Forgot your password?
typodupeerror
Biotech Science

Bacterial Prisoner's Dilemma and Game Theory 95

Posted by Soulskill
from the sporulate-is-the-word-of-the-day dept.
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.'"
This discussion has been archived. No new comments can be posted.

Bacterial Prisoner's Dilemma and Game Theory

Comments Filter:
  • Maybe someone will update Conway's game of life with these new findings... ..and I'll get a cool new screensaver.

    • Re: (Score:2, Funny)

      by Sulphur (1548251)

      I for one welcome our new cell automaton overlords.

    • Re: (Score:3, Interesting)

      by JoshuaZ (1134087)
      Conway's Game of Life wasn't made to simulate life in any meaningful sense. It was designed by Conway because he was investigating simple cellular automata that had non-trivial behavior. http://en.wikipedia.org/wiki/Conway's_Game_of_Life [wikipedia.org]. It happened that the simplest interesting form he found happened to have rules that could be stated with very very rough analogs to living creatures. Some of the rules are very much stretches. For example, while bacteria can die from overcrowding, they cannot die from bein
      • by bytesex (112972)

        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...

      • Yes, the "life" part was a metaphor. The basic point was that simple rules can result in highly complex behaviour. Classical examples from nature are the "hive minds" of bees and ants.

        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
  • by Anonymous Coward

    "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.

  • Thinking Bacteria (Score:4, Insightful)

    by icebike (68054) on Sunday December 13, 2009 @01:48PM (#30424056)

    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.

    • Re: (Score:3, Insightful)

      by selven (1556643)

      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,

      • Re: (Score:3, Funny)

        by Anonymous Coward

        > 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?

        • Re: (Score:2, Funny)

          by Anonymous Coward

          > 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.

      • by Thanshin (1188877)

        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.

    • by Wordplay (54438)

      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.

      • by easyTree (1042254)

        Only at the point that the water is has done so for the greater good of the lake.

        Whenever I tried to read this, my brain throws an exception.

        • by lilomar (1072448)

          Only at the point that the water is has done so for the greater good of the lake.

          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.

          • by easyTree (1042254)

            That is because you reject the 4-Corner time-cube! [timecube.com]

            Yay, 48-pt text - always a good indicator of article quality.

            • by lilomar (1072448)

              Um, less I get modded troll, the joke is that the line

              Only at the point that the water is has done so for the greater good of the lake.

              Sounds like a line from TimeCube, even though it was probably just Wordplay (appropriate nick) typing too fast.

              • by easyTree (1042254)

                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.

        • by Wordplay (54438)

          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

          • by easyTree (1042254)

            Evolution is pretty much all about coincidental behavior becoming non-coincidental.

            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 :(

            • by hrimhari (1241292)

              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)

      by fuzzyfuzzyfungus (1223518) on Sunday December 13, 2009 @02:25PM (#30424284) Journal
      Obviously the bacteria aren't "thinking" in any way that could usefully be crammed into the usual definition of the word; but I don't think that either "sophisticated" or "decision" are being distorted at all.

      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.
      • I take all this to mean that there are several inputs, a complex process that determines the output (what action is performed), and the output is one that an intelligent being would be likely to come to, given the same limited available information and amount of time available to deliberate. Given enough complexity, "sophisticated decision-making" could easily be appropriate terms.
    • 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.

      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

      • by icebike (68054)

        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".

        • Human decision making is taking inputs and deciding on an output based on the inputs + internal biases. This is the same process as in software and in bacteria. Humans can do this process in a generic way, where in the other two examples they are limited to pre-defined scenarios - but its not really that different. I think there is a confusion here between decision making and consciousness, which is strictly speaking not necessary for decision making (i.e. rational decision making).
          • by icebike (68054)

            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

            • Re: (Score:3, Interesting)

              Why do you need intelligence to do decision-making? This seems an arbitrary requirement - and the literature on decision-making doesn't use intelligence as a prerequisite, rather it refers to cognition - which is more rigorously defined and can be automated.

              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
        • by juhaz (110830)

          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.

    • Re: (Score:3, Insightful)

      by BigSlowTarget (325940)

      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

    • Re: (Score:3, Interesting)

      by hazem (472289)

      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

      • by icebike (68054)

        There is no "decision" being made. Period.

        • Re: (Score:3, Interesting)

          by TapeCutter (624760) *
          Please explain how the chemical process in your head do not lead to your decision that there is no decision.
          • Re: (Score:1, Troll)

            by huckamania (533052)

            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

        • by hazem (472289)

          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

      • Water molecules do not do this.

        http://www.youtube.com/watch?v=DpiUZI_3o8s [youtube.com]

      • Re: (Score:3, Funny)

        by DriedClexler (814907)

        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.

