Malevolent Designer News - How A Bacterium Is 'Intelligently Designed' To Turn Plants Into Zombies

The Life Cycle of a 26S Proteasome.

From: Marshall, R.D. & Vierstra, R.D. (2019)
Figure 6)

From Infamy to Ingenuity – Bacterial Hijack Mechanisms as Advanced Genetic Tools | John Innes Centre

Scientists working at the John Innes Centre, Norwich, Norfolk, UK., have worked out the sneaky way a bacterium converts an internal cell mechanism in plants to suit its own purpose at the expense of the host, in another example of how a parasite can zombify its host.

Creationists looking at this mechanism from the arrogant perspective that sees their own ignorant incredulity as scientific data, would conclude that it must be intelligently designed, but would then need to perform intellectual summersaults to explain why, even though their own putative creator god is the only supernatural entity capable of designing complex living organisms, something called 'Sin' also creates complex living organisms, so their omnipotent god is not responsible for parasites.

The parasitic Phytoplasma bacterium is transmitted by insects and causes diseases like Aster Yellows, significantly diminishing yields in leaf crops including oilseed rape, lettuce, carrots, grapevines, onions, and a variety of ornamental and vegetable crops worldwide. It is also responsible for the familiar 'witches' brooms' in trees in which the plant produces a proliferation of thin branches and leave.

How it does this is explained in an open access research paper in PNAS. It does it by hijacking the protein recycling function of a cell organelles, the 26S proteasome, so first a little AI background about the 26S proteasomes:

Creationism in Crisis - Humans and Other Apes Are Born With Similar Brains

A new study challenges the belief that human newborns have significantly less developed brains than other primates. The study found that humans are born at a typical development level for primates, but their brains grow more after birth, leading to the impression of underdevelopment.

Contrary to current understanding, the brains of human newborns aren’t significantly less developed compared to other primate species but appear so because so much brain development happens after birth.

Brains of newborns aren't underdeveloped compared to other primates | UCL News - UCL – University College London

Scientists are revising what was believed about the state of development of a human baby's brain at birth compared to that of a newborn Chimpanzee - but not in a way that brings any comfort to creationists.

This research compares the brain development of a human baby with that of other apes because the scientists have no doubt that humans are apes, so comparisons are scientifically valid.

It had been thought that a newborn human's brain was underdeveloped, or altricial, compared to the other apes, but this paper shows that to be a false impression caused by the fact the a human baby's brain grows more quickly and becomes more complex than that of our close relatives, however, the starting point is very similar to that of a chimpanzee.

The paper by researchers Aida Gómez-Roblesa and Christos Nicolaou of the Department of Anthropology, University College London (UCL) together with colleagues Jeroen B. Smaers of the Department of Anthropology, Stony Brook University, New York, USA and Chet C. Sherwood of the Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC, USA, is published open access in Nature Ecology & Evolution.

The research and its significance are explained in a UCL News release:

Unintelligent Design - Or Is It Malevolence? How Bacteria Are Designed to Exploit Our Mucus

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[Right caption/credit]

Movement of mucus in the respiratory tract

Blausen.com staff (2014). "Medical gallery of Blausen Medical 2014"
Via Wikimedia (CC BY 3.0)

Bacteria's mucus maneuvers: Study reveals how snot facilitates infection | Penn State University

The mucous membrane lining our respiratory system has evolved (or, according to creationists, been intelligently [sic] designed) to keep our respiratory system clean as we breathe in air containing particles of dirt, dust, pollen and bacteria. It does this by secreting mucus that traps the particles, then ciliated cells on the surface sweep them towards our pharynx to be swallowed and disposed of in our digestive system where the proteins in the mucous are recycled.

Other body cavities are lined by a mucous membrane that serves to protect and keep the cavity moist and lubricated.

But, in one of those research papers that creationists have to avoid reading, a team of researchers from Penn State University, have shown how bacteria have evolved (or been intelligently [sic] designed, according to creationists) to exploit the mucous, the better to infect us and make us sick, and the thicker the mucus, the better it is for these would-be pathogens.

Infections by bacteria, known medically as opportunist infections, especially in the nasal sinuses and lungs, are a frequent complication of viral infections such as a common cold or influenza. These opportunist infections can be more dangerous than the virus infections that facilitate them.

The team showed that bacteria find it easier to swim, swarm and form colonies in thick mucus than in thin, watery mucus and that this swarming probably helps protect them from the antibacterial enzymes in the mucus.

Their research is explained in a Penn State news release:

Creationism in Crisis - A Monster Virus Is A BIG Problem For Creationists

Pithovirus sibericum

Legendre, Matthieu; Bartoli, Julia; Shmakova, Lyubov, et al. (2014)

Pithovirus sibericum

Pithoviruses Are Invaded by Repeats That Contribute to Their Evolution and Divergence from Cedratviruses | Molecular Biology and Evolution | Oxford Academic

Regular readers with very long memories may remember how I wrote about something big and potentially nasty emerging from Siberian permafrost back in 2014.

The 30,000-year-old monster in question was a form of giant virus then unknown to science, now named Pithoviruses sibericus. It came back to life when thawed. Since then, several other related pithoviruses have been discovered in soil and aquatic sources. Fortunately, all those discovered so far are parasitic only on one species of amoeba, Acanthamoeba castellanii and don't pose a threat to humans or multicellular life.

The question was, why are they so large, or more particularly, why do they have such a massive genome, including some genes normally found in complex cells. the Pithovirus species so far discovered have a genome of between 460 to 686 kb. Their genome, moreover, is similar to that of bacteria and archaea, in that it is DNA-based and forms a single circular 'chromosome'.

But it's not the fact that the first one was found in permafrost dating back 20,000 before 'Creation Week', difficult though that little inconvenience is for creationists; it is the account of how they acquired this massive genome that is the thing of nightmares for any creationists who understand the biology.

They acquired it by processes that give the lie to their basic dogma that new genetic information can't arise in a genome without 'God magic'.

