Does Science Have the Best Explanation - For EVERYTHING?

It's a claim I made a couple of posts back and was disputed by commenter "cl" (not of the Hanson variety). I've asked him to give a couple of examples of things science does not explain better than religion does. So far, he hasn't met the challenge. He did offer up the notion (I assume now know facetiously) that religion itself is better explained by religion, than by science. (For instance - The Crusades or the Papal rejection of Galileo's claims re: heliocentric solar system. I tossed in the Inquisition and Pope Johnny The Rat's notion that the AIDS epidemic in Africa is better battled with faith than with condoms). But really, that's a weird circular reasoning. "We some crazy-ass mother fuckers and no one can explain how fucked up we are like we can"! Theories of mind and consciousness have already made great strides in explaining why people gravitate toward religion or cult figures and why they can do evil things while claiming moral high ground (and being able to convince most people that they are indeed righteous).

"Great Strides" you say, eh Evo? Sounds like science hasn't fully explained it yet.

True. But that doesn't change my position.

A mere 500 years ago, the following questions were beyond the scope of man's knowledge - The Universe (how it began, how long ago, the immensity of it, it's expansion), disease caused by microbes such as bacteria and viruses, atomic structure (everything being made up of trillions of atoms), evolution (that every life form is connected to every other life form in common ancestry), Consciousness (that there is no need to invoke a ghost in the machine. That everything we know and feel happens within the material structure of the brain and that once there is no chemical and electrical activity, there is no consciousness).

Back then, all of these and many more could have been explained as "rationally" by any religious belief as from the empirical knowledge humans had gathered. We can look back at the knowledge achieved in 500 years and say, "well sure. We know all that. But there is still a place for religious explanations of some things".

What things?

Yes, there are many mysteries that science has barely begun to scratch. There are mysteries coming that we aren't even aware of now - in much the same way that Pope Pius III in 1509 didn't dispute particle physics because no one knew what an atom was. But how different are any of today's (or tomorrow's) mysteries from those of 500 years ago? "Love" may be great challenge, but it is not beyond science's scope. Science has proven itself over and over, as the battered and dead bodies of religious certainty littering it's march attest. I won't be around to say I told you so, but today's "religious mysteries" will be chuckled at in 500 years if we are wise enough to keep from destroying civilization. And science will be our best guide in how to avoid that calamity. Religion will be, as it always has been, our worst enemy.

I could be wrong. I kind of hate using an absolute like "everything". But so far I've yet to hear a convincing argument to contrary.