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<Link> Junk DNA might be really, really useful for biocomputing
#1
This article suggests that redundant 'junk' DNA in our genome could be repurposed as a DNA-based biocomputer.
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#2
Biocomputing is an interesting field, it's a shame that there's not more attention to it.
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#3
It has passed quite a lot of time since I studied DNA base constructs but technically, with the right sequence, you can fold it into almost any nanostrucutre.
The problem with biocomputing compared to silicon based transistor, IIRC, is more on the speed of the signals among components (which could be made of mRNA, proteins, peptides, small molecules, twisting of the same DNA) which is governed by diffusion and thus way slower than the electric field in a processor.
This if you can solve the assembling and manteinance of a DNA based chip. IIRC our 3 billion bases long genome breaks 1 million times a day and the machinery to repair it is not trivial. And for breaking I mean breaking of the chemical bonds in the double strand, then you have that pesky thing that is oxidative stress to cope with...
You also have a lot of other problems like the input-output trasducers, contamination, mutations in the DNA, etc...

Still is indeed true that the structure of the DNA and the genome allow for very fine and complex cascade signaling sequences: a single DNA gene can be influenced by enancher, silencers, promoters, DNA methilation, micro-RNA and RNA silencing in general, etc...


Quote:Biocomputing is an interesting field, it's a shame that there's not more attention to it.

From my point of view, at the moment, is already a small miracle we have a tool like the CRISPR-Cas9 to edit DNA in general with a very high fidelity (was a real pleasure sweating like a pig for the test on the techniques to manipulate DNA and having the CRISPR disclosed a few months later Big Grin Rolleyes ).

Pretty sure we will have commercial quantum computer before biocomputing, we really still can't manipulate the DNA perfectly and even if our capabilities of sequencing has gone through the roof in the last years the understanding of how the genes works has not increased at the same rate.

Last but not least: the "junk" term is quite misleading as the DNA in these sequences can be quite relevant for the cell life and was already disregarded since I graduated a few years ago. Pretty a shame reading it in a 2020 article Sad
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#4
I would say yes DNA molecules are definitely really useful for computing, but it would probably be best if we don't use them in situ in living organisms whose welfare we care about.

Junk DNA - even if it's never expressed and never affects the expression of anything - is usually valuable in some degree. Much of It is what it is, and where it is, because at some point in the evolutionary past some version of it served our ancestors well. We got a switch here, a switch there, this sequence activated, that sequence deactivated, and now it's "junk." But next week or a century from now, we get a switch there, a switch here, this sequence deactivated, that sequence activated, and the trait - or some related trait, or some part of that trait, or some combination of it with current traits - shows up in the current environment. Junk DNA is DNA recombining across time rather than just across gametes. If you go rewriting it, using it to compute, etc, you are disrupting the process of recombination across time, and suddenly tiny little mutations that might otherwise have reactivated something potentially useful or combined it with something we now have making a new useful thing, become lethal.
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#5
Quote:because at some point in the evolutionary past some version of it served our ancestors well.

Plus viruses integrating in it, transposons and repeating sequences overflowing.

Quote:If you go rewriting it, using it to compute, etc, you are disrupting the process of recombination across time, and suddenly tiny little mutations that might otherwise have reactivated something potentially useful or combined it with something we now have making a new useful thing, become lethal.

I guess that "computing" here can go from activating a very simple, very localized scavenging gene package in response to a toxine entering the cell or binding to a receptor to the membrane, to "true" biocomputing, in the OA sense. In the latter case you need a knowledge of the orgainsm nearly perfect, the former is quite similar to what we do now to select recombinanting bacteria, but it would be madness do it on a genome as complex as the human one right now. Too many things that can go wrong.
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#6
(12-22-2020, 07:53 AM)Vitto Wrote:
Quote:because at some point in the evolutionary past some version of it served our ancestors well.

Plus viruses integrating in it, transposons and repeating sequences overflowing.
Well, in the sense of beings whose DNA we inherit.... those viruses are in fact among our ancestors.
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