A team of researchers have shown that they acquired new genetic information and such a massive genome by:

1. Horizontal gene transfer (5% -7 %)
2. Gene duplication (14% - 28%)
3. Massive inversions of repeated sequences of DNA.

All these are familiar mutations in which the genome size is increased, and by which 'spare' copies of genes and novel sequences are free to mutate and give rise to new genes and new functions.

And this gives the lie to the ludicrous creationist dogma that no new information can arise by mutation because all mutations are deleterious. There is nothing deleterious in having a spare copy of a gene, nor in mutations in that spare copy, least of all if it gives a new function that increases fitness.

The researchers, from the Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix–Marseille University, Centre National de la Recherche Scientifique, Marseille, France were led by Matthieu Legendre. Their findings are published, open access, in Molecular Biology and Evolution:

Creationism in Crisis - Evolution of Rock Doves & Domestic Pigeons

Rock dove, Colmba livia neglecta (Iran)

Picture: Γεωργός via Wikimedia (CC BY-SA 4.0)

Rock dove, Columba livia.
The wild ancestor of the domestic or town pigeon

Redefining the Evolutionary History of the Rock Dove, Columba livia, Using Whole Genome Sequences | Molecular Biology and Evolution | Oxford Academic

A great deal is understood about how the many different varieties of domestic pigeon were produced ever since Charles Darwin used them to illustrate the role of selection in evolution. In this case, selection is human selection rather than natural selection, although the difference is a matter of semantics if you regard human selective breeders as part of the domestic pigeon's environment.

Incidentally, creationists should note that Darwin never claimed evolution always resulted in new species. As he showed with his selective breeding examples, it produced new varieties too. Some of these have become so far removed from their wild ancestors that they rank as subspecies, like the domestic pigeon, Columba livia domestica

Although the radiation of domestic varieties is now well understood, the wild ancestors, the rock doves, have received far less attention until now. Now a paper by a team led by Germán Hernández-Alonso of the Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark, redresses that discrepancy by analysing the entire genomes of 65 historical rock doves that represent all currently recognized subspecies and span the species’ original geographic distribution. 3 of these specimens were from Charles Darwin's collection.

This works shows that rock doves have diversified into a number of subspecies across their range, stemming from a subspecies now restricted to a small coastal strip of Northwest Africa, C. livia gymnocyclus. One of these subspecies received a substantial ingression of genes from a related species, C. rupestris after it split from the West African population but before it became domesticated. The result is that C. livia gymnocyclus should now probably rank as a species in its own right, C. gymnocyclus.

First a little about the evolution of domestic pigeons:

Wonderful World - Ten Reasons to Like Spiders

Top left: Giant trapdoor spider Euoplos dignitas

Bottom left: European garden spider, Araneus diadematus

Top right: Gooty Sapphire Ornamental tarantula, Poecilotheria metallica

Bottom right: Banded Garden spider, Argiope trifasciata

Female house spider, Tegenaria domestica

Don't like spiders? Here are 10 reasons to change your mind

Back in the past, in what now seems like a lifetime ago, I managed the Emergency Operations Centre for my local Ambulance Service which was housed in a single-storey building in the grounds of the Church Hospital, Oxford. One of my nicknames was 'Spiderman' because of my fondness for spiders.

The roof space of this building was home to a population of 'house spider' or Tegenaria domestica, a good-sized one of which can be 4 inches or more across its outstretched legs. They frequently paid us a visit by coming through the light fittings or round the edges of the aircon unit.

The house spider is well-named, being one of those commensal species that, like barn swallows, can't exist without human habitation and so must have evolved after we became settled and built permanent dwellings.

Despite its large fangs, it is entirely harmless to humans, even if it does manage to pierce the skin - something I tried to impress on my staff, whose first response to one running across the floor was to stamp on it.

Despite this reassurance, one of my assistants was so arachnophobic she refused to enter the room until the spider was gone - although what she thought it would do to her was a mystery, so one of my tasks was to gently catch the spider in my hands and put it outside, whereupon I would deliver my famous (or maybe infamous) spider talk, in which I explained why spiders are such fascinating creatures - their very long evolutionary history from a common ancestor with scorpions; their multiple eyes (some for binocular vision and some for detecting movement) and above all their amazingly engineered webs.

Orb web spiders like the common garden spider, Araneus diadematus, make two sorts of silk - one to act as scaffolding and the radial threads of the web and sticky one to form the circular strands. Each thread of silk consists of multiple fine filaments that stretch very quickly to catch a flying insect without it bouncing off, then recoil slowly to avoid throwing the insect free. All this is controlled by the fine molecular structure and electrostatic bonds between the filaments. The result is a thread that, weight for weight, is stronger than steel.

One small spider that is common on walls and buildings in Oxford is the zebra spider, Salticus scenicus, a tiny black and white-striped spider, only a few millimeters long, that has amazing eyes. It is a hunting spider that preys on small insects, even some three times its size, by jumping on them. Its modus operandum is to crawl over the surface of walls and roofs and, when it sees its prey, it approaches slowly and when close enough, judges the distance perfectly and pounces. It will also jump across gaps, again with a perfectly judged jump, many times its own body length, rather like a human jumping the Grand Canyon from a standing start, but before it does so, it dabs the tip of its abdomen down to fix a 'safety line' of silk, just in case. To perform these feats, the zebra spider needs a high degree of visual acuity and binocular vison. The amazing thing about this spider is the way it overcomes the problem for visual acuity of such a small retina; it rapidly moves the retina up and down, effectively increasing its size.

The jump is accomplished, not by muscles in the legs, but by a sudden increase in haemocoelic blood pressure which straightens the front and back legs, so the spider always jumps with its legs extended.
I always hoped my spider talk would impress my staff enough to take an interest in spiders rather than seeing them as creepy-crawly things to be half-feared and killed simply for sharing the building with us. Alas, only one or two ever followed my example and picked them up to put them out of a window.

All that was by way of introduction to an article in The Conversation in which Leanda Denise Mason, an Associate Lecturer, Curtin University, Australia give her ten reasons to like spiders, or at least change your mind it you don't. Her article is reprinted here under a Creative Commons licence, reformatted for stylistic consistency. The original can be read here.

