Creationism in Crisis - How Our Need For Vitamin D Was A Bad Design That Went From Bad To Worse

Permanent Central Maxillary Incisors showing evidence of Vit. D deficiency.

Fig 3. Permanent central maxillary incisors of CL 66.
Plane form hypoplasia is exhibited on the occlusal and labial surfaces.

Archaeological evidence of seasonal vitamin D deficiency discovered | University of Otago

The human need for vitamin D to ensure proper bone growth and development and various other health-related needs, is an example of how we were not intelligently designed but are the result utilitarian evolutionary compromises that balance benefit against detriment and that balance depends on the environment in which we evolved. It shows that we evolved in sunny climates where the sun comes directly through the atmosphere as it does in the tropics, rather than obliquely, as it does in the northern and southern parts of the globe.

We do not generally get enough vitamin D from our diet, so we need to manufacture it in our skin by the action of sunlight, in particular the ultraviolet B (UVB) spectrum. However, UVB sunlight is also harmful, so our skin needs to be protected from it with the pigment, melanin, which gives our skin its varying shades of brown or black. Generally, the darker the skin, the better protection it has from UVB but the less it can produce vitamin D.

This AI explanation outlines the problem:

Creationism in Crisis - Neanderthals And Modern Humans Lived Together in Northern Europe 35,000 years Before 'Creation Week'

Stone tools from the Lincombian–Ranisian–Jerzmanowician technocomplex at Ranis.

© Josephine Schubert, Museum Burg Ranis, License: (CC-BY-ND 4.0)

Neanderthals and humans lived side by side in Northern Europe 45,000 years ago | Berkeley

35 thousand years before creationism's god decided to create a small flat Earth centred on the Middle East and put a dome over it to keep the water above the sky out, anatomically modern humans were living alongside Neanderthals in Northern Europe.

The problem was that the Bronze Age people who wrote the creation myth, which they assumed all happened in their small part of the planet, were completely unaware of Northern Europe, the people living there, or that it had a history of a different species of humans living there for half a million years. If they had been, they might have invented a different tale to compensate for what they didn't know, but being human, and humans always want a story, they made one up with what little knowledge and understanding they had, and hardly surprisingly, got it spectacularly and laughably wrong, as we now know.

We know this because science is finding out what really happened and it's turning out to be nothing like the story the Bronze Age story-tellers made up.

That Neanderthals and modern humans met, co-existed and occasionally interbred has been known to science for some time now, but there was uncertainty about how long ago they first came into contact and where. Now a large team of archaeologists which included researchers from the Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, have discovered evidence that they coexisted in Northern Europe, 45,000 years ago and lived together for several thousand years before Neanderthals became extinct.

The evidence of this is the finding of bone fragments which DNA analysis shows to be modern human DNA, dated to at least 40,000 years old, at a site in Germany at Ranis. Their finding also suggests that it was an invasion of Europe and Asian by modern humans that drove the Neanderthals to extinction, having lived in Europe for about 500,000 years. Although there is a school of thought that says Neanderthals, who existed in low population density, never became extinct so much as merged with the much larger population of modern humans. There is now probably more Neanderthal DNA in modern humans (who carry 1-3% Neanderthal DNA) then ever existed prior to the two species coming into contact.

The work of the team who made this discovery is the subject of three papers, two in Nature Ecology & Evolution and one in Nature. It is also the subject of an article by Robert Sanders in Berkely News:

Creationism in Crisis - Scientists Have Shown How The Evolution Of Bird Flight Was Connected To Growth in The Brain's Cerebellum

Digital reconstructions of endocasts of a woodpecker, Melanerpes aurifrons (top), and a troodontid dinosaur, Zanabazar junior (bottom). The blue area is the cerebellum.

Credit: Amy Balanoff

An artist's conception shows Archaeopteryx, a creature that had the wings of a bird but the tail and teeth of a dinosaur.

John Sibbick / NHM

Scientists Pinpoint Growth of Brain’s Cerebellum as Key to Evolution of Bird Flight | Johns Hopkins Medicine

Powered flight has evolved three times in vertebrates, the long-extinct Triassic pterosaurs, in a Jurassic dinosaur lineage that would become birds and in the Early Cenozoic ancestors of today's bats.

Of those, the easiest to study the evolution of flight in is the dinosaur lineage that became birds, because there is a large and available group of birds and a rich fossil record to study.

