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

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.

Ten Reasons To Lose Faith: And Why You Are Better Off Without It

This book explains why faith is a fallacy and serves no useful purpose other than providing an excuse for pretending to know things that are unknown. It also explains how losing faith liberates former sufferers from fear, delusion and the control of others, freeing them to see the world in a different light, to recognise the injustices that religions cause and to accept people for who they are, not which group they happened to be born in. A society based on atheist, Humanist principles would be a less divided, more inclusive, more peaceful society and one more appreciative of the one opportunity that life gives us to enjoy and wonder at the world we live in.

Available in Hardcover, Paperback or ebook for Kindle


What Makes You So Special? From The Big Bang To You

How did you come to be here, now? This books takes you from the Big Bang to the evolution of modern humans and the history of human cultures, showing that science is an adventure of discovery and a source of limitless wonder, giving us richer and more rewarding appreciation of the phenomenal privilege of merely being alive and able to begin to understand it all.

Available in Hardcover, Paperback or ebook for Kindle




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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.

Wednesday 13 December 2023

Creationism in Crisis - How Wrong The Bible's Authors Were! Why Would Anyone Believe Anything Else They Wrote?


The Universe as described in Genesis 1: 6-10
NASA’s Webb Stuns With New High-Definition Look at Exploded Star - NASA

The description of the Universe in the Bible is so naïve and radically different to the real universe, it beggars belief that there are grown adults who think the Bible is the inerrant word of a creator god.

There is nothing about the authors' description of it which can be described as allegorical or metaphorical, without the most contorted of mental gymnastics. It is not metaphorical or allegorical; it is quite simply wrong; spectacularly and conspicuously, with no shadow of a doubt, wrong!

What we now know are hundreds of billions of galaxies, each with maybe half a trillion stars, many with planetary systems, the authors of the Bible thought were little lights stuck to the underside of a dome over a flat Earth, that can be shaken loose and will fall down to Earth where they can be trampled on by a goat! (Daniel 8:10).

They described this flat Earth with a dome over it as standing on pillars and the fixed and immobile center of the Universe, round which a small sun orbits. They described the sky above the dome as being made of water. Their universe ran on magic.

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:

Wednesday 1 November 2023

Creationism in Crisis - The Universe is Much Bigger Than Our Prophets Said, Grander, More Subtle, More Elegant..


The Crab Nebula Seen in New Light by NASA’s Webb - NASA

NASA’s James Webb Space Telescope has gazed at the Crab Nebula, a supernova remnant located 6,500 light-years away in the constellation Taurus. Since the recording of this energetic event in 1054 CE by 11th-century astronomers, the Crab Nebula has continued to draw attention and additional study as scientists seek to understand the conditions, behavior, and after-effects of supernovae through thorough study of the Crab, a relatively nearby example.
The Crab Nebula seen by NASA’s James Webb Space Telescope

How is it that hardly any major religion has looked at science and concluded, “This is better than we thought! The Universe is much bigger than our prophets said, grander, more subtle, more elegant?” Instead they say, “No, no, no! My god is a little god, and I want him to stay that way.” A religion, old or new, that stressed the magnificence of the Universe as revealed by modern science might be able to draw forth reserves of reverence and awe hardly tapped by the conventional faiths.

Carl Sagan, Pale Blue Dot: A Vision of the Human Future in Space
The Universe as described in Genesis 1: 6-10

The Crab Nebula - a tiny fragment of the universe as seen by science:

Sunday 15 October 2023

Creationism in Crisis - Colliding Planets Falsify Creationism


October: Exoplanet collision | News and features | University of Bristol

The reason creationism is so easy to refute is that its claims are simplistic, designed as they are to appeal to those who think like children and who know little or no science.

This means we can construct simple hypotheses and predictions and test them against the real world. When we do that, we invariably find the hypotheses are easily falsifiable and the predictions fail to be fulfilled.

Science readily accepts, for example, that much of the observable universe emerged from chaos under the directional force of gravity, which turns a chaotic system into a progressively ordered system, so galaxies, superclusters, black holes, suns and planetary systems all emerged from the background chaos of the Big Bang and quantum fluctuations. This view of the universe predicts that there is still a degree of chaos and unpredictability about the universe.

M1: The Crab Nebula from Hubble.
The chaotic remnants of an exploding supernova.

Credit: NASA, ESA, J. Hester, A. Loll (ASU)
Creationists however, insist that the universe, and everything in it was created in a few days by a perfect, omniscient, god, casting magic spells and commanding everything to appear from nowhere, made out of nothing, in a perfectly ordered and designed universe. It then either micromanages it or sits back and watches while it runs on a prepared a set of rules that govern it (depending on the flavour of creationism and how much the superstition has tried to accommodate science while still believing in magic and the fairy tales they were told in childhood).

