Indeterminism in developmental biology

There's a review article in this week's Science (v.320, April 4 2008, 65-68) that is potentially of philosophical interest, "Stochasticity and Cell Fate". The bumper sticker version: although a cell's transformation into a specialized subtype is deterministic in most cases, "[i]n some cases, however, and in organisms ranging from bacteria to humans, cells choose one or another pathway of differentiation stochastically, without apparent regard to environment or history."

Discussions of indeterminism in biology have usually been restricted to the 'random' mutations that drive evolutionary change. This, if it holds up, looks to be a quite different kind. And interestingly, the authors point out reasons why a certain degree of indeterminism may confer selective advantage upon organisms whose development contains stochastic elements.

confusion and prokaryotes

One of my recurrent interests is confusion, especially in science. The way I understand this concept is as follows: a term or concept is confused = that term or concept takes 2 or more entities to be one entity (where 'entity' covers individual objects, properties, relations, etc.). In other words, a confused concept or term conflates distinct things. I think the phenomenon of confusion is important in science because part of what happens in many scientific revolutions is that, from the point of view of the new scientific framework, the old scientific framework is confused -- or vice versa. (Re: 'vice versa': Einstein's principle of equivalence, for example, would be seen as an unjustified conflation from the viewpoint of a classical physicist: gravitation and inertia are two separate things, and running them together as Einstein does is an unjustified conflation.)

I've recently started looking at another potential case of confusion in science, but I'm a bit uncertain about it, and would like to air it to get reactions.

In high-school biology class, we are told that the highest/ most basic division among life on Earth is between 2 kingdoms: prokaryotes and eukaryotes. Eukaryotes are all those organisms whose genetic material is encapsulated within a nucleus; Prokaryotes are organisms whose genetic material is not. In other words, Prokaryote=df not-Eukaryote.

However, in the last 2-3 decades, the highest taxonomic level has slowly switched to a three-group classification: Eukaryotes, Archaebacteria, and (Eu)bacteria. Why? The short answer is: "on the molecular level, [archaebacteria] resemble other procaryotes, the eubacteria, no more (probably less) than they do the eukaryotes" (C. Woese et al., PNAS 1990 p.4577).

The upshot for present purposes is that there are actually two distinct highest taxa whose genetic material is not enclosed within a nucleus, viz. the archaebacteria and the eubacteria. From this point of view, it appears that 'prokaryote' conflates the archaebacteria and the eubacteria. But if we recall the earlier characterization of 'prokaryote' as simply 'not-eukaryote,' then 'prokaryote' does not appear to be a confused term. So the question is: Is 'prokaryote' confused, or not? (And why?) I'm happy to hear just intuitions, as well as intuitions backed up with some sort of argument or evidence.

P.s. -- For some readers, this discussion will immediately call to mind Quine's solution to the 'grue' paradox in his paper "Natural Kinds" (in Ontological Relativity and other essays). There, Quine notes that if the predicate P picks out a natural kind, then not-P usually doesn't. A hackneyed example: 'gold' picks out a natural kind (any matter with atomic number 79), but 'not-gold' does not, because it covers many, many completely disparate things -- there are too many ways to be not gold for 'not-gold' to refer to a natural kind.

This might make us think that many/ most predicates of the form not-P are, in fact, confused, since such predicates most often apply to many different natural kinds. All I can say at this point is: that sounds counterintuitive to me... it doesn't feel to me like 'not-gold' conflates distinct things.

On the Darwinian explanation of the success of science

I really don't have time to post now, but I'm going to anyway. Van Fraassen writes: "I claim that the success of current scientific theories is no miracle. It is not even surprising to the scientific (Darwinian) mind. For any scientific theory is born into a life of fierce competition, a jungle red in tooth and claw. Only the successful theories survive--the ones which in fact latched on to actual regularities in nature." (Scientific Image, p.40)

James Robert Brown, in "Explaining the Success of Science" (Ratio, 1985) agrees that this Darwinian explanation can account for the first two aspects of success, but not the third:
(1) The sciences "are able to organize and unift a great variety of known phenomena.
(2) This ability to systematize the empirical data is more extensive now than it was for previous theories.
(3) A statistically significant number of novel predictions pan out; that is, our theories get more predictions right than mere guessing would allow." Brown says of (3): "Here the Darwinian analogy breaks down since most species could not survive a radical change of environment, the analogue of a novel prediction."

First a small point: I don't think a novel prediction needs to be analogized to a radical change in environment -- perhaps some should be, but it's not necessary. If an organism can handle living and reproducing in any new environment, i.e., one for which its various features were not historically adapted, then that seems a decent enough analogy to a novel prediction (which makes a prediction different from the cases the thoery was originally designed to handle). A 'radical' change in environment might precipitate a scientific revolution -- i.e., the science (like the organism) might not survive.

