Bacterial Prisoner's Dilemma and Game Theory 95
dumuzi writes "Scientists studying how bacteria under stress collectively weigh and initiate different survival strategies say they have gained new insights into how humans make strategic decisions that affect their health, wealth and the fate of others in society. The authors of the new study are theoretical physicists and chemists at the University of California, San Diego's Center for Theoretical Biological Physics. In nature, bacteria live in large colonies whose numbers may reach up to 100 times the number of people on earth. Many bacteria respond to extreme stress — such as starvation, poisoning and irradiation — by creating spores. Alternately the bacteria may 'choose' to enter a state called competence where they are able to absorb the nutrients from their newly deceased comrades. 'Each bacterium in the colony communicates via chemical messages and performs a sophisticated decision making process using a specialized network of genes and proteins. Modeling this complex interplay of genes and proteins by the bacteria enabled the scientists to assess the pros and cons of different choices in game theory. It pays for the individual cell to take the risk and escape into competence only if it notices that the majority of the cells decide to sporulate,' explained Onuchic. 'But if this is the case, it should not take this chance because most of the other cells might reach the same conclusion and escape from sporulation.'"
High Scientific Goals (Score:2)
Maybe someone will update Conway's game of life with these new findings... ..and I'll get a cool new screensaver.
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I for one welcome our new cell automaton overlords.
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Cells can be 'lonely' when they're in a place without food. Without food, the cell dies. I agree that it's doing the switcheroo on cause and effect, but hey...
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As for wether it is usefull, Conway's article in SciAm was what piqued my interest in computers and lead me to buying a second hand AppleII in the early 80's. It may not be as usefull to mankind as the Principa but on a personal level it was the start of a journey that lead me out of what American's call a "trailer park" an
Bah. nothing new (Score:2, Funny)
"Alternately the bacteria may 'choose' to enter a state called competence where they are able to absorb the nutrients from their newly deceased comrades."
The vultures on Wallstreet do this all the time.
Re:Bah. nothing new (Score:5, Funny)
Wall street are earning billions - trillions (Score:2)
And you? You're giving it to them, *every* which way.
Who's competent and incompetent?
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"Soylent Green is people! We've got to stop them somehow!".
Thinking Bacteria (Score:4, Insightful)
Each bacterium in the colony communicates via chemical messages and performs a sophisticated decision making process...
I'm sorry, but that stretches the meaning of "sophisticated" and "decision" beyond all reason.
One might just as well argue that water flowing down hill has made a sophisticated decision.
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Uhh, no. The essence of evolution is that your particular combination of genes make you more or less:
* adapted to your environment,
* capable of surviving to rear young.. leading to more (variations of) those genes in the gene-pool as a whole (every organisms genes).
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A rock is a computer 10 billion times more powerful than all of our computers on the planet combined. The hard problem is putting that power to good use,
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Not at all the same thing. The molecules in the rock are making trillions of trillions of computations per second. They're just not in a useful arrangement. As for the molecules in water, you have to introduce an infinite amount of energy from outside to accelerate it to the speed of light.
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> A rock is a computer 10 billion times more powerful than all of our computers on the planet combined.
Is that including the other rocks?
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> A rock is a computer 10 billion times more powerful than all of our computers on the planet combined.
Is that including the other rocks?
Yes. It's only that particular rock that's so powerful. All of the rest of them are dumb as, well, rocks.
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A rock is a computer 10 billion times more powerful than all of our computers on the planet combined. The hard problem is putting that power to good use,
I think you forgot to turn the computer on.
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I'm sorry, but that stretches the meaning of "sophisticated" and "decision" beyond all reason.
One might just as well argue that water flowing down hill has made a sophisticated decision.
Only at the point that the water is has done so for the greater good of the lake.
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Whenever I tried to read this, my brain throws an exception.
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Whenever I tried to read this, my brain throws an exception.
That is because you reject the 4-Corner time-cube [timecube.com]!
YOU can't handle Cubic Time, Cubic Life
or Cubic Truth - for insideof Time Cube
equates the most magnificient symmetry
of opposites existing within the universe -
for every corner has an equal opposite corner,
every 2 corners has an equal opposite 2
corners, every tri-corner has an equal
opposite tri-corner and every 4 corners has
an equal opposite 4 corners. No human or
god can utter such powerful ineffable
opposite Cubic Truth.
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Yay, 48-pt text - always a good indicator of article quality.
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Um, less I get modded troll, the joke is that the line
Sounds like a line from TimeCube, even though it was probably just Wordplay (appropriate nick) typing too fast.
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Thanks for the heads-up :D
timecube is painful - I can't help wondering if the author suffered a head-injury prior to writing it.
