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Origin of Life -


Origin of Life - Natural Processes, Pre-biotic World, Proto-ribosome, A Scenario

Origin of Life

There is an extensive expose on the "Origin of Life" in another section of this website. In spite of all the circumstantial evidences, it is still unclear why the transition to life from non-life did not need a helping hand (a.k.a. God). The mystery could be dispelled by learning
Origin of Life more about the concepts of self-assembly, self-organization and the phenomena of emergence (from the prebiotic soup, Figure 01). The explanations are all based on the science of physics and chemistry although ultimately life could be better described at the level of biology. Giving enough time, life is inevitable provided the condition is right. For example, the hydrogen bond so important for maintaining the structure of life will be disrupted by thermal agitation at few tens

Figure 01 Origin of Life
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of degrees above room temperature; and the structure becomes frozen if temperature is low enough for the van der Waals force to take over.



Self-assembly is the process in which a disordered system with many components turns into an orderly and stable structure (at equilibrium with minimum energy configuration, like a ball rolling down the hill to rest at the bottom of the valley) without external direction. The process has the following features : Self Assembly produces only lifeless objects which may be components in living organism. It is created under the requirement of minimum free energy in chemical equilibrium.



Even though both the self-assembly and self-organization processes refer to the spontaneous formation of orderly structure, they are different in that while self-assembly arrives at an equilibrium configuration, the self-organization drives the system off equilibrium which requires an infusion of energy to maintain. Self-organization is created from small fluctuations, which are amplified by positive feedback loop. The process is non-linear similar to chaos. Another major difference is the interaction. While the interaction in self-assembly is
Self Organization more elementary, which can be traced back to the electromagnetic force; the interaction in self-organization involves the kind of action that affects many facets. The size of the resulting structure from self-assembly is mostly mesoscopic, but it can be considerably larger for self-organization. Figure 03 illustrates the continuum of open thermodynamic systems from ordered, near-to-chaotic, to far-from-equilibrium states. As energy consumption increases, systems move further from equilibrium and pass through a phase transition between order and chaos. Complex systems such as proto-ribosome exist in this phase transition.

Figure 03 Self-organization
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The diagram also shows the assembly and self-organizational activity of the proto-ribosome under the sun (for energy infusion). It is supposed to be the ancestor of the modern ribosome making protein from genetic codes.
Self-organization involves non-equilibrium processing driven by external energy source. It is still lifeless because life requires an internal energy source such as ATP to become self-sufficient. Life also involves reproduction.


Emergent Phenomena

Auto-systems Self-organization is different from emergent phenomena. While both are dynamic processes arising over time, emergence emphasizes the presence of novel coherent macro-level emergent property, behaviour, structure, ... as a result from the interactions between micro-level parts (rectangles in Figure 04b). Self-organisation emphasises the spontaneous increase in order (circle in Figure 04a). When both the self-organizing and emergent processes

Figure 04 Three Auto-systems

are involved in creating the system (as in Figure 04c), it is often mistaken that they are the same process. It is this kind of process that is most important for the origin of life.

An example of self-organization without emergent phenomena is the cooling of gas (e.g., via infrared radiation) - a process lower the entropy but evokes no new phenomena. The microscopic description of gas molecules in "kinetic theory of gas" and its
Examples of Auto-systems macroscopic correspondence offer an example of emergent phenomena without self-organization - it is a change of perspective from individual molecules to thermodynamics without any change in the entropy of the system. The example of slime moulds life cycle is for

Figure 05 Examples of Auto-systems [view large image]

the case of simultaneous occurrence of self-organization and emergent phenomena (Figure 05).

Slime Mould The self-organization and emergent phenomena occur simultaneously when the slime moulds (see more in "Slime Moulds Life Cycle") run out of food. As shown in Figure 06, The parts are the individual amoebae, the interaction is the adhesive molecules, the energy is supplied by their favorite food - the bacteria and yeast, and the emergent phenomena is the moving slug and fruiting body.

