Creationism in Crisis - Evolution By Loss Of Complexity - How A Mutation Cost Our Ancestors Their Tails

A mutation cost our simian ancestors their tails

Photo: Getty / Steve Adams

Change in Genetic Code May Explain How Human Ancestors Lost Tails | NYU Langone News

In that distant, pre-'Creation Week' history of Life On Earth, 25 million years before creationists think Earth was created out of nothing, and all living things on it were magicked into existence without ancestors, a 'jumping gene' inserted a short length of DNA termed AluY, into the gene which controls tail length in monkeys, and the resulting tailless monkeys went on to diversify into the apes - gibbons, siamangs, orangutans, gorillas, chimpanzees, bonobos, and the hominins which were to evolve into the Australopithecines and the Homo genus, including Homo sapiens, all of which still possess that short insertion in the TBXT gene, which otherwise is identical to one of the gene which grow the tail of the simians.

As an example of design, it is one of the least intelligent, since, instead of removing all the genes required to grow a tail, the 'designer' simply broke an essential gene and left all the others to do nothing apart from having to be replicated in every cell in every ape that ever lived, as an example of the massive waste and unnecessary complexity that characterises an evolved process and gives the lie to any notion of any intelligence being involved.

By inserting the AluY snippet into a mouse BBXT gene the researchers found a variety of tail effects, including mice born without tails. They also showed that there was a small increase in the incidence on neural tube defects (spina bifida) in mice.

Quite why tailless would have been selected for during the evolution of these ancestors of the modern apes is a matter for speculation; maybe a tail was becoming an encumbrance for a brachiating mode of locomotion as opposed to running along the top of branches and jumping from branch to branch, which the smaller monkeys used, where a tail was an important balance organ. For a heavier ape hanging beneath the branches by its arms, there would have been less need for a balance organ and a tail would have been liable to damage and infection.

How this was discovered by a team led by researchers at New York University Grossman School of Medicine, is the subject of an open access paper in Nature and a NYU Langone Health news release:

Malevolent Designer News - How Creationism's Favourite Sadist May Use Climate Change To Increase The Suffering In The World

Nematode movement

Parasitic worms cause huge economic loss to farmers and can infest humans too.

Temperature, humidity may drive future transmission of parasitic worm infections | Penn State University

Creationists who believe nothing happens unless their invisible magic god wants it to have to have all manner of intellectual gymnastics to avoid giving it credit for all the nasty things to be found in nature, such as parasitic worms.

Their favourite strategy is the old trick of believing two mutually exclusive ideas simultaneously - that only their god is capable of designing living systems, so anything too complex for them to understand must have been created by it, whilst simultaneously believing that all pathogens are created by another entity, called 'Sin', no matter how complex or difficult to understand they may be.

And of course, they are forbidden by dogma to believe in more than one creator and must believe, also by dogma, that that creator is omni-everything - omnibenevolent, omniscient and omnipotent - so they have to believe that whatever its designs do, they were designed to do it, and whatever the future may bring, they were aware of that whilst designing their creations.

What percentage of the surface of Earth is habitable to humans without special equipment? Approximately 29% of the Earth's surface is comprised of land, which is habitable to humans without special equipment. The remaining 71% is covered by water, primarily in the form of oceans, which generally require specialized equipment for prolonged habitation. Therefore, without considering other factors such as climate, terrain, and resources, roughly 29% of Earth's surface is habitable to humans without special equipment.

That means, creationists have no choice but to accept that the results of climate change were part of their designer creator's plan, as was the response of their creations to it. And one of those responses to climate change may be an increase in parasitic worms in parts of the world they have not been prevalent in before.

Many of these worms are, or have been, confined to the tropics and sub-tropical zones, and the northern and southern part of the world, where most advanced economies are based, have been relatively free from them. But, as Earth gets warmer, the 'habitable zone' for parasitic worms expands to incorporate more of the advanced economies, but the habitable zone for humans shrinks even further.

This is the prediction of a team of researchers from the Center for Infectious Disease Dynamics and Department of Biology, The Pennsylvania State University (PennState), Pennsylvania, USA, and Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milano, Italy, led by Professor Isabella Cattadori and Dr. Chiara Vanalli of PennState, who have just published their findings, open access, in the journal Ecology Letters. Their work is explained in a PennState news release:

Unintelligent Design - How The Same Function Evolved Twice - Once in Vertebrates And Again in Insects

Sunset over University of California - Irvine

Diagram of an insect compound eye.

Credit: Bugboy52.40 via Wikipedia (CC BY-SA 3.0 Deed)

UC Irvine study shows similarities and differences in human and insect vision formation – UCI News

Regardless of the different structures in the compound eyes of insects and the eyes of vertebrates, at the heart of them both is a light-sensitive molecule, 11-cis-retinal, also known as 'visual Chromophore', but these are produced in two different ways from the same starting compound - β-carotene - which in humans is obtained from eating plants like carrots which are rich in Vitamin A from which β-carotene is derived.

