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Let $h: \mathbb{R}^3 \to \mathbb{R}$ be the usual height function (i.e. $h(x,y,z) = z$). One way that Morse functions on $S^2$ are often described is by picking an embedding $i: S^2 \to \mathbb{R}^3$ and then considering $h \circ i$ which, for a generic embedding will be a Morse function.

Does there exist a Morse function $f : S^2 \to \mathbb{R}$ so that there is no embedding $i: S^2 \to \mathbb{R}^3$ with $f = h \circ i$?

I think that this shows that every Morse function on $S^2$ can be factored through an immersion, but I am interested in embeddings.

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    $\begingroup$ If you allow slightly more liberal usage of the word "height function" then the answer is yes. For example, every morse function can be realized as the distance from the origin for a suitable embedding of $S^2$ in $\mathbb R^3$. You similarly have no problem if your embedding space is $S^2 \times \mathbb R$. But in $\mathbb R^3$ you likely can't get away from the immersion condition. $\endgroup$ Commented Jun 14, 2019 at 1:59

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Any Morse function on $S^2$ may be realized by an embedding $S^2\hookrightarrow \mathbb{R}^3 \to \mathbb{R}$. For a Morse function $F:S^2\to \mathbb{R}$, take the equivalence relation with equivalence classes given by the components of the level sets of the Morse function $F$. The quotient of the sphere by this equivalence relation is a cubic tree $\mathcal{T}$, with inducted function $f:\mathcal{T}\to\mathbb{R}$ on the quotient.

Hatcher Thurston

This was used more generally by Hatcher and Thurston to obtain a presentation of the mapping class group (the figure is from their paper).

Hatcher, Allen E.; Thurston, William P., A presentation for the mapping class group of a closed orientable surface, Topology 19, 221-237 (1980). ZBL0447.57005.

Now we may embed the tree $\mathcal{T}\hookrightarrow \mathbb{R}^3 \to \mathbb{R}$ so that the composite is $f$ (essentially by general position). Then taking a regular neighborhood of $\mathcal{T}$, we get an embedding $S^2 \hookrightarrow \mathbb{R}^3\to \mathbb{R}$ that induces the Morse function $F$.

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