On the Origins of Life

A new experimental system demonstrates that precursors of ribonucleotides, amino acids, and lipids may have simultaneously arisen from the same prebiotic chemistry.

By | March 17, 2015

© KEVIN HANDOrigin-of-life researchers have traditionally been categorized into a “genetics first” camp, which ascribes to the notion that some sort of information molecule was a necessary prerequisite for life, and a “metabolism first” group, in which studies focus on understanding the chemical cycles that led to the synthesis of organic molecules. But in a paper published this week (March 16) in Nature, scientists presented evidence that both genetics and metabolism may have arisen simultaneously, via a reaction involving ?hydrogen cyanide and hydrogen sulfide, driven by ultraviolet (UV) light.

“This is a very important paper,” Jack Szostak, a molecular biologist and origin-of-life researcher at Massachusetts General Hospital in Boston, told Science. “It proposes for the first time a scenario by which almost all of the essential building blocks for life could be assembled in one geological setting.”

In 2009, John Sutherland of the Medical Research Council Laboratory of Molecular Biology in the U.K. and his colleagues demonstrated that the basic sugars glycolaldehyde and glyceraldehyde could be used to create RNA’s pyrimidine nucleotides, cytidine (C) and uridine (U), under conditions consistent with early-Earth geochemical models. Then, in September 2012, Sutherland’s team found that these sugars could be derived from the even simpler hydrogen cyanide, which itself is suspected to have been present on prebiotic Earth.

Expanding on this system, Sutherland and his colleagues found that hydrogen cyanide, along with hydrogen sulfide and UV light, could spawn not just precursors of ribonucleotides, but also the building blocks of amino acids and lipids, the core components of proteins and fatty acids. The details of each reaction are slightly different, however, and all three of these components are not likely to have arisen in close enough proximity to spontaneously form some sort of proto-cell, Sutherland told Science. Other factors, such as rain, could have then brought the compounds together.

“This general scenario raises many questions,” Szostak told Science, “and I am sure that it will be debated for some time to come.”

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Avatar of: James V. Kohl

James V. Kohl

Posts: 436

March 19, 2015

“This is a very important paper,” Jack Szostak, a molecular biologist and origin-of-life researcher...

See also: Luis P. Villarreal: We Need a Nonlinear Language for Life

Nobelist Jack Szostak has told me this about autocatalytic sets: the people who came up with the original idea, like Stuart Kauffman, rather than admit being wrong kept changing their story until it was basically the same concept everybody was already working on.

My comment: Researchers continue working on "origin of life" issues but they ignore Villarreal's perspective. It links viral microRNAs and the anti-entropic epigenetic effects of nutrient-dependent microRNAs from entropic elasticity to epigenesis and epistasis manifested in cell type differentiation in all genera. 

"Origin of life" theorists seem to be stuck with theoretical physics that cannot be linked via RNA-mediated amino acid substitutions to the biophysically constrained chemistry of RNA-mediated protein folding that differentiates all animal cell types.

Will Kauffman and others keep changing their story until it is the same one told by Villarreal? If not, will they simply accept the fact that they've been wrong about cell type differentiation for at least 50 years.

Dobzhansky (1964) wrote:

...the only worthwhile biology is molecular biology. All else is "bird watching" or "butterfly collecting." Bird watching and butterfly collecting are occupations manifestly unworthy of serious scientists!

Dobzhansky (1973) wrote: 

...the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla.

Excerpted from this article:

Sutherland and his colleagues found that hydrogen cyanide, along with hydrogen sulfide and UV light, could spawn not just precursors of ribonucleotides, but also the building blocks of amino acids...

That suggests viral microRNAs and nutrient-dependent microRNAs are driving cell type differentiation via RNA-mediated amino acid substitutions that stabilize protein folding in the organized genomes of species from microbes to man. If  Villarreal is right, everyone will need to change their story to the one that accurately represents how the virus-driven origin of life led to cell type differentiation via light-induced amino acid substitutions in plants and nutrient-dependent pheromone-controlled amino acid substitutions in all animals.

See also: No need for extrasolar delivery by comet: Nitrogen fingerprint in biomolecules could be from early Sun

Ammonia molecules, a nitrogen atom bound to three hydrogen atoms, makes up a fundamental chemical group, the 'amines' the characterize amino acids, which link up in long chains to form proteins.

Quantum Criticality at the Origin of Life (co-author Stuart A. Kauffman)

The number of proteins grows exponentially with the number n of amino acids...

That story may start with "Let there be light" and the differentiation of cell types by nutrient-dependent microRNAs that repair the DNA damage caused by viral microRNAs.

In any case, the story does not seem to start with mutations and evolution. Does it?

Avatar of: JonRichfield

JonRichfield

Posts: 122

March 21, 2015

I have a growing suspicion that there is an element of cross-purposes in this discussion. Some of the following concepts are just a few that should be borne in mind

*Before there were complex molecules (such as nucleotides, nucleosides and sugars, which, please note, are not simple, except in comparison with far larger molecules) there was no question of DNA, RNA, or their evolution or chemistry coming into existence, let alone into action.

*To develop meaningfully complex nucleic acids and proteins, by which I mean those adequate to permit meaningful discussion of viroids, let alone viruses, it is not clear how it possible to speak in terms of life at all, even in precellular electron-cascade terms.

