Undefining life's biochemistry: implications for abiogenesis

Abstract

In the mid-twentieth century, multiple Nobel Prizes rewarded discoveries of a seemingly universal set of molecules and interactions that collectively defined the chemical basis for life. Twenty-first-century science knows that every detail of this Central Dogma of Molecular Biology can vary through either biological evolution, human engineering (synthetic biology) or both. Clearly the material, molecular basis of replicating, evolving entities can be different. There is far less clarity yet for what constitutes this set of possibilities. One approach to better understand the limits and scope of moving beyond life's central dogma comes from those who study life's origins. RNA, proteins and the genetic code that binds them each look like products of natural selection. This raises the question of what step(s) preceded these particular components? Answers here will clarify whether any discrete point in time or biochemical evolution will objectively merit the label of life's origin, or whether life unfolds seamlessly from the non-living universe.

Disproving two widely accepted notions regarding entropy

“…Notably, Google Scholar showed at the end of 2023 that Schrödinger's book, What is life, had been positively cited approximately 10,000 times mainly due to the inclusion of this notion. In 2022 and 2023, this book was cited for more than 1,000 times by authors from various countries (e.g., [32][33][34][35][36][37][38][39]) with few doubts about this notion. Coinciding with the popularity of this notion, English Wikipedia and other academic websites deliberately added the word "negative" with brackets in Boltzmann's statement in Box 2 before "entropy" [40,41].…”

“…The second law of thermodynamics, which states that heat can flow spontaneously from hot objects to cold objects and cannot flow reversely, has been frequently misused. For example, it was assumed by researchers from various fields that many natural or social systems tend to become more disordered over time due to the second law of thermodynamics [2, [4][5][6]18,19,32,[35][36][37][38][39][40][41][42]. The assumption that many natural or social systems tend to become more disordered over time is inherently correct due to some statistical probabilities because it is more probable for these systems to stay at a disordered status than at an ordered status.…”

Early Selection of the Amino Acid Alphabet Was Adaptively Shaped by Biophysical Constraints of Foldability

“…The role of peptides and proteins in life’s emergence has historically been sidelined as they have been, at times, perceived as only relevant after the evolution of nucleotide-based polymers, the genetic code, and a translation apparatus. However, the prebiotic abundance of amino acids and their ease of condensation resulting in polymers capable of creating functional hubs along with various cofactors (such as metal ions and organic compounds) has prompted some chemists to reconsider peptides’ role during life’s early evolution. − While extant proteins are built from a sequence space spanned by the 20 canonical amino acids (cAAs) and rely on the specificity of the Central Dogma, early peptides (and peptide-like polymers) likely arose from a larger pool of prebiotically plausible monomers.…”

Early selection of the amino acid alphabet was adaptively shaped by biophysical constraints of foldability

“…The role of peptides and proteins in life's emergence has historically been sidelined as they have been, at times, perceived as only relevant after the evolution of nucleotide-based polymers, the genetic code, and a translation apparatus. However, the prebiotic abundance of amino acids and their ease of condensation resulting in polymers capable of creating functional hubs along with various cofactors (such as metal ions and organic compounds) have been recently re-centering peptides' role during life's early evolution (1)(2)(3)(4). While extant proteins are built from the sequence space spanned by the twenty canonical amino acids (cAAs) and rely on the specificity of the Central Dogma, early peptides (and peptide-like polymers) likely arose from a larger pool of prebiotically plausible monomers.…”

“…However, the prebiotic abundance of amino acids and their ease of condensation resulting in polymers capable of creating functional hubs along with various cofactors (such as metal ions and organic compounds) has prompted some chemists to reconsider peptides' role during life's early evolution. [1][2][3][4] While extant proteins are built from a sequence space spanned by the twenty canonical amino acids (cAAs) and rely on the specificity of the Central Dogma, early peptides (and peptide-like polymers) likely arose from a larger pool of prebiotically plausible monomers.…”