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LaTomate's Avatar Joined about 6 years ago
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Go to: Biology Enters 'The Matrix' Through New Computer Language

LaTomate's Avatar Jump to comment 61 by LaTomate

LISP = LISt Processor - a pretty old but constantly evolving programming language still widely in use today.

Lots of stuff to know about it. Should have its own article on Wikipedia (if not I'm outraged) which you can check out.

Mon, 28 Jul 2008 09:12:00 UTC | #208868

Go to: Biology Enters 'The Matrix' Through New Computer Language

LaTomate's Avatar Jump to comment 45 by LaTomate


I've noticed that people with little or no background in computing often tend to think programming a computer to do something is out-of-this-world.

Yeah, we're magicians. We do magic. There's nothing we cannot do, no problem we cannot solve. Yet nothing we can do well.

When something goes wrong in any part of your company, it's probably our fault. If something goes right, it definitely has nothing to do with us though.

Common knowledge :p

Mon, 28 Jul 2008 01:46:00 UTC | #208589

Go to: Biology Enters 'The Matrix' Through New Computer Language

LaTomate's Avatar Jump to comment 17 by LaTomate


When I was in school I thought that there would soon be programs that could instantly determine what 3D shape a protein would take based only on its peptide sequence, or the reverse. Just type in the shape and properties of the active site you're looking for and BLAMO: instant biopharmaceuticals.

It's been a while (I have stopped in this field for over 5 years) but determining the 3d structure of a protein based on its peptide sequence algorithmically is utter hell - it's an exponential computation and so is practically impossible.

What we can try and do is use artificial intelligence to try and guess the 3d structure based on training using the proteins we already know (and which have been determined using other chemical and physical techniques). Of course, these guesses won't be 100% correct, and so is not absolutely trustworthy. At the time I would have thought that the domain would have moved forward, but it seems we are still blocked by the complexity of the problem.

I once worked on the prediction of RNA secondary structures using dynamic programming. It was an extremely complex thing for technical reasons - recursive pseudoknots can give you quite a few sleepless nights :)

Anyways, I believed that using a multi-agent system - an agent per peptide would be a good place to start looking - attempting to minimize some sort of energy function, would perhaps be worth investigating to solve these folding problems. I have never suggested it though (this is a first for me) and have never heard of it being used.

As I said, I have left this domain of science (did not get phd funding at the time) but I'm still very interested in it, although time lacking, I am not up to par on the literature.

[Edit] thanks for the link ChewToy. I'll check it out :)

Sun, 27 Jul 2008 17:56:00 UTC | #208476

Go to: Biology Enters 'The Matrix' Through New Computer Language

LaTomate's Avatar Jump to comment 10 by LaTomate

I'm a software engineer, having specialized in bio-computing and artificial intelligence in uni. Ok, so now I'm in 3D graphics and video games, but hey.

I'm actually very surprised that this had not been done before. Inference engines (implemented using LISP or Prolog which are ideal for the job) have been around for decades.

Maybe it's our understanding of the cells that was behind and is now sufficient to implement this sort of thing.

My interest in the field is artificial selection to develop "intelligent" programs, extremely well adapted to their task, and better (though often less consistent) than anything an engineer would have come up with. We now metaprogram, rather than program. I love it :)

[Edit] for artificial selection, check this out. it's old, but hot.

Sun, 27 Jul 2008 15:16:00 UTC | #208423

Go to: Escape or betrayal.

LaTomate's Avatar Jump to comment 22 by LaTomate

It is a pretty well known fact that many women who suffer from domestic abuse, be they Muslim or not, have a very difficult time severing their bond with the abuser. It is very hard to help them get out of their situation as well.

One of my good friends who suffered for years (her daughters also got beaten sometimes) is divorcing and is now fighting back. She is not a Muslim at all, rather a "secular catholic". I wish her all the best.

What is sure though is that in the Muslim world it is a lot harder to get out of the situation, since most Sharia courts would grant custody of the children to the abusive father.

Fri, 25 Jul 2008 00:48:00 UTC | #206851

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