Refuting Creationism - First Steps to Abiogenesis

Diagram of the atmospheric evolution of Earth's ancient atmosphere estimated by this study

© Yoshida et al.

Research News - How Life Began on Earth: Modeling Earth's Ancient Atmosphere | Tohoku University Global Site

The fact that living organisms arose on Earth from inorganic sources rather than being made of nothing by magic, is an indisputable fact because there are living organisms on Earth and the chemicals they are composed of all exist on the planet in inorganic minerals and gases. 'Life' contains nothing that 'non-life' doesn't contain.

This much we know, but what we don't yet know and can probably never know with certainty, is precisely how and where that happen. In fact, we don't even know whether it did all start in the same place at the same time because the reason there are two different prokaryote cells - bacteria and archaea - could be because life arose on Earth not once but twice, by two different processes in two different places at two different times.

What we have though is lots of working hypotheses in the process of being validated.

What role would Earth's atmosphere have played in abiogenesis? Earth's early atmosphere was crucial in creating the right conditions for abiogenesis—the process by which life originated from non-living matter. While the exact composition of Earth’s primordial atmosphere is still debated, its unique conditions likely contributed in several essential ways:

1. Provision of Basic Building Blocks
   
   • Earth’s early atmosphere likely contained simple molecules like methane (CH₄), ammonia (NH₃), hydrogen (H₂), carbon dioxide (CO₂), nitrogen (N₂), and water vapor (H₂O). These molecules are rich in carbon, nitrogen, oxygen, and hydrogen—elements that are vital for organic compounds and, ultimately, for life.
   • When exposed to energy sources like ultraviolet (UV) radiation from the Sun or electrical discharges from lightning, these molecules could recombine into more complex organic molecules, such as amino acids and nucleotides, which are the building blocks of proteins and nucleic acids, respectively.
   
   
2. Facilitation of Prebiotic Chemistry
   
   • Experiments like the famous Miller-Urey experiment in 1953 showed that simple gases (methane, ammonia, hydrogen, and water vapor) in an atmosphere subjected to electrical sparks could produce amino acids. This suggests that Earth’s early atmosphere could have been instrumental in initiating chemical reactions that synthesized complex organic molecules.
   • Without a protective ozone layer, the early atmosphere allowed substantial UV radiation to penetrate the Earth’s surface, providing the energy necessary to drive these prebiotic reactions.
   
   
3. Supporting a Reducing Environment
   
   • The presence of reducing gases (such as methane and ammonia) would favor the formation of organic molecules because such conditions prevent the oxidation (and hence destruction) of organic compounds. Oxygen is highly reactive and can break down organic molecules, so the absence of free oxygen in the early atmosphere was likely a key factor that allowed these molecules to accumulate and react.
   • This reducing environment might have helped organic compounds to survive long enough to form stable, self-replicating systems.
   
   
4. Encouraging Geochemical Interactions
   
   • The interaction between the early atmosphere and the oceans, along with geothermal activity like volcanic eruptions and hydrothermal vents, provided a diverse range of chemical environments. In particular, hydrothermal vents may have supplied essential minerals and additional energy sources, further driving complex chemical reactions that are believed to be important in the formation of life.
   • The cycling of materials between the atmosphere and oceans would have contributed to creating localized "hotspots" for prebiotic reactions.
   
   
5. Protection and Concentration Mechanisms
   
   • The atmosphere also played a protective role by preventing the immediate dissipation of important compounds into space. It allowed the concentration of molecules and gases at Earth’s surface, increasing the chances of interactions among the essential precursors to life.
   • Early atmospheres may have helped regulate surface temperatures, preventing extreme fluctuations that would have been hostile to complex chemistry.
   
   
6. Encouraging Self-Organization and Membrane Formation
   
   • Interactions in the early atmosphere could have contributed to the formation of lipid molecules that could aggregate to form primitive cell-like structures or vesicles. These structures would eventually help in containing and protecting reactions necessary for early metabolic pathways.
   • These early "proto-cells" or vesicles would have been necessary to create a boundary for molecular interactions, which is a critical step toward the organization needed for cellular life.

In summary, Earth’s early atmosphere provided a chemically conducive, energetically rich environment that fostered the synthesis and concentration of organic molecules necessary for abiogenesis. This atmosphere also shielded these nascent molecules, allowing them to organize and evolve toward increasingly complex systems, eventually leading to the first living organisms.

One of which is the precise details of the atmosphere on the Early Earth, which is important because it would have had a major impact on the rest of the environment in which life arose. To gain a better understanding of that, a team from Tohoku University, Tokyo University and Hokkaido University, Japan, led by Tatsuya Yoshida have succeeded in modelling that atmosphere, as explained in a Tohoku University press release and published in the journal Astrobiology:

How Life Began on Earth: Modeling Earth's Ancient Atmosphere

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The key to unlocking the secrets of distant planets starts right here on Earth. Researchers at Tohoku University, the University of Tokyo, and Hokkaido University have developed a model considering various atmospheric chemical reactions to estimate how the atmosphere - and the first signs of life - evolved on Earth.

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Ancient Earth was nothing like our current home. It was a much more hostile place; rich in metallic iron with an atmosphere containing hydrogen and methane.

Shungo Koyama, co-author
Graduate School of Science
Tohoku University, Sendai, Japan.

