Tuesday, August 18, 2015

Is DNA the Earliest Foundation of Life?

It has been noted several times in this blog that the lack of understanding of the origin of life is a major impediment for deducing why no aliens are in evidence in our corner of the galaxy. There needs to be more work done on this, which is dependent on more funding. Let’s amuse ourselves by walking through the process.

One potential pathway for life might have been some self-replicating molecules, which then diversify and eventually become cells. All our cells are built by DNA, which controls the proteins manufactured by each cell. Proteins make up the structure of the cell.

How exactly did some self-replicating chemical become a coding for proteins, which are then used to make the whole cell? Perhaps it was the other way around, with DNA being formed first, and later it manufactured proteins, which eventually found their way to making cell walls and other components. Maybe even the cell wall was generated first, prior to DNA starting to manufacture proteins.

The basic idea for self-replicating molecules becoming something else comes from a very simple mathematical model. If you have a molecule, such as some form of DNA or something similar but simpler that can replicate itself, it will very soon become more prevalent than any molecule that simply catalyzes the production of a different molecule. One leads to exponential growth and the other, linear growth. Let’s assume there is some replication period, and at the beginning you have molecule A, which replicates, and molecule B, which produces molecule C. At the end of the replication period, you have two molecule A’s, and one molecule B and one molecule C. At the end of the second replication period, you have four molecule A’s, and one molecule B and two molecule C. Exponential growth! This is a nice precursor to evolution happening via competition for sustenance. The self-replicating molecules start with a large advantage.

Even if the replication time for molecule A is longer than the production time for molecule B, A will eventually win out. So, back before life began, the oceans were essentially on a hunt for the first self-replicating molecule. Once one was found, it took over from there. Any change to the molecule which preserved its ability to self-replicate, and shortened the time, given available materials, would have given it an advantage in numbers over the slower one. Thus, not only would the oceans hunt for self-replicating molecules, they would hunt for better and better ones by tweaking the original one.

Self-replication is a tricky business, and is not exactly like catalysis. Self-replication in a stew of precursor molecules means all of the components needed have to be gathered, and put into the right place. Catalysis is often thought of as a change in the form of a target molecule, or the addition of a component to the target molecule, or the merging of two target molecules. For self-replication to work, the precursor molecules have to be held in place while the other ones are being collected. Thus there must be a binding of each of the precursors to the original molecule. When there is a collection made, then the components must be joined, or that may have occurred earlier as each component falls into place. There is also a third step. The original molecule must let go of the newly formed copy of itself.

This evokes the idea of some cycling. It is hard to imagine some control mechanism completely within the original simple molecule which releases the copy. Thus, some external, environmental cycling would have to take place. When the cycle changed is not a concern, as any time after the new copy was completed, it would work. The cycling would determine the replication time, if the average time needed for collection was smaller than the cycling time. If the inverse held, the original molecule would release its components before a copy was made. If some joining had occurred, the released parts would be further along toward becoming a copy that they were before they were transiently collected by the original molecule.

Changes of temperature, pH, salinity, pressure or the presence of other molecules could create this cycling. There was certainly many examples of cycling on early Earth, from diurnal heating, tides, interaction of fresh water flows from rivers with sea water bodies, winds stirring up the upper layers, geostrophic flows, annual changes, and likely many others.

Could a molecule something like a very short strand of DNA have been the original self-replicating molecule? DNA is formed of a string of amino acids, and these molecules are believed to form in several environments, including in clouds in space. In cells, DNA does not self-replicate as there is a polymerase which performs that task. But perhaps a simplified DNA could self-replicate. If so, self-replication would be done and evolution is ready to take off, but what about DNA’s other tricks, such as producing proteins for things like cell walls. There is apparently a gaping chasm between self-replicating pseudo-DNA and the cell walls of Archea, the first known cellular organisms.

The chasm might be overcome by considering substrates. If one end of the self-replicating molecule developed a chemical method of binding to some surface, it might have a large evolutionary advantage. While free-floating, it is swept along with all the surroundings, and essential components for self-replication might be nearby, but never brought into contact. If the molecule was bound on one end to some surface, such as a grain of sand or a rock, the flow of the water past the binding point would sweep these components into the self-replicating molecule. Almost no living creatures in the ocean fails to take advantage of this process; even jellyfish move through the water or change the water inside themselves.

Once adherence was achieved, evolution would favor stronger adherence if the initial bonding to the surface was only transient. This would not have to be part of the self-replication process if a second process was evolved to deal with adherence, the catalysis or formation of some molecules useful for linking the molecule and the substrate. In other words, if one form of self-replicating molecule shed some other molecule, perhaps made as an incomplete copy of itself, which would serve to hold the molecule and the substrate together, then this one would have an immediate immense evolutionary advantage. If the production of the linking molecule could occur multiple times, and if each one of these linking molecules was tied to the other ones as well as to the substrate, a type of chemical pad would evolve. Then adherence would grow stronger, provided only that the linking molecule could attach to the substrate, to other copies of itself, and to the end of the self-replicating molecule. The generation of such as molecule by the incidental production of partial copies seems a simple evolutionary path to follow.

As the attachment pad was favored by evolution, it might grow. Since the molecule which formed it liked to adhere to itself, at least along the edges of the pad, sooner or later there might be enough to form a film partially detached from the substrate. This might serve to slow down water flow and allow more components for self-replication to occur. If evolution was clever enough to devise such a linking molecule that would form holes in the film, porous to the components needed by its self-replicating partner, the pad could continue to become a larger film, and voilá, a cell is formed when the pad closes on itself.

Properly permeable film formation and a self-replicating molecule which secondarily produces film molecules seems to be all that is needed for the most primitive form of cell. From here on in, the substrate can soon be dispensed with. Evolution has a new toy to play with, and here comes intelligent life. You might say that the self-replicating molecule has one gene, for a cell wall molecule. It is child’s play to imagine the cell wall becoming large enough to split into two with the self-replicating molecule doing its replication at the same time. Having multiple copies inside is probably an advantage, so the initial steps of cell duplication can be done with few modifications of the original concept.

If this hypothetical sequence of molecular changes is a good facsimile of the process that actually occurred, we can search through it for Great Filters. Clearly, cycling is necessary, so a planet which was phase-locked to its sun and had no satellite might not be a candidate for life. Perhaps a large satellite is necessary; the idea that the moon is necessary for life, or at least strongly facilitates its origination, is popular. Since our satellite is particularly large as a fraction of the planet’s mass, it might be rare in the galaxy. The current hypothesis for the origin of the moon is a collision between the proto-earth and another planet. Such collisions are probably quite rare, since the cross-section of the planet compared to the size of the empty space in the inner solar system is very small. The process of planetary collision has not yet been worked out in any detail. Perhaps most of them make such changes in planetary orbits that staying inside the habitable zone is rare following such a collision. This really has the markings of a Great Filter.

The other requirement is a soup of amino acids. Experiments have shown lightning can form them; it is thought that meteors and comets have some. Perhaps they are easily produced by a variety of mechanisms. The mechanisms by which they might form should be investigated more intensely, as they seem to be fundamental to the origin of life. Amino acid broth does not seem to warrant being a Great Filter, so the score is one for two.

If this hypothesis about the origination of life, that it goes backwards from what might initially be thought, it would be easy to prove that it existed. Just take some very simple DNA-like molecules, plunge them into a bath of amino acids, and fool around with the conditions, like temperature and salinity, to try and get the originator prototype to attach to a replica strand. Finding one might take several trials, but these are easy to do and cheap as well. Then dissociation experiments could begin. This is far simpler than looking around the planet for interesting life-origination sites.

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