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 - Humans Were Making Beads In North America 2,900 Years Before 'Creation Week' - And The Evidence Survived The Legendary Genocidal Flood!

12,940-year-old bead made of hare bone, discovered at Wyoming’s La Prele Mammoth site.

Photo: Todd Surovell.

UW Archaeology Professor Discovers Oldest Known Bead in the Americas

The problem with having counter-factual beliefs that are only believed because you want to feel more important than you're afraid you really are, is that you need a vast array of strategies for ignoring the vast amount of evidence that your beliefs are wrong. This is especially important if you live in a technological society where there is free access to that vast amount of evidence and news such as this discovery of what could be the oldest known bead from the western hemisphere, dated to 12,940 years ago.

It was recovered from a site in Wyoming, USA at an archaeological site known as the La Prele Mammoth site:

What information do you have on the La Prele Mammoth site in Wyoming, USA?

Atheism - Eight Things You Probably Didn't Know

8 facts about atheists | Pew Research Center

Atheism is the lack of belief in the existence of any god or gods, nothing more and nothing less. This position is based on the self-evidence fac that the only intellectually honest basis for belief is evidence and the equally self-evidence fact that there is not (and cannot be) any definitive evidence for the existence of anything supernatural because, by definition, nothing supernatural can be detected. All there is, is the material universe and anything beyond that has nowhere and no time to exist in and could not interact with or influence events in the material universe, so is indistinguishable from nothing. Belief in anything supernatural is thus a superstition for which there is no supporting evidence.

Atheism is a belief position, not a knowledge claim. Since again the only intellectually honest position is that all knowledge has a degree of uncertainty, atheism is not Agnosticism since Agnosticism allows for the possibility of Atheism being wrong, but any assessment of the probability of the existence of any god must be subjective since there can be no observations to base it on. So, an Agnostic cannot express that probability without it becoming a belief position. As it is, Agnosticism is a pedantic knowledge claim which has no measurable probability of being different to Atheism, in the accuracy of its claim.

Recently, the Pew Research Center published 8 facts about Atheism based on its opinion polling in the USA and elsewhere. Most of them refer to Atheism in the USA, where Atheists make up 4% of U.S. adults, according to their 2023 National Public Opinion Reference Survey. That compares with 3% who described themselves as atheists in 2014 and 2% who did so in 2007.

That figure of 4% for the USA lags someway behind the UK (12%), Netherlands (17%), Sweden (18%), France (23%) and even once staunchly Catholic countries of Spain (10%) and the Republic of Ireland where 14.2% gave Atheist/No religion, as their religion, (if any) in the 1922 census (an increase of 187% since 2011). However, with a great deal of stigma still attached to Atheism in the USA and pressure to conform with regular church attendance, the true figure for Atheism is probably very underestimated and hidden within the large and growing 'Nones, which currently stands at 28% in the USA.

Pew Research Center's eight fact about Atheism are:

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 - More Bad News For Creationists - 12 Million-Year-Old Colored Snail Shells

Coloured fossil snail shells (left) and a snail shell from modern times (large specimen on the right)
Scale bar represents 1 cm.

Photo: Klaus Wolkenstein

Examples of coloured Miocene and modern gastropods used for Raman measurements. A, Pithocerithium rubiginosum, Miocene, Nexing, Austria, NHMW 2023/0101/0001. B, Tiaracerithium pictum, Miocene, St Margarethen, Austria, NHMW 2023/0103/0001. C, Potamides disjunctus, Miocene, Fertőrákos, Hungary, NHMW 2023/0104/0002. D, Sarmatigibbula podolica, Miocene, Fertőrákos, Hungary, NHMW 2023/0104/0003. E, Megalotachea sylvestrina, Miocene, Nexing, Austria, NHMW 2023/0101/0003. F, Thericium vulgatum, modern, Mediterranean Sea, Malacological Collection of NHMW, NHMW 2023/0105/0001. Scale bar represents 1 cm.

Photo: Klaus Wolkenstein

Fossil shell of Pithocerithium rubiginosum (height is 1.5 cm) from the Miocene sediments of Nexing in Austria (left) and isolated reddish polyene pigments on calcium fluoride disc (diameter of disc is 2 cm) (right).

