The Origin of Life and Self-Replication: A Perspective on Polymer Conversion Systems
Regarding the origin of life, I have been conducting personal research from a systems engineering perspective. Until now, I have focused on the evolution of chemical substances leading up to the birth of life.
In this context, I paid attention to the structure where ponds and lakes are connected by rivers on Earth’s terrain, and the water flows through rivers via ponds and lakes, evaporates at the sea to become clouds, and then rains down on the mountains. Numerous ponds and lakes would have accumulated chemical substances in various proportions, and these chemicals would have been transported by water flows, upward drafts during evaporation, winds, and clouds. I hypothesized that this facilitated the encounter of a diverse range of new chemical substances and formed a feedback loop, leading to a system where groups of chemical reactions reinforced and maintained themselves.
Furthermore, during the process of chemical evolution, it’s believed that viscous lumps, fibrous organic matter, and lipid membranes appeared. Therefore, not just chemical evolution, but structural evolution also progressed. I also proposed a hypothesis of an evolutionary model that both chemical and structural evolution jointly pushed forward the birth of life.
In this article, I will discuss the origins of the mechanism of self-replication, similar to DNA, and the central dogma mechanism where DNA generates RNA, and RNA produces proteins.
A point of focus here is that DNA, RNA, and proteins are all chain-like chemicals called polymers. By considering the mechanism in which a polymer, composed of basic chemical units called monomers, is converted into another polymer, I aim to unravel this mystery.
Polymer Conversion System
Living cells have a mechanism by which messenger RNA is translated into proteins by ribosomes.
There’s also a mechanism where one strand of DNA is transcribed into its complementary DNA strand by DNA polymerase, and another where messenger RNA is transcribed by RNA polymerase.
Both transcription and translation can be viewed as types of polymer conversions.
Therefore, organisms have a mechanism to produce various proteins through polymer conversions from DNA, and it can also be said that the replication of DNA is made possible by polymer conversion. From this perspective, organisms have an aspect of being a polymer conversion system.
Of course, such abstraction omits many details, but to thoroughly understand the essential mechanisms, it’s necessary to pare down to the basics.
Mechanism of Polymer Conversion
Polymer conversion requires a constant polymer converter. Then, the converter changes the varying input codes into output codes following a set rule.
Though not exactly fitting the definition of a polymer converter, the simplest schema is when chemical substance A comes into contact with chemical substance B, chemical substance C is produced from surrounding materials.
If chemical substance A produces chemical substance E upon contact with chemical substance D, it gets closer to being a polymer converter. This is because it outputs chemical substance C when in contact with chemical substance B and chemical substance E when in contact with chemical substance D, much like word conversion in a dictionary.
If chemical substance A outputs a polymer composed of chemicals C and E when given a polymer of chemicals B and D, then it becomes a full-fledged polymer converter.
Mechanism of Polymer Replication
If the given polymer is a sequence of chemicals B, C, D, and E, and the converted polymer is a sequence of C, B, E, and D, then chemical substance A can replicate the polymer. A polymer converted once by chemical substance A appears as if it’s the inverse of the original polymer. When this is converted again by chemical substance A, it becomes a replication of the original polymer.
Furthermore, if the given polymer and the polymer converted once by chemical substance A bond as a double-strand, it becomes capable of self-replication.
DNA self-replication might seem like a special mechanism, but in essence, it’s a system established by a polymer that meets specific conditions and its corresponding polymer conversion.
Polymer and Polymer Converter
If the original polymer and the polymer converter can regenerate through polymer conversion, they can proliferate.
The need for both to be generated is a rather challenging demand.
If this requirement were to be relaxed, it would be convenient if the polymer converter itself was of the same substance as the original polymer.
Considering the presence of ribosomal RNA contained in ribosomes, if RNA had a mechanism to replicate and evolve first, it can be assumed that ribosomal RNA later appeared, enabling the synthesis of proteins.
RNA can produce a single strand of DNA by reverse transcription, and RNA can be generated from DNA by transcription. However, both reverse transcription and transcription require special enzymes. This system cannot explain the generation of these special enzymes.
About the Origin of the Polymer and Polymer Converter
For very short RNA and DNA, perhaps reverse transcription and transcription occurred as a natural phenomenon without needing enzymes. For example, a substance dissolved in water naturally crystallizes as the water temperature decreases.
The prototype of RNA might have been able to naturally produce DNA under certain environmental conditions, even without a polymer converter. Likewise, the generation of RNA from DNA could naturally form in the same way without a polymer converter.
If such a mechanism existed, substances closely related to early RNA and DNA could have self-replicated without enzymes.
Of course, if the chains of RNA and DNA are long, the likelihood of complete reverse transcription and transcription being successful becomes low, so this mechanism probably wouldn’t occur for longer chains.
During the self-replicating process, RNA and DNA underwent diverse mutations. From these, the prototype of ribosomal RNA might have emerged, and the initial stages of protein formation could have been realized.
Once the mechanism for synthesizing proteins was established and evolved, enzymes constituting ribosomes, reverse transcription enzymes from RNA to DNA, transcription enzymes from DNA to RNA, and other refined polymer converters could have been produced.
Considering from the DNA Perspective
Let’s think from a DNA standpoint. Assume there’s a very short single strand of DNA, and under the right environmental conditions, it can naturally produce its complementary single DNA strand even without a polymer converter.
In this case, a short chain length is also assumed. If short, DNA could separate as a single strand without twisting into a double helix.
Considering this, if you think from the DNA standpoint, only the mechanism of transcription from DNA to DNA needs to naturally occur without a polymer converter. This seems simpler for self-replication than reverse transcription and transcription between RNA and DNA.
