Open source Digital Bacteria 125
FiReaNGeL writes "Scientists have constructed a software capable of simulating organisms at the molecular, single-cell and population levels. The program, called AgentCell, will soon be available, open sourced under a BSD license. "With AgentCell we can simulate the behavior of entire populations of cells as they sense their environment, respond to stimuli and move in a three-dimensional world". The researchers have designed their digital bacterial system in modules, so that additional components may be added later - "The hope is that people will modify the code or add some new capabilities". AgentCell has possible applications in cancer research, drug development and combating bioterrorism. Lots of movies and pictures are available, along with a detailed press release describing the program."
True AI? (Score:1, Insightful)
Re:True AI? (Score:4, Insightful)
If you want a "AI" that borders on a consciousness, you don't want to start at this level - that's way too much work. You want to algorithmicly be simulating entire cells or even groups of cells at once, instead of components of cells. The higher up you can shift the behavior, the more computation you can get done.
Hmm... this may tempt me to play with Framsticks and [alife.pl] Avida [caltech.edu] some more.
Re:True AI? (Score:5, Insightful)
Except for one problem: You're assuming that we actually know how the brain functions. Neural networks are interesting, but to date they've failed to show the levels of intelligence of a comparable animal. On top of that, they don't actually model the brain's neural patterns correctly.
Experiments at a lower level may produce greater insight, especially if we're missing something tricky such as encoded waveforms in neural pulses. Lower level simulations would allow us to explore the differences between the simulation and the real thing, thus producing loads of data on things we might be missing.
Re:True AI? (Score:2)
The further distanced you get from precisely simulating our universe, the less of the potential search space you're covering.
Re:True AI? (Score:1)
Re:True AI? (Score:2)
Re:True AI? Read the Numbers (Score:3, Insightful)
An average neuron has 1500 signal connections to other neurons.There are about 0.15 quadrillion of these "synapses" in the brain.
The senses transduce external stimuli into neural action which modifies the states of connected neurons. Each of the 100 Billion neurons in your brain is in a changing state at every instant
It is interesting to estimate how many arith
Re:True AI? Read the Numbers (Score:2)
But then I went and calculated your first calculation, and that's where the error was; you added one too many zeros, but then took one away with the exponential. So the rest of the numbers are valid, and it's just a typo, not a math error as I at first thought.
Incentive? (Score:1, Insightful)
Re:Incentive? (Score:3, Insightful)
Because people who work for companies are fake open source people? Sometimes the only people who can still eat, have a roof over their head, and still be able to put in 14 hours a day on a large project (open source or otherwise) are those working for an organization with some actual money to spend. Some of those are (gasp!) corporations.
Now, if you're suggesting that "big biotech" is going to deliberately break a license clause, that's another story. But the big
Re:Incentive? (Score:2)
Umm... The BSD license doesn't have to be broken in order for some random person or company to close up their version. The software isn't licensed under the GPL, which would prevent this.
Re:Incentive? (Score:2)
All that hate (Score:1)
But seriously. What good is free software that can be locked down by some corp the moment it is released?
Re:All that hate (Score:1)
Y = # of users using project X code
Z = Average usage of project X code, from 0-1
"Goodness" of license = Sum Y*Z over all projects X.
However, given that you'd need to do some serious analysis of survey data to find out how close people are to reporting the truth, it very probably is impossible.
Am I the only one? (Score:2)
core wars and other games (Score:2)
I haven't actually played core wars, but I know what you mean.
What intrigues me is using this kind of bacterial model in a first-person shooter, maybe a Half-Life mod where you fight hostile bacteria in a microscopic maze. The heads-up display elements might resemble FreeAgent diagrams....
-kgj
Huh? (Score:1, Funny)
Re:Huh? (Score:3, Funny)
There are 10 kinds (Score:3, Funny)
Re:There are 10 kinds (Score:3, Funny)
* Those that have off-by-one errors in the code,
* and those that don't.
Re:There are 10 kinds (Score:5, Funny)
Re:There are 10 kinds (Score:2)
Poor server... (Score:4, Funny)
Re:Poor server... (Score:1)
Sounds like a good plan to me.