These molecules contain an important clue to how life was initially formed. When exposed to solar ultraviolet (UV) radiation, they undergo a chemical reaction that produces organics (also known as the "building blocks of life"). Part of these organics were precursors to essential biomolecules, such as amino acids and nucleic acids. However, understanding the role of UV radiation is difficult. Firstly, this type of atmosphere is unstable and likely underwent rapid changes due to atmospheric chemical reactions. Secondly, when UV radiation efficiently breaks down water vapour in the atmosphere and forms oxidative molecules, the precise branching ratio and timescale has not been determined. In order to address these issues, a 1D photochemical model was created to make accurate predictions about what the atmosphere was like on Earth long ago.

The calculation reveals that most hydrogen was lost to space and that hydrocarbons like acetylene (produced from methane) shielded UV radiation. This inhibition of UV radiation significantly reduced the breakdown of water vapour and subsequent oxidation of methane, thus enhancing the production of organics. If the initial amount of methane was equivalent to that of the amount of carbon found on the present-day Earth's surface, organic layers several hundred metres thick could have formed.

There may have been an accumulation of organics that created what was like an enriched soup of important building blocks. That could have been the source from which living things first emerged on Earth.

Tatsuya Yoshida, lead author
Graduate School of Science
Tohoku University, Sendai, Japan.

The model suggests that the atmosphere on ancient Earth was strikingly similar to what we see on current day neighbouring planets: Venus and Mars. However, despite their proximity, Earth evolved into a completely different environment. Researchers are trying to understand what makes Earth so special. As such, this model allows us to deepen our understanding of whether atmospheric evolution and the origin of life on Earth are unique or share common patterns with other planetary systems.

These findings were published in the journal Astrobiology on October 22, 2024.

Publication Details:

Tatsuya Yoshida, Shungo Koyama, Yuki Nakamura, Naoki Terada and Kiyoshi Kuramoto
Self-Shielding Enhanced Organics Synthesis in an Early Reduced Earth's Atmosphere Astrobiology DOI: 10.1089/ast.2024.0048

Abstract
Earth is expected to have acquired a reduced proto-atmosphere enriched in H₂ and CH₄ through the accretion of building blocks that contain metallic Fe and/or the gravitational trapping of surrounding nebula gas. Such an early, wet, reduced atmosphere that covers a proto-ocean would then ultimately evolve toward oxidized chemical compositions through photochemical processes that involve reactions with H₂O-derived oxidant radicals and the selective escape of hydrogen to space. During this time, atmospheric CH₄ could be photochemically reprocessed to generate not only C-bearing oxides but also organics. However, the branching ratio between organic matter formation and oxidation remains unknown despite its significance on the abiotic chemical evolution of early Earth. Here, we show via numerical analyses that UV absorptions by gaseous hydrocarbons such as C₂H₂ and C₃H₄ significantly suppress H₂O photolysis and subsequent CH₄ oxidation during the photochemical evolution of a wet proto-atmosphere enriched in H₂ and CH₄. As a result, nearly half of the initial CH₄ converted to heavier organics along with the deposition of prebiotically essential molecules such as HCN and H₂CO on the surface of a primordial ocean for a geological timescale order of 10–100 Myr. Our results suggest that the accumulation of organics and prebiotically important molecules in the proto-ocean could produce a soup enriched in various organics, which might have eventually led to the emergence of living organisms.

Yoshida, Tatsuya; Koyama, Shungo; Nakamura, Yuki; Terada, Naoki; Kuramoto, Kiyoshi
Self-Shielding Enhanced Organics Synthesis in an Early Reduced Earth’s Atmosphere Journal of Astrobiology (2024) DOI: 10.1089/ast.2024.0048

© 2024 Mary Ann Liebert, Inc.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.

So, by the action if UV radiation from the sun on the inorganic molecules in Earth's early atmosphere for a period of some 10-100 million years, the oceans could have accumulated the basic building blocks for organic organisms to get started, and all th result of chemistry and physics with no magic gods involved at any point.

And, as usual with scientific discoveries, the truth is shown to have little resemblance to the origin myths the parochial Bronze Age pastoralists made up to fill the yawning chasm in their knowledge and understanding of the world around them, with their belief that Earth had only existed for a few thousand years, so were blissfully ignorant of the 99.9975% of its history that occurred before then.

Refuting Creationism - LUCA Had Evolved 4.2 Billion Years Ago And Already Suffered From Viral Parasites

A digital representation illustrating how LUCA was already under attack from viruses even at 4.2 billion years ago.

Science Graphic Design

A digital representation illustrating how LUCA was already under attack from viruses even at 4.2 billion years ago.

Science Graphic Design

July: LUCA | News and features | University of Bristol

Contrary to the Bible's laughable model of a 10,000-year-old universe consisting of a small flat planet with a dome over it, containing nothing that was unknown to the Bronze Age hill farmers whose best guess became part of the Hebrew creation myth, scientists at the University of Bristol have shown that the last universal common ancestor of all living organisms (LUCA) had evolved within 400 million years of Earth forming some 4.6 billion years ago.

They have calculated that LUCA was about as complex as a prokaryote, had already evolved an immune system and was engaged in an arms race with viruses.

Abiogenesis News - RNA's Hidden Potential & Role In Early Cells

Ribozyme

RNA's Hidden Potential: New Study Unveils Its Role in Early Life and Future Bioengineering | Tokyo University of Science

In a recent open access paper in the online journal, Life, a Tokyo University of Science team led by Professor Koji Tamura of the Department of Biological Science and Technology, has given support to the 'RNA World' hypothesis that explains the beginnings of self-replicating organisms as self-catalysing RNA assemblies known as 'ribozymes'.

