Evolution of DNA - Eight Molecule Life
Introduction
First Protein Transcription
First Genetic Replication
First Feedback
Puddle Evolution
First Dispersal & Evolution
First Parasite
First Organism
First Cell Metabolism
First Self-Sufficiency
Aromatic Assistants
First Assimilation
First Transfer Molecules
Eight Molecule Life
Complementary Base Pairs
Energy Sources
Conquering the Oceans
First Cells
Cellular Explosion
Gene Regulation
Chromosomes
First DNA
Introns
Wider Reading Frames
Complementary Triplets
Cellular Scripts
The Spread of Foxy
Second Parasite-- Transposons
First Schism
Improved Gene Regulation
Cell Structures
Eukaryote Explosion
Multi-Cellular Scripts
Cambrian Explosion
Epilog
Appendix 1-- Prebiotic Earth
Appendix 2-- Primordial Puddles
Appendix 3-- Primordial Catalysts
Appendix 4-- C Value Enigma
Cast of Characters

When a Caleb and alt-Caleb merged successfully, and mastered four-molecule replication and transcription, there was a new organism that was built from eight different molecules-- four amino acids, and four aromatic chain molecules.

That may finally be enough chemistry to support our very first self-sufficient Cassius.

It's not really critical to determine when the first Caleb reached full Cassius status, but this seems as good a time as any to make the switch. So in this stage in the evolution of almost-life, it seems reasonable to suppose that the first self-sufficient organism would appear. This new, actual Cassius probably contained a few dozen genes and a few dozen proteins, plus a large assortment helper chains that performed much of the catalytic action.

Since Cassius could build its own ingredients, it was no longer restricted to those rare, special puddles that had high concentrations of some ingredients . It still couldn't live in the open ocean, but it could live in any restricted puddle where it could create high concentrations of its own ingredients, and then use them to build more of itself.

Third Explosion

Splashing waves would gradually have washed multiple copies of Cassius out of the first pools where it formed. Once in the open water, they would have drifted the ocean currents, and then splashed up into new shoreline pools and puddles. Once they arrived there, they could immediately have started to reproduce.

The result would have been a third and larger explosion of new organisms that were one step closer to life than anything that had gone before. It would have been a much more extensive expansion than the previous explosions-- first of Freds and Sofias (which may not have even happened), then of Calebs. It seems reasonable to suppose that the Earth would be supporting large numbers of Cassius organisms, probably mixed with various surviving Calebs, and combinations of Caleb and alt-Caleb. It's possible that most of the shoreline puddles had some sort of life-like activities occurring in them .

Evolutionary Speed

Once Cassius was able to build its own ingredients, it could live in perhaps a billion large puddles along the shorelines of the early Earth. More importantly, it could also prosper in quadrillions of micro-puddles, nestled between sand grains, in small fissures, and in any other place where a microliter of water and a trillion organic molecules could reside.

With such huge numbers of homes, Cassius could have increased its population to enormous numbers-- up into the quadrillions or more.

In turn, having such huge numbers of organisms would have sped the pace of evolution enormously. Whenever a chance mutation produced a version of Cassius with some new life-like skill, it would have increased its population via an advanced form of 'puddle evolution'. Then it could spread first to neighboring puddles, and eventually, to more distant locations.

Each of those waves of improvements might have taken only a few years or decades to spread to all the puddles surrounding the local ocean.

Eight Molecule Life

The eight-molecule organism is a significant milestone for our emerging life forms. On the one hand, it's probably the first organism with enough chemical diversity to build a good repertoire of enzymes. On the other hand, it's also the maximum possible level of complexity that Fred can manage, when it comes to specifying protein sequences.

Let's make some guesses about the chemical nature of eight-molecule life:

The first Cassius probably contained two polar amino acids, and two hydrophobic ones. That's because it's built from a Fred and an alt-Fred, each of which probably starting with one polar and one hydrophobic component (simply because that's the most effective way for Fred to actually function).
Its amino acids were probably very simple. They had to be extremely easy to produce catalytically, or else very common in the soup.
The four amino acids were moderately distinct from each other. If not, the organism would have a harder time reaching full Cassius status, since it would have a less diverse 'toolbox' for creating enzymes. Fred and alt-Fred would also have interfered with each other, if their components were too similar. It seems reasonable to guess that the most successful merged Clem was built from one big and one small polar amino acid, along with one big and one small hydrophobic one.
It seems possible that the first four amino acids are still used with higher frequencies in modern proteins, particularly in 'old' proteins that evolved very early in life. Leucine is the most common amino acid in modern proteins, which makes it a very good candidate for the 'large hydrophobic' molecule in the first successful Cassius. Serine is the next most common, so it's a good bet for the 'small polar' component. Alanine seems possible for the 'small hydrophobic' niche, while either lysine or glutamate is a good possibility for the 'large polar' molecule.

Cassius had to make extensive use of helper chains. They were the only components capable of moving electrons around, so they would have been highly necessary in the first synthetic enzymes.

Chirality

Nearly all of the amino acids and aromatic chain molecules come in two different forms that are mirror images of each other (called enantiomers). They are classified as dextro-rotary and levo-rotary, for the way each form rotates polarized light.

The early primordial soup was formed by various natural processes that almost certainly produced a mixture of both forms (called a racemic mix).

Fred and Sofia were each built from just one of the mirror-image forms of their molecules-- and in fact, the other, mirror-image enantiomer would probably have been a poison for them. Most likely it was just coincidence that they were built from levo-rotary amino acids, and there may have been alt-Calebs that used dextro-rotary molecules instead.

The appearance of Cassius was the first time when the racemic mix of random amino acids started to shift. The chain-based enzymes in Cassius were able to place atoms much more precisely than raw chemical processes, and they would have created just one of the two possible mirror-image forms.

As versions of Cassius became more common, the early soup that was composed of a huge variety of compounds would have gradually given way to a predominance of compounds that were created by some enzyme-- most likely levo-rotary amino acids, and dextro-rotary sugars, as we have today.

Our current amino acid composition may be entirely the result of a random event-- the choice of amino acids that happened to be contained in the Fred that was present in the first complete Cassius. A slightly different puddle splash, and maybe we'd be dextro instead .