New advances in abiogenesis

[shunyadragon]

New discoveries about natural Peptide formation an important step for RNA/DNA formation. The simplicity of the solution is amazing.

Source: https://www.vice.com/en/article/n7z4g8/scientists-breakthrough-origin-life-could-change-everything

Scientists Made a Breakthrough on Life’s Origin and It Could Change Everything


A new study shows that ingredients for life can form from non-living chemicals on any given beach, and it could help develop new drugs and search for alien life.
[IMG]https://video-images.vice.com/contributors/5846d2ab856950029f1efb93/lede/1596819376514-img0192-copy-2.jpeg?crop=0.5844xw:1xh;0xw,0xh&resize=100:*[/IMG]
By Becky Ferreira
October 3, 2022, 3:39pm

Scientists have achieved a major breakthrough toward unraveling the mystery of how life first arose on Earth and whether it might exist elsewhere in the universe, reports a new study.
A longstanding mystery—perhaps the mystery, existentially speaking—is how life originated from non-living, or abiotic, chemicals. For the first time ever, researchers at Purdue University have shown that peptides, which are strings of amino acids that are crucial building blocks of life, can spontaneously form in droplets of water during rapid reactions that occur when water meets the atmosphere—for example, when a wave hits a rock and throws up a misty spray. This could occur in conditions similar to those that existed on Earth some 4 billion years ago, when life first took hold on our planet.

The discovery provides “a plausible route for the formation of the first biopolymers,” which are complex structures produced by living organisms, according to a study published Monday in Proceedings of the National Academy of Sciences. The team says the discovery could even speed up the development of novel drugs and medical treatments by providing a new medium for fostering rapid chemical reactions.

“There are a very large number of studies showing peptide formation, but they all use catalysts or modified amino acids to make species unlikely to exist naturally,” said R. Graham Cooks, who serves as the Henry B. Hass Distinguished Professor of Analytical Chemistry at Purdue and senior author of the study, in an email.

Cooks and his colleagues have now shown that peptides readily form in the kinds of chemical systems that existed on ancient Earth, such as sea spray from our planet’s primordial oceans or freshwater dribbling down slopes.

“The most interesting implication is that similar chemistry explains other essential biological polymers, not just peptides,” he noted, adding that his team plans to publish more on this topic soon.

In other words, the new study has opened a rare window into the murky early years on our planet when nonliving compounds somehow assembled themselves into living organisms, a still-unexplained transformation known as abiogenesis. The formation of peptides is an important step in abiogenesis because these structures form the basis of biomolecules such as proteins, which can perform the self-replicating mechanisms that are necessary for life.

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[shunyadragon]

Source: https://theconversation.com/did-this-chemical-reaction-create-the-building-blocks-of-life-on-earth-216843

How did life begin? How did chemical reactions on the early Earth create complex, self-replicating structures that developed into living things as we know them?

According to one school of thought, before the current era of DNA-based life, there was a kind of molecule called RNA (or ribonucleic acid). RNA – which is still a crucial component of life today – can replicate itself and catalyse other chemical reactions.

But RNA molecules themselves are made from smaller components called ribonucleotides. How would these building blocks have formed on the early Earth, and then combined into RNA?

Chemists like me are trying to recreate the chain of reactions required to form RNA at the dawn of life, but it’s a challenging task. We know whatever chemical reaction created ribonucleotides must have been able to happen in the messy, complicated environment found on our planet billions of years ago.
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I have been studying whether “autocatalytic” reactions may have played a part. These are reactions that produce chemicals that encourage the same reaction to happen again, which means they can sustain themselves in a wide range of circumstances.

In our latest work, my colleagues and I have integrated autocatalysis into a well-known chemical pathway for producing the ribonucleotide building blocks, which could have plausibly happened with the simple molecules and complex conditions found on the early Earth.
The formose reaction


Autocatalytic reactions play crucial roles in biology, from regulating our heartbeats to forming patterns on seashells. In fact, the replication of life itself, where one cell takes in nutrients and energy from the environment to produce two cells, is a particularly complicated example of autocatalysis.

A chemical reaction called the formose reaction, first discovered in 1861, is one of the best examples of an autocatalytic reaction that could have happened on the early Earth.The formose reaction was discovered by Russian chemist Alexander Butlerov in 1861. Wikimedia
In essence, the formose reaction starts with one molecule of a simple compound called glycolaldehyde (made of hydrogen, carbon and oxygen) and ends with two. The mechanism relies on a constant supply of another simple compound called formaldehyde.