This is one of those examples which are so common in biology, of where, had it been intelligent, the same designer could have used a process it had designed earlier but did not, instead it designed an even more complex way of doing the same thing, giving the lie to claims that the same 'intelligent' designer designed living things, insects and vertebrates have two different ways to achieve the same product - 11-cis-retinal; the second being the more complicated of the two.


Although the earliest vertebrates appeared about 518 million years ago, so predating the first insects by about 130 million years, the creationists dogma of omniscience which they traditionally ascribe to their putative designer god, would mean this alleged designer was already aware of the less complex way to make 11-cis-retinal, when if supposedly designed the vertebrate method.

Besides, creationist dogma also says they were all created on the same day - 10,000 years ago.

Creationism in Crisis - What Made Snakes Able To Evolve So Quickly 100 Million Years Before 'Creation Week'?

Lialis burtonis. Not a snake, but a legless gecko.

Image credit: Pascal Title, University of Michigan/Stony Brook University.

A false boa, Pseudoboa nigra, eating a lava lizard, Tropidurus hispidus.

Image credit: Ivan Prates, University of Michigan.

Snakes do it faster, better: How a group of scaly, legless lizards hit the evolutionary jackpot | University of Michigan News

100 million years ago the ancestral snake was just another lizard but then suddenly (on the evolutionary timescale) something happened that enables snakes to diversify into thousands of different species while the other lizards plodded along slowly, diversifying at a much slower rate than the snakes.

But what was it that allowed this sudden radiation into so many species and why did it give the snakes the edge over their cousins the lizards? It was an event that an international team led by University of Michigan biologists have called an evolutionary singularity, in an analogy with whatever was at the start of the Big Bang.

The team has estimated that snakes have evolved up to three times faster than lizard, an ability that was facilitated by three things - an elongated body and loss of legs; enhanced sensory detection enabling them to find and track prey, and a flexible skull that enabled them to swallow large prey.

In an attempt to understand this, the team assembled a large database of lizard and snake diets from examining the stomach contents of tens of thousands of museum specimens. They also sequenced the partial genomes of almost 1,000 species from which they were able to construct the evolutionary trees of lizards and snakes.

Their findings are the subject of a paper in Science and of a news release from the University of Michigan:

Abiogenesis News - Closing Creationism's Favourite Gap On Their Ever-Shrinking Little God

Hot Springs in Yellowstone National Park

Credit: iStock / tomolson54

Hot Spring in Yellowstone National Park.

Credit: iStock / tomolson54

Compound vital for all life likely played a role in life’s origin | UCL News - UCL – University College London

Abiogenesis is the gap creationists prefer to shoehorn their ever-shrinking little god into because they feel safer placing it there, believing that they have an unarguable claim that 'you can't get life from non-life'. Hilariously, you can sow confusion in their smug certainty in two simple ways:

1. Ask them to define 'life' and state whether it is a substance, a process or something else, because it only takes a moment's thought to realise 'life' is what we call the metabolic processes that organic molecules perform, so is simply the laws of chemistry and physics in operation. There is no magic ingredient needed.
2. Ask them what happens when the non-living food they eat becomes living tissues during the processes of digestion and assimilation if it is 'impossible'?

Their claim is nonsense of course; it's simply slogan delivered in response to trigger words which creationists no more understand than a parrot understands the meaning of the words it squawks.

There is nothing in the laws of chemistry or physics that makes abiogenesis impossible; given the right conditions there is no reason the inorganic chemicals present on the early Earth couldn't build more complex molecules or why those molecules couldn't perform the necessary processes to grow, repair and replicate. And once replication is possible, then selection would have been inevitable, and with selection, the processes which performed best would inevitably produce more copies.

Of course this can't be replicated easily in a laboratory because what no laboratory process can replicate is the long period of time, possibly millions of years, the process had on the early Earth, but what scientists can do is show that essential molecules to kick-start the processes could have arisen on the early Earth in the conditions that pertained then.

This is exactly what a team from University College London have shown in respect of a molecule which is the functional unit of one of the basic enzymes involved - Coenzyme A. The molecule is pantetheine. In earlier studies, pantetheine failed to be produced leading some to think that it would not have formed on early Earth and would therefore be absent and unable to play its essential role in metabolism.

Molecular structure of pantetheine

Creationism in Crisis - 250 Million Years of Butterfly And Moth Evolution

Butterfly and moth genomes mostly unchanged despite 250 million years of evolution

It'll no doubt come as a surprise to those creationists who believe Earth was created from nothing by magic just about 10,000 years ago to learn that the butterflies and moths have been evolving for 250 million years.

