|Evolution of DNA -
So far we have imagined Fred jumping onto the scene as a fully functional protein-- one that is capable of reading a chain, polymerizing amino acids, and flopping between two different conformations while doing so.
It's easy to explain that way, but it's also possible that Fred was a completely different polypeptide. Remember, this is still 4 billion years ago, and we have to make some pretty wild guesses about the chemistry that might have occurred.
One alternative is that the Sofia chain might have acted as more than just a passive clump of data. For example, each of the two molecules in the Sofia chain may have had an affinity for a different amino acid, so the Sofia chain itself could have helped 'choose' each new amino acid, whenever Fred used it to produce a new Roscoe or Fred.
In that case, Fred could be a much simpler molecule that would only need to hold the incoming amino acids up close to Sofia, and then catalyze the amino acid dehydration.
From a probability point of view, a 'direct match' Fred could have been shorter, and therefore more likely to have developed (along with a matching Sofia chain). On the other hand, it needed a much rarer set of conditions-- not only did its puddle need to contain just two chain molecules and two amino acids, but they had to be complementary in such a way that they would match up.
There are plenty of other possibilities for the early evolution of Fred and Sofia.
Fred may have taken advantage of a local concentration of phosphate ions as a temporary energy-bearing bonding aid, similar to the way phosphates work in modern DNA.
It may have 'piggy backed' on some local catalysts that were present in a puddle neighborhood-- perhaps mineral crystals or clay templates with the right chemical shapes to help polymerize amino acids and/or chain molecules.
Fred may also have used some precursors as a shortcut to its synthesis-- perhaps a concentration of amino acid dimers or polymers that were already present in a puddle, thanks to local catalysts and templates.
It may also have taken advantage of coenzymes or metal ions that were present in quantity, or followed some other more obscure chemical path in its production of more Freds.
We'll stick with our original Fred model in the following chapters, as we move further along with this story. But it's important to remember that any attempts to trace evolution from 4 billion years ago is going to involve a healthy dose of speculation and guesswork.
Fred and Sofia could have been very different in their initial method or composition, and yet still have followed a path that eventually created DNA.