Creationism in Crisis - Scientists Show How a Dynamic And Changing Earth Influenced Evolution Over Millions of 'Pre-Creation' Years

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[Right caption/credit]

Landscape dynamics determine the evolution of biodiversity on Earth - The University of Sydney

A dynamic and changing Earth.

From Salles, T., Husson, L., Lorcery, M. et al. (2023

Again, it's the turn of geologists to refute creationism without even trying, like so many biologists do with their daily work.

Creationists insist that Earth is 'fine-tuned' for life; but as anyone who understands biology will know, life is 'fine-tuned' for Earth and the tuning process is called evolution by natural selection.

The observable fact that, over time, species have either evolved or gone extinct gives the lie to the 'fine-tuned for life' assertion because, if that were true, there would be no selection pressure for change and the fossil record would show no change.

In fact, the fossil record wouldn't exist as we know it because there would have been no evolution beyond the first free-living, single-celled prokaryote organisms because their environment would have been perfect for them.

Yet, as we know from daily observation, Earth is a changing and dynamic planet with periodic climate change, earthquakes and volcanoes caused by the slow process of plate tectonics, changing oxygen and carbon dioxide levels caused by the rise and fall of major ecosystems, and changing ocean currents caused by a number of different factors, not the least of which are climate change and plate tectonics. Then there are the cosmological changes caused by the Milankovitch cycles.

One of the consequences of this dynamic change is the way the Earth's surface is continually being recycled over geological time by erosion, transportation in water and sedimentation in ocean deposits as nutrients, then subduction and mountain-building and eventual resurfacing through volcanic activity. This gives changing levels of nutrients in the oceans that affect biodiversity both in the seas and on land.

This is the conclusion of a study by a team of geologists jointly led by Dr Tristan Salles of The University of Sydney, Sydney, New South Wales, Australia, and Dr Laurent Husson of Université Grenoble-Alpes, Grenoble, France. They have shown an association between changes in nutrient levels due to sedimentation and mass extinctions. Their findings are published open access in Nature and are explained in a University of Sydney news release:

Creationism in Crisis - How America's East Coast Formed - 230 Million Years Before 'Creation Week'

Vector graphic of the land mass of the supercontinent Pangea.

Credit: Rainer Lesniewski

Vector graphic of the land mass of the supercontinent Pangea.

Credit: Rainer Lesniewski

Study Illuminates Formation of U.S. East Coast During Breakup of Supercontinent Pangea - SMU

It's not just the biologists who are incidentally refuting creationism with just about every peer-reviewed research paper; now the geologists are doing the same.

The problem for creationists is that their superstition has no basis in facts because it didn't happen and the record of how it did happen is in the evidence that science is revealing, so inevitably that evidence is going to refute the childish fairytale that creationists were taught by their parents who were taught it by their parents...

Take this piece of geological research into the formation of the East Coast of the USA, for example. It was carried out by scientists from the University of New Mexico, Southern Methodist University seismologist, Professor Maria Beatrice Magnani, and scientists from Northern Arizona University and the University of Southern California. It occurred in that long 'pre-Creation' history before creationists think Earth was magicked up out of nothing.

It is based on the knowledge that the East Coast of America formed when the supercontinent, Pangea, broke up some 230 million years before creationists think Earth existed.

Because it wasn't known about by the parochial and scientifically illiterate Bronze Age authors of their holy books, creationists are completely unaware of the way the present land-masses were formed on the breakup of Pangea, despite the abundant tectonic evidence in the form of mid-ocean ridges with their embedded record of multiple magnetic reversals over millions of years, subduction zones, earthquakes, volcanoes and uplift folds to form hills and mountains at tectonic plate margins.

Geology is a science about which my education has been somewhat lacking (I'm a biologist, physiologist and biochemist by training) but as I understand it, the edges of continents that were the site of the original rifts that opened up to form the oceans, particularly the Atlantic Oceans, will also show evidence of magma that would have welled up in the initial stages of the split.

In the case of the North American Atlantic coast, which is passive in this process because it is simply being pulled away from what is now Northwest Africa, and has not been subject to collisions with other plates, or any significant volcanic activity, these traces of magma are still to be found in the edges of the continental shelf beneath the ocean floor. Associated with the passive margin is a magnetic anomaly, The East Coast Magnetic Anomaly (ECMA), that runs parallel to the American East Coast.

My knowledge of the American East Coast is limited to two week vacation in Boston about 12 years ago, during which I tried bathing in Cape Cod Bay from a beach near South Wellfleet, to discover that I was standing barefoot on king crabs, either dead or alive (their remains littered the beach along Cape Cod), so I didn't spend long in the water - not that they were any threat to me but because they are not very pleasant to walk on.

As the Southern Methodist University news release explains:

Malevolent Design News - How 'Intelligently Designed' Pathogens Use The Tactics Of A Burglar To Make Us Sick

Model pathogen, Toxoplasma gondii

[Right caption/credit]

Pathogens use force to breach immune defenses, study finds: IU News

Creationists trying to defend their magic creator god argue that it didn't create pathogenic parasites and instead blame it on 'Sin'. Sadly for them, however, one of their leading cult gurus, Michael J. Behe, has pulled that rug from underneath them by writing a book in which he used the supposedly irreducibly complex flagellum of a common pathogen, Escherichia coli (E. coli) to argue that it must have been intelligently designed, (so God did it!). Behe's book, 'Darwin’s Black Box' is constantly being cited as 'proof' that the reputedly omniscience, omnipotent creator god of the Bible and Qur'an is real and creates things.

So, let's go with their 'proof of God' argument and assume therefore that pathogens are the intentional design of their putative designer god and were designed for the function they perform - making us sick, while producing more copies of themselves to make others sick too.

