Microbiology, biochemistry, and Evolution

Sorry to start a new topic, but I wanted this one to be separate. I understand that the main evolution topic has quite a few philosophical dissertations and I want to be as specific as possible in this one. This may have actually been brought up once or twice in it, but I definitely don't feel like searching a hundred pages to find out.
Soooo... as prologue, a lot of you on both sides of the debate probably know that I've generally taken the stance that evolution is clearly a theory well supported by science, and therefore I, like many Catholics, accept it.
Well, a curious thought popped into my head a few weeks ago, and in the time between now and then I did some reading which has led me to question the concept of macroevolution being the cause of the complexity and diversity of life today.
In essence, I was by chance reading a wikipedia article about cell structures and bacteria, etc. I was fascinated by the biochemistry of it all. Processes in cells are much like processes in robotic factories. All a cell is is just proteins and molecules reacting in a certain way; there's no intelligent body directing it, and yet somehow it manages to work in an almost cosmopolitan or factory-like way.
In my mind it didn't seem to add up that 3.7 billion years worth of natural selection could ever add up to a structure as complex as even a bacteria, let alone ultimately create structures composed of many of these already complex little bodies into even more complicated systems. This was just a hunch, but I decided to follow it up with some reading.
So I did some basic research on biochemistry. By my basic understanding, molecules don't "think", they just react to each other in certain ways; they fit together due to shape, attract due to charge, etc. Cells are made up of these molecules, especially proteins. Proteins then combine to make insanely and irreductibly complex structures with moving parts. Factories, transportation systems, etc.
I don't think that natural selection can adequately explain the complexity of a cell. They're just composed of too many complex parts. Remember that natural selection only preserves traits that are beneficial to an organism, ie traits that give it an advantage. Each intricate part of a cell is composed of several different specifically arranged proteins; oftentimes a structure is composed of parts which are composed of even more parts which are composed of constituent protein.
But how could natural selection preserve these otherwise useless parts? Darwin was fairly specific in saying that natural selection is a slow process; organs and structures don't just pop up in one generation. It takes time for certain small mutations to occur. So in order for this to fit with natural selection, it would mean that each individual part must be present in the cell for some reason or another. But there would be no reason for that part to be present at all because alone each part is useless, so natural selection wouldn't preserve it.
These are just my thoughts so far, and in my reading I was surprised to see an oddly large amount of biochemists who used this data to become evolutionary skeptics. As a guy who's been an evolutionist for years, I'd like to know how Darwinists explain the evolution of these microorganisms. After all, the complexity of a cell is so immense that some mathematicians estimate that the chances of some of the structures occurring by chance in the amount of time life has existed is about nil. That said, there are many such structures in existence in the cell, not to mention many such structures within multi-celled organisms as well! The odds against evolution just seem staggering to me, the more I research biochem.
Soooo... as prologue, a lot of you on both sides of the debate probably know that I've generally taken the stance that evolution is clearly a theory well supported by science, and therefore I, like many Catholics, accept it.
Well, a curious thought popped into my head a few weeks ago, and in the time between now and then I did some reading which has led me to question the concept of macroevolution being the cause of the complexity and diversity of life today.
In essence, I was by chance reading a wikipedia article about cell structures and bacteria, etc. I was fascinated by the biochemistry of it all. Processes in cells are much like processes in robotic factories. All a cell is is just proteins and molecules reacting in a certain way; there's no intelligent body directing it, and yet somehow it manages to work in an almost cosmopolitan or factory-like way.
In my mind it didn't seem to add up that 3.7 billion years worth of natural selection could ever add up to a structure as complex as even a bacteria, let alone ultimately create structures composed of many of these already complex little bodies into even more complicated systems. This was just a hunch, but I decided to follow it up with some reading.
So I did some basic research on biochemistry. By my basic understanding, molecules don't "think", they just react to each other in certain ways; they fit together due to shape, attract due to charge, etc. Cells are made up of these molecules, especially proteins. Proteins then combine to make insanely and irreductibly complex structures with moving parts. Factories, transportation systems, etc.
I don't think that natural selection can adequately explain the complexity of a cell. They're just composed of too many complex parts. Remember that natural selection only preserves traits that are beneficial to an organism, ie traits that give it an advantage. Each intricate part of a cell is composed of several different specifically arranged proteins; oftentimes a structure is composed of parts which are composed of even more parts which are composed of constituent protein.
But how could natural selection preserve these otherwise useless parts? Darwin was fairly specific in saying that natural selection is a slow process; organs and structures don't just pop up in one generation. It takes time for certain small mutations to occur. So in order for this to fit with natural selection, it would mean that each individual part must be present in the cell for some reason or another. But there would be no reason for that part to be present at all because alone each part is useless, so natural selection wouldn't preserve it.
These are just my thoughts so far, and in my reading I was surprised to see an oddly large amount of biochemists who used this data to become evolutionary skeptics. As a guy who's been an evolutionist for years, I'd like to know how Darwinists explain the evolution of these microorganisms. After all, the complexity of a cell is so immense that some mathematicians estimate that the chances of some of the structures occurring by chance in the amount of time life has existed is about nil. That said, there are many such structures in existence in the cell, not to mention many such structures within multi-celled organisms as well! The odds against evolution just seem staggering to me, the more I research biochem.