Evolution of DNA - First Assimilation

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

Adding helper chains to assist with the enzymatic action definitely increased the chances for Caleb to develop a wider range of useful enzymes. However, we really can't expect miracles from the chains either, since they were also composed of just two types of molecules. Even having four different molecules for building enzymes was probably not enough.

Our theoretical Cassius with just 14 components is an elegant piece of theoretical simplicity, about as minimal you can get for something capable of assembling itself from scratch. However, there's a good chance that Cassius could never have really developed a sufficient set of enzymes to get that far, if it was restricted to the chemical tools we've described so far.

Fortunately, there is one more event that is poised to occur during this stage of Caleb's development. It creates another boost in the number of molecules that Caleb can use, and also takes it one further step along the evolutionary path towards modern life.

The Mixed Caleb World

To understand what happens next, let's go back in time for a moment, and consider the conditions shortly after the original Caleb explosion.

The first Calebs that migrated to other shoreline pools were able to survive and replicate in locations that contained high concentrations of their own ingredients (two amino acids and two chain molecules).

Meanwhile, some Calebs drifted into puddle neighborhoods with different sets of raw materials, and gradually evolved into alt-Calebs that used a different set of amino acids and chain molecules from the original. In addition, all of the variations were busy evolving better Freds and Roscoes which could distinguish more reliably between their own components and similar compounds.

In some places, the net result would be populations of Calebs and alt-Calebs relatively close to each other-- two similar organisms that were each based on a different pair of amino acids and a different pair of chain molecules, living just a few puddles away from each other.

In between the two populations (and the two sources of raw materials that fed them) there would have been a gradient of raw material densities.

Life on the Gradient

We already have talked about gradients as a way to create new alt-Freds and alt-Sofias, but let's take a closer look at how the two Caleb populations might also have evolved under its influence.

To start with, let's look at the amino acid contents in some sample pools (see diagram below).

The pool on the left contains supercatalysts that create leucine and glutamate (two amino acids that might be the components of one version of Fred). The pool on the right contains supercatalysts that create valine and lysine (two amino acid components of a possible alt-Fred). In between are several pools that contain intermediate amounts of the four amino acids. Each of the 'middle' pools would have received raw materials from both sides, as waves splashed things around at high tide. In other words, there is a concentration gradient between the two pools.

The first Caleb arriving in the neighborhood would have been intolerant of alternate amino acids, and could have lived only in the far-left pool that exclusively contained its ingredients. Likewise, an alt-Caleb that used valine and aspartate could only survive in the far-right puddle, which was heavily stocked with its ingredients .

As the Fred and alt-Fred became better at distinguishing between 'good' amino acids and the competitors, the Calebs and alt-Calebs could expand into a wider range of pools along the gradient.

Eventually the Caleb and alt-Caleb would have become so selective about their amino acids, that they could survive even when there was a high density of competing amino acids. At that point, the ranges of Caleb and alt-Caleb would extend so far into the intermediate puddles, that they overlapped. That mean that both versions could survive and prosper in the same intermediate puddles.

A Merger of Calebs

Once that overlap happened, it's likely at some point that a Nathaniel or alt-Nathaniel would have accidentally bound up a combination of proteins and chains from both a Caleb and an alt-Caleb. That would have created a more complex organism with the capacity to use all four amino acids, and all four chain molecules.

After some adapting, the newly merged organism could have included all of the enzymes and genetic chains from both of the Calebs.

What would that have gained?

Doubled Metabolism

When a Caleb merged with an alt-Caleb, it would have picked up two sets of enzymes for the basic replication of chains and transcription of proteins-- a Fred, alt-Fred, Roscoe and alt-Roscoe. So far, that would not have given the merged Caleb any selective advantage, but at least the combined version of Caleb could manage with four amino acids and four chain molecules instead of two.

However, things are much more interesting if the Calebs had already started on the road to Cassiushood. If they had already developing any useful enzymes, then the combined organism would have all those new enzymes from both of its parents. That would be synergistic if the two Calebs had each developed some useful proteins that the other one didn't have, yet.