It'll maybe come as a bigger surprise to those creationists who have been fooled into believing that the Theory of Evolution is being discarded by mainstream biologists in favour of their childish fairy tale of magic and supernatural spirits, that yet another group of mainstream biologists regard it as the foundation of modern biology, and are participating in the Darwin Tree of Life Project, which aims to sequence the genome of 70,000 eukaryote species from Britain and Ireland, to learn their evolutionary relationships.

This project also contributes to the much larger, Earth BioGenome Project.

One of the teams taking part in this project, based at the Wellcome Sanger Institute and the University of Edinburgh, Scotland, has just completed the sequencing of 200 high-quality genome of the Lepidoptera order of insects (moths and butterflies) and discovered some interesting facts about the evolution of the order, including that there are some elements in the genomes, which they term 'Merian elements' after the 17th century entomologist Maria Sibylla Merian, which have remained relatively stable over the 250 million years the order has been evolving.

The research is published in the journal Nature Ecology & Evolution and is described in a Welcome Sanger Institute news release:

Creationism in Crisis - How An Ancient Retrovirus Evolved To Create The Vertebrate Brain

A myelinating oligodendrocyte (green)

Credit: Peggy Assinck,
ALTOS Labs-Cambridge Institute Of Science

Ancient retroviruses played a key role in the evolution of vertebrate brains | ScienceDaily

Schematic diagram of a neuron show the myelin sheath as the electrical insulator of the axon.

Wikimedia Commons (CC BY-SA 3.0)

Extinct Late Devonian placoderm Bothriolepis canadensis. Myelin first appeared in these primitive early fish

Credit: Nobumichi Tamura / Stocktrek Images / Getty.

Creationists generally hate endogenous retrovirus (ERV's) because:

1. They are one of the strongest pieces of evidence of common descent appearing in the same locations in the genome of all organisms in a clade, forming nested hierarchies exactly as the Theory of Evolution predicts. The probability of the same viral DNA appearing in the same locus in all species in a clade by chance is, of course, so small it can be dismissed as an explanation.
2. They form a large part of the 'junk' DNA carried by all organisms, which, although a small proportion of it is transcribed into RNA, the RNA doesn't get translated into proteins and most of it doesn't serve any purpose. Some, but by no means all of it may have some regulatory functions.
3. Occasionally, an ancient ERV may have become exapted for some useful purpose unrelated to the original virus, so showing how new genetic information can enter a genome, flatly contradicting creationist's claims that no new information can arise within a genome because the second law of thermodynamics [sic] and Shannon Information Theory somehow forbids it.
4. An ERV serving a useful purpose also contradicts creationist claims that, while their favourite creator god is responsible for all the good stuff, another creator, called 'Sin', is responsible for the harmful stuff like parasites and viruses. Yet in those exapted ERVs we have viruses providing something that is beneficial and therefore, according to creationist dogma, must have been provided by their god!
5. Lastly, the examples of where ancient ERVs have mutated and provided some additional ability or function, such as enabling the formation of the myeline sheath in vertebrates, can't be regarded as detrimental mutations, yet creationist dogma, courtesy of the hapless Micheal J. Behe, is that all mutations are 'devolutionary'[sic].

How Science Works - Correcting Earlier Mistakes With Modern Technology

280-million-year-old Tridentinosaurus antiquus.
Black outline, not skin, but paint!

Latest News and Views from University College Cork (Coláiste na hOllscoile Corcaigh)

There are few things that creationist like more than reports of 'soft' tissues being found in ancient fossils, because they imagine this 'proves' the fossils are much younger than palaeontologists claim, and places them well within the 10,000 years they believe Earth has existed for. It's nonsense, of course, because fossilised 'soft' tissues are not the same as actual soft tissues since, under the right circumstances, there is nothing to prevent soft tissue being mineralised by the same processes that hard tissues are mineralised. The results are not soft; they are hard, mineralised fossils. The term 'soft tissue' simply relates to what they started out as, not what they ended up as.

That point is probably too subtle for most creationists to appreciate.

Given the propensity of creationist frauds to misrepresent the science to their dupes, it's perhaps surprising that they don't wave the fossil of Tridentinosaurus antiquus. as 'proof' of a young Earth because it was believed to have its skin preserved and was thought by some to be an example of the rare preservation of soft tissue in a fossil.

However, a paper in Palaeontology a few days ago, not only destroys that notion, but shows how the scientific method eventually corrects mistakes and even deliberate hoaxes, in much the same way that the scientific method eventually exposed the Piltdown hoax as a forgery.

This paper shows that what was interpreted as fossilised skin was actually black paint. Whether this was a deliberate attempt to mislead or simply an attempt to make the fossil stand out from the surrounding rock matrix in which it is embedded may never be known, but one thing of which we can be sure, is that it isn't fossilised skin, so there is no mystery for science too explain.

