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Origin of Life - Self-assembly, Self-organization, and Emergent Phenomena


Origin of Life
Emergent Phenomena
A 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 )

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 more about the
Origin of Life 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

Figure 01 Origin of Life
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agitation at few tens 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 :



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
Self Organization is non-linear similar to chaos. Another major difference is the interaction. While the interaction in self-assembly is more elementary, which can be traced back to the electromagnetic force; the interaction in self-organization means the kind of action that affects many sides. 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

Figure 03 Self-organization
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through a phase transition between order and chaos. Complex systems such as life exist in this phase transition. The diagram also shows the creation of life from a cell and its individual parts (the organelles).

Unfortunately, self-assembly and self-organization are often used interchangeably creating a lot of confusion.


Emergent Phenomena

Auto-systems Self-organization is different from emergent phenomena. While both are dynamic processes arising over time, emergence emphasises the presence of a 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

Figure 04 Three Auto-systems

emergent processes 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 macroscopic
Examples of Auto-systems 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 the case of simultaneous

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

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

Figure 06 Slime Mould
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and fruiting body.

    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 is coherent and could maintain itself as a whole over some 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.


A 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.

    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 17 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 role of aaRS
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".