(Maybe not Competitor.. but government?!)
This is of course just speculation.
Re:Poor server... (Score:2)
Re:Poor server... (Score:1)
Re:Poor server... (Score:1, Funny)
This Is New? (Score:5, Funny)
That, and news on free "sword sharpeners", if ya get my meaning.
I remember the old game of "Life" that simulated growth with very simple rules. Sounds like the game has grown up.
Re:This Is New? (Score:2)
To be technical, Life simulated cellular automata, which can demonstrate, but is not limited to, growth.
Re:This Is New? (Score:5, Interesting)
Re:This Is New? (Score:3, Funny)
I think maybe you have a virus.
Re:This Is New? (Score:2)
Of course, you were simply trolling and pretending to be a newbie, but I have a nasty habit of feeding trolls.
Re:This Is New? (Score:1, Insightful)
Re:This Is New? (Score:2)
Re:This Is New? (Score:2)
First, nice program, it looks huge and very fast. I like to play with CA too, but in java (quite a difference.) I came up with a variation on Conway's which doesn't tend to die of "heat death" as I call it, but it also tends to be a little too chaotic to develop anything real as well.
Here is a link to the Java sim I wrote... [skeeze.net] My documentation sucks, but if you click on the "Fill" button until it reads "Life2", then cl
Great... (Score:3, Funny)
Re:Great... (Score:1)
Next Obscure Programming Game (Score:1)
Re:What about us? (Score:5, Funny)
Well, first, no - if we're in a giant box, and the laws of physics defined therein cause us to see and experience what we're seeing and experiencing, then... no. That's the framework of our universe. We can't operate outside of that framework, so kvetching about it isn't very productive.
And second, you'll be getting the munchies very soon, I'm guessing.
Re:What about us? (Score:1)
Re:What about us? (Score:3, Interesting)
It's also possible to have a simulation that's good enough to simulate matter behaving as a brain, in which case any life being simulated has no existence at all outside of the simulation. It's not impossible for that life to be intelligent, conscious, or self aware, and there would be no way for them to tell they were in a simulation, other than by saying that things looked like someone d
Re:What about us? (Score:2)
It features in Hoffstader & Dennett 'Minds I'
Re:What about us? (Score:2)
Re:What about us? (Score:2)
My point is that it is also possible to have a non Matrix like simulation, in which your brain is actually simulated too. In that situation, there would be no way to tell what was happening and no way out, as you would have no existence outside of the simulation.
Re:What about us? (Score:1)
Re:What about us? (Score:2)
(No I am not a creationist)
Re:What about us? (Score:2)
Daylight and everything.
Re:What about us? (Score:2)
Let's not dis this development - (Score:5, Funny)
Next, the Computer Virus (Score:1)
Its the game of life (Score:1)
Digital disease (Score:5, Funny)
Anybody know the cure for digital chlamydia?
I networked with this infected computer and didnt have my firewall turned on.
oh no! (Score:2)
If that computer was connected to the Internet, you end up networking with everyone they network with.
On top of that, if you're connected to the Internet you can really *screw yourself* in the end.
Re: (Score:1)
Pathogen games for the PS3 (Score:3, Funny)
I can't wait until this becomes an actual game:
"Cell-Wars 3D. Engineer your own pathogens and destroy up to 5000 different types of organisms! Experience multiplayer action over the Internet in a race to be the quickest and most destructive pathogen.
Be sure to enter in our annual contest. The winner will get to see their pathogen recreated in real life by our molecular engineers and injected into a mouse! Total insane action!"
Cyberterrorism (Score:2)
And with the addition of malware modules and networking might be used to promote cyberterrorism said lead engineer 133t h@x0r.
So... (Score:1)
Digital Bacteria (Score:1)
If it were GPL, it'd be a digital virus.
I can see them writing the press release now... (Score:3, Funny)
Bob: Oooh ooh...and maybe the frontpage on some reputable internet discussion board *cough*.
-Nano.
