F Rosa Rubicondior: Abiogenesis
Showing posts with label Abiogenesis. Show all posts
Showing posts with label Abiogenesis. Show all posts

Tuesday 5 March 2024

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


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:

Friday 1 March 2024

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:

Thursday 29 February 2024

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:

Saturday 24 February 2024

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


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

Friday 26 January 2024

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


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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Thursday 25 January 2024

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


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:

Tuesday 16 January 2024

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


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.

Sunday 17 December 2023

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:

Friday 24 November 2023

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":

Wednesday 15 November 2023

Creationism in Crisis - Biochemists are Homing In On Abiogenesis


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.

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:

Tuesday 12 September 2023

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


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.

Wednesday 9 August 2023

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


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.

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.
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:

Thursday 29 June 2023

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


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:

Saturday 17 June 2023

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:

Monday 29 May 2023

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


Chiral molecules
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).

Sunday 28 May 2023

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:

Saturday 29 October 2022

Creationism In Crisis - Plate Tectonics Billions of Years Before Creationists believe Earth Existed

Harvard researchers provide stronger proof of plate tectonics billions of years ago – Harvard Gazette
New evidence points to the role of plate tectonics in early Earth’s release of internal heat and the swapping of geomagnetic poles.

Illustration by Alec Brenner
The surprising thing is not so much that Creationists ever existed. Given the power of the Medieval Christian and Islamic religions to coerce the population and force on them simplistic dogma from the ignorant and fearful infancy of our species, and to supress contradicting science, it would have been surprising it they hadn't existed in those days. The really surprising thing is that, despite the massive amount of information which flatly contradicts the childish superstitions and the advanced technological societies in which most of them live, there are actual adults, leading otherwise normal lives, who still believe that childish nonsense.

There really are grown adults who believe Earth was magicked into existence, as is. less than 10,000 years ago!

And these ignorant people exist despite evidence such as this paper, that there were continental movements, known to geologists as plate tectonics, billions of years before they believe Earth was magicked up by a spell from an invisible magician, the existence of which has never been explained, let alone demonstrated with evidence, and the modus operandum which has never been observed.

And, if that wasn't bad enough for the Creation cult, the paper even alludes to the geological clock that has been recording the magnetic reversals of Earth that have occurred 183 times in the last 83 million years and perhaps several hundred times in the past 160 million years, according to NASA.

The scientists led by Harvard geologists, Alec Brenner and Roger Fu, point out that the stability of the early Earth, where basically the same tectonic forces were working as are working still, means the conditions were conducive to the appearance and evolution of self-replicating systems we call life.

As the Harvard Gazette article by Juan Siliezar explains:
New research analyzing pieces of the most ancient rocks on the planet adds some of the sharpest evidence yet that Earth’s crust was pushing and pulling in a manner similar to modern plate tectonics at least 3.25 billion years ago. The study also provides the earliest proof of when the planet’s magnetic north and south poles swapped places. The two results offer clues into how such geological changes may have resulted in an environment more conducive to the development of life on the planet.

The work, described in PNAS and led by Harvard geologists Alec Brenner and Roger Fu, focused on a portion of the Pilbara Craton in Western Australia, one of the oldest and most stable pieces of the Earth’s crust. Using novel techniques and equipment, the researchers show that some of the Earth’s earliest surface was moving at a rate of 6.1 centimeters per year and 0.55 degrees every million years.

That speed more than doubles the rate the ancient crust was shown to be moving in a previous study by the same researchers. Both the speed and direction of this latitudinal drift leaves plate tectonics as the most logical and strongest explanation for it.

“There’s a lot of work that seems to suggest that early in Earth’s history plate tectonics wasn’t actually the dominant way in which the planet’s internal heat gets released, as it is today, through the shifting of plates,” said Brenner, a Ph.D. candidate in the Graduate School of Arts and Sciences and a member of Harvard’s Paleomagnetics Lab. “This evidence lets us much more confidently rule out explanations that don’t involve plate tectonics.”
Geologists Alec Brenner and Roger Fu, focused on a portion of the Pilbara Craton in Western Australia, one of the oldest and most stable pieces of the Earth’s crust.
Photo by Roger Fu
For example, the researchers can now argue against phenomena called “true polar wander” and “stagnant lid tectonics,” which both can cause the Earth’s surface to shift but aren’t part of modern-style plate tectonics. The results lean more toward plate tectonic motion because the newly discovered higher rate of speed is inconsistent with aspects of the other two processes.

In the paper, the scientists also describe what’s believed to be the oldest evidence of when Earth reversed its geomagnetic fields, meaning the magnetic North and South Pole flipped locations. This type of flip-flop is a common occurrence in Earth’s geologic history, with the poles reversing 183 times in the last 83 million years and perhaps several hundred times in the past 160 million years, according to NASA.

