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

Monday 11 March 2024

Unintelligent Design - RuBisCO Is Slowly Evolving - And Becoming Even More Embarrassing For Any Creationist Who Understands It


The world’s most prolific CO2-fixing enzyme is slowly getting better | University of Oxford

The world’s worst enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase, or RuBisCo as it is known, has featured in these blog posts several times and it described in my book, The Unintelligent Designer: Refuting the Intelligent Design Hoax as an example of the lack of intelligence in biological systems, and, as such, why it would be a major embarrassment to creationists - if they understood it.

Briefly, RuBisCo is one of the most ancient enzymes known and became an essential component of photosynthesis early on in the history of life on Earth when the first cyanobacteria evolved the ability to use the energy from sunlight to fix the carbon in atmospheric carbon dioxide (CO2) to build the sugar glucose. Eventually, these photosynthesising cyanobacteria became incorporated into plant cells as the chloroplasts to produce the green plants at the base of most food chains. Because it is so inefficient, it quickly became probably the most abundant enzyme on Earth, making up with quantity what it lacked in quality.

But, evolution, unlike good intelligent design, is a one-way, utilitarian process in which whatever works better than preceded it will be retained and will provide the next basis for further evolution, because evolution has no mechanism to scrap a bad design and start again as any backward step will inevitably be worse, so will be quickly eliminated.
Tell me all about RuBisCo and why it's so inefficient. RuBisCo, or ribulose-1,5-bisphosphate carboxylase/oxygenase, is an enzyme crucial for the process of carbon fixation in plants, algae, and some bacteria. It catalyzes the first major step of the Calvin cycle, which is the primary pathway for carbon dioxide fixation in photosynthesis. Despite its importance, RuBisCo is often considered inefficient for several reasons:

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.

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 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.

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:

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:

Tuesday 9 August 2022

God of the Gaps News - Creationism's Little Skrinking God Just Got a Lot Smaller

Olivine basalt
Scientists announce a breakthrough in determining life's origin on Earth—and maybe Mars

The basic problem with Creationism's favourite 'argument' - 'the God of the Gaps' - is not only that it is based on two fallacies - the argument from ignorant incredulity and the false dichotomy fallacies, but also that it tends to disappear every time the gap is subjected to scientific scrutiny.

That's exactly what has just happened with one of their favourite gaps - the origin of living organisms, which they always conflate with the theory of evolution of which it is not and never was a part. Evolution is what happened after ‘life’, or more precisely, self-replication, got started.

Essentially, living organisms can trace their origins back to a self-replicating molecule because once that had arisen, everything else follows naturally by Darwinian natural selection acting on small variations in the copies (the sieve of natural selection acting on each generation to filter out the best at producing copies of themselves and remove those least able to). Just such a molecule known to exist is a short length of RNA which has been shown to self-catalyse copies of itself in a mixture of nucleotides, by nothing more complex than the operation of the basic laws of chemistry.

But the question is, how did such a molecule first assemble?

Friday 13 May 2022

Abiogenesis News - Closing in to Fill Creationism's Favourite Gap - No God Found.

a, tRNA structure showing selected ribose and nucleobase modifications. The 3′-amino acid-acylated adenosine is located at the CCA 3′ end in contemporary tRNAs. 5-Methylaminomethyl uridine, mnm5U, is found in the wobble position 34. The amino acid-modified carbamoyl adenosine, (m6)aa6A (aa, amino acid), is present at position 37 in certain tRNAs. b, General RNA–peptide synthesis cycle based on mnm5U and m6aa6A. The structures of oligonucleotides are simplified and only terminal nucleobases are drawn.
The origin of life: a paradigm shift - LMU Munich

It doesn't seem to have dawned on creationists who forlornly claim, despite the daily torrent of evidence to the contrary, that the Theory of Evolution is a theory in crisis. Far from the TOE being a 'theory in crisis', the reality is that it's the childish notion of creationism that's in crisis and which is being increasingly rejected even by religious people as a valid explanation for how life diverged. It's only by creative misrepresentation of the data, or by dismissing it out of hand, that creationist frauds are still able to pull the wool over the eyes of their credulous dupes, to maintain their cult’s superstitions.

One of their mainstays as an 'argument' which they invariably fall back on when confronted with unarguable evidence for evolution by natural selection and other mechanisms, is that none of the mechanisms explain the origin of 'life' itself (abiogenesis, life from non-life'), and without that, evolution would have nothing to work on. It is, of course, irrelevant to the mechanisms by which life diversified once replicators did get going, but, as usual with childish notions, the relevance of using the false dichotomy fallacy is lost on creationists who lack the critical thinking skills to spot the trick, and few if any of them could define the term 'life' in a scientifically meaningful way, anyway, so assume it means some magic ingredient that separates organic' molecules from inorganic ones. It is one of the last remaining gaps which they insist must contain their god and their belief is that, of all the gaps closed by science, this will be the one where a god is found. Their ever-shrinking little god has degenerated to the size of this one remaining gap. The magician that magicked 'life' from non-life and made them 'speshul'.

There are, of course, many possible alternative explanations for how a simple replicator could have got going and, indeed, there doesn't even need to be a single explanation since two or more replicators could have got together early on. If the result had given them an advantage over remaining separate, then this symbiosis would have been almost inevitable.

