posted by brooke .
Why do some scientist think that areas protected from the atmosphere might have favored the production of organic compounds on early life?
Multiple post. Please look at your later post.
One reason is oxygen, or its absence.
IF molecular oxygen was present in the prebiotic atmosphere - even at levels far less than are present today - then the formation of complex organic molecules would have been thwarted due to the thermodynamic spontaneity of combustion. So organics could accumulate much more readily in regions protected from the atmosphere and its molecular oxygen.
HOWEVER, most scientists studying the origin of life don't think that there was enough molecular oxygen to be of any concern. But then a problem might be, with little to no molecular oxygen in the atmosphere, there would have been little to no ozone. DNA and RNA absorb UV light readily, causing problems (as one example, covalent bonds forming between adjacent thymines). Ozone in the atmosphere absorbs UV light, and the more ozone, the less UV light reaches the surface. And conversely, the less ozone in the atmosphere, the more UV light would strike the earth's surface, and cause problems for DNA/RNA.
Those are rather superficial looks. For example, protective layers other than ozone are possible.
PS: It is quite possible that life arose near deep-sea hydrothermal vents, in which case the atmosphere is pretty much completely irrelevant.