Evolution of DNA - First Dispersal and Evolution

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

Once the Fred/Roscoe/Sofia/Sorrel combination formed, positive feedback would have ensured that more of each were created, and puddle evolution would have gradually improved the effectiveness of the Fred and Sofia enzymes.

As the tides rolled and the waves splashed, Freds, Roscoes, Sofias and Sorrels would have gradually spread into neighboring puddles and pools. Some would have splashed into the open ocean and drifted on currents to new locations many kilometers from their origins.

We can consider this to be the first explosion-- a dispersal event that invades a larger geographical area with a new and improved form of life (or in this case, preliminary partial maybe sort-of almost life forms).

Let's take a closer look at what would have happened to our first self-replicating chemicals, as they diffused into new regions, far from their home.

Open Ocean

First of all, Fred and Roscoe would have been completely useless in the open ocean, or in any large body of water. The problem is that they were still only capable of choosing between two different types of molecules. That was good enough in the home puddle, with its high concentration of just two specific amino acids and two chain molecules. However, in the open ocean, there would have been many different types of molecules that were similar to the components of Fred, Roscoe, Sofia and Sorrel. The result is that Fred and Roscoe would have merely produced chains with a completely random sequence of many molecules, making them entirely non-functional.

At this stage of chemical evolution, pretty much anything would act as a 'poison' to our primitive self-replicating system

Not only that, but the Fred/Roscoe/Sofia/Sorrel combination had a very basic problem, when it came to surviving far from the home puddle. Because they were four separate molecules, that had to all get to the same place at the same time in order to work . It's plausible to imagine a single Fred or Sofia drifting and diffusing into a hospitable place far from home, but much less likely for all the necessary molecules to get there.

Even worse, they were just small raw molecules, all alone in a hostile sea that was full of all sorts of hazards. There would have been volcanic hot spots, and enzymatic blobs, metal ions, ultraviolet radiation, gamma rays and radioactive decay particles-- all of them poised to decompose a Fred or a Sofia back into its individual components.

New Puddles

It's probably too much to expect that a complete set of the Fred/Roscoe/Sofia/Sorrel components would ever drift kilometers from home, with any chance of success. But closer to home, they probably would have managed to drift into an occasional new shoreline pool or puddles, all at the same time.

What happened next would depend on the contents of the puddle.

Deadly Puddles

Nearly all of the puddles and pools along the primeval coastlines would have contained a mixture of many different amino acids and chain molecules, similar to the open ocean. They would have been entirely poisonous to any Freds or Roscoes that drifted into them.

Likewise, some puddles would have contained a shortage of amino acids or chain molecules, perhaps because they were washed clean by rainwater, or had their organic contents removed by some natural process. Those puddles would have starved any Freds or Roscoes that happened to arrive there.

Many puddles would also have contained catalysts or chemical agents that would decompose large chains. Those locations would merely add Fred or Sofia back to the soup, in the form of single amino acids or chain molecules.

Finally, an occasional puddle may have contained high concentrations of just two amino acids and just two chain molecules, similar to the home puddle. However, in nearly all cases, those molecules would have been too different from the normal constituents of our four chains. Fred and Roscoe might still have managed to duplicate new amino acids and chains in the new puddle. However, the resulting compounds would be very different from the originals, with very different chemical properties. Because of that, the children would not be effective Freds, Roscoes, Sofias or Sorrels, and self-replication would cease.

Heavenly Puddles

On the opposite extreme, there may have been a few rare puddles and pools that contained high concentrations of the same, original two amino acids and two chain molecules as in the first Fred puddle. Once a Fred, a Sofia and a Sorrel simultaneously diffused into such a puddle, they would create another production center, and start flooding their own neighborhood with Freds, Roscoes, Sofias and Sorrels.

Of course, the first home puddle was just a very small puddle on the edge of a huge ocean. It probably wasn't producing that many Freds, Sofias and Sorrels, and it is unlikely that they would have simultaneously diffused over a very long distance.

However, it's possible that by some quirk of chemistry, there were similar puddles relatively close by. Or perhaps a full set of self-replicating molecules may have been engulfed by a glob of natural tar or mucus, and then traveled together to a distant heavenly puddle.

It's nice to think of new little colonies of Freds starting up, even at this early stage of proto-life. But as hopeful as it may seem, those new colonies would not actually have had much affect on the pace of evolution. After all, they were merely identical to the home puddle. All they would have done is increase the global concentrations of self-replicating compounds, by a little.

Pretty Good Puddles

In between the deadly puddles and the perfect ones, there may have been a few puddles with intermediate conditions.

For example, a 'pretty good' puddle might contain the same chain molecules as the original Fred puddle, and one of the same amino acids-- but have one amino acid component that was similar to the original, but just a little different.

Roscoe would work fine there, and Fred could probably replicate new polypeptides there too, though they wouldn't be effective Freds. However, such a 'pretty good' puddle would still have been extremely interesting-- since it could help our 'life-like' chemicals to evolve into new forms.

Let's take a closer look at that now.

New Raw Materials

Let's consider a 'pretty good' puddle with a concentration of three of the four 'home puddle' molecules, along with a high concentration of something else.

For example, we built our first Fred example from leucine and lysine (two modern amino acids), but a Fred, Sofia and Sorrel may have one day diffused into a nearby puddle that contained high concentrations of leucine and 5-methyl-lysine instead (almost the same molecule, but with a side chain containing an extra carbon).


In that new puddle, Fred would still read Sofia, but it would produce a new amino acid chain built from a slightly different molecule.

If the new molecule was similar enough to the old, it might not have much impact on the folding or chemical action of Fred. Which means that the new proteins transcribed by Fred in the new environment might work passably well on their own.

Even if the change did have some impact, it's possible that a mutant form of Sofia would 'undo' the chemical and structural changes caused by the new molecules, and create a fully functional Fred using the new components. Since the chemical change in the raw materials was small, the genetic change to compensate for it might also be small.

The result would have been a mildly different version of Fred that we'll call an alt-Fred. This new molecule would work with the new combination of components, and it would be created by a chain that we'll call alt-Sofia (with a slightly different sequence from the original Sofia).


Of course, the same kind of 'chemical drift' could also occur in the chain molecules used as raw materials by Roscoe. Consider a puddle the contained the original two amino acids, plus one of the original chain molecules, and another that was just a wee bit different from its original.

If the difference wasn't too extreme, Roscoe could probably still 'read' the difference between the two types of chain molecules, and still link chain molecules in approximately the right order at its knee. It probably wouldn't work nearly as well as with the original molecules, but it might eventually mutate into an alt-Roscoe (coded by an alt-Sorrel) that would work better.

Since Fred also was affected by changes in the chain composition, a change of chain molecules would also result in an alt-Fred (coded by an alt-Sofia) that would be a bit different at its elbow end.

Almost Perfect Puddles

Of course these gradual changes the chemistry of Fred and Sofia would have worked best in puddles that contained three raw materials that were exactly the same as in the 'home puddle', and a fourth compound that was only a little bit different. That kind of slightly-different puddle would actually have been much more common than puddles with exactly the same raw materials as in the original Fred puddle.

There are four possible raw materials that could have been different in a 'favorable' puddle, and perhaps a half-dozen chemical variations in each ingredient that might have been similar enough so an alt-Fred or alt-Sofia could have evolved into using them.

That means that there would have been approximately 24 times as many 'almost perfect' puddles as perfect ones.

Evolutionary Jumps

Once a new alt-Fred and alt-Sofia formed from a slightly different set of raw materials, they in turn could have colonized other nearby puddles. Each time a new 'almost perfect' puddle was colonized, one of the raw materials might have shifted slightly, creating a new alt-Fred, alt-Roscoe, alt-Sofia and alt-Sorrel combination that could self-replicate, using slightly different molecules.

After a sufficient number of evolutionary jumps like that, there would eventually have been a new set of alt-Fred, alt-Roscoe, alt-Sofia and alt-Sorrel molecules which could self-replicate from amino acids and chain molecules that were entirely different from the originals.

Given enough time and enough 'almost perfect' puddles, new versions of alt-Fred and alt-Sofia could have gradually evolved into use of extremely different components, one small chemical step at a time.

The alt-ification of Fred and Roscoe wouldn't have increased their ability to exist outside of puddles that had the right concentrations of contents. But it would have allowed them to expand into more just-right puddles that contained different chemistry.


The evolution of Fred and Roscoe into alt-Freds and alt-Roscoes may have also been assisted by chemical gradients between two sets of pools. The right gradients might have allowed Fred or Sofia to start using new raw materials more quickly, by providing intermediate conditions.

For example, let's look at the formation of Freds in a puddle complex that contains a gradient in one of the amino acids contained in Fred. At the north end is a high concentration of glutamate (E, polar), and at the south end is a high concentration of aspartate (D, polar). In between are many small puddles and micro-puddles containing different combinations of the two molecules.

These two molecules have similar chemical properties, but aspartate is a wee bit bigger, with one extra carbon.

In the north, Fred would read a Sofia and create more Freds built from leucine and glutamate, just like normal.

In the south, Fred would create mutant proteins built from leucine and aspartate that would be so different that they would not function at all.

Somewhere in between, Fred would find itself in a chemical mix with both glutamate and asparatate. If it were close to the glutamate side of the gradient, it might build structures with just a couple of aspartate substitutions, like this:

This new polypeptide would have a slightly different shape than the original Fred, but it's possible that it would still have some or all of Fred's functionality, since there was only a difference of a couple of atoms, and the locations of charged area was still exactly the same.

Now there would be puddle evolution that would select for Sofias that created Freds with a more reliable structure that functioned well, even with a few random arginines substituted into the chain. That might mean an adjustment in the chain sequence. Likewise, puddle evolution would tend to produce new versions of Sorrel in the intermediate zone that created effective Roscoes, even when aspartate substituted for some of the glutamates.

Some of the new aspartate-tolerant Freds and Roscoes might then in turn diffuse further south into a higher-aspartate neighborhood, and make a further jump into aspartate tolerance.

With enough time and enough small puddles in the gradient, the end result might be an alt-Fred and alt-Roscoe that were built completely from aspartate instead of glutamate (along with the alt-Sofia and alt-Sorrel chains that produced them).

In a world of puddles that had different concentrations of amino acids, there would have been many gradients like this, and they would have provided a second way that alt-Freds and alt-Sofias could have evolved from the originals.

Functional Evolution

We have talked about Fred and Roscoe using polar and non-polar (hydrophobic) amino acids for their action, since proteins typically use both types of amino acids to build a chemically effective enzyme .

If an alt-Fred contained different molecules, but the same arrangement of polar and non-polar amino acids, it would already have a head start on the correct structure to work effectively. There might need to be some small changes to compensate for the different size of the new molecules, but that would only require some small changes in sequence, so it could act like the original.

You might think of Fred's structure as a combination of different 'domains', some of them hydrophobic, some polar, and some a combination. An alt-Fred simply needed to fill the same domains with similar structures, using a different set of molecules.

Larger Evolution

You might notice that the appearance of alt-Fred variations would create an additional sort of genetic selection for our extremely primitive original organisms.

If an alt-Fred developed that used a pair of amino acids that gave those alt-proteins some kind of advantage over other alt-proteins, then organisms based on that particular set of proteins would have spread further and faster than the other Fred variations.

Likewise, if a pair of chain molecules created genetic chains that were particularly good, those alt-chains would have become established at a faster rate than other Sofia progeny.

The selective advantage for the early proteins and chains might have been ease of synthesis, or chemical stability, or effective catalysis.

The shifting towards more effective chemistry for Fred and Sofia could have started during the first explosion, and it would have increased during later explosions as more and more effective organisms developed.

In other words, even if the first Fred was based on a poor choice of amino acids, it would have eventually been replaced by a superior alt-Fred that used more effective ingredients.

Chicken and Egg

Many past efforts to explain early biogenesis have relied on one chemical class to provide two functions in the earliest chemical stage of evolution. The 'RNA world' hypothesis puts RNA in both information-carrying and catalytic roles, and various other theories have proposed some sort of information-carrying role for proteins or other substances.

One big advantage of the Fred/Sofia system that we have discussed so far, is that it's a lot like life, right from the beginning.

Fred and Sofia still have a long ways to go before they are completely life-like, but all of the subsequent evolutionary steps can proceed with a similar division of labor. There is no need for an awkward switch from one chemical system to another.