Now a team of Evolutionary biologists at Johns Hopkins Medicine, including assistant professor of functional anatomy and evolution, Amy Balanoff, Ph.D. have combined PET scans of modern pigeons with studies of fossil dinosaurs to answer one of the enduring questions in evolutionary biology - how did powered flight evolve in birds?

Having established the role of the cerebellum in flight with the PET scans on pigeons, they then found that there was a progressing increase in the size and complexity of the cerebellum in the ancestral dinosaurs as they evolved into flying birds.

Their results are published in Proceedings of the Royal Society B.

As the Johns Hopkins Medicine news release explains:

Creationism in Crisis - Evolution Of The Human Imune System - By Repurposing An Existing Protein

The Joining chain (J chain) that helps bind and regulate the subunits that make up antibodies was evolutionarily co-opted by the human immune system from another biological process, according to a study by researchers from Penn State, the University of Maryland and the University of Chicago. The J chain, shown here in purple, assembles and stabilizes, from left, immunoglobin A (IgA) and immunoglobin M (IgM) antibodies. It is also required to move IgA and IgM across the mucus-producing tissue lining body structures with external exposure, like the intestine, nasal cavity and lungs.

Credit: Ttsz/Getty Images.

Evolutionary origin of mysterious immune system molecule in humans revealed | Penn State University

The human immune system is a problem for creationists who insist that their putative creator god designed humans perfectly but didn't create pathogenic parasites, which were created later by another creator called 'Sin' because of 'The Fall' after which this 'Sin' thing was free to create everything that increases the suffering in the world, so the question that throws creationists into confusion is when was the human immune system created?

If it was created before 'The Fall' then their designer god was planning for 'The Fall' all along and Adam & Eve had no choice but to comply with this god's plan for them, so there was no disobedience; just compliance with the plan.,

If, on the other hand, the creator had to upgrade its design later to protect its creation from pathogens, then it had failed to anticipate 'The Fall' so can't be omniscient.

And, since pathogens can and do get passed our immune defences, then a perfect, omnipotent creator did not design the immune system because it fails to work as designed, or 'Sin' can outwit it.

And now creationists have another problem, especially those who have been fooled into believing there is evidence of intelligent design to be found in 'irreducibly complex' structures and processes, because the simple biological explanation for such structures and processes is that they are composed of elements that originally evolved for other purposes and were later exapted for a novel function as part of the 'irreducibly complex' structure. For example, almost all the elements of the bacterial flagellum are to be found in the Type III secretion system (T3SS) which bacteria used to bind themselves to their potential host, but motility was such an advantage that the T3SS was repurposed for a flagellum with a few additional proteins and a slight modification of others to improve its efficiency.

Two of the components of the immune system are protein complexes which are the antibodies produced in response to infection by pathogens. These are the immunoglobin M (IgM) and immunoglobin A (IgA). Both these are stabilised by a Joining chain (a short length of protein) called the J chain. And this is the component that was co-opted from an entirely unrelated biological process, as a team of researchers at Penn State University, which included Kazuhiko Kawasaki, associate research professor of anthropology, discovered.

Their research was published a few days ago in Proceeding of the National Academy of Science (PNAS) and is explained in a Penn State University news release:

Creationism in Crisis - The Universe Is Much Bigger Than Our Prophets Said...

The James Webb Space Telescope observed 19 nearby face-on spiral galaxies in near- and mid-infrared light

NASA, ESA, CSA, STScI, Janice Lee (STScI), Thomas Williams (Oxford), PHANGS Team, Elizabeth Wheatley (STScI)

NASA’s Webb Depicts Staggering Structure in 19 Nearby Spiral Galaxies - NASA Science

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

Face-on spiral galaxy, NGC 628, is split diagonally in this image: The James Webb Space Telescope’s observations appear at top left, and the Hubble Space Telescope’s on bottom right. Webb and Hubble’s images show a striking contrast, an inverse of darkness and light. Why? Webb’s observations combine near- and mid-infrared light and Hubble’s showcase visible light. Dust absorbs ultraviolet and visible light, and then re-emits it in the infrared. In Webb's images, we see dust glowing in infrared light. In Hubble’s images, dark regions are where starlight is absorbed by dust.

NASA, ESA, CSA, STScI, Janice Lee (STScI), Thomas Williams (Oxford), and the PHANGS team

Continuing with the theme of how different the universe really is compared to the laughably naive description of it in the Bible where the sun, moon and stars were stuck to a dome over Earth above which there was just water. And the stars could even be shaken loose by earthquakes when they would fall to Earth and could be trampled on by goats.