So, our simple hypothesis then is that a universe created according to creationist superstitions would be perfectly ordered and free from chaos, and of course had the ultimate purpose of providing humans with somewhere nice to live, like America. Such a well-ordered universe would never have planets colliding, or comets being knocked out of stable orbit in the outer reaches of the solar system and moving into elliptical orbits around the sun, for example. Nor would it have had a minor planet colliding with a young Earth as is believed to account for the Moon and the axis tilt that causes the seasons.

Thursday 12 October 2023

Creationism in Crisis - How We Can Tell The Bible Is Not The Work Of The God Described in It


A creator god would not have got so much wrong when it tried to describe the world it had created and described is as though it knew no more than a parochial Bronze Age pastoralist who knew almost nothing and had to rely on guess-work and folkloric superstitions from the fearful infancy of our species.

A picture is worth a thousand words:
The universe from descriptions of it in the Bible.

And God said, Let there be a firmament in the midst of the waters, and let it divide the waters from the waters. And God made the firmament, and divided the waters which were under the firmament from the waters which were above the firmament: and it was so. And God called the firmament Heaven. And the evening and the morning were the second day.

And God said, Let the waters under the heaven be gathered together unto one place, and let the dry land appear: and it was so. And God called the dry land Earth; and the gathering together of the waters called he Seas: and God saw that it was good.

Genesis 1: 6-10.

How the Universe really is, as revealed by science:

Tuesday 10 October 2023

Creationism in Crisis - Now it's Tree Rings Recording Solar Storms 4,300 Years Before The Universe Existed! Oops!


The Miyake Event is the biggest yet discovered.

Alamy/PA
Researchers identify largest ever solar storm in tree rings | University of Leeds

It's probably unkind to laugh at creationists, who probably genuinely don't know any better and are too dim to learn any science. But they leave us little choice when they wave aside all the evidence of a 14 billion-year-old Universe and a 3.8 billion-year-old Earth as 'wrong' or 'scientists lying' or 'planted by Satan to mislead us', or even 'faked by God the liar almighty as a test of faith', in favour of an evidence free-superstition they were taught by their parents and which they are too terrified to let go off in case they get a zap from an invisible, magic mind-reading sky thug, stories about which they were terrorized by as children, or worst of all, they don't feel important enough?

Their infantile superstition is, of course, that Earth is 8-10,000 years old and was created by magic pretty much as we find it today, just because a bunch of Bronze Age pastoralists thought so.

And then along comes an international team of those pesky scientists who only go and produce evidence that a tree was alive on Earth 4,300 years before the Universe supposedly existed and recorded in its annual tree rings a massive solar storm from a sun that supposedly hadn't yet been magicked into existence, and which is allegedly hanging like a lamp from a dome over Earth so we can tell it's not night! (Remember! It's unkind to laugh! LOL!)

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.

Friday 1 September 2023

Creationism in Crisis - A 4.5 Billion-Year-Old Meteorite Helping to Understand How The Solar System Formed


Erg Chech 002 (EC 002) Meteorite

Sahara space rock 4.5 billion years old upends assumptions about the early Solar System

According to creationists, a magic supernatural god magicked a flat Earth into existence from nothing and put a dome over it to keep the water about the sky out. It then hung a sun and a moon from the dome and the sun has been orbiting Earth ever since. In its Bronze Age account of this creation, the magic god 'forgot' to say where the sun went at night, and creationists have puzzled over that problem for centuries, never reaching a conclusion.

Nowadays, 25% of Americans still believe Earth is the centre of the universe and the sun orbits it, although most of them now accept that Earth is no longer flat or has a dome over it, whilst believing the Bible, which says otherwise, is the inerrant word of the god who created everything from nothing.

Science, on the other hand, is providing evidence that the universe is some 14 billion years and the solar system, with the sun at the centre and Earth orbiting it, formed some 4.5 billion years ago.

One of the pieces of evidence is a meteorite, recovered from a sand dune in the Saharah Desert which has been dated to 4.5 billion years old, using the aluminium-26 – magnesium-26 (26Al-26Mg) decay system combined with the Uranium/Lead system.

First, a little AI information from ChatGPT3.5 about the dating methods used, their accuracy and limitations. Creationists especially might want to skip this since it refutes many of their claims about radiometric dating in general, and shows their responses to be parrot squawks, regurgitated on cue without the slightest understanding of the subject:

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:

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 20 May 2023

Creationism in Crisis - Does Reality Really Exist? Science is Still Working On It.

Creationism in Crisis

Does Reality Really Exist? Science is Still Working On It.

Great Mysteries of Physics: does objective reality exist?

One of the more hilarious arguments against science that I have had levelled at me by a Creationist is that you can't prove reality exists, and yet the whole of science claims to be a description of reality and the scientific method is an examination of it based on materialist principles.

The conversation was ended abruptly with the traditional condescending insult when I pointed out that he was trying to persuade me that reality doesn't exist in order to justify his belief in a creator of it!

