[Taxacom] molecular nonsense

Tue May 5 14:41:48 CDT 2009

'Hidden' in the sense that molecular phylogeny is so often portrayed as
the silver bullet of phylogenetic reconstruction.

John Grehan

> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
> bounces at mailman.nhm.ku.edu] On Behalf Of Neil Bell
> Sent: Tuesday, May 05, 2009 11:52 AM
> To: Taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] molecular nonsense
> 
> This is a paper about bad data, not any "hidden problems" of molecular
> analysis as a method. The equivalent would be to claim that there are
> hidden problems in morphological taxonomy simply because some
published
> papers aren't very good.
> 
> > John Grehan wrote:
> > <<<<I read this statement to the effect that unless you are
> > experienced and trained in handling molecular genetic data and
trained
> > in molecular evolutionary analyses you will have no clue as to what
is
> > going on regarding the validity of the data.>>>>
> 
> Well, one would hope that most people who are publishing molecular
> phylogenetic analyses have some knowledge of how to handle molecular
> data (although admittedly this paper casts some doubt on that). Nearly
> all of the errors in the molecular sequences referred to are pretty
> basic, and should not be made by anyone who is both competent and
> thorough. Simply checking for uninterrupted open reading frames in
> protein coding regions covers most of the problems mentioned, and
that's
> something everyone should be doing. It's also something that can
easily
> be checked by anyone properly examining the online GenBank accessions
> after publication, so in that sense the "raw data" is there and the
> errors are transparent.
> 
> The paper does touch on some issues of non-transparency that are much
> more problematic if you are trying to assess the validity of a
published
> study using just the universally available data, namely the lack of a
> requirement to submit sequence chromatograms (we are asked to trust
the
> researcher's competence and honesty in producing a trustworthy
sequence
> from a chromatogram), and the fact that many published sequences do
not
> cite voucher specimens.
> 
> Of course there is some "molecular nonsense" out there, but most of it
> is just old-fashioned nonsense that happens to be molecular.
> 
> 
> > I was interested to read in the paper by Buhay (2009) on "COI-like
> > sequences are becoming problematic in molecular systematic and DNA
> > barcoding studies" that there appear to be pervasive problems with
> > questionable sequences and the lack of verification of data. In her
Fig.
> > 2 she notes that "anyone can inset any [molecular] text into a nexus
> > file and output a phylogenetic tree, even one with 100% support for
a
> > bogus clade." And she also notes that "A thorough understanding of
> > phylogenetic methods and theory is not required to push buttons in
PAUP
> > [or any other program for that matter] and generate a tree.
> >
> >
> >
> > She also warns that "Without experience in handling molecular
genetic
> > data and training in molecular evolutionary analyses [presume this
means
> > molecular manipulations], a researcher might not recognize exactly
(if
> > anything) is wrong if the sequence chromatograms were clean." I read
> > this statement to the effect that unless you are experienced and
trained
> > in handling molecular genetic data and trained in molecular
evolutionary
> > analyses you will have no clue as to what is going on regarding the
> > validity of the data. I think this is a critical observation given
the
> > extraordinary amount of faith that is given to molecular results
over
> > morphology. At least in morphology anyone can directly access the
raw
> > data (when it is provided - which is not always the case as in most
> > hominid studies) and make an evaluation of homology.
> >
> >
> >
> > More comments by Buhay:
> >
> >
> >
> > "molecular data errors are not just negligible issues anymore - they
are
> > cause for serious concern which must be addressed."
> >
> >
> >
> > "it is an issue that can involve some or all of the following:
> > re-sequencing, re-editing and re-checking chromatograms, cloning,
> > re-analyzing phylogenetic input and output, re-examining systematic
> > conclusions, and re-accessioning GenBank sequences.
> >
> >
> >
> > I know I am in the minority on this, but the more I read about the
> > hidden problems of molecular analysis the more it seems to be
imbedded
> > with a lot of 'crap' that even molecular theorists admit, while at
the
> > same time some results are touted as the holy truth of life, the
> > universe and everything (the proclaimed FACT of the chimpanzee
> > relationship is iconic in this respect).
> >
> >
> >
> > John Grehan
> >
> >
> >
> >
> >
> > Dr. John R. Grehan
> >
> > Director of Science
> >
> > Buffalo Museum of Science1020 Humboldt Parkway
> >
> > Buffalo, NY 14211-1193
> >
> > email: jgrehan at sciencebuff.org
> >
> > Phone: (716) 896-5200 ext 372
> >
> >
> >
> > Panbiogeography
> >
> > http://www.sciencebuff.org/biogeography_and_evolutionary_biology.php
> >
> > Ghost moth research
> >
> >
http://www.sciencebuff.org/systematics_and_evolution_of_hepialdiae.php
> >
> > Human evolution and the great apes
> >
> > http://www.sciencebuff.org/human_origin_and_the_great_apes.php
> >
> >
> >
> >
> >
> > _______________________________________________
> >
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> >
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> >
> >
> >
> 
> 
> --
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Neil E. Bell
> Postdoctoral Researcher
> (Bryophyte Systematics)
> 
> Kasvimuseo
> PO Box 7
> 00014 University of Helsinki
> FINLAND
> 
> +358 9 191 24463
> neil.bell at helsinki.fi
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 
> 
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> 
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