Religion, Creationism, evolution, science and politics from a centre-left atheist humanist. The blog religious frauds tell lies about.
Tuesday, 19 December 2023
Creationism in Crisis - The Periodic Greening Of The Sahara In That Vast Expanse of 'Pre-Creation' History.
The Sahara Desert used to be a green savannah – new research explains why
Having visited the Sahara Desert in April about 10 years ago, I can assure readers that it is not the hot, dry place of repute but can be cold and wet, at least in the Tunisian part. It was so cold with a fine drizzle, that, shivering in a t-shirt, I offered to buy the thick, hooded duffle coat a local troglodyte guide was wearing, but he quoted me 5000 dinars (about £400) with a knowing twinkle in his eye. I elected to shiver until I got back on the coach and the driver turned the heating on. Yes, there are troglodytes in Tunisia!
There have been times in the past when rain in the Sahara was not just freak weather in Spring to annoy tourists, but the norm in much of the year, so much so that the Sahara was mixed savannah and scrub with lakes and rivers, especially the western part.
Readers may recall how I mentioned the periodic greening of the Sahara in my article about the evolution of rock doves and feral pigeons. Briefly, a species of dove resident in West Africa crossed the Sahara during one such period when there was forest, grassland and water in place of sand. Then when the Sahara became desert the two populations diverged and the one which had made it as far as the Middle East hybridized with a resident related dove. This hybrid quickly became the normal form of the rock dove north and east of the Sahara and diversified further into several subspecies, one of which was domesticated and selectively bred to produce lots of different varieties. Some of these eventually reverted to a feral existence and became the ubiquitous town pigeon with a very different lifestyle and habitat to the original rock dove.
This process of African species moving into and across the Sahara during these periods of greening, and then becoming isolated from the African population, is known as the Saharah Pump and accounts for some of the sub-Saharan African species having a closely related counterpart in North Africa and Eurasia.
And this process has been going on since about 8 million years before creationists think Earth was created and may account for the migration of humans out of Africa some 40-50,000 years ago. More recently, however, there was certainly a population of humans living in a green and fertile Sahara up to at least 11,000 years ago (i.e., at least 1,000 years before 'Creation Week'. We know this because they left a record in rock carvings at Tassili N’Ajjer plateau in present-day Algeria, which show us some of the animals that lived there too.
These periods of greening have occurred approximately every 21,000 years and now two geoscientists from Helsinki University, Finland together with colleagues at Birmingham and Bristol universities, UK., have developed a climate model that explains how the climate changed so regularly and so radically. They have published their findings, open access, in Nature Communications. One of them, Edward Armstrong of Helsinki University, has also written an article about their research in The Conversation. His article is reprinted here under a Creative Commons licence, reformatted for stylistic consistency:
Sunday, 17 December 2023
Creationism in Crisis - The Woolly Dogs Of The American Coast Salish People Predate 'Creation Week'
Researchers, Coast Salish People Analyze 160-Year-Old Indigenous Dog Pelt in the Smithsonian’s Collection | Smithsonian Institution
This is the sort of nonsense that creationism requires you to believe in order to reconcile the scientific evidence with the creation myths of a bunch of Bronze Age Canaanite farmers who thought Earth was small, flat and had a dome over it to keep the water above the sky out. Obviously, these people had almost certainly never heard of Siberia or North America or realised that there were other people living there and were as ignorant of most of Earth's long history as they were of cosmology, biology and geology.
One of the things the Bronze Age Canaanites would never have guessed was that some of the domestic dogs the Siberians took with them had genes for a dense wooly fur that could be woven into blankets and other fabrics, but now a team of researchers from the Smithsonian’s National Museum of Natural History have carried out a detailed DNA analysis of the pelt of the last known example of this breed of dog (a dog known as Mutton). Mutton died in 1859 and his pelt was sent to the Smithsonian Institute where it remained until it was rediscovered in the early 2000's.
The analysis has shown that the line diverged from the other dogs about 5,000 years ago (i.e., before creationist superstition says all life on Earth was exterminated in a genocidal flood when their 'all-loving' god flew into a rage because its creation wasn't working as intended).
They have shown that its closes genetic relationship is with the pre-colonial dogs from Newfoundland and British Columbia. The Indigenous Coast Salish communities in the Pacific Northwest (in Washington state and British Columbia) for millennia held these wooly dogs in high esteem, regarding them almost as family members and often keeping them in pens or on islands to prevent them interbreeding with other dogs, to maintain the quality of their wool. This isolation prevented the ingress of genes from other dogs and even from the dogs later colonists brought with them. The genes recovered from Mutton's pelt show that 85% of his genes were from pre-colonial dogs.
