An Open Dialogue

Ignoring my poor qualifications, I recently threw caution to the wind and engaged in a lively email discussion with a fine young man that largely involved science and Torah. On the chance that someone else might find it useful, here's how it went.
My correspondent's questions are indented and in bold type. I've used the regular boring text for my contributions.

I will first mention that I'm not sure there is any 100% empirical proof for (or against) the existence of God. I believe that the human mind and the world we live in are too complex for absolutes. What we can do is treat Torah the same way we would other important questions in our lives and look for the approach which is supported by the strongest evidence. As Rabbi Dovid Gottlieb (who used to be a professor of analytic philosophy at Johns Hopkins University) wrote, just like you will make life-and-death medical decisions without knowing 100% that a particular therapy will be successful and won't kill you, you could also comfortably rely on God and Torah as long as their existence clearly fits the facts of life on earth *better* than any other explanation.
Perhaps we can get a good start by having a text from which we can both work. I briefly summarized Rabbi Gottlieb's four main arguments here. I'm not sure it's correct to say that most evidence points to a universe that doesn't require a God to have created it. There might be possible theoretical scenarios explaining the variety of life and the development of the world's key physical forces, but I'm aware of no solid working model that currently explains the existence of matter and the existence of life. The absence of such viable models wouldn't by themselves prove the existence of God, of course, but it do certainly add credibility to the various classes of historical evidence for Him.
Let me explain. Since the scientific community rejected the solid state model of the universe (meaning that the universe had always existed as it is today) in favor of what they now call the big bang theory (meaning that the universe and all the matter in it has only existed since a great explosion of an infinitely small and dense mass that somehow, inexplicably, came to exist), they have been unable to explain where this dense mass came from. The problem is that the first law of thermodynamics states that energy (and, thus, mass) can be transformed, but not created or destroyed. In other words, if there was a time when the universe contained no matter at all, matter could not possibly have subsequently come to exist.
Now a God Who stands outside the physical universe and is independent of the laws of physics could theoretically suspend this first "law." But a purely secular perspective does not allow for anyone outside the universe. Cosmologists (the scientists who study this field) have, to my knowledge, no alternative explanation. Similarly, the existence of life. There is, as of yet, no serious theoretical model explaining how living matter developed from non-living ingredients (known as abiogenesis). The various theories which are currently popular are at best inconclusive (this is from the Wikipedia page on abiogenesis: "The sequence of chemical events that led to the first nucleic acids is not known.") Some of them are downright useless (like the theory that primitive organisms came from space...which, of course, begs the question of how they came to exist in space in the first place). So I don't think you can say that there are serious secular models explaining all key aspects of our natural world. Well, even if all that supported the "creation theory" were disproofs of competing theories (and even if the disproofs were not convincing), there would still be at least one compelling positive reason to consider sticking with creation: it might be true.
Of course, that alone, without any evidence at all, wouldn't be enough for an intelligent person. But I believe that that isn't all there is (besides the current weaknesses of abiogenesis and the origin of matter that we've already mentioned). There is some pretty solid historical evidence (like R' Gottlieb's four classes of evidence that I summarize on my site). Without any viable theory explaining abiogenesis or the existence of matter? I don't think so. It seems to me that proposing the existence of a God solves far more real-world scientific problems than it causes. It is apparently a very strong theory, but it alone has very little bearing on the existence or non-existence of God - because He's possible either way. Our belief is that He is eternal which means he didn't come from anywhere. The key point here is, though, that, unlike the existence of matter and life in a mechanistic universe, in and of itself, God's existence doesn't run counter to any physical laws. And even if it did, we could simply say that He is above physical there's no philosophical problem tied up in belief. However, big bang requires that energy and mass that formerly did not exist, somehow came to be, and that does run counter to physical laws - which is a particular problem for someone who insists of looking at the universe from a purely secular - or mechanistic - perspective. Regardless of how strong evolutionary theory might be, it won't help to address your hypothetical scenario in which you propose a purely religious model of creation to someone who had only been aware of the physical evidence. All it takes is one gap for the religious model to at least demand serious investigation...and we've now got two gaps: abiogenesis and the origin of matter.
But we do know about Him. Our claim is that He spoke to us as a nation and directly and publicly interacted with us for the decades between Egypt and Israel. This claim of direct large-scale revelation is falsifiable - and therefore it is verifiable (see Rabbi Gottlieb's Kuzari argument).
In fact, the Kuzari himself acknowledges that if the Torah would have only told us that God created the world (which, of course, no human could have seen) and nothing about Matan Torah etc., then we would be unconvinced. It's the subsequent personal contact that verifies everything else. Well, let's compare. You are proposing a purely mechanical origin for the universe. You have an admitted problem in that there are two major gaps. Of course, it is possible that those gaps may one day be filled in with some new theoretical model, but even then it will only be theoretical as none of us will have been there to see it.
Now I am proposing a religious model in which there are no holes (that's not to say it's proven, but that the theory itself has no holes comparable to the holes of your model). My model has external evidence (historical) that may be submitted for verification (via the Kuzari argument).
I think that this difference is fairly significant. Perhaps I'm being fair in saying that, looking only at this element, the religious model has an advantage at this point. They don't have to explain "why". Right now we're discussing the evidence for this model over that one. If we should later conclude that God was, indeed, behind everything, then we can always come back to "why". In the meantime it's enough to remember that even if human existence is overwhelmingly cold and cruel (which I believe isn't necessary in any case), that by itself is not a disproof of God. Perhaps God is cold and cruel (which, of course, I don't believe) - there's nothing philosophically impossible with that... I don't think that there are any older religions around today, but it's true that some are pretty ancient. So you make a valid point. Gottlieb addresses it.
The key difference is that the other religions and cultures that have persisted have done so in an unremarkable way: they have been consistently dominant forces in their local populations and haven't been subject to sustained religious persecution. We could have predicted their survival from the outset. Judaism's longevity, however, could never have been predicted. Gottlieb summarizes the evidence pretty well here. Again you are correct in that this could use more detail. And again I'll direct you to Gottlieb himself who has already done the work. I will, however, offer two observations. Rabbi Gottlieb does not include the prediction of conquest - as that indeed would have been relatively simple to predict. Exile, on the other hand, was something which was (and is) quite rare.
Also, the prediction is not that our enemy would not speak our> language (Hebrew), but that the Jews would not speak their language. I believe that it is safe to say that, for most of our history, most Jews were at least familiar with the languages of their neighbors. Absolutely not. The Kuzari argument proposes that:
    an event which, by its definition, should have left behind a great deal of evidence will not be accepted later by a large population if that evidence is absent. But an event which would not necessary have left widespread evidence is not affected one way or the other.
The forty years two million of us spent being fed mann miraculously in the midbar should have left behind lots of evidence (there is no doubt that such an event today would be discussed and written about for centuries afterwards). A half a dozen or so disciples having seen Jesus resurrected would not.
In other words, if you were a tribal pagan confronted by two missionaries on the same day, one claiming that some guys saw a fellow crucified and resurrected 2000 years ago and one claiming that your ancestors were fed mann for forty years - in the absence of any personal social memory of either event, which one will you know immediately is false? The mann one, of course. Therefore, if millions of "pagans" did accept the mann story, it must be because they did have the evidence.