Now a team of researchers have shown the lengths this alleged designer god has gone to to continue making us sick and suffer. The team, led by Professor Yan Yu, of the College of Arts and Sciences’ Department of Chemistry, Indian University, Bloomington, IN, USA have shown that the intracellular pathogens like Toxoplasma, tuberculosis, malaria and chlamydia don't use subtlety to gain entry into the cell, probably because this would provoke an immune response as our immune system, allegedly designed by the same intelligent designer to protect us from the pathogens it designed to harm us, tried to fight back. Instead, they use brute force to break into the cell and once inside use the same force to break into a cell vacuole where they are protected by the internal cell membranes.

How the research team which included Professor Yan Yu's colleagues from Indiana University with Thomas K. Gaetjens and Steven M. Abel of the Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, USA, made this discovery is explained in an Indian University new release:

Creationism in Crisis - How Snakes Evolved To Meet The Demands Of Their Habitat And Food Sources

There are more than 800 species of dipsadine snakes, ranging from less than 12 inches to more than 9 feet in length.

Photos: Gregory G. Pandelis.

Dipsas catesbyi, a snail-eating species

Snake skulls show how species adapt to prey - News Center - The University of Texas at Arlington

The ability to catch and consume prey species is a key aspect of evolutionary biology in carnivorous species, for obvious reasons, and so is a major source of divergence and radiation of species as each species become more and more specialised at catching different prey species.

An example of this was published recently in the journal BMC Ecology and Evolution in which three researcher, led by Gregory G. Pandelis of the Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas at Arlington, Arlington, Texas, USA with two colleagues from the Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA, showed a correlation between prey species and skull morphology in dipsadine snakes.

How Science Works - Facing The Challenges of New Information

Artistic rendering of the possible view from LHS 3154b towards its low mass host star. Given its large mass, LHS 3154b probably has a Neptune-like composition.

Credit: Penn State
Creative Commons

Discovery of planet too big for its sun throws off solar system formation models | Penn State University

Theists embrace certainty at the expense of truth because it feels safe in an uncertain world in which truth is subordinate to opinion. Scientists embrace doubt because it leads them closer to the truth in a world full of wonder and begging to be understood, where truth is supreme and leads opinion wherever it may go.

In other words, religion is unreasonable certainty; science is reasonable uncertainty.

So, if there is one thing theists hate, it's being challenged with new information. It's not just scientific information that shows how far removed from reality their founding myths, such as those in the Bible, are, but information that shows, for example, that several of the 'epistles' attributed to Paul were forgeries trading on his name to give them added authority, or that the description of his 'conversion' on the road to Damascus was actually a description of a temporal lobe epileptic seizure and that his reason for being there didn't make any sense in the geo-political and legal context of the times.

So heavily invested are most devout theists that inconvenient facts like these are not considered reasons to change their minds; they are considered reasons to look for excuses to deny and dismiss the evidence. There is a vast and very lucrative industry, especially in the USA, which specialises in selling people 'reasons' to deny the science and believe the myths in the Bible, for instance. Remaining stoically ignorant of science is even considered virtuous in some parts of the world where religions still have a strangle hold.

Contrast that with science, where the most exciting news is that someone has discovered something that means we need to revise our thinking and change our minds. With science, when the facts change, the intellectually honest change their minds; with religion, when the facts change, they try to change the facts because the beliefs are sacred.

An example of how science welcomes and embraces new evidence is the news that cosmologists have probably discovered a massive planet orbiting a sun that is too small for such a large planet orbiting so close to it. This might not sound dramatic but if confirmed, it will demand a reassessment of how we think planetary systems form.

Creationism in Crisis - Evolution of a Carnivorous Pitcher Plant by Gene Duplication - New Genetic Information Created Naturally

Genomic study sheds light on how carnivorous Asian pitcher plants acquired signature insect trap - University at Buffalo

East Asian pitcher plants, Nepenthes gracilis.

Photo: Pierre-Louis Stenger

East Asian pitcher plants capture insects using their highly specialized pitcher-shaped leaves, which may have resulted from duplicated genomes.

Photo: Pierre-Louis Stenger.

Genomic study sheds light on how carnivorous Asian pitcher plants acquired signature insect trap - University at Buffalo

Unlike so many biology, geology and palaeontology papers published recently, this paper doesn't refute creationism by showing how much of Earth's history occurred before creationism's mythical 'Creation Week', although the genetic changes almost certainly did occur in the long period of 'pre-Creation' history.

Instead, it refutes two more of creationism's favourite fallacies:

1. Genetic information can't be created without the magical assistance of a creator god. This is a fundamental axiom, taught to creationists by cult leaders such as William Dembski, who fooled them by equating 'information' with energy and citing the Third Law of Thermodynamics. It's a belief clung to despite the repeated evidence of gene duplication and repurposing of resulting redundancy.
2. The fallacy of irreducible complexity which wrongly assumes that a complex system must have arisen as a single event and was so highly unlikely that a magic god must have created it. This is taught to them by another cult leader, Michael J. Behe, despite the evidence that 'irreducibly complex' systems can and do arise by exaptation of pre-existing, redundant structures or steps in a metabolic pathway that arise in parallel in the species gene pool, not all at once in a single event in one individual or cell.

The paper, by a large team of researchers that included Victor Albert, PhD, Empire Innovation Professor in the University at Buffalo Department of Biological Sciences, within the College of Arts and Sciences, concerns the evolution of the carnivorous East Asian pitcher plant, Nepenthes gracilis, in particular the 'pitcher' traps and the condition of dioecy, which is unique in this genus of plants.

And, just in case creationists declare that mere gene duplication wouldn't create enough new genetic information, this species doesn't have just one or a few genes duplicated and repurposed; they don't even stick with a whole genome duplication, They actually have five whole genome duplications making them decaploid, an extreme example of polyploidy!

Creationism in Crisis - Scientists Identify a Possible Cause of a Mass Extinction - 201 Million Years Before 'Creation Week'

An algal bloom

Ichthyosaurs, marine reptiles that went extinct during the Triassic–Jurassic mass extinction.

