Biology Enters 'The Matrix'
by JoyYep. That's the headline. Whole thing reads…
Biology Enters 'The Matrix' Through New Computer Language
Bradford posted about a Protein Folding Game, where scientists are hoping humans turn out to be more efficient than computer modeling programs have been at functional folding. This article is about a new computer language that can mimic the 'mind' of a cell.
Yep. You read that right. Enter "Little b," working off an AI programming language called LISP…
"LISP isn't like typical programs, it's more like a conversation," says Gunawardena. "When we input data into Little b, Little b responds to it and reasons over the data."
For example, Gunawardena's lab works on kinases, a kind of protein that transfers phosphate chemicals to other proteins in order to regulate their activity. While this property is common to all kinases, there is a great deal of variety in how particular kinases carry this out. Little b, however, understands this basic property of kinases, this abstraction.
Little b promises to model complex protein folding, molecular machine construction (with function built-in) and complex biochemical interactions.
"This language is stepping into an unknown universe, when your computer starts building things for you," says Gunawardena. "Your whole relationship with the computer becomes a different one. You've ceded some control to the machine. The machine is drawing inferences on your behalf and constructing things for you."
So. The question seems obvious to me. If you design a machine that designs, and it in turn informs you that indeed the designs are designed, will the Darwinian die-hards believe it?
July 26th, 2008 at 1:22 am
Joy:
No. Some anti-designists have a cultish attachment to their view.
Comment by Bradford — July 26, 2008 @ 1:22 am
July 26th, 2008 at 5:10 pm
Bradford:
"Cultish" is a harsh word to use here, Bradford. Given that it equally applies to Creationists of all varieties as well as anyone whose metaphysical belief system encompasses design in life and evolution.
But it is a "metaphysical" commitment. No matter how hard they try to assert that it's not an a priori metaphysical commitment (answers before questions asked), they're only fooling themselves. From both ends of the spectrum of a priori metaphysical commitments to be made about life and evolution.
Science isn't really about metaphysics, so it doesn't answer metaphysical questions or seek to confirm anyone's metaphysical views. Yet it is also true that the questions we ask – and expect science to answer – arise from metaphysics. Understanding that much will allow philosophy to participate as it should, instead of being the ugly red-headed stepchild of both theology and science.
I have read some threads over on PZ's hate-rag over the past couple of weeks that serve no purpose other than to allow utterly irrational haters to back-slap each other on how vehement their hatred is (and how 'well' they express it). That has nothing whatsoever to do with science. It never will have anything whatsoever to do with science. It's just semi-mentally handicapped antisocial wannabe mind-tyrants getting together for a hate-fest. Ho, hum.
I've seen hundreds of 'em screaming to high heaven (in print) that there is no God, no one should be allowed to believe there might be a God, and kill 'em all, let God sort it out. Basic juvenile crap from people who never actually reached puberty.
They don't know. Any more than the Pope knows. We all just believe, because we can and we're inclined to. From our beliefs our science flows. Or stagnates, depending on who's in charge at the time. All mere history, yet another entirely human endeavor.
Comment by Joy — July 26, 2008 @ 5:10 pm
July 26th, 2008 at 5:24 pm
Some anti-designists have a cultish attachment to their view.
You reminded me of something I had overlooked. Some of the harshest critics of ID are creationists who think IDers have cut God out of the mix. Of course that is not the case- at least for this IDer. It is simply a matter of the type of evidence cited and what it is that one is attempting to support with that evidence.
I find that there is a core group of anti-ID fanatics who show cult-like behavior. They are those who are so desperate to discredit those, not holding their preferred metaphysical outlook, that stooping to trolling and sock puppeting, to get around blog rules, is not too low. Gossip and mean spirited commentary also is par for the course with these types.
Comment by Bradford — July 26, 2008 @ 5:24 pm
July 26th, 2008 at 5:51 pm
LISP is cool, but I think what they missed was not LISPs ability to define domain-specific languages, but rather the genome's ability to do so. This was the topic I covered at the BSG meeting a few years ago. If biologists wanted to think with their design caps, they should be looking for these suckers. This year at BSG, I'll be talking about how to detect higher-order mechanisms at work in the genome.
Comment by johnnyb — July 26, 2008 @ 5:51 pm
July 26th, 2008 at 5:56 pm
Bradford:
Unless we wish to label all adamant, reality-ignoring belief systems "cults," I'd avoid the term. The personality traits that lead one to behave in such socially aberrant ways belong to individuals, not to institutions (though institutions can exist to amplify such traits).
The pure obsession displayed by some of our more notorious commenters and puppets is indeed fairly amazing. But more for the personality deficit it reveals than that they'd physically attempt such garbage. I honestly don't care that I'm called names over at the Swamp, or that they'd engage in obviously libelous epithetic screeds against me personally on top of that. I've never actually met a single one of them, they obviously don't know what they're talking about. They just like to hear themselves talk, and really, really enjoy the civilizationally seditious expansions on a theme. Juvenile delinquents. My favorite tactic is to spank 'em (or slap 'em hard).
I don't have a mean spirit. I have a mean streak. Earned quite honestly, and wielded in the same fashion. I tend not to hold grudges, though. Unless someone has earned it. In which case, I figure they know they deserve it. I'm sure they care about as much as I do – not much at all.
But if I ran my own blog on the subject, I'd have no compunction at all against consigning 'em to purgatory (or hell) sans appeal. If I made a living on my reputation as an honest dealer, I'd sue the shit out of any inter-pseud who wasted entire threads on calling me dishonest. I'd win, too. Fortunately for our unfriendly swamp denizens, I am not important enough to have an ego they can destroy. There's much to be said in that position's favor.
Comment by Joy — July 26, 2008 @ 5:56 pm
July 26th, 2008 at 7:11 pm
johnnyb:
Wow, that's very cool! Can you elaborate on this some? I'm not sure (or even semi-confident) that I understand what's been reported, and what's actually going on.
Don't give us the farm, but again – more details please!
Comment by Joy — July 26, 2008 @ 7:11 pm
July 26th, 2008 at 8:11 pm
Why wouldn't they? Machines are quite capable of design.
Comment by Zachriel — July 26, 2008 @ 8:11 pm
July 27th, 2008 at 2:45 am
Joy -
I went ahead and posted a summary of my 2006 BSG presentation about metaprogramming and V(D)J recombination. The 2008 BSG is in two weeks, so I'll try to remember to record a video of a practice presentation and post it in the next three weeks.
Comment by johnnyb — July 27, 2008 @ 2:45 am
July 27th, 2008 at 5:38 pm
Thanks so much, Johnny! I've downloaded the pdf and bookmarked the publisher's page. It may take me awhile, and I may need some remedial education, but it looks very interesting indeed!
Comment by Joy — July 27, 2008 @ 5:38 pm