Ribozymes have the ability to catalyse the production of new ribozymes, so overcoming the 'problem' for abiogenesis that proteins are needed to catalyse the assembly of DNA but DNA is needed to create proteins, leading to a classic 'chicken and egg' paradox. Since ribozymes don't need proteins, this solves the problem.

How Professor Tamura' team did this is the subject of a Tokyo University of Science news release:

Creationism in Crisis - Closing The Last God-Shaped Gap - How The Simplest Cells Could Have Evolved, Naturally

Last Chance Lake in British Columbia

Credit: Zachary R. Cohen

Last Chance Lake in September 2022. At the end of the summer, the water has almost all evaporated, leaving a salty crust on the surface.

Credit: Zachary R. Cohen/Washington University

Did the first cells evolve in soda lakes?

According to a new study by Zachary R Cohen of the Chemistry Department of Washington University, Seatle, WA, USA and colleagues, soda lakes which are rich in sodium and carbonates could have provided the right conditions for the simplest, RNA-based cells to have arisen.

It is widely assumed that the earliest simple cells were based on RNA enclosed in a lipid membrane but there is a problem in that RNA requires divalent ions such as Magnesium (Mg²⁺ to function, but Mg²⁺ damages lipid membranes, so it isn't easy to explain how they could have co-existed within the same cell structure.

So the question is whether the low levels of (Mg²⁺ found in soda lakes, such as the Last Chance Lake in British Columbia, Canada, could have provided the right conditions of enough (Mg²⁺ for RNA to function but not so much as to prevent the formation of an enclosing membrane.

To explore this possibility, Zachary Cohen and his colleagues collected water from Last Chance Lake and the similar but subtly different Goodenough Lake after seasonal evaporation. According to information from Washington University published in phys.org:

These soda lakes each contained ~1 M Na⁺ and ~1 mM Mg²⁺ at pH 10. The authors found that spontaneous extension of short RNA primers occurred in lake water at a rate comparable to the rates in standard laboratory conditions.

The authors added fatty acids, which could have been available on the early Earth, to the lake water to see if the molecules would assemble into membranes. The membranes formed in dilute water that simulates a rainfall event, and the membranes persisted even when surrounded by concentrated lake water from the dry season.

According to the authors, soda lakes on the early Earth could have supported key features of protocell development, with RNA copying and ribozyme activity taking place in the dry season and vesicle formation occurring during the wet season.

The scientists give more technical details in their open access paper in PNAS Nexus:

Abiogenesis News - New Evidence For The 'RNA World' Hypothesis

Hammerhead sequences copied by the lower-fidelity polymerase drift away from their original RNA sequence (top) and lose their function over time. Hammerheads catalyzed by the higher-fidelity polymerase retain function and evolve fitter sequences (bottom).

Credit: Salk Institute

Stylized rendering of the full-length hammerhead ribozyme RNA molecule

Source: Wikipedia

Modeling the origins of life: New evidence for an “RNA World” - Salk Institute for Biological Studies

On way of looking at cellular life is that it is based on RNA, not DNA. In that model, DNA is RNA's data store. All the functional processes that DNA codes for are first transcribed into RNA and short lengths of RNA still regulate some of the cell processes. RNA can even act as a catalyst playing the role normally performed by protein enzymes - proteins that are themselves transcriptions of RNA triplet codes for amino acid sequences.

On that model, early self-replicating systems were based on RNA, and DNA was late to the game.

Now three researchers at the Salk Institute for Biological Studies, La Jolla, California, USA, have shown how such a system could have bootstrapped from simple, self-catalysing lengths of RNA which not only self-replicate but can continue to do so even when there are variations stemming from faulty replications. This system would have created the variation needed for Darwinian evolution by natural selection as some variant performed better in terms of competing for resources and ultimately making more copies, so coming to predominate in the pool of RNA-based organisms.

How the scientists discovered this is the subject of a research paper in PNAS which sadly is behind a paywall with only the abstract and statement of significance freely available. It is also the subject of a news release from the Salk Institute.

Since the team refer to an RNA structure known as the 'hammerhead ribozyme', it might help to understand a little about it first:

Abiogenesis News - That God-Shaped Gap Just Keeps On Shrinking

Scripps Research scientists reveal how first cells could have formed on Earth | Scripps Research

It's been a bad week so far for creationists. Coming so soon after scientist announced they had solved the 'chirality problem, is news that another team have shown how simple cells could plausibly have formed in the pre-biotic conditions that pertained on early Earth.

Creationists are generally black & white thinkers who value certainty above truth, so, for them there is no such thing as a plausible explanation; either something is proven beyond doubt, even passing an especially impossible standard of evidence, or it is wrong (so God did it!).

And one of their 'certainties' is their absolute faith in the slogan, "You can't get life from non-life!", which is chanted like a protective mantra in any debate about evolution (conveniently switching the debate from evolution to what they think is safer ground, abiogenesis). But ask them to define 'life' in such a way that you can test for it to tell if something is alive or not, or to explain how the non-living food they eat gets converted into living tissues, if that's impossible, and you're likely to get an ad hominem or an indignant, condescending flounce and a swift termination of the conversation.

It is an essential ingredient of creationism that the belief that abiogenesis is 'impossible' be maintained as the last refuge for their ever-shrinking creator god to be located in, as all the other gaps are closed to it.