A reaction between glycolaldehyde and formaldehyde makes a bigger molecule, splitting off fragments that feed back into the reaction and keep it going. However, once the formaldehyde runs out, the reaction stops, and the products start to degrade from complex sugar molecules into tar.

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The formose reaction shares some common ingredients with a well-known chemical pathway to make ribonucleotides, known as the Powner–Sutherland pathway. However, until now no one has tried to connect the two – with good reason.

The formose reaction is notorious for being “unselective”. This means it produces a lot of useless molecules alongside the actual products you want.
An autocatalytic twist in the pathway to ribonucleotides


In our study, we tried adding another simple molecule called cyanamide to the formose reaction. This makes it possible for some of the molecules made during the reaction to be “siphoned off” to produce ribonucleotides.

The reaction still does not produce a large quantity of ribonucleotide building blocks. However, the ones it does produce are more stable and less likely to degrade.

What’s interesting about our study is the integration of the formose reaction and ribonucleotide production. Previous investigations have studied each separately, which reflects how chemists usually think about making molecules.Chemistry often focuses on clean, efficient and productive reactions, rather than messy combinations. Shutterstock
Generally speaking, chemists tend to avoid complexity so as to maximise the quantity and purity of a product. However, this reductionist approach can prevent us from investigating dynamic interactions between different chemical pathways.

These interactions, which happen everywhere in the real world outside the lab, are arguably the bridge between chemistry and biology.
Industrial applications.

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[shunyadragon]

Source: https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14507

Abiogenesis through gradual evolution of autocatalysis into template-based replication

Polina Pavlinova, Camille N. Lambert, Christophe Malaterre, Philippe Nghe
First published: 06 October 2022

https://doi.org/10.1002/1873-3468.14507
Polina Pavlinova and Camille N. Lambert are joint first authors

Edited by Claus M. Azzalin
Abstract


How life emerged from inanimate matter is one of the most intriguing questions posed to modern science. Central to this research are experimental attempts to build systems capable of Darwinian evolution. RNA catalysts (ribozymes) are a promising avenue, in line with the RNA world hypothesis whereby RNA pre-dated DNA and proteins. Since evolution in living organisms relies on template-based replication, the identification of a ribozyme capable of replicating itself (an RNA self-replicase) has been a major objective. However, no self-replicase has been identified to date. Alternatively, autocatalytic systems involving multiple RNA species capable of ligation and recombination may enable self-reproduction. However, it remains unclear how evolution could emerge in autocatalytic systems. In this review, we examine how experimentally feasible RNA reactions catalysed by ribozymes could implement the evolutionary properties of variation, heredity and reproduction, and ultimately allow for Darwinian evolution. We propose a gradual path for the emergence of evolution, initially supported by autocatalytic systems leading to the later appearance of RNA replicases.

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[Diogenes]

I find it quite humorous Man goes to so much trouble intelligently designing experiments when the crux of rejecting intelligent design (of any sort) is lack of agency. Of course, the broader problem is that the experiments are done under the assumption of early conditions. The hard empiricism often employed by atheists has to be jettisoned to smuggle in "best guesses" of early Earth environment.

[shunyadragon]

I find it quite humorous Man goes to so much trouble intelligently designing experiments when the crux of rejecting intelligent design (of any sort) is lack of agency. Of course, the broader problem is that the experiments are done under the assumption of early conditions. The hard empiricism often employed by atheists has to be jettisoned to smuggle in "best guesses" of early Earth environment.

The religious agenda of ID is not humorous it is tragic intentional ignorance.

Your reference to Intelligent Design is unclear. Intelligent Design is a theological hypothesis that the complexity of life cannot be explained by science in this case the origin of life. The design of experiments cannot take into consider claims of ID, because the claims of ID are not based on science. The claims are a negative assumption of what science is capable of explaining. The negative assumptions of the theological hypothesis of ID does not have "agency" of any sort The belief in ID is based on Divine Intelligent Creation not based on human intelligence. Human intelligence creates science.

The research concerning the chemical and physical environment of abiogenesis is not based on blind assumptions, but based on the assumption that Natural Laws and natural processes have consistent predictable properties that is the basis of scientific knowledge.

