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It is natural for physicists to consider the group $SO(3)$. Presumably, $SU(2)$ came into physics because of quantum mechanics. How did people realize that when studying rotation of a physical system that sometimes, it is the group $SU(2)$ instead of the group $SO(3)$ that really matters?

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It came to physics a bit earlier than quantum mechanics. The homomorphism $SU(2)\to SO(3)$ was discovered by Cayley (1843), Hamilton (1847), and Klein (1875) in their pure mathematical studies, and came to the attention of physicists through the theory of rigid body rotation (classical mechanics). It was Klein who brought it to the attention of physicists.

In old books on mechanics this is called the "Cayley-Klein's parameters". Klein explained this correspondence to physicists in his 1895/6 lectures which were later published as a book under the title "Theory of the top" (joint with his student A. Sommerfeld). (A concise exposition in English is in his 1897 Princeton lectures on the same subject. But the 4 volumes of Klein and Sommerfeld has been also translated into English).

In his Princeton lectures Klein says:

Instead of either of these commonly used systems of parameters, I propose to introduce another, which so far as I know has not yet been employed in dynamics.

Later he writes in the same lectures:

There is nothing essentially new in these considerations. I have merely attempted to throw a method already well known into the most convenient form for applications in mechanics.

Among the predecessors of Cayley, Hamilton, and Klein, Euler has to be mentioned: he discovered a rational parametrization of the rotation group which is equivalent to quaternion parametrization, in his work on arithmetic. It was apparently not noticed by physicists, but Klein credits the "quaternion parametrization" to Euler.

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    $\begingroup$ I think there's some absolutely fantastic stuff lying around in the history of science (and mathematics). $\endgroup$ Commented Nov 9, 2019 at 17:11
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    $\begingroup$ @John Duffield: can you be more specific? (The word "fantastic" has several meanings:-) $\endgroup$ Commented Nov 9, 2019 at 19:57
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    $\begingroup$ Why does it appear in classical mechanics? Is it because of the double cover? Wouldn't its true use in physics appear with the discovery of spin? $\endgroup$
    – Mauricio
    Commented Dec 9 at 22:44
  • $\begingroup$ @Mauricio: as I explained in my answer it appeared in physics a bit earlier, namely in the study of rotating top. It is because this the universal cover (which happens to be double in this case). $\endgroup$ Commented Dec 10 at 11:46
  • $\begingroup$ @AlexandreEremenko can you just describe the top with SO(3) only? SU(2) only seems truly necessary once you need to describe two level quantum systems. $\endgroup$
    – Mauricio
    Commented Dec 10 at 12:18

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