The fossil is embedded in volcanic rock, so the 'mystery' was how the skin survived the high temperatures involved in the production of the rock, and various theories were proposed for this, including the lizard-like reptile sheltering in a crack in the rock.

How the 'forgery' was exposed is the subject of the paper in Paleontology and a news release from the University of Cork, Ireland:

Creationism in Crisis - How The Fossil Record Provides Evidence For Evolution - No Magic Needed

Desert sand dune landscape of the Upper Cretaceous Djadokhta/Baruungoyot Formations
Foreground: the large-bodied monstersaurian lizard Estesia mongoliensis

Illustration by Nathan Dehaut

Desert sand dune landscape of the Upper Cretaceous Djadokhta/Baruungoyot Formations. Foreground: the large-bodied monstersaurian lizard Estesia mongoliensis predating on the enantiornithine bird Gobipteryx minuta.

Illustration by Nathan Dehaut

A Lighthouse in the Gobi Desert | Natural History Museums of Los Angeles County

We are regularly told by creationists who have either been fooled by a lie, or are trying to fool us with one, that biomedical scientists are increasingly rejecting the Theory of Evolution and replacing it with the notion of intelligent design.

This was, of course, the aim of the Discovery Institute's 26-year-old, 5-year[sic] strategy detailed in The Wedge to insert Bible literalism into mainstream science, apparently believing that for the first time in the history of science, a well-established scientific theory is going to be replaced by a an evidence-free superstition based on misrepresentation of the data and including unproven supernatural entities doing magic.

Intelligent design creationism, of course, doesn't meet the basic criteria to be called a science, which is why any scrutiny of the relevant scientific literature will find no hint that the TOE is inadequate for explaining the data or that magic explains it in a more scientifically satisfying way. Indeed, as I repeatedly show in these blog-posts, virtually every piece of scientific research casually refutes creationism by revealing the evidence and not a single peer-reviewed biomedical science paper ever concludes that intelligent design is the only way to explain the observations.

As Michael J Behe was forced to admit in the Kitzmiller case, "There are no peer-reviewed article by anyone advocating for intelligent design supported by pertinent experiments or calculations which provide detailed rigorous accounts of how intelligent design of any biological system occurred". And that situation has not changed since Behe effectively sank the Wedge Strategy with that grudging admission under oath in an American court. Instead, we find papers like this technical one in which a team of researchers led by Dr. Hank Woolley, a Postdoctoral Research Fellow at the Dinosaur Institute, Natural History Museum of Los Angeles County, and the Department of Earth Sciences, University of Southern California, Los Angeles, California, discuss and evaluate the degree to which exceptional collections of fossils, such as those found in the Gobi Desert of Central Asia can influence our understanding of evolutionary relationships between fossil groups - what they term the lagerstätten effect .

The team have explained their research in a news release from the Natural History Museums of Los Angeles County:

Creationism in Crisis - The Inner Ear Of A 6 Million-Year-Old Hominoid Fossil Gives A Clue To The Evolution Of Bipedalism In Humans

Reconstruction of the locomotor behavior and paleoenvironment of Lufengpithecus

Illustration by Xiaocong Guo;
image courtesy of Xijun Ni,
Institute of Vertebrate Paleontology and Paleoanthropology,
Chinese Academy of Sciences.

InformedHealth.org How does our sense of balance work?

How Did Humans Learn to Walk? New Evolutionary Study Offers an Earful

To walk upright successfully needs a fully functioning balance organ in the inner ear, as anyone suffering from Ménière's disease will testify, so the study of the origins of bipedalism in the remote ancestors of humans needs to take into account changes in the inner ear that would facilitate it.

Humans and our closest relatives, the great apes and the simians, display a range of locomotion but only humans are normally fully bipedal, although chimpanzees can use bipedal locomotion when carrying a load for example.

The monkeys normally run along branches on all fours, balanced on top of them and jumping from branch to branch; the apes hang beneath the branches in locomotion known as brachiation, but humans are ungainly in trees and prefer bipedal locomotion on the ground. The question is, when did this ability evolve in our ancestry?

We can be sure our hominin ancestors the Australopithecines, were fully bipedal because we have a record of their footprints in volcanic ash at Laetoli, and their lower limbs and feet were almost indistinguishable from those of Homo sapiens. 'Lucy' (Au afarensis) was probably mostly bipedal but may have taken to trees for safety and possibly to sleep on constructed platforms like chimpanzees do. The evidence of injuries to her fossilised skeletal remains suggests she may have died by falling out of a tree.

To investigate this stage in our evolution a group of researchers, led by Professor Xijun Ni, which included Yinan Zhang, a doctoral student, both of the Institute of Vertebrate Paleontology and Paleoanthropology of the Chinese Academy of Sciences (IVPP), and Terry Harrison, a New York University anthropologist, used 3-dimensional CT scanning to examine the inner ear of a 6-million-year-old fossil ape, Lufengpithecus, unearthed in China’s Yunnan Province in the early 1980s, and compared it to the inner ear of other living and fossil apes and humans from Asia, Europe, and Africa.