By contrast, here are the latest clutch of images from NASA's James Webb Space Telescope (JWST). They are all of face-on spiral galaxies taken in the infra-red spectrum. Compare them to the description in Genesis where the entire Universe has a small, flat Earth at the centre of it.

Creationism in Crisis - The Billion-Year Evolutionary History of Plants On Earth

Since the first plants appeared, they have diversified into a vast range of forms, and sizes from pond scum to massive trees.

How did plants first evolve into all different shapes and sizes? We mapped a billion years of plant history to find out

Plants come in all manner of shapes and sizes, varying in complexity from simple single-celled algae, through mosses, liverworts and ferns to flowering plants and massive trees.

But how did they get this way?

A team of scientists led by Philip C J Donoghue, Professor of Palaeobiology, University of Bristol, James Clark, Research Associate, School of Biological Sciences, University of Bristol and Sandy Hetherington, Plant Evolutionary Biologist, The University of Edinburgh, set out to answer this question by looking at certain traits in each major plant group. The traits ranged from fundamentals like the presence of roots, leaves or flowers to the fine details such as the surface topography of pollen grains. All in all, the team collected data on 548 traits from more than 400 living and fossil plants, amounting to more than 130,000 individual observations.

They then used this data to plot the positions of plants, living and extinct in a 'design space', i.e., the theoretical range of possible forms for each major group.

What they found was that there tended to be a burst of diversification soon after the evolution of a major new trait, with the new lineage then tending to settle down to improve on what they had, rather than to innovate - until the next major innovation.

This what we would expect from the way a major new trait, such as the evolution of pollen as the male reproductive cell which could be transferred to the female by wind, insects, etc., so freeing the plants from the need to live in water or damp conditions so the motile male cells could 'swim' to the female, as it still does with the gametophytes - mosses, liverworts and ferns.

This innovation meant plants were not free to diversify into the dryer land between rivers, lakes and coastal margins and so colonise much more of the planet.

The same phenomenon is seen in animals where, for example, terrestrial living freed the early amphibians from dependence on water, except to breed, and the evolution of eggs, freed them even from that dependence; the evolution of flight freed the birds and bats to diversify into the new niches now open to them.

The team's work was published, open access in Nature Plants and is the subject of an article in The Conversation by the three lead authors. Their article is reprinted here under a Creative |Commons license, reformatted for stylistic consistency:

Creationism in Crisis - How An Iconic Australian Plant Originated in Africa - 132 Million Years Before 'Creation Week'

Banksia serrata photographed in the Australian Blue Mountains

Bjørn Christian Tørrissen via Wikipedia
(CC BY-SA 3.0)

Banksia spinosa inflorescence

Credit: Nadiatalent via Wikipedia (CC BY-SA 3.0)

Banksias are iconic Australian plants, but their ancestors actually came from North Africa

No real scientists these days sets out to refute creationism as such, but most do anyway, because creationism is so counter-factual that almost any scientific facts, especially in the fields of biology, cosmology, archaeology, geology and palaeontology refute it. It takes a resolute and determined ignoramus to not be aware of that. The problem creationists have is that they get all their beliefs from an ancient text that is demonstrably wrong, even when explained away as allegorical or metaphorical. It is neither. It is quite simply wrong on every level.

So, creationists are left desperately trying to defend the childishly absurd claim that the entire Universe, including Earth and all living things on it, were all created out of nothing in a few days, about 10,000 years ago, by a magic man also made of nothing who designed himself before he existed then self-assembled according to that plan, with all the complexity and information needed to create and micromanage an entire Universe.

This, despite the fact that there are fossil remains of plants and animals from hundred, even thousands of millions of years before then and despite the fact that all the evidence points to a long, slow, evolutionary process of divergence from a common ancestor that lived well over a billion years ago, which was itself the result of a symbiotic associations of much earlier organisms.

One such paper, which casually and incidentally refutes creationism, recently published in Perspectives in Plant Ecology, Evolution and Systematics by three Australian botanists and plant ecologists and a South African Professor of botany, traces the origin of the family of iconic Australian plants, the Banksias, to North West Africa, 132 million years ago.

The story of this migration meshes in with the sciences of plate tectonics and oceanography allowing the plants to migrate across then contiguous land masses from what is now North West Africa to what is now Australia via South America and Antarctica, as land-masses split and diverged and sea-levels rose and fell to reveal land bridges where there is now ocean.