So, having committed themselves to the certainty that abiogenesis is 'impossible', they have unwittingly committed themselves to accepting that any plausible process which can be shown to be viable, refutes the notion of impossibility and everything they conclude from it. So, their next step is the intellectually bankrupt technique of moving the goal-posts or demanding scientist provide an impossible standard of evidence such as showing it happening - billions of years ago. Never will they concede that evidence of plausibility refutes the claim of impossibility because, to a black & white thinker, plausibility doesn't give enough certainty, so can be dismissed until proven.

So, we can expect that predictable display of intellectual bankruptcy in response to the news that scientists at the Scripps Institute, La Jolla, CA, USA have discovered a plausible mechanism for the formation of simple self-replicating cells in the prebiotic conditions that pertained on early Earth.

Their findings are published in the Cell Press journal Chem and are the subject of a Cripps Institute press release:

Creationism in Crisis - Biological Chirality Explained - And Another Favourite Creationist Gap Slams Shut With No God(s) Found

How molecular “handedness” emerged in early biology | Scripps Research

Back in the 1980's when I first encountered (mostly) American creationists on the emerging Internet, one of their arguments from personal incredulity was that 'no-one can explain' why amino acids occur naturally in two stereo forms, yet only one is found in nature (therefore God did it!).

This 'problem' for evolutionary biologist now seems to have dropped out of favour with creationists, probably because, as more and more former creationists realise they've been fooled, only the lower tail-end of the IQ bell curve remain, and this phenomenon, known as chirality, is a little difficult to understand and requires a modicum of understanding of chemistry.

Basically, at the heart of an amino acid is a carbon atom with four different atoms of groups attached. This structure can be thought of as a pyramid with a triangular base (known as a tetrahedron) with the carbon atom in the centre and each of the four atoms or groups at each point of the tetrahedron. These groups can be attached to the carbon in two separate ways so that one is a mirror image of the other. These are known as chiral forms or stereo-isomers. No matter how you rotate one, it can never be the same as its opposite chiral form.

These chiral forms have the same chemical properties and the same physical properties apart from one - the way they interact with polarised light. One form causes the plane of polarity of polarised light to rotate in one direction, the other in the other direction; so they are also known as optical isomers.

The chiral forms of amino acids are prefixed with 'D' or 'L' (upper case; Dextro and Laevo (right and left)) according to the physical structure, or 'd' and 'l' (lower case) according to which direction they rotate the plane of polarity of polarized light.

ChatGPT explains it more succinctly:

Abiogenesis News - Closing Creationism's Favourite Gap On Their Ever-Shrinking Little God

Hot Springs in Yellowstone National Park

Credit: iStock / tomolson54

Hot Spring in Yellowstone National Park.

Credit: iStock / tomolson54

Compound vital for all life likely played a role in life’s origin | UCL News - UCL – University College London

Abiogenesis is the gap creationists prefer to shoehorn their ever-shrinking little god into because they feel safer placing it there, believing that they have an unarguable claim that 'you can't get life from non-life'. Hilariously, you can sow confusion in their smug certainty in two simple ways:

1. Ask them to define 'life' and state whether it is a substance, a process or something else, because it only takes a moment's thought to realise 'life' is what we call the metabolic processes that organic molecules perform, so is simply the laws of chemistry and physics in operation. There is no magic ingredient needed.
2. Ask them what happens when the non-living food they eat becomes living tissues during the processes of digestion and assimilation if it is 'impossible'?

Their claim is nonsense of course; it's simply slogan delivered in response to trigger words which creationists no more understand than a parrot understands the meaning of the words it squawks.

There is nothing in the laws of chemistry or physics that makes abiogenesis impossible; given the right conditions there is no reason the inorganic chemicals present on the early Earth couldn't build more complex molecules or why those molecules couldn't perform the necessary processes to grow, repair and replicate. And once replication is possible, then selection would have been inevitable, and with selection, the processes which performed best would inevitably produce more copies.

Of course this can't be replicated easily in a laboratory because what no laboratory process can replicate is the long period of time, possibly millions of years, the process had on the early Earth, but what scientists can do is show that essential molecules to kick-start the processes could have arisen on the early Earth in the conditions that pertained then.

This is exactly what a team from University College London have shown in respect of a molecule which is the functional unit of one of the basic enzymes involved - Coenzyme A. The molecule is pantetheine. In earlier studies, pantetheine failed to be produced leading some to think that it would not have formed on early Earth and would therefore be absent and unable to play its essential role in metabolism.

Molecular structure of pantetheine

Closing In On Abiogenesis - How Amino Acids Become Peptides in Water Droplets - No Magic Required

Professor R. Graham Cooks has studied the chemistry of water droplets for decades, discovering insights into cancer detection, drug discovery and early Earth chemistry.

Purdue University file photo/Andrew Hancock

A tripeptide (example Val-Gly-Ala) with green marked amino end (L-valine) and blue marked carboxyl end (L-alanine)

Chemistry professor R. Graham Cooks expands research of water droplet interfaces that offer the secret ingredient for building life - Purdue University Department of Chemistry

One of the puzzles of how the earliest proteins were built from amino acids was that the reaction of joining two amino acids together is a condensation reaction in which a molecule of water is eliminated when the -C-OH of one amino acid binds to the H₂N-C- of the other amino acid in what is known as a peptide bond:

-C-OH + H₂N-C- → -C-NH-C + H₂O;
but how could this happen in an aqueous solution?

In 2022, Professor R. Graham Cooks' team at Purdue University found the answer: It is due to the peculiar properties at the surface of droplets of water. Because of the way electrostatic forces align the water molecules at the surface, it behaves as though it is extremely dry, and highly acidic. These conditions provide the perfect conditions for a condensation reaction to occur, resulting in a peptides.