The formation the fossil was found in has been previously dated magnetobiostratigraphically to about 6 million years. This technique depends on the record of periodic changes in Earth's polarity trapped in magnetic particles in sedimentary rocks and by recording the microfossils such as pollen associated with these changes:

Malevolent Design - Another Arms Race Between A Parasitic Worm And Its Host - Or is It Just Unintelligent Design?

Cane Toad, Rhinella marina

Cane Toad, Rhinella marina

A secret war between cane toads and parasitic lungworms is raging across Australia

The subject of parasitic arms races throws creationists into a bout of cognitive dissonance from which they can only emerge with a hefty dose of double-think and self-deception, telling themselves that it's perfectly logical to hold two diametrically opposite and mutually contradictory views simultaneously, like believing that the term 'circle' describes a spere but the term 'square doesn't describe a cube.

They need to believe that, whilst it is central to their dogma and the belief on which all their god of the gaps and false dichotomy fallacies relies - that there is only one creator god capable of whatever it is they are waving as 'proof' or its existence, and at the same time believing that parasites were created by a different creator, over whom their omnipotent god has no powers and who goes toe to toe with it in parasite-host arms races.

Sadly for creationists, they were denied the argument concerning a second creator by their guru and Deception Institute flunky, Michael J Behe, who used the evolution of parasites like Escherichia coli and Plasmodium falciparum (the malaria parasite) as 'proof that their god is the intelligent designer behind the 'design' of all living things.

So, let's do what Behe unwittingly did and remove the second, evil designer from the equation, and see where it leads.

A case in point is the recently discovered arms race between the Australian cane toads and the lung worm parasite that infests their lungs:

Creationism in Crisis - Hundreds of Fossils From France From 470 Million Years Before 'Creation Week'

Biomineralized taxa of the Cabrières Biota

Saleh, F., Lustri, L., Gueriau, P. et al. (2024)

New fossil site of worldwide importance uncovered in southern France - UNIL L'ACTU

Artistic reconstruction of the Cabrières Biota.

Credit: Christian McCall (Prehistorica Art).

The news just keeps getting worse for creationism as the relentless scientific refutation of all their sacred dogmas continues unabated.

Today, it's the turn of palaeontologists from the Faculty of Geosciences and Environment at the University of Lausanne (UNIL), Switzerland, who, together with international colleagues, have just announced the discovery of a large collection of exceptionally well preserved fossils in the Lower Ordovician formation at Montagne Noire, in the Hérault department of France. The Lower Ordovician deposits were formed between about 485.4 and 470 million years before creationists believe Earth was magicked out of nothing.

Tell me all about the Lower Ordovician period particularly in the Montagne Noire, in the Hérault department of France, including how its age was determined. The Lower Ordovician period is a significant geological epoch characterized by a diversification of marine life, particularly marine invertebrates such as trilobites, brachiopods, and mollusks. It spans from approximately 485.4 to 470 million years ago. The Lower Ordovician is part of the larger Ordovician period, which is divided into three stages: Tremadocian, Floian, and Dapingian.

Montagne Noire, located in the Hérault department of France, is a region renowned for its Lower Ordovician sedimentary rocks, which provide valuable insights into the Earth's geological history during this period. The geological formations in Montagne Noire contain a wealth of fossils and sedimentary structures that have been studied extensively by geologists and paleontologists.

Creationism in Crisis - Now It's Fossils of Air-Breathing Fish From Australia - From 380 Million Years Before 'Creation Week'

Life reconstruction of Harajicadectes zhumini, a 40 cm long lobe-finned fish that is not too distantly related to the fishes that gave rise to the earliest limbed tetrapods.

Brian Choo/Flinders University

A 380-million-year-old predatory fish from Central Australia is finally named after decades of digging

It seems every day brings a new scientific refutation of creationism that the frauds who lead the cult and feed it disinformation need to keep hidden, or at least give the half-baked strategies for ignoring. The scientists are lying; the scientists get their dates wrong; no matter what the evidence shows, God's holy word trumps it; if you weren't there to see it, it probably didn't happen.

Maybe creationists can be satisfied with such obvious logical fallacies and evidence free assertions, but normal people will allow the evidence to lead their opinions, not the misrepresentations and lies of frauds who know nothing of the subject.

And what better evidence that the world wasn't created out of nothing by magic in a few days about 10,000 years ago, than yet more evidence that there were creatures like fish living on Earth 380 million years before creationist mythology says the magic creation happened; creatures like this fossil air-breathing, lobe-finned fish found in Devonian rocks in Central Australia.

