"The only thing I am skeptical about is the medium in which the proteins are sorting. "
I am not so sure that the sorting was independant of the nucleotides. My view is it would NOT be independant.
Think of the ionosphere and the cloud top as cathode and anode, and cirrus particles first as water droplets with the nucleotide/protein molecules in a rising mass of air. As they reach a thinning atmosphere, they cool and freeze. The particle, now frozen, is water, protein, and nucleotide. If the particle is light AND carries a charge, it stands to levitate better than a particle that is heavier and less charge. Levitating, the particle then begins, along with other similar weighted and charged particles, to trap infra red heat and cause further updrafts of warm, moist air underneath it. The structure of the protein will cause it to "fly" or fall in the gravitational field opposing the friction of air.
Where I think proteins gain most of their importance in connection with the growing complexity with nucleotide sorting is that proteins will rise to the surface of water by trapping air bubbles, allowing for them to be blown back into the air. Again, will the particle fly or fall. They may be as a nucleotide/protein particle to attrack water vapor and further gain phase energies to the surrounding air, causing uplift. I think this is where some of the folding can be a surviving trait.
"First, if banding were to occur they would have to carry an overall neutral charge (also called the isoeletric point or pI). In the lab, pI gradients are artificially constructed before protein banding occurs."
I am not sure how this matters. The particle will have a mass and an ability to hold a charge, and will be sorted as such. Similar massed and wieghted particles will behave in a manner where they will levitate opposing gravity in the same way. The mechanical process of electrophoresis and what I am discussing, thus, probably differs. It is true that at the cloud top there will be a mass "charge" or mass electrical state but that doesn't mean that each particle within that mass will have the exact same charge. Individual particles that have a tendency to lose an electron to another in the mass of particles will lose it--and then move accordingly in relation to the ionosphere and cloud top above and below the particle, and, of course, move in relation to its mass and gravity and size in the winds.
"The gradients are usually set up with small molecular weight acids and bases with varying pKa values that are at higher concentrations than the protein. I don't know the chemical composition of clouds, but it seems improbable that sorting could happen at an appreciable level."
Again, the process you are describing is without consideration of gravity and how the particle interacts with the winds or air pressure . . .
"Secondly, I don't know if clouds as a medium would be conducive to transporting proteins by electrostatic charge. You would have to show how winds, charges within the clouds themselves, and gravity will not disrupt sorting. That, and you usually need a continous liquid medium for this to happen instead of a nebulous water vapor."
The water vapor condenses on particles and moves with updrafts up into the higher atmosphere, where it freezes, releasing phase change energies into the air and warming it further. If the particle further traps infra red heat, the air further warms under the cirrus. However, if the process stops feeding it, the particle begins to lose water directly from ice to water vapor and that TAKES phase change energies from the air and causes the air mass to cool and to become dense and fall. It is a complex process but none-the-less electrical movements would find feedbacks that would further the sorting processes and feedback more powerful cloud making heat.
"My experience with meterological cycles and phenomena are not that great, but those are some of the hurdles I see."
No hurdles have been put up, but perhaps I don't understand what you are talking about.
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