Evolution of DNA - First Cell Metabolism
Caleb was quite an accomplishment, for its time, but it was still a rather pampered creature, capable of reproducing only in a very specific environment that was extremely concentrated in its own raw materials. Any given Caleb or alt-Caleb would only trive in an minuscule percentage of the Earth's shoreline puddles and pools, and it was completely helpless in the open ocean. Without the right densities of raw materials, Caleb was just another useless clump in the soup.
Caleb was also rather self-absorbed, with no skill at doing anything else other than assembling its own components from exactly the right materials.
But despite all those limitations, Caleb was the first organism able to self-replicate.
Evolution of Better Calebs
So far we have talked about Caleb just containing genetic chains that code for its three polypeptides. However it seems likely that on occasion, a Nathaniel would meet some other type of random genetic chain, and attached it to Caleb along with its regular components. What would happen then?
Fred would transcribe the new chain into a polypeptide, and what happened next would depend entirely on what that new polypeptide did.
The likeliest case is that the new polypeptide would do nothing-- just some random molecule with no enzymatic action. In that case the local population of Calebs would survive less well than those in neighboring puddles (since some raw materials were going into production of useless polypeptides and useless chains). Over time, Calebs with the useless baggage would decrease in number, and the useless chain would become less prevalent, too.
In some cases the new polypeptide might have done something lethal-- a protease enzyme that digested Fred and Roscoe, or an enzyme that created some metabolic poison. In that case all of the Calebs in the local puddle would die out quickly, and the bad chain would die out too.
And then every once in a rare while, a new chain might create a protein with some sort of survival value for that particular Caleb. When the enhanced Caleb hit a new puddle, it would survive better than its neighbors in nearby puddles, and thanks to puddle evolution, the new chain would gradually become established in the overall population.
What kinds of things would be useful to an ambitious and evolving Caleb?
There are a whole host of structural or metabolic features that might have appeared at this early evolutionary stage. For example, Caleb could have made good use of a cell membrane, enzymes that produced energy, and molecules like ATP to store energy and transfer it to chemical reactions. Those improvements may have happened to early Calebs, but we won't focus on them quite yet.
Instead, there are two specific improvements that would have the most immediate impact on Caleb survival-- enzymes that helped produce Caleb's raw materials from any simpler compounds that were available locally, and more selective versions of Fred and Roscoe that could survive in places where their ingredients were mixed with other compounds.
Let's take a closer look now, at those two enhancements.
Raw Material Synthesis
Adding a new enzyme to a Caleb so it could synthesize one of its own amino acids or chain molecules is an obvious improvement-- what could be better than building one's own building blocks?
Any Caleb that added an enzyme that produced one of its ingredients could survive and prosper in any puddle neighborhood that contained the other three raw materials. And there were probably thousands of times as many of those less well-endowed puddles, as compared to the relatively rarer four-ingredient puddles.
Any Calebs that included synthetic enzymes would also have a jump start on the production of other, similar enzymes, which might produce other useful raw materials. So we can expect that natural selection would have gradually produced Calebs that could produce more and more of the materials that they needed to survive.
Selective Freds and Roscoes
There was a different sort of selective advantage for any Calebs that developed better versions of Fred and Roscoe (produced from mutations in Sofia and Sorrel).
For example, Calebs containing a Fred that was better at selecting the correct amino acids, even when there were competing molecules, would be able to prosper in environments with a wider mixture of raw materials. That means they could spread to new puddles and regions where older Calebs couldn't survive.
A more selective Fred might work by having a larger and more selective protein-binding region, or by adding a helper enzyme that would help bind only the two appropriate amino acid molecules, or by having a side chain that would repel inappropriate materials.
It seems unlikely that Fred's simple-minded approach to protein transcription could ever have become completely reliable in a mixed open-ocean soup (which would probably have had hundreds of compounds similar to each of the two Fred amino acids). But at least a more selective Fred could have worked reliably in a wider range of pools-- for example, in places that contained a concentration of three or four amino acids, instead of just the correct two.
With the help of 'puddle evolution', any Calebs with a Sofia that produced a more selective Fred would reproduce faster than older Calebs. Because of that, they would eventually become established in the population.
Likewise, more selective Roscoes would have been beneficial, since they would have allowed their Calebs to reproduce in puddles that contained a wider mixture of chain molecules. Because of that, it seems likely that Sorrel would have undergone similar selective pressure, producing a Roscoe that could assemble two-molecule genetic chains, even when in a pool containing other, similar chain molecules.
One more thing to consider, as Caleb became more sophisticated, is that its choice of amino acids and chain molecules could also evolve.
Remember, Caleb is now invading more puddles, and forming alt-versions that are built from entirely different molecules.
Some combinations of amino acids and chain molecules will be better at working together then others, and alt-Calebs built from the 'cooperative' molecules will be able to form new enzymes much more quickly than other variations of Caleb.
Up until now, we have considered Caleb as being built from some random chemicals that might have been completely different from the molecules found in modern life. However, this is probably the time when its amino acids and chain molecules started to 'drift' into something that was much closer to the modern selection of biological molecules.