Adonis Diaries

Archive for October 18th, 2022

For millions of years, millions of living species died, became extinct,…and we have no ideas what they were and how they vanished.

Millions of living species failed to adapt to their environment (climate change…), surrounding nature…

Thousands went extinct due to human behavior, and now a few of these species are being re-created by modern sciences and technologies, a few are being considered becoming rare and need protection…

Even human species is still debatable as to its origin (One origin or many origins and continents), kinds of intelligent/adaptable species…and time span.

It is a fact that evolution occurs. It has not only been verified in the fossil record but also been observed to occur over small time scales.

Likewise, we observe flaws in the design of the body that show that it evolved in a different environment and was adapted to a new one.

A common example in the evolutionary process is the eye which works better in water than air since it mostly evolved under the sea. Clues can be found in our DNA that point to how long ago our species split off from others.

Offspring with harmful traits either die off or fail to reproduce. The effect is natural selection which vastly raises the probability that beneficial traits will be retained and carried forward to the next generation. Once natural selection gets started, you can’t help but arrive at complexity.

Imagine that each of the amino acid, a small protein, and finding the box with their number is equivalent to finding a place in a long protein chain that leads to evolutionary success, the beginnings of the natural selection process.

They don’t have to communicate to strategize, simply have to follow the strategy blindly, connecting together via peptide or hydrophobic bonds, but not randomly.

Rather, they must connect in such a way that the configuration of amino acids or small proteins leads to another configuration, via reconnection and folding, on a cycle that ultimately leads to a successful configuration.

If the process is random, then the chances of any viable configuration are almost nil.

While the chances of this happening for a large collection of amino acids or protein sections randomly is vanishingly small, if each follows a reconfiguration strategy similar to the prisoner’s problem, then they have a good chance of success.So far so good,

But how would this Non random process occur naturally?

Let’s look at our analogy.

How do the proteins “know” where to go next without having a mind to direct them there?

To answer this question, we have to grok the strategy. At its core, the strategy follows a cycle, but why is the cycle there in the first place? The cycle is there because the slips of paper represent a permutation of the drawer numbers.

A permutation can be thought of as a sequence of exchanges between an ordering of numbers.

Thus, any permutation contains a cycle representing the sequence of exchanges that occurred or would need to occur to reproduce that permutation.

You can think of it like this. If no permutation had been done, each drawer would contain a slip with its own number on it and point to itself. The cycles would have one element. If I exchange the slips of paper between two drawers, say 1 and 2, this single permutation creates a cycle of length two. Drawer 1 points to 2 and 2 back to 1.

If I then permute one of them with another drawer such as exchanging the slips in drawers 2 and 3, the cycle grows, now 1 to 2 to 3 and back to 1. Thus, there is a direct relationship between the length of the cycle and the number of exchanges.

Going back to proteins, suppose we consider that there exists a successful protein configuration, the one that represents all the prisoners finding their own numbers, i.e., starting natural selection going.

Permutations of this configuration are on average failed configurations. Randomly assembling a protein in the right configuration is unlikely to succeed.

But if that protein builds itself up with each segment following a permutation cycle, it is far more likely to succeed.

Now, suppose that the successful protein configuration is precisely that, a configuration that builds itself up according to permutation cycles. That is, we aren’t trying to find some magical, natural selection configuration but, rather, the natural selection configuration is precisely the one that satisfies the strategy! That is enough.

The reason is that a protein that follows this strategy would have a property that all life possesses: the ability to reproduce.

It has this ability because it constructs itself (copies itself) with high probability despite its structure being very complex.

Each segment finds its place by following a permutation cycle rather than encouraging random configurations.

If the property of Reproduction were to exist among proteins, even one amid trillions, it would be able to kickstart natural selection even if the protein had no other characteristics of life and there were nothing otherwise special about it.

It would be the beginnings, indeed, of the transcription ability that we see in DNA and RNA.

Proteins do not configure themselves randomly at all but connect to one another via exposed bonds. These bonds are exposed based on the way the protein folds.

Thus to construct a successful permutation cycle protein only requires that each of the segments have this special property, via how they fold and expose their bonds, so that they connect in the right way to reproduce.

Likely this would work via a sequence of proteins (rather than one self-reconfiguring protein) with each segment following a predictable pattern of where in the chain it is positioned.

Each iteration of the prisoners opening a drawer would be a new generation for the protein, but, since the cycles are all closed, the resulting proteins would all be part of a related family of proteins that would continuously reproduce in a never ending cycle that nevertheless is far from random.

These sequences, by following permutation cycles, would guarantee reproduction. This might be a simple enough way for life to be far more probable than you would think.

Note: This article was inspired by Tim Andersen, Ph.D. Sep 29, 2022. “The 100 Prisoner problem could explain the origin of life” and I had to edit many of the sections.




October 2022

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