Re: [DIYbio] Re: I want to test my own food - where do I start

On Thu, Aug 27, 2015 at 11:47 PM, Cathal (Phone)
<cathalgarvey@cathalgarvey.me> wrote:
> I think the question was "For any given gene how would you detect
> modification of that gene". More of an informatics exercise than a molecular
> one: I imagine hidden markov modelling of the surrounding genome would help
> identify areas that are "too simple" because of our present difficulty and
> disinclination towards matching deep genomic patterns.
>

Yeah I was thinking along these lines... the answer to the question
"is this stuff (contaminated with) GMO" seems lie in some sort of
statistics or mathematical analysis.

That said, Cory's answer is perfect for a question like "aside from
statistical analysis, what is a good way to start checking for common
agro-industry-standard GMO". Rightfully as he pointed out, this is a
very crude test, as sequence construction can change at any point when
industry developments alternatives.

At that point, if you're really concerned about presence of GMO, you
might have much much bigger problems. If you want to /just/ detect Bt
corn, you can search for CaMV promoters, if that comes up empty you
can search for Bt protein sequence fragments, if that doesn't turn up
results maybe you want to check a Western Blot or ELISA for
functional/binding domains of Bt protein, if that doesn't turn up
results well who knows... maybe the engineers altered the structure
vastly and that turns up nothing. Or maybe this is really a GMO-free
sample.

So at that point the logic and procedure becomes quite circular in
terms of GMO, detection, form, function, role, etc...

If you screen only for common standards, you may find all standard
GMOs, but you will not catch non-standard (or newer standards that you
are not updated to, because they are trade-secrets, etc...). The only
reasonable thing to do at that point seems to be statistical analysis,
unless you have a BIG engineering budget and some serious reason to
get into blotting and enzyme function assays.

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