V. Life's Corporeal Evolution Develops, Encodes and Organizes Itself: An Earthtwinian Genesis Synthesis

1. The Origins of Life

Takeuchi, Nobuto, et al. On the Origin of DNA Genomes: Evolution of the Division of Labor between Template and Catalyst in Model Replicator Systems. PLoS Computational Biology. Online March 24, 2011. As the extensive Abstract explains, bioinformatic researchers Nobuto, NIH, Paulien Hogeweg, Utrecht University, and Eugene Koonin, NIH, achieve notable insights into how life’s replication process initially got its evolving act together. We resultant people are just beginning to learn the rest of the story. And might one imagine that since material nature innately appears to develop this way, it might in fact be made for this purpose?

At the core of all biological systems lies the division of labor between the storage of genetic information and its phenotypic implementation, in other words, the functional differentiation between templates (DNA) and catalysts (proteins). This fundamental property of life is believed to have been absent at the earliest stages of evolution. The RNA world hypothesis, the most realistic current scenario for the origin of life, posits that, in primordial replicating systems, RNA functioned both as template and as catalyst. How would such division of labor emerge through Darwinian evolution? We investigated the evolution of DNA-like molecules in minimal computational models of RNA replicator systems. Two models were considered: one where molecules are adsorbed on surfaces and another one where molecules are compartmentalized by dividing cellular boundaries. Both models exhibit the evolution of DNA and the ensuing division of labor, revealing the simple governing principle of these processes: DNA releases RNA from the trade-off between template and catalyst that is inevitable in the RNA world and thereby enhances the system's resistance against parasitic templates. Hence, this study offers a novel insight into the evolutionary origin of the division of labor between templates and catalysts in the RNA world. (Abstract)

Takeuchi, Nobuto, et al. The Origin of a Primordial Genome through Spontaneous Symmetry Breaking. Nature Communications. 8/250, 2017. Veteran theoretical and experimental biologists NT and Kunihiko Kaneko, University of Tokyo and Paulien Hogeweg, Utrecht University go on to perceive a whole genomic complementarity amongst replicative nucleotides in rudimentary bounded cells and autocatalytic processes. As the Abstract notes, an efficient self-organized critical poise between these dual functional stages is then becoming apparent.

The paper is included in an Early Earth Collection on this site which has Nucleoside and Nucleotide, Early Cells, and Early Earth Conditions segments. See, e.g., Considering Planetary Environments in Origin of Life Studies by Laura Barge, Life as a Guide to Prebiotic Nucleotide Synthesis by Stuart Harrison and Nick Lane, and Prebiotic Plausibility and Networks of Paradox-Resolving Independent Models by Stephen Benner.

The heredity of a cell is provided by a small number of non-catalytic templates. How did these genomes originate? We demonstrate the possibility that genome-like molecules arise from symmetry breaking between complementary strands of self-replicating molecules. Our model assumes a population of protocells, each containing a population of self-replicating catalytic molecules. The protocells evolve towards maximising the catalytic activities of the molecules to increase their growth rates. Conversely, the molecules evolve towards minimising their catalytic activities to increase their intracellular relative fitness.

These conflicting tendencies induce the symmetry breaking, whereby one strand of the molecules remains catalytic and increases its copy number (enzyme-like molecules), whereas the other becomes non-catalytic and decreases its copy number (genome-like molecules). This asymmetry increases the equilibrium cellular fitness by decreasing mutation pressure and increasing intracellular genetic drift. These results implicate conflicting multilevel evolution as a key cause of the origin of genetic complexity. (Abstract)

Thomsen, Kristoffer, et al. Metabolism, information, and viability in a simulated physically-plausible protocell. arXiv:2405.04654. University of Southern Denmark, and ICREA-Complex Systems Lab, Universitat Pompeu Fabra, Barcelona including Artemy Kolchinsky and Steen Rasmussen provide a highly technical quantification of life’s occasion by its tendency to form and foster rudimentary cellular assemblies. We sample a long abstract and another notice of the tripartite metabolism, biocode, and boundary model.