The reversal tells a great deal about the planet’s magnetic field 3.2 billion years ago. Key among the implications is that the magnetic field was likely stable and strong enough to keep solar winds from eroding the atmosphere. This insight, combined with the results on plate tectonics, offers clues to the conditions under which the earliest forms of life developed.

It paints this picture of an early Earth that was already really geodynamically mature. It had a lot of the same sorts of dynamic processes that result in an Earth that has essentially more stable environmental and surface conditions, making it more feasible for life to evolve and develop.

Alec R. Brenner lead author
Department of Earth and Planetary Sciences
Harvard University, Cambridge, MA, USA.
Today, the Earth’s outer shell consists of about 15 shifting blocks of crust, or plates, which hold the planet’s continents and oceans. Over eons the plates drifted into each other and apart, forming new continents and mountains and exposing new rocks to the atmosphere, which led to chemical reactions that stabilized Earth’s surface temperature over billions of years.

Evidence of when plate tectonics started is hard to come by because the oldest pieces of crust are thrust into the interior mantle, never to resurface. Only 5 percent of all rocks on Earth are older than 2.5 billion years old, and no rock is older than about 4 billion years.

Finally being able to reliably read these very ancient rocks opens up so many possibilities for observing a time period that often is known more through theory than solid data. Ultimately, we have a good shot at reconstructing not just when tectonic plates started moving, but also how their motions — and therefore the deep-seated Earth interior processes that drive them — have changed through time.

Professor Roger R. Fu,
Department of Earth and Planetary Sciences,
Harvard University, Cambridge, MA. USA
Overall, the study adds to growing research that shows that tectonic movement occurred relatively early in Earth’s 4.5-billion-year history and that early forms of life came about in a more moderate environment. In 2018, members of the project revisited the Pilbara Craton, which stretches about 300 miles across. They drilled into the primordial and thick slab of crust there to collect samples that, back in Cambridge, were analyzed for their magnetic history.

Using magnetometers, demagnetizing equipment, and the Quantum Diamond Microscope — which images the magnetic fields of a sample and precisely identifies the nature of the magnetized particles — the researchers created a suite of new techniques for determining the age and way the samples became magnetized. This allows the researchers to determine how, when, and in which direction the crust shifted as well as the magnetic influence coming from Earth’s geomagnetic poles.

The Quantum Diamond Microscope was developed in a collaboration between Harvard researchers in the Departments of Earth and Planetary Sciences (EPS) and of Physics.

For future studies, Fu and Brenner plan to keep their focus on the Pilbara Craton while also looking beyond it to other ancient crusts around the world. They hope to find older evidence of modern-like plate motion and when the Earth’s magnetic poles flipped.
In the abstract to their published open access paper in PNAS, the scientists say:
Significance

The modern Earth is geologically dynamic. Convection in its rocky mantle drives plate tectonics that reshapes its surface, and currents inside its metallic core generate a strong planetary magnetic field. However, it is uncertain whether these processes had begun to shape Earth in its deep past. Our measurements of magnetic signals preserved in 3.25-billion-year-old rocks provide the earliest quantitative evidence of both rapidly moving crust—a hallmark of plate tectonics—and a stable ancient magnetic field that episodically alternated polarity. These observations suggest that the early Earth was remarkably geologically mature from its surface to its deep interior, potentially contributing to stable surface conditions for the evolution of early life.

Abstract

The paleomagnetic record is an archive of Earth’s geophysical history, informing reconstructions of ancient plate motions and probing the core via the geodynamo. We report a robust 3.25-billion-year-old (Ga) paleomagnetic pole from the East Pilbara Craton, Western Australia. Together with previous results from the East Pilbara between 3.34 and 3.18 Ga, this pole enables the oldest reconstruction of time-resolved lithospheric motions, documenting 160 My of both latitudinal drift and rotation at rates of at least 0.55°/My. Motions of this style, rate, and duration are difficult to reconcile with true polar wander or stagnant-lid geodynamics, arguing strongly for mobile-lid geodynamics by 3.25 Ga. Additionally, this pole includes the oldest documented geomagnetic reversal, reflecting a stably dipolar, core-generated Archean dynamo.

Just another example there of how Creationism is refuted quite incidentally, simply by revealing the real world evidence with which it is of course entirely inconsistent simply because the people who made up the origin myths in the Bronze Age were entirely ignorant of the science. Incidentally, it's also an example of the way different strands of evidence mesh so neatly to support the idea that life originated on Earth several billion years ago, just as you would expect if the current theories were correct.