The Smithsonian researchers have, with the assistance of Coast Salish Elders, Knowledge Keepers and Master Weavers, now traced the place of the woolly dogs in Coastal Salish culture and the reasons for its decline. Their findings are published in Science and tell a sorry tale of colonial destruction of a people and their culture. Instead of, as has been suggested, the arrival of machinery and woven blankets made the wooly dogs expendable, the truth is that, due to disease and colonial policies of cultural genocide, displacement and forced assimilation, it likely became increasingly difficult or forbidden for Coast Salish communities to maintain their woolly dogs and a 1000 years or more of careful selective breeding was wiped out within a couple of generations.
Creationism in Crisis - A French 7-Year Scientific Program To Disover The Origin Of Life!
Although it's nothing to do with evolution, which is the science of how living organisms respond to environmental pressures and diversify over time, abiogenesis is a favourite of creationists because they imagine, without being able to define 'life', that it must involve some magical, God-given quality that turns 'non-life' into 'life'. But then when did facts bother creationists?
So it must be disconcerting to those of them who are still in touch with reality, that 28 French scientific organisations, involving over 100 scientists, have formed a partnership (Programme et Équipement Prioritaire de Recherche - PEPR) led by the Centre National de la Recherche Scientifique (French National Center for Scientific Research - CNRS) to research into the origins of life, not only on Earth but on other planets. The project is already being known as 'Origins'.
According to the CNR News release by Mehdi Harmi:
Saturday, 16 December 2023
Malevolent Design - How A Chicken Virus Got More Deadly - Malice Or Evolution?
Ancient DNA reveals how a chicken virus evolved to become more deadly | University of Oxford
Marek's Disease Virus (MDV) is a serious infection in chickens that costs th4e poultry industry over $1 billion annually. Now an international group of virologists and archaeologists led by researchers from Oxford University, Ludwig-Maximilians-Universitat, Munich, Germany, have discovered how it has evolved over time to become more virulent and deadly, or, as creationists insist, has been intelligently redesigned.
The team reached this conclusion from an analysis of the virus in modern and ancient chickens going back over the past 1000 years. The ancient samples were obtained from DNA extracted from chicken bones recovered from 140 archaeological sites in Europe and the Near East. This analysis showed that MDV was widespread in European chickens for at least 1000 year before being first described in 1907.
Friday, 15 December 2023
Creationism in Crisis - How Early Humans Caused A Decline In Megafauna Numbers Thousands Of Years Before 'Creation Week'
People, not the climate, caused the decline of the giant mammals
About 90,000 years before creationist superstition says the Universe was created, humans, who had been evolving in Africa, began to expand their range into Eurasia and eventually into Austronesia and the Americas.
About 500,000 years later most large species show a sudden decline in their numbers, and now researchers led by Professor Jens-Christian Svenning, head of the Danish National Research Foundation's Center for Ecological Dynamics in a Novel Biosphere (ECONOVO) at Aarhus University, believe they have shown that this was due to human predation and habitat destruction.
They reached this conclusion from an analysis of the genomes of 139 species. This involved crunching the data from 3 billion or so data points to build evolutionary trees of the mutations in the genomes. The bigger the population, the more mutations there will be in the species genome, so this data shows the population changes over time.
Their work is published, open access, in Nature and is explained in a news release from Aarhus University:
Creationism in Crisis - Human Intelligence Is Not So Much A Matter of Quantity But Of Quality
Human intelligence: how cognitive circuitry, rather than brain size, drove its evolution
Researchers have shown that human intelligence does not depend primarily on the size of our brain - there are animals with bigger brains (elephants, orcas) - but on the cognitive circuitry.
The team, led by Valentin Riedl of the Department of Neuroradiology at Klinikum rechts der Isar, TUM School of Medicine and Health, Technical University of Munich, Munich, Germany, have published their findings, open access, in the journal Science Advances. It is explained in an article in The Conversation by two Cambridge University professors who were not involved in the research.
Their article is reprinted here under a Creative Commons license, reformatted for stylistic consistency:
Thursday, 14 December 2023
Unintelligent Design - Why Some Women Experience Morning Sickness during Pregnancy.
1-3% are severe enough to require hospital treatment
Why seven in ten women experience pregnancy sickness
'Morning sickness, which is common in the earlier stages of pregnancy, and which, in its more severe form, hyperemesis gravidarum, can be seriously debilitating and may even require admission to hospital and iv fluids to prevent life-threatening dehydration, is now known to be caused by a protein hormone, known as GDF15, produced by the foetal part of the placenta.
This discovery, published yesterday in Nature, by a team from Cambridge University, UK, led by Professor Sir Stephen O’Rahilly, and including researchers in Scotland, the USA and Sri Lanka, points to a potential way to prevent pregnancy sickness by exposing mothers to GDF15 ahead of pregnancy to build up their resilience.
Wednesday, 13 December 2023
Creationism in Crisis - The Evolution of the Mammalian Eye From A Common Origin Over 400 Million Years Before 'Creation Week'.
Cell types in the eye have ancient evolutionary origins | Berkeley
Despite the claims of creationists frauds who cite Charles Darwin, whom they falsely claim admitted the structure of the eye couldn't be explained, the evolution of the mammalian eye from a simple patch of light-sensitive cells is well known to biological science.
Darwin, of course, was setting out the problem before explaining the solution in a typical literary technique of his time. The paragraph that creationists often try to get away with citing is:
To suppose that the eye with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest degree.
'Origin of Species', page 100
What they always fail to cite is the very next paragraph:
Yet reason tells me, that if numerous gradations from a perfect and complex eye to one very imperfect and simple, each grade being useful to its possessor, can be shown to exist; if further, the eye does vary ever so slightly, and the variations be inherited, which is certainly the case; and if any variation or modification in the organ be ever useful to an animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, can hardly be considered real.
'Origin of Species', page 100
Creationism in Crisis - How Wrong The Bible's Authors Were! Why Would Anyone Believe Anything Else They Wrote?
D. Milisavljevic (Purdue University),
T. Temim (Princeton University),
I. De Looze (University of Gent)
NASA’s Webb Stuns With New High-Definition Look at Exploded Star - NASA
The description of the Universe in the Bible is so naïve and radically different to the real universe, it beggars belief that there are grown adults who think the Bible is the inerrant word of a creator god.
There is nothing about the authors' description of it which can be described as allegorical or metaphorical, without the most contorted of mental gymnastics. It is not metaphorical or allegorical; it is quite simply wrong; spectacularly and conspicuously, with no shadow of a doubt, wrong!
What we now know are hundreds of billions of galaxies, each with maybe half a trillion stars, many with planetary systems, the authors of the Bible thought were little lights stuck to the underside of a dome over a flat Earth, that can be shaken loose and will fall down to Earth where they can be trampled on by a goat! (Daniel 8:10).
They described this flat Earth with a dome over it as standing on pillars and the fixed and immobile center of the Universe, round which a small sun orbits. They described the sky above the dome as being made of water. Their universe ran on magic.
Tuesday, 12 December 2023
Creationism in Crisis - Here Be Monsters! - 72 Million Years Before Creation Week
Today's scientific refutation of the childish creationists superstition that even some otherwise normal adults still believe in, comes from a paper published in Journal of Systematic Palaeontology by Associate Professor Takuya Konishi of Cincinnati University and an international team of co-authors.
It describes a giant mosasaur the size of a great white shark that hunted in the Pacific seas, 72 million years before creationist dogma says Earth was created. And this is no ordinary mosasaur but displays a number of features that show how a similar environment and lifestyle can lead to parallel evolution, just as the Theory of Evolution by Natural Selection predicts.
These mosasaurs have a dorsal fin, just like the only very distantly-related bony fish, sharks (cartilaginous fish), and whales and dolphins. This gives them greater control and mobility in water.
This species of mosasaur was named after the place where it was found (Wakayama Prefecture, Japan) and a mythical creature from Japanese folklore, Soryu (blue dragon).
According to the press release from Cincinnati University:
Sunday, 10 December 2023
Creationism in Crisis - What A Juvenile Tyrannosaurid Was Eating 75 Million Years Before 'Creation Week'
Royal Tyrrell Museum
What’s for dinner? UCalgary paleontologist finds out through remarkable specimen | News | University of Calgary
75 million years before creationists think Earth was created, a juvenile Gorgosaurus, a species of tyrannosaur, was catching young avian dinosaurs like Cities but then selectively eating the fleshiest parts, the legs.
At this stage in its life, the Gorgosaurus was slender, had a narrow skull and blade-like teeth and was able to catch small, swift running dinosaurs, but had it lived to grow into an adult, it's body and particularly its head and teeth, would have become massive and capable of catching the large vegetarian dinosaurs and crushing their bones.
We know this because this particular juvenile Gorgosaurusdied and its body became fossilised, complete with the leg bones of two young Citipes still in its stomach, one more digested than the other, showing they were eaten at different times.
This was discovered by a group of palaeontologists led by Dr. Darla Zelenitsky, PhD, an associate professor in the Department of Earth, Energy and Environment at the University of Calgary, and Dr. François Therrien from the Royal Tyrrell Museum. Their finding is published, open access, in the journal Science Advances. It is described in a University of Calgary news item:
Saturday, 9 December 2023
Unintelligent Design - The Late Devonian Mass-Extinction Or How Earth Is Badly Designed For Life
Way back 370 million years before the mythical 'Creation Week' the seas were full of life and angiosperm plants were rapidly replacing the tree ferns and other Tracheophytes and life was looking good, despite the fact that the single large landmass, Pangea, was on the point of breaking up.
Then something happened to cause another of those periodic mass extinctions that have punctuated Earth's long 'pre-Creation' history. What exactly it was has been the subject of ongoing debate by geologists, biologists and climatologists ever since evidence of it was found in the fossil record, particularly in Devonian rocks like those in Greenland.
But whatever the cause, it's not good news for creationists who have been duped by their cult leaders into believing Earth is fine-tuned for life by a designer god, and, by the circular reasoning that characterises creationism, therefore this fine-tuning 'proves' their designer god exists. A cynic might wonder, if faith is any good, why creationists are so desperate to find scientific 'proof' of their god that they perform all manner of ludicrous mental gymnastics and commit just about every logical fallacy in the book, to tell themselves and their target dupes that they have discovered it - and will be producing it any day now, real soon!
But that's by the by.
Sadly for creationists the evidence is that Earth is anything but finely tuned and perfect for life. The simple truth is that an Earth that was perfectly designed for life would never have extinctions, let alone mass extinctions like the ones that ended the Devonian and Cretaceous eras, and the one that's in progress right now. In fact, there would not even be biodiversity on such a planet because there would be no reason to adapt to adverse conditions because since these would not exist on a perfectly designed Earth, so life would not have progressed beyond the simplest of self-replicating molecules.
So, just for any creationists still under the delusion that Earth is finely tuned for life, here is a brief description of the Devonian and the mass extinction at the end of it:
Creationism in Crisis - How De Novo Genes Arise (And Another Creationist Dogma Bites The Dust)
New genes can arise from nothing | HiLIFE – Helsinki Institute of Life Science | University of Helsinki
Present a creationist with a puzzle like, where does new genetic information in the form of new functional genes come from and a typical response will be, "Er... I can't imagine how that's possible... so God did it!". This of course is based on the foundational fallacies of creationism, and most religious apologetics - the argument from ignorant incredulity, and the false dichotomy fallacy.
This intellectual dishonesty appeals to people who are satisfied with not knowing and aren't bothered about the truth, so long as they have an excuse for pretending they know the answer
By contrast, present a scientist with the same question, and the response will probably be, "I don't know, so how can we find out?", because admitting ignorance is the foundation of good science. This approach appeals to people who have the humility to admit they don't know and who are interested enough in truth to want to find out.
An example of this was published recently by three researchers from the Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland, who decided to address the question of where de novo genes arise in the genome, seemingly from nowhere.
This question arose from the observation that a comparison between human and other primate genomes shows that a number of microRNA (miRNA) sequences arose within the human genome, and the genome of other apes apparently as single mutation events.
In addition to the 20,000 genes in the human genome, there are thousands of miRNA sequences of about 22 base-pairs which have a regulatory function. Their role is to stop messenger RNA (mRNA) from continuing to make proteins when enough have been made. They do this by blocking the mRNA molecules and to do this they need to be folded in half like a hairpin. This folding means that they need to be 'palindromes', i.e., reading the same forward as backward, so, when folded in half, each base lines up with a copy of itself.
So, the question was, how do these palindrome miRNAs arise?
Friday, 8 December 2023
Creationism in Crisis - Chemical Fossils Show How Life Evolved Over A Billion Years Before 'Creation Week'
via Getty Images
A simplified animal phylogeny, with the hypothesized presence of smt visualized with blue lines. This tree provides a conservative estimate of the number of smt losses, as it excludes many understudied animal phyla that may also lack the protein.
Early organisms, particularly from before animals with hard body parts like teeth, bones and hard exoskeletons had evolved, leave few traces in the fossil record, but that's not to say they leave no trace whatsoever. What they leave is a chemical signature in the rocks that can last for hundreds of millions, even billions of years.
Sterol lipids, for example are highly stable chemicals that come from cell membranes and can be found in rocks dated to 1.6 billion years old. Since they can only be produced by living organisms, they are compelling evidence for the existence of life when those rocks were laid down.
In the present day, most animals use cholesterol — sterols with 27 carbon atoms (C27) — in their cell membranes. In contrast, fungi typically use C28 sterols, while plants and green algae produce C29 sterols. The C28 and C29 sterols are also known as phytosterols.
C27 sterols have been found in rocks 850 million years old, while C28 and C29 traces appear about 200 million years later. This is thought to reflect the increasing diversity of life at this time and the evolution of the first fungi and green algae.
Early organisms needed to synthesise their own sterols and did so using a gene called smt, but, as more sources of sterols became available by eating fungi and algae, so this gene became redundant and was eventually lost from many evolutionary lines. When this gene disappeared from these lines shows when they began consuming these new sources of sterols.
By constructing a family tree for this gene using data from first annelids then across animal life in general, the UCDavid team were able to map when this gene was lost onto changes in the sterol record in rocks - and they mapped closely to the chemical record in the rocks.
According to a news release from the University of California Davis (UCDavis), where David Gold, associate professor in the Department of Earth and Planetary works in this new field of molecular paleontology, using the tools of both geology and biology to study the evolution of life:
Thursday, 7 December 2023
Unintelligent Design News - How A Badly Designed Protein Causes Autoimmune Diseases
Fungus-fighting protein key to overcoming autoimmune disease and cancer | Australian National University
The more you learn of creationism's putative intelligent [sic] designer, the more like William Heath Robinson it becomes.
The main difference is that, no matter how ramshakled they were, William Heath Robinsons inventions actually worked, even if they didn't produce the required result. The same can't be said for creationism's god's designs. They resemble piecemeal designs where each part is designed in isolation in response to a problem, often a problem somewhere else in the design, where near enough is good enough and there is no joined up thinking.
Rather like a William Heath Robinson machine, conbbled together from disparate parts, but where when a knotted piece of string breaks, instead of replacing it with a new piece of string or tying the broken ends together, like Heath Robinson would, a different, weaker sort of string is designed and tied across the broken ends, but then that keeps breaking too.
An example of this inept design was discovered recently and found to be the cause of autoimmune diseases such as iritable bowel syndrome (IBS), type 1 diabetes, eczema and other chronic disorders. The problem is with a protein called DECTIN-1 (also known as CLEC7A) which is producd by the immune system in response to fungal infections. Researchers at The Australian National University (ANU) have discovered that a mutated form of DECTIN-1 limits the production of T regulatory cells or so-called ‘guardian’ cells in the immune system.
Mutations arise, of course, because of another poor design - the process for replicating DNA, which is so prone to errors that another mechanism for repairing it is needed. However this is also prone to errors, the result of which means that many of our cells carry mutations, some of which cause cancers.
The research is publshed in Science Advances and ex[lained in an Australian Nationa University News release:
Creationism in Crisis - A 15 Million-Year-Old Former Lake in Southern Germany Is Drowning Creationism With Facts
15 million years before 'Creation Week', when creationists think Earth was magically created out of nothing, a meteorite struck in what is now southern Germany, just north of the Danube, creating a circular crater that filled with water to form a lake, in an area surrounded by the hills known as the Nördlinger Ries.
Now the sedimentary rocks formed on the lakebed are revealing their locked-up record of the geological and biological changes in the intervening 15 million years of Earth's 'pre-Creation' history.
They are also providing useful information about what any signs of life in Martian craters might look like.
First, a little AI information about Nördlinger Ries:
Wednesday, 6 December 2023
Malevolent Designer News - How A Bacterium Is 'Intelligently Designed' To Turn Plants Into Zombies
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
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
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
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:
- Horizontal gene transfer (5% -7 %)
- Gene duplication (14% - 28%)
- Massive inversions of repeated sequences of DNA.
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:
Tuesday, 5 December 2023
Creationism in Crisis - Evolution of Rock Doves & Domestic Pigeons

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:
Monday, 4 December 2023
Wonderful World - Ten Reasons to Like Spiders
Bottom left: European garden spider, Araneus diadematus
Bottom right: Banded Garden spider, Argiope trifasciata
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.
Sunday, 3 December 2023
Creationism in Crisis - Scientists Show How a Dynamic And Changing Earth Influenced Evolution Over Millions of 'Pre-Creation' Years
Landscape dynamics determine the evolution of biodiversity on Earth - The University of Sydney
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'
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:
Saturday, 2 December 2023
Malevolent Design News - How 'Intelligently Designed' Pathogens Use The Tactics Of A Burglar To Make Us Sick
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
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
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.
Friday, 1 December 2023
Creationism in Crisis - Evolution of a Carnivorous Pitcher Plant by Gene Duplication - New Genetic Information Created Naturally
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:
- 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.
- 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.
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'
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'
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:
Wednesday, 29 November 2023
Creationism in Crisis - Early European Humans Hunted Beavers 400,000 Years before 'Creation Week'
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:






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