Deoxygenation levels similar to today’s played key role in marine extinctions during major past climate change event - News & Events | Trinity College Dublin

201 million years before creationists believe Earth was created, something happened to cause one of the pivotal moments in Earth's long 'pre-Creation' history, when very many species went extinct, providing the opportunity for the few survivors to evolve to occupy the vacant niches, so putting the evolutionary trajectory of Earth's ecosystems on a course that led us to where we are today.

This was the Triassic–Jurassic mass extinction.

Creationism in Crisis - Ancestral Geckos from 150 Million Years Before 'Creation Week'

The black banded gecko, Coleonyx fasciatus, is a good approximation of the physical appearance of Helioscopus dickersonae

Francisco Farriols Sarabia
via Wikimedia (CC BY 4.0)

Skeleton of Eichstaettisaurus, an early member of the gecko lineage from the Late Jurassic, Germany

Yale study gives grandmother gecko a place of honor — and a new name | YaleNews

If you want to see the origin of today's species, the best place to find them will be in the fossil record of all the millions of species that lived in that vast expanse of pre-'Creation' time, when some 99.97% of Earth History happened and 99% of all known species lived and went extinct - before creationists believe Earth was created.

For example, and for yet another example of a science paper that casually refutes creationism with no effort to do so on the part of the authors, a team of palaeontologists from Yale have identified a new fossil lizard as the ancestor of modern geckos that lived during the late Jurassic period, 163.5 to 145 million years ago. This pushes the date of the earliest known member of the gecko line in North America back 100 million years.

The team have named the new species, Helioscopus dickersonae and have published their find open access in the journal Proceedings of the Royal Society B. The publication is accompanied by a Yale University press release:

Creationism in Crisis - Early European Humans Hunted Beavers 400,000 Years before 'Creation Week'

Cut marks on the left femur of a beaver

Eurasian beaver, Castor fiber,
Hunted by early hominins in Europe.

Early humans hunted beavers, 400,000 years ago | Press and Public Relations

You know, this is so much like shooting fish in a barrel, that I would feel sorry for creationists. If only they were so smugly certain and lacking in self-doubt, but here's another of those so predictable scientific papers that refute creationism without even trying.

Previously, it was thought that Middle Pleistocene humans in Europe hunted large game such as bovids and rhinoceros for food, but this may be because the bones of large animals are better preserved than the bones of smaller mammals.

Now, a new study by a team from Johannes Gutenberg University Mainz (JGU), the Leibniz Zentrum für Archäologie (LEIZA), also in Mainz, and Leiden University in the Netherlands, shows that Middle Pleistocene humans hunted beavers as a food resource and possibly also for their pelts, 400,000 years before creationists think Earth was created.

The beavers they hunted were the now extinct Eurasian giant beaver, Trogontherium cuvieri, and the still living European beaver, Castor fiber.

The team have published their findings in the journal Scientific Reports.

The publication is accompanied by a brief press release from Johannes Gutenberg University:

Creationism in Crisis - How Elephants Got Their Trunks and Tusks 20 Million Years Before 'Creation Week' - No Magic Required

Artist's impression of Platybelodon grangeri

Credit: Tim Bertelink via Wikimedia (CC BY-SA 4.0)

Platybelodon grangeri (artist's impression)

How shifting climates may have shaped early elephants’ trunks | For the press | eLife

As expected of scientific research papers, this one deals with events that occurred in that vast expanse of time before creationists think Earth was created, when 99.97% of Earth's history occurred.

This one, published open access in eLife, explains how the ancestors of modern elephants and their recently extinct relatives, the mammoths, got their long flexible trunks and used them for their unique feeding method.

The paper by lead author, Chunxiao Li, and colleagues from the Key Laboratory of Vertebrate Evolution and Human Origins of the Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China, and including Burt Wolff of the Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL, USA and Fajun Sun of the Department Environmental Science & Technology, University of Maryland, MD, USA, "combines multiple analyses to reconstruct feeding behaviours in the extinct longirostrine elephantiforms - elephant-like mammals characterised by elongated lower jaws and tusks."

It seems that, as they grew larger, for reasons not yet fully understood, but possibly to give a larger 'vat' in which to ferment their high-cellulose diet, these early ancestors of the elephants had to evolve a longer jaw to reach the grasses and shrubs on which they grazed. The trunk extended as part of this process of facial elongation. This in turn created the opportunity for the end of the truck to play a part in holding the plants as they were cut off by the incisor teeth at the end of the lower jaw. This was more of an advantage in the open grasslands that Platybelodon inhabited, so, when climate change meant loss of habitat and eventual extinction for the two related gomphotheres, Platybelodon's prehensile trunk gave it enough advantage to survive.

A press release by eLife explains the research and its significance for understanding how elephants got their trunks:

Antivax COVIDiot News - Study Shows Vaccines Halted The Rise In Prem Births Caused By COVID-19

Covidiot Trumpanzees.
Risking the lives of unborn babies for political ends.

Study: Spike in premature births caused by COVID, halted by vaccines

About the last thing the politically-motivated, far right antivaxxers covidiots are interested in is protecting human life. With characteristic hypocrisy, many of the same frauds are also active campaigners against legal abortions and a woman's right to choose which, together with COVID-19 denialism and antivaxx conspiracism, have become major talking points in the Trumpanzee far right playlist.

The hypocrisy of these frauds was revealed yesterday in a study which shows there was a huge spike in the number of premature births during the early phase of the COVID-19 pandemic when women infected with the virus spontaneously aborted their baby. The same study also shows that in those areas where the vaccine uptake was high, the premature birth rate quickly fell back to pre-pandemic levels, but in areas where uptake was low, it took another year to return to pre-pandemic levels.

The study was carried out by Professor Jenna Nobles of Wisconsin–Madison University and Professor Florencia Torche, of Stanford University who have published their findings in Proceedings of the National Academy of Sciences (PNAS).

As the Wisconsin–Madison University press release explains:

Creationism in Crisis - The Daily Life of a North American Mammoth - 7,100 Years Before 'Creation Week'

An illustration of an adult male woolly mammoth as it navigates a mountain pass in Arctic Alaska, 17,100 years ago. The image is produced from an original, life-size painting by paleo artist James Havens, which is housed at the University of Alaska Museum of the North.

