Context problems

context problems

The passage below is from ‘the Blank Slate’ by Steven Pinker.

http://evolbiol.ru/blankslate/blankslate.htm

The study of neural development is often framed in terms of nature and nurture, but it is more fruitful to think of it as a problem in developmental biology — how a ball of identical cells differentiates into a functioning organ. ?Doing so ?stands ?the conventional assumptions of associationism on their head. Primary sensory cortex, rather than being the firmest part of the brain on top of which successive stories can only be even more plastic, may be the part of the brain that is most dependent on the input for proper development.

In this passage I have three questions.
(I know I can ask one question per thread, but these questions are in a string so I think they cannot be separated.)
?First, what does 'doing so' refer to?
Does it refer to after 'think of it as...'?
?Second, does 'stands' can be replaced by 'turns' as in 'Marx turned Hegel on his head'?
?Last, does 'the conventional assumptions of associationism' refer to 'primary sensory cortex is the firmest part of the brain on top of which successive stories can only be even more plastic'?

Hope for your replies.

Regards.