October 05, 2006

Microbial Grice

In response to my call for "a description of bacterial fermentation in cheese that's as appetizing as Mary Falk's prose poem about the molds", Rosie Redfield tunes up with

Yeast transform dreary starches and sugars into intoxicants and fragrances.

but concedes that she'll "need to work on the bacterial perspective".

Rosie also sent along a paper about bacterial quorum sensing (Rosemary Redfield, "Is quorum sensing a side effect of diffusion sensing?", Trends in Microbiology 10(8), August 2002), which seems to me to raise some interesting questions about what we mean by "communication".

There's a familiar issue with intention in human communication, as in Grice's analysis of "speaker's meaning":

A (an agent) meant something ... by x (an utterance or gesture) if and only if A intended the utterance or gesture x to produce some effect in an audience by means of the recognition of this intention.

This seems to make sense of much of our reasoning about communication. For example, if someone says something hurtful or insulting, we typically try to figure out "what they meant by it" in terms of an analysis of their intentions. Did they understand that their remark would be taken as an insult, or did they think it was really neutral or even a compliment? Did they perhaps intend to refer to something completely different from what we thought they were talking about? Our evaluation and response depends on the answers.

But even for humans, it's often obscure who had which intentions when, and the application of this kind of reasoning to non-human animals is even murkier, as all of the debates about animals' "theory of mind" show. From a certain common-sense point of view, it may seem preposterous to imagine that a bacterium could have a communication-intention of Grice's kind. However, Daniel Dennett and other smart people think that thermostats and alarm clocks have beliefs and intentions, and bacteria are much more complex machines than that.

What's interesting about Rosie Redfield's paper, in this context, is that it deals in detail with a parallel sort of reasoning about certain acts performed by bacteria:

Many bacteria appear to communicate by releasing and sensing autoinducer molecules, which are believed to function primarily as sensors of population density.However, this quorum-sensing hypothesis rests on very weak foundations, as neither the need for group action nor the selective conditions required for its evolution have been demonstrated. Here, I argue for a more direct function of autoinducer secretion and response – the ability to determine whether secreted molecules rapidly move away from the cell. This diffusion sensing allows cells to regulate secretion of degradative enzymes and other effectors to minimize losses owing to extracellular diffusion and mixing.

As Rosie explained her theory in email to me, "the whole process is more like radar than radio, in that they're emitting 'signals' to sense the properties of their environment rather than to change the behaviour of recipients".

Note that everyone agrees about what the bacteria do -- they emit certain molecules, and also sense the local concentration of those molecules and modify their behavior as a result. The argument, in some sense, is about what the bacteria mean. At least, it's about the purpose of what they're doing -- is it their intention to give a shout-out to their peeps? or are they just trying to figure out what the local diffusion rates are like? And again, I think that everyone agrees that what they do has both of those effects, at least in principle; but there's still a diagreement about the purpose of the behavior.

I suppose that "purpose" is a way of talking about evolutionary forces here, rather than a claim about any individual bacterium's state of mind. Though perhaps Dan Dennett would say that bacteria do have purposes as well as beliefs and intentions, I'm not sure.

[On a completely different topic -- When Rosie wrote that "Yeast transform dreary starches and sugars into intoxicants and fragrances", was "yeast" taking the game-animal zero plural? Historically, "yeast" was a mass noun, referring to the froth or sediment that forms during fermentation of certain fluids. At some point in the last couple of centuries, people realized that these substances were composed of single-celled fungi, who thus came to be called "yeasts" -- but the OED's earliest citation for the plural is from 1906:

1906 G. MASSEE Text-bk. Fungi III. 275 Symbiotic relationship between yeasts and bacteria is not uncommon.

Whatever the explanation, Rosie's usage ("yeast" with a plural verb) seems to be a common one:

Yeast ferment glucose and thus depend heavily on the glycolytic pathway.
Ale yeast ferment at warmer temperatures than will lager yeast.
Yeast grow in colonies that are generally isogenic, so survival of the genes of a single colony is guaranteed even if only a few organisms survive.
This system can compensate the absence of pyruvate dehydrogenase when yeast grow aerobically on glucose or lactate...

However, "yeast" with singular agreement seems to be roughly as common:

... confirmation of a theory originally proposed by Hopkins that yeast ferments the furanose form of fructose.
When yeast ferments glucose in the presence of potassium chloride K+ is taken up by the cells and an equivalent amount of H+ is excreted.
When yeast grows, it makes carbon dioxide and alcohol.
Yeast grows best in a warm, moist environment.

And examples with plural "yeasts" generally have the "types of X" interpretation typical of mass-noun plurals:

In contrast, tel1 mutant yeasts grow normally at 37°C.
...about 30% of all yeasts grow either on methanol (about 10%) or on hydrocarbons (about 20%)...
However, while many yeasts ferment hexoses, they are usually considered to be unable to ferment aldopentoses.

This is probably covered at length somewhere in CGEL, but I've got a meeting to go to. ]

Posted by Mark Liberman at October 5, 2006 09:39 AM