Droplets of water are everywhere in nature, from the spray of breaking waves, the splash of raindrops, waterfalls, trickling streams to aerosols of water in clouds and fog.

And Professor Cooks's team at Purdue have now shown that these conditions also occur at the macro, centimeter scale as water evaporates on, for example rocks or the margins of hydrothermal pools. They have also shown that these reactions, in the presence of oxazolones (produced by the dehydration of amino acids) preserve the chirality of the peptides so the resulting peptides are 'L' enantiomers, as found in all living organisms.

As the Purdue University press release says:

The study adds to the body of evidence that the surface of water drops represents a uniquely active physical and chemical system. Present are very high electric fields and extreme acidity that drives dehydration of amino acids to form peptides. Studies of the chemistry at water droplet interfaces offer new insights into the early stages of life's chemical evolution.

Significance

This study provides experimental evidence identifying oxazolones as the key intermediates in prebiotic peptide synthesis. These compounds yield the dipeptides upon reaction with water and generate tripeptides in the presence of other amino acids. These key steps in protein formation occur in pure water droplets. Amino acid chirality is preserved in forming the oxazolone and the addition of amino acids during peptide chain extension shows a strong chiral preference, viz. the aqueous droplet chemistry represents a simple route to chirally pure polypeptides. A direct connection between this intermediate and the dipeptide isomer, oxazolidinone, is demonstrated by simple hydration/dehydration. The oxazolone/oxazolidinone-mediated mechanism also occurs in macroscopic wet–dry cycling, establishing a strong connection between macroscopic and microscopic peptide synthesis.

Abstract

Peptide formation from amino acids is thermodynamically unfavorable but a recent study provided evidence that the reaction occurs at the air/solution interfaces of aqueous microdroplets. Here, we show that i) the suggested amino acid complex in microdroplets undergoes dehydration to form oxazolone; ii) addition of water to oxazolone forms the dipeptide; and iii) reaction of oxazolone with other amino acids forms tripeptides. Furthermore, the chirality of the reacting amino acids is preserved in the oxazolone product, and strong chiral selectivity is observed when converting the oxazolone to tripeptide. This last fact ensures that optically impure amino acids will undergo chain extension to generate pure homochiral peptides. Peptide formation in bulk by wet-dry cycling shares a common pathway with the microdroplet reaction, both involving the oxazolone intermediate.

Qiu, Lingqi; Cooks, R. Graham
Oxazolone mediated peptide chain extension and homochirality in aqueous microdroplets
Proceedings of the National Academy of Sciences (PNAS) 121(2). DOI: 10.1073/pnas.2309360120

© 2024 PNAS.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.

And so that day that creationist frauds must be dreading, when science finally closes their favourite gap in which to force-fit their ever-shrinking little god finally slams as shut as all the other gaps it used to occupy in the minds of scientifically illiterate believers, gets a little closer. Only yesterday we learned how simple metabolic biochemical cycles can be produced from simple precursors, all of which were present on the pre-biotic Earth and without protein enzymes, and here we see how the proteins that could catalyse and improve those processes could also arise from simple precursors that were also present.

I wonder what disinformation the frauds who feed pseudo-science to the creation cult are preparing for that eventuality.

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Abiogenesis News - Scientists Harness The Massive Computing Power of Blockchain Technology To Show How Metabolic Processes Arose

[left caption]

[Right caption/credit]

Chemists use the blockchain to simulate over 4 billion chemical reactions essential to the origins of life | ScienceDaily


As though to give a two-fingered salute to those creationist frauds who tell their dupes that scientists are turning their back on materialism and accepting that magic creation is a better explanation for abiogenesis and evolution than the operation of the laws of chemistry and physics, scientists from the Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland with colleagues in IBS Center for Algorithmic and Robotized Synthesis, Ulsan, South Korea, have used the massive computing power of blockchain technology to simulate all possible reactions between pre-biotic chemicals such as water, methane and ammonia and their products, and shown that simple metabolic processes such as the citric acid cycle can arise without enzymes.

A few of these metabolic cycles were found to be capable of self-replication (believed to be a prerequisite for evolution) but these were comparatively few in number, so the scientists believe they may not have played a significant part on early abiogenesis.

These primitive metabolic processes could have provided the necessary energy for more complex processes to evolve including enzymes, each of which, if it catalyzed the reactions in the metabolic cycles, would have given it additional advantage and been quickly incorporated into the process.

the The scientists have published their findings in the Cell Press journal Chem and explain their research in a Cell Press news release.

First, a brief AI explanation of blockchain technology and its use in cryptocurrencies:

Abiogenesis News - Going! Going! Gone! - How Creationism Favourite Gap Just Got Smaller

Geothermal hot spring in Haukadalur Valley, Iceland

ancient hot springs - Press Office - Newcastle University

Hardly any debate about evolution with a creationist will go more than a few exchanges before the creationist gives up trying the traditional fallacies and avoidance tactics and falls back onto ground he or she feels safer on - abiogenesis - with the demand that you explain how the first cell arose fully developed, with the parrot squawk assertion that 'you can't get life from non-life'.

But ask them to define 'life' and they'll break off the debate because it's a term creationists think involves something that science can't explain, but they've no idea what it is or why it should present science with a problem. Ask them to explain how dead food becomes living tissue through the process of digestion and metabolism, if it's impossible, and you probably won't hear from them again.

The gap creationists are trying to shoehorn their favourite creator god into is what they've been programmed to believe is unclosable by science, so it must have been done by the locally popular god. They will of course be unaware of the fallacy of the false dichotomy because it's probably what someone fooled them with, so they just assume it'll work on everyone else.

