Evolution of DNA - First Parasite
While all the new Freds and alt-Freds were moving out into the world, they would have met other, random aromatic chains with a sequence entirely different from Sofia or Sorrel.
Some of those chains may have resulted from an extremely bad copy of a Sofia or Sorrel. Some may have started out as a real Sofia or Sorrel, with sequence changes caused by some sort of tragic chemical accident in a bad neighborhood. Still others may have been formed on their own via a template (see Appendix 2) or random chemistry, built from the same chain molecules, but with an entirely different sequence.
By simple diffusion, Fred would sometimes attach to one of those non-Sofia chains, and produce an entirely new and different polypeptide chain. Most of those new chains would have been non-functional, but at some point we can imagine Fred meeting a new aromatic chain that we'll call a Serena (short for SEquence Replicating NAthaniel).
As usual, Fred would hook up for a brief fling, and transcribe the chain sequence to form a new polypeptide that we'll call Nathaniel (short for Nasty And Troublesome Hellish Adhesive NItrogenous ELement).
This new Nathaniel polypeptide had no catalytic activity at all, but it did have a snaky sort of amino acid chain structure, and two ends that were particularly good at attaching to aromatic chains and polypeptides.
Nathaniel would have quickly latched onto the first chemicals it saw, namely Fred and Serena-- so there would suddenly be a larger Fred-Nathaniel-Serena complex instead of three separate compounds.
With that particular Fred held captive next to Serena, it would spend most of its time transcribing Serena, and creating still more Nathaniels .
Our free and independent Fred has suddenly become a dedicated Nathaniel producer, and the local puddle would soon be filled with many additional copies of Nathaniel.
Welcome to the first parasite!
The Nathaniel Explosion
A puddle full of Nathaniel is bad enough, but things would have gone from bad to worse very quickly, once a Nathaniel linked a Serena to a Roscoe, instead of a Fred.
Since it was bound captive next to Serena, Roscoe would spend most of its time replicating more Serenas.
The result is a permanent Serena-producing machine, and that would cause the neighborhood situation to really get out of hand.
The Nathaniel-Roscoe-Serena combinations would spend all day making more Serenas. Some of those Serenas would hook up with a Fred, which would promptly produce a Nathaniel that would bind into a Nathaniel-Fred-Serena complex. That would create extra Nathaniels which would bind Serenas to Freds and Roscoes, right and left. Positive feedback and then some.
Each of the Nathaniel-connected complexes probably produced hundreds of times as much product as the unconnected forms, since the Serena chain was always right there next to the Fred or Roscoe, with no need for a lengthy diffusion before it could start being transcribed.
Because of that efficiency, it's easy to imagine that the entire local puddle complex would soon be filled with Fred-Nathaniel-Serenas (producing more Nathaniels) and Roscoe-Nathaniel-Serenas (producing more Serenas). Our first tidy experiment with self-replication has been almost entirely subverted by a clever parasite.
Coevolution of Nathaniel
You might expect that the end result would be a world permanently dominated by small Nathaniel-based proteins. However, and fortunately for us all, Nathaniel was subject to the principles of host and parasite evolution, just the same as any modern disease organism.
In a nutshell, parasites that are too good at killing their host will tend to die out, while parasites that are less lethal will survive. As long as there are enough isolated populations and enough time, parasites eventually become less dangerous. In fact, the ideal parasite will evolve into a cooperative or commensual relationship, which benefits both the parasite and the host.
Let's take a closer look at how that may have developed, in our early world of self-replicators.
Serena and Puddle Evolution
As the population of Serena and Nathaniel increased, there would have been various bad transcriptions of Serena that produced different versions of Nathaniel. One important difference would be at the chain-gripping end. Presumably, different sequences of amino acids there would have affected which chains Nathaniel would attach to, most frequently.
Let's look at the consequences when different versions of Serena and Nathaniel inhabited a puddle region, along with a reasonable supply of Fred, Roscoe, Sofia and Sorrel.
Some Serenas might have produced a 'greedy' Nathaniel, that only connected to Serenas. Those Nathaniels would soon grab all available Freds and Roscoes, and connect them to Serenas.
In the local puddle, the Fred-Nathaniel-Serena complexes would create more Nathaniels, and the Roscoe-Nathaniel-Serena complexes would produce more Serenas. Each new Serena would link with a Nathaniel, but they would remain incomplete, since the puddle was producing no new Freds or Roscoes.
The Serena-Nathaniel combinations would be a highly infectious parasite that could invade neighboring puddles, and take over their Freds and Roscoes.
There might be a local explosion of greedy Serenas and Nathaniels that extended throughout an entire region, but it would eventually fade out, as the local Freds and Roscoes drifted away or decomposed.
Some other Serenas would have coded for a 'cooperative' Nathaniel, that connected to Sofias and Sorrels, as well as Serenas. Those Nathaniels would soon grab all available Freds and Roscoes, and connect them to all of the various chains in the neighborhood.
A 'cooperative' Nathaniel might link up a Fred with a Sofia, and create a more efficient unit that could transcribe many more new Freds than the original, disconnected versions of Sofia and Fred.
Other 'cooperative' Nathaniels might link a Fred with a Sorrel, and create a more efficient unit that could produce many more new Roscoes than the originals.
Still other Nathaniels might link a Roscoe and a Sofia, or a Roscoe and a Sorrel, and make a more efficient unit that would replicate additional chains much faster than the original.
The overall result is a thriving population of all the self replicating molecules.
Puddles with a cooperative Serena would end up with a much larger net population of Serenas than the greedy version, since there would be a steady supply of new Roscoes, some of which would replicate more Serenas.
Within the range of a few meters, there would be competition between the different versions of Serena and Nathaniel. The greedy versions would sometimes invade a new puddle, but they would be limited in the number of progeny that they could produce there (since they eventually eliminated the local supply of Fred and Roscoe).
On the other hand, the cooperative Serenas would create a thriving colony whenever they wandered into a new puddle, and that puddle in turn would start creating many more copies of cooperative Serenas, which in turn would invade new puddles.
Over a period of months or years, the overall result is that any Nathaniels that were generous about linking up to the original self-replicating units would have better 'survival value' than the Nathaniels that totally took over and ended the production of new Freds and Roscoes (which, in a short time, would also end the local production of Nathaniels and Serenas).
With some puddle evolution at play, improved versions of the linked protein and chain structures would soon have become the dominant almost-life forms in the local puddles.
Of course, many of the replications of Serena would be imperfect, and a few of those mutations might produce Nathaniels that were 'better' than the original. With the help of puddle evolution, there would be some selective pressure that would help produce Serenas that made Nathaniels with better connection abilities.
For example, a better Nathaniel might have a third binding zone which could combine a Fred with a Sofia and a Sorrel, and transcribe two different proteins at once.
That would create a jump in the number of Freds and Roscoes in the local puddle, which would then increase the numbers of the better Nathaniels and Serenas, too.
A better Serena might also create a Nathaniel that would bind a Roscoe, a Sorrel and a Serena, to create a more efficient chain-replicating complex. That combination, in turn, would eventually create more proteins, that would transcribe more Nathaniels and replicate more Serenas.
Serena mutants might also create Nathaniels that could bind to other Nathaniels at a third site, and create even larger complexes of polypeptides and chains.
All of these new Nathaniels would contain some of their own replicating machinery when they invaded a new puddle. Because of that, they would create more net Nathaniels and Serenas than their more primitive ancestors. And over time, 'chemical evolution' would result in higher concentrations of the improved Nathaniels and Serenas in the local population.