One of the more popular hypotheses amongst biologists is the 'RNA world hypothesis' that says, because RNA is still the functional unit of biological activity and it is simpler than DNA, it probably came first and DNA followed on as an evolved improvement, acting as RNA's data store and so became the functional organ of inheritance of genetic data.

This is the idea currently being expanded by a team at the Ludwig-Maximilians-Universität München, Germany. Their work has just been published, open access in Nature. They believe they have solved one of the outstanding problems with the theory - how RNA began catalysing the production of chains of amino acids to form peptides and short proteins without the peptides it codes for - a classic chicken and egg conundrum.

Like all chicken and egg conundrums, if this scenario is correct, it turns out that neither of them came first; they both emerged simultaneously and part of a developing complex out of simple pre-existing precursors.

As the Ludwig-Maximilians-Universität news release explains:

Friday 6 May 2022

Quantum Evolution - How A Quantum Fluctuation Can Cause Mutation

The Double Helix of DNA
Getty Images
Quantum mechanics could explain why DNA can spontaneously mutate | University of Surrey

Another of creationism’s central dogmas was unintentionally laid to rest by science yesterday, when three scientists from Surrey University's Leverhulme Quantum Biology Doctoral Training Centre, which includes the famous science broadcaster, Professor Jim Al-Khalili, published a paper which showed that DNA can spontaneously mutate due to nothing more than a random quantum fluctuation. Creationist dogma insists, with no evidence to support it and in spite of evidence to the contrary, that no new information can arise in the genome without violating the Second Law of Thermodynamics [sic]. Don't ask! It's based on some half-baked notion that information is like energy and can't be created, or rather, in creation world, can only be created by magic.

But, as the Surrey University team say in their open access Communications Physics paper:

Due to the significance of the quantum tunnelling even at biological temperatures, we find that the canonical and tautomeric forms of G-C inter-convert over timescales far shorter than biological ones and hence thermal equilibrium is rapidly reached. Furthermore, we find a large tautomeric occupation probability of 1.73 × 10−4, suggesting that such proton transfer may well play a far more important role in DNA mutation than has hitherto been suggested.

The Surrey University news release explains what that means:

Tuesday 18 January 2022

Abiogenesis News - Science Is Closing the Gap - Still no God(s) Found or Magic Needed

New Study Sheds Light on Origins of Life on Earth | Rutgers University

A team of researchers led by scientists from Rutgers University, New Jersey, USA, have brought us a little closer to understanding how the first self-replicating organisms arose on earth. And it didn't need magic supernatural deities to make it happen.

The Rutgers-led team have discovered the structures of proteins that may be responsible for the origins of life in the primordial soup of ancient Earth. They have published their findings, open access, in Science Advances
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Writing in Rutgers Today, John Cramer explains:

Saturday 31 July 2021

Malevolent Designer News - A Nasty Little Trick for Making Malignant Melanomas

Melanoma
VAI Study reveals source of DNA mutations in melanoma - VAI

Creationist mode:


Back in 2014 I wrote an article about malignant melanoma, inspired by a holiday on the Côte d'Azur, explaining why people with pale skin are at risk because of poor 'design' creating the need for a balance between getting melanoma and producing enough Vitamin D in the skin to avoid rickets due to Vitamin D deficiency. In Eurasia, where the sun is lower in the sky, meaning it has more atmosphere to travel through, and the weather is more cloudy, than in our ancestral homelands in Africa, pushed this balance towards pale skin and therefore an increased risk of melanomas.

Now, however, judging by the way creationists seem to admire the many examples of malevolence in their beloved, putative intelligent [sic] designer, there may be another reason - mendacity and delight in watching us suffer, if we buy into this childish explanation for a moment...

So, if you've been taken in by the Intelligent Design Hoax and believe that nothing of this sort ever happens without the positive intervention of a magic designer to make it happen, and that this magic designer is an omniscient god, then you must accept that the recent findings of a research group at the Van Andel Institute (VAI), Grand Rapids, Michigan, USA, point to deliberation and not accident - which is excluded by the dogma of omniscience.

Thursday 25 February 2021

Abiogenesis News - Creationism's Favourite God-Shaped Gap Just Got Smaller Again

“Protocells” containing bubble-like compartments formed spontaneously on a mineral-like and encapsulated fluorescent dye. This could have been what happened 3.8 billion years ago when cells first began to form.

Image: Karolina Spustova.
Evidence That Earth’s First Cells Could Have Made Specialized Compartments

No wonder Creationists often come across as paranoid. At times it must feel as though their favourite dogmas and god-shaped gaps are under siege by science and constantly in danger of being overthrown or closed altogether, like so many former gaps in which they sat their favourite god(s); all found to be empty when science shone a light in them.

One of their favourites, and often their only fall-back position, is that abiogenesis hasn't been explained by science, and that easily becomes a claim that it can't be explained without resort to magic by a magic man because living things contain special god-magic called 'life' that can't be identified or even explained.

Then along comes another paper, like this one from scientists at the University of Oslo, published by the Biophysics Society, that chips away a little more at this dogma, by showing not only how simple cells got started but by showing how 'life' is simply chemical and physical processes, all understandable as properties of matter, with no magic involved.

This paper is yet another in a long line of papers all reducing the size of creationism's god-shaped abiogenesis gap, and deals with how proto-cells became internally organised, in this case, with the formation of 'bubbles' or vacuoles that are a fundamental part of living cells today.

The Biophysical Society press release explains:
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