Photo: Klaus Wolkenstein

Information for the Media: Surprisingly vibrant colour of 12-million-year-old snail shells - Georg-August-Universität Göttingen

Another terrible week for creationists is continuing today with news that a team of researchers from the University of Göttingen and the Natural History Museum Vienna (NHMW) have shown that the red pigment frequently found associated with the shells of fossilised snails from the Middle Miocene is the pigment that would have been present in the living shells, and not, as had been suggested, the product of later reactions.

This makes these pigments, from the chemical group of polyenes which includes the carotenes that give the colour to the plumage of some birds and to carrots, the oldest known pigments ever discovered. The fossil snails, Pithocerithium rubiginosum, so named from the 'rusty red' pigment they often contain, are from the Middle Miocene deposits in the geologically important Vienna Basin:

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:

Trust in The Clergy Falls To An All-Time Low in USA

Joel Osteen

Church of the Almighty Greed

Ethics Ratings of Nearly All Professions Down in U.S.

According to the latest Gallup Poll, trust in the ethical standards of almost all identified professional groups in the USA has declined in the four years up to 2023 with trust in the clergy reaching an all-time low at 32 percent of those polled rating their trust in them as very high or high. The clergy now rank alongside chiropractors and psychiatrists in the public perception of their ethical trustworthiness.

All the 5 major professions in the USA fell steadily between 1976 when polling began but the profession which fell furthest and fastest was that of clergy. in 1977, 61 percent of adult Americans polled, gave their trust in clergy as very high or high; this has now fallen to 32 percent, a 29 percentage points decline to almost half what it was in 1977.

And this downward trend has accelerated since 2012, declining by an average of slightly over 1.8 percentage points per year, against an average of just over 0.38 percentage points between 1977 and 2012. This represents about a four-fold increase in the rate of decline which, projected forward, if this rate continues, no-one in America will rate the ethical trustworthiness of clergy as very high or high by mid-2032.

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:

Creationism in Crisis - How A Pterosaur Flew Like A Bird On The Wing, Over The Sea To Skye - 165 Million Years Before 'Creation Week'

Reconstruction of Ceoptera evansae.

© NHM & Witton 2021

Skeleton of the new pterosaur Ceoptera evansae from the Middle Jurassic of the Isle of Skye.

Trustees of the Natural History Museum London

---

3D models of skeleton.

Natural History Museum London

February : New species of Jurassic pterosaur discovered | News and features | University of Bristol

In another of those casual refutations of the creation myth in the Bible, archaeologists have discovered a new species of pterosaur that flew in the skies of what if now the Isle of Skye, Scotland, about 165 million years before creationism's fabled god decided to magic up out of nothing, a small flat planet with a dome over it in the Middle East.

They are thought to have lived for some 5 million years between the late Early Jurassic up to the Late Jurassic.

The fossilised skeleton fills another of those gaps in the fossil record so beloved of creationist, where the scarcity of fossils meant that the evolution of pterosaurs was poorly understood. This fossil shows that all the main clades of pterosaurs had evolved before the end of the Early Jurassic and earlier than previously thought.

The team from the University of Bristol Natural History Museum, the University of Leicester, and the University of Liverpool have named the new species, Ceoptera evansae: Ceoptera from the Scots Gaelic word Cheò, meaning mist (a reference to the Gaelic name for the Isle of Skye, Eilean a’ Cheò, or Isle of Mist - Scots Gaelic is still widely spoken on Skye), and the Latin -ptera, meaning wing. Evansae honours Professor Susan E. Evans, for her years of anatomical and palaeontological research, in particular on the Isle of Skye.

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:

Unintelligent Design - How Scientists Are Learning to Do What Creationism's 'Intelligent' Designer Found Too Difficult - Or Didn't Want To Do!

The proteins needed to create limb progenitor cells are marked with different colors under a microscope.

Images: Yuji Atsuta/Tabin lab

The proteins needed to create limb progenitor cells are marked with different colors under a microscope.

Images: Yuji Atsuta/Tabin lab

The Surprisingly Simple Recipe for Starting to Grow a Limb | Harvard Medical School

Visit any site of a supposed Marian miracle, such as Lourdes, now selling 'miracle cures' that almost never work and those that do can be attributed to the medication the pilgrim was receiving prior to the visit, or to spontaneous regression, the placebo effect or a psychosomatic condition, and you may find lots of crutches supposedly left there as testament to the cure of mobility disorders, but what you will never find is the artificial limb discarded by someone who had a spontaneous regeneration of an amputated limb.

