Life on Earth arose about as soon as it was possible for life to arise

[Junkdrawer]

24. My guess....

One of the biggest mysteries still outstanding in 21st century science is this: How did life originate from inanimate matter. With Darwinian evolution, we believe we have a handle on how primitive, replicating life evolved into more and more complex life forms, but, as far as I know, we have little idea how even the most primitive life forms originally developed.

Life on Earth is currently protein based with DNA and RNA nucleotides controlling the replication of cells. Proteins, in turn are comprised of amino acids and we do, thanks to the 1952 Miller-Urea experiment, have a pretty good idea how amino acids may have arisen on a planet with a carbon dioxide, nitrogen, hydrogen sulfide, and sulfur dioxide atmosphere. But here we seem to be stuck waiving our arms saying that somehow, given enough time, life must have spontaneously appeared – the Primordial Soup hypothesis. The problem is that even the most primitive self-replicating cell we know of is so incredibly complex, that spontaneous generation is beyond credulity.

As a lay person looking into the field of evolutionary biology, I see an enormous amount of effort trying to overcome the first step of the problem: exactly what sort of pre-life structures are capable of spontaneous generation? And this is an important question, but certainly not the only question. Other fundamental questions would include “How does Nature select between the different structures capable of spontaneous generation?” and “Why did Nature choose to combine these spontaneous generated structures into something like a cell capable of that Rube-Goldberg-like thing we call mitosis?”

In order to not get bogged down in the initial question of what sort of pre-life structures are capable of spontaneous generation, I will speak of Black Box processes. In engineering, especially electrical engineering, a Black Box is a system described solely in terms of its inputs and outputs - with the internal workings undetermined. In the rest of this paper the Black Box models will be exceptionally simple. This is by design so that we can get a flavor of the concepts involved. Later, we could add complexity to the models and, with computer simulations, see if the concepts identified sill hold.

Let’s begin with the problem of selection. How would nature select one pre-life process over another? Well, if we were talking about how Darwinian evolution would select one organism over another, we would look to see which organism is best able to gather and consume the scarce resources of a given environmental niche and then replicate. Since the main resource in the Primordial Soup scenario is the amino acids themselves, let’s consider a few thought experiments and see how far this takes us.

We begin with the simplest scenario I can think of: two Black Box processes, say BBA and BBB, both are able to join together the same three amino acids, but each produces unique proteins we’ll call ProteinA and ProteinB. We’ll also assume BBA joins the amino acids twice as fast as BBB, and that there is a finite amount of amino acids. Clearly, at the end of this experiment there will simply be twice as much ProteinA as ProteinB. However, if we further assume that both ProteinA and ProteinB naturally break down to their constituent amino acids at a rate slower than their formation, a more interesting result occurs. As the newly freed amino acids will form ProteinA twice as fast as ProteinB, given enough time, only ProteinA will exist in any quantity and only a trace amount of ProteinB will be found. Now both BBA and BBB still exist, but as far as impact on the environment, as measured by their eventual outputs, it’s as if BBB never existed. This may be how Nature selects between different pre-life processes.

In order to attack the next question(s), I have found that it was necessary to put some precision of language around the problem. Indeed, in the rest of this paper, I will offer some insights this more precise language has given me to date.

Let BB0 represent the set of all pre-life Black Box processes capable of spontaneously generating in a given environment containing only amino acids. Let’s notate each member of this set as BB0,M where M is an integer starting with 1. Let E0,M represent the number of BB0,M members that will spontaneously generate in a given volume over a given time. We’ll call this the Existential function for the BB0 set. A fractional number such as 0.5 will mean that it takes two time periods before a BB0,M member will appear.

Now, the next insight is that once we have BB0 processes occurring, the environment has changed. We now have primitive proteins as well as amino acids in the new environment. This will allow us to define the next set:

Let BB1 represent the set of all pre-life Black Box processes capable of spontaneously generating in a given environment containing amino acids and at least one of the primitive proteins generated by the BB0 set. The important thing to note here is that the E1,M existential functions will all contain a term that represents the number of one or more BB0 set members currently existent since, by the very definition of the set, BB1 members only spontaneously generate in the presence of one or more BB0 members.

We can now proceed and define BBN as the set of all pre-life Black Box processes capable of spontaneously generating in a given environment containing amino acids and the at least one of primitive proteins generated by BB(N-1) set. And we can refer to the increasing N subscript as “generations” with BB0 as the 0th generation, BB1 as the first generation, etc. etc.

Currently, without the introduction of additional concepts, all we have here is perhaps a more formal statement of the extremely low order of probably of the spontaneous generation of a complete cell capable of mitosis. But consider this thought experiment:

Imagine that there are a large number of BB0 processes possible, and they all have very, very small probabilities of forming. However, let’s posit that as we move to later generations, the probability of formation would increase were it not for the fact that they are dependant on the less likely formation of their predecessors. Now, what happens when a member of later generation starts to produce the protein(s) of the dependent BB0 set? Well, we would introduce a feedback loop, something like indirect replication. And, as there are in this example many BB0 processes possible, we may have many independent and, perhaps interlocking loops, each competing for the finite amino acid resource.

Another possibility in the preceding example is that, instead of replacing the protein of an earlier generation, the new protein creates a “helper” structure that simply increases the likelihood of an intermediate BB process spontaneously generating. This also could create or increase feedback loops. It would also help explain the creation of structures within current cells not directly related to protein generation.

It is important to note that, until now, we are talking about open solution processes. So, how and when do we move from open solution processes to replicating cells? I believe the answer may lie in enzymes. Suppose that one or more of the competing closed loop processes described above happens upon a protein that acts as an enzyme that breaks down a critical protein of a competing loop. This would certainly be a plus for the enzyme-generating loop as it both increases the amount of free amino acids while removing from competition the prey loop. But it would also setup a circumstance where the BB process which generates a protein that forms defensive semi permeable membranes (allowing amino acids in and keeping enzymes out) are more likely to remain in competition.. I would further guess that the development of cell walls is a late development as the walls that keep enzymes out may also keep out the proteins needed to form a cell capable of mitosis.

While I hope the ideas expressed in this paper shed some light on how inanimate matter may organize into something approximating life, it is, currently, a weak and insufficient light. I focus on protein generation and leave the incredible complexity of DNA/RNA in the shadows. But it is a beginning and I hope that it points in a direction that would eventually allow us to unravel this great mystery.