And to make matters worse for creationists, this fish was a close relative of one of the lobe-finned fish that evolved into the terrestrial tetrapods from which all terrestrial vertebrates are descended. Taxonomists have now named this fish, Harajicadectes zhumini.

Creationism in Crisis - Social Learning Is Part of Beaked Whale Culture - Just Like Humans

Baird's beaked whale is the largest of the beaked whales, reaching a length of up to 10 meters.

Surprising Behavior in One of the Least Studied Mammals in the World - SDU

Continuing where I left off with the account of how orcas (killer whales) form distinct cultures based on food, hunting strategies, location and dialect, which parallel human cultures in many way, we now have evidence that at least one of the 24 known species of the beaked whales, Baird's beaked whale, form cultural groups, and that another 'human' trait - social learning - is involved in the formation of these cultures.

Creationists, of course, continue to insist that only humans form cultures and have the social ethics that hold them together because they were specially created in a way that makes them materially different to all other animals, and by the circular reason that often typifies creationist arguments, this proves they were specially created by a god who holds them in the highest esteem.

s But as we are learning, almost all the traits creationists try to claim are uniquely human and therefore proof of our special creation, are turning out to be common to many other species, especially mammals, and so are evidence for common ancestry and evolution by descent with modification.

The little-known beaked whale, a relative of orcas and dolphins, has recently been observed changing its habitat and hunting strategy by a process of social learning. This is the same process by which growing children adopt the social norms and customs of their culture and how people from other cultures can assimilate into unfamiliar cultures. Essentially it means observing others and memorizing what they do in any given situation.

This observation was made by researchers from the University of Southern Denmark (SDU) led by Olga Filatova, a whale expert and postdoc at Department of Biology and SDU Climate Cluster. She led the study which showed that some pods of orcas in the Pacific have occupied the same area since the last Ice Age glacial maximum, 20,000 years ago when they occupied warmer refugia and adopted them as permanent territories. The same study showed how orcas form distinct 'ecotypes' which are genetically isolated from other ecotypes by cultural barriers to interbreeding.

For the beaked whale study, the team observed a population of Baird's beaked whales, which has unexpectedly been found near the coast and in shallower waters than previously observed.

Their work has been published, open access, in the journal Animal Behaviour and is explained in a SDU press release by Birgitte Svennevig:

Creationism in Crisis - How Killer Whales Were Evolving Cultural Groups - 20,000 Years Before 'Creation Week'

Researchers find 20,000 years old refugium for orcas in the northern Pacific - SDU

The northern Pacific near Japan and Russia is home for several different groups of orcas. They have no contact with each other, do not seek the same food, do not speak the same dialect, and do not mate with each other. Some are the descendants of a pod that moved there during the last Ice Age.

Any study of whales, such as dolphins and they larger cousins, the orca's or killer whales will quickly dispel one of the myths creationists use to try to justify their absurd belief that humans are somehow materially different to the rest of life on Earth in a way which isn't just because we are a variation on the general mammalian theme with enough distance between us and related species to justify a separate taxon, because we were specially created - humans form cultures and have languages and traditions, etc.

Of course, it's not just the whales that have cultures and languages; chimpanzees and bonobos and other primates also have distinct cultural groups that differ significantly from one another, but this article deals specifically with orcas and the research which has shown that they moved into Ice Age refugia at the last glacial maximum, some 20,000 years ago, and some have slayed there ever since.

The article also illustrates a problem of modern taxonomy in how to define a species with hard and fast rules when the distinction in reality is fuzzy. Some of the pods studied form isolated cultural groups that seek different foods to the others, which speak a different dialect, move in a specific area, and never interbreed. This cultural barrier to hybridization is as much a barrier as is the different plumage and mating rituals that are the pre-zygotic barriers to interbreeding that justify classifying many related birds as distinct species because the barriers ensure an isolated gene pool in species that could successfully interbreed and do so in captivity. Killer whales exist in many pods with cultural barriers to interbreeding and so form isolated gene pools, yet they are regarded as a single species.

To overcome this problem, biologists have classified the different killer whale pods into 'ecotype', but it is this genetic isolation that enables genetic analysis to determine how long the pod has been isolated.

A research team led by whale biologist, Olga Filatova, of the University of Southern Denmark recently published an open access paper in the journal Marine Mammal Science showing how environmentally stable marine regions may have preserved refugial populations of the killer whale that retained historical genetic and cultural diversity. These whales are believed to have moved into the warmer refugia during the last Ice Age.

The team's work is explained in a University of Southern Demark (SDU) press release by Birgitte Svennevig:

Unintelligent Design - The Heath Robinson Way Legumes Get Nitrates

Image by Miha Creative/Shutterstock

Mechanism of Plants Obtain Nitrogen by Supplying Iron to Symbiotic Bacteria | Research News - University of Tsukuba

Creationism's 'intelligent' designer is nothing if not inventive. In fact, it's so inventive that it keeps on reinventing things it's already invented and designing new ways to do things it's already designed a way to do. It's almost exactly like it has no way of remembering what it did yesterday and using those designs and inventions today - a bit like a motor-car manufacturer who reinvents the wheel, or the steering mechanism every time it designs a new model.