How they discovered this is the subject of an article in The Conversation by the four scientists. Their article is reprinted here under a Creative Commons licence, reformatted for stylistic consistency:

Creationism in Crisis - Something For Creationists to Squawk About - Parrot-Like Dinosaurs from 67 Million Years Before 'Creation Week'

Artist’s depiction of Eoneophron infernalis (top left), MOR 752 (bottom left), and Anzu wyliei (right) in the Hell Creek Formation.

Illustration by Zubin Erik Dutta
Atkins-Weltman et al., 2024, PLOS One,
CC-BY 4.0

OSU-CHS student discovers new dinosaur species, publishes findings | Oklahoma State University

Between about 67 and 66 million years ago, during a period that geologists call the Maastrichtian, there was a thriving ecosystem of dinosaurs in what is now the Hell Creek formation which spans parts of Montana, Wyoming, and North and South Dakota. We know this because their remains are frequently found in this fossil-rich formation known as the Hell Creek Formation.

The great thing about this formation is the way, as the layers built up, nearby volcanoes periodically spread a layer of ash (or tufa) over it forming neat bands that can be accurately dated using one of the most accurate radiometric dating methods - Uranium-Lead (U-Pb) in zircons. This gives a maximum and minimum age of the fossils found between these layers of tufa.

I wrote about U-Pb dating in a recent blogpost, but for the sake of creationists who are about to squawk "Radiometric dating is false!", I'll expand on what I said here:

Unintelligent Design - How A Virus Saved The Unintelligent Designer's Blushes Early In Multicellular History

A virus that infected animals hundreds of millions of years ago has become essential for the development of the embryo

I've remarked before how similar biological systems are to the machines the late William Heath Robinson designed for solving simple, everyday problems. Simple solutions were eschewed for more complicated ones and unlikely items were used in ways they weren't intended for, such as a grandfather clock standing on a piano to support a platform balanced on top. Everything was held together by pieces of knotted string and labour-saving devices took far more people than would have been needed to do the job more simply.

And yet, the whole contraption worked, or at least looked as though it would if were ever made, but take any part away and the whole thing would fail, in an example of what creationists call 'irreducible complexity'.

So, let's pretend that creationism's, 'intelligent'[sic] designer really is behind the design of living organisms and see how closely Heath Robinson unwittingly parodied it:
Just such an example of a Heath Robinson machine in biology was revealed a few days ago in an open access paper published in Science Advances, explaining how a virus which became incorporated in the genome of an early multicellular organism provided a solution to a problem of the designer's own making. The problem it solves was how to overcome the problem created by choosing the same method of cell replication in multicellular organisms that single-celled organisms use, where the entire genome needs to be replicated at each division.

The entire 'point' of multicellularity, and what gave it its success over single-celled organisms is division of labour, in other words, specialisation, so the organisms can be divided into tissues and organs that perform a specialised task. This means that every cell has to have the potential to carry out every function, in the genes it inherits from its parent cell, yet only a few genes are need for its particular specialty.

The process by which this is achieved is the complicated epigenetic system which turns off unneeded genes as the cells differentiate into different cell lines in the developing embryo, and these settings can't normally be reversed.

However, the sperm and egg which then fused to form the zygote from which a new embryo develops, are themselves specialised cells with all the epigenetic settings of their parent cells with an additional few of their own, and these are inherited by the zygote, so to make cell differentiation possible again, the zygote is quickly (within minutes of fertilisation) reset to a state of totipotency.

So, to overcome the epigenetic settings problem that is a problem of the designer's own making, the zygote needs to be epigenetically reprogrammed and this happens in two stages: first to produce a 'totipotent' cell with the potential to produce all the different cells in the embryo as well as the placenta, umbilical cord, and amniotic sack in which the embryo will develop, and then, soon after cell division begins, 'pluripotent' cells from which the different stem cells for the required specialised cell lines will develop.

