leveled has no
necessary bearing on whether the accusation has a substantiated
foundation).

"Do you think those people don't care about what they find?"

Of course everyone cares about what they find. I never implied
otherwise.

"Why don't you actually try to do some real work and understand these
things?"

Again it's all relative. I am sure you would might not like it if I said
the same about you (which I do not intend).

"The entries below suggest that you have no idea how molecular
systematics is actually done."

Perhaps, perhaps not. 

"It is just a waste of time"

Then don't waste your time.

"for those of us who actually work on taxa taxonomically and
phylogenetically, and try to use this Listserve as a way of keeping up
on things."

I don't work on taxa taxonomically and phylogenetically? News to me.

"There are lots of
useful bits of information from many on this list, but unfortunately
they
get buried in this other stuff..."

What's that phrase? - one person's food is another person's poison

"Checking out now. Not sure why I bothered."

Good for you. Neither am I (sure about why you bothered)!

John Grehan

> With apologies to those tired of this subject (hence my change of the
> subject so this email can be deleted in advance).
>
> -----Original Message-----
> From: jwhitfie at life.illinois.edu [mailto:jwhitfie at life.illinois.edu]
> Sent: Wednesday, April 20, 2011 12:53 PM
> To: John Grehan
> Cc: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] Why Taxonomy does NOT matter
>
> A brief respite between thesis defenses...
>
> "I think your statement that DNA homologies are only a measure of
> overall
> similarity is patently ridiculous."
>
> And I think otherwise
>
> "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."
>
> Interestingly these studies are still quoted (at least in
human-primate
> molecular systematics) as still valid.
>
> "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."
>
> One may, but in primate systematics algorithms are used and it is a
> matching process of gaps vs substitutions which requires a
compensatory
> solution based on the best overall fit (according to whatever that may
> be)
>
> "The argument of purported homology only meaning similarity could be
> made
> FAR more cogently for most morphological homologies."
>
> But has not yet.
>
>
> "Molecular bioinformatics works because these DNA correspondences DO
> mean something!"
>
> They might mean 'something' but what they mean is another matter.
>
> "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."
>
> I'm not so sure it is difficult as so much that it is time consuming.
In
> human-primate systematics the morphology gives a pretty clear cut and
> unambiguous answer.
>
>
> "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..."
>
> In the case I work on - human-primate systematics DNA 'homologies' are
> very LOWLY congruent with morphogenetics (i.e. morphology which is the
> product of morphogenetic processes).
>
> John Grehan
>
> 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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>>>> Exhibition 9 April - 7 August 2011
>>>> The Australian Museum.
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>>>> _______________________________________________
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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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>> _______________________________________________
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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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>>
>> Taxacom Mailing List
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>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>>
>> The Taxacom archive going back to 1992 may be searched with either of
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>>
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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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>
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>
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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