origin of life Archives

Topological alteration of a state graph. a) A system being coarse-grained and receiving arbitrary labels from an external observer. The example macrostate (u) labels are vectors of three binary-valued microstate variables denoted (v1, v2, v3). Panels b to d display the topologies of the physicallyreachable state graph after constraining a variable of the labeling vector. The nodes and edges that became inaccessible as a consequence of applying a conservation law are displayed with lighter colors. The top row corresponds to setting value 0, while the bottom row corresponds to setting the variable to 1. b) Constraining variable v1. On the one hand (b.1), a conservation law for v1 = 0 leads the system to state u1. On the other hand (b.2), with v1 = 1, the system cannot escape from u2. c) Constraining variable v1. In the case v1 = 1 in c.2), the graph is restricted to u3 and has no possible transitions. The node does exist under a conservation law setting v1 to 1 but there is no way to reach this node due to the topology of the unconstrained graph. d) Constraining variable v3. This variable is constant and equal to 1 in the unconstrained graph in a), so a conservation law setting v3 = 0 such as in panel d.1 is meaningless for this case. -- physics.bio-ph

Biophysics, Biosignatures & Paleobiology, Nanotechnology & SynBio, Origin & Evolution of Life, Status Report

An Open-Ended Approach to Understanding Local, Emergent Conservation Laws in Biological Evolution

by Keith CowingSeptember 24, 2024September 24, 2024

While fields like Artificial Life have made huge strides in quantifying the mechanisms that distinguish living systems from non-living ones, particular mechanisms remain difficult to reproduce in silico.

Examples of the >100 macrocycles generated in this study. Colored components represent new-to-nature amino acids that were incorporated into either peptide. Credit Scripps Research

Biochemistry & Organic Chemistry, Biophysics, Biosignatures & Paleobiology, Commercial & Private Sector, Genomics, Proteomics, Bioinformatics, Nanotechnology & SynBio, Origin & Evolution of Life, Press Release

Earth Life’s Genetic Alphabet Has Been Expanded To Create Novel Proteins

by Keith CowingSeptember 17, 2024September 17, 2024

It’s a dogma taught in every introductory biology class: Proteins are composed of combinations of 20 different amino acids, arranged into diverse sequences like words. But researchers trying to engineer […]

Hadean Earth - credit: Alec Brenner via Harvard University

Atmospheres, Climate, Weather, Biochemistry & Organic Chemistry, Biogeochemical Cycles & Geobiology, Biosignatures & Paleobiology, Fossils & Paleontology, Habitable Zones, Microbiology & Virology, Status Report, Water/Hycean Worlds & Oceanography

New Estimates of Nitrogen Fixation on Early Earth

by Keith CowingSeptember 17, 2024September 17, 2024

Fixed nitrogen species generated by the early Earth’s atmosphere are thought to be critical to the emergence of life and the sustenance of early metabolisms.

Cold RNA misfolding and phase transitions. (A) Illustration of a multi-colored free-energy landscape (FEL) at different temperatures. The temperature arrow indicates the tendency to explore low-lying energy states with the FEL becoming rougher upon cooling: from high (red) to intermediate (green) and low (blue) temperatures. Transition state (TS) distances are typically shorter for M than N, denoting disordered and compact misfolded structures. The encircled schematic folds are for illustration purposes. (B) Temperature-dependent entropy (black) and enthalpy (grey) of N for H1L12A (empty symbols) and H1L4A (full symbols). The results are reported in Table S5 and S6, Supp. Info. Fits to the entropy values in the hot (red) and cold (blue) regimes for H1L12A (solid lines) and H1L4A (dashed lines) are also shown. The transition between the two regimes occurs at TG ⇠ 293K ⇠ 20C (dashed grey band) with a sudden change in Cp. Inset. Stability curves of H1L12A (empty black circles) and H1L4A (solid grey squares). Maximum stability is found at TS ⇠ 278K ⇠ 5C (vertical black line) with melting temperatures at TH ⇠ 370K ⇠ 100C (red lines). Extrapolations of G0(T) in the cold regime predict cold denaturation at TC ⇠ 220K ⇠ 50C for both hairpins (blue lines). -- PNAS