How this was helped by a virus is the subject of the paper by researchers from the Spanish National Cancer Research Centre (CNIO), Madrid, Spain. First, a little AI background:

Creationism in Crisis - A Multicellular Organism 1.63 Billion Years Before 'Creation Week'

1.63-billion-year-old multicellular fossils from North China
The oldest record of a multicellular eukaryotes

(Artist’s concept.)
Credit: SciTechDaily.com

Fig. 1. Transmitted-light (TL) photomicrographs of Q. magnifica from the Chuanlinggou Formation.
(A to D and K) Filaments with cells of varying length and width. (E) Four-celled filament with hemispherical terminal cell. (F and G) Filament with notably decreasing cell width toward one end. Note that (F) and (G) represent the same specimen; (F) lost the narrowest part of the filament as shown in (G). (H to J) Filaments displaying more uniformity of cell dimensions. (L) Two-celled filament with ovoid terminal cell. All specimens were handpicked from organic residues of acid maceration and photographed in wet mounts, except for (K), which was photographed from a permanent strew mount. Solid and empty gray triangles in (A), (C), and (K) indicate the longest and the shortest cells, respectively, within single filaments. tb, transverse band (interpreted as cross wall); tr, transverse ring (interpreted as partially preserved cross wall). Scale bar, 50 μm [(A) to (E), (I), (J), and (L)] and 100 μm [(F) to (H) and (K)].

Fossils from North China indicate eukaryotes first acquired multicellularity by at 1.63 billion years ago---- Nanjing Institute of Geology and Palaeontology Chinese Academy of Sciences

As though the abundant evidence of life on earth before about 10,000 years ago wasn't bad enough for creationists who believe the Universe and everything in it were was magicked out of nothing in 6 days around about then, a team of scientists led by led by Professor ZHU Maoyan from the Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences (NGIPAS), has now pushed the date of oldest-known multicellular, eukaryote organism back another 70 million years to a whapping 1.63 billion years before the supposed 'Creation Week'.

This would mean, if their superstition had any merit that creationists believe Earth has been around for just the last 0.0006% of the time that multicellular eukaryotes have existed on it.

And they wonder why people laugh!

The fossils were discovered in the Yanshan area of North China in the late Paleoproterozoic Chuanlinggou shale Formation which is about 1,635 million years old. The age of the fossils is constrained by a layer of volcanic ash ~40 m above the fossil horizon in the Kuancheng area, which has yielded a U-Pb zircon age of 1634.8 ± 6.9 Ma (23).

All complex life on Earth, including diverse animals, land plants, macroscopic fungi and seaweeds, are multicellular eukaryotes. Therefore, multicellularity is key for eukaryotes to acquire organismal complexity and large size, and often regarded as one major transition in Earth’s life history by scientists. However, it is still poorly understood when eukaryotes first evolved this innovation in their deep evolutionary history.

Fossil records with convincing evidence show that eukaryotes with simple multicellularity already appeared at 1.05 billion years ago, including red and green algae, and putative fungi. Older records claimed to be multicellular eukaryotes, but most of them are controversial due to their simple morphology and lack of cellular structure.

Unintelligent Design - The Unintelligent Evolution of Sea Grasses 100 Million Years Before 'Creation Week'

Neptune grass (Posidonia oceanica) in the Mediterranean Sea.

Photo: Gabriele Procaccini, Stazione Zoologica Anton Dohrn Naples.

Little Neptune Grass (Cymodocea nodosa).

Photo: Thorsten Reusch, GEOMAR

Use it or lose it: How seagrasses conquered the sea - GEOMAR - Helmholtz-Zentrum für Ozeanforschung Kiel

Sea grasses are the only flowering plants to become fully submerged, having evolved from three independent lineages some 100 million years ago in fresh water and transitioned into marine plants. This appears to have been facilitated some 86 million years ago by a whole genome tripling, which created plenty of spare DNA which could mutate harmlessly to create new genetic information - something deemed 'impossible' by creationist dogma. Since then, they have undergone further evolutionary adaptation by gene loss - something else that creationist dogma says is impossible.

Now an international group of 38 researchers coordinated by Professor Dr. Yves Van de Peer, Ghent University, Belgium, Professor Dr. Jeanine Olsen, University of Groningen, Netherlands, Professor Dr. Thorsten Reusch, GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany, Dr. Gabriele Procaccini, Stazione Zoologica Anton Dohrn of Napoli, Italy, and the Joint Genome Institute, Berkeley, California, United States of America, sequenced and analyzed the genomes of three of the most important seagrass species – the iconic Mediterranean endemic Neptune grass (Posidonia oceanica), the broadly distributed Little Neptune grass (Cymodocea nodosa) and the Caribbean endemic Turtlegrass (Thalassia testudinum), to discover what evolutionary changes had enabled this transition.