Figure 06 Slime Mould
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Emergent Phenomena is the appearance of novel property via change in the system. It could emerge with living or lifeless entity.
    In summary, the minimum requirements for emergent biologic phenomena out of self-organization include :

  1. There are interactions between components parts to build the structure.
  2. An open thermodynamic system with many parts to allow the infusion of energy and removal of entropy.
  3. A positive feedback loop causing nonlinear dynamic behavior (for amplifying small fluctuations).
    It follows that the resulting characteristics of the biological emergent phenomena are :

  1. Novel properties not observed previously in those component parts - the total is more than the sum (via interaction).
  2. The resulting entity can reproduce, is coherent and could maintain itself as a whole over period of time (by energy infusion).
  3. It can evolve to something else. This is the Darwinian selection, which determines the outcome of the evolution according to changing environment (in positive or negative feedback loop).
See "Active Matter" for 21st Century research on the transition of inanimate substance into active matter.


2018 Update on the Theory of "Prebiotic World"

                 ( Evolution of Ribosome,   Evolution of aaRS,   Requirements for the Origin of Life,   A Scenario of prebiotic World )

Evolution of Ribosome : starting from recent observations to some evidences from the ancient world.

RNA World Most theories on the origin of life adopt a "bottom-up" approach from simple to complex and from unknown to known. Another method is to trace the evolutionary path from a known point at present. The path is narrowing down by observing a conversed organelle called ribosome inside all life including bacteria and human. Although difference exists on the ribosome across different species, there is a core structure inside that is present in all of them. The following is an attempt to reach the origin by such scenario from "The Modern Day Ribosome" (structure and function) to "History of Ribosome" (looking backward to LUCA).

Figure 07 RNA World
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Figure 07 portrays one of the bottom-up theories - the hypothetical "RNA World" in a evolutionary sequence from some nucleotides ~ 4.5 Gyr ago to LUCA (Last Universal Common Ancestor) ~ one billion years later. See relationship to the "RNA-Protein World" in Step C.
[2022-10-05 Update] - Ribosome Self-Replication (Biogenesis) :
    Here's a summary of the evolution of the Protein/RNA World (forward in time) with the development of the aminoacyl-tRNA synthetase (aaRS) playing the central role as illustrated in Figure 16 (see more in "Peptide/RNA Partnership") :

  1. Biology emerged from a reciprocal partnership in which small ancestral oligopeptides and oligonucleotides initially both contributed rudimentary information coding and catalytic rate accelerations.
  2. The superior information-bearing qualities of RNA and the superior catalytic potential of proteins emerged from such complexes only with the gradual invention of the genetic code.
  3. The two aminoacyl-tRNA synthetase (aaRS) ATP binding sites (including a 46-amino acid sequence - the 46mers, see Figure 16 for location of the site) arose as translation products from opposite strands of a single gene. This is the key intermediates on a path from simple catalytic peptide/RNA complexes to contemporary aminoacyl-tRNA synthetases. This scenario provides a path to increasing complexity that obviates the need for a single polymer such as the RNA to act both catalytically and as an informational molecule.
  4. The pattern persisted until the evolution of the modern aminoacyl-tRNA synthetases (aaRS), tRNAs, and ribosomes enabled higher-specificity genetic coding. The LUCA emerged at this stage. The early steep raise of the evolutionary curve in Figure 16 indicates relatively easy steps in synthesizing macromolecules such as RNA and protiens, while the nearly flat portion of the curve later signifies the more difficult task of making them to perform useful functions such as replication of a strand of RNA. That is, synthesis is relatively easy by just adding another unit randomly selected, while replication involves one to one copying of a specific sequence.

This "Protein/RNA World" scenario is different from the "RNA World" mainly in Phase 1 and 2 as depicted in Figure 14 in which the
aaRS role of aaRS is only implied in the formation of the proto-CCA (Figure 10). The RNA World follows the evolution of ribosome to arrive at the ancestral rRNA. While the Protein/RNA World as portrayed in Figure 16 emphasizes the role played by aaRS, which bears evidence of ancestral protein (enzyme) in the very beginning of the evolution of life. These two theories are complementary to each other. Evolution on both ribosome and aaRS should be considered in any future investigation into the "Origin of Life". For example, there would be no translation by the ribosome without the tRNA charged by the aaRS. See "Origin of Translation" for more info on aaRS in action.