Whether or not reality exists as we see and experience it, or whether what we see is an optical illusion or an emergent product of the underlying structural chaos of spacetime is irrelevant to our everyday lives, or course. If you're shot to death by a gun, or hit and killed by a bus, you're just as dead, whether or not the gun or bus actually exists.

Wednesday 26 April 2023

Creationism in Crisis - Stuff The Bible's Scientifically illiterate Authors Never Imagined

Creationism in Crisis

Stuff The Bible's Scientifically illiterate Authors Never Imagined

Figure 1: Illustration of gravitational lensing by a galaxy. Light from a more distant and reddish galaxy is bent by a more nearby and bluish galaxy, which acts like a natural cosmic telescope to magnify the more distant galaxy. In this instance, multiple images of the reddish galaxy are created, forming a reddish ring-like feature referred to as an Einstein ring around the bluish galaxy.





Image credit: ALMA, L Calcada, Y. Hezaveh et al.

Howe the authors of Genesis saw the Universe
HKU Astrophysicists Reveal the Nature of Dark Matter through the Study of Crinkles in Spacetime - All News - Media - HKU

Back in the bronze Age, in the days that Christopher Hitchens described as 'the fearful infancy of our species', before we had even invented the wheel and isolated tribes still thought Earth was flat, the best explanation they could think of for where everything came from was the result of some magic spells cast by an invisible magician who lived above the sky. Agency in all things and magic, were assumed to be behind everything, just as they are today by creationists.

So, imagine these ignorant hill farmers, who thought stars were hanging from a dome over a flat Earth, struggling to come to terms with concepts such as deep space where celestial bodies are millions of light years apart and most of it is composed of invisible matter?

Magic and agency in all things
(Bible moralisée, French, 13th century)
How on Earth were these simple, ignorant people going to guess at an accurate description of the cosmos and its origins?

They weren’t of course. The best they could do was to describe a world which ran on magic and give magical explanations for everything they didn't understand, confident that those who were going to read their guesses were equally ignorant.

Contrast that situation about 3000 years ago with today's astrophysicist trying to make sense of what can be observed.

Having abandoned magic and supernatural agency as an explanation for anything, about 200 years ago, modern scientists have to rely on what can be observed, either directly or indirectly, and one of their observations is that the Universe has far more mass in it than can be accounted for by observation of that which can be seen. In other words, the observable universe has a lot of stuff that can't be seen but which is giving it mass.

How then do we know about it? Because we now understand the relationship between mass and gravity, so we can observe dark matter indirectly by observing the effect its gravity has on things we can see, such as galaxies.

You wouldn't expect the simple-minded hill farmers who wrote Genesis to have any inkling that such substance even existed, let alone come up with an explanation of what this 'dark matter' is, other than the product of magic words, of course.

This is why there is no mention, not even the tiniest hint, of dark matter in the Bible, or even that the universe is as massive as it is. In the ignorant minds of the authors, 'stars' (whether galaxies or suns) were points of light stuck on the underside of the dome that kept the water above the sky out. Of course, you wouldn't expect scientifically illiterate and ignorant people to describe and explain the origins of dark matter, but you WOULD expect any creator god who filled the Universe with dark matter to be able to describe and explain it.

Wednesday 12 April 2023

Creationism in Crisis - Stuff the Authors of Genesis Never Even Guessed At

Creationism in Crisis

Stuff the Authors of Genesis Never Even Guessed At
A view of Stephan’s Quintet, a visual grouping of five galaxies from the James Webb Telescope.

Image credit: NASA, ESA, CSA, STScI
Creationism in Crisis

Stuff the Authors of Genesis Never Even Guessed At
The Atacama Cosmology Telescope

New map of the universe’s cosmic growth supports Einstein’s theory of gravity

Atacama Cosmology Telescope (ACT)
The Atacama Cosmology Telescope (ACT), Chile
It has been said that, like the Qur'an, if the Bible were discovered for the first time today, we could date it accurately by the scientific ignorance in it.

There is no hint of knowledge about Germ Theory, electricity, atoms, photosynthesis, thermodynamics, relativity, quantum mechanics, gravity, or dark matter and dark energy, anywhere in the Bible, unless you stretch the meanings of words beyond breaking point and add things that are not there.

It's as though the authors knew no more than the little that was already known at the time and didn't realise that much of what they thought they knew was fundamentally wrong. But you would expect a creator god who wanted us to believe it knew everything and most importantly, had a vital message for mankind, would have included something new and even something useful - like electricity or antibiotics, for example, but it couldn't even describe the scientific method, let alone a null hypothesis or the need for controls in an experiment.

So, it took until the early part of the 20th century for a scientist to discover that matter and energy are interchangeable because they are different aspects of the same thing, and so why planets orbit suns and Earth has enough gravity to stop us and the atmosphere floating off into space. Einstein’s discovery of Relativity is now a fundamental of cosmology and theoretical astrophysics.

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