Take, for example, the way most plants obtain the essential nitrates they need to make proteins. Nitrogen is abundant in the atmosphere (about 79%) where it exists as diatomic molecules N₂, in which form plants can't assimilate it. Instead they depend on soil bacteria, the 'nitrogen-fixing' bacteria such as Azotobacter and Clostridium which convert N₂, into ammonium (NH₄⁺ which forms salts with other minerals in the soil, in which form it can be taken in through the roots of plants. Apparently, it was too simple to give plants the same metabolic pathways that the nitrogen-fixing bacteria have so they could make their own ammonium, so a more complex and less energy-efficient way to get nitrates into plants had to be invented.

A small amount of ammonia (NH₃ is also produced by the action of lightening on atmospheric nitrogen and this, together with nitrates produced by industrial pollution is dissolved in rainwater and finds its way into the soil. Other bacteria, fungi and other soil organisms also release nitrates from decaying plant and animal matter in the soil.

Unintelligent Design - How A Design Blunder Causes Inflammatory Diseases, Especially In Later Life

Endosomes (magenta) collect around mitochondria (blue) after infection with virus HSV-1, which attacks mtDNA (green) and causes its release.

Credit: Salk Institute

Faulty DNA disposal system causes inflammation - Salk Institute for Biological Studies

In another example of the ramshackle Heath Robinson design process that created humans, scientists today published their findings that show how when a cell process goes wrong, as it frequently does, the result can be a serious health condition, causing suffering and unhappiness.

And of course, it’s another example of how we can tell humans weren't intelligently designed by an omnibenevolent god who wants to minimise the suffering in the world, but by a mindless, amoral natural process that has no option but to settle for the sub-optimal as long as it’s better than nothing.

The discovery, by researchers at the Salk Institute and their colleagues at UC San Diego , is the way when mitochondrial DNA (mtDNA) goes wrong and the cell tried to dispose of it, some of it leaks out into the cell, the cell’s immune system treats it like the DNA of a parasitic organism and sets up an immune response which caused inflammation.

Given the origin of mitochondria in our Heath Robinson contraptions we call cells, this is hardly surprising since mitochondria started out, probably as the free-living bacterial prey of another prokaryote, possibly an archaeon. They then became symbiotic, providing the cell with free ATP in return for protection and nutrients in the form of sugar, water and oxygen. Because they need to provide a handful of enzymes to do this with, and they are self-replicating, they retained a small amount of their original DNA while giving up most of it to the host cell's nucleus.

Creationism in Crisis - A New Endogenous Retrovirus Caught In The Act Of Invading a Genome

white-bellied mosaic-tailed rat Melomys leucogaster.
The species is being infected with the gibbon leukemia retrovirus.

Photo by Carlos Bocos

A rare recent case of retrovirus integration: An infectious gibbon ape leukemia virus is colonising a rodent’s genome in New Guinea - Leibniz Institute for Zoo and Wildlife Research

Researchers have discovered that a retrovirus is currently in the process of invading the genome of a rodent in New Guinea. This will add to the extensive list of known endogenous retroviruses. The virus, which appear to be harmless to the rodent - a mosaic tailed rat of the Melomys genus - is an infectious virus that causes leukemia in gibbons.

A retrovirus is an RNA virus that 'hides' in its host's DNA by inserting the DNA template for its RNA, using the enzyme reverse transcriptase that is coded for in its RNA. Once inserted it is replicated by every daughter cell. If it is inserted into the DNA of a germline cell, it can be passed on to the next generation.

Endogenous retroviruses (ERVs) are common in the genomes of all multicellular organisms and even some single-celled organisms, and as such constitute a large proportion of the non-coding or 'junk' DNA. A few may have been exapted for other purposes, but most are simply strands of viral DNA with a few mutations that broke them and rendered them harmless way back in our evolutionary history.

ERV's provide some of the most compelling evidence for common descent, especially since they appear at the same locus in the genomes of almost all members of a clade such as the vertebrates, including fish ancestors or the terrestrial vertebrates. The probability of the same ERV with the same mutations in in the same genetic locus to make it look like they form nested hierarchies, is vanishingly small, yet they do it over and over again.

The fact that they are present in all members of the same major clade tells us they must have been present in the last common ancestor of that clade, so they are a double embarrassment for creationists. They are both evidence of descent with modification and that there was no intelligence in the design of our genomes, because an intelligent designer would have no reason to include broken viral DNA which adds nothing by way of functionality yet must be replicated in every cell.

