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Open source Digital Bacteria

Hemos posted more than 8 years ago | from the create-your-own-share-it-with-your-friends dept.

Software 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."

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125 comments

True AI? (2, Insightful)

AviN456 (863971) | more than 8 years ago | (#12736935)

This brings up the question of could this be used to create a true AI, or perhaps even a way to store a human conciousness, which would have useful applications for people with major illnesses or injuries.

Re:True AI? (3, Insightful)

Rei (128717) | more than 8 years ago | (#12736987)

Seems to just be a more realistic version of something like PolyWorld [beanblossom.in.us] . Still quite interesting.

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? (4, Insightful)

AKAImBatman (238306) | more than 8 years ago | (#12737147)

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.

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? (0)

Anonymous Coward | more than 8 years ago | (#12737315)

I think the real issue here is people are afraid of what they might discover if they dig deep enough to discover how neurons work at the lowest level.

Some scenarios:

- This discovery causes the casual evolutionary enthusiast to question his thinking. Perhaps there was a creator who planned it all out? You don't have to look far back in history to find examples of egos getting in the way of scientific discovery.

- We find that quantum-level interactions and randomness do indeed play a part in the development and functioning of neuron cells. Not because it was thought to be necessary, rather, because it evolved that way without rules or guidelines, so to speak. Yet again this discovery would create controversy and divide scientists into groups of believers and doubters.

- We discover that there is only one possible way neurons could have evolved. This will no doubt be unsettling to the open-source camp, the kind of folks who extol the virtues of choice. For Word, there is Wordperfect and OO.o. For windows, there is Mac OS X. For carburetors, there is electronic fuel injection, and so on. But for neurons? There is no other choice. It might be go neuron or go home, which means that it will nearly be computationally impossible to create a real AI that will interact with human players in future fantasy computer games.

So what's holding us back?

Re:True AI? (1)

Rei (128717) | more than 8 years ago | (#12737443)

Not going to happen. Your scenarios require eliminating every other possibility, which is clearly impossible. Even if we could precisely simulate this universe, and had the preposterous amount of CPU necessary to simulate an entire universe, the number of "possibilities" at each step along the way rules out practicable encountering of the specific route that led to our existance.

The further distanced you get from precisely simulating our universe, the less of the potential search space you're covering. Absense of evidence is not evidence of absense until one has covered a relevant portion of the search space.

What we can do with this is find possible ways for intelligence to occur - positive confirmation, as opposed to negative confirmation.

Re:True AI? (1)

AviN456 (863971) | more than 8 years ago | (#12737641)

Obviously this is nowhere near the complexity you would require to mimic the human brain, but is it a start?

Re:True AI? (1)

MightyMartian (840721) | more than 8 years ago | (#12737720)

I don't think anything like that is holding anybody back. The problem is that we simply don't know enough about how the brain functions to get a good model that we could transfer over to silicon (or whatever material we end up building computers out of). The brain is not a piece of end-user engineering. It's a complicated organ that has gone through a lot of modification during its evolutionary history, and it's pretty tough to reverse engineer something like that.

Mindcreators (0)

Anonymous Coward | more than 8 years ago | (#12737776)


http://www.mindcreators.com/ [mindcreators.com]

This is an interesting site which displays some fascinating results from simulating cockroach behavior. Big deal, you may think, but this guy simulated not the cockroach as a whole, but various pieces, such as antennae, muscle control, leg synchronization, etc.
I was unable to find the source code - the author doesn't claim to make it available - but there is an incredible amount of detail regarding the hows and whys of the development process.

And oh, yeah, there are lots of movies and pictures... ;)

Re:True AI? (0)

Anonymous Coward | more than 8 years ago | (#12737678)

No it doesn't.

Incentive? (1, Insightful)

m50d (797211) | more than 8 years ago | (#12736952)

Why are those who improve this going to release their changes? Hopefully some real open source people will pick it up and add good things to the public version, but I wonder about a big company making their own version and keeping it propriety. Big biotech is hardly a historically open environment, is it?

Re:Incentive? (2, Insightful)

ScentCone (795499) | more than 8 years ago | (#12737015)

Hopefully some real open source people

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 ones are publicly help companies, and are under unbelievable scrutiny, with a lot at stake if they do the wrong things IP-wise.

Re:Incentive? (1)

Omnifarious (11933) | more than 8 years ago | (#12737177)

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? (0, Flamebait)

REBloomfield (550182) | more than 8 years ago | (#12737030)

It's a BSD license. No one has to release any changes. And whether you hippy idealists disagree doesn't matter.

Re:Incentive? (0)

Anonymous Coward | more than 8 years ago | (#12737255)

Which is precisely why I like the GPL. I just like the feeling of slapping the corporate fascists in the face.

Re:Incentive? (1)

m50d (797211) | more than 8 years ago | (#12737372)

No, exactly, no one has to release any changes. That makes me wonder whether anyone will. So their "hope" may be unfounded.

All that hate (1)

Enoch Lockwood (889602) | more than 8 years ago | (#12737660)

Sigh. How can you hate Freedom so much? ;-)

But seriously. What good is free software that can be locked down by some corp the moment it is released?

Re:All that hate (0)

Anonymous Coward | more than 8 years ago | (#12737801)

We use BSD licensed software, and we give back changes that we make.

Next time we pull from the head of CVS, we don't have to merge to get our changes back in. They are already in the tree.

If you don't understand that, you never will.

Am I the only one? (1)

kabocox (199019) | more than 8 years ago | (#12736960)

Am I the only one the looked at the pictures and thought of core wars?

Am I the only one?-Digital Terrorism. (0)

Anonymous Coward | more than 8 years ago | (#12737008)

Yes, I was thinking about better viruses, trojans, and worms.

Re:Am I the only one? (0)

Anonymous Coward | more than 8 years ago | (#12737773)

nope! count me in.

core wars and other games (1)

handy_vandal (606174) | more than 8 years ago | (#12737868)

Am I the only one the looked at the pictures and thought of core wars?

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

Combatting bioterrorism? (-1, Troll)

Gothmolly (148874) | more than 8 years ago | (#12736962)

Rather, how long before the nice Men in Black show up at their door, confiscate the code, throw them all in jail, and get Con-gress to pass a law against this sort of thing, on the grounds that it could be used to ADVANCE bioterrorism?

Re:Combatting bioterrorism? (2, Interesting)

ScentCone (795499) | more than 8 years ago | (#12737100)

Rather, how long before the nice Men in Black show up at their door, confiscate the code, throw them all in jail, and get Con-gress to pass a law against this sort of thing, on the grounds that it could be used to ADVANCE bioterrorism?

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 people fast enough in that area, they pay's good, the need is real... oh, never mind. That sort of info takes all fun out of wearing the hat. My bad!

Re:Combatting bioterrorism? (1)

corrosive_nf (744601) | more than 8 years ago | (#12737108)

Thats is a stupid analogy, thats like saying they would put you in jail for taking physics because it could advance nuclear terrorism.

Probably after the actually release it. (2, Funny)

955301 (209856) | more than 8 years ago | (#12737158)


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.

Open Sores. (0)

Anonymous Coward | more than 8 years ago | (#12737330)

"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."

Open Source AIDS.

-1, Groupthink (2, Insightful)

Gothmolly (148874) | more than 8 years ago | (#12737542)

How is this a troll? The FAA is considering banning cell phone usage on airplanes, since attackers could use it to coordinate hijackings. Uncle Sam is the one with the tinfoil hat.

Huh? (1, Funny)

yanndug (832046) | more than 8 years ago | (#12736965)

Will my anti-virus interfere with this software?

Re:Huh? (2, Funny)

Leroy_Brown242 (683141) | more than 8 years ago | (#12737187)

Virii and bacteria are totally different. I think you're fine. :)

Re:Huh? (0)

Anonymous Coward | more than 8 years ago | (#12737705)

Virii and bacteria are totally different.

Yes. "Bacteria" is the proper plural of "bacterium."
"Virii" is not a proper plural of anything.

Poor server... (4, Funny)

Cobra_666 (777517) | more than 8 years ago | (#12736972)

Saying "Lots of movies and pictures are available" in a Slashdot article is like a death sentence to the poor server running the site...

Re:Poor server... (1)

Kjuib (584451) | more than 8 years ago | (#12737018)

Maybe that was the whole plan. Competitors Post site on slashdot... destory servers... Info is not lost to the world... 3. Profit
Sounds like a good plan to me.

(Maybe not Competitor.. but government?!)

This is of course just speculation.

Re:Poor server... (1)

Stibidor (874526) | more than 8 years ago | (#12737365)

I'm getting 159 KB/sec. Seems to be working fine so far. :)

Re:Poor server... (1)

iwan-nl (832236) | more than 8 years ago | (#12737764)

Must be a pretty nice server; The biggest movie is 172 Mb, but it's still doing fine. Maybe this proves no one reads TFA.

Re:Poor server... (1, Funny)

Anonymous Coward | more than 8 years ago | (#12737394)

Oh boy, I can't wait until that "joke" is repeated again in the *next* article. :-/

I, for one, (-1, Redundant)

null etc. (524767) | more than 8 years ago | (#12736977)

...welcome our new digital bacterium overlords.

Ugh. Yes, I know. You don't have to say it.

This Is New? (5, Funny)

Spencerian (465343) | more than 8 years ago | (#12736981)

It seems that Windows users receive free copies of stuff like this each time they connect to the Internet and get their mail.

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? (1)

null etc. (524767) | more than 8 years ago | (#12737016)

I remember the old game of "Life" that simulated growth with very simple rules. Sounds like the game has grown up.

To be technical, Life simulated cellular automata, which can demonstrate, but is not limited to, growth.

Re:This Is New? (4, Interesting)

Rei (128717) | more than 8 years ago | (#12737093)

This isn't really a variant on Conway's Game of Life - it's closer to a variant on Polyworld. Of course, if you want a grown up Conway's Game of Life, I wrote one called Megaconway [daughtersoftiresias.org] a while back - massive worlds made possible by using each byte to store 8 squares and doing operations in bulk wherever possible. It also keeps entropy in the world with occasional random inputs of randomness of varying sizes. My big hope, although I doubt it will occur, is that eventually it will come up with a system that is stable, self-perpetuating, and can "heal" from random damage. Who knows... I leave it running niced to 19 at all times.

Re:This Is New? (2, Funny)

Blue-Footed Boobie (799209) | more than 8 years ago | (#12737215)

I tried to run your program from the link, but there wasn't a Setup.exe. Just a bunch of strange files.

I think maybe you have a virus.

Re:This Is New? (1)

Rei (128717) | more than 8 years ago | (#12737245)

Yes. Those strange files are called "code" and "output". Note the ".c" extension and the files starting with the word "outfile".

Of course, you were simply trolling and pretending to be a newbie, but I have a nasty habit of feeding trolls. :)

Next Obscure Programming Game (1)

N3Roaster (888781) | more than 8 years ago | (#12736991)

It looks very cool, but it also looks like it could make a neat programming game.

What about us? (0)

Thauma (35771) | more than 8 years ago | (#12736993)

And just how do we know our entire reality isn't simply a large scale version of this? Is our universe simply the inside of a box? Does it even matter?

Re:What about us? (4, Funny)

ScentCone (795499) | more than 8 years ago | (#12737052)

And just how do we know our entire reality isn't simply a large scale version of this? Is our universe simply the inside of a box? Does it even matter?

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? (1)

Brahgam (774597) | more than 8 years ago | (#12737393)

Hey! haven't you learned anything from "The Matrix"? Tell Neo if he can't operate beyond the framework of his universe!

Re:What about us? (2, Interesting)

bcmm (768152) | more than 8 years ago | (#12737517)

Trouble is, in The Matrix, Neo's brain (and, for that matter, a functional body) are physically outside the simulation.

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 designed them.

I wonder if any of the theories that constants like the speed of light or the cosmological constant are changing are correct, and if so if whoever coded that kludge got in trouble...

Re:What about us? (1)

N3Roaster (888781) | more than 8 years ago | (#12737103)

We don't (if we did, it would be a lousy simulation), no way to know (I'll bet no), and not in the slightest (unless you like being pathetic). Not bad to think about, but if you don't have an exploit that removes you from the simulation while preserving yourself beyond it, there isn't anything to be gained by considering the simulation to be anything but either reality or indistinguishable from reality (meaningless).

Re:What about us? (1)

bcmm (768152) | more than 8 years ago | (#12737447)

But it is a lousy simulation! Doesn't quantum uncertainty look like a kludge? Doesn't the strong force look like it's been played with to make things work nicely?

(No I am not a creationist)

Re:What about us? (1)

mizhi (186984) | more than 8 years ago | (#12737508)

Maybe for the professional navel gazers out there, but the practical applications of such knowledge are nil. Except maybe to stick our tongues every once in a while at some uber unix geek observing our universe.

...and combating bioterrorism (0)

Anonymous Coward | more than 8 years ago | (#12736994)


or creating it
knowledge can be used for good and bad
guess which side you are on

Cell hardware + Cell software = (0)

Anonymous Coward | more than 8 years ago | (#12737028)

Skynet, is that you?

This is pointless (-1, Troll)

Anonymous Coward | more than 8 years ago | (#12737080)

That piece is of software is retarted. Why should someone emulate an E.Coli and it's reaction to stuff with a Computer, rather than looking through a Microscope?