Figure 17 aaRS in Action
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BTW, most cells contain 20 different aaRS enzymes, one for each amino acid. The editing function of the aaRS as indicated in Figure 17 is to ensure high fidelity of tRNA charging.

See original article : "What RNA World? Why a Peptide/RNA Partnership Merits Renewed Experimental Attention".

[2022-5-19 Update]
Even the virus (the most primitive modern day life) uses an aggregate of 6 proteins to replicate its RNA (see step 8 in Figure 19f). Thus, the protein (aka peptide chain) is one of the indispensable components in supporting life. Recently in 2022, the research paper "Origin of life theory involving RNA–protein hybrid gets new support" reveals a very primitive way to produce peptide chain long before the emergence of life. Some of those ingredients and processing methodology are still hidden inside the present day ribosome.

Unlike most enzymes, the ribosome itself is made of not only proteins, but also segments of RNA — and these have an important role in synthesizing proteins. Moreover, the ribosome contains modified versions of the standard RNA nucleosides A, C, G, and U. These exotic nucleosides have long been seen as possible vestiges of a primordial broth (see "Exotic Nucleotides").

    Here's a summary of the novel experiment and comparison to the modern process (in italic, see also corresponding diagrams in Figure 17b,b). The formation of bonds in the process requires energy, which the researchers provided by supplying various reactants in the solution (in place of the energy supply from the ATP to the aaRS in charging the modern tRNA, see Figure 17b,b).

    RNA/Protein World
  1. A RNA molecule is synthesized by joining two pieces of RNA commonly found in living cells with two exotic nucleosides. At the first exotic sites, the synthetic molecule could bind to an amino acid.
    These RNA segments correspond to the charged/un-charged modern day tRNA but carrying only 1 nucleoside instead of 3 (the codon carrying the genetic code in modern version).
  2. The amino acid then moved sideways to bind with the second exotic nucleoside adjacent to it.
    This step corresponds to the transfer of amino acides from the 1st tRNA to the next one within the ribosome (see Figure 10).
  3. The original RNA strands are separated and a fresh one is brought in, carrying its own amino acid.
    This step corresponds to the advance of mRNA fetching the next tRNA to the ribosome (Figure 10).
  4. The second amino acid would form a strong covalent bond with the first amino acid. The process
  5. Figure 17b RNA/Protein World [view large image]

    then returns to step 3 and keeps on repeating, growing a short chain of amino acids — a mini-protein called a peptide — that grew while still attached to the RNA - the process is uncontrollable.
    This one corresponds to the elongation after processing each tRNA in the ribosome (Figure 10) - the process is regulated by mRNA in the ribosome.

    Here's an illustration with chemical formulas for the exotic processe :
This experiment suggests a possible evolutionary path from non-life to life, and that trace of its remnants are still lingering on inside the living organelle called ribosome. See original article "A prebiotically plausible scenario of an RNA–peptide world".

[End of 2022-5-19 Update]

[2023 Update]

This update is about the proto-ribosome, which is believed to be the ancestor of life in the lifeless era. It still resides in every organism on Earth today. There are experimental observations to support the assertion on its role in the origin of life. The discovery has earned a Nobel prize for its principle researcher (see the "video about the investigation of Proto-ribosome" from the horse's mouth, also an extensive "review article on Peptidyl Transferase Center (PTC)" dated 2021 ).
peptidyl transferase center (PTC) Evolution of Ribosome
    In Figure 17c (see "Is This RNA a Key Ingredient in the Origin of Life?") :

  • (a1) shows the location of the proto-ribosomes within the PTC of modern ribosome.
  • (a2) reveals the 3-D tertiary structure of the proto-ribosome pair in blue and green (short line = nucleobase).
  • (a3) displays the evolutionary change of the proto-ribosomes over the eon in secondary structures.

Figure 17c PTC

Figure 17d Evolution of Ribosome

   Figure 17d shows the evolution of ribosome in quaternary structures.

More information about the PTC within the LSU of the ribosome is shown by Figure 17h.

The roles of these nucleotides and their pairing is summarized below :