Even more amazing than the fact the otherwise normal people believe the childish Bronze Age Creation myths despite this sort of refutation, is that these same people are prepared to perform the most idiotic mental gymnastics to dismiss them, as though being ignorant of scientific evidence is something to take great pride in, because their mummies and daddies were also ignorant of them.

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Tuesday 4 October 2022

Creationism In Crisis - Another 'God-Filled' Gap Just Got a Lot Smaller

Molecular dynamic simulation of ADP and acetyl phosphate

Aaron Halpern, UCL (CC-BY 4.0)

What is perhaps the favourite of all Creationism's 'God-filled' gaps - abiogenesis - just go a lot smaller with the news today that Nick Lane and colleagues of University College, London, UK, have shown how ATP became the universal energy currency used by all living organisms, so adding another layer to our understanding of how the earliest self-sufficient, self-replicating organisms arose from pre-existing molecules.

As always, the process evicts Creationism's shrinking little god because it is explained using just the natural laws of chemistry and physics acting on pre-existing molecules, with no place for magic or supernatural powers.

The mystery was, how the system for producing ATP could have evolved when the process used by cells today is a multi-step process which itself utilises ATP at six different points. Clearly, there must have been a simpler process for creating ATP early on in the evolution of living organisms and, because of it's universality, this was almost certainly in a common ancestor to all forms of life.

In prokaryote cells such as bacteria, the process occurs in the cell itself but in eukaryote cells the process takes place in the mitochondria - the descendants of bacteria originally incorporated into other prokaryote cells to give rise to the eukaryotes.
What is ATP and how is it synthesised? Wikipedia - Adenosine triphosphate
As explained in information provided ahead of publication by PLoS Biology:

Tuesday 27 September 2022

Creationism in Crisis - Scientists Show How Large Molecules Self-Assemble - No Gods Required Again

Self-assembled large molecule
Attraction between the dipoles of several macromolecules leads to their mesomorphic assemblies, in contrast with typical polyelectrolyte behavior.
Credit: Shibananda Das
Game-changing New Theory Upends What We Know About How Charged Macromolecules Self-assemble : UMass Amherst

The recent rum of bad news for Creationism just got worse, with the news that scientists from the University of Massachusetts Amherst have discovered how large molecules such as proteins and DNA can self-assemble with nothing more than the laws of chemistry and physics. As always when one of Creationism's favourite gaps is snapped shut by science, no gods were found and the 'mystery' required nothing more than the operation of the natural laws of chemistry and physics.

In the words of one of the researchers:

The significance of the discovery that dipoles drive the assembly of polymers is immense because it throws new light on one of the fundamental mysteries of life’s processes, [how biological materials know how to self-assemble into coherent, stable structures]. The theory changes the paradigm of how we think about these systems, and highlights the unacknowledged role that dipoles play in the self-assembly of biological materials.

Professor Murugappan Muthukumar, senior author
Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA, USA
As the University of Massachusetts Amherst news release explains:

Monday 5 September 2022

Space News - First Exoplanet Photo. No Life Yet, But It's Only a Matter of Time

The Webb telescope has released its very first exoplanet image – here's what we can learn from it

NASA's James Webb Space telescope, which is performing much better than expectations, has just produced the first image of an exoplanet. The planet, HIP 65426b, is a gas giant rather like Jupiter, orbiting HIP 65426. It's presence had been inferred from data in 2017.

As a gas giant, it is not suitable for living organisms to have evolved but, with so many exoplanets being discovered, with over 5,000 discovered so far, and so many stars with potential planetary systems, it can't now be long before signs of life are detected on one or more of them.

When that happens, of course, it will destroy any remaining arguments from Creationists that the probability of a self-replicating molecule arising by chance is too small to be credible as an explanation for how life got going on Earth. It will show that, if the conditions are right, chemistry and physics alone are quite capable of producing that and the probability of a planet with those conditions being discovered, increases with every new exoplanet discovered.

The chances of finding such a planet are greater the closer the planetary system is to Earth for the simple reason that telescopes such as the James Webb, see distant objects as they were when the light left them, so a planet say, 10 billion lightyears away, will appear as it was 10 billion years ago. We know it took the Universe 10-11 billion years to give rise to Earth before life could get going some 500 million years later, so distant object may not have had time when we are seeing them, to have reached that stage. Closer objects will have had more time.

The image from the James Webb Space Telescope, and its significance is explained in an open access article in The Conversation by Professor Jonti Horner, Professor (Astrophysics), University of Southern Queensland, Australia. The article is reprinted here under a Creative Commons licence, reformatted for stylistic consistency. The original article can be read here.
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