Biochemistry & Organic Chemistry, Biophysics, Biosignatures & Paleobiology, Cryobiology, Genomics, Proteomics, Bioinformatics, Press Release

A New Biochemistry For RNA At Low Temperatures

by Keith CowingSeptember 11, 2024September 11, 2024

Ribonucleic acid (RNA) is a biological molecule with crucial functions in the genetics of organisms and plays a key role in the origin and evolution of life. With a composition […]

A hairpin loop from a pre-mRNA. Highlighted are the nucleobases (green) and the ribose-phosphate backbone (blue). -- Wikipedia

Biochemistry & Organic Chemistry, Biophysics, Biosignatures & Paleobiology, Genomics, Proteomics, Bioinformatics, Origin & Evolution of Life, Status Report

RNA World: Overcoming Nucleotide Bias In The Nonenzymatic Copying Of RNA Templates

by Keith CowingSeptember 6, 2024September 6, 2024

The RNA World hypothesis posits that RNA was the molecule of both heredity and function during the emergence of life.

Astrochemistry, Biochemistry & Organic Chemistry, Biophysics, Biosignatures & Paleobiology, Genomics, Proteomics, Bioinformatics, Origin & Evolution of Life, Status Report

The Astrochemical Evolutionary Traits Of Phospholipid Membrane Homochirality

by Keith CowingSeptember 3, 2024September 3, 2024

Compartmentalization is crucial for the evolution of life. Present-day phospholipid membranes exhibit a high level of complexity and species-dependent homochirality, the so-called lipid divide. It is possible that less stable, […]

Structure and protein subunits of ATP synthase from F- and A/V-types. Figure based on Mahendrarajah et al. (2023)

Genomics, Proteomics, Bioinformatics, Microbiology & Virology, Origin & Evolution of Life, Status Report

The Unfinished Reconstructed Nature of the Last Universal Common Ancestor

by Keith CowingSeptember 3, 2024September 2, 2024

The ultimate consequence of Darwin’s theory of common descent implies that all life on earth descends ultimately from a common ancestor. Biochemistry and molecular biology now provide sufficient evidence of […]

Origins of Terrestrial and Extraterrestrial Life -- Grok

Astrobiology (general), Astrochemistry, Origin & Evolution of Life, Status Report

Alternative Pathways in Astrobiology: Reviewing and Synthesizing Contingency and Non-Biomolecular Origins of Terrestrial and Extraterrestrial Life

by Keith CowingSeptember 3, 2024September 2, 2024

The pursuit of understanding the origins of life (OoL) on and off Earth and the search for extraterrestrial life (ET) are central aspects of astrobiology.

Polymetallic nodules, also called manganese nodules, on the floor of the Pacific Ocean; surprising new research suggests deep sea rocks are capable of producing oxygen without help from plants or the sun. Photo via Wikimedia Commons/Geomar Bilddatenbank/ROV KIEL 6000, GEOMAR

Atmospheres, Climate, Weather, Biochemistry & Organic Chemistry, Biogeochemical Cycles & Geobiology, Biophysics, Biosignatures & Paleobiology, Habitable Zones, Icy Worlds, Origin & Evolution of Life, Planetary Protection & Biosafety, Press Release, ROVs/Submersibles/Diving, Sample Return, Water/Hycean Worlds & Oceanography

Oxygen Produced In The Deep Sea Raises Questions About Extraterrestrial Life

by Keith CowingAugust 27, 2024August 27, 2024

Over 12,000 feet below the surface of the sea, in a region of the Pacific Ocean known as the Clarion-Clipperton Zone (CCZ), million-year-old rocks cover the seafloor. These rocks may […]

The temporal distribution of our candidate hard steps.

Biosignatures & Paleobiology, Habitable Zones, Intelligence & Language, Origin & Evolution of Life, SETI & Technosignatures, Status Report

A Reassessment of the “Hard-steps” Model For The Evolution Of Intelligent Life

by Keith CowingAugust 27, 2024August 27, 2024

While there exist more contentious geochemical and molecular clock estimates for these steps that would place them each farther back in time, we have chosen the least controversial evidence to […]