The point I think the commenter was making is that the statement "The goal was to understand how abstract thought arises from brain structure" suggests there may be some begging the question in the study design.
If you start with the assumption that that brain structure produces abstract thought, your evidence will support it, because you already believed it in the first place.
The main challenge to any hypothesis about the nature of thought or consciousness is that our fundamental tool for contemplating the topic is our consciousness - which is precisely what we're trying to understand.
On that basis, the argument goes, it's impossible to objectively determine what consciousness really is, because we have no way of separating the consciousness we're studying from the consciousness we're using to study it.
Alternative theories to the one that says the brain produces consciousness are that the brain is a carrier or receiver of consciousness, which somehow originates elsewhere.
Various forms of such theories have been proposed by reputable scientists including Roger Penrose[1], John Eccles[2] and - somewhat ironically - Karl Popper[3].
I personally don't have any strong opinions about the validity of these theories; it's enough for me to know that they exist and to keep an open mind until someone can develop a truly testable and falsifiable hypothesis.
Until then, it's all pretty much philosophy.
[1] https://en.wikipedia.org/wiki/Roger_Penrose#Physics_and_cons...
[2] http://www.theosophy-nw.org/theosnw/science/prat-bra.htm
[3] https://en.wikipedia.org/wiki/Mind%E2%80%93body_problem#Popp...