    • by NonSequor (230139)

      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.

    • 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

    • Re: (Score:3, Insightful)

      by TapeCutter (624760) *
      The water had no choice, gravity decided for it. Besides the human brian is basically a colony of single celled automata that communicate via chemical messages and perform a sophisticated decision making process (well sometimes anyway).
      • by icebike (68054)

        Exactly my point.

        The bacteria had no choice. The chemicals decided for it. They have no mechanism that can choose.

        • "They have no mechanism that can choose.

          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.
  • by v1 (525388) on Sunday December 13, 2009 @01:53PM (#30424076) Homepage Journal

    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?

    • by TubeSteak (669689) on Sunday December 13, 2009 @02:45PM (#30424444) Journal

      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.

      • by bar-agent (698856)

        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.

      • by hawkfish (8978)

        Stock markets do not allow for equal access to information.

        This is also what stabilises them...

    • 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

      • by v1 (525388)

        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

    • 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.

    • This begs the question "Can't we all just not switch back to greedy?"

      Yeah yeah, I know... -1 Utopian fantasy.
  • by Anonymous Coward

    That's so easy even I could do it!

    First, assume the world's population is an ideal gas in a frictionless vacuum...

    • Re: (Score:3, Funny)

      by Wonko the Sane (25252) *

      First, assume the world's population is an ideal gas in a frictionless vacuum...

      So the population of the world = 0? No wonder it's frictionless.

  • 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?

    • by wellingj (1030460)
      I don't think we will like the implications if they say yes.
    • by TheMeuge (645043)

      Have you been following our recession?

    • Re: (Score:2, Insightful)

      by easyTree (1042254)

      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.

    • by tnk1 (899206)

      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?

    • by Cassius Corodes (1084513) on Sunday December 13, 2009 @08:12PM (#30426764)
      They are - and for good reason. Game theory has been very successful in understanding some of the basic trade-offs involved in individual vs group decision-making. Certain set-ups such as the http://en.wikipedia.org/wiki/Prisoners_dilemma [wikipedia.org] are generic forms of common problems that are encountered both in the human world and the natural world. Having worked in this area I can tell you that solutions found in the natural world often end up as inspiration for real life applications - such as regulation of industry and organisational psychology. At the end of the day one of the most re-occurring problems is how to get selfish people to co-operate as a group - and this problem has been solved so many times by nature in so many ways its basically a handy repository of tried and true solutions just waiting to be discovered.
  • by theNAM666 (179776) on Sunday December 13, 2009 @02:27PM (#30424296)

    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...

  • So, globally, considering the number of bacteria, could they be the most advanced intelligence? Of course being loosely coupled their time-scale of thought would be extremely slow. They would also exist in a reality very much different than ours.

    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.
    • by linhares (1241614)
      I can't refrain from pointing out that you seem to have a very adequate userid
      • by headkase (533448)
        :D ;) Wiki Metaphysics. What makes a rock a rock and not just a collection of atoms. Its taking pieces and drawing an abstract boundary around them. We call such groupings many things.
  • 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!

  • by DynaSoar (714234) on Sunday December 13, 2009 @03:51PM (#30424958) Journal

    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.

  • by Main Gauche (881147) on Sunday December 13, 2009 @05:23PM (#30425690)

    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.

    • by kressaty (1699650)
      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. It's more of a "Sneetches" game, where all the bacteria know that the majority need to survive in order for them to obtain a "stable" outcome and keep living as a whole. Suppose there are an odd number of bacteria.
      • Re: (Score:2, Informative)

        by zarzu (1581721)

        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.

        • by zacronos (937891)

          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

          • by zarzu (1581721)
            well yes, the interesting part of PD is if it's not a one-shot game, and as you pointed out in reality you will hardly ever face a one-shot. but there is no actual dilemma in a one-shot PD if you only care about yourself (which is what i was answering to), however there is still a dilemma present if you consider empathy and the hope that everyone can work together and be happy (in a real life experiment you will see that in a one-shot PD many people will not choose the dominant strategy even though they're
    • by radtea (464814)

      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.

  • As has been said: Asking if machines can think is like asking if submarines can swim. And the answer may not be what you expect.
  • the optimal solution in a situation like that requires each cell to make probabilistic and independent decisions.

Passwords are implemented as a result of insecurity.

Working...