Creationism in Crisis - A French 7-Year Scientific Program To Disover The Origin Of Life!

Aerial view of the construction site of the Extremely Large Telescope (ELT) in the Atacama Desert, Chile.

© G. Hüdepohl (atacamaphoto.com)/ESO

Investigating the origins of life | CNRS News

Although it's nothing to do with evolution, which is the science of how living organisms respond to environmental pressures and diversify over time, abiogenesis is a favourite of creationists because they imagine, without being able to define 'life', that it must involve some magical, God-given quality that turns 'non-life' into 'life'. But then when did facts bother creationists?

So it must be disconcerting to those of them who are still in touch with reality, that 28 French scientific organisations, involving over 100 scientists, have formed a partnership (Programme et Équipement Prioritaire de Recherche - PEPR) led by the Centre National de la Recherche Scientifique (French National Center for Scientific Research - CNRS) to research into the origins of life, not only on Earth but on other planets. The project is already being known as 'Origins'.

According to the CNR News release by Mehdi Harmi:

Creationism in Crisis - Scientists Show LUCA (Last Universal Common Ancestor) Lived 4.32-4.52 Billion Years Before 'Creation Week'

Figure 1: A schematic tree of life with the primary domains, the Archaea and Bacteria shown in purple and blue, respectively and the secondary domain, Eukaryotes in green. The figure highlights key nodes in the tree of life that have been calibrated against absolute time scales of Earth history. Estimates are given in Ga referring to billions of years (or giga annum).

Looking for ‘LUCA’ and the timing of cellular evolution - NIOZ

My previous two blog posts dealt firstly with the discovery of Neanderthal art in a cave in France which had been sealed with river debris since at least 40,000 years before creationism's supposed 'Creation Week' and secondly with the discovery of fossil trilobites in Thailand in rocks independently dated to about 490 million years before 'Creation Week'.

This one is bound to send creationists into deep denialism, shouting abuse at the fact and bearing false witness against the scientists who discovered it; it is the dating of the Last Universal Common Ancestor (LUCA), i.e., the primitive free-living organism from which all life on Earth is descended, to between 4.32 and at the most 4.52 billion years ago, in other words, to soon after Earth was really formed.

This of course means that abiogenesis occurred quite quickly once Earth had coalesced from the accretion disc around the new sun and had recovered from the collision with another minor planet which gave rise to the moon and tilted Earth on its axis.

Biologists Tara Mahendrarajah of the Royal Netherlands Institute for Sea Research (NIOZ) and senior author Anja Spang discovered this, in collaboration with colleagues from Universities in Bristol, Hungary and Tokyo.

The research is published open access in Nature Communications and is explained in an NIOZ press release entitled "Looking For 'LUCA' and the timing of cellular evolution":

Creationism in Crisis - Biochemists are Homing In On Abiogenesis

Deep-sea hydrothermal vent chimney from the Mid-Atlantic Ridge. Many new microbial genomes have been described from these environments.

Credit: Anna-Louise Reysenbach and Woods Hole Oceanographic Institution

Did this chemical reaction create the building blocks of life on Earth?

Scheme 2 Some pathways for the proposed reaction network of formose intermediates and cyanamide based on the autocatalytic cycle proposed by Breslow³² and experiments herein. It is hypothesised that the formation of tetrose and pentose aminooxazolines via the addition of 2-NH2Ox with glycolaldehyde and glyceraldehyde (gray dashed arrows), respectively, is likely not the dominant pathway as originally hypothesised in Scheme 1. See ESI Table S3† for more proposed structures. Note, that although the Breslow autocatalytic cycle is shown for simplicity, the full reaction network is much more complex; see ref. 30, 41 and 42.

Tran, Quoc Phuong; Yi, Ruiqin; Fahrenbach, Albert C.(2023)

Stand by for another bout of petulant histrionics from creationists when biochemists and biophysicists finally work out how a self-replicating molecule could have arisen on Earth, then, through a process of evolution by natural selection, gradually improved its efficiency until free-living, self-replicating organisms emerged. The traditional anti-science rhetoric normally includes abusing the scientists, misrepresenting their findings, and claiming it proves intelligence was needed.

It is generally assumed that this process took place in deep ocean hydrothermal vents, or 'black smokers' where the right chemicals and catalysts were present with sources of energy in the form of geothermal heat, and a rich chemical soup of the basic ingredients needed. It is also assumed that the earliest forms of self-replicating organisms were RNA- based, and only became DNA-based later on. In fact, there is a school of thought that says living things are still essentially RNA-based, using DNA as a data store, since DNA is always transcribed into its RNA counterpart to be useful to a cell in transporting amino acids and producing proteins.

Whatever the final pathway turns out to have been, we can be sure it all started with a relatively simple, self-catalyzing molecule, that just needs a supply of the right raw materials to proceed, and there is a simple chemical reaction, known as the formose reaction, that we have known about since 1861 which fits that requirement. Basically, the formose reaction is where the molecule glycolaldehyde, given a supply of formaldehyde, will keep producing copies of itself and will only stop when the supply of formaldehyde runs out.

The following article by Quoc Phuong Tran a PhD Candidate in Prebiotic Chemistry at the University of New South Wales, Sydney, Australia, is reprinted from The Conversation under a Creative Commons license, reformatted for stylistic consistency. In it, he discusses this reaction and the role it could have played in abiogenesis:

Creationism in Crisis - Signs of Life on an Exoplanet 120 Million Lightyears Away.