Enzyme Cousins

Aside from the direct benefit from picking up two sets of enzymes, the combined Caleb would also have gained an advantage from 'genetic drift' in the metabolic enzymes.

For example, picture a Caleb that had already developed an enzyme that synthesized its polar amino acid component from raw materials, and an alt-Caleb that included an enzyme that synthesized its hydrophobic amino acid.

Since alt-Caleb's polar amino acid was similar to Caleb's, it would not have required a huge change in the Caleb enzyme to synthesize a different polar molecule for alt-Caleb. Likewise, alt-Caleb's hydrophobic-synthesizing enzyme could have drifted a bit, and started to create Caleb's version, as well.

The net result is that the combined Caleb could probably reach Cassius-hood faster than either could alone.

Helper Chains

The merged version of Caleb would have also picked up an immediate advantage from the additional molecules available for building helper chains.

A functional Caleb protein that used a helper chain built from its own two chain molecules might have 'drifted' into a slightly different enzyme by using a similar helper chain from alt-Caleb.

In other words, the merger of Caleb and alt-Caleb would have allowed any existing Caleb proteins to instantly take on a greater variety of forms, since they could get enzymatic help from four chain molecules, instead of just two. In a sense, the chemical repertoire available for enzyme 'design' jumped immediately from four to six, just as soon as the merger occurred.

Future Expansion

Aside from the immediate benefits for a combined Caleb, there were also some long-term advantages.

For example, the combined Caleb might be able to build an enzyme using the alt-Fred amino acids, that would synthesize one of the Fred amino acids, even if that enzyme couldn't be built from the original Fred amino acids. Or likewise, the original Fred amino acids might be just right for building alt-Fred's components.

In other words, the merger gave Caleb a bigger chemical toolbox, even while it was still confined to the original style of proteins that were built from just two amino acids.

Mixed Chain Transcription

Snazzing up the existing enzymes was a pretty good improvement for the new Caleb/alt-Caleb organism. But better yet, a mixed Caleb had the potential to create some brand new proteins which included all four of the combined amino acids.

How could it have done that? Well, let's look at a slight variation of the original Fred protein-transcription method. This one could take advantage of all four chain molecules, instead of just two.

We'll start with a regular Fred, plus a four-molecule chain (perhaps formed by a Roscoe or alt-Roscoe that wasn't quite adapted completely to the mixed chain neighborhood). In this example, the clear ovals represent Caleb's gene molecules, and the shaded ones come from alt-Caleb.

1. Fred's elbow binds to the first element of the new mixed backbone chain. It brings in the first amino acid, just like normal.

2. Fred jiggles to the next element, and brings in a different amino acid. So far Fred is working exactly the same as it always has.

3. Fred doesn't jiggle any further because the next backbone molecule is something it finds completely unattractive . However alt-Fred is perfectly comfortable with that type of chain. When one diffuses into the neighborhood, it shoves the first Fred out of the way, and adds a third amino acid to the chain.

4. Alt-Fred jiggles, changes conformation and adds a fourth amino acid. Note that we are now including four different amino acids in this protein--two from the original Caleb, and two from the alt-Caleb.

5. Alt-Fred can't go any further because the next backbone molecule is something it's not attracted to. However, Fred is fine with those, so one diffuses in, kicks out the alt-Fred, and takes over the chain again.

6. The process continues, and eventually we have a polypeptide chain built from four different amino acids.

With more choices of side branches, this new four-molecule protein could most likely do some sorts of chemical tricks that were not possible in the simpler two-molecule proteins.

Four Molecule Roscoe

Of course, transcribing proteins from a four-molecule chain does no good if Roscoe can't replicate those chains reliably.

However, that would not be hard to arrange, since a Roscoe and an alt-Roscoe could use an almost identical process to replicate four-element backbone chains. Roscoe would jump in to replicate Sofia chain molecules, and alt-Roscoe would take over to replicate molecules from alt-Sofia .

The system of 'alternating Roscoes' would have worked just as well as 'alternating Freds'.

