Yes, it does.
There are far more properties of matter that we are only beginning to test for.
No, there aren't.
I’m sure there are countless others that we don’t even know of.
Wrong, again. You're batting 1000.
Different methods of synthesis and production have long been known to affect the actions of drugs even though they appear identical when tested.
The differences found are accounted for by cofactors which mobilize or inhibit uptake, not because the same compound has different effects when produced by different processes.
I’m sure the same would not apply to sugar and other compounds found in foods.
It might, if what you were saying was anything but errant nonsense. But it isn't, because everything you've written in this post has no basis in science.
For example, the fructose synthesized by the agave plant is surely different from the fructose found in processed HFCS.
Nope. No difference. Fructose, is, by definition, fructose. Always is fructose and never is anything else, not even if made by little elves in a hollow tree.
How different or how it affects us remains to be seen. It is more difficult to study and confirm because foods don’t have as profound and immediate effect as drugs.
More nonsense. Some drugs have no effect on some people at all. Some foods kill some people almost instantly.
I'm sure this is going to be lost on you, but for the sake of people who are educable: A molecule is a molecule. When that molecule has the same number of atoms, the same kinds of atoms, and the same structure, it is physically indistinguishable from any other identical molecule. There is no physical test, no chemical experiment, and no biological process, including eating, drinking or snorting it that will produce a different effect.
I tremble for my country when I reflect that our scientific education has produced anyone who can make such a collection of completely false and nonsensical statements in a single post.
Humans use D sugars and L amino acids. L sugars and D amino acids are toxic. That optically active carbon is important. Racemization is the characteristic of having a mix of D and L forms. In the case of vitamin E, only the D isomer is biologically active. Cheap drugstore vitamin E is often half inactive racemized junk. Review your biochemistry.
“When that molecule has the same number of atoms, the same kinds of atoms, and the same structure, it is physically indistinguishable from any other identical molecule.”
Indistinguishable by our current level of understanding. There is far more to atomic structure than we can measure or even imagine.
I am a nuke engineer and did research for many years. Once you dig down, you see we are far from truly understanding anything.
Again, we are only beginning to understand and there will be properties discovered that we can't even imagine.
http://www.newscientist.com/mobile/article/dn20130-fly-sniffs-molecules-quantum-vibrations.html