From ScienceNOW Daily News, this story, entitled “Pavlov’s Bacteria?”:
Researchers already know that microbes can mount simple responses to changes in their environment, such as acidity fluctuations, by altering their internal workings. If the changes are regular enough, bacteria can respond ahead of time. But systems biologist Saeed Tavazoie of Princeton University wondered if microbes were capable of more sophisticated reasoning. Could they, for example, learn to match a signal that didn’t occur regularly to a probable future event? If so, the bacterium could improve its chances of survival by turning on a preemptive response to that event.
Tavazoie and colleagues first ran a computer simulation to determine if a simple system could evolve such behavior. They created an environment inhabited by evolving virtual bugs. The organisms garnered more energy if they could “learn” that certain signals preceded the arrival of food and launch a preemptive metabolic response. Even when the signal combinations grew more complex, the population was able to evolve the correct responses, the team reports online this week in Science.
The researchers then looked for evidence of this ability in the bacterium Escherichia coli. Because E. coli gets warmer when it enters a human mouth–ferried in on some old meatloaf, perhaps–and then must soon contend with low oxygen levels as it passes into the large intestine, the team reasoned that the bacterium might use temperature as a cue to prepare for the upcoming lack of oxygen. Indeed, when the researchers turned up the heat in a dish of E. coli, the bugs dialed down activity in genes that normally operate in high-oxygen conditions. But the true test came when the team flipped the normal association, growing the bacteria in conditions in which high oxygen levels followed temperature increases. Less than 100 generations later, the bacteria stopped turning on their low-oxygen response after exposure to high temperatures, suggesting that they had evolved to break the association.
The study is the “first convincing demonstration” that bacteria can use environmental cues to anticipate events, says Michael Travisano, an evolutionary biologist at the University of Minnesota, Twin Cities. The work could open up new ways to explain puzzling behavior of microbial pathogens, which might use predictive signals to change their cell surfaces and avoid a host’s impending immune attack. “If it does something you don’t understand, maybe it’s anticipating an environmental shift,” he says.
Consider the final quote:”If it does something you don’t understand, maybe it’s anticipating an environmental shift”.
What does it mean to say “If it [i.e.,the organism] does something you don’t understand”? Clearly, if an organism exhibits some behavior (call it B), then there is some causal grounds (call it X) which induces B. Doesn’t it suffice to know that X causes B, and once we have discovered the physical (e.g., biochemical) mechanism of X and how it biochemically/mechanically/etc. induces B then our answer is complete? What more is there to understand?
From a strictly contemporary physics or chemistry point of view, there may well be nothing else to understand – this may exhaust the “why?” questions concerning B. From a biological perspective, however, the phrase “If it [i.e.,the organism] does something you don’t understand” implicitly refers to the relationship between the behavior B and the organism (call it S) of which is is a part. What we want to understand is: ‘what does B do for S?’, or restated, ‘Why B, with respect to S?’.
From the author’s perspective, the answer to:
Why B, with respect to S?
Because B, at time t1, may anticipate an environmental change E at time t2, where t2 > t1.
Previously, in terms of “why B?” answers, we had only:
X at time t0 entails B at time t1
Now, we additionally have the effect of B as “why B?” information. Namely, we have:
The effect of B is to alter S for condition E, even though E is not yet physically the case.
In biological functional terms, we can say that ‘the function of B is make S favorable to future condition E’.
It is now apparent why contemporary physics and chemistry has no “why B?” answers beyond those which fall into the realm of ‘X causes B’. Since E is not yet physically the case at time t1, then in a physics paradigm in which causal properties flow unidirectionally from past states to present states there is no meaningful way to pose or encode causal statements which refer to a non-existent state, much less to such a state which is in the future, and which furthermore may or may not come to pass. From a biological perspective, however, is it obvious that it is a perfectly good causal and physical answer to say that ‘The effect of B is to alter S favorably to condition E, even though E is not yet physically the case (and may possibly never be physically the case)’.
Thus, we see that contemporary physics cannot adequately encode either function or anticipation. Now, this situation leaves us with two possibilities: either 1) contemporary physics is exhaustive yet remains fundamentally incommensurable with biology, or 2) contemporary physics fails to be large enough to include biology. The first case strikes us as highly unlikely; as far as we can tell, biological organisms are indeed physical systems in a physical universe subject to physical laws. Therefore, the second possibility must be the case; it must be that physics, in its current paradigm, is lacking. Specifically, it must be that contemporary physics fails to possess formalisms into which one can encode causal statements such as the one under discussion — what current physics can encode is just some subset of a more inclusive physics.
Robert Rosen remarked on this situation [2, p. 133-134]:
Now we can understand why finality is so resolutely excluded from Newtonian encodings. First, as we have seen, entailment in that picture is embodied entirely in the recursiveness of state transition sequences. There is nothing in that picture for a state to entail except a subsequent state. Furthermore, a state can itself be entailed only by a preceding state. The presence of time as a parameter for state transition sequences translates into an assertion that causes must not anticipate effects. Therefore, whether we express final causation in terms of “intentionality,” or equivalently in terms of what its effect entails, final causation in the Newtonian picture involves the future acting on the present. And of course, this is clearly inconsistent with the encoding of the other causal categories in the Newtonian picture.
This is a basic point, so let us recapitulate. In the Newtonian picture, a state can only entail subsequent states. (That is all the entailment present in the Newtonian encoding, as we have seen). Subsequent states are necessarily later in time than present states. Finality is expressible only in terms of what is entailed by a state, and hence, in the Newtonian picture, only in terms of future states. Ergo, final causation, as a separate causal category, cannot exist in that picture.
There is nothing unphysical about functional entailment. What is true is that functional entailment has no encoding into an formalism of contemporary physics; it represents a notion of final causation that is unencodable in any such formalism from the outset. On the other hand, it reflects basic features of material organization per se. At root, it is the resolute exclusion of these features, these manifestations of matter, that makes contemporary physical formalisms so special. Put baldly, there is simply not enough entailment in these formalisms to encompass biology. But that is a fault of the formalisms, and in the encodings into them; it certainly does not connote anything vitalistic or transphysical in material nature.
 Kwok, R. “Pavlov’s Bacteria?”. ScienceNOW Daily News. 05/09/2008. Link.
 Rosen, R. 1991. Life Itself. Columbia Univ. Press.
 Rosen, R. 1985. Anticipatory Systems. Pergamon Press.