The referenced first known life is in rocks formed in hydrothermal vents are the same rocks forming now in hydrothermal events which is a known hydrothermal environment, The hydrothermal vents provide the energy and nutrients in an aqueous environment suitable for abiogenesis..The Continental drift that formed the spreading zones where hydrothermal vents formed occurred before the first evidence of life is found ~4.0 billion years ago. Based on the earliest life found in these rocks abiogenesis took place between ~3.6-3.9 billion years ago.

[rogue06]

I think the points is that 4 billion years ago the chemical composition of our atmosphere and any seas was likely profoundly different from what we now have, so everything is at best an educated guess.

[Diogenes]

I find it quite humorous Man goes to so much trouble intelligently designing experiments when the crux of rejecting intelligent design (of any sort) is lack of agency. Of course, the broader problem is that the experiments are done under the assumption of early conditions. The hard empiricism often employed by atheists has to be jettisoned to smuggle in "best guesses" of early Earth environment.

I have no problem with assumptions or best guesses, merely the inevitable incredulousness of using intelligently designed experiments to try to argue there is no God. The problem is not the science but rather the intentional distortion and abuse of the science.

[shunyadragon]

I think the points is that 4 billion years ago the chemical composition of our atmosphere and any seas was likely profoundly different from what we now have, so everything is at best an educated guess.

Yes the seas of the world were sterile and unsuitable for life and remained so until the beginning of the Tonian 1 billion years ago with some diversification of primitive tife life and more diversification in the Cryogenian ~720 million years ago. The geologic strata describes this hostile environment to life. Things began to change ~4 billions of years ago when continental drift began and the hydrothermal vents formed around the spreading zones. We can determine the environment of the seas, and land by analyzing the rocks, and to certain extent extrapolate the nature of the atmosphere, The rocks where the first life were found ~3.5 billion years ago was the same as the rocks forming around the hydrothermal vents throughout the the history of the earth since indicated a very consistent environment around the spreading zones suitable for abiogenesis and early life. Sort of the hot aqueous incubator for life on earth. Even the Cryogenian was a hostile world of extreme glaciation.

[rogue06]

Yes the seas of the world were sterile and unsuitable for life and remained so until the beginning of the Tonian 1 billion years ago with some diversification of primitive tife life and more diversification in the Cryogenian ~720 million years ago. The geologic strata describes this hostile environment to life. Things began to change ~4 billions of years ago when continental drift began and the hydrothermal vents formed around the spreading zones. We can determine the environment of the seas, and land by analyzing the rocks, and to certain extent extrapolate the nature of the atmosphere, The rocks where the first life were found ~3.5 billion years ago was the same as the rocks forming around the hydrothermal vents throughout the the history of the earth since indicated a very consistent environment around the spreading zones suitable for abiogenesis and early life. Sort of the hot aqueous incubator for life on earth. Even the Cryogenian was a hostile world of extreme glaciation.

The most hostile time might well have been during the Great Oxidation Event some 2.3 Billion years ago.

But the point is that we don't know much about conditions were like back then. For instance, we're still trying to figure out why the planet was warm during a time when the Sun was only producing something like 70% of the energy it now produces. A leading theory is that there was a LOT more methane in the atmosphere, but any evidence that this was the case is pretty scant.

[shunyadragon]

The most hostile time might well have been during the Great Oxidation Event some 2.3 Billion years ago.

But the point is that we don't know much about conditions were like back then. For instance, we're still trying to figure out why the planet was warm during a time when the Sun was only producing something like 70% of the energy it now produces. A leading theory is that there was a LOT more methane in the atmosphere, but any evidence that this was the case is pretty scant.

Yes, the e5ath in general was in hospitable to life, and al you say is true. The upper oceans and land remained sterile until much later. The problems you mentioned did not effect the origins and early evolution of life on the sea floor, which based on the evidence made the gradual evolution of life possible on the sea floor over more than a billion years The key for abiogenesis is the environment of the spreading zones with hydrothermal vents had a very consistent geochemical environment once the formed based on the chemistry of the rocks throughout the history of the spreading zones and the vents.to today,

[rogue06]

Yes, the e5ath in general was in hospitable to life, and al you say is true. The upper oceans and land remained sterile until much later. The problems you mentioned did not effect the origins and early evolution of life on the sea floor, which based on the evidence made the gradual evolution of life possible on the sea floor over more than a billion years The key for abiogenesis is the environment of the spreading zones with hydrothermal vents had a very consistent geochemical environment once the formed based on the chemistry of the rocks throughout the history of the spreading zones and the vents.to today,

Even so, the chemical composition of the oceans would be different given that they consist of H₂O and oxygen was in very support supply. What's more when oxygen levels increased it caused oxidation allowing iron and other metals to enter the waters.

