Evolution of DNA - First Cells
Back in the 'old days' of Caleb and earlier, we could pretty much describe the entire organism, and draw out its molecules in a little picture. But from this point forward, it's going to be much more difficult to picture the whole, exact organism. We will also need to skip over many vital parts of the emerging biochemistry, so we can concentrate on DNA .
It's important to keep in mind that many changes were probably happening in parallel, as Caleb gradually became Cassius, and as Cassius gradually became modern life. Small advances in any 'life like' feature would have increased the speed of further advances in others. And none of these features could have happened on their own, without the gradual appearance of the other improvements, at approximately the same time.
Aside from self-replication, probably the most momentous thing Cassius could do was to separate itself from its surroundings, and become a real cell. That probably happened shortly after Cassius first stumbled upon some genetic chain which produced enzymes capable of synthesizing phospholipids, terpenes or other membrane-forming materials.
Those substances are amphiphilic, which means they contain a polar (water-loving) group at one end and a hydrophobic (oily) group at the other. In water, they will form a two-layer film with the oil on the inside and the polar groups on the outside (in this illustration, the circles are the polar, water-loving exterior of the membrane, and the squiggles are the hydrophobic, oily interior)).
If there are enough of the amphiphilic molecules, they will spontaneously form a micelle or simple cell, which could have surrounded the main Cassius complex. Being inside a membrane would have created a portable, concentrated local soup where Fred and Roscoe could function properly, not just in specific puddles, but anywhere .
Any Cassius with a membrane would have synthesized more efficiently, and also suffer less trouble from proteolytic enzymes and other soup hazards. Adding a boundary between a cell and its surroundings is such a useful improvement that it would have revolutionized the prebiotic world, once it developed.
Of course, early versions of Cassius couldn't just move to the inside of a bubble of lipids immediately, since they still needed access to their raw materials in the surrounding soup. A full lipid layer would prevent most compounds from diffusing into the cell interior, and that would eventually starve Cassius.
Since early versions of Cassius were not yet ready to live inside a cell, they probably started out by living on or near a lipid film on some other surface, or they may have even taken up residence on the outside of a membrane, for a while, and only later moved to the interior.
Regardless of its shape, even a simple lipid layer would have given Cassius a quick selective advantage, by providing it with a substrate to anchor its enzymes. Let's take a look at how that might have worked.
Membranes are very interesting from a chemical point of view, since they provide a small strip of oil or other hydrocarbon that is surrounded by water. One of the first amino acids in Fred was probably a hydrophobic (oil loving) molecule and the other was probably polar (oil repelling), so Fred and other early proteins would have interacted with a membrane in some specific ways.
For example, a protein that contained both polar regions and hydrophobic regions would take up a specific position within such a film, with its hydrophobic areas imbedded in the hydrophobic core of the film, and its polar parts sticking out.
A protein with a hydrophobic middle and polar groups at the two ends might 'bridge' the membrane, and have both ends sticking out on opposite sides.
Proteins embedded in a membrane have restricted motion-- they can easily slip sideways through the film and twirl about their own axis, but they can't move very much at right angles to the film, nor rotate in any direction other than axially. The hydrophobic attraction between the lipid core and the hydrophobic amino acids keeps the protein in a relatively fixed position.
We have already talked about the use of backbone chains as a way to confine enzymes into a fixed position, so they can work together as a supercatalyst. Membranes could also have served a similar function. Several proteins might all be imbedded in a film, which would hold them together rigidly so they could perform as a supercatalyst.
You might think of a membrane as an extremely effective way to impose some two-dimensional order onto a three-dimensional assembly of free-floating enzymes.
Once there were sufficient types of proteins floating within membranes, some of them may have formed a 'ring' structure within a membrane, which would have created a pore that allowed a connection from one side to the other. In fact, a single protein with just the right placement of hydrophobic and polar amino acids could clump up with others of its kind within a membrane, and pierce a hole through to the outside.
With the right types of pores, an advanced membrane-building Cassius would become a true cell. As with modern cells, it could control the chemistry of its local environment by restricting what went through the pores. Once that happened, all of its chemistry could occur within a wrap-around membrane, with all the advantages it entailed.
Of course, the ideal pores would let in any useful raw materials from the outside, without allowing useful cell contents to seep out. So pore proteins would have been under enormous selective pressure to improve their skills at regulating the cell contents.
Membranes and Nathaniel
Once there were membranes to hold in Cassius's contents, there would have been no particular need for Nathaniels to hold together the different proteins and chains.
Of course, some Nathaniel connections may have still remained in place as a way to keep various components close to each other within the cell.
For example, the linkage between Fred and the various chains (Sofia, Sorrel etc) would still have provided a selective advantage, since it would have made protein transcription happen more easily.
It is possible that phospholipids were present in the early soup, in which case they may have formed natural membranes even before Fred and Sofia came onto the scene . In that case, much of the molecular evolution that we have discussed so far may have occurred within micelles or vesicles (cell-like structures created from natural membrane materials)
A micelle with a few supercatalysts inside may have provided the exact right conditions for early replication chemistry, without the need for tidal pools or puddles. Of course such early 'pseudo-cells' would have only been a temporary, dead-end stage of cell development, since they had no way to synthesize more membrane material (at least not from an enzyme coded from a genetic script). Any Caleb or Cassius that used natural phospholipids would have been completely at the mercy of the natural processes that formed them locally.
Because of that, the first versions of Cassius that could synthesize their own membranes would still have gained an enormous selective advantage, even if earlier cells had formed by natural processes, before the first Cassius-synthesized membrane.
Phenotype and Genotype
An important genetic consequence of the cell membrane is that it fully enables true Darwinian selection. By separating the genetic material from the outside world, the membrane enforces a complete linkage between a cell's genotype (Sofia, Sorrel and other genetic chains) and its phenotype (Fred, Roscoe, Nathaniel and metabolic proteins).
A mutant Cassius with a new genetic chain that created an effective new protein would no longer share any of its genes with surrounding copies of Cassius . That means that it would thrive, increase in size, split, and then spread much more quickly then its less-endowed neighbors. That could happen anywhere, so there was no longer any need for isolated micro-puddles to provide separation and evolution.
In other words, once there were cells, a new gene could now become established in the entire population by the 'classic' forces of natural selection.