I can't help but chime in here. What seems to be missing from the original w/u is the notion of sample size. We've all heard the phrase 'large N.' If these unlikely conditions only have to occur once, what if the soup is the size of a planet? Take Earth's oceans. If you divide up their volume into spaces the size of these potential proteins, then what happens?

There's also the notion of time. If we assume that a 'snapshot' of the soup state (God I miss my Newton) lasts for as long as it takes these potential protein spaces to completely slide past each other, then you have even more chances. If it takes a minute, even, for the soup to mix, how many minutes has the Earth been around?

The problem with these arguments, as The Alchemist has properly noted, is that they can be reduced or extended ad absurdum. It's all in the assumptions, baby.