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It was an unfortunate typo--I fail preview. :)
My point was that coincidental behavior is only coincidental until such point that it starts fulfilling basic life criteria, such as self-survival, and is passed between generations. Evolution is pretty much all about coincidental behavior becoming non-coincidental.
What is interesting here is that coincidental behavior has bridged self-survival and species-survival, and performs at a sophisticated enough level to be interesting but at a simple enough level to b
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Yah, who knows what societies we've missed-out on because 'way-back-when', aggression was more useful than cooperation, from a survival perspective.
Hopefully those from 10,000 years into the future won't say the same thing :(
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Fear not! Gene variety and mutation can bring back nearly anything lost on that dry, careless evolution process... as long as there's sufficient time to adapt to the new challenges.
Re:Thinking Bacteria (Score:5, Interesting)
It is quite common, for instance, to refer machines that have a fair number of parts and are good at what they do as "sophisticated"("a sophisticated inertial navigation mechanism"). Even unicellular procaryotes have a fair amount going on inside, so they could easily fall under this definition.
As for "decision", that certainly can imply a process of rational, reflective cogitation; but it is also quite commonly applied to fairly simple, entirely mechanistic, things. "Decision Algorithms", for instance, are explicitly designed to be mechanistic and, as their name suggests, make decisions. The idea that the process whereby a cell enters either stateA or stateB depending on certain inputs is a "decision process" seems wholly reasonable to me.
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That's hardly a good comparison. If you wrote a piece of software that had a similarly sophisticated decision making process you would call it just that although the process is completely deterministic. Water flowing downhill is just shaped by the terrain although the turbulence is complex. The water contains no complex m
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Software is an even WORSE comparison.
Software is encapsulated human knowledge and decision making.
Bacteria have no such knowledge, no way to make decisions, and no intelligence to support them, unless of course you adhere to a certain religious view, in which case why would anyone be surprised at the bacteria's survival "strategy".
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Decision making requires intelligence. It requires the ability to choose or not choose.
Dogs can choose. They can decide to bark or wag.
Grass can not choose. It blows in the wind. It can not "decide" to lay down and avoid being blown.
Chemicals swirled in a beaker can not Decide to combine or not combine, to react, or remain inert. It can not decide which molecules will combine with another chemical and which ones will not.
Bacteria can not choose. They are sacks of chemicals and micro-structures that re
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Your example of grass and dogs seems quite confused - grass lacks the ability to move in real time so the notion of it being unable to choose to lay down seems bizarre, unless I am missing something. According to this one could argue that a failure of
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Bacteria have no such knowledge, no way to make decisions, and no intelligence to support them, unless of course you adhere to a certain religious view, in which case why would anyone be surprised at the bacteria's survival "strategy".
Of course they do. Bacteria have knowledge instilled into them by evolution rather than by humans.
Software produced by a genetic algorithm would be a pretty good match - external factors (humans/environment) enforce the wanted outcome, but the system does make decisions that help it reach that result.
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Bingo, there is some major over generalization going on in this article. The chemical reactions of bacteria to a chemical threat, even honed by millions of years of evolution, are not directly comparable to human reactions to information or threat. Even with billions of members a colony of bacteria has less chemical and informational content than a much smaller number of humans.
"Everyone knows the need to try to postpone important decisions until the last moment but apparently there are simple creatures t
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One might just as well argue that water flowing down hill has made a sophisticated decision.
Actually, the behaviors and communication of groups of bacteria are much more complex than water flowing downhill. Consider that when you get a bacterial infection, the bacteria will typically work in a "growth phase" where they are multiplying but not doing being virulent. When the bacteria reach a certain population size (or density), they all switch on their virulence. Individuals are making decisions that actu
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There is no "decision" being made. Period.
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I'll give it a shot. The chemical/electrical processes in his head gets really turned on by the fact that individual bacterium communicate using chemicals. Feedback from the chemicals in his head make him dizzy thinking of the little notes passed back and forth like "good luck" and "you've changed since the last time we talked". Not one to RTFA, the chemicals in his head move on to the next story.
There, I explained how the chemical processes in his head could have not lead him to his decision that there
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There is no "decision" being made. Period.
Well, then what do you mean by "decision"?
At its fundamental level, a decision the selection of one option from among more than one, based on some input information.
A bacteria, taking in information about how many of its own species are nearby, and information about the overall population of all types bacteria, determines if its species is in the majority and if there are enough of them. It uses this information to decide whether to keep reproducing or to become vi
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Water molecules do not do this.
http://www.youtube.com/watch?v=DpiUZI_3o8s [youtube.com]
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Not true. Once, I introduced a colony of water molecules onto a table. As is typical, they work in a "spread phase" where increase the area-to-water-stack-height ratio. Once they've detected the edge of the table, they begin "burrow mode" and start propagating a message for other water molecules to replaced the ones that started burrowing.
