This is really the "final frontier" of evolution: How did that first self-replicating molecule, protein, creature — whatever it was — come into existence in the first place? We understand virtually every aspect of evolution, from the high-level theory right down to the molecular mechanics of mutation. But we don't know where it all started. Or do we?
There are really three separate parts to the answer, which I'll call: 1) God in the gaps; 2) What we actually know; and 3) Innumeracy. So let's get started!
God in the Gaps
The "God in the Gaps" argument asks: Just because we don't yet understand something, does that mean it's magical?
To surrender to ignorance and call it God has always been premature, and it remains premature today."God in the Gaps" is a phrase that describes what's happened to God with the rise of science. Long ago, pretty much everything was a mystery, and God was seen as the reason and motivating force behind everything. A baby's conception, a bird's ability to fly, the regularity of the moon and stars, were all simply due to God's guiding hand.
— Isaac Asimov
As science started to learn more and more, God's active participation became less necessary. Science started demystifying vast bodies of knowledge, leaving only occasional gaps where God's magic was still needed. As science advanced even more, the gaps became smaller and smaller, squeezing the need for God to just the farthest reaches of time and space. God used to have to guide the planets and stars daily, but science pushed Him back to the Big Bang. God used to have to cause a miracle for every birth, but now we know how sperm and ova work so only the unquantifiable "soul" is left to God. And so forth. As science progresses, the gaps get smaller, and God gets squeezed even more.
Let's now go back to our original question: Where did evolution start?
It's been less than 100 years since serious research on the biochemistry of life's beginnings started in earnest. Darwin published Origin of the Species just 150 years ago, and since then science has filled in vast swaths of knowledge, leaving very few "gaps" indeed.
Just because a few of those gaps are still with us is no reason to give up and resort to magical explanations. The answer is, we don't know yet what that first molecule was that started it all. But that doesn't mean we won't know some day.
There are unanswered questions about evolution, but that doesn't make it false. It means that there is still room for some great scientific work.
Next: Part 2, What we actually know