|Evolution of DNA - Energy Sources
When looking at the gradual transformation of Caleb into a self-sufficient Cassius, so far we have only focused on its self-replication needs. But in fact, to be a really successful organism, it needed many other skills, besides the ability to produce its own ingredients. These additional improvements probably evolved in parallel with the changes we've already mentioned.
First and foremost was energy management-- the ability to tap some source of energy, and use it to drive chemical reactions.
Back in the very early days, Fred and Roscoe assembled proteins and chains without any energy inputs, using exothermic or weakly endothermic reactions that did not require a significant source of outside energy to complete. Because of that, they couldn't survive in many places. Most likely they were most confined to highly concentrated pools where the hydrodynamic forces made it easier to polymerize long chains.
Any Caleb that could generate energy, and then deliver it to drive reactions more reliably, would have gained an enormous selective advantage. So it seems likely that energy management became a part of the repertoire of some Cassius, fairly early in its existence.
Fortunately, that were plenty of possible sources for raw energy. Nothing had been 'eating' the soup, yet, so there was a wealth of possible chemical reactions that a Caleb or Cassius could use.
Nowadays, plants and cyanobacteria absorb photons in the visible range, and convert them to usable energy via complex chemical pathways. Meanwhile, nearly all animals and many bacteria grab organic compounds from somewhere or another, and oxidize them with oxygen from the atmosphere to 'burn' themselves some energy.
These are both highly energetic reactions that allow for a modern, rapid lifestyle, but neither would have been very convenient for Caleb. Most likely, free oxygen was not yet available, and photosynthesis requires far too many clever enzymes for such a primitive organism.
On the other hand, some modern Archaea and bacteria rely on a variety of anaerobic reactions as an energy source. Compounds of iron and sulfur in particular provide smaller, easily managed amounts of energy, as they shift between valence states. One of these simpler reactions was probably the first energy source for a Caleb or Cassius.
It's not usually convenient to drive a biochemical reaction directly from a raw energy source, so any Caleb that could store and deliver manageable amounts of energy would gain a huge selective advantage.
It doesn't take very much energy to shove two amino acids or two chain molecules together. Even in a dilute solution, the energy required to bind peptides and nucleotides is on the order of .2 electron volts per molecule, which is about 1/10 the energy of a typical light photon. Since polymerizing was the most important reaction performed by early versions of Caleb, it seems likely that the best energy storage unit would be for about that much energy.
When one of the common purines (adenine) links up with a ribose sugar and a few phosphate groups, it can store about .3 electron volts of energy-- just about the perfect amount of energy to assist a Fred or Roscoe.
The reactions of AMP (adenosine monophosphate), ADP (adenosine diphosphate) and ATP (adenosine triphosphate) are extremely important to modern life, and it's quite likely that they appeared in early version of Caleb as well . Conveniently, adenosine is also one of the components of RNA and DNA, and it's very likely that it was one of the chain molecules in early forms of Caleb.
The adenosine phosphates are so vital to life that the probably deserve an 'Evolution of' book of their very own, but we'll try to confine ourselves to DNA in this one, and skip over the details of ATP's appearance.
When we talked about genetic chains in the early days of Fred and Sofia, we were deliberately vague about their composition. The first chains really could have been almost anything. In fact, since the ribophosphate 'backbone' of RNA is rather hard to assemble under soup conditions, it seems likely that the early chains were not true RNA, but rather simpler polymers of purines and/or pyrimidines, or possibly some entirely different chain-forming molecules.
As ATP-based energy management appeared, Calebs would have gradually become more proficient at managing all types of chemical reactions that used phosphate bonds to store a bit of energy.
The phosphate content of RNA gives it an important advantage, since it carries a small jolt of energy that helps speed up replication and other reactions. That means that the first Caleb that stumbled upon chain molecules linked by ribophosphates would have gained a significant advantage over its less energetic cousins.