Unintelligent Design - How Scientists Are Overcoming The "Designer's" Incompetence

Credit: Dingzeyu Li via Unsplash

Systemic lupus erythematosus

World-first discovery may enable an effective long-term lupus treatment - Monash University

Readers may recall my recent article on Lupus and why women are nine times more likely to suffer from it than men, because the epigenetic process for switching off genes on their X-chromosome sometimes goes wrong and produces proteins that induce an immune response to their own tissues.

From a creationist perspective, this can only be for one of two reasons: either the designer was incompetent, or this was by design. The choice being either incompetence, or malevolence and misogyny.

Now a team of researchers at Monash University, Clayton, VIC, Australia, have reported success in finding a way to overcome this design defect - which begs the question: if scientists can do it, why couldn't an omnipotent intelligent designer? Could the answer be that the human immune system was not designed by an omnipotent, intelligent designer, but is the result of a mindless, utilitarian process that inevitably produces sub-optimal 'designs' that can't be scrapped and redesigned?

But that is the kind of thought that would cause panic in the mind of most creationists because it would raise the terrible spectre of wondering if they could be wrong.
The Australian team have just published their results, open access, in Nature Communications. They are also explained in a Monash University news release:

Unintelligent Design News - A Newly-Discovered Virus-Like Particle That Doesn't Appear to Do Anything Other Than Replicate Itself

Streptococcus sanguinis bacteria, which live in the mouth, may host replicators named obelisks

UK Health Security Agency/
Science Photo Library

Figure 2.

Obelisks encode putatively well-folded proteins
a) Obelisk open reading frame 1 (Oblin-1) is predicted (total mean-pLDDT ± SD = 83.8 ± 13.4, see methods) to fold into a stereotyped N-terminal “globule” formed of a three alpha helix (orange) bundle partially wrapping around an orthogonal four helix bundle, capped with a beta sheet “clasp” (blue, globule mean-pLDDT = 90.1 ± 8.7), joined by an intervening region harbouring the conserved domain-A (magenta) with no predicted tertiary structure, to an arbitrarily placed C-terminal alpha helix. “Globule” emphasised on the right. b) a to-scale (secondary structure) topological representation of Oblin-1 with the “globule” shaded in grey, and the domain-A emphasised with this bit-score sequence logo (see methods). c) Obelisk Oblin-2 is confidently predicted (mean-pLDDT = 97.1 ± 4.6 ) to fold into an alpha helix which appears to be a leucine zipper. Sequence logo of an “i+7” leucine spacing emphasised in red, with hydrophobic “d” position residues emphasised in yellow (expanded in Supplementary Figure 4b). d) homo-multimer predictions of Obelisk-alpha Oblin-2. top: dimer (mean-pLDDT = 94.6 ± 0.6), bottom: trimer (mean-pLDDT = 93.6 ± 0.6). Side-on representations of homomultimers shown with numbers of inter-helix salt-bridges (see Supplementary Figure 5).

A new virus-like entity has just been discovered – ‘obelisks’ explained

At least with most of creationism's putative 'intelligent' designer, there is something that they appear to be for, other than simply reproducing themselves - even if it is, in the case of viruses and bacteria, increasing the suffering in the world by making other organisms sick.

But scientists have just discovered a small particle that seems to be in the edge of life, less so even than a virus, which doesn’t appear to do anything other than replicate, although it seems to need bacteria in which to do this. It’s not clear what harm it does to its bacterial host or even if it has some symbiotic function. But it appears to be almost everywhere, especially in our mouths and gut, where it appears to have speciated into several different forms. The team have named it 'obelisk' because it forms a rod-like shape.

It was discovered by a team of Stanford University researchers led by Andrew Z. Fire, a previous recipient of the 2006 Nobel Prize for Physiology or Medicine who have reported to have 'identified 29,959 Obelisks (clustered at 90% nucleotide identity), with examples from all seven continents and in diverse ecological niches'. Their report has been provided with free access ahead of peer-reviewed publication, in the preprint server, bioRxiv.

The question remains, what do these particles do exactly and are they potentially harmful, or are they beneficial in some way? At least one of their hosts in which they replicate is one of the bacteria responsible for the plaque on our teeth that is responsible for dental caries and gum disease that can result in lost teeth, Streptococcus sanguinis.
Like most viruses, obelisks are a single, circular strand of RNA, but unlike viruses, they don't have a protein coat. They have one and maybe two genes which code for proteins named 'oblins' which are unrelated to any other known proteins. In this respect they differ from other recently (1970) discovered free-living strands of RNA called viroids, which don't have any recognisable genes but are known to cause serious diseases in plants.

In the following article, reprinted from The Conversation under a Creative Commons license, Professor Ed Feil, Professor of Microbial Evolution at The Milner Centre for Evolution, University of Bath, explains the significance of this discovery. His article is reformatted for stylistic consistency: