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4. A Mechanistic Version of Inference to the Best Explanation

I suggest that the Meselson-Stahl experiment selects the semi-conservative hypothesis by an inference to the best explanation (IBE).5 In order to make this thesis good, I first need to elaborate on the relevant concept of scientific explanation. For the purposes of this paper, I shall adopt a mechanistic account of explanation. According to such an account, to explain a phenomenon means to describe a mechanism that produces this phenomenon. We are thus talking about a causal-mechanical account of explanation (Salmon 1984). A highly influential account of the relevant concept of mechanism has been given by Machamer, Darden, and Craver (2000), who define mechanisms as “entities and activities organized such that they are productive of regular changes from start or set-up conditions to finish or termination conditions”. A considerable body of scholarship exists know that shows how much experimental research in biology is organized around mechanisms in this sense (Craver and Darden 2001; Darden and Craver 2002; Craver, forthcoming).6


For the purposes of my analysis, I will need to distinguish between two kinds of mechanisms: a) physiological mechanisms and b) experimental mechanism. Physiological mechanisms are mechanisms that operate in a living cell. This kind of mechanism has received much attention lately. By contrast, to my knowledge, no-one has discussed experimental mechanisms in the context of the recent debates in mechanisms in philosophy of science. I want to leave the meaning of the term ‘mechanism’ itself pretty much the same, but allow the entities and activities as well as the changes, set-up and finish conditions to include parts of the experimental system used. In other words, the artificially prepared materials as well as the characteristic manipulations and measurement devices used in the experiment also qualify as parts of a mechanism – an experimental mechanism.7


In order to motivate this move a little, note that it makes perfect sense to speak of the mechanism that produced the UV absorption bands in Meselson’s and Stahl’s experimental setup. This mechanism includes the heavy nitrogen added to the growth medium, as well as the transfer of the growing bacteria into a medium containing light nitrogen. Furthermore, the mechanism includes the mechanical devises used to grind up the cells, extract the DNA and transfer them onto the CsCl gradient (which, needless to say, is also part of the mechanism). The only difference between this experimental mechanism and a physiological mechanism is that the latter occurs in nature, while the former requires external interventions (not necessarily human; the manipulations could be carried out by a lab robot). Of course, this difference is methodologically relevant. Interventions are crucial in generating experimental knowledge and in testing causal claims (Woodward 1993). What is also important is that the physiological mechanism – i.e., the mechanism of DNA replication in this case – is somehow embedded in the experimental mechanism. In other words, it is responsible for some of the regular changes that constitute the experimental mechanism. Mechanisms often form hierarchical structures where particular entities and activities can be themselves decomposed into lower-level mechanisms (Craver and Darden 2001). The lower-level mechanisms may be responsible for some of the activities that feature in higher-level mechanisms. But such a hierarchical organization is not necessary. Mechanisms may be related by one mechanism providing the substrate that another mechanism operates on. Biochemical pathways are a nice example for this. Thus, mechanisms may be vertically linked. Such vertical links exist in our present example: the heavy nitrogen is an entity of the experimental mechanism, and it is a substrate on which the physiological mechanism can act if it is provided instead of the usual substrate (i.e., light nitrogen).


Why this extension of the notion of mechanism? What I would like to suggest is that the experimental mechanism provides an explanation for the actual patterns that Meselson and Stahl saw in their experiment. Further, I want to claim that this explanation is better than the two alternative explanations that involve the dispersive or conservative replication mechanism instead of the semi-conservative one. In other words, the experimental mechanism in combination with the semi-conservative physiological mechanism is the best explanation for the banding patterns obtained by Meselson and Stahl, at least in the group of experimental mechanisms that involve either the semi-conservative, the dispersive or the conservative mechanism and are otherwise identical. Therefore, the semi-conservative mechanism is inferred by an IBE.


Such an account requires that we be able to say (1) why the semi-conservative mechanism is a part of the best explanation, and (2) why this provides grounds for the truth of the statements that describe the mechanism. For this purpose, I would like to refer to Lipton’s distinction between the “likeliest” and the “loveliest” explanation. The former is the explanation that is most probable. The latter is “the one which would, if correct, be the most explanatory or provide the most understanding” (Lipton 2004, 59). As Lipton shows, IBE can only be used in a non question-begging way if there are reasons to believe that loveliness is a guide to likeliness. I will come back to the question of whether we could have such reasons in this case in Section 6. The question right now is if there is any sense in which the experimental mechanism in combination with the semi-conservative scheme is more explanatory, i.e., provides more understanding than the experimental mechanisms containing the alternative schemes.


I think there is clearly such a sense. For if we assume any of the other schemes to be correct (the dispersive and conservative schemes), then we would expect different banding patterns. On the conservative scheme, we would not expect bands intermediate in density. By contrast, on the dispersive scheme we would expect more bands of intermediate density than just one after further rounds of replication. But Meselson and Stahl observed exactly one.


At this stage, the question arises why we cannot simply say that the semi-conservative scheme was the only one to survive the test to which Meselson and Stahl subjected it, while the alternative schemes did not survive this test and were therefore falsified? This would mean that we could do without IBE. But note that this would amount to an eliminative induction, which is exactly the kind of reasoning that is not possible according to Duhem. If we construe the experimental reasoning like this, both of Duhem’s objections can be raised: First, it can be argued that the dispersive and conservative hypotheses could still be true because one or several auxiliary assumptions might have been false. For example, it could be that Meselson and Stahl were wrong about the molecular units that they resolved in their ultracentrifuge. Technically, what the centrifuge data show is merely that there are three colloidal substances of different density. It does not show that these substances were simple DNA duplexes. In other words, the identification of this:





with this:





could have been false. This is all the more so because it is known today that Meselson and Stahl were wrong about the length of the molecules they saw floating in their gradients. Although the length of total E. coli DNA had been determined pretty accurately, the hypodermic syringes that Meselson and Stahl used to load the DNA onto the gradient must have mechanically sheared the DNA molecules into much smaller pieces – unbeknownst to these scientists in 1957!8 This did not alter the result because the CsCl-gradient technique separates DNA molecules according to density, not length. Quite to the contrary: the interpretation of the data would have been much more difficult had the DNA not been sheared. The reason is that if the samples had contained intact E.coli genomic DNA, some proportion of the molecules could have been incompletely replicated, which would have meant a whole smear of material of intermediate density. Sometimes it’s good of experimentalists don’t know too much about their experimental system!


In fact, Meselson and Stahl were quite cautious in stating their conclusions:


The structure for DNA proposed by Watson and Crick brought forward a number of proposals as to how such a molecule might replicate [the semi-conservative, dispersive and conservative mechanisms, M.W.] These proposals make specific predictions concerning the distribution of parental atoms among progeny molecules. The results presented here give a detailed answer to the question of this distribution and simultaneously direct our attention to other problems whose solution must be the next step in progress toward a complete understanding of the molecular basis of DNA duplication. What are the molecular structures of the subunits of E.coli DNA which are passed on intact to each daughter molecule? What is the relationship of these subunits to each other in a DNA molecule? What is the mechanism of the synthesis and dissociation of the subunits in vivo? (Meselson and Stahl 1958, 681).


As this passage makes clear, Meselson and Stahl did not even draw the inference from their data to the semi-conservative mechanism, at least not officially. The questions they raise toward the end of this passage are exactly those that their experiment is supposed to have answered! In print, Meselson and Stahl did obviously not want to go beyond what their data said. However, unofficially they showed less caution. Meselson sent J.D. Watson a little poem9:


Now 15N by heavy trickery / Ends the sway of Watson-Crickery. / But now we have WC with a mighty vengeance … or else a diabolical camouflage.


