Not a biologist, but I've been in bio labs and it is _meticulous_ work. Very, very clever processes for detecting molecules as they pass through (or don't pass through) certain organelles, a good dose of math, some inference, and sometimes luck.

Not being able to see (and as the toothpick -> truck of floss poster mentioned above, this isn't going to help with biological systems much at this point) does mean there are significant gaps in what biologists know. On the other hand, biologists have been visualizing larger structures for some time (even proteins via xray etc.)