Tuesday, 12 December 2023

Creationism in Crisis - Here Be Monsters! - 72 Million Years Before Creation Week


The Wakayama Soryu was about the size of a great white shark and lived more than 72 million years ago during the age of Tyrannosaurus rex and other late-Cretaceous dinosaurs.
Illustration/Takumi
UC paleontologist describes Wakayama 'blue dragon' that ruled prehistoric waters off Japan | University of Cincinnati

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'


A Gorgosaurus feeding on a Citipes

Illustration by Julius Csotonyi
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


Fieldwork at Trail Island in East Greenland, near a Late Devonian rock outcrop.
Photo by John Marshall, University of Southampton
Study reshapes understanding of mass extinction in Late Devonian era: IU News

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'


Fig. 6: Summary of smt gene loss in the animals.
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.

Molecular Fossils Shed Light on Ancient Life | UC Davis

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


William Heath Robinson
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


Drill core from borehole taken in 1981 from the Nördlinger Ries. There are distinctive layers of light-coloured dolomite between fine-layered dark sediments of the former crater lake.
Photo: Gernot Arp, Göttingen University
Information for the Media - Georg-August-Universität Göttingen

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


The Life Cycle of a 26S Proteasome.

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


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


Movement of mucus in the respiratory tract

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
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:

Tuesday, 5 December 2023

Creationism in Crisis - Evolution of Rock Doves & Domestic Pigeons


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:

Monday, 4 December 2023

Wonderful World - Ten Reasons to Like Spiders


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.

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
A dynamic and changing Earth.
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:
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