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."

Comments

True AI?

[AviN456]

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?

[Rei]

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. :)

Re:True AI?

[AKAImBatman]

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.

Incentive?

[m50d]

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?

[ScentCone]

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:This is pointless

[Spy der Mann]

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 New?

[Anonymous Coward]

I think it might have been attempting humour...

-1, Groupthink

[Gothmolly]

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.

Re:True AI? Read the Numbers

[Quirk]

From Man and Machine An average human brain contains about 100 Billion neurons, although, at this point in your life, you may have fewer.

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.