Now, a more substantive point, and one which perhaps pushes the analogy farther than is fair. The paleobiologist David Jablonski has shown that genera that are more geographically widespread are more likely to survive mass extinction events (such as the meteor that killed off lots of the dinosaurs). The analogy would be, I suppose, to groups of related theories that 'organize and unify' a greater variety of phenomena -- which are precisely the groups of theories that we (including van Fraassen) count as most successful. So it appears that a van Fraassenite Darwinian has a nice answer to J.R. Brown: viz., the more successful groups of theories will be more likely to deliver novel predictions.

But unfortunately for the van Fraassenite, the biological story doesn't end there. What is strange about Jablonski's results is that a species' being geographically widespread has no statistical correlation with its probability of surviving a mass extinction event. The correlation only appears at the level of genera. (Side note: For the philosophers and biologists who think about group selection, this looks like an instance of it.) So, the analogy would go, the more unifying particular theories do not enjoy any advantage in novel prediction over the less unifying, but the more unifying groups of theories would. Hopefully you can see why I suggested that this may be pushing the analogy too far: I'm not sure there's anything in the domain of science that would correspond nicely to the concepts of genus and species in the evolutionary domain. Although (and now I'm really stretching), if one could be made out, perhaps the structural realists could cash out their notion of structure at the level of the genus, and thereby capture why particular theories come and go, but the structure tends to survive through revolutions.

p.s. -- Can anyone recommend a good article completely devoted to arguing for or against this Darwinian explanation of science's success? I've seen several parts of book chapters or parts of papers dealing with it, but I can't recall seeing a fine-tooth-comb analysis of it.

Fantastic new Darwin resource

Today my faith in the web as an instrument of enlightenment was restored: the complete works of Darwin will soon (December 15th) be freely available online. The site, which currently has a detailed project description posted, is:

http://darwin-online.org.uk

Thanks to the Philosophy of Biology blog for the pointer. (Does anyone else wonder whether we would have this ID controversy in the US if Darwin were an American? The UK (from what I've seen) holds him up as a national hero of sorts, and this project is just the latest instance of their Darwin valorization.)

Einstein and the Units of Selection

No, the title of this post is not a typo. I just finished reading through the first three articles in the most recent issue of Philosophy of Science. They are an argument-response-rebuttal between Elisabeth Lloyd ("Why the Gene Will not Return"; "Pluralism without Genic Causes?") and Ken Waters ("Why Genic and Multilevel Selection Theories Are Here to Stay"), who is one of her targets in the original essay. As the biologically-inclined among you will have inferred, this is the latest installment in the long-standing units of selection debate; very roughly, the question in these debates is: Upon what does natural selection operate? Organisms? Genes? Groups of organisms?

Ken Waters' basic response to this question -- which he first articulated in "Tempered Realism about the Force of Selection" (Philosophy of Science 1991) -- is that there is no determinate fact of the matter about whether selection is really acting at the level of the gene or the organism/ genotype. Mathematical models can be constructed in terms of genes and in terms of genotypes, and both kinds of model suffice to represent the facts of dynamic changes in populations. (See "The Dimensions of Selection," P. Godfrey-Smith and R. Lewontin, Philosophy of Science 2002, for an excellent treatment of the niceties of of the situation.) Since these different models do not represent different facts, Waters concludes that we will choose between them on pragmatic grounds. In the language of his current paper, Waters says that different models "parse" the causal structure differently.

For the purposes of this post, I will assume Waters is correct to maintain that there is no fact of the matter about whether the true cause of any particular evolutionary change lies at the level of the gene or the genotype. What I want to do is to compare this situation with Einstein's reaction in (what I consider) an analogous situation.

At the beginning of Einstein's 1905 paper that introduces special relativity, he asks us to imagine a conductor and a magnet in relative motion with respect to each other. If the take the conductor to be at rest and the magnet moving, then Maxwell's theory says that an electromotive force is generated in the conductor, which gives rise to an observable electric current C. If, on the other hand, we assume the conductor is moving and the magnet is at rest, then Maxwell's theory says that no electromotive force is generated in the conductor, but an electric field is generated around the magnet -- and this field induces exactly the same electric current C as before. Einstein's conclusion is that we are not actually dealing with two physically different situations here; rather, our theoretically distinct models are representing one and the same set of facts. This is exactly Einstein's argumentative maneuver in his famous elevator thought-experiment as well: though the pre-Einsteinian theory would distinguish between the cases in which I am being uniformly accelerated through a gravitation-free region and in which I am at rest in a homogenous gravitational field, Einstein maintains that there is in fact no difference between these two cases. This is (one version of) the Principle of Equivalence.

Note that Einstein does not say is that 'we choose between the competing descriptions of the magnet-and-conductor case on pragmatic grounds,' or that 'we parse the causes differently: either as an electromotive force or as a electric field.' Rather, he re-arranges the permitted causal structures of the theory to eliminate these pseudo-differences, so that the theory no longer "leads to asymmetries which do not appear to be inherent in the phenomena." He replaces the separate categories of 'inertial effects' and 'gravitational effects' with a single category (which we could call gravitational-inertial effects) via his principle of equivalence.

What I am curious about is whether Einstein's maneuver can be carried over into the biological case. I am hoping someone better-informed than I am can tell me why this has no prayer of working, or why Einstein's cases are not analgous to the situation in evolutionary biology. Of course, I wouldn't mind hearing suggestions for how this might work, either.

Editorial note. Posting here will probably be sporadic for the next few months: I am going on the job market this year, and that process has been (and, I imagine, will continue to be) time-consuming.

On Rosenberg and Kaplan's "Physicalism and Antireductionism in Biology"

I've just finished reading Alex Rosenberg and D. M. Kaplan's "How to Reconcile Physicalism and Antireductionism about Biology" in the current issue of Philosophy of Science. The title describes its contents perfectly, and I can unequivocally recommend it to anyone interested in the topic (which is more than I can say for my foray into the subject). I'll quote the key part of the introduction:

In considering the relation between the PNS [Principle of Natural Selection] and physical science, three alternatives suggest themselves:
a. The PNS is an underived law about biological systems, and is emergent from purely physical processes. ...
b. The PNS is a derived law; it is derivable from some laws of physics and/or chemistry. ...
c. The PNS is an underived law about physical systems (including non-biological ones), and from it the evolution of biological systems can be derived... This is an alternative no one has canvassed, and one which we shall defend here.

Before continuing, let me give their version of the PNS:

For all x, y, and E: If x is fitter than y in environment E at generation n, then probably there is some future generation n', after which x has more descendants than y.

Note that the domain of quantification has no restrictions.

Their basic rationale for calling the PNS a law of physical science -- in particular, of chemistry (59, 62) -- is this: if there is a kind of chemical molecule that (in some sense) replicates itself and has higher rates of 'survival' than other molecules in a given reaction (say, as a reaction moves towards equilibrium, this kind of molecule is favored), that molecule will be subject to the PNS. (It's not a law of physics simply because (sub)atomic particles cannot be construed as replicating.) Calling the PNS a law of chemistry instead of biology "is just a picturesque way of drawing attention to the fact that selection for effects only begins to operate at the level of chemical interactions... Similarly, we call the second law of thermodynamics a law of physics, even though it obtains for all systems -- physical, chemical, and biological -- since it is at the level of the physical that it begins to operate" (61). As an example of such chemical natural selection, they point to current models of origins of life research.

So far, so good. But I'm less comfortable with the other half of their claim in c. above, viz., that from the physico-chemical PNS a fully biological PNS can be derived. They rephrase this point later in the article:

According to this view, at each level of the organization of matter there turns out to be a PNS, and each one should be in principle derivable from the PNS for the immediately lower level or some other lower level(s), all the way back down to the PNS for molecules. (61)

The problem is that they do not explain how this (in principle) derivation would proceed. They phrase the point slightly differently elsewhere (the PNS's "operation at higher levels of the aggregation of matter is a consequence of the operation of the underived PNS for molecules together with the rest of physical law" (62)), but they never actually spell out the derivation beyond this -- as far as I can tell. (In one place (top of p.62: "The rest is natural history"), they appear to hint that any higher-level PNS is a 'consequence' of chemical PNS in a historical sense: because the PNS acted on the primordial soup, today's organisms came into existence -- yet that is completely unlike any sort of reduction any philosopher of science that I know of has talked about. So I assume they can't mean that.)

So the question to Rosenberg and Kaplan is: does natural selection operate on the biological realm (whether it be genes, individuals, or even groups) because it operates on the chemical-molecular level? -- where that 'because' has the same force as the one in 'This mole of gas has a higher temperature than that one because this one's molecules have a higher mean kinetic energy.' Here's one way to press this worry. Look at their definition of the PNS quoted above, and convert it into 'the PNS for molecules':
For any molecule x and molecule y, if x is fitter than y, then...
Now they say that from this (and perhaps other PNSes), we should be able to derive higher level PNSes:
For any gene x and gene y, if x is fitter than y, then...
For any organism x and organism y, if... then...

But these higher-level PNSes don't appear to follow at all. Certainly, each follows from the general PNS quoted at the beginning; but from the fact that all chemical molecules behave a certain way, you cannot infer that organisms will behave a certain way -- unless organisms are chemical molecules. Rosenberg and Kaplan might say at this point: but all we are is an aggregate of chemical molecules: that is just the physicalist thesis which we profess in the title of our paper. But 'Aggregates of As are B' does not in general follow from 'As are Bs,' even for the most determined physicalist.