Anyone who has holidayed on the Mediterranean coast may be familiar with the 'Poseidon balls' that wash up on beaches. These example of emergence of order from chaos are the result of the fibrous remains of Poseidon grass leaves being rolled along the seabed at the tidal interface to form long rolls which then break up and get rolled further into balls, as I relate here.

But the question the team addressed was not how the Poseidon balls form but how did the sea grasses evolve? This is the subject of their paper in Nature Plants and a press release from GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany:

Creationism in Crisis - Evolution In Progress As a Tiny Ant Changes The Ecosystem.

'Big headed' ant, Pheidole megacephala (soldier cast).

Tiny ant species disrupts lion’s hunting behavior - News - University of Florida

As well as species evolving, there is another form of biological evolution that is often not recognised as such - the evolution of ecosystems as the populations of species that exist within it changes.

Environmental change is the prerequisite of evolutionary change on the classic Darwinian evolution by natural selection model, so we would expect to see an evolutionary change to significant environmental change, given time, but changes to delicately-balanced ecosystems can occur very quickly - in a matter of years or even months, whereas evolutionary change in the species gene pool will normally take many generations to occur, and that slow response to ecosystem change often results in extinction or sometimes, in favourable conditions, a population boom.

And one such ecosystem change is currently underway in Africa due to a small, invasive species of ant, as Professor Todd Palmer, an ecologist and professor in the Department of Biology at the University of Florida, with colleagues including University of Wyoming doctoral candidate and Kenyan scientist Douglas Kamaru, Jake Goheen, from the University of Wyoming, and Corinna Riginos, with The Nature Conservancy reported recently in Science.

I have remarked several times elsewhere how, because the giraffe's long neck and legs have evolved in an arms race with acacia trees, if acacia trees disappeared what is now an advantage to giraffes, would become a handicap as they find drinking difficult and are vulnerable to predation by lions and leopards as they drink because they can't raise their heads up rapidly without a dangerous fall in blood pressure to their brain and that, together their spread-eagled legs, mean they can't suddenly get up and run. Their long necks and legs only make sense in the presence of acacia trees.

And acacia trees have also been evolving in this expensive -do-or-die arms race with giraffes and other browsing species, in which the massive cost of producing enough sugar to build such a tall trunk would also be a handicap in the absence of giraffes. But, in one of those serendipitous turns of good fortune, acacia trees have an ally in this arms race in the form of vicious ants of the Pseudomyrmex and Crematogaster genera that take up residence in swellings at the base of thorns in the crown of the tree. These ants vigorously defend the trees against not only giraffes, but also elephants which can reach to lower branches with their trunks and will even push them over to get at the leaves.

The close interdependence of acacia trees and these ants is an example of co-evolved mutualism:

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

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

Purdue University file photo/Andrew Hancock

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

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

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

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

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

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

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

As the Purdue University press release says:

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

Significance

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

Abstract

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

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

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

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

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

---

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

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Malevolent Designer News - How The SARS-CoV-2 Virus Has Been Redesigned to Have Another Go

The emergence of JN.1 is an evolutionary ‘step change’ in the COVID pandemic. Why is this significant?

To anyone but a reality-denying creationist, the SARS-CoV-2 virus that causes COVID-19, is a classic example of evolution by natural selection, as it continually mutates and those mutations that make it more successful are retained, so it continually improves in its ability to infect and be passed on to another victim, so producing more offspring in the virus gene pool than rival versions.

The latest version to gain predominance, JN.1, currently spreading across the world, is yet another variation on the omicron version, which itself ousted delta as the predominant variety. This new improved version may prove to be so different to omicron that is should be given a new Greek letter designation.

One point that shouldn't go unnoticed is that because, unlike the original, the virus now exists in an environment in which most of its potential victims have a degree of immunity to it, either by vaccination or by previous infection. Because that immunity usually means the ability to produce antibodies to the 'spike' proteins on the surface of the virus, most of the mutations of progressively more successful variants are in the genes that code for those proteins - making it more difficult for antibodies to bind to them.

To a creationist, the SARS-CoV-2 virus, like all the other pathological viruses, presents the paradox of trying to believe their putative designer god is the supreme ruler of and creator of everything in, the universe and is the only entity capable of creating biological organisms, but, because it is omnibenevolent, it would not have designed SARS-CoV-2 and would not be responsible for continually redesigning it to continue making us sick, by evading the immune system it supposedly also designed to protect us from viruses and other pathogens.

