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Patent on cladistic analysis involving unknown species

PARSONS_at_AFIP05 at EMAIL.AFIP.OSD.MIL PARSONS_at_AFIP05 at EMAIL.AFIP.OSD.MIL
Thu Aug 3 23:23:54 EST 1995


     
     I also feel it is a shame to grant patents for such obvious scientific 
applications as this (original posting follows).  It is not justified, and is a 
burden on the scientific and biotechnology communities.  The use of phylogenetic
analysis in biological identification is widespread, and cladistics (parsimony) 
is a standard phylogenetic technique; therefore the use of cladistics in 
identification is a trivially obvious extension.  I, and no doubt many others, 
have used this approach without ever having heard of Davidson and Bartlett or 
"FINS."  There is no question that the approach would be just as widely in use, 
"discovered" independently by multiple scientists, if Davidson and Bartlett had 
never used it.  I also suspect that the priority of their citations is not 
valid.  I put my hands on a couple of examples of earlier studies that have 
employed conceptually equivalent approaches, and there are probably quite a few 
others.

Example 1:  E. Smith et al., Ibis 133:227-235 (submitted, accepted 1990).  "A 
new species of Shrike (Laniidae: Laniarius) from Somalia, verified by DNA 
sequence data from the only known individual."  The authors use mtDNA (cyt b) 
sequence from an unknown bird and run parsimony analysis with other shrike 
species to identify the bird in question as a new species, rather than a hybrid 
or color morph of an existing species.

Example 2:  R. Thomas et al., Nature 340:465-467.  "DNA Phylogeny of the extinct
marsupial wolf."  This paper is a parsimony-based (PAUP program) phylogenetic 
analysis of mtDNA sequences from a specimen of the extinct marsupial wolf, but 
the phylogenetic analysis is also used in the paper as an identification tool.  
In ancient DNA research, contamination with human or other contemporary 
sequences is a serious and common problem.  Phylogenetic verification of the 
source of DNA sequences is standardly employed to identify the source of the PCR
amplicon (strictly speaking, this is all that "FINS" does as well).  In the 
Thomas paper, the source of an amplicon was identified as human from one sample,
but from another sample the phylogenetic analysis demonstrated unambiguous 
marsupial sequences.

    I hope others will be able to provide additional early citations that employ
the same conceptual basis as "FINS," and also will voice their opinion that 
using cladistics as the method for phylogenetic analysis in identification 
studies is not conceptually novel and deserving of a patent.

Tom Parsons
Armed Forces DNA Identification Lab
Rockville, MD
These views are my own, not necessarily those of my employer.


______________________________ Reply Separator _________________________________
Subject: Patent on cladistic analysis involving unknown species
Author:  Frank Wright <frank at sass.sari.ac.uk> at INTERNET
Date:    8/3/95 10:07 AM


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