Saturday, September 3, 2016

Combinatorical Templating

Biological evolution seems a bit easier to understand than chemical evolution, which is what happens to create the first biological cell, defined as having some coded genetic information used to make new cells. The basic principle is the same, that a simple change occurs, and then an increase in fitness happens or it doesn’t. When a change happens so fitness increases, the change has to stick.

In the origin of life theory concocted here, called organic oceans, the first thing to form is a membrane of ambiphilic molecules on the meniscus between the organic ocean and the water ocean. If the theory is to be complete, there has to be some pathway from this to a biological cell. A lot of guesswork has to go into finding some simple step that can lead away from this first stopping place.

One simple step is the concatenation of a chain of amino acids attached to a strand of the membrane. These would build up only if energized by something in solution before they reach the attachment point, so the process would be slow. Evolution is a billion year thing, however, so slow is not an objection. If there are chains formed, and they cross-link, there is some structure that might fold over the membrane into something like a tube. This increases the cross-sectional area for more attachment area from a thin layer below the membrane to the size of the tube, which can be much larger. This is certainly a fitness improvement. Random attachment can go on, but there has to be replication as part of this puzzle, so only those attachments which can template themselves or in a group will replicate, and then when the membrane tears into two, these auto-templating ones will be the ones to be present on both pieces, as a form of reproduction.

The big problem with chemical evolution is the transition to biological evolution. Templating is a simple means of replication, but some simple steps have to be found to transform it into coded replication. The current means of tRNA and mRNA, ribosomes and ATP, etc. doesn’t have to spring into being all at once, but what is needed is some simple initial steps that will get the process started.

Here’s the rub. A genetic code has to do two things: it has to replicate itself when the cell it is in reproduces, and it has to generate other things in the meantime. Templating only does the first thing, not the second. So something a little more complicated has to be thought of. Consider group templating. Molecule A is a template for molecule B and molecule B is a template for molecule A. As many molecules can be inserted into this chain as desired, but it still does not break loose of the original set of molecules. Suppose templating to make molecule Z needs two molecules, X and Y. Maybe X and Z together produce Y and Y and Z together make X. Still no progress is expanding generation of molecules beyond what is the starting set.

Suppose Z does need X and Y, but some fourth molecule, W, is needed in combination with Z to make X and in combination with X to produce Y. W and Y make W, so replication of the originals is complete. Now suppose that Z and X make A and Z and Y make B. Now there is production outside of the original set. In other words, there can be schemes for production of other molecules as long as four molecules are present in the original set. So, to fill in the details of such a proposal, there would have to be some way in which two molecules interact in order to produce one molecule, the same or different, and there has to be sufficient participants to produce more than the original numbers, which easily happens with combinatorics. A thousand different schemes can be thought of, with molecules K, L and M working together to produce J, and J alone produces K, and so on and so on. The general idea is simply that with combinatorics, the hurdle of moving with templating beyond some original set of molecules is passed.

Other types of schemes are certainly possible, for example, two-state schemes. Suppose molecule A produces molecule A when it is in one state, but it produces molecule B when in the other state. It could be a state controlled by the torsion on a carbon chain, or polarization caused by some other molecule, or something else entirely, methylation or some other modification. It could be something as intriguing as a molecule being quite long, and folding back on itself in a loop to make one molecule, but staying straight to replicate itself.

Replication undoubtedly needs energy, so there has to be some scheme, involving some other molecule, to activate molecules which will participate in replicate, either of themselves or something different. This is another aspect of what has to go on next to the original membrane.

It doesn’t seem really necessary that the molecules involved be completely detached. As chemical evolution proceeds, perhaps two of them, say A and B, join, and when C, with a frontal length that matches A and B separately, connects to either A or B, the requisite production happens. If there is another molecule, D, which just moves C from A to B, we have the absolutely simplest abstraction of a ribosome. And if it is necessary that molecule E join with C before can do the replication with A and F must join for B, then we have the simplest abstraction of tRNA.

It might be possible to do some simple experiments to find out about what membranes could form in this hypothetical situation, and then to see what is necessary to have concatenation with something like an amino acid. These experimental steps would have to be worked through before any replication experiments were started, but with the knowledge of how to bind the template molecules to some experimental apparatus, replication might be studied in a laboratory setting as well. These would represent the first tiny steps toward understanding the real origination of life processes.

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