I go birdwatching on a regular basis--my favorite birds are waterfowl, and at this time of year there are a lot of migratory species coming through Holland (it's a very good time to have a pair of 8 x 56's). As with any region, you have your native common fauna, which consists of the same old 15-20 species you see EVERY time you go out, your native less-common fauna (the 10-15 species you don't see every time and are excited when you do), the non-native fauna (10-15 species that are SOO COOL! when you see them), and the rare birds.
When you pick up a birdwatching guide, it will contain a long list of field markers, habitats, songs, behaviors, notes about plumage changes, differences between age groups--there is no way to memorize all of the information. Yet I can tell you, sitting in a train whizzing by at 60 mph, that that white-ish goose is a domestic goose and that other white-ish goose is a dark variation of the snow goose.
OK, so compulsively reading my bird guide probably has something to do with this. But more than that is practice. It's how you learn to tell black-headed gulls apart from common gulls (red feet, red bill) during the winter, when they don't have their black heads. I don't check plumage points, behaviors, habitats, unless I'm really uncertain about a new strange bird--and the only reason it's new and strange is because I haven't seen it in the wild before, as most of the time I know where it is in my book and I can turn right to it.
But if you were to ask me how I go about quickly spotting birds and making my identificataions--what thoughts go through my head--I couldn't tell you. Just as I couldn't tell you exactly what makes my cells healthy and what makes them not--why I say they're "not behaving" even though they look plump and otherwise healthy. I don't think anybody who does cell culture can accurately describe what "healthy" cells look like, but they know "unhealthy" cells when they see them.
You might wonder why there's any fuss over the health of cells at all. Turns out that many of the assays run depend on the cells being "healthy"--i.e., not contaminated, in the log phase of their growth, not newly-split, not "hungry" (believe it or not, you can tell when they are), with a slightly-acidic-but-not-too-much media, evenly dispersed--the criteria go on and on, but the gestalt picture is that the cells just look "healthy".
When you work in science, you eventually acquire a feeling as to what should work and what doesn't. The minutiae of your system become intuitive--you know that's not a pigeon, even if all you can see is a black blob against a blue sky. You know your cat isn't feeling well, even if it's not doing anything other than what it normally does. You know that even if the protocol says nothing about gently stirring your reaction mixture, you'd better do it gently if you want results. You know that some equations are better than others.
This is the daily in-and-out of experimental science, ladies and gentlemen. It is predicated on a long list of assumptions, some of which only may be true. It is not very scientific at all.