This illustration shows what exoplanet K2-18 b could look like based on science data. K2-18 b, an exoplanet 8.6 times as massive as Earth, orbits the cool dwarf star K2-18 in the habitable zone and lies 120 light years from Earth.
In this illustration, the exoplanet K2-18 c is shown between K2-18 b and its star.

Nikku Madhusudhan (IoA)/NASA, ESA, CSA, Joseph Olmsted (STScI)

Webb Discovers Methane, Carbon Dioxide in Atmosphere of K2-18 b | NASA

Abiogenesis, like the conditions that produced the Big Bang, is one of creationism's favourite gaps in which they try to fit their ever-shrinking little god and play their false dichotomy fallacy - if science can't explain it, "God did it!".

That ploy depends for its success of a couple of things, not the least of which are scientific illiteracy and cultural chauvinism of their target dupes. Creationists, while telling their targets that science can't explain how abiogenesis occurred, then pretend they know anyway and have calculated the probability of it. Of course, without knowing the precise conditions and chain of events, it is impossible to do that calculation, but nevertheless, creationist frauds will confidently proclaim it to be infinitesimally small.

However, if the precise mechanism were known, and the conditions could be replicated (temperature, pressure, catalysts, chemicals and time) the mechanism would not be impossible, it would be inevitable (i.e., certainty) since it is a basic principle of chemistry that if the conditions are right, a reaction will occur. No ifs or buts, it will occur since chemical reactions are not governed by laws of probability but by laws of physics. No chemist has ever needed to set up ten thousand test tubes to ensure at least one will produce the expected result. He/she would get ten thousand identical results.

But now, as scientists improve their ability to detect and examine the atmosphere of distant exoplanets orbiting other suns in the galaxy, so they are improving their ability to detect the inevitable signs of life on those planets and many people think it is only a matter of time before we have strong evidence of life elsewhere in the universe.

Abiogenesis News - Self Organising Organic Molecules Add Another Possibility to The Theory of Abiogenesis

A new model describes the self-organization of catalysts involved in metabolic cycles. Different species of catalysts (represented by different colors) form clusters and can chase each other.

© MPI-DS / LMP

Fig. 4: Oscillatory dynamics for an odd number of species with chasing cross-interactions.

A schematic representation of the oscillatory dynamics (left), snapshots of molecular dynamics simulations (middle, see also Supplementary Movie 8), and a diagram of the corresponding species interactions and pairing (right) are shown side by side. Here, dashed and dotted lines represent respectively the pairs on the left and right of the schematic representation. The eigenvalues of the system are as in Fig. 3b, but now Re(λ)<Im(λ) for the most unstable conjugate pair, so that the dynamics of the system are oscillatory.

Ouazan-Reboul, V., Agudo-Canalejo, J. & Golestanian, R. (2023).

Exploring the origins of life | Max Planck Institute for Dynamics and Self-Organization

Creationists would have us believe that science can't explain how 'life' arose from 'non-life', as though 'life' is some magical, mysterious substance, which, when added to inorganic chemicals, turns them into organic, living, substances. whereas of course, 'life' is simply a term for the active metabolic processes that resist entropy by using the energy stored in organic molecules, involving nothing more than the operation of the laws of chemistry and physics. That energy ultimately comes from the sun via photosynthesis, or, more rarely, geothermal energy via chemosynthesis.

What is life?

The question for science then, is how did inorganic molecules become organised in such a way that they can carry out these metabolic processes, and for that there is almost an embarrassment of explanations, most of which require conditions and time that would be impossible to replicate in a laboratory.

For a plausible ten-step process towards abiogenesis, see: Perfectly Plausible Abiogenesis.

And now to add more to the embarrassment of riches that is the growing science of abiogenesis, scientists from the Max Planck Institute for Dynamics and Self-Organization (MPI-DS), Göttingen, Germany have shown in two studies that catalytic molecules can form metabolically active clusters by creating and following concentration gradients.

As explained in an MPI-DS news release:

Abiogenesis News - Urea May Have Been The Precursor to Life.

Potential witness to the origins of life: a urea dimer.

Visualisations: Adobe Stock / Montage

Why urea may have been the gateway to life | ETH Zurich

Artist's impression of the pre-biotic Earth.

A new technique for observing chemical reactions with an extremely high temporal resolution has enabled Swiss scientists working at Eidgenössische Technische Hochschule, Zürich (ETH Zürich) and Geneva University to see what happens when urea in water is subject to ionizing radiation - the conditions that would have existed on pre-biotic Earth, billions of years ago.

The dominant theory explaining abiogenesis is that it took place around deep ocean hydrothermal vents, or black smokers, but a rival theory, which harks back to Darwin's 'warm little pond', is that it could have occurred in shallow pools subjected to ionizing radiation from the sun. The team's observation of how urea reacts lends support to the latter theory.

Urea is a highly reactive molecule that exists in concentrated solutions as a dimer (two molecules chemically bonded). The researchers observed that ionizing radiation causes a hydrogen ion (i.e., a proton, which carries a positive charge) to move from one molecule in the dimer to the other, creating a negatively charged urea^- radical from one molecule and a protonated urea⁺ molecule from the other. The former is highly reactive and can then form malonic acid - believed to be the first step in creating larger molecules such as RNA. This happens so fast (in about 1 femtosecond, or 150 billionths of a second) that it effectively monopolizes the dimer and prevents other chemical reactions from occurring, so favouring the formation of malonic acid.