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Each bacterium in the colony communicates via chemical messages and performs a sophisticated decision making process...
I'm sorry, but that stretches the meaning of "sophisticated" and "decision" beyond all reason.
One might just as well argue that water flowing down hill has made a sophisticated decision.
In the same sense that a neuron in your brain isn't "thinking" when it does or doesn't fire.
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Or that yer puny humans, caught in ludicrous four dimensions, would be able to do such things!
And one of ’em isn’t even rolled out! *ha ha ha ha ha* *wipes tear*
Greets,
Pirate Zombie Cthulhu Ninja, the IIIrd.
First Rank Transdimensional Overlord
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Exactly my point.
The bacteria had no choice. The chemicals decided for it. They have no mechanism that can choose.
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And yet they clearly do.
I think you are confusing choice with consious choice. But even if we define choice as a consious choice, philosophically speaking you cannot show that a highly intergrated colonoy of bacteria do not posses some kind of "mind" unless you make one of two assumptions...
1) Mind does not emerge from the physical process of the brain
OR
2) Only brains can produce a mind.
strategy sounds familiar (Score:5, Interesting)
a case of where the individuals are all trying to make decisions that are selfish, but if everyone is selfish, no one wins, so some have to be selfish and some have to fold, for any to survive. I seem to remember playing games like that as a kid, where it was basically a game of chicken, where no one could do anything until everyone was generous, and so everyone then starts building up, and whoever managed to switch back to greedy first won. Also reminiscent of the stock market during a bubble, eh?
Re:strategy sounds familiar (Score:5, Interesting)
I seem to remember playing games like that as a kid, where it was basically a game of chicken, where no one could do anything until everyone was generous, and so everyone then starts building up, and whoever managed to switch back to greedy first won. Also reminiscent of the stock market during a bubble, eh?
Stock markets do not allow for equal access to information.
That inequality seriously skews any game theory in favor of the well connected.
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Stock markets do not allow for equal access to information.
That inequality seriously skews any game theory in favor of the well connected.
I'd guess that the same is true for the bacteria. Information will diffuse out chemically; they won't all know something at the same time. Of course, statistically, it probably doesn't matter, since the first movers among the bacteria world aren't going to be first by much. They'll all decide things more-or-less at the same time, by happenstance.
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Stock markets do not allow for equal access to information.
This is also what stabilises them...
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I think the problem is your definition of “one”. In fact, if everyone is selfish, exactly one wins. But if they work together, they may all together win more. Maybe even more than what they would have won by being selfish. It also depends on the resources available.
But “one” can really be everything, from the whole planet, over whole humanity, over a whole social group, down to one individual, or even just a part of it.
And so, one “one” winning or everybody winning, essen
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play a game with friends. Top couple players by points win at the end. Everyone either chooses A, B, or C for maybe 10 rounds.
If you pick A, you get one point
if you pick B, you get two points for everyone else that picked B, minus 3 points for everyone that picked C
if you pick C, you get five points, plus two points for everyone that picked B, minus ten points for everyone else that picked C
Run that ten rounds and see what happens.
At the start it's clear that B is a good pick because everyone builds point
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FYI this is formally known as The Tragedy of the Commons [wikipedia.org]. From a bacteria-level perspective it describes the rather unfortunate fate of brewing yeast, which grows to the point where its own alchoholic excrement kills it.
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Yeah yeah, I know... -1 Utopian fantasy.
Pfft... predicting social behaviour... (Score:1, Funny)
That's so easy even I could do it!
First, assume the world's population is an ideal gas in a frictionless vacuum...
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So the population of the world = 0? No wonder it's frictionless.
Bacteria analogous to human beings? (Score:2)
Yes because the way that a colony of bacteria reacts is totally similar to how a population of human beings would react.
Are they serious?
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Have you been following our recession?
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I'm more interested in how various strategies used by scientists when making the "latest wild claim" (tm) affects their level of success within the game of scientist-gene evolution.
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Yes because the way that a colony of bacteria reacts is totally similar to how a population of human beings would react.
Are they serious?
I know, right? Don't they know that humans are actually a virus?
Re:Bacteria analogous to human beings? (Score:4, Interesting)
James Cagney as a Bacterium... (Score:3, Funny)
Now look here guys, see, I'll spore as soon as each of you spore, but if any one of you display any signs of competence, it's...
Numbers (Score:2)
But then again, once you get inclusive and start using words like "ecosystems" then you can "sum" the "intelligence", everything only has meaning in relation to something else. Together, Earth, is a mind.