If something similar to early DNA could self-replicate through such natural mechanisms, it might have acquired the function of transcribing to RNA while undergoing random mutations. From there, it might have gained the ability to synthesize proteins. Thus, enzymes for transcription from DNA to DNA and other polymer converters could have been produced and refined.
Origin: RNA or DNA?
RNA seems to be more favored as the origin of life phenomena given its simpler structure compared to DNA and the fact that RNA not only serves as a medium for genetic information storage but also acts enzymatically.
However, as discussed in the previous section, replication is possible even for simple single-stranded DNA, not just the complete double helix. Such replication may even be more advantageous. If transcription occurred naturally, whether or not it has enzymatic functions would not influence the formation of the initial replication mechanism.
For RNA to acquire a self-replicating mechanism, it either needs to undergo reverse transcription and transcription through natural processes or express one of these functionalities as an intrinsic enzymatic capability.
On the other hand, for single-stranded DNA, if transcription naturally occurs from one single strand to another, replication is possible.
The key point here is the hypothesis that initial self-replication didn’t require enzymes. While this might be challenging with the complete DNA or RNA seen in present-day organisms, it’s conceivable if we consider precursors to DNA or RNA with similar properties, starting from very short chains. Chemical substances that could replicate themselves might have emerged even without enzymes.
Under such assumptions and premises, a polymer, like single-stranded DNA capable of transcribing its complementary chain, would likely have been the first self-replicating mechanism.
Palindromic DNA
Single-stranded DNA can replicate itself by transcribing twice. However, in a natural setting, successfully transcribing twice without errors is improbable. If the speed of potential failures or DNA structural damages outpaces the speed of successful double transcription, replication won’t be successful.
I’ve heard that palindromic genetic information partially exists within DNA. Palindromic genetic sequences are ones where if you transcribe from ABCD, you get DCBA, which is just the reverse. If you rotate the transcribed DCBA by 180 degrees, it becomes ABCD, meaning the same genetic information is produced in just one transcription.
If you have single-stranded DNA with palindromic genetic information, it can self-replicate with only one transcription, offering a significant advantage in the rate of replication versus the rate of damage.
Therefore, I believe that short, single-stranded polymers with DNA-like properties and palindromic genetic sequences might have been the origin of self-replicating polymers. This could also explain why palindromic genetic sequences are still found in today’s DNA.
Conditions for the Original Self-replicating Polymer
When considering DNA as a specific chemical substance, we might get bogged down by its complexity. Additionally, in the context of the origin of life, entirely different polymers might have self-replicated initially. Through chemical evolution, DNA or RNA emerged, and the initial polymers became extinct.
Considering our previous discussions, whether it’s an unknown polymer or a precursor to DNA, certain conditions must be met for self-replication. The simplest chemical substance meeting these conditions is likely the original self-replicating polymer.
The conditions are:
a) It should be a polymer composed of at least two types of monomers.
b) It should be capable of transcribing to a polymer composed of the same monomers.
c) Transcription should be possible without complex enzymes, instead relying on natural conditions or simpler catalytic substances.
d) It should have a palindromic sequence.
e) The speed of transcription due to natural processes should exceed the rate at which the polymer structure gets damaged.
Considering conditions c) and e), the simplest polymer that meets these conditions is likely the origin of life on Earth in the form of a polymer conversion system.
Considering Binding Sites
Let’s assume we have chemical substance X and chemical substance Y. For these to bind, let’s say X and Y have binding sites a and b respectively, and a and b can bind together. This makes X and Y monomers that can form a polymer.
Furthermore, if X has a binding site x and Y has a binding site y, the polymer formed from monomers X and Y would satisfy the conditions of the aforementioned self-replicating type of polymer.
Moreover, it’s essential that the bond between a and b is stronger, whereas the bond between x and y is weaker. This ensures that when environmental conditions change, the single-stranded polymer remains intact, but it doesn’t become stuck in a double-stranded state.
Let’s assume that a sufficient amount of these chemical substances X and Y exist in water. Once minimal environmental conditions are met, the binding sites a and b of X and Y combine, forming a short polymer. The basic units are XX, XY, and YY. Note that among these, XY possesses a palindromic structure.
Once more suitable conditions are present, molecules will bind at the x and y binding sites of this polymer. This can be visualized as Y binding to the earlier mentioned XY. As time progresses, another Y binds, forming pairs of XY and YX polymers. If the conditions slightly change, the bond at x and y separates, leading to the separation of XY and YX. Since YX structurally is the same as XY, through this process, XY effectively doubles in number.
Through such processes, the polymer grows longer due to the binding of x and y, and transcription occurs due to the binding of a and b. If the polymer has a palindromic structure, its transcription would mean the same as replication, making the palindromic polymer grow at twice the speed of other polymers. Given the same probability of damage, the overall quantity of palindromic polymers should dominate.
In Conclusion
In this article, by contemplating polymers and their transformation mechanisms, we have delved deeper into the generation of DNA, RNA, and proteins.
We have also explored the possibility of polymer transformation driven by natural environmental changes, stepping away from the premise that complex enzymes are necessary. Theoretically, we discovered that short palindromic polymers can self-replicate simply by environmental fluctuations.
What remains to be seen is whether such chemicals fulfilling these conditions truly exist. Moreover, until now, we’ve only discussed the existence of self-replicating polymers. Going forward, we need to ponder whether a polymer transformation system like that of DNA, RNA, and proteins can emerge.
Regardless, realizing a simple mechanism that could be the origin of self-replication is a significant discovery.
We know that complex enzymes are involved in the transformation of DNA, RNA, and proteins. It’s easy to assume that these enzymes were the origin of polymer transformation. However, if self-replication was realized before the advent of complex enzymes, as suggested by our idea, our understanding of the chemical evolution sequence in the origin of life might dramatically change.