Curiously, creationists who continually present what they think is evidence of design as evidence for their magic creator on the grounds that it is the only entity capable of biological design, never use evidence of malevolent design as evidence for the same magic creator. That has to be ascribed to another entity with even greater powers than their supposedly supreme-in-all-things god and with the ability to outwit it, even though that claim is blasphemous within their own religious beliefs. They need to hold those two diametrically opposite views of 'creation' simultaneously to continue to deny the evidence for evolution by natural selection of which the SARS-CoV-2 virus is a perfect example.

And those creationists who do actually believe the religion they purport to believe and who won't contemplate blasphemy, have no recourse but to believe that the SARS-CoV-2 virus was not only designed by their putative designer god but that it also regularly updates it to continue making us sick despite the efforts of biomedical scientists, because the alternative it to accept the unthinkable and ascribe it all the a god-free natural process of evolution by natural selection, just as science claims.

The following article by Suman Majumdar, Associate Professor and Chief Health Officer - COVID and Health Emergencies, Burnet Institute; Brendan Crabb, Director and CEO, Burnet Institute; Emma Pakula, Senior Research and Policy Officer, Burnet Institute; and Stuart Turville, Associate Professor, Immunovirology and Pathogenesis Program, Kirby Institute, University of New South Wales, Australia, explains why the emergence of the JN.1 variant of SARS-CoV-2 is a significant evolutionary step change. It is reprinted from The Conversation under a Creative Commons licence, reformatted for stylistic consistency:

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

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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:

Unintelligent Design - How Ovulation Goes Wrong Because It Wasn't Intelligently Designed

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Gene expression atlas captures where ovulation can go awry | Cornell Chronicle

Back in the late 1960s and early 1970, in what seems like a different lifetime now, I was a senior research assistant in the Oxford University/MRC Neuroendocrinology Research Unit, researching the hormonal control of ovulation in guinea pigs. Two of our tools were radioimmunoassays I had adapted for measuring extremely low levels of a hormone in guinea pig anterior pituitary glands known as luteinizing hormone (LH), and another similar assay for measuring the level of the steroid progesterone in guinea pig blood.

Sadly, having worked for close on two years towards producing a research paper with hundreds of assay results, thousands of microscope slides, hundreds of electron micrographs and a freezer full of samples waiting to be assayed, the government pulled the rug from under our feet by withdrawing our research funding, and I was made redundant, so my work was never published. Disillusioned and with a young family to support, I left research and perused a career in the NHS Ambulance Service instead - but that's a different story, and not relevant to the subject of this blogpost, which illustrates how much science has progressed in the last 50-60 years.

Researchers are no longer researching the hormonal control of ovulation but the fine details of the genetic control of the process of ovulation at the cell level, and what they've found is that the process is far from intelligently designed by anything resembling a perfect, omniscient, omnipotent designer. It is a process that is so complex that it can, and does, go wrong. An intelligent designer who didn't want random women to be unable to shed viable eggs, could have designed a less complicated process, but you can depend on creationism's putative intelligent[sic] designer to never do something simple when there is a far more complicated and wasteful way to achieve the same result.

The research, published a few days ago in Proceedings of the National Academy of Sciences, was led by Iwijn De Vlaminck, associate professor of biomedical engineering in Cornell Engineering, and Yi Athena Ren, assistant professor of animal science in the College of Agriculture and Life Sciences. The paper’s lead author is Madhav Mantri, Ph.D., now a postdoctoral researcher at Stanford University.

The team used a form of RNA tagging to map the gene expressions that occur during ovarian follicle maturation and ovulation in mice.

This spatial transcriptomics map depicts the cell types of a mouse ovary undergoing hormone-induced ovulation

The research is explained in a Cornell University Press release:

Bible Blunders - How Bronze Age Goat-Herders Described The Universe - And How It Really Is

N79, a star-forming region in the Large Megallanic Cloud

Credit: ESA/Webb, NASA & CSA, O. Nayak, M. Meixner

The Universe as described in Genesis 1: 6-18

Galactic Genesis: Webb Space Telescope Reveals Massive Star-Forming Complex

If you asked any 6-year-old to draw a picture of what they thought the world with the sky, sun, moon and stars would look like if you could stand outside it, chances are they would come up with something not massively different to the way it is described in Genesis:

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

And God made two great lights; the greater light to rule the day, and the lesser light to rule the night: he made the stars also. And God set them in the firmament of the heaven to give light upon the earth.