Or visit any of the lucrative travelling, carefully stage-managed 'faith healing circuses' where people appear to be 'cured' of all manner of ailments at the touch of a 'healer', who, for perhaps obvious reasons, never works in a hospital, and you will never witness the regeneration of a limb, or even part of a limb. Not even a finger or toe.

And before some-one cites, the 'Miracle of Calanda', this is such an obvious hoax that it's a miracle anyone believes it.

Despite having allegedly created a universe from nothing and all living things from dirt, creationism's god appears to be incapable, even with the help of his miracle-working mother, to be able to regrow a human limb.

The problem is one of the designer's own making (if you believe creationists) because it would involve the epigenetic resetting of the cells at the end of the stump, so they become stem cells again, capable of making all the different specialist cells in a limb, like bone, muscle, skin, nerves and blood vessels and growing to the right shape in the right place. That was a once-only ability in the developing embryo.

Epigenetics, as I have written about many times, is necessary because the cells of a multicellular organism replicate the same way our single-celled ancestors did - by replicating the entire genome every time in every daughter cell. But the benefit of multicellularity is that cells are specialised so only need a few genes, not the entire genome and having the wrong genes active in a specialist cell would be detrimental, so most of them need to be switched off by the epigenetic system. A problem which could have been avoided by any omniscient, omnipotent designer by just replicating those genes that were going to be needed by the specialist cells, but not something a mindless, natural process with no foresight, no reverse gear and no means of scrapping a bad design and starting again, could have avoided.

And yet medical scientists investigating the problem believe they have discovered the basic principles involved, which turn out to be "surprisingly simple", so well within the capabilities of even creationism's rather limited god.

The scientists, led by Harvard Medical School geneticists, have published their findings in an open access paper in a Cell Press journal, Developmental Cell and explain it in a Harvard Medical School news release by Stephanie Dutchen:

Creationism in Crisis - Scientists Are Understanding More About How Plants Evolve and Diversify - No God-Magic Required

Top Left: Penstemon newberryi
Bottom Left: Penstemon cardwellii

Top Right: Penstemon rupicola
Bottom Right: Penstemon cerrulatus

Ecological Diversification in an Adaptive Radiation of Plants: The Role of De Novo Mutation and Introgression | Molecular Biology and Evolution | Oxford Academic

An effective way to refute the counter-factual claims of a wackaddodle cult like creationism is simply to reveal the facts and show how different they are to the cult beliefs. Sadly, this approach won't convince many creationists of course, especially those too arrogant to think their beliefs can be contradicted with mere facts, because part of being a creationist is to hold the self-idolatrous belief that your beliefs are inerrant, so trump anything science can produce, but one can but try.

In fact, researchers in biomedical sciences don't even try, they have more important things to do than try to convince fools who reject evidence before they see it and who are proud of the fact that nothing can make them change their minds. Scientists just discover the facts and add to the mountain of evidence that creationists have been conditioned to ignore or dismiss as lies or otherwise relegate to the realm of the unimportant.

For example, this week’s edition of Oxford University Press' journal Molecular Biology & Evolution has 10 different open access papers dealing with the minutia of evolution and not one of them shows any sign that the scientists are abandoning the Theory of Evolution as not fit for purpose and adopting instead, creationism's childish superstition complete with magic and unproven supernatural entities, as creationist cult leaders regularly tell their dupes.

None of these papers mention creationism or point out how the research findings refute it, of course, because they are written for people who understand the science, so don't need that to be pointed out to them. These are:

Creationism in Crisis - A Strange Shaped Tree 360 Million Years Before 'Creation Week'.

Enigmatic fossil plants with three-dimensional, arborescent-growth architecture from the earliest Carboniferous of New Brunswick, Canada: Current Biology

Creationism's designer is not known for creating a design then sticking to it. If you believe creationists, it has designed something like 500,000 beetles, for example, and, although they all do basically the same thing, hundreds of different trees.

And, if you believe creationist mythology, it created almost everything on Earth, hundred, even thousands of millions of years before it created the small flat planet with a dome over it, centred on the Middles East. Sadly, the Bronze Age story-tellers who wrote about it were oblivious of what had been living 360 million years earlier in the Tournaisian age in what is now New Brunswick, Canada, so said nothing about it in their tales. They said nothing about Canada either for that matter, because they were ignorant of anywhere outside their small area of the Middle East, as can be seen from the naive way they describe their world as they imagined it.

