DNA barcoding analogy

Vince Smith vsmith at INHS.UIUC.EDU
Fri Nov 4 11:18:53 CET 2005


Dear all,

Perhaps a real world analogy might be useful. There are comparisons
between this discussion and the DNA barcoding debate, particularly on
the question of ascribing identity and separating notions of identity
from concepts about that identity. In DNA barcoding a string of DNA
bases can be generated from a  biological specimen, much in the same
way that a taxonomist might generate or apply a taxonomic name. The
DNA barcode (like a taxonomic name) might not be unique, but quite
separately we can apply concepts to these strings that add meaning
(e.g. these DNA barcodes / taxonomic names do / do not refer to the
same 'thing', what ever that 'thing' [e.g. a species] might be). The
first step to doing this is to uniquely identify all the elements
(DNA barcodes or taxonomic names) by applying GUID's to them. Keeping
up with the DNA barcoding analogy, NCBI already do this with Genbank
accession numbers that uniquely identify DNA sequences. Genbank will
give any DNA sequence an identifier independently of any taxon
concept ascribed to a particular sequence or even if a DNA sequence
is a duplicate (although they try to avoid the latter). The number is
just an identifier.

Given that generating GUID's is easy, and can be done in a
distributed manner (e.g. with LSID's) there is no reason why we can't
do this for taxonomic names. As in DNA barcoding the hard part will
be in ascribing concepts to taxonomic names (e.g. does this group of
DNA barcodes / taxonomic names identify the same concept). Some of
this can be automated by applying rules across the metadata (i.e DNA
sequences or authority data for a taxon name) identified by GUID's.
There will always be disputes about these rules, and to some extent
there are real question over how much of this can be automated for
taxonomic names (uBio seem to be making a lot of headway with this).
For me the real debate is over these rules and the concepts behind
them, not the (Globally Unique) identifiers.

Regards,

Vince Smith

____________________________________________________

Dr. Vincent S. Smith
Illinois Natural History Survey
607 East Peabody Drive
Champaign, IL  61820-6970
USA
Tel: +1 (217) 265-0831
Fax: +1 (217) 333-4949

E-mail: vsmith at inhs.uiuc.edu
Web: http://darwin.zoology.gla.ac.uk/~vsmith/
iChat Video Conferencing: vsmithuk at mac.com (invitation only)
Skype: vsmithuk; or try SkypeIn (call whichever is nearer you)
SkypeIn London: 020-755-88950; or Chicago: (312)-239-0950
____________________________________________________


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<HTML><BODY style=3D"word-wrap: break-word; -khtml-nbsp-mode: space; =
-khtml-line-break: after-white-space; "><DIV>Dear all,</DIV><DIV><BR =
class=3D"khtml-block-placeholder"></DIV><DIV>Perhaps a real =
world=A0analogy might be useful.=A0There are comparisons between this =
discussion and the DNA barcoding debate, particularly on the question of =
ascribing identity and=A0separating notions of identity from concepts =
about that identity. In DNA barcoding a string of DNA bases can be =
generated from a=A0 biological specimen, much in the same way that a =
taxonomist might generate or apply a taxonomic name. The DNA barcode =
(like a taxonomic name) might not be unique, but quite=A0separately we =
can apply concepts to these strings that add meaning (e.g. these DNA =
barcodes / taxonomic names do / do not refer to the same 'thing', what =
ever that 'thing' [e.g. a species] might be). The first step to doing =
this is to=A0uniquely identify all the elements (DNA barcodes or =
taxonomic names) by applying GUID's to them. Keeping up with the DNA =
barcoding analogy, NCBI already do this with Genbank accession numbers =
that uniquely identify DNA sequences. Genbank will give any DNA sequence =
an identifier=A0independently=A0of any taxon concept ascribed to a =
particular sequence or even if a DNA sequence is a duplicate (although =
they try to avoid the latter). The number is just an =
identifier.=A0</DIV><DIV><BR =
class=3D"khtml-block-placeholder"></DIV><DIV>Given that=A0generating =
GUID's is easy, and can be done in a distributed manner (e.g. with =
LSID's) there is no reason why we can't do this for taxonomic names. As =
in DNA barcoding the hard part will be in ascribing concepts to =
taxonomic names (e.g. does this group of DNA barcodes / taxonomic names =
identify the same concept). Some of this can be automated by applying =
rules across the metadata (i.e DNA sequences or authority data for a =
taxon name)=A0identified by GUID's. There will always be disputes about =
these rules, and to some extent there are real question over how=A0much =
of this can be automated for taxonomic names (uBio seem to be making a =
lot of headway with this). For me the real debate is over these rules =
and the concepts behind them, not the (Globally Unique) =
identifiers.</DIV><DIV><BR =
class=3D"khtml-block-placeholder"></DIV><DIV>Regards,</DIV><DIV><BR =
class=3D"khtml-block-placeholder"></DIV><DIV>Vince =
Smith</DIV><DIV><DIV><BR><DIV> <P style=3D"margin: 0.0px 0.0px 0.0px =
0.0px"><FONT face=3D"Helvetica" size=3D"3" style=3D"font: 12.0px =
Helvetica">____________________________________________________</FONT></P>=
 <P style=3D"margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica; =
min-height: 14.0px"><BR></P> <P style=3D"margin: 0.0px 0.0px 0.0px =
0.0px"><FONT face=3D"Helvetica" size=3D"3" style=3D"font: 12.0px =
Helvetica">Dr. Vincent S. Smith</FONT></P> <P style=3D"margin: 0.0px =
0.0px 0.0px 0.0px"><FONT face=3D"Helvetica" size=3D"3" style=3D"font: =
12.0px Helvetica">Illinois Natural History Survey</FONT></P> <P =
style=3D"margin: 0.0px 0.0px 0.0px 0.0px"><FONT face=3D"Helvetica" =
size=3D"3" style=3D"font: 12.0px Helvetica">607 East Peabody =
Drive</FONT></P> <P style=3D"margin: 0.0px 0.0px 0.0px 0.0px"><FONT =
face=3D"Helvetica" size=3D"3" style=3D"font: 12.0px =
Helvetica">Champaign, IL<SPAN class=3D"Apple-converted-space">=A0 =
</SPAN>61820-6970</FONT></P> <P style=3D"margin: 0.0px 0.0px 0.0px =
0.0px"><FONT face=3D"Helvetica" size=3D"3" style=3D"font: 12.0px =
Helvetica">USA</FONT></P> <P style=3D"margin: 0.0px 0.0px 0.0px =
0.0px"><FONT face=3D"Helvetica" size=3D"3" style=3D"font: 12.0px =
Helvetica">Tel: +1 (217) 265-0831</FONT></P> <P style=3D"margin: 0.0px =
0.0px 0.0px 0.0px"><FONT face=3D"Helvetica" size=3D"3" style=3D"font: =
12.0px Helvetica">Fax: +1 (217) 333-4949</FONT></P> <P style=3D"margin: =
0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica; min-height: =
14.0px"><BR></P> <P style=3D"margin: 0.0px 0.0px 0.0px 0.0px"><FONT =
face=3D"Helvetica" size=3D"3" style=3D"font: 12.0px Helvetica">E-mail: =
<A =
href=3D"mailto:vsmith at inhs.uiuc.edu">vsmith at inhs.uiuc.edu</A></FONT></P> =
<P style=3D"margin: 0.0px 0.0px 0.0px 0.0px"><FONT face=3D"Helvetica" =
size=3D"3" style=3D"font: 12.0px Helvetica">Web: <A =
href=3D"http://darwin.zoology.gla.ac.uk/~vsmith/">http://darwin.zoology.gl=
a.ac.uk/~vsmith/</A></FONT></P> <P style=3D"margin: 0.0px 0.0px 0.0px =
0.0px"><FONT face=3D"Helvetica" size=3D"3" style=3D"font: 12.0px =
Helvetica">iChat Video Conferencing: <A =
href=3D"mailto:vsmithuk at mac.com">vsmithuk at mac.com</A> (invitation =
only)</FONT></P> <P style=3D"margin: 0.0px 0.0px 0.0px 0.0px"><FONT =
face=3D"Helvetica" size=3D"3" style=3D"font: 12.0px Helvetica">Skype: =
vsmithuk; or try SkypeIn (call whichever is nearer you)</FONT></P> <P =
style=3D"margin: 0.0px 0.0px 0.0px 0.0px"><FONT face=3D"Helvetica" =
size=3D"3" style=3D"font: 12.0px Helvetica">SkypeIn London: =
020-755-88950; or Chicago: (312)-239-0950</FONT></P> <P style=3D"margin: =
0.0px 0.0px 0.0px 0.0px"><FONT face=3D"Helvetica" size=3D"3" =
style=3D"font: 12.0px =
Helvetica">____________________________________________________ <SPAN =
class=3D"Apple-converted-space">=A0</SPAN></FONT></P>  =
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