Getting Beyond the Toy Domain. Meditations on David Deamer’s “Assembling Life”

Bains, William

doi:10.3390/life10020018

Cited by 14 publications

(13 citation statements)

References 56 publications

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“…The origin of life is summarized as " container-enabled chemistry first" or "self-assembling" [45,46]. Perhaps some people will ask why molecules did not stay silently in the organic soup but struggled to shift from chaos to order?…”

Section: Perspectives: Where To Go?mentioning

confidence: 99%

ATP-Hypothesis: A New Conceptual Framework for the Origins of Genetic Codes

Xie¹

2020

Preprint

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The origin of genetic codes is the key to reveal life’s origin on the earth as it is a prerequisite for the existence of life. More than half a century has passed since the discovery of genetic codes, while their origin is still one of the greatest mysteries. Are the origins of genetic codes really unknowable? Do they really require external design? Here, I present an ATP-hypothesis that explains how the genetic codes came into being with the coevolution of biochemical system. ATP has several properties that make it suitable as the initiator of the origin of genetic codes. First, ATP is the only energetic product of photosynthesis. Second, ATP is at the heart of the extant biochemical systems. Third, ATP serves as carriers of both energy and information. Fourth, ATP could energetically elongate chains of both polynucleotides and polypeptides, thus providing a bridge between them, and eventually mediating prebiotic biochemical transaction from energy to information. This hypothesis shows how primitive life emerged through a series of processes from energy to information mediated by ATP. Informatization (processes of creating and managing information) was inevitably coupled with structuralization (processes of organizing or incorporating into a cellular structure), making polynucleotides and polypeptides be cyclized into a system of reciprocal causation. The triplet codon might just be for stereo-chemical handing of amino acid through e.g. Watson–Crick pairing interactions. It is an evolutionary completion for genetic codes from RNA to DNA, only which, a reverse to the Central Dogma, marked the dawn of cellular life when Darwinian evolution began to operate. ATP-hypothesis shades lights on the origin of life, together with the formations of both photosynthesis and biochemical systems, which have been largely unknown so far.

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Section: Perspectives: Where To Go?mentioning

confidence: 99%

ATP-Hypothesis: A New Conceptual Framework for the Origins of Genetic Codes

Xie¹

2020

Preprint

View full text Add to dashboard Cite

show abstract

“…The origin of life is summarized as -container-enabled chemistry first‖ or -self-assembling‖ [45,46]. Perhaps some people will ask why molecules did not stay dormant in the organic soup and instead struggled to shift from chaos to order?…”

Section: Perspectives: Where To Go?mentioning

confidence: 99%

The ATP Hypothesis: A New Conceptual Framework for the Origin of the Genetic Code

Xie¹

2020

Preprint

View full text Add to dashboard Cite

The origin of the genetic code is the key to revealing the origin of life on Earth, as it is a prerequisite for the existence of life. More than half a century has passed since the discovery of the genetic code, but its origin is still one of the greatest mysteries. Is the origin of the genetic code truly unknowable? Does the code truly require external design? Here, a hypothesis is proposed, according to which ATP is at the origin of the genetic code by its coevolution with the pristine biochemical system. ATP has several properties that make it suitable as a plausible initiator of the genetic code. First, ATP is the only energetic product of photosynthesis. Second, ATP is at the heart of the extant biochemical systems. Third, ATP serves as a carrier of both energy and information. Fourth, ATP could energetically elongate chains of both polynucleotides and polypeptides, thus providing a bridge between these molecules and eventually mediating prebiotic biochemical innovation from energy transformation to informatization. This hypothesis shows how primitive life emerged through a series of processes from energy to information flow mediated by ATP. Informatization (processes for creating and managing information) was inevitably coupled with structuralization (processes for organizing or incorporating cellular structures), cyclizing polynucleotides and polypeptides into a feedback loop of reciprocal causation. The triplet codon might be only for stereochemical handling of amino acids through, e.g., Watson–Crick pairing interactions. It is only the evolutionary completion of the genetic code from RNA to DNA that, contrary to the central dogma, marked the dawn of cellular life, when Darwinian evolution began to operate. The ATP hypothesis sheds light on the origin of life, together with the formation of both photosynthetic and biochemical systems, which remains largely unknown thus far.

show abstract

“…The origin of life is summarized as -container-enabled chemistry first‖ or -self-assembling‖ [60,61]. Perhaps some people will ask why molecules did not stay dormant in the organic soup and instead struggled to shift from chaos to order?…”

Section: Perspectives: Where To Go?mentioning

confidence: 99%

The ATP Hypothesis: A New Conceptual Framework for the Origin of the Genetic Code

Xie¹

2020

Preprint

View full text Add to dashboard Cite

A plenty of theories on the origin of genetic codes have been proposed so far, yet all ignored its energetic relation to the biochemical system. Here, a new hypothesis is proposed, according to which ATP is at the origin of the primordial genetic code by its coevolution with the pristine biochemical system. This hypothesis aims to show how the genetic code was produced by photochemical reactions in a protocell that derived from a lipid vescile enclosing various life’s building blocks (e.g. nucleotides and peptides). At extant cell, ATP is the only energetic product of photosynthesis, and is at the energetic heart of the biochemical systems. ATP could energetically elongate chains of both polynucleotides and polypeptides, thus providing a bridge between these bio-polymers and eventually mediating cellular biochemical innovation from energy transformation to informatization. ATP was not the only one that could drive the formation of polynucleotides and polypeptides, but favored by precellular selection. The protocell innovated a photosynthesis system to produce ATP efficiently and regularly with the aids of proteins and RNA/DNA. The completion of the genetic code from RNA to DNA marked the dawn of cellular life operated by Darwinian evolution. The ATP hypothesis supports the photochemical origin of life, shedding light on the formation of both photosynthetic and biochemical systems, which remains largely unknown thus far.

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Getting Beyond the Toy Domain. Meditations on David Deamer’s “Assembling Life”

Cited by 14 publications

References 56 publications

ATP-Hypothesis: A New Conceptual Framework for the Origins of Genetic Codes

ATP-Hypothesis: A New Conceptual Framework for the Origins of Genetic Codes

The ATP Hypothesis: A New Conceptual Framework for the Origin of the Genetic Code

The ATP Hypothesis: A New Conceptual Framework for the Origin of the Genetic Code

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