Slashdot Mirror
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."
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.
Seems to just be a more realistic version of something like PolyWorld. 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 Avida some more.
We should start dealing in those black-market beagles.
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
Bacteria may be the only culture some people have.
I don't know the meaning of the word 'don't' - J
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.
Don't disappoint your bird dog. Go to the range.
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.
Don't disappoint your bird dog. Go to the range.
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.
Anybody know the cure for digital chlamydia?
I networked with this infected computer and didnt have my firewall turned on.
"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]
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.
Javascript + Nintendo DSi = DSiCade
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?
Virii and bacteria are totally different. I think you're fine. :)
Pretty Pictures!
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
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.
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.
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.
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...
# cat
Damn, my RAM is full of llamas.
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