Selective Advantage

What would be the selective advantage to the first four-molecule genetic chain?

Well, to begin with, probably none.

Nearly all of the new four-amino-acid polypeptides would have given Caleb zero or negative advantage. Random new proteins are rarely beneficial.

However, by sheer random happenstance, at some point a useful chain eventually did occur, and the merged Caleb that contained it prospered, and spread more quickly than its two-amino-acid cousins.

Over a period of time, mixed chains coding for four-molecule proteins would have gradually become more and more common, since their ability to use four amino acids would let them create a wider range of new enzymes or useful structural proteins, once they got over the hurdles of transcribing and replicating four-molecule chains.

Backwards Compatibility

This new transcription system of 'old style' conformational changes combined with the new 'alternating Freds' has a very interesting property. It still works fine with Sofia and Sorrel, and also with the alt-Sofia and alt-Sorrel that were assimilated from the alt-Caleb. In a sense it is backwards compatible with all of the existing genetic information from both Caleb and alt-Caleb.

This change also allows for entirely new proteins to evolve that use four different amino acids. In other words, the combined Caleb can ease into the formation of new 4-amino-acid proteins, while still keeping the old, essential 2-amino-acid proteins around.

Evolutionary Pressures

The merge of a Caleb and an alt-Caleb might not always be an enzymatic bed of roses. Some combinations would be much better than others, and this is a good time to look at some of the details.

For one thing, a Caleb and an alt-Caleb whose amino acids were too similar would have problems. When Fred or alt-Fred tried to transcribe proteins, they would mix up the two molecules too frequently, and produce too high a percentage of lethal or dysfunctional enzymes .

Likewise, if the genetic chain molecules in Caleb and alt-Caleb were too similar, Fred and alt-Fred would make many mistakes when transcribing polypeptides, and Roscoe and alt-Roscoe would make mistakes when replicating genes.

Besides not dying, a Caleb/alt-Caleb that had sufficiently different amino acid and chain molecules would have gained a selective advantage, since it would have contained a wider repertoire of chemical actions that it could use, when developing new enzymes and structural proteins.

On the other hand, a Caleb and alt-Caleb that were too different, would have also been at a disadvantage. For example, mixing a Caleb that used L-rotary amino acids with an alt-Caleb that used the mirror image D-rotary ones, probably would have created problems. Each set of enzymes would not fit so well with the others' raw materials, and the enzymes producing combined chains would have a harder time merging them.

Further Assimilation

Could Caleb be assimilate still more alt-Calebs, and expand the number of amino acids it could use even further?

Well, probably not. Unfortunately, trying to build proteins from more than four amino acids would probably have caused problems, because of the physical shape of Fred and Sofia, and how they interacted.

Fred's knee was perfectly fine, and could have handled more than four different amino acids. There is plenty of room to maneuver there, which means the knee could wrap almost completely around each amino acid that it selected. With all that contact area, Fred could find a way to distinguish between many different amino acids, using their size, shape or chemical properties as a guide. There could easily have been twenty different versions of the knee in different alt-Freds, capable of selecting between twenty different amino acids.

However, things were not so easy at the elbow, the part of Fred that reads a single molecule in the genetic chain. The problem arises from the physical structure of the chain molecules, and how they link up with each other.

Purines, pyrimidines and other chain-forming molecules consist of a flat 'plate' built from carbon, hydrogen and nitrogen, and those plates will line up in parallel to form the chain, looking much like a stack of very tiny coins.

Fred's elbow would have a very hard time squeezing in between the plates-- in fact, if it did so, it would probably break the chain. That means Fred's elbow could only have matched with a few atoms sticking out on the edges, when it tried to distinguish between different chain molecules. You might think of it as trying to identify coins in a stack, by just feeling their rims.

There's only so much information to be had in the six or ten atoms that might be jutting out from the aromatic rings, and it's quite possible that four different chain molecules is as much as Fred's elbow could manage.

That means that any super-Caleb that absorbed more then one species of alt-Caleb would probably have created a toxic level of confusion, and then died out.