*It is very well to argue that this is niggling on my part, because everyone knows that these are obviosities, but in fact, whether they know it or not, many of the loudest voices gloss over such fundamental points continually if not continuously.

*It is puzzling that there should be any suggestion, however tacit,  that one could reasonably  ignore a discontinuity between a stage of prebiotic chemistry and the development of a basis for storing, transmitting, accumulating, and  controlling digital information and developing reproductive life forms based on and dependent on such.

*It would make no sense to deny that the development of the more complex prebiotic molecules would involve the accumulation of information-rich structures, though not in general digitally encoded information.

*It would be equally senseless to argue that the first such informationally complex structures (such as proto-enzymes or structural polymers) would be biotic or in any direct way homologous with nucleic acid based Darwinian processes.

*It would be necessary for anyone to assemble his arguments with great care and force, who wished to deny that the development of the NA-based Darwinistic processes was a class of emergent development, whether in its early forms it was proto-cellular, viroidal or viral, or indeed based on chemical structures that could not sensibly be equated with any of those classes of structure.

And so on and on. Books worth.

Now, this HCN, H2S proposal is, as I see it, strictly of importance to the development of those first complex biochemicals, and presumably thereafter no doubt into the first protocellular forms, give or take a few hundred million years. I hold no brief for or against some of the structures that have been claimed to be probiotic fossils in the oldest cherts. No doubts some of them are significance, but equally doubtless many must be artefacts.

Personally I am certain that such processes must have been key to the infrastructure that led to NA structures, though I am equally certain that there must have been many other chemical process in parallel with those. Such processes might well have included the HCN/H2S reactions proposed. Other candidates might well include aldol condensations, which immediately suggest themselves as sources of simple sugars for example.

I hold no brief for or against the work of Luis P. Villarreal, not even having studied it to any depth, but I am sure that it does not deny any of the foregoing principles; he certainly speaks of viruses/viroids as the first life/protolife. I have seen very little work detailing a coherent chain of events intervening between the primeval soup or porridge and the first undoubted life forms and Darwinian processes. Personally I am of the opinion that the transitions did happen, and good luck to anyone who would like either to deny or detail the intervening developments.

Avatar of: James V. Kohl

James V. Kohl

Posts: 436

Replied to a comment from JonRichfield made on March 21, 2015

April 4, 2015

The supporters of the evolution industry and "big bang" cosmology industry are stuck with their dogma at a time when serious scientists have made more progress than most people could imagine.

The progress during the past decade links microRNAs to RNA-mediated cell type differentiation via amino acid substitutions in all cell types of all individuals of all genera. See: RNA society

See also: MicroRNA control of protein expression noise, which was reported as: MicroRNAs silence the noisy genome, and see the incessant denial of biologically-based facts in Our Cosmic Selves.

Review the obfuscating comments made by Jon Richfield (above). Place them into 1) the Biblical context of "Let there be light;" 2) the de novo creation of amino acids; and 3) the first self-replicating cell.

If viruses are the source of entropic elasticity, 1) the sun appears to supply the energy required for the creation of life and also 2) the anti-entropic energy for its maintenance. 3) The Biblical perfection of the first created self-replicating cell also appears to be pertubed by viruses.

The viruses are linked to physiopathology via the perturbed chemistry of biophysically constrained RNA-mediated protein folding that links metabolic networks and genetic networks to the morphological and behavioral phenotypes manifested in all extant and extinct biodiversity. Extinct biodiversity represents the failure to ecologically adapt.

For example, DNA repair of damage caused by viruses is nutrient-dependent. The nutrient-dependent physiology of reproduction enables the fixation of amino acid substitutions in the organized genomes of all individuals of all species that have ecologically adapted to variations in their epigenetic landscape.

If the de novo creation of the first cell came before viral microRNAs began to perturb the chemistry of protein folding, what is currently known about physics, chemistry, and the conserved molecualr mechanisms of RNA-mediated cell type differentiation makes sense.

The questions arise: Would Dobzhansky's claim to be both a creationist and an evolutionist force him to choose between the two if he 1) was not still dead, and 2) if he knew what is now known about viral microRNAs, nutrient-dependent microRNAs, and the RNA-mediated amino acid substitution he claimed differentiated the cell types of three primate species?

"...the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla" (p. 127). Nothing in Biology Makes Any Sense Except in the Light of Evolution

Is it possible that a single amino acid substitution differentiates all cell types of man and the chimpanzee? Or would that make too much sense?

Avatar of: Vladimir Matveev

Vladimir Matveev

Posts: 2

July 28, 2016

Vladimir Matveev. The great basic question of science: Membrane compartment or non-membrane phase compartment is a physical basis for origin of life? Oral presentation at The 2nd All-Russian Conference on Astrobiology. Moscow, Pushchino, 5-9 June 2016. Video in English: https://youtu.be/Hn7A-1w0tuQ   Presentation slides in English as pdf: http://www.bioparadigma.spb.ru/conf/Matveev-2016-The.great.basic.question.of.science_Eng_Slides.pdf   Comments for slides in English:  http://www.bioparadigma.spb.ru/conf/Matveev-2016-The.great.basic.question.of.science_Comments_Eng.pdf

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