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I agree that deciding what is relevant is not always the sort of question that can be decided by scientists. 

And not only that, but after we have decided that something is relevant, it may not be the sort of thing that can be identified by scientists.

Consider the case of the embryo/fetus/unborn child. Pro-life writers often stress the physical similarities between a fetus and an infant. By applying the 'treat equal cases equally' rule, they hope to persuade others that abortion is as immoral and unjust as infanticide. Pro-choice writers often stress the differences between a fetus and a fully developed human being. The embryo or fetus, for example, cannot reason. By noting that we can justly treat different cases differently, they hope to persuade others that abortion is morally permissible.

Which of these similarities and differences are relevant? If they are all relevant, which ones are the most important so far as justice is concerned?

It seems to me that there is something other than a scientific question at issue here. Pro-life and pro-choice people could agree on all the scientific facts about embryos and babies but still disagree about the moral status of the embryo/unborn child. What kind of a question is moral status? It doesn't sound like a scientific question to me.

And moral status connects with other issues. For example, for some writers, the key question is "What is a person" or "When does the fetus become a person? For some pro-life writers, the key question is "When does the unborn child bear the image of god?" These are not scientific questions. But they are clearly very relevant to any final conclusions about the morality and justice of abortion.