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Good Bacteria interaction overview (good watching) (Score:2, Informative)
Very strange - I just finished watching this lecture video this morning. I've all so seen her talk in TED.com
http://microbeworld.libsyn.com/index.php?post_id=516458&utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+asm+(MicrobeWorld+Video)# [libsyn.com]
Cool Stuff!
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I think that's called Black Mesa.
Great Program, Wrong Channel (Score:3, Insightful)
They've done a bang up job investigating how bacteria adapt, and from the names and departments listed, I can see how they'd be quite able to do so as well as apply it to an expanded game theory scenario.
But applying it to human decision making, strategic or otherwise? Sorry, but they should have included someone on the team from behavioral science that could have pointed out the glaring differences.
They happen on one themselves in saying the bacteria don't lie. The level of stress they're talking about is equivalent to massive drought/starvation. Humans under such conditions do and say all kinds of things, most of it to some degree hiding real intentions.
To extend that, some of human behavior is rational under normal conditions, some isn't (emotionally driven isn't, for instance). With increased stress, less and less is rational. Their very nicely done description of possible decisions at various points based on DNA is entirely rational throughout. Not that the bacteria think, but that the decision is predetermined by being programmed in. There is no irrational result, no off-the-wall craziness drastic behavior resulting in novel solutions. Humans do this. In fact, novel results is a major difference between their work and pretty much any higher organism.
I don't find it particularly instructive that bacteria put off "decision making" until the last moment. As if people don't? It's human nature to constantly refine decisions according to the situation, including attempting top adapt to the situation after a decision has been implemented and the crucial point passed.
The final point they make, where one has to decide based on best guess of others' future behavior, is fairly telling of a major difference between bacteria and humans. Humans can coordinate their decisions so that none obtain an optimal result but all obtain a satisfactory result. That flies in the face of traditional game and economic theory. It also earned John Nash a Nobel. Bacteria can't discuss with predictive insight, they can only wait until the last moment to react.
NOT a prisoner's dilemma (Score:5, Insightful)
Why is it that anyone who's learned the slightest bit of game theory suddenly thinks everything is a Prisoner's Dilemma?
In a (1-shot) Prisoner's Dilemma, one action is always better for you than another, leaving little to analyze.
In the Bacteria's game, the bacteria are obviously programmed to do what is best to ensure the survival of the species. (FTFA: "bacteria usually do not cheat their friends and inform them by sending chemical messages about their true intensions.") Whether a bacterium should spore or not depends on the proportion of other bacteria doing each action. This is not the structure of a P.D. It's one thing for journalists to make a bad reference, but the physicist himself refers to Prisoner's Dilemma.
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Actually, that's not really 100% either. In a single play of a prisoner's dilemma, you still don't know what's best because you don't know what your opponent is going to do; you can only hope that he's going to hold his tongue, but since he won't, you'll both rat each other out no matter what.
no, the whole point of it is that every player has one dominating strategy, meaning no matter what the opponent does, this one strategy is always the best. what your opponent does changes your actual win, but in a one-shot PD it never influences your choice.
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Actually, that's not really 100% either. In a single play of a prisoner's dilemma, you still don't know what's best because you don't know what your opponent is going to do; you can only hope that he's going to hold his tongue, but since he won't, you'll both rat each other out no matter what.
no, the whole point of it is that every player has one dominating strategy, meaning no matter what the opponent does, this one strategy is always the best. what your opponent does changes your actual win, but in a one-shot PD it never influences your choice.
I was under the impression that the important part of PD was that the dominating strategy is not globally optimal -- hence the "dilemma": if you both choose the dominating strategy, you both do worse than if you both choose the vulnerable strategy. The idea of a one-shot is, in my opinion, the most artificial aspect of PD, as in the real world even a one-shot PD is merely one of a series of PD games played among one large player pool, and thus I believe many people consider that "what goes around comes aro
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the bacteria are obviously programmed to do what is best to ensure the survival of the species.
Why does everyone who's learned the slightest bit of evolutionary theory suddenly think everything is about the survival of the species?
It's never about the survival of the species. In this case, where some kin-selection has unsurprisingly being going on, it's about survival of the most closely related individuals.
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Evolution is always about what is best for the single organism, i.e. no group selection, contrary to what you imply.
Wow, biology fail. Evolution is about what is best for an organism's genes. An organism and its siblings and cousins share genes, and therefore share an evolutionary fate. Group selection is all over the place.
And the answer, please? (Score:1)
solution (Score:2)
the optimal solution in a situation like that requires each cell to make probabilistic and independent decisions.