One aspect of Christianity that is prominent is belief in a virgin birth – Mary conceived of Jesus ‘directly’ from God. If we take the story literally (it resonates with various other myths, many of which would have been known in the Mediterranean at the time, so it is not clear to me what the reader is supposed to take from the claim), then an argument against it goes as
a) The claim is that Jesus was conceived from God by a virgin, but we now know that virgin births do not occur naturally among humans. Therefore, Jesus was not conceived by a virgin.
I think many secularists actually follow this line of thinking when denying the virgin birth. Yet, a moment’s reflection shows it is not a good argument.
The problem here is that ancients also knew that virgin births among humans do not occur naturally. The whole point of the virgin birth is that it is an unusual (perhaps unique) event. Saying we don’t see it happening today or that it doesn’t occur in nature (which would condition our sense of what can or can’t happen) is true but not to the point.
Rather, there is a premise required for the argument a) above, which is
There is no such thing as miracles.
If there are no miracles, and if virgin births don’t occur naturally, then the conclusion is much stronger.
However, now the argument has to rely upon a much more sweeping argument, namely, the argument to show there is no such thing as miracles.
My guess is that most debates about supposed miracles between secularists and theists aren’t primarily about the evidence for the miracle in question, but a more general claim. As in many beliefs, there is a cyclical component to this (if you don’t believe miracles can occur, you are less likely to think a specific instance of a supposed miracle actually occurred, which in turn helps support your more general belief).