There's no simple answer as to the exact processes that put everything here, IMO. We can poke around all we want, but I seriously doubt we'd be able to find out just how God chose to put everything together in the foreseeable future.
I've never been a fan of 'pure' science, personally. With all the money being dumped into it, I feel scientific research should concentrate more on the application of what we already know to develop technologies and solutions that improve our daily lives and can be used to improve the quality of life for people in impoverished and technologically underdeveloped parts of the world. You know, make things cheaper, easier to make, easier to distribute, stuff like that.
Obviously, we need to keep doing some of this sort of poking around - think how many technologies in our everyday lives today were just theoretical fifty years ago. But I think a lot of time, effort, and money is being wasted on too many dead ends in science as it is, and if we concentrate too much on this debate as to how we got here, we'll just walk ourselves into that many more dead ends. The possibilities for scientific discovery may seem limitless, but some things are a lot easier to get to than others, and they're escaping our notice at the moment because we can't seem to be able to prioritize.