To what is the Doctor referring when he tells Marlow,"The changes take place inside, you know"?
This statement is part of Conrad's backlash against Enlightenment thinking. Proponents of the ideology believed all questions could be eventually be answered by science; Conrad casts some serious doubts on the theory throughout his novel.
Here, the doctor is measuring Marlow's skull, using a now-discredited practiced known as phrenology. Phrenologists postulated that they could tell a person's propensity for violence, passion, reason, etc., from the bumps and shape of one's head. This is the "outward" purpose of the exam. Internally, Marlow will be going through psychological changes that can never be measured scientifically. Here is the verbiage from this particular exchange. Marlow has just agreed to the examination.
Doctor: Don't be alarmed..these calipers here measure your dimensions back and front and..and every way.. one hundred and thirty centimetres..I always ask leave, in the interests of science, to measure the crania of those going out there...
Marlow: And when they come back, too?
Doctor: Oh, I never see them...and, moreover, the changes take place inside, you know. Two hundred and forty..So! You are going out there. Famous. Interesting, too. One hundred and seven point five.....Ever any madness in your family?
Marlow: Is that question in the interests of science, too?