I have absolutely no formal training in biology, and because of that there are tons of basic things I don't know. However, lately I've really enjoyed being a biology nerd and doing lots of reading mostly on genetics and development. Also, the Theory of Evolution is a major piece of my atheistic worldview, so the more understanding I can gain the better I can support my position.
Recently I was involved in a discussion with a creationist, which is why I ended up watching the Boonstra movie. One of the major portions of the Boonstra argument (and I think this is a standard creationist position) was that the theory of evolution doesn't explain the origin of life therefore god did it. In my discussion I repeatedly demanded that a distinction be made between evolution and abiogenesis. My point was that evolution works if life developed spontaneously, was seeded by an advanced alien race or was sneezed into existence by the Great Green Arkleseizure. I still believe that this is a correct understanding, but I need to be careful how I phrase the statement. For rhetorical purposes it is useful to make a distinction between origins and evolution, but based on the some recent research on chemical replicators (the the biology nerd in me gets really excited about) it would probably be false to say that natural selection had no part in the origin of biological life.
In the study reviewed on pharyngula and neurologica some enzymes were able to assemble themselves spontaneously from simpler chemicals. The researchers relied on natural selection to optimize the reaction. From PZ Myers:
"They started with a very rough sequence, one that inefficiently catalyzed an A + B → E sort of reaction, but that not only worked slowly, but also produced faulty products that eventually killed the reaction after a few cycles. Then they tweaked it to form a minus-strand enzyme, and then they subjected both the plus and minus strand forms to — natural selection! They made copies with mutagenic PCR (so they had a range of random variants), ran it through several cycles of in vitro selection for more efficient forms, and ended up with two RNA enzymes that were good at building copies of each other."
And from Steven Novella:
"Specifically, what they found was that when they added different versions of their self-replicating RNA with limited raw material to the same test tube, the different RNA “species’ competed with each other. The more “fit” RNA species, those better able to compete for raw material and replicate, dominated the resulting brew of RNA. Further, different RNA species combined together to form new versions of RNA - the molecules evolved - with more fit molecules being selected for."
While this is almost certainly not how life started on this planet, this is a nice proof of concept that more complex chemical structures can build themselves from simpler components.