Evolution of DNA - First DNA
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

A few chapters back, we mentioned the emergence of complementary base pairing, and all the advantages it had for Cassius. It was an extremely cool improvement for cell metabolism, but it also created a huge genetic problem that would have only grown worse, the more cells used it.

Each set of complementary pairs would tend to cause the RNA chain or chains to link up with other sections of the chain, whenever complementary sections came close together. The result would be a tangled mess-- hard to transcribe, hard to replicate, and prone to breakage of the sequence.

Roscoe and the Ribozymes

In fact, it was even worse than that. Since some genes were carrying the sequence for ribozyme enzymes, what was to prevent the main genetic material from curling up into ribozymes, too?

To help solve these problems, cells probably developed 'snagbuster' versions of Fred and Roscoe. These slightly more clever chain-reading molecules would have had some sort of leading edge that could break any complementary pairs as they traveled along the RNA chain, so the main part of Fred or Roscoe could transcribe or replicate a single chain .

It would have helped a little, but there was another genetic problem we need to consider, and a better solution for both.

The Master Copy

Up until now, we've been rather vague about cellular RNA, which was sometimes a gene coding for protein sequences, and sometimes an actual working chemical that was involved in cell metabolism.

In early versions of Clem and Cassius, presumably Roscoe just replicated any RNA strands that it ran into, and the cell coped with the results. Not a particularly efficient process, but good enough for such early life forms.

However, as genes became consolidated into fewer chains, it was also time for cells to become more 'professional' about their gene management.

Ribonuclease

Up until now, we've only talked about the creation of new RNA chains. But a healthy cell would go through different stages of growth, and it would be very advantageous to get rid of the various enzymes and helper chains when they were no longer needed.

Some types of RNA need to be permanent, but others were pretty much just 'day use' molecules that could be digested back to their original nucleotides, when their task was over.

It would have been very beneficial to 'mark' the main genetic chain in some way, so cells could digest the temporary RNA chains, without harming the main genetic RNA.

Faster Evolution

There was also an evolutionary advantage to reducing clutter within the genetic material.

The earliest cells probably had several copies of each gene. So when a new, improved gene made its appearance, it would have had only a limited impact within the cell, since the old genes were also still present.

If cells could switch to just one 'master copy' of the genetic chain, the impact of any genetic change would be much more thorough. Any improved genes would improve the cell completely and immediately .

Master Marker

How could cells 'mark' the main genetic material, so it could be treated differently from plain old metabolic RNA? Probably the easiest method was to make a chemical change of some kind in the chain itself.

RNA is built from three different types of molecules-- the nucleic acids, ribose sugars, and phosphate. Switching to a different set of nucleic acids would have been extremely hard to arrange, and the phosphate bonds were far too simple to change.

So what was left was the ribose.

Deoxy Roscoe

The switch to the 'master chain' may have started with a mutant form of Roscoe that included an enzyme (probably a ribozyme) which removed an oxygen from the ribose, as it added each new nucleotide. It would replicate RNA chains just like a regular Roscoe, but the product would be DNA rather than RNA .

The bad news was that the new DNA molecules were useless as ribozymes, since DNA is somewhat more rigid than RNA, and the molecules wouldn't have been able to bend into their enzymatic shape so easily. However, the good news was that the added stiffness made them much better as genetic chains, since they wouldn't curl up into ribozymes.

That means that a regular Fred would have an easier time converting them to proteins, and a regular Roscoe would have an easier time reading them, and converting them back to a functional RNA enzyme.

The differences between DNA and RNA are small enough that the switch would not have required much new chemistry. And it would have solved enough problems for the cell, that it would have conferred an enormous selective advantage.

Intermediate Molecules

If cells were not able to make the evolutionary leap from RNA to DNA in one step, they may have used some sort of intermediary molecule, to act as the first ‘master chain’ genes that were different from the functional forms of RNA.

One possibility for that role is methyl-RNA , which is a more stable form of RNA that is less prone to chain breakage. It is not as capable of forming ribozymes, but it makes a much better genetic chain than RNA itself .

The Double Helix

Remember DNA? The subject of this book? Well, it finally has appeared!

For the moment, we only have a single strand of it. But eventually, some clever cell managed to protect it with a set of complementary base pairs. The result was the well known double helix, with all the nucleotides snug in the center of the molecule, and no risk of tangling at all.

DNA chains are chemically much more stable than RNA, with chains that are much stronger. They are more resistant to chemical attack, since the more reactive nucleic acids are snug in the center, surrounded by a relatively inert wrapping of ribose and phosphates.

The double helix of DNA also encodes its genetic information in a redundant form, which is much easier to maintain and repair.

What that means is that there would have been a huge genetic advantage for any Cassius that could convert its RNA genes into a separate 'master copy' stored in DNA form, and then replicate them back to mRNA, as needed.

DNA is positively such a cool molecule that it's a shame that we delayed so long in seeing it.

DNA and RNA Maintenance

The DNA chain is very similar to RNA, so most of the enzymes that cells had previously developed for replicating and maintaining DNA genes would have worked fine on DNA as well, with only minor modifications. The process of switching from RNA as the primary genetic carrier to DNA would have required some new enzymes and new processes, but nothing that was nearly as dramatic as the previous steps of genetic evolution that we've described.

At some point, the uridine used in RNA was methylated and changed to thymidine. There is no strong evidence for when or why that happened. It may possibly be an artifact of two different strains of Cassius that each developed a portion of the DNA/RNA system, and then later merged. It may have been helpful in some early transition period, or it may have arisen millions of years later, for some other reason.

When Did DNA Appear?

Well, now it's time to admit to some literary license. Delaying the appearance of DNA may have been a little sadistic, and it's possible that DNA first appeared much earlier, perhaps even during the days of Caleb and Cassius.

Back when 'helper chains' first appeared, Caleb had a management problem-- since it needed to replicate those chains, but not transcribe them.

We talked earlier about using a 'header' sequence to mark the chains, and that probably was the first solution-- since it also provided a 'landing site' for Fred and/or Roscoe.

However, it's possible some version of Caleb may have accomplished the same thing by storing the protein-coding genetic chains as DNA, and the helper chains as RNA. If it then had a Fred that only read DNA, and Roscoes that replicated both DNA and RNA, it would have been all set. Its Fred would avoid accidental protein transcriptions from the RNA chains, and Roscoe (most likely in two different versions) would keep the genetic chains and helper chains in stock.

If that didn't happen, there would have been increasing pressure for cells to switch to DNA, after the appearance of ribozymes. Since their very structure depended on many complementary stretches, they would have been particularly tangle-producing. Any cells that could switch the main ribozyme genes to a more rigid form would have gained a serious advantage.

Of course, locking the genetic material into a double helix was a drastic step, and it's also possible that there was a long period of plain old RNA chemistry (that is the gist of the 'RNA world' theory). Its appearance certainly would have been easier if there were already operons, gene ID, and cells with sophisticated metabolisms.

Unfortunately, there's no sure way to know when DNA appeared. By the time it made the scene, organisms were growing more and more complex, and it's not easy to sort through all of the evolutionary possibilities and affix a specific order to each improvement.

The Star of the Show

We could write much more about the DNA double helix and its chemistry, but this is an area that has already been well explored by other authors.

It is rather an anticlimax to treat the entry of DNA with so little fanfare, but at least we will make up for it, by devoting the rest of the book to its quirks and personality.

In fact, it's time to start looking at some of the odder aspects of modern DNA, and why they are important.