Had they been better informed though, they might have mentioned one of the more bizarre tree designs which consisted of a straight trunk about 15 feet tall, with long thin leaves radiating out from the top third and measuring about 18 feet in length, the whole thing resembling a giant green bottle brush. It doesn't appear to have had any branches.

Fossils of this tree have been described by an international team led by Robert Gastaldo of Colby College in Waterville, Maine, USA in collaboration with Matthew Stimson and Olivia King of the New Brunswick Museum, Saint John, and Saint Mary's University in Halifax, Nova Scotia, Canada, and others.

Their work is published, open access, in Current Biology and described in a Cell Press article reprinted in Science Daily:

Unintelligent Design News - Why Women Are More Prone To Lupus Than Men - Evolution, Or Does Creationism's God Just Hate Women More?

The classic 'butterfly rash' of systemic lupus erythematosus (SLE)

Lupus and other autoimmune diseases strike far more women than men. Now there's a clue why

In my days as an operational paramedic, I once had to move a 26 your old women to hospital because lupus had made her so ill her blood pressure was below the safe level to maintain her renal function.

It was so low I couldn't even sit her up to carry her down stairs without her losing consciousness, so I had to run a couple of units of IV fluid into her to bring it up enough to make it safe to move her. She really was profoundly ill and at death's door. But such was the nature of the profession that, having delivered her safely to hospital and handed her over to the care of doctors and nurses, that was the end of my role in her care, so I never heard the outcome.

The autoimmune condition, lupus erythematosus, is caused by a malfunction of the immune system in which something triggers it to turn against the sufferer's own body instead of the invasive pathogens from which it has evolved to protect us. Although, of course, a creationist would hotly dispute the idea that a system like our immune system evolved at all, and would insist that it was intelligently [sic] designed by their favourite, evidence-free, supernatural deity without whom nothing can be created, presumably because they believe chemistry and physics don't know how to behave without a magic god telling them.

But an intelligently-designed immune system would only malfunction and turn against the person it is supposedly designed to protect if it were either incompetently designed or malevolently designed and is doing what it was designed to do - randomly increasing the suffering in the world. The evidence is that lupus is far more common in women than in men by a ratio of 9:1, which begs the question, does the designer just hate women more than men or was he more diligent when designing men's immune system then when designing women's?

The answer, as anyone who understands anatomy and physiology and particularly, evolution, will tell you, is that as an evolved system, we can expect compromises and a lack of perfection because evolution is a utilitarian process with no foresight and no reverse gear, so we are stuck with a sub-optimal immune system that evolved in an ancient ancestor, maybe even a pre-vertebrate ancestor. Certainly, all known vertebrates have one, and some, like that of bats, is far superior to ours.

Now a team of researchers at Stanford University School of Medicine, Stanford, CA, USA have worked out why lupus is far more common in women than men. Ther results are published, open access, in Cell and explained in a Stanford Medical news release. But first, a little AI background:

Malevolent Designer News - Creationism's Divine Malevolence Has Just Released An E. Coli Upgrade With Added Malice

Escherichia coli

New and highly infectiousE. coli strain resistant to powerful antibiotics - University of Birmingham

Escherichia coli is a pathogenic bacterium that is loved by creationists because they have been taken in by Michael J. Behe's book, Darwin's Black Box, that made him a millionaire because so many creationists bought it (though few appear to have read it) and which they love to wave around as 'proof' that the locally popular god exists.

Behe, a leading light in the Deception Institute, which was set up to try to win converts for fundamentalist, Bible literalist Christianity, by spreading disinformation about science, had argued, falsely, that the flagellum of E. coli must have been intelligently designed, since all the components need to be present for it to work (the 'irreducibly complex' fallacy) and it is too complex to have evolved in a single step because, so he claimed none of the components on their own could have given an advantage for natural selection to select for (which of course ignores genetic drift as a cause of evolution).

What Behe neglected to do was tell his readers that almost all the components of the flagellum and the proton pump that drives it, were present in a structure called the Type III Secretory system with which bacteria bind themselves to their host and kill them, and this could easily have evolved from simpler beginning over the billions of years that bacteria were evolving into their present forms.

Since its publication, Behe has been repeatedly told of the errors in it, and as a professional microbiologist, he should be aware of the growing body of research explaining how the E.coli flagellum evolved^{1,2, 3, 4, 5}, yet he refused to correct his errors in later editions and continues to promote and defend the misinformation in it, whilst pocketing the royalties from sales, in a classic case of bearing false witness.