The pronoun problem

The passage below is from The Blank Slate written by Steven Pinker.

https://books.google.co.kr/books?id=ePNi4ZqYdVQC&pg=PA12&lpg=PA12&dq=%22He+derived+the+policy+after+consulting+not+just+with+scientists+but+with+philosophers+and+religious+thinkers%22&source=bl&ots=kKu5EnLlP1&sig=nk00oXDc5sHH-KQbEL1C02IHvlM&hl=en&sa=X&ei=j6g7VeW7NOP6mQXV2YCoBQ&ved=0CBwQ6AEwAA#v=onepage&q=%22He%20derived%20the%20policy%20after%20consulting%20not%20just%20with%20scientists%20but%20with%20philosophers%20and%20religious%20thinkers%22&f=false

He derived the policy after consulting not just with scientists but with philosophers and religious thinkers. Many of them framed the moral problem in terms of “ensoulment,” the moment at which the cluster of cells that will grow into a child is endowed with a soul. Some argued that ensoulment occurs at conception, which implies that the blastocyst (the five-day-old ball of cells from which stem cells are taken) is morally equivalent to a person and that destroying it is a form of murder. That argument proved decisive, which means that the American policy on perhaps the most promising medical technology of the twenty-first century was decided by pondering the moral issue as it might have been framed centuries before: When does the ghost first enter the machine?

In this passage I’m not sure what the underlined ‘it’ stands for.
In a way it seems to represent, ‘the moral issue.’
In another it can stand for ‘the American policy.’
Can you make it clear for me?

Thanks in advance.