The hint with the “diabolical camouflage” is quite revealing. It suggests that Meselson thought it unlikely in the extreme that their experiment had turned out the way it did had the semi-conservative hypothesis been false. This suggests yet another construal of the case: It could be argued that what Meselson and Stahl actually provided was a severe test in the sense of Deborah Mayo’s error-statistical theory of scientific reasoning (Mayo 1996). A severe test in this sense is a test with a low error probability, in other words, a low probability that the hypothesis passes a test in spite of being false. The problem with such a construal is to say what justifies the judgment that this probability was low or sufficiently low. The mechanism does not imply a probability distribution for different outcomes, which are the classic cases where a Neyman-Pearson test can be run. Thus, introducing error probabilities does not solve any problem here. We need to know why Meselson thought it unlikely that the DNA would behave as it did, had the semi-conservative scheme been false. How could this judgment be justified on Meselson’s and Stahl’s behalf?


I can’t think of a better answer than just saying that it would be a strange coincidence if Meselson’s and Stahl’s experiment behaved as if a semi-conservative mechanism was at work while, in fact, there was some other physiological mechanism at work. But this is just another way of expressing the intuition that this was unlikely; it does not really give a justification for it. Therefore, I think a construal of the case as a severe test with a low error probability does not really solve the problem.10


I want to claim that my construal of the case as an IBE does solve the problem. On this view, the reason why the experiment supported the semi-conservative hypothesis was because there is an experimental mechanism that interacts with the semi-conservative mechanism in such a way that it explains the banding pattern obtained by Meselson and Stahl in a very lovely way (in Lipton’s sense). By contrast, there is no mechanism involving the conservative or dispersive mechanisms that would explain this result. In theory, there are of course possible epicycles that one could introduce to make them do so. One possibility of doing this is as follows. As already mentioned, what the experiment showed was merely the symmetrical distribution of heavy nitrogen in replication, not that the bands correspond to single DNA duplexes. It was technically possible that the intermediate band represents an end-to-end association of parental DNA duplexes with newly synthesized duplexes rather than hybrid molecules composed of a light and a heavy strand (this would make the results compatible with the conservative hypothesis). This interpretation was ruled out about five years later, when Meselson’s student Ron Rolfe showed that the DNA can be broken into smaller fragments by sonication without affecting its density (Hanawalt 2004).


At this point, we face a juncture: Either we could say that before this additional test was done, Meselson and Stahl had no decisive evidence for the semi-conservative hypothesis (i.e., evidence that provides grounds for holding the hypothesis to be true, see Achinstein 2001). In fact, this was Meselson’s and Stahl’s own official view as stated in the conclusions of their paper (see above). However, this throws us on a slippery slope toward skepticism. For it is always possible to come up with an interpretation of Rolfe’s data that make them compatible with one of the alternative hypotheses (perhaps there were covalent crosslinks between the parental and newly synthesized duplexes that were resistant to the sonication treatment, and so on). This move allows Duhemian underdetermination to run amok. Furthermore, this does not reflect how many scientists really thought about the experiment at that time.


Fortunately, there is another way. Instead of saying that the jury was in only in once all the auxiliary assumptions had been tested (i.e., never), IBE allows us to argue that the Meselson-Stahl experiment supported the semi-conservative hypothesis by its own wits, that is, even without the help of additional tests that ruled out possible errors in the interpretation of the data. This is because the semi-conservative mechanism, together with what I have called the experimental mechanism, can explain the data without any help. By contrast, the alternative schemes have no such explanatory force with respect to the data actually obtained (they do have the power to explain different banding patterns, but those were not actually obtained). Even if there are possible epicycles that one can introduce to make them fit, these would have a strong ad hoc character and go totally unexplained. For instance, nothing in the conservative scheme implies that the parental and progeny molecules would remain covalently attached to each other, thereby tricking scientists into believing they are seeing hybrid molecules composed of one conserved and one newly synthesized strand. Even if such an epicycle can be added, the conservative mechanism wouldn’t explain it by itself. This, I suggest, is an epistemically important difference between the conservative and semi-conservative schemes. The latter requires no further assumptions, not even extra mechanistic detail, in order to explain the banding pattern, except for the experimental manipulations carried out by Meselson and Stahl. This, I suggest, is what made the experiment compelling evidence for Watson’s and Crick’s replication scheme. Thus, Duhem’s first predicament can be solved with the help of my mechanistic version of IBE.


In the following section, I shall address a further complication to the story.

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