Genesis 1:16-18

And it gets even more laughable when you read in Daniel:

Therefore the he goat waxed very great: and when he was strong, the great horn was broken; and for it came up four notable ones toward the four winds of heaven. And out of one of them came forth a little horn, which waxed exceeding great, toward the south, and toward the east, and toward the pleasant land. DANI And it waxed great, even to the host of heaven; and it cast down some of the host and of the stars to the ground, and stamped upon them.

Daniel 8:8-10

And it doesn't get any better in the New Testament, where the authors also though Jesus would believe the stars would fall to Earth when they broke loose.

Immediately after the tribulation of those days shall the sun be darkened, and the moon shall not give her light, and the stars shall fall from heaven, and the powers of the heavens shall be shaken.

Matthew 24:29
(Quoting Jesus)

And the stars of heaven shall fall, and the powers that are in heaven shall be shaken.

Mark 13:25
(Quoting Jesus)

And the stars of heaven fell unto the earth, even as a fig tree casteth her untimely figs, when she is shaken of a mighty wind.

Revelation 6:13

Malevolent Designer News - How To Keep Ahead In The COVID Game Against Creationism's Divine Malevolence - Keep Being Boosted

How long does immunity last after a COVID infection?

Creationists stuck with the evidence of parasites and viruses that appear to be designed for two purposes only - making more copies of themselves and increasing the suffering in the world by making us sick and die - traditionally try to ride two horses. They blame something else, like 'The Fall' or 'Sin' for them, whilst still arguing that their putative designer god is supreme in all things and the only entity capable of creating complex organisms.

They also get in a terrible muddle when asked whether their 'designer' god included an immune system to protect us from these parasites when it designed us before 'The Fall', in which case it was planning for it all along, or whether there was a subsequent upgrade to V.1.2, in which case it couldn't have been omniscient and had to redo its design to account for the unforeseen.

But whatever rationalisation creationists can think up for these mutually contradictory beliefs, we are left with the fact that viruses like the SARS-CoV-2 virus and our immune system are locked in an arms race, in which human medical science has had to get involved because the immune system isn't fit for purpose, and the protection it gives us is only temporary.

Meanwhile, medical scientists, aware of the fact that evolution by natural selection is going to continually produce new variants of the virus and that these viruses may become better at evading our defences, continue to apply that knowledge and develop new vaccines against the latest variants.

The following article by Lara Herrero, Research Leader in Virology and Infectious Disease, and Wesley Freppel, Research Fellow, Institute for Glycomics, both of Griffith University, Australia explains why regular vaccination with boosters to keep out immune system primed for the latest iteration of the arms race with a latest version of the virus. The article is reproduced from The Conversation under a Creative Commons licence, reformatted for stylistic consistency:

Malevolent Designer News - How Bacterial Pathogens Are Cleverly Designed to Invade Their Victim's Body

The exceptional secretion mechanism of Tc Toxins.

MPI MOPH

Functional model for Yen-Tc toxicity. Following ingestion of the Tc, it is likely that the surface-bound chitinases bind to and/or degrade the chitin-rich peritrophic membrane of the insect midgut. Cell surface recognition is likely facilitated by motifs within the A subunits prior to internalization. Similarities to the well characterized bacterial binary toxin systems (e.g., anthrax, cholera, diphtheria) suggest a mechanism involving receptor-mediated endocytosis followed by pore formation and translocation of the B and/or C components into the cytosol (I), although alternative mechanisms (e.g., II, III) cannot be ruled out.

Landsberg, MJ., Jones, SA., Rothnagel R., et al (2011)

24-01-18 | Max Planck Institute of Molecular Physiology

Imagine you're in charge of an invading army laying siege to your enemy's outer defences. How do you neutralise them?

One way would be to send a small group of soldiers, packed with high explosives and deadly toxins on a kamikaze mission into the defences, with instructions to detonate their explosives and so spread the toxins when inside to destroy the defences and kill the defenders. You could improve on that by removing any temptation the suicide bombers might have to not detonate their defences by automating the trigger to fire as soon as they encountered the defender.

That's exactly what a team at the Max Planck Institute for Molecular Physiology (MPI MOPH), Dortmund, Germany, have found bacteria use to gain access to their victim’s body and make their hosts sick and die. The team, led by Stefan Raunser, Director of MPI MOPH, have published their findings, open access, in Nature Microbiology. Their work is described in a MPI MOPH press release: