How can scientists determine exactly what happens at really small scales inside our bodies?


Over time I have seen very detailed descriptions about the mechanisms of certain pharmaceuticals and also about biological processes. Things like “this molecules works by binding to this very specific type of receptor found in these areas of the brain/”. How do scientists observe these processes? How do they figure what exactly happens inside the body on those small scales? Also, I do know about autopsies but I’m talking about active processes inside actual living humans.

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Disclaimer: I am not an expert, a lot of what I say might be wrong.

We can’t observe things on the molecular level.
However, we can *model* things on the molecular level.

If we know that drug X has a certain molecular shape, and that receptor Y has an X-shaped hole in it, then it is reasonable to infer that drug X binds to receptor Y. This can be tested by looking at people who have a malformed receptor Y, and what effects drug X has on them; or comapring the effects of drugs that are shaped similarly to X and how well they bind to Y, etc.

We can then tell that the receptors are in part Z of the brain by looking at people who have damage in part Z and what effects that damage has on them, and then testing how they respond to X, etc.

The answer is sort of a cop out: they don’t, not usually. Not inside the body.

If you want to determine what the actual mechanisms are, a lot of the time drugs are tested on cell cultures and tissue analogues in the lab. Or, if it’s sufficiently simple or they’re already dialled in on a particular protein, the might do pure chemistry with synthetic receptors and some sort of predefined marker. That’s because those are very controllable and repeatable conditions, something essential for proper scientific study. Actual living people are too… Messy.
Of course drugs have to eventually pass clinical trials, because you can’t replicate all aspects of a human body in the lab. There’s always something to be missed.

Same really goes for biological processes, we’re made of cells and you can study those closely in a lab. That’s why biopsies are taken. Then you make a theoretical model of how you think it works, and check its predictions with real data from a more complex organism, including people. You’re either right, or you go refine your model with new information.