In Einstein's theory of General Relativity, the universe is a 4-manifold that might well be fibered by 3-dimensional time slices. If a particular spacetime that doesn't have such a fibration, then it is difficult to construct a causal model of the laws of physics within it. (Even if you don't see an a priori argument for causality, without it, it is difficult to construct enough solutions to make meaningful predictions.) There isn't usually a geometrically distinguished fibration, but if you have enough symmetry or even local symmetry, the symmetry can select one. An approximate symmetry can also be enough for an approximately canonical fibration. Once you have all of that, the topology of spacelike slices of the universe is not at all a naive or risible question, at least not until you see more physics that might demote the question. The narrower question of whether the Poincaré Conjecture is relevant is more wishful and you could call it naive, but let's take the question of relating 3-manifold topology in general to cosmology.
The cosmic microwave background, discovered in the 1964 by Penzias and Wilson, shows that the universe is very nearly isotropic at our location. (The deviation is of order $10^{-5}$ and it was only announced in 1992 after 2 years of data from the COBE telescope.) If you accept the Copernican principle that Earth isn't at a special point in space, it means that there is an approximately canonical fibration by time slices, and that the universe, at least approximately and locally, has one of the three isotropic Thurston geometries, $E^3$, $S^3$, or $H^3$. The Penzias-Wilson result makes it a really good question to ask whether the universe is a 3-manifold with some isotropic geometry and some fundamental group. I have heard of the early discussion of this question was so naive that some astronomers only talked about a 3-torus. They figured that if there were other choices from topology, they could think about them later. Notice that already, the Poincaré conjecture would have been more relevant to cosmology if it had been false!
The topologist who has done the most work on the question is Jeff Weeks. He coauthored a respected paper in cosmology and wrote an interesting article in the AMS Notices that promoted the Poincaré dodecahedral space as a possible topology for the universe. But after he wrote that article...
There indeed is other physics that does demote the 3-manifold question, and that is inflationary cosmology. The inflation theory posits that the truthful quantum field theory has a vaguely stable high-energy phase, which has such high energy density that the solution to the GR equations looks completely different. In the inflationary solution, hot regions of the universe expand by a factor of $e$ in something like $10^{-36}$ seconds. The different variations of the model posit anywhere from 60 to thousands of factors of $e$, or "$e$-folds". Patches of the hot universe also cool down, including the one that we live in. In fact every spot is constantly cooling down, but cooling is still overwhelmed by expansion. Instead of tacitly accepting certain observed features of the visible universe, for instance that it is approximately isotropic, inflation explains them. It also predicts that the visible universe is approximately flat and non-repeating, because macroscopic curvature and topology have been stretched into oblivion, and that observable anisotropies are stretch marks from the expansion. The stretch marks would have certain characteristic statistics in order to fit inflation. On the other hand, in the inflationary hot soup that we would never see directly, the rationale for canonical time slices is gone, and the universe would be some 4-manifold or even some fractal or quantum generalization of a 4-manifold.
The number of $e$-folds is not known and even the inflaton field (the sector of quantum field theory that governed inflation) is not known, but most or all models of inflation predict the same basic features. And the news from the successor to COBE, called WMAP, is that the visible universe is flat to 2% or so, and the anistropy statistically matches stretch marks. There is not enough to distinguish most of the models of inflation. There is not enough to establish inflation in the same sense that the germ theory of disease or the the heliocentric theory are established. What is true is that inflation has made experimental predictions that have been confirmed.
After all that news, the old idea that the universe is a visibly periodic 3-manifold is considered a long shot. WMAP didn't see any obvious periodicity, even though Weeks et al were optimistic based on its first year of data. But I was told by a cosmologist that periodicity should still be taken seriously as an alternative cosmological model, if possibly as a devil's advocate. A theory is incomplete science if it is both hard to prove, and if every alternative is laughed out of the room. In arguing for inflation, cosmologists would also like to have something to argue against. In the opinion of the cosmologist that I talked to some years ago, the model of a 3-manifold with a fundamental group, developed by Weeks et al, is as good at that as any proposal.
José makes the important point that, in testing whether the universe has a visible fundamental group, you wouldn't necessarily look for direct periodicity represented by non-contractible geodesics. Instead, you could use harmonic analysis, using a suitable available Laplace operator, and this is what used by Luminet, Weeks, Riazuelo, Lehoucq and Uzan. I also that I have not heard of any direct use of homotopy of paths in astronomy, but actually the direct geometry of geodesics does sometimes play an important role. For instance, look closely at this photograph of galaxy cluster Abell 1689. You can see that there is a strong gravitational lens just left of the center, between the telescope and the dimmer, slivered galaxies. Maye no analysis of the cosmic microwave background would be geometry-only, but geometry would modify the apparent texture of the background, and I think that that is part of the argument from the data that the visible universe is approximately flat. Who is to say whether a hypothetical periodicity would be seen with geodesics, harmonic expansion, or in some other way.
Part of Gromov's point seems fair. I think it is true that you can always expand the scale of proposed periodicity to say that you haven't yet seen it, or that the data only just starts to show it. Before they saw anisotropy with COBE, that kept getting pushed back too. The deeper problem is that the 3-manifold topology of the universe does not address as many issues in cosmology, either theoretical or experimental, as inflation theory does.
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