Image by James Havens,
The Havens Studio

Study takes unprecedented peek into life of 17,000-year-old mammoth | uOttawa

A view of the excavation site of the mammoth tusk from north of the Brooks Range in Alaska.

Photo by Pam Groves, University of Alaska Fairbanks

According to creationist superstition, a magic man made of nothing created the entire Universe, Earth, and all life on Earth, out of nothing, using magic words spoken in a language that no-one else spoke, and, using the rotation period of a planet that didn't exist, completed it all in 6 days during what creationists call 'Creation Week'.

7,000 years before that, mammoths were living their daily lives in what is now Alaska, and leaving tusks that carried a daily record of where they were living and consuming vegetation, in the form of 'signature' ratios of isotopes of strontium.

Strontium finds its way into the plants that animals eat from the underlying rocks where the ratio of the different stable isotopes of strontium (⁸⁷Sr and ⁸⁶Sr) in it changes very little over millions of years, giving a characteristic 'signature' that can be used to identify where the food plants were growing. This signature strontium was deposited in the growth layers of mammoth tusks, starting at the tip when the mammoth was born, and ending in the root when the mammoth died. In between the two is a complete record of where the mammoth roamed.

But first, scientists need to build a strontium isotope map so they can match up the record in the tusks with the geographical location in which the food grew that day. And this is where voles come in. Voles also eat the strontium-containing grasses that mammoths eat and so build up a record in their teeth. However, voles are mostly very sedentary in their habits so have a very restricted range and because the strontium in the rocks changes little, even present-day voles can be used to build up a strontium isotope map.

Using that knowledge, an international research team led by Clément Bataille, an assistant professor and researcher in the Department of Earth and Environmental Sciences in the Faculty of Science, Ottawa University, Canada have analysed the strontium content of a mammoth tusk found on Alaska’s North Slope above the Arctic Circle, to build up a picture of its daily life and travels.

The study is explained in a press release from Ottawa University:

Malevolent Designer News - Scientists Have Disovered the Sneaky Way Creationism's Putative Designer Created Childhood Leukaemia

Pediatric oncology: Scientists discover new Achilles heel of leukemia cells | Current news from the Goethe University Frankfurt

In leukemia, white blood cells divide uncontrollably.

Acute myeloid leukaemia, micrograph

Pediatric oncology: Scientists discover new Achilles heel of leukemia cells | Current news from the Goethe University Frankfurt

With the double-think that characterises creationsm, creationists will use, depending on what facts they are disputing, two mutually exclusive arguments:

1. A combination of the argument from ignorant incredulity and the false dichotomy fallacy. This argument depends on the assumption that there is only one supernatural entity capable of creating something as complex as DNA, with the conclusion "Therefore, God did it!", which of course is also a non-sequitur and an intellectually dishonest presupositional invocation of something unproven as evidence that it exists.
2. On another day, presented with something so patently evil as childhood cancer or nasty parasites that kill many and make life a misery for millions more (and not just humans, but just about every living thing) creationists invoke somethign called 'Sin' as being responsible for its design and/or creation.
   

In other words, they will argue both that their god is the only entity capable of creating anything, and that 'Sin' can create things too; and their supposedly omnipotent god is powerless to prevent it.

So, it will be interesting to see what arguments creationists will come up with to counter the argument that, if creationism has any substance, the same designer must have designed childhood leukaemia, in full knowledge of the suffering and grief it would cause not just to the child but to his/her parents and relatives.

But I suppose they could always cite William Lane Craig's repugnant defence of religiously-inpired infanticide - "killing children is not wrong because they go straight to heaven so it makes them happy".

But whatever excuse they make, creationists are hoist by their own petard in arguing the false dichotomy fallacy, so they are stuck with portrying the god they purport to worship as the designer of childhood leukaemia - a position they seem to prefer to having people accept that evolution by natural selection is responsible for the nastiness in nature as well as the wonderful.

So, given that a favourite subject for their argument from ignorant incredulity, is the structure of DNA, how will creationists react to the fact that a team of researchers from the Department of Pediatrics and the Institute for Experimental Pediatric Hematology and Oncology at Goethe University, Frankfurt, Germany has discovered a site in the DNA of cancer cells that is essential for leukemia cells to survive?

Unintelligent Design - Why Skunks Have Evolved Different Colour Patterns

Four skunks, four different patterns

Striped skunk, Mephitis mephitis

November: Skunks' warning stripes | News and features | University of Bristol

It's better to warn than to attack because attacking is costly and carries risks, but a warning is often free or takes minimal effort.

This is why many creatures advertise the fact that they can be dangerous so leave them alone - yellow and black wasps; the warning rattle of a rattlesnake, the bright colours of a poison dart frog, or the black and white pattern of a skunk, for example.

But these patterns only work as a deterrent, if the potential threat has some experience or has evolved in their presence so has a genetic aversion.

Creationism in Crisis - Human Footprints from a million years before 'Creation Week'

Children in the Upper Awash River, Melka Kunture, Ethiopia, 1.2 million - 850,000 years ago

Artist's reconstruction

Children in the water one million years ago: human fossil footprints discovered in a prehistoric river in Melka Kunture | Sapienza Università di Roma

About a million years ago hominin children were wading in the Awash River, near what is now Melka Kunture, Ethiopia. Shortly afterwards there was an eruption of a nearby volcano and their tracks in the river mud got covered in volcanic ask, or tuff, preserving a record of their passing, along with the tracks of several other species and freshwater molluscs. These are now the oldest child footprints known.

Like 99.97% of history this was taking place before creationists believe the universe was magicked out of nothing by a magic man made of nothing who said some magic words in a language that no-one spoke because it hadn't made anyone yet, and using as a basis of time, the rotation period of a planet that didn't exist. Creationists, even some adult ones, believe this magic man had earlier self-assembled out of nothing using a design it made before it existed.

Creationists believe this explains reality better than anything science can discover.

These weren't the children of modern humans but the children of an earlier species that walked upright on legs and feet that were almost indistinguishable from those of modern humans, possible Homo erectus, Home ergaster or maybe even Homo heidelbergensis, but until we have more than just footprints there is no way to be sure. All we know is that they were not Homo sapiens, which wasn't around a million years ago.

The volcanic ash buried more than just the footprints; it buried the remains of butchered animals showing the cutmarks of the obsidian tools used to butcher them, the obsidian tools and the flakes made from knapping them to shape the blades.

How these footprints were discovered by a team led by archaeologists from Sapienza University, Rome, is explained in a press release:

Children footprints.

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Animal tracks

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Mollusc traces

Melka Kunture, 50 km south of Addis Ababa, is an important complex of Pleistocene archaeological sites located along the upper basin of the Awash River, on the Ethiopian plateau. In this area, archaeological research began more than 50 years ago, and since 2011 has been carried out by the Italian mission led by Margherita Mussi and her team of the Department of Ancient World Studies of Sapienza University of Rome.

Dozens of archaeological levels have been identified over the years, found mainly along the gullies cut by the streams of the area. In 2018, in one of these incisions called the Gombore Gully, the Sapienza team had already found numerous human footprints of adults and children, tools made from volcanic stones (such as obsidian and basalt) and remains of hippos butchered by the hominins. These discoveries, sealed by a 700,000-year-old tuff, helped the researchers to reconstruct a scenario in which children assisted adults engaged in knapping stone and butchering large animals, proving that in the prehistoric environment the acquisition of skills and techniques useful for survival began at an early age.

Today, a new study on the archaeological layers of the Gombore Gully, dating back to the end of the Early Pleistocene, offers another rare image of childhood in the most ancient periods of prehistory. The research, coordinated by Flavio Altamura and Margherita Mussi of Sapienza University in collaboration with researchers from the University of Cagliari, Bournemouth University (UK) and the Urweltmuseum GEOSKOP (Germany), focused on another site of the gully, even more ancient, called Gombore II Open Air Museum where new footprints of children were found on the edge of what was a prehistoric river. The results, which shed further light on the behaviours and habits of our distant ancestors, have been published in the scientific journal Quaternary Science Reviews.

The excavations have documented a sequence of archaeological layers about 3 meters thick, which, according to the researchers, probably formed along a river and in marshy environments, cyclically invested by ashes erupted from volcanoes several tens of kilometers away. The volcanic tuffs allowed to date the layers between 1.2 million and 850,000 years ago using the method called Argon/Argon.

The excavations notably brought to light 18 fossil surfaces with footprints left by hippos, hyenas, some herbivores similar to today's wildebeests, gazelles and birds. Three of the levels have also revealed human footprints, almost all attributable to children and adolescents of the prehistoric human species Homo erectus/ergaster or possibly already to an archaic Homo heidelbergensis.

"These footprints - says Margherita Mussi, director of the Archaeological Mission to Melka Kunture - are among the oldest in the world and the earliest ever discovered made by children. Further proof of human presence near the river are the numerous stone tools: some obsidian flakes were probably trampled by hippos, which made them sink into the mud at the bottom of their footprints, indicating the coexistence of man and these dangerous animals."

In many levels, there are also prints formed by curvilinear trails with small almond-shaped hollows, the traces left by bivalve freshwater mussels, which live anchored at the bottom of rivers and lakes with clean and well-oxygenated running waters. This is an excellent indicator to reconstruct the paleo-environment and also allows to indirectly confirm the existence of fish, on which the molluscs depend during their reproductive cycle.

The children's footprints close to the prints of herbivores and molluscs show that the little hominins entered shallow and clean waters, as did the other animals. "Probably, even a million years ago" - says Flavio Altamura, who carried out the excavations - "the Pleistocene children entered the water for reasons very similar to those of modern children: to drink, to wash themselves or to try to catch fish and molluscs with their bare hands. Or more simply to play."

"This research, – Mussi concludes – carried out thanks to funding by Sapienza University and the Italian Ministry of Foreign Affairs, provides a snapshot of Pleistocene childhood and confirms that the children's attraction to watery environments and ponds - puddles included! – is deeply rooted in human behaviour. This is, in a way, the first scientific evidence of "bathing" children."

The age of the volcanic tuff was determined by the argon/argon method:

What is the Argon/Argon method for dating volcanic tuff and what are possible sources of error? The Argon-Argon (Ar-Ar) dating method is a radiometric dating technique used to determine the age of rocks, especially volcanic rocks and minerals. It is a refinement of the more widely known potassium-argon (K-Ar) dating method. Both methods are based on the radioactive decay of potassium-40 (⁴⁰K) to argon-40 (⁴⁰Ar) in minerals. Here's a brief overview of the Ar-Ar dating method and some potential sources of error:

1. Principle of the Method:
   • The Ar-Ar dating method involves irradiating a sample of the mineral or rock with neutrons in a nuclear reactor.
   • This irradiation converts a portion of the stable isotope potassium-39 (³⁹K) into ³⁹Ar.
   • After irradiation, the sample is heated, releasing argon isotopes, including ⁴⁰Ar, from the mineral lattice.
   • The released argon is then measured using a mass spectrometer to determine the ratio of ⁴⁰Ar to ³⁹Ar, which allows the calculation of the age of the sample.
2. Calculation of Age:
   • The age is calculated using the equation derived from the principles of radioactive decay and isochron plots.
   • The presence of ³⁹Ar in the sample is crucial for the precision of the method, as it helps correct for any argon loss during the heating process.
3. Sources of Error:
   • Argon Loss: If the rock or mineral has experienced partial argon loss due to metamorphism or other processes, the calculated age may be too young.
   • Excess Argon: Presence of excess argon, which was not produced by in situ decay, can lead to an overestimation of the age.
   • Inherited Argon: Some minerals may contain argon inherited from their formation, which can affect age calculations.
   • K-Ar System Resetting: If the rock has undergone significant thermal events, the K-Ar system may have been reset, leading to inaccurate age determinations.
   • Neutron Fluence: The accuracy of the method depends on the precise knowledge of the neutron fluence during irradiation.
4. Advantages:
   • Ar-Ar dating can provide more accurate and precise age determinations compared to the conventional K-Ar method.
   • It is particularly useful for dating volcanic rocks and minerals with complex thermal histories.
5. Applications:
   • Ar-Ar dating is widely used in geochronology, especially for dating volcanic tuffs, lavas, and other igneous rocks.

