[Taxacom] molecular nonsense

[John Grehan]

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