When I was very little the question was easy. I simply assumed the whole Bible was true, albeit in a mysterious, grown-up sort of way. But once I learned something of science, at school and then at university, that unquestioning belief slid away.
Mathematics was especially important here, and I remember how entranced I was when I first saw the power of axiomatic systems. Those were logical structures that were as beautiful as complex crystals — but far, far clearer. If there was one inaccuracy at any point in the system, you could trace it, like a scarcely visible stretching crack through the whole crystal; you could see exactly how it had to undermine the validity of far distant parts as well. Since there are obvious factual inaccuracies in the Bible, as well as repugnant moral commands, then — just as with any tight axiomatic system — huge other parts of it had to be wrong, as well. In my mind that discredited it all.
What I've come to see more recently is that the Bible isn't monolithic in that way. It's built up in many, often quite distinct layers. For example, the book of Joshua describes a merciless killing of Jericho's inhabitants, after that city's walls were destroyed. But archaeology shows that when this was supposed to be happening, there was no large city with walls there to be destroyed. On the contrary, careful dating of artifacts, as well as translations from documents of the great empires in surrounding regions, shows that the bloodthirsty Joshua story was quite likely written by one particular group, centuries later, trying to give some validity to a particular royal line in 7th century BC Jerusalem, which wanted to show its rights to the entire country around it. Yet when that Joshua layer is stripped away, other layers in the Bible remain. They can stand, or be judged, on their own.
A few of those remaining layers have survived only because they became taken up by narrow power structures, concerned with aggrandizing themselves, in the style of Philip Pullman's excellent books. But others have survived across the millennia for different reasons. Some speak to the human condition with poetry of aching beauty. And others — well, there's a further reason I began to doubt the inanity of everything I couldn't understand.
A child age three, however intelligent, and however much it squinches his or her fact tight in concentration, still won't be able to grasp notions that are easy for us, such as 'century', or 'henceforth', let alone greater subtleties which 20th century science has clarified, such as 'simultaneity' or 'causality'. True and important things exist, which young children can't comprehend. It seems odd to be sure that we, adult humans, existing at this one particular moment in evolution, have no such limits.
I realized that the world isn't divided into science on the one hand, and nonsense or arbitrary biases on the other. And I wonder now what might be worth looking for, hidden there, fleetingly in-between.