The details are given in the ETH Zürich press release:

Creationism in Crisis - Key Ingredient for Abiogenesis Found on Jupiter's Moon, Enceladus

Creationism in Crisis

Key Ingredient for Abiogenesis Found on Jupiter's Moon, Enceladus

Enceladus has the whitest and most reflective surface that astronomers have yet observed, and it’s known for spraying out tiny icy silica particles.

Source: UCLA

Key building block for life found at Saturn’s Moon Enceladus | Southwest Research Institute

Artist's impression of the south polar region of Enceladus shows massive jets of water ice being blasted into space.

Image credit: Karl Kofoed / NASA.

Creationist frauds playing the 'Big Scary Numbers' tactic and the false dichotomy fallacy, which argues that the probability of self-replicating molecules arising on Earth is so small as to be indistinguishable from zero, and therefore it must have been done by the locally-popular god their mummy and daddy believed in, usually include the notional idea of the 'Goldilocks zone' which is assumed to be a zone round the sun where the conditions are 'just right' for life to exist.

They then argue that the Universe must be fine-tuned for human life on Earth, therefore God did it!

This is, of course, a statistical sleight of hand because the probability of something happening that has already happened is 1 (certainty), not some infinitesimally small fraction of 1. It has happened, therefore it happened. For some reason, the logic in that escapes the hard of thinking on whom the creationist frauds prey.

So, anything which shows that self-replicating molecules, i.e., life arising elsewhere in the Universe, and especially in the solar system far away from the 'Goldilocks zone', is anathema for creationists who must find a way to deal with another inconvenient fact.

Nevertheless, this is exactly what happened recently when an international team of scientists led by Frank Postberg, of the Institut für Geologische Wissenschaften, Freie Universität Berlin, Berlin, Germany, and including Christopher R. Glein of the Space Science Division, Space Sector, Southwest Research Institute, San Antonio, TX, USA have shown that the ocean beneath the ice covering on Enceladus, one of Saturn's moons, has a key building block for 'life', phosphate. Phosphates are essential for life as we know it, not only as the main mineral in the bones of vertebrates but also as a component of metabolic pathways in the form of adenosine diphosphate (ADP) and adenosine triphosphate (ATP) and the nucleotides in DNA and RNA.
The discovery was made in data from NASA’s Cassini mission.

A Southwest Research Institute press release explain how this was done:

Creationism in Crisis - Another Mystery of Abiogenesis May Have Been Solved

Creationism in Crisis

Another Mystery of Abiogenesis May Have Been Solved

Image by Triff/Shutterstock

Chirality in a generic amino acid (-NH 2 : amine,-COOH: caboxyl,-R: rest of the molecule). (a) Left-handed (LH) enantiomer: with thumb along the C→H axis, it takes the left hand for the fingers to point from COOH to NH 2 through R. (b) Righthanded (RH) enantiomer: with thumb along the C→H axis, it takes the right hand for the fingers to point from COOH to NH 2 through R.

Picture: Wikimedia Commons

New Study Provides Novel Insights into the Cosmic Evolution of Amino Acids - University of Tsukuba

One of the enduring problems in biology is explaining why just about all organic molecules in biological organisms have the same chirality. Creationists often latch onto this problem as evidence of something that science "can't explain", as though not (yet) being able to explain something renders the entire body of science wrong, so their "God did it!" superstition wins by default.

Of course, creationism can't explain it either other than by declaring it to be one of their creator god's mysteries.

But, properly understood, chirality is evidence of common descent since the earliest molecules from which self-replicating organisms evolved had one particular chirality - a property which has been inherited by all its descendants. The mystery is why one chirality came to dominate so completely to the exclusion of the other.

Chirality arises because an atom of carbon can form a molecule with four different groups which can be in one of two stereo-spacial arrangements, a levo (L) and a dextro (D) form, known as enantiomers. All amino acids from which proteins are built, and all fatty acids, are L-enantiomers.

Chiral molecules also display 'optical isomerism' in that the different enantiomers rotate the plane of polarisation in polarised light in opposite directions. 'L' enantiomers rotate it to the right 'd' (dextro rotation) and 'D' enantiomers rotate it to the left 'l' ( levorotation).

Creationism in Crisis - The Evolution of Life and the Genetic Code.

Genetic information is stored as long, complex sequences of the four different bases in DNA: adenine (A), thymine (T), guanine (G) and cytosine (C). Triplets of these bases are interpreted by the genetic machinery as instructions to add a certain amino acid to a protein.

Alfred Pasieka/Science Photo Library/Getty Images Plus

Did life evolve more than once? Researchers are closing in on an answer

By way of an introduction to this article on abiogenesis, I'm going to try to dispel the common, but evidence-free claim from creationists that the genetic code is so complex that it must have been designed by an intelligent designer.

This is, of course, nothing but the usual argument from ignorant incredulity and a false dichotomy fallacy - I don't know enough, I can't be bothered to learn, and I can't imagine how something could have arisen naturally, so God did it - and of course it must be the locally popular god because there are only two possibilities; the current science or the local god. It's an argument that demonstrates better than most the scientific illiteracy, intellectual bankruptcy and cultural chauvinism of creationism.

First, I look at the genetic codes and how it could have evolved naturally, without a supernatural magician making chemistry and physics do things they couldn't do without it, or making the highly improbable happen - as though the notion of an undetectable entity existing outside space and time but able to influence things inside space and time makes any sense.

This comes in two forms: a conversation with an AI chat bot, and the book, Life Ascending by Nick Lane.

Firstly, a conversation with ChatGPT3: