orbitals, flowers, quantum puzzlement;

I have heard it said that there is exist shapes in the world, shapes such as
the shapes and symmetries of flowers, crystals (and cabbages and kings)
exactly because atoms aren't all spherically symmetric. Most atoms (taking
higher orbitals of hydrogenic atoms as a guide) have orbitals that have
definite shape. Or do they? We have all seen the pictures of the spherical
harmonics etc. But wait! The choice of the z-direction is arbitrary and
implies that an experiment is being done that looks for the z component of
angular momentum. But then an atom out there in nature doesn't really have
the electron cloud shape implied by the graphs of spherical harmonics after
all. Why not? Well what or who chooses the direction of z? The positions or
orientations of the lobes doesn't seem to be an objective fact independent
of out experimental preparations (like a bean of atoms in a uniform magnetic
field etc.). So how can these lobes of orbitals (which have no objective
orientation) account for "shape' in nature. One might jokingly ask "who is
measuring L_z?". God? :)---and how does /he/she/it choose the direction of z
when making a flower?
I am begining the think that I (like Lee Smolin) do not understand QM; I
wonder if quantum mechanics as taught is not conceptually coherent. There is
a definite mathematical structure (rigged Hilbert spaces etc.) but the
application is piecemeal and involves equivocations and hand waving.
Little puzzles like the one I give here always have answers but those
answers apply ontological strategies that seem ad hoc and directed only to
the particular puzzle at hand. One interpretation of QM may help with one
puzzle while making a different one incomprehensible.
Sometimes I think we should work harder to understand QM as such before we
try to quantize everything under the sun (gravity, strings, spacetime etc.)

In the article http://www.edge.org/q2005/q05_5.html#smolin
Smolin wrote " am convinced that quantum mechanics is not a final theory. I
believe this because I have never encountered an interpretation of the
present formulation of quantum mechanics that makes sense to me. I have
studied most of them in depth and thought hard about them, and in the end I
still can't make real sense of quantum theory as it stands. Among other
issues, the measurement problem seems impossible to resolve without changing
the physical theory."

.

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