Many "why" questions are really "how" questions in disguise. For instance, if you ask: "Why does water boil at 100C?" what you are really asking is: "What are the processes that explain it has this boiling point?" – which is a question of how.Critically, however, scientific "why" questions do not imply any agency – deliberate action – and hence no intention. We can ask why the dinosaurs died out, why smoking causes cancer and so on without implying any intentions. In the theistic context, however, "why" is usually what I call "agency-why": it's an explanation involving causation with intention.So not only do the hows and whys get mixed up, religion can end up smuggling in a non-scientific agency-why where it doesn't belong.This means that if someone asks why things are as they are, what their meaning and purpose is, and puts God in the answer, they are almost inevitably going to make an at least implicit claim about the how: God has set things up in some way, or intervened in some way, to make sure that purpose is achieved or meaning realised. The neat division between scientific "how" and religious "why" questions therefore turns out to be unsustainable....But for the moment, we can say that any religious belief that involves an activist, really-existing God and claims that religion has something to say about why things happen, must also be encroaching on questions of how they happen, too. And if that's true, the easy peace which many claim should exist between science and religion just isn't possible.
It's not unidirectional, though. Perhaps politeness forbids him from suggesting that science and rationality can, in the course of delineating the hows, do away with the whys by process of elimination, leaving them nowhere to rest but in incoherence. The more we learn about how things work, the more we come to see the futility of trying to make the universe fit the Procrustean bed of purpose and meaning on a human scale. I speak to you from personal experience here, my friends: when you allow your desperate need for objective meaning rooted in abstract universal truth to atrophy, wither and fall away, life is still worth living.