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

1. The Origins of Life

Hogeweg, Paulien and Nobuto Takeuchi. Multilevel Selection in Models of Prebiotic Evolution. Origins of Life and Evolution of the Biosphere. 33/4-5, 2003. Life arose due to self-organizing dynamics which formed bounded vesicles and spatial hierarchies.

It appears not only that the formation of multiple levels of selection shaped living systems on this planet, models show that the occurrence of new level of selection is an inevitable property of eco-evolutionary processes when interactions occur locally in space. (375)

Huang, Wentao, et al. Near-collapse of the geomagnetic field may have contributed to atmospheric oxygenation and animal radiation in the Ediacaran Period. Communications Earth & Environment. Vol. 5/Art. 207,, 2024. A seventeen member international team at the University of Rochester, across the US onto Brazil and South Africa perceptively identify and qualify an additional planet scale factor which seems to have influenced life’s often stochastic but oriented evolutionary development.

Earth’s magnetic field is known to be in an unusual state when macroscopic animals of the Ediacara Fauna diversified and thrived (635 – 540 MYA). But any connection between these events remains unclear. Here, we present single crystal paleointensity data from pyroxenites and gabbros that define an intensity decline from a strong Proterozoic field like today to an Ediacaran value 30 times weaker. This concurrence raises the question of whether enhanced H ion loss in a reduced magnetic field contributed to the oxygenation, ultimately allowing diversi fication of macroscopic and mobile animals.

Hud, Nicholas and David Lynn, eds. Model Systems From Life’s Origins to a Synthetic Biology. Current Opinion in Chemical Biology. 8/627, 2004. Of especial note is Benner, Steven, et al. Is There a Common Chemical Model for Life in the Universe?. Whenever there is a thermal disequilibrium and temperatures consistent with chemical bonding, living systems of some kind will appear. Further features of a habitable environment are a solvent bath, availability of carbon, hydrogen, oxygen and nitrogen, and relative isolation.

These inevitable developments will open the field of a new synthetic science, beyond defining the origins of living systems, where the powerful principles of biology can be extended and enriched in new ways, ways that both benefit mankind and deepen our understanding of the Universe. (628)

Humphries, Courtney. Life’s Beginnings. Harvard Magazine. September/October, 2013. A Boston science writer interviews major players in this field conveniently at Harvard and environs for a succinct update. Inspired by recent exo-planet findings and implications, astronomer Dimitar Sasselov, paleontologist Andrew Knoll, Nobel laureate chemist Jack Szostak, geneticist George Church, and mathematical biologist Martin Nowak, along with MIT astrobiologist Sara Seager, offer scientific intimations of a conducive cosmos that by way of “universal principles” is innately made for life to appear and evolve.

Life requires more than just getting the right molecules together—it’s an engine propelled by evolution. Martin Nowak, professor of mathematics and of biology and a member of the (Origins of Life) initiative, says that most biologists think of evolution as a process that takes place among organisms that reproduce; evolution at the level of molecules is unfamiliar. But Nowak looks at the problem from a mathematical perspective; to him, evolution “is a well defined process that can be described as precise mathematical equations.” Accordingly, he believes that the same principles governing complex life forms must have been present at the simplest levels—otherwise scenarios for the origins of life depend on a collection of random events. (74)

Ingber, Donald. The Origin of Cellular Life. BioEssays. 22/12, 2000. Nature’s employ of a tensegrity geometry forms hierarchical cell and skeletal structures facilitated by “self-renewing functional webs through the emergence of autocatalytic sets.”

My premise in this article is that evolution is the process by which matter self-organizes in space and, thus, that the origin of life is merely one aspect of the natural evolution of the cosmos. (1160)

Jortner, Joshua. Conditions for the Emergence of Life on the Early Earth. Philosophical Transactions of the Royal Society B. 361/1877, 2006. A reflective summary of a dedicated issue on this subject. One of the most complete and up-to-date sources on the origin and ramifications of life, but within a mechanistic frame. A noteworthy aspect is an accepted recognition of intrinsic self-organizing dynamics.

The arsenal of self-organization of complex biological matter driven by information acquisition, storage, retrieval and transfer, which allows selection, adaptation, self-reproduction, evolution and metabolism may constitute many of the missing links… (1879)

Keenan, Peter, et al. Measuring competing outcomes of a single-molecule reaction reveals classical Arrhenius chemical kinetics.. Nature Communications. 15/10322, 2024. As scientific techniques advance into the collaborative 2020s, University of Bath, UK and University of Potsdam, Germany nanoresearchers are able to peer deeper to discrete biomolecules where they find further verifications of life’s preordained insistence.

Programming matter one molecule at a time is a long-standing goal in nanoscience. The atomic resolution of a scanning tunnelling microscope (STM) can induce single-outcome single-molecule reactions. Here we show it is possible to influence the outcome of a single-molecule reaction with multiple competing outcomes. By precise injection of electrons from an STM tip, toluene molecules are induced to react with two outcomes: switching to an adjacent site or desorption. Using known values, ab initio DFT calculations and empirical models, we conclude that this excess energy leads to a heating of a common physisorbed state and gives control over the two outcomes. (Excerpt)

Crucially, our results indicate that it is possible to go beyond setting up the initial conditions of a charge-stimulated chemical reaction and instead gain control by using the whole range of the molecular dynamics at play. In the future, if we can map the electronic excitation of adsorbates to specific vibrational modes of the molecule, we could achieve direct selectivity over the reaction outcome. (8)

The (Svante) Arrhenius equation describes the relation between the rate of reaction and temperature for many physical and chemical reactions.]

Kempes, Christopher, et al. The Thermodynamic Efficiency of Computations Made in Cells Across the Range of Life. Philosophical Transactions of the Royal Society A. Vol. 375/Iss. 2109, 2017. Kempes and Juan Perez-Mercader, Harvard University, David Wolpert, Santa Fe Institute, and Zachary Cohen, University of Illinois propose that living systems from amoebae to people ought to be seen as constantly performing computations. Such information processing involves genomes in translation making proteins, which is said to go on with inherent efficiency at a minimum energetic cost. Another way that cosmic nature seems made to foster evolutionary life can thus be entered. See also the November 2017 SFI Parallax Newsletter for a commentary on the paper.

Biological organisms must perform computation as they grow, reproduce and evolve. Moreover, ever since Landauer’s bound was proposed, it has been known that all computation has some thermodynamic cost. Accordingly an important issue concerning the evolution of life is assessing the thermodynamic efficiency of the computations performed by organisms. This issue is interesting from the perspective of how close life has come to maximally efficient computation. Here we show that the computational efficiency of translation, defined as free energy expended per amino acid operation, outperforms the best supercomputers by several orders of magnitude. However, this efficiency depends strongly on the size and architecture of the cell in question. In particular, we show that the useful efficiency of an amino acid operation, defined as the bulk energy per amino acid polymerization, decreases for increasing bacterial size. This cost of the largest bacteria does not change in cells as we progress through the major evolutionary shifts to both single- and multicellular eukaryotes. (Abstract excerpts)

Kim, Kyung Mo and Gustavo Caetano-Anolles. Emergence and Evolution of Modern Molecular Functions Inferred from Phylogenomic Analysis of Ontological Data. Molecular Biology and Evolution. 27/7, 2009. A paper from the Evolutionary Bioinformatics Laboratory, University of Illinois, offers still another insight upon preexisting properties at work to impel life’s quickening metabolism. See also from this group: “The Origin, Evolution and Structure of the Protein World” in the Biochemical Journal (417/3, 2009).

Knoll, Andrew, et al. Life: The First Two Billion Years. Philosophical Transactions of the Royal Society B. Vol. 371/Iss. 1707, 2016. This lead paper in a New Bacteriology issue by Harvard, MIT, and Dartmouth scientists reconstructs how microbial phases successfully achieved oxygenation and photosynthesis as a crucial basis for and step to multicellular evolution.

Microfossils, stromatolites, preserved lipids and biologically informative isotopic ratios provide a substantial record of bacterial diversity and biogeochemical cycles in Proterozoic (2500–541 Ma) oceans that can be interpreted, at least broadly, in terms of present-day organisms and metabolic processes. Archean (more than 2500 Ma) sedimentary rocks add at least a billion years to the recorded history of life, with sedimentological and biogeochemical evidence for life at 3500 Ma, and possibly earlier; phylogenetic and functional details, however, are limited. Geochemistry provides a major constraint on early evolution, indicating that the first bacteria were shaped by anoxic environments, with distinct patterns of major and micronutrient availability.

Archean rocks appear to record the Earth's first iron age, with reduced Fe as the principal electron donor for photosynthesis, oxidized Fe the most abundant terminal electron acceptor for respiration, and Fe a key cofactor in proteins. With the permanent oxygenation of the atmosphere and surface ocean ca 2400 Ma, photic zone O2 limited the access of photosynthetic bacteria to electron donors other than water, while expanding the inventory of oxidants available for respiration and chemoautotrophy. Thus, halfway through Earth history, the microbial underpinnings of modern marine ecosystems began to take shape. (Abstract)

Kocher, Charles and Ken Dill.. The prebiotic emergence of biological evolution.. arXiv:2311.13650. Into 2023, SUNY Stony Brook biophysicists (search) post extensive theoretic and empirical quantifications which achieve a robust affirmation of natural life-bearing propensities as they seem to arise from an innate ecosmic fertility. See also a companion paper Origins of life: first came evolutionary dynamics, by the authors in QRB Discovery (March 2023, Cambridge Press open journal)

The origin of life must have been preceded by Darwin-like evolutionary dynamics that could propagate it. How did that adaptive dynamics arise and from what prebiotic molecules? Using evolutionary invasion analysis, we develop a universal framework for describing any evolutionary dynamics. We find that cooperative autocatalysts whose reproductive rate grows as their population increases are able to cross a barrier from their initial degradation-dominated state to a growth-dominated state. (arXiv Excerpt)

The question we have raised in this paper is how prebiotic non-catalytic reactions could have transitioned to autocatalytic growth processes toward biology. Of necessity, this requires explaining the molecular bases of cooperativities and their bootstrapping origins. An explanation of origins requires a plausible microscopic model that has a basis in molecular physics and tenable grounding in prebiotic processes. The Foldcat hypothesis is found to satisfy these criteria. As random peptides grow longer, they fold, protecting their cores from degradation, and they catalyze the further growth of peptides as a plausible basis for the origins of biological evolution. (7)

When life arose from prebiotic molecules 3.5 billion years ago, what came first? Informational molecules (RNA, DNA), functional ones (proteins), or something else? We argue here for a different logic: rather than a molecule type, a dynamical evolutionary process is proposed which was rooted in the peptide folding process. Our models show how short random peptides can catalyse the elongation of others, powering increased folding stability and emergent autocatalysis through a disorder-to-order process. (QRD Discovery Abstract

Koonin, Eugene and William Martin. On the Origin of Genomes and Cells within Inorganic Compartments. Trends in Genetics. 21/12, 2005. The last universal common ancestor (LUCA) is proposed to be housed in iron sulfide matrices in the vicinity of warm submarine hydrothermal vents. Initial natural selection was for molecular self-replication, which favored increasingly complex ensembles. Even at this early stage, a reciprocity between competition and “altruism” is noted with the formation of “selfish cooperatives.” But what kind of a universe does such life arise from – is it innately fertile or basically “inorganic?”

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