Re: Barcoding Life

[David Farber <dfarber () cs cmu edu>]

Begin forwarded message:

From: David Magda <dmagda () ee ryerson ca>
Date: January 2, 2008 8:58:14 PM EST
To: dave () farber net
Subject: Re: [IP] Re:   Barcoding Life
Reply-To: David Magda <dmagda () ee ryerson ca>

For IP if you wish,

Daniel Janzen gave a talk at the Long Now Foundation a few years back.  
Search for his name (April 9th 02004 entry) for his talk:

        http://www.longnow.org/projects/seminars/

The first part of the talk is about bio-diversity, and then he goes  
into the "barcorder".

They use the COI mitochondrial gene for identifying things:

        http://en.wikipedia.org/wiki/DNA_barcoding

On Jan 1, 2008, at 18:17, David Farber wrote:

> ________________________________________
> From: Jim Fruchterman [Jim.F () Benetech org]
> Sent: Tuesday, January 01, 2008 3:15 PM
> To: Allen Smith; tt () postbiota org
> Cc: Jim () Benetech org; David Farber
> Subject: RE: [tt] [IP] Barcoding Life
>
> You'll need to find multiple regions to distinguish all life, because
> what works on vertebrates may not work with invertebrates or plants or
> bacteria, as you point out.
>
> The "barcoding" concept is slightly misleading: you aren't expecting
> identical sequences for all members of a species like you would if it
> were a 12 oz. bottle of Classic Coke.  The real issue is whether
> intra-species variation is significantly smaller than inter-species
> variation: I believe they are aiming for a 10X difference in variation
> for barcoding techniques to be workable (I think it's called the
> barcoding gap, say .5% variation intra-species and 5% variation
> inter-species).
>
> But, the great thing is that it's testable, and that's the phase  
> they're
> in: collecting a bunch of data and evaluating different loci.  One
> region did perfectly for birds in an article I saw cited.  If one  
> region
> isn't enough, it's not hard to imagine a second one.  And, if you have
> two regions that are both 95+% discriminating and relatively
> independent, you can build a pretty cheap gizmo that would be pretty
> darn accurate.
>
> But, I'm not a biochemist...


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