I'm about to run to the airport for an observing run, so must be brief.
I've been aware of this result some time, and I agree that it is interesting, and if I had done that experiment, I might have leapt to the same conclusion. However, it is premature to do so.
One actually has to do the analysis in terms of the specific theory that is being tested; Clowe et al. have not done this. They merely point out (correctly) that the mass does not seem to be where the light is. This is certainly the naive expectation for modified gravity theories, but does not suffice as a falsification.
If this "bullet cluster" were a nice stable system, they might be correct. However, the whole point here is that it is in the midst of the titanic collision, and is far out of equilibrium. In such a situation, the simple "mass traces light" reasoning might fail, and one has to do a rather involved calculation to check it. One complaint dark matter advocates have long had is that this calculation could not be done in certain theories (e.g., MOND). That has been rectified recently with theories that extend MOND into the relativistic regime, like TeVeS (of Bekenstein).
As it happens, a recent paper by Angus, Famaey, & Zhao that addresses this specific case in TeVeS. Their finding is that "we can generate a multi-centred baryonic system with a weak lensing signal resembling that of the merging galaxy cluster 1E 0657-56 with a bullet-like light distribution." I.e, the observation that is claimed as direct evidence for dark matter can happen in modified gravity theories, so we have to be more cautious about the interpretation.
More generally, I am skeptical about any claim of "direct" detection of dark matter by astronomical means. All the astronomical data tell us is that something is wrong - EITHER we need dark matter OR the equation of gravity we're using needs to be modified. I have had many experiences where I thought the evidence pointed firmly one way or the other, only to find later that the opposite idea could do just as well (or better!) This may be such a case. At any rate, a "direct" detection of dark matter particles would mean (to me) grabbing them in the laboratory, not just infering that their effects can be the only possible explanation for an observation before the alternatives have actually been checked.
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