Open-source biotechnology

Posted Mar 31, 2010 16:39 UTC (Wed) by flewellyn (subscriber, #5047)
In reply to: Open-source biotechnology by nix
Parent article: Open-source biotechnology

Given that protein folding is a problem for, well, protein, and not DNA...

Open-source biotechnology

Posted Apr 1, 2010 6:49 UTC (Thu) by mitchskin (subscriber, #32405) [Link] (7 responses)

A lot of DNA expresses itself through proteins. The point nix is making is that a biological system is much, much more difficult to engineer than a software system. The protein folding problem is part of it; that problem makes it very difficult to predict what your DNA modifications will do (you have to solve an n-body problem with a very large n just to figure out what shape your protein will have, and that doesn't necessarily tell you very much about how it will behave).

A big part of engineering (certainly software engineering) involves encapsulation: the hiding of complex behavior behind a simple interface. But in biological systems this is very hard to achieve; there are a lot of processes going on all mixed together in the same solution. That's what nix meant when he sarcastically described "every bit of the program able to modify every other bit"; of course we don't program that way because doing software that way would be total madness. But in biological systems, that's the way things are.

So (to restate what nix was saying): Imagine trying to program a computer system where 1. the behavior of the system is not at all deterministic, 2. the system prevents encapsulation, 3. you can't predict what effects your changes will have.

Evolution has had billions of years on Massively, Massively, Massively parallel hardware to come up with the complex systems we have today. Humans are now only barely able to scratch the surface of the complexity of those systems. There's a lot of excitement now about engineering biological systems, but it's a very long-term project.

Point being, be very careful about making facile analogies between biological systems and computer systems. There are some similarities but there are also very, very significant differences.

Re: the point about other systems trying to eat yours - I actually think internet-connected computer systems are kind of like biological systems that way.

Open-source biotechnology

Posted Apr 1, 2010 6:52 UTC (Thu) by mitchskin (subscriber, #32405) [Link]

I was speaking a little loosely; by "encapsulation" I was also referring to things like process isolation. So it's also like programming a computer without an MMU.

Open-source biotechnology

Posted Apr 1, 2010 14:40 UTC (Thu) by nix (subscriber, #2304) [Link] (2 responses)

Quite so. Note that there *are* modular components in biology: things like
the Hox genes are conserved because so much other stuff depends on them
that if they change, the organism dies. But conserved components like this
are often little more than genetic switches, at most generating protein
that binds to regulatory regions of the DNA: the things that actually do
the *work* are rarely so conserved. (Sometimes they are, but even truly
ancient and insanely well-conserved things like hsp83 occasionally
mutate.)

More generally: conserved stuff has lots of stuff depending on it, so is
often hard to use in isolation; non-conserved stuff often depends upon
conserved stuff, so is often hard to use in isolation.

Open-source biotechnology

Posted Apr 1, 2010 16:45 UTC (Thu) by flewellyn (subscriber, #5047) [Link] (1 responses)

I understand that programs created by genetic algorithms often have similar issues, as far as interdependency and nontrivial interactions between components go. Do you know if this is true?

Open-source biotechnology

Posted Apr 2, 2010 13:47 UTC (Fri) by nix (subscriber, #2304) [Link]

Yes, and for similar reasons. But GA programs have tiny population sizes
and tiny runtimes compared to the sizes and runtimes which have brought us
present-day biology, so they have had less time to accumulate arcana.

Open-source biotechnology

Posted Apr 1, 2010 16:44 UTC (Thu) by flewellyn (subscriber, #5047) [Link] (2 responses)

Yeah, I get all that. I just thought nix had made a mistake attributing the protein folding problem to DNA.

But, it seems I was wrong on that score.

Open-source biotechnology

Posted Apr 2, 2010 16:57 UTC (Fri) by nix (subscriber, #2304) [Link] (1 responses)

Well, technically they're disconnected, but if you want to make DNA that
*does* anything useful, you need to solve the protein folding problem as
well, because the machines that DNA builds are all protein-based. (I think
the only stuff this doesn't apply to is siRNA, which uses antisense
matching, which is of course trivial, particularly given how short siRNAs
are.)

... actually, that's an oversimplification. Some machinery DNA builds
(generally really ancient stuff) is catalytic-RNA-based (e.g. parts of the
ribosome). However, *that* gets its function in the same way as protein
does: it folds into strange 3D shapes, and those shapes have their effects
via the strange intermingling of chemistry and quantum physics which
affects interactions at that scale. So that doesn't help you much. You
still have the horrible folding problem to solve.

Open-source biotechnology

Posted Apr 2, 2010 19:58 UTC (Fri) by mjg59 (subscriber, #23239) [Link]

The last few years have shown that the role of miRNAs are more significant than people had
previously expected, so I wouldn't go so far as to say that the problem domain is pretty much
limited to that impacted by the protein folding problem - on the other hand, I think this is pretty
way off topic at this point...