It looks more like Microbiologists are lazy people who are just trying to save a little bit work.

BUT: The open source part is cool! ;)

Re:This is pointless (2, Insightful)

Spy der Mann (805235) | more than 8 years ago | (#12737138)

It looks more like Microbiologists are lazy people who are just trying to save a little bit work.

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 (2, Informative)

macklin01 (760841) | more than 8 years ago | (#12737228)

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 control. Want to test the effect of a different mutation rate in gene X? No problem. Vary that effect in your model only and don't change anything else. There's some good science to be conducted once the numerical implementation and the biophysical models have been validated.

Then there's cost. You can run many simulations and obtain a vast amount of data in the same time and for much less cost than it would take to run a few physical experiments. So, run a few hundred computer sims to determine which physical experiments are worth conducting; now physical lab time is more focused and more efficient. -- Paul

Digital disease (5, Funny)

lilrowdy18 (870767) | more than 8 years ago | (#12737117)

Anybody know the cure for digital chlamydia?

I networked with this infected computer and didnt have my firewall turned on.

oh no! (1)

ImaLamer (260199) | more than 8 years ago | (#12737699)

You've got to be careful.

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. /Rimshot

Re:Digital disease (0)

Anonymous Coward | more than 8 years ago | (#12737782)

Sure,

On Unix, become root and type:
rm -f /

and on Windows, become admin and type
format C:

That should clear the problem up in no time.;-)

(Newbie warning, note the ;-) and beware)

Re:Digital disease (1)

lilrowdy18 (870767) | more than 8 years ago | (#12737951)

OK so what your saying to do is go to start>run type in cmd and hit enter.

OK now type in format C: and I hit enter.

Just great. My computer wont boot now and I still have the discharge and itching. I mean my computer still has the discharge and itching.

Yeah my computer. Thats what i meant.

space invaders (1)

milktoastman (572643) | more than 8 years ago | (#12737119)

I think I'll add a modification to this code to make all the little bacteria make the space invaders noise...'VOOMP-voomp-voomp-voomp-VOOMP-voomp-vomp- voomp....CHUH-CHUH-CHUH-CHUH-CHUH-DZZZZ...' You've been eaten.

Pathogen games for the PS3 (3, Funny)

CardiganKiller (854899) | more than 8 years ago | (#12737123)

"For instance, if you mix a pathogenic strain with a friendly strain, which one is going to win, and with what kind of speed?"

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 (1)

Perl-Pusher (555592) | more than 8 years ago | (#12737229)

"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

And with the addition of malware modules and networking might be used to promote cyberterrorism said lead engineer 133t h@x0r.

Why BSD? (0, Troll)

Adam Avangelist (808947) | more than 8 years ago | (#12737233)

If it is released under the BSD liscense, it will not encourage terrorists to give back to the community.

Re:Why BSD? (0)

Anonymous Coward | more than 8 years ago | (#12737454)

like they give a shit anyway??? Are you being funny?

So... (1)

suitepotato (863945) | more than 8 years ago | (#12737241)

...who's going to write the open-source simulator code to model the Fritos crumbs, dirty socks, and body soil and sweat for the sim-bacteria to feed on, and who's going to write the sim anti-bacterial spray to clean it up and... will anyone get the message?

I can see them writing the press release now... (3, Funny)

nanoakron (234907) | more than 8 years ago | (#12737281)

Alice: Yeah...make sure we stick 'combat terrorism' in there somewhere. That'll make sure we get the cash.

Bob: Oooh ooh...and maybe the frontpage on some reputable internet discussion board *cough*.

-Nano.

Re:I can see them writing the press release now... (0)

Anonymous Coward | more than 8 years ago | (#12737338)

Bob: Oooh ooh...and maybe the frontpage on some reputable internet discussion board *cough*.

How did it end up here?

SIMS X? (1)

COMON$ (806135) | more than 8 years ago | (#12737297)

Ahhh yes, one step closer to having myself cloned into a virtual sim, this way I can see whether or not I will survive a gunshot, fall or if I should procreate....

combating bioterrorism (3, Interesting)

exp(pi*sqrt(163)) (613870) | more than 8 years ago | (#12737309)

!!!

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 (2, Informative)

Daniel Dvorkin (106857) | more than 8 years ago | (#12737666)

The thing is, anything that helps us fight infectious disease in general may also help with "combating bioterrorism." And a good simulation of the response of bacterial populations, which often show emergent behavior, respond to biochemical stimuli may very well be helpful in coming up with new methods of diagnosis and treatment. (For an understanding of why this is so, check out work on swarming behavior [nih.gov] , and the research interests page of Leah Edelstein-Keshet [math.ubc.ca] , one of the leading researchers in the field.) I'm not any happier than you are about how the bioterrorism card is played in every grant application, but it really is one of many valid applications here.