Vital experimental issues connecting energy transduction and inheritable information within a protocell are explored and elucidated. The protocell design utilizes a photo-driven energy transducer to turn resource molecules into building blocks in a manner that is modulated by a combinatorial DNA-based co-factor. This co-factor molecule serves as part of an electron relay for the energy transduction mechanism, where the charge-transport rates depend on the sequence that contains an oxo-guanine….. Functional information of the co-factor molecules is used to probe sequences from a limited population of co-factors molecules, where a good co-factor can enhance both metabolic biomass production and its own replication rate. (Abstract brief)
The work is based on an operational definition of minimum life that can be supported by four interconnected functionalities: a metabolic energy transducer, an informational co-factor, and a container, which must all be situated in an appropriate environment. (39)

Trefil, James. How Life Began. Santa Fe Institute Bulletin. Winter, 2006. A substantial NSF grant has been awarded to SFI to systematically study how life first occurred, directed by Harold Morowitz. Two concurrent approaches are planned – bottom up from biomolecules and top down in a reverse-engineering fashion from cellular forms.

…what is exciting and new about this multi-pronged approach to the origin of life is its focus on the fundamental physical and chemical processes that we know were present early in the history of our planet – the processes we know must have given rise to life in the first place. It encourages us to see life not as some highly improbable accident but as a natural outcome of the workings of the physical universe. (7)

Trefil, James, et al. The Origin of Life. American Scientist. May-June, 2009. With co-authors Harold Morowitz and Eric Smith, a state of the art update noted more with quote in An Organic Universe.

Vaidya, Nilesh, et al. Recycling of Informational Units Leads to Selection of Replicators in a Prebiotic Soup. Chemistry & Biology. 20/2, 2013. Vaidya and Niles Lehman, Portland State University chemists, and Sara Walker, Arizona State University astrobiologist, propose that a biomolecular redundancy is at work to aid in life’s complex initiation.

Our studies take two complementary approaches, one computational and one empirical. In that regard, the results presented here are relatively uncommon. The computational approach allowed a thorough search of parameter space and concluded that catalytic recycling could lead to the selection of high-fitness genotypes, especially when rate constants were in an intermediate range. This result mirrors a common feature of biology: that reaction rates need to be attenuated to be neither too rapid nor too slow. The empirical approach, while unable to explore as many combinations as could be done on the computer, allowed an imposition of chemical reality to the recycling system. These studies show that recycling with a known recombinase of biological origin not only is facile but can lead to evolutionary self-selection. (250-251)

Vanchurin, Vitaly, et al. Thermodynamics of Evolution and the Origin of Life. arXiv:2110.15066. This is a companion paper by Vanchurin, Wolf, Koonin and Katsnelson to their Evolution as Multilevel Learning entry (2110.14602) so to provide a physical and chemical basis for life’s evident proclivity to progressively achieve an referential accumulated knowledge repository. Along the way a maximum entropy principle is seen to be involved. A Table compares thermodynamic qualities with machine learning methods and evolutionary biology, which are then fitted into a major transitions frame. Into the 2020s, these postings suggest that a composite explanatory synthesis which links many heretofore separate aspects into a single sweep from universe to us is newly possible.

We outline a phenomenological theory of evolution and the origin of life by combining classical thermodynamics with a statistical description of learning. The maximum entropy principle is employed to derive a canonical ensemble of organisms (population), their macroscopic fitness and free energy of additive fitness). We model evolution as a function of the biological temperature and potential development, This thermodynamics framework then allows major transitions in evolution such as from biomolecular stages to an ensemble organisms to be identified. As a further result, the origin of life, can be appreciated as a special case of physical phase transitions. (Abstract)

We employ the conceptual apparatus of thermodynamics to develop a phenomenological theory of evolution and of the origin of life that incorporates both equilibrium and non-equilibrium evolutionary processes within a mathematical framework of the theory of learning. The threefold correspondence is traced between the fundamental quantities of thermodynamics, the theory of learning and the theory of evolution. Under this theory, major transitions in evolution, including the origin of life, represent specific types of physical phase transitions. (Significance)

The key idea of our theoretical construction is the interplay between the entropy increase in the environment dictated by the second law of thermodynamics and the entropy decrease in evolving systems (such as organisms or populations) dictated by the second law of learning (19)

Vaneechoutte, Mario. The Scientific Origin of Life. Jerry Chandler and Gertrudis Van de Vijver, eds. Closure: Emergent Organizations and Their Dynamics. Annals of the New York Academy of Sciences, 2000. The author contends that early life and the scientific enterprise develop in the same way by corresponding molecular and linguistic codes.

Villarreal, Luis and Guenther Witzany. That is Life: Communicating RNA Networks from Viruses and Cells in Continuous Interaction. Annals of the New York Academy of Sciences. Online March, 2019. A UC Irvine biologist and a Telos–Philosophische Praxis, Austria philosopher (search each) continue their project to better explain how life’s biomolecular origins came to be. Herein a novel finesse of ribonucleic and deoxyribonucleic acids, along with viral–like modes, is seen to provide a fuller, more accurate reconstruction.

The conserved results of evolution stored in DNA must be read, transcribed, and translated via an RNA‐mediated process for the development and growth of each individual cell. Thus, all living organisms depend on these RNA‐mediated processes. The precellular evolution of RNAs was crucial to the emergence of cellular life. Here we argue that RNA networks and RNA communication can interconnect precellular and cellular levels. With the reemergence of virology in evolution, it became clear that communicating viruses and subviral infectious genetic parasites are bridging these two levels by invading, integrating, coadapting, exapting, and recombining constituent parts in host genomes for cellular requirements in gene regulation and coordination aims. Therefore, a 21st century understanding of life is of an inherently social process based on communicating RNA networks, in which viruses and cells continuously interact. (Abstract excerpts)

Wachtershauser, Gunter. Chemoautotrophic Origin of Life: The Iron-Sulfur World Hypothesis. Barton, Barry, et al. Geomicrobiology: Molecular and Environmental Perspectives. Dordrecht: Springer, 2010. I once heard the author, a Munich patent attorney and Ph.D. chemist, speak on the subject at a 1984 AAAS meeting in New York City. He has stayed on the case, and is now recognized for crafting a unique integration which this lead chapter summarizes. In so doing, as the quotes express, dichotomous methods of close analysis or overall synthesis, discrete molecule or relational metabolism, can be resolved. In support of an organic cosmos, significant aspects can be gleaned. By way of our human “retrodiction” some twenty “bio-elements” such as Sulfur, Magnesium, Phosphorous, Zinc, and Vanadium are found well suited, as if “preordained,” which seem to act in concert for life to arise and evolve.

But, in a mix of some terms, it begs notice that while said “mechanisms” do not augur for a deeper reality, a perceived animate “teleology” across life’s long history would imply a greater, conducive milieu, something rather than nothing. A “bio-anthropic principle” could accrue if the periodic table is appreciated as a fertile materiality for creatures and planet. In this latter regard, as other book chapters add, if a “geologic-chemical-biology” truly graces the earth, a biological universe would be inferred as well.

At the philosophical level we still are faced with the conflict between mechanistic explanations and teleological judgments. Biochemistry is providing ever more refined mechanistic explanations of the chemistry of life, down to the finest molecular details. A theory of biology, by contrast, would have to treat organisms, i.e., organized beings, as integrated wholes. Biochemistry is reductionistic and mechanistic while biology is holistic and teleological. (1) This then is our problem: to postulate a primordial organism – here termed “pioneer organism,” which is at the same time mechanistic and organizational. Central to this effort will be the notion of a “synthetic autocatalysis,” the chemical equivalent of biological reproduction, which is a chemical reaction mechanism and at the same time a functional whole, and by being synthetic it is endowed from the start with the primary vector of complexity increase. (2)

The theory of Wallace and Darwin is based on the assumption of stochastic micromutations, which suggests to most biologists that there is no inner directionality in the process of evolution. The prebiotic broth theories and notably the RNA world theories extend this stochasticity down to the very beginning of life. By contrast, the theory of a chemoautotrophic origin of live forces us to view the overall process of evolution in a fundamentally novel manner, recognizing aspects of both directionality and uniqueness in the early process of evolution. (31) These factors jointly amount to a “chemical determinism” that is bound to hold in the farthest reaches of the Universe as on Earth. (31)

Wagner, Andreas. The Large-scale Structure of Metabolic Networks: A Glimpse of Life’s Origin? Complexity. 8/1, 2003. As the ‘universal character’ of network dynamics becomes known, their activity in organizing biomolecules and protocells into organic systems brings a novel feature to explain how life began and became increasingly complex.

Walde, Peter, ed. Prebiotic Chemistry. Berlin: Springer, 2005. Volume 259 in the Topics in Current Chemistry. series. Much recent progress via theory and experiment is reported about the procession from simple amphiphilic molecules, which combine both hydrophilic and hydrophobic (water affinity or aversion) properties, to the self-assembly of membrane-bounded minimum protocells. Typical papers discuss rudimentary cell structures, chirality, and amino acid synthesis, whose authors include David Deamer and Eors Szathmary. The tacit implication is a fertile cosmos which innately complexifies to its current human reconstruction and self-witness.

[Prev Pages]   Previous   | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18  Next