IOW, the chemical composition of things aren't anything like they are now.

[shunyadragon]

Even so, the chemical composition of the oceans would be different given that they consist of H₂O and oxygen was in very support supply. What's more when oxygen levels increased it caused oxidation allowing iron and other metals to enter the waters.

IOW, the chemical composition of things aren't anything like they are now.

I already agreed with this, and yes, regardless of what we may know or not know about the oceans they hostile to life until the Siderian when anerobic cyanobacteria dominated in a world mostly without oxygen ~2.5 billion years ago. The abiogenesis of life and early evolution is dependent on the environment of the hyfrothermal vents not the ocean in general which is dependent on many factors,. The fossil evidence has demonstrated that about ~3.5 billion years ago there was life at the hydrothermal vents, and geochemical environment has been relatively constant since. .

[shunyadragon]

Even so, the chemical composition of the oceans would be different given that they consist of H₂O and oxygen was in very support supply. What's more when oxygen levels increased it caused oxidation allowing iron and other metals to enter the waters.

IOW, the chemical composition of things aren't anything like they are now.

I edited my previous post because of errors and it was incomplete.

Despite the unknowns we do know a lot about our oceans from the geochemical nature of the rocks, which gradually became dominated by oxygen from the evolution of life. I already agreed with the above, and yes, regardless of what we may know or not know about the oceans they were hostile to life ~3.5 billion years ago until the Neoarchean Era began to diversify the evolution of sea life. Life dominated the Siderian when anerobic cyanobacteria dominated in a world mostly without much oxygen ~2.5 billion years ago. The abiogenesis of life and early evolution is dependent on the environment of the hyfrothermal vents not the ocean in general which is dependent on many factors, The fossil evidence has demonstrated that about ~3.5 billion years ago there was life at the hydrothermal vents, and geochemical environment has been relatively constant since. .

As far as the subject of the thread let us focus on what we know about the geochemical nature and environment of the hydrothermal vents and the spreading zones of the ocean floor.

[rogue06]

I think my point is that we know enough to know that conditions were radically different then than they are now, but not enough to know what exactly those differences were, much less the role they would play. At this point it is still largely guesswork.

[shunyadragon]

I think my point is that we know enough to know that conditions were radically different then than they are now, but not enough to know what exactly those differences were, much less the role they would play. At this point it is still largely guesswork.

Because your responces are vague without specidic references I am not sure what your point is.

Your accusing science as guess work, and without more specifics than vague 'arguing from ignorance' your argument fails. I have a background geochemistry and yes a great deal of our past environments can be determined by the chemistry of the rocks, I believe my references have documented this concerning th ehisotry of the hydrothermal vents, Yo have at present offered nothing but vague speculations,

This research di not conclusively reach the conclusion of the origin of life, but id is a sound beginning that primitive life lived at this time under these conditions.

Source: https://sciworthy.com/3-42-billion-year-old-fossilized-microbes-in-an-ancient-hydrothermal-vent/

Scientists studying structures that might be fossils of very early life follow careful standards to assess whether or not the structures are truly fossilized microorganisms. The scientists who studied the 3.42 billion-year-old fossils from South Africa analysed the specimens visually using a light microscope. Then they analysed the chemical composition of the specimens using several techniques, including mass spectrometry, Raman spectroscopy, electron energy loss spectroscopy, and x-ray fluorescence spectroscopy.

The results of this suite of analyses indicated that the structures, which look like modern thread-like microorganisms, are made of fossilized organic matter. The fossilized organic matter on the outside of structures is chemically different from the fossilized organic matter on the inside of the structures. The scientists who discovered the microstructures suggested that these chemical differences are because the outer layer of fossilized organic matter was once a sheath or cell-wall, similar to what is seen in modern thread-like microorganisms.

The analyses further revealed the presence of nickel associated with the organic matter of these structures. Nickel is found in the enzymes that some modern microorganisms living in hydrothermal vents use to produce energy and grow. The scientists also studied the minerals that these structures were preserved within and found that they fossilized when a type of quartz deposited on the walls of the deep sea vents where the ancient microorganisms lived.

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References please . . .