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Open source Digital Bacteria
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."
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.
- Just because we CAN do a thing, does not mean we SHOULD do that thing.
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?
I am trolling
Am I the only one the looked at the pictures and thought of core wars?
Will my anti-virus interfere with this software?
of bacteria in this world ...
Saying "Lots of movies and pictures are available" in a Slashdot article is like a death sentence to the poor server running the site...
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.
Vos teneo officium eram periculosus ut vos recipero is.
As if Windows didn't have to deal with enough computer viruses, now it has to deal with computer bacteria as well.
multifariam.net -- yet another nerd blog
It looks very cool, but it also looks like it could make a neat programming game.
Remember RFC 873!
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?
or creating it
knowledge can be used for good and bad
guess which side you are on
Bacteria may be the only culture some people have.
I don't know the meaning of the word 'don't' - J
Yes, I was thinking about better viruses, trojans, and worms.
Skynet, is that you?
Can I run the bacteriosim inside my favorite online game?
--
make install -not war
Hey thats the game of life http://www.math.com/students/wonders/life/life.htm l. I remember programming that one for multiple school classes. One of my friends even made it his screen saver.
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!
Don't disappoint your bird dog. Go to the range.
Thats is a stupid analogy, thats like saying they would put you in jail for taking physics because it could advance nuclear terrorism.
"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?"
/ qid=1118074934/sr=2-1/ref=pd_bbs_b_2_1/104-4255005 -2249561
http://www.amazon.com/exec/obidos/ASIN/0312313586
"Kick a rock".
Anybody know the cure for digital chlamydia?
I networked with this infected computer and didnt have my firewall turned on.
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.
"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!"
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]
Whoa... so that's what happens when you get released under the BSD licence?
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.
You are checking your backups, aren't you?
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
OpenSource.MathCancer.org: open source comp bio
And with the addition of malware modules and networking might be used to promote cyberterrorism said lead engineer 133t h@x0r.
If it is released under the BSD liscense, it will not encourage terrorists to give back to the community.
...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?
If my grammar and spelling are off, I am [distracted/tired/careless] (take your pick)
If it were GPL, it'd be a digital virus.
Remember, You are unique...just like everyone else.
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.
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....
CS: It is all sink or swim...oh and did I mention there are sharks in that water?
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 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.
Doesn't it make you feel good to know that our freedoms are protected by politicans, lawyers and journalists.
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.
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.
This post encoded with ROT26. If you can read it, you've violated the DMCA. Handcuffs please, sergeant.
"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.
Bob: Oooh ooh...and maybe the frontpage on some reputable internet discussion board *cough*.
How did it end up here?
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.
Moderator hint: a comment is neither "Flamebait" nor "Troll" if it is true.
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....
EvilCON - Made Famous by
Read the title and thought it was another of those "the GPL is a virus" rants/FUD articles...
Try not. Do... or do not. There is no try. ~Yoda
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.
I want to delete my account but Slashdot doesn't allow it.
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.
If telephones are outlawed, then only outlaws will have telephones.
But seriously. What good is free software that can be locked down by some corp the moment it is released?
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!
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
You've got to be careful.
/Rimshot
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.
Get your Unix fortune now!
If IBM ran AgentCell on their virtual brain, perhaps we could find ways to reduce the damage caused by brain infections
- Just because we CAN do a thing, does not mean we SHOULD do that thing.
http://www.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...
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
-kgj
>> The researchers have designed their digital bacterial system in modules, so that additional components may be added later
K00l!!! Do they have a level editor? I'll do the "capture the flag" mod.
Well according to TFA they have writted "a software", so they jolly well are the lazy chappies! I and my most esteemed Indian chums could have written several softwares in this time.
select * from base where originalOwner = 'you' and currentOwner != 'us'.
0 rows returned.
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 arithmetic operations might be required to simulate an average human brain. If this simulation is done in the simplest possible way - by adding the contribution of every synapse to every neuron we could proceed as follows:
Number of synapses in a brain =
synapses per neuron * neurons in a brain =
1500 * 100 000 000 000 = 1 500 000 000 000 000 = 1.5 x 1014
Number of calculations per synapse = 2 (read current state of synapse, add to sum for connected neuron. Note these are integer operations (not floating point))
Number of calculations per second per synapse = 1000 (allows for a maximum firing rate of 500Hz for each synapse, which is about 2 to 5 times higher than normally recorded)
Total number of integer operations per second = 1.5 x 1014 * 2000 = 3.0 x 1017
Brain:
300,000,000,000,000,000 iOps / second
To Simulate 1 Brain requires 120,000,000 Pentium-4 Processors (each P4 operating at 3Ghz)
We work with models, model are based on presuppositions underlying suppositions which if correct give the model predictive power. We aren't going to map the brain one on one for a long, long, time, if ever. What we can try to do is construct models that allow us to predict how the brain will work given any set of restrictions.
"Academicians are more likely to share each other's toothbrush than each other's nomenclature."
Cohen
An average human brain contains about 100 Billion neurons, although, at this point in your life, you may have fewer.
Oh yeah. I may have had a lot of fun in my youth, but boy - do I have fewer brain cells!
Why is it that when some interesting new technology is developed, the first question that gets asked is "How can we use it for the military?"
in true...this is just an initial step in biological modelling. We yet need more experimental data to develop reliable models, and build oriented models. Real biological systems are much more complex than our modelling capacity today. References?? http://www.nature.com/msb/index.html http://www.fosbe.org/ http://ieeexplore.ieee.org/xpl/RecentIssue.jsp?puN umber=9270
---- Where is my mind?
"But seriously. What good is free software that can be locked down by some corp the moment it is released?"
Funny how with movies,music,and games. It can't be "locked down"(arrrr). But when the converstation switches to GPL vs BSD, suddenly digital CAN BE "locked down". Now don't you guys get tired of talking out of both sides of your mouth?
Here is an interesting idea. Will we prove the validity of the Theory of evolution by going through it with computers and our quest for artificial intelligence. Are we bound to repeat mother nature's path to intelligence? If so, shouldn't it be clear to AI researchers that they need to master the description of each organism as it appeared on Earth?
I've recently implemented a small (6 node) openmosix cluster.
I'll have to try this out on it.
Agent Cell?
Didn't Maxwell Smart have one of those in his shoe?
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.
I feel fantastic, and I'm still alive.
now that we have open source bacteria, i guess ballmer was right when he said "linux is a cancer..."
How could they possibly simulate bacteria, if they are not completely understood yet? You would have to simulate every single molecule of the bacteria. A quick guess is, that bacteria have several billion molecules (a bacteria has a size of about 1 micrometer; that are 1000 to 10000 atoms, which taken to the third power are 10^9 - 10^12. roughly).
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 simulate it on a higher level (proteins, rna and dna) it is too complicated and not fully understood.
And here we are talking about one individual bacterium. To calculate whole colony of those AND their interactions (wich are even less understood): that is a little bit much for me to believe.
They might have a framework, which is able to simulate several "agents" and their interactions in a 3D-world. But it still needs to be fed with a complete description of a bacteria. A _formal_ description. But we are as far away from knowing that as a chemical rocket is from achieving interstellar travel.
I do not doubt it will help researchers all over the world to understand certain aspects and test some theories, but it is only a first step, and a very small one at that.
But IANAMB, so YMMV. Is there a module somewhere in there, that says "mysterious stuff"
Keep open minded - but not that open your brain falls out...