Evolution of DNA - Conquering The Oceans
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
First DNA
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
Appendix 1-- Prebiotic Earth
Appendix 2-- Primordial Puddles
Appendix 3-- Primordial Catalysts
Appendix 4-- C Value Enigma
Cast of Characters

So far, Cassius has gradually been gaining more and more metabolic skills, to the point where it can thrive in just about any shoreline puddle or pool. With eight catalytic molecules to choose from, it's capable of building an enzyme that can do just about anything.

But it's still not capable of living in the open ocean. It's all a matter of concentrations.

Stuck in Puddles

First of all, the oceans were much more dilute than the shoreline puddles, since they hadn't had the benefit of evaporation and concentration. Because of that, they wouldn't have contained sufficient raw materials within a reasonable distance of any given Cassius. Fred, Roscoe, and the catalytic enzymes would have spent far too much time waiting for their raw materials to diffuse into reach.

Secondly, the oceanic Cassius would have fought an uphill battle every time it tried to link amino acids or chain molecules into smaller chains. The thermodynamic equilibrium would have encouraged polypeptides to split, rather than lengthen. Without a source of energy to drive endothermic reactions, or high densities of raw materials, Fred would have been ineffective .

On top of all that, the Fred in Cassius would have been confused by the huge number of possible amino acid choices in the open ocean. In a puddle, Cassius's synthetic proteins could create a large excess population of the 'right' amino acids so Fred could work reliably, but in the open ocean those synthetic products would have drifted away, and Fred would have been poisoned too easily by the great variety of similar compounds nearby.

The same problems also apply to Roscoe-- dilute ingredients, difficult polymerizations, too many poisons.

Still, there would have been enormous selective advantage for any Cassius that managed to conquer the open oceans. Since the total volume of all coastal puddles was tiny relative to the total volume of the ocean, anything that would have allowed a Cassius to survive in open water would have given its descendants a gigantic niche to live in, with no competitors.

Let's take a look at some of the early evolutionary upgrades that may have helped Cassius 2.0 to conquer the oceans, after Cassius 1.0 had established itself in the shoreline puddles of the world.

Positioning Structures

One way Cassius could survive in the open ocean is by positioning its enzymes just right so Fred and Roscoe could grab their raw materials, as soon as they were formed by enzymes within the organism.

To do that would require careful positioning of the compounds in Cassius, extra structural 'channeling' to direct molecules to the right places, and perhaps multiple copies of each enzyme to put their products in the places where they were needed.

The right protein shapes would help in this regard-- which means there was evolutionary pressure on Nathaniel and the other proteins in Cassius to position themselves so they could create a more closed system with their metabolism.

We have also talked about positioning chains and 'blueprint' chains that place enzymes and raw materials close together. They would have made each enzyme complex more efficient, by creating an 'assembly line' of enzymes that could take in raw materials at one end, and spit out finished molecules at the other.


Cassius could also protect itself from the ocean by surrounding itself with a protective barrier of some kind. That might be a gel of proteins, a mucus built from sugar polymers, or an oily froth of phospholipids or terpenes.

With a less fluid cell structure, the compounds produced by Cassius's enzymes would stay close. That would give Roscoe the high concentration of nucleotides that it needed for replicating RNA chains, even when in a dilute environment. Likewise, Fred and Fatcat would have the high concentration of amino acids they needed for effective protein transcription.

A gel or mucus coating would have kept Cassius's compounds inside of Cassius, and it would also have helped protect Cassius from the hazards that were outside of Cassius: including cell-destroying enzymes, toxic chemicals, UV, and just about anything else that might infringe on the chemical happiness of a Cassius.


Another way Cassius could have set up local concentrations for Fred and Roscoe was to form a cell wall or a cell membrane-- a continuous barrier to separate its enzymes from the outside world. That way Cassius could maintain a 'puddle-like' environment even while floating in the open ocean, with its many competing ingredients.

Cell membranes are such an important feature of living organisms that we'll devote an entire chapter to them (coming up next!)

Membranes would have been the most effective way to isolate Cassius's chemistry from the outside world, but keep in mind that even within a membrane, positioning chains and gelatinous cytoplasm would have still been useful. As Cassius grew larger and larger, its components would have grown further and further apart, and anything in the interior that helped to position its molecules effectively, would still have been beneficial.