Re:combating bioterrorism (2, Interesting)

Frumious Wombat (845680) | more than 8 years ago | (#12737671)

Strangely enough, sometimes theoretical underpinnings are crucial to end-user applications. Yes, maybe this should have been funded by a grant from NIH (new bacterial simulator), NSF (ibid), FDA/DoAg (food contamination), or DOE (model potential industrial organisms), rather than DoHS, but e. Coli is both (a) well-understood and (b) a real problem in our food supply. A good e. coli simulator could, as they've already demonstrated, teach us quite a bit about potential pathogens, or be generalized into an organismal simulator for other, more potentially useful, bacteria.

In principle, presume that you model various strategies of optimizing for methanogens, leading to a shorter development time for biofuels, or even optimize e. coli for better use in industrial synthesis (i.e. an e. coli that will produce 20% more HGH for the same feed input). As long as the model is directly related to experiments, this is a great idea, and will lead us towards a future where eukaryotes (such as your cells, or more plausibly food crops), can be digitally screened and optimized for their response to various promotors and inhibitors.

What's the worst that happens; someone has figured out how to get DoHS to pay for an improved version of Life, and fabulous new screensavers are developed! In all seriousness, the outcome should be much more promising than that. This is one more step to placing usable molecular biology tools into everyone's hands. You could look at individual molecules, and now you can simulate the workhorse of microbiology, without having to have petri dishes or autoclaves around until the last stages of the experiments. I, for one (remembering the smell of agar in the morning), welcome this development.

Re:combating bioterrorism (1)

macklin01 (760841) | more than 8 years ago | (#12737750)

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, e.g., on a water supply.

-- Paul

mo3 up (-1, Redundant)

Anonymous Coward | more than 8 years ago | (#12737313)

successes with the* is the group that the reaper BSD's

Interesting Issues (2, Funny)

stevev007 (887227) | more than 8 years ago | (#12737318)

How many times have we all complained about having to use non-OSS because it was our only option that accomplished what we wanted it to. I personally have felt this way dozens of times.

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? (2, Funny)

tilleyrw (56427) | more than 8 years ago | (#12737327)

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? (2, Funny)

c0d3h4x0r (604141) | more than 8 years ago | (#12737371)

Scientists have constructed a software capable of simulating organisms at the molecular, single-cell and population levels.

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? (1)

Eric604 (798298) | more than 8 years ago | (#12737516)

No, but I am the only one that predicted that someone would misread it like that and scrolled down to search for that post.

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? (0)

Anonymous Coward | more than 8 years ago | (#12737902)

Imagine the military applications of software capable of simulating orgasms at the population level!

That's the secret holy grail of the military subcontractors collectively known to the outside only as the "porn industry."

Aha! (1)

Comatose51 (687974) | more than 8 years ago | (#12737382)

Aha! I knew OSS supports terrorists, communists, and is anti-American. What else would a digital bacteria be for?! Other than to infect the computers of law-abiding, copyright-fearing, Windows users?! Isn't that what all bacterias do after all....

Anyone else think this? (1)

malikvlc (889549) | more than 8 years ago | (#12737503)

Read the title and thought it was another of those "the GPL is a virus" rants/FUD articles...

AgentCell? (1)

tekrat (242117) | more than 8 years ago | (#12737638)

Sounds like it should be one of those Tom Clancey videogames for the Xbox where you walk around with night-vision goggles and shoot people.

Open Source Everything (0)

Anonymous Coward | more than 8 years ago | (#12737681)

I know that this isn't what the article is about, but what if instead of drugs and anti-bodies being owned by the companies that created them, we could have "open source drugs," like a grad student cooks up a drug and just releases it as public knowlege, like anyone can look at the formula and make changes. Maybe even a REAL open source bacteria! like the DNA is open source!

Stocks as living entity (0)

Anonymous Coward | more than 8 years ago | (#12737698)

What would be the potential of it being used to simulate stocks. I'm gonna buy a really really big virtual petri-dish for my primordial Stock portfolio, I'm gonna be virtually rich and I welcome our virtual bacterial Overlords

IBM + UofC + ANL = digital meningitis? (1)

AviN456 (863971) | more than 8 years ago | (#12737718)

If IBM ran AgentCell on their virtual brain [slashdot.org] , perhaps we could find ways to reduce the damage caused by brain infections
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