SIMS X? (Score:1)
combating bioterrorism (Score:4, Interesting)
I'd put money on this work being completely bogus. There's quite a bit of funding going to researchers from Fath^H^H^H^HHomeland Security. I'm pretty astonished by the types of reserach these people are doing which really has no practical applications whatsoever. But on paper it makes it look like the department are investing in our security. This sounds like a prime example of such a project. There simply isn't a situation involving bacteria that is both (1) something we can model on a computer and (2) relevant to combating bioterrorism. Sure, we might be able to qualitatively model a population in a petri dish, but that has nothing whatsoever to do with the reality of a terrorist releasing bacteria into the atmosphere, say. But the ignorant politicians working at the department have no way of understanding this for themselves and fund it anyway. Remember, these are the same people who think this [ready.gov] is useful.
So...politicans might be taken in by BS about the applications of these methods, but there's no need for /. readers to be decieved the same way.
Re:combating bioterrorism (Score:3, Informative)
Re:combating bioterrorism (Score:2, Interesting)
Re:combating bioterrorism (Score:2)
I'll bite. Here are two I can think of off the top of my head:
Application one: A collection of bacterial species was selected to detect specific toxins and/or biological agents. This can quantify how they would respond, aiding in the design of a biotoxin and/or chemical detector.
Application two: Species X is known to break down chemical agent Y. A computer model is used to determine the optimal temperature, oxygen, and other environmental settings to use this species in cleanup after a chemical attack
Re:combating bioterrorism (Score:2)
Interesting Issues (Score:2, Funny)
Now, it seems the tables have turned. OSS has turned into the exact thing that it despises. I personally think this article raises some interesting issues, particularly concerning living organisms being forced to use open source just because that is the only option available to them.
Where's the birdie? (Score:2, Funny)
OK, someone was actually given a research grant to produce a new version of Life?
Yes, I'll have what they're smokin', thank you.
Orgasms? (Score:3, Funny)
Am I the only one who had to read that thrice to verify that it in fact did not say "orgasms"?
Imagine the military applications of software capable of simulating orgasms at the population level!
Maybe I just need caffeine.
Re:Orgasms? (Score:1)
Now, before you say you predicted that someone would predict that it would be misread as orgasms... that's impossible, that would require a brain the size of a jumbojet.
Re:Orgasms? (Score:2)
Man, think about something else. You'll go friggin' blind or somethin'.
Aha! (Score:2)
Anyone else think this? (Score:1)
AgentCell? (Score:2)
IBM + UofC + ANL = digital meningitis? (Score:1)
K00l!!! (Score:2)
K00l!!! Do they have a level editor? I'll do the "capture the flag" mod.
fixation on using new tech for military (Score:1)
oops... (Score:1)
openmosix (Score:1)
I'll have to try this out on it.
Open Source Cancer? (Score:1)
I do not believe that (Score:2)
Fully calculating all those parts' movement in all 3 degrees of freedom could prove tricky. Especially taking quantum effects into account.
Even if they do simula
Re:Combatting bioterrorism? (Score:3, Interesting)
Why is that tinfoil-clad perspective any better (more likely) than wondering how long it will be before they're offered jobs at Fort Dietrich or at any of a number of big contractors that are working on exactly this sort of stuff with defense in mind? They can't hire good p
Probably after the actually release it. (Score:3, Funny)
Blockquoth the article:
"As soon as this is done the code will be available for download. Stay tuned."
Besides, the MiB don't operate on the entire planet. Perhaps that's the best argument for releasing something which may have questionable applications as open source - you can't undo it once it's done.
-1, Groupthink (Score:1, Insightful)
Re:This is pointless (Score:3, Insightful)
Yeah, and nuclear scientists are too lazy to build a gazillion particle accelerators so instead of doing hard work, as they SHOULD, they try their tests in a computer simulation, instead. This is outrageous! There's nothing worse than a lazy scientist! [/sarcasm]
Re:This is pointless (Score:3, Informative)
There are many reasons. For one thing, not all physical quantities are easily and accurately measurable. But in a situation like this, you can measure whatever you simulated and gain new insights, right down to the molecular level. Chemical reaction rates in individual cells, intracellular pressures and mechanical stresses, the effects of different mutation rates, the distribution of nutrient concentrations both within the cells and between them, and so forth.
Then there's the issue of experimental cont