[Taxacom] molecular nonsense

Tue May 5 10:52:00 CDT 2009

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from a chromatogram), and the fact that many published sequences do not 
cite voucher specimens.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
>
>  
>
>  
>
> _______________________________________________
>
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>
> The Taxacom archive going back to 1992 may be searched with either of these methods:
>
> (1) http://taxacom.markmail.org
>
> Or (2) a Google search specified as:  site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
>
>
>   

-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
~~~~~~~~~~~~~~~~~~~~~~~~~~~~