It's important to note that careful sample selection and analysis are critical to obtaining reliable results. Researchers must consider potential sources of contamination and thoroughly understand the geological history of the samples being dated. Additionally, advances in analytical techniques and calibration methods continue to improve the accuracy of Ar-Ar dating.

The team's findings are published in Quaternary Science Reviews:

Abstract

New ichnological data are available at the prehistoric site of Melka Kunture, Upper Awash Valley in Ethiopia. Excavation of new test pits enabled us to explore the volcanic and fluvio-lacustrine sequence at the Gombore II Open Air Museum archaeological site (ca. 0.85 Ma). This has allowed a detailed reconstruction of the palaeoenvironment and of the fauna present in the time interval between 1.2 and 0.85 Ma. Various-sized mammals, birds, molluscs as well as hominins left tracks throughout the sequence, and document a varied fauna and associated behaviours. Most of the hominin tracks were made by young individuals on the basis of size and are some of the earlier child tracks to be reported. The mollusc traces document the presence and orientation of water streams which, according to the associated vertebrate traces, were visited by hominins, mammals and birds. Most of these traces were found within levels traditionally considered barren for archaeology, yet they all document life activity and are always in situ. This confirms the potential of the ichnological research as an important complementary tool for archaeological investigations.

Graphical Abstract

And so, the casual refutation of the childish fairytale of magic creation by science continues on its inevitable course, showing with every pertinent discovery that the vast majority of Earth's history and the slow evolution of species such as Homo sapiens all happened in that vast expanse of time before 'Creation Week'.

Creationism in Crisis - Hippos Were Living Near Rome About Half a Million Years Before 'Creation Week'

Modern hippos, Hippopotamus amphibius, arose from African ancestors during the Quaternary and were present in Europe during the Pleistocene.

Photo: Sue Roehl/Flickr

Modern Hippopotamus, Hippopotamus amphibius, present in Europe in the Pleistocene

Earliest known European common hippopotamus fossil reveals their Middle Pleistocene dispersal | EurekAlert!

One of the easiest predictions to make is that, in the next few days there will be more science papers casually refuting creationism, without the slightest intention of doing so on the part of the authors.

This is inevitable, of course, because creationism is so profoundly counter-factual that just about every fact is inconsistent with creationism, so, by merely revealing the facts, scientists refute creationism.

And today's example is the revelation that there were hippos living around Rome during the Pleistocene, about half a million years before creationist superstition says Earth was magicked up out of nothing in 'Creation week'. The amazing thing isn't that there were Hippos living near Rome half a million years ago, but the fact that there are grown adults who believe the creationist superstition of a 'Creation Week' 10,000 years ago, before which, there was nothing and nowhere for anything to happen in.

This news comes in the form of an open access paper in PLOS ONE by Beniamino Mecozzi of the Sapienza University of Rome, and colleagues, and a press release from PLoS:

Unintelligent Design - A Bat That Has Non-Penetrative Sex

A common serotinus, Eptesicus serotinus

© Alona Shulenko

An 'intelligently designed' device for making holes in Swiss Cheese

William Heath-Robinson

Discovery of a new method of mating: a bat reveals its secret to us, size XXL - L · NEWS

It's almost as though creationism's putative designer took lessons from William Heath-Robinson, and then lost its sense of humour, the ludicrously complicated ways it designs to carry out simple tasks.

The evolutionary advantage of penetrative sex is that the male is able to deposit sperm close to the egg, using his penis, and the female is able to exercise a degree of selection in her choice of who is to father her babies. It is a considerable advantage over the more primitive forms of external fertilisation such as those used by amphibians where the sperm is shed onto the eggs as the female lays them, or by fish, where the sperm is deposited near the eggs and then swims towards them. The later method, especially, frequently allows opportunist males to sneak in and fertilise some of the eggs when another male has done all the work.

However, for reasons which are not entirely clear, most male birds have lost their penis and deposit their sperm into the female's reproductive opening by a 'cloacal kiss', a notable exception being the swans, geese and ducks which have retained a penis and sex is penetrative. This may be because a strategy used by male members of this order of birds is forcible penetration or, frankly, rape.

Of course, being unintelligently designed, birds lost their penis, not by simply losing the genes that grow one during embryonic development, but by have a gene that literally kills the growing penis soon after it starts to develop. Inhibit that gene in chickens and the male chick is born with a penis. Give it to a goose, and the male gosling is born without one.

William Heath-Robinson

And now, in what looks like another example of unintelligent design (by that I mean, of course, evolution) there is a species of bat in which the male's penis is too big to penetrate the female, so he uses it to transfer his sperm into the vagina by pressing the tip against her vulva and holding it there until the deed is done. which usually takes about 53 minutes but can take over 12 hours.

The bat is the common serotinus, Eptesicus serotinus. It is the only known example of non-penetrative sex in a mammal. Quite why it evolved is something of a mystery, but it could be something to do with needing to get round the female's tail membrane resulting in a penis that, when erect is 22% of the bat's body length. The tip is large and bulbous and almost seems designed to prevent penetration.

The study began when Nicolas Fasel, an evolutionary biologist at the University of Lausanne in Switzerland, and his colleagues noticed that the serotine bat has a rather large and unusual penis. When erect, it is 22% of the bat’s head–body length and has a bulbous, heart-shaped tip. “We were thinking it would be really difficult for it to enter anything,” he says.

It is described in a University of Lausanne (UNIL) news release and published Current Biology:

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

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

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

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

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

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

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

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