Wednesday, February 24, 2016

Options for the Origin of Life

Around the edges or ends of a word, there are sometimes fuzzy areas, where the definitions are not so obvious. Take 'Life'. What exactly is something, or alternatively, when is something alive? Like most words, there are lots of dictionary definitions for the various uses of the word that exist, but only one relates to the questions surrounding the origin of life. That is, something is alive if it does four things: has the capability for growth, change, reaction to stimuli, and reproduction. Obviously this is not very good.

When the dictionary says growth, it implies under certain conditions. In a mine, a photosynthetic plant doesn't grow, but it is still alive. What that means is that if you brought it out into the sunlight, it could grow. In a mine, a herbivore would not do well, but again, if you brought it out into the sunlight where some plants were growing, it could grow. Things like certain insects which reach a fixed size, and do not add any mass for the rest of their existence aren't dead, so growth isn't necessary anyway. Maybe the dictionary was talking about growth in the past, so if something has a history of growing, even though it had maxed out at the end, it was still alive.

The capability for change is also a bit uncertain. Growth is change, and so those insects we talked about weren't growing nor changing, except they were going to different places, so perhaps that's what the authors of the dictionaries were trying to convey. Plants cannot reach a maximum extent or they are not alive, and everything else can get blown around or walk around or float around and therefore they are alive.

Reaction to stimuli is pretty good. A person in a coma doesn't react to some stimuli, but their lungs would react to a lessening of oxygen in the room, meaning that non-autonomous change is okay in this definitional slice. Tardigrades or other creatures that can survive being frozen don't turn from dead to live every time the temperature fluctuates, so the definition must mean that a there has to be a reaction under some conditions, like unfrozen, rather than always.

Reproduction is a strange one. Old people can't reproduce. Sterile people can't reproduce. Ant drones can't reproduce. This one must mean something a bit exotic, like belonging to a species that can reproduce, even though the individual cannot. So the concept of life is somehow wrapped up in the definition of a species and what belongs to one. Messy!

This means it is going to be hard to talk about the origin of life, as it is not going to be clear just where the boundary gets drawn. As some replicating chemical begins to become more complex, is it alive yet? The exact difference probably does not make much difference to the research being done to investigate how life could spring out of non-life, but instead just makes the terminology tricky.

The first block of options for the origin of life, meaning options in a combinatorial way, relates to how the not-yet-living chemicals that are capable of reproduction, or replication if you prefer, stay in the conditions allowing replication. Just like the plant in a mineshaft, without the chemical flow coming out of a sea vent, the chemical cannot replicate. This is all under the assumption that the current most popular hypothesis of sea vent origination is valid. So here is the molecule, trying to make another molecule. How does it stay in the flow? There are three options. One is that it attaches to a substrate, meaning some particular deposit of minerals at or near the sea vent efflux point. It hangs on there, and materials it needs flow past it. Viscosity is nice, and means that the flow near the surface will be going nice and slow, so some component chemical can be grabbed by the molecule.

A second option means it is in the water, but the water does not move. Why? Because it is trapped by some geometry of the vent, like small deep pores, or overhanging ledges on the outside. Water flows by the outside of the pore, and there is some chemical exchange there, but deeper in the molecule has a residence time more than long enough to replicate. If it replicates enough, it won't matter that some copies slip out the pore opening, perhaps to be decomposed or perhaps to land in another pore. Numbers can still build up to some saturation level, and then a bit of mutation can go on.

A third option also involves being in the water, but the water flows in a cyclic fashion, perhaps a slow vortex somewhere down the sides of the vent stack. Exchange takes place, but just as in the second option, if replication rates beats residence time, the molecule will still build up its numbers.

The second block of options relates to how the energy to generate the replication gets to the molecule which will do it. Two options are immediately obvious. Either there has to be some source of energy, in other words an energetic molecule from the flow, interacting with the replicating molecule and putting it into a metastable state. The metastable state contains some of the energy that the energetic molecule that bumped into it had; the rest might be lost. The other option is that one or more of the components that the replicating molecule will assemble contain the energy needed for the assembly. A subsidiary option is that the molecule, either the one doing the replication or the identical one which is the product of replication, is a lower energy state that the components being separate. This might only be true in the exact location of the replication site, or alternatively everywhere near the vent.

The third option relates to how many pieces need to be assembled to make a copy. This has to do with the richness of the flow that washes over or surrounds the replicating molecule. Is it full of amino acids, or even peptides, or some other carbohydrate? How much building has to be done, and how much was already done by random chemical reactions in the vent flow? The vent flow would be at much higher temperatures, and there could be reactions in that flow during the very long time when it migrates down to the maximum depth and then back up. These reactions could make some handy precursors.

Now everything is nice and tidy for some chemistry to be done. 1) What organic molecules can bond to what mineral surfaces? 2) What energetic molecules can excite a metastate in what organic molecules? 3) Does replication occur in a linear fashion, with components being added linearly and perhaps attached to the end of the replicator, or in a close hugging fashion, the way DNA and proteins hug each other with complementary folding? Is it some combination of that, with multiple bonding sites onto one component, which then linearly attaches to another?

A nasty option, meaning more work to be done before the answer to origination is clear, is about symbiotic molecules. For example, do certain molecules have to be adhering to some part of the substrate to produce a precursor molecule that the actual replicator will use? Instead of the precursors being made in the flow, perhaps there is a tiny, little factory producing them a bit upstream. Figuring that out could be done sequentially, provided that the experiments to find the components needed for replication weren't restricted to only those which were known to be produced in a hot flow of seawater through rocks.

Let's just hope there are labs working on these options, and that someday, soon we hope, results will be announced.

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