Rosa Rubicondior

Thursday 21 March 2024

Creationism in Crisis - How Hair Evolved From A Keratin Gene In A Frog-Human Common Ancestor

Genetic basis for the evolution of hair discovered in the clawed frog

Western Clawed Frog, Xenopus tropicalis
Carries the precursor gene for mammalian hair.

"When sorrows come, they come not single spies but in battalions" - Claudius in Hamlet.

That was never more true of creationism than it is today with the publication of not just the usual casual refutation of creationism we've come to expect most days, but of four disparate papers each of which casually and unintentionally refutes creationism to anyone who understands biology and is familiar with the basic dogmas of the creation cult, simply by revealing real-world facts.

The papers range from this one, which shows how mammalian hair has its genetic origins in a common human-amphibian ancestor, through how a female butterfly evolved Batesian mimicry, through the discovery of a giant Amazonian dolphin from 16 million years before creationists think Earth existed, to how early modern humans survived a super-volcano eruption in South-West Ethiopia a mere 64,000 years before 'Creation Week'.

With so many papers I'll do my best to cover all of them in the next few days, so keep checking back!

Firstly, the evolutionary origin of mammalian hair.

The gene for this originated in a common ancestor of humans (and the other mammals) and a modern clawed frog. The gene controls the growth of keratin, of which the claws of a clawed frog are composed, as is mammalian hair. The evidence for this common origin was found by researchers from the Medical University of Vienna, Austria, led by led by Leopold Eckhart. The team have published their findings open access in Nature Communications and described their work in a Medical University of Vienna new release:

A typical fairy circle on the Kamberg on the edge of the Namibian Desert

Photo: Stephan Getzin.

Information for the Media - Georg-August-Universität Göttingen

Scientists are hotly debating how the 'fairy circles' which arise in the vegetation on the edge of the Namib desert actually form. Whatever the process, they are examples of order emerging from chaos by the operation of natural forces. The debate is over what exactly those forces are.

Typical of the mindless parroting that constitutes creationism in the social media, is the claim that 'you can't get order from chaos', which of course is nonsense, since any chaotic system will tend to order if a directional force is applied to it.

Suns and galaxies condense out of the chaos of dust and gas clouds under the directional force of gravity; raindrops form in clouds under the directional forces of gravity and electrostatic attraction; and 'fairy rings' form in grassland under the influence of fungal hyphae and nutrient depletion, and rings form in ell grass because of a build-up of toxic sulphides in the marine sediment, just to cite a few examples

Here's a little bit of fun which you can use to show any creationist acquaintance what nonsense they've been fed. Next time you're playing Scrabble, place all the tiles in the upturned box lid and make sure no tile is on top of another. Ask them to swirl it round to show you're not cheating. Observe that the tiles are in a chaotic arrangement. Now apply a directional force in the form of gravity by tipping the box lid about 15 degrees to produce a slope and tapping it or shaking the lid gently to provide a little energy to the system. Observe now that the tiles have formed themselves into neat rows and columns at one end of the lid. If not, give it a little more shaking or tapping.

Order has emerged out of chaos under nothing more magical than the directional force of gravity.

More examples of emergence of order out of chaos are:

Creationism in Crisis - Closing The Last God-Shaped Gap - How The Simplest Cells Could Have Evolved, Naturally

Last Chance Lake in September 2022. At the end of the summer, the water has almost all evaporated, leaving a salty crust on the surface.

Credit: Zachary R. Cohen/Washington University

Did the first cells evolve in soda lakes?

According to a new study by Zachary R Cohen of the Chemistry Department of Washington University, Seatle, WA, USA and colleagues, soda lakes which are rich in sodium and carbonates could have provided the right conditions for the simplest, RNA-based cells to have arisen.

It is widely assumed that the earliest simple cells were based on RNA enclosed in a lipid membrane but there is a problem in that RNA requires divalent ions such as Magnesium (Mg²⁺ to function, but Mg²⁺ damages lipid membranes, so it isn't easy to explain how they could have co-existed within the same cell structure.

So the question is whether the low levels of (Mg²⁺ found in soda lakes, such as the Last Chance Lake in British Columbia, Canada, could have provided the right conditions of enough (Mg²⁺ for RNA to function but not so much as to prevent the formation of an enclosing membrane.

To explore this possibility, Zachary Cohen and his colleagues collected water from Last Chance Lake and the similar but subtly different Goodenough Lake after seasonal evaporation. According to information from Washington University published in phys.org:

These soda lakes each contained ~1 M Na⁺ and ~1 mM Mg²⁺ at pH 10. The authors found that spontaneous extension of short RNA primers occurred in lake water at a rate comparable to the rates in standard laboratory conditions.

The authors added fatty acids, which could have been available on the early Earth, to the lake water to see if the molecules would assemble into membranes. The membranes formed in dilute water that simulates a rainfall event, and the membranes persisted even when surrounded by concentrated lake water from the dry season.

According to the authors, soda lakes on the early Earth could have supported key features of protocell development, with RNA copying and ribozyme activity taking place in the dry season and vesicle formation occurring during the wet season.

The scientists give more technical details in their open access paper in PNAS Nexus:

Creationism's Heath-Robinson Designer - Muddling Through With Even More Ramshackle Complexity

Gut Bacteria Make Neurotransmitters to Shape the Newborn Immune System | Newsroom | Weill Cornell Medicine

The story so far, according to the Creationists Gospel:

Once upon a time, just a few thousand years ago, a magic man in the sky magicked a small flat planet with a dome over it in the Middle East, and then made some people to live on it.

It also made lots of harmful bacteria and other parasites to live in them and make them sick, but luckily, it also gave the humans an immune system to stop the parasites it made to make them sick, from doing what it designed them to do.

The only problem was that the ramshackle immune system it designed, which often doesn't do what it was designed to do, is also a little hypersensitive and prone to treating other things like the body it should be protecting as a parasite and mounting an attack on it so we suffer from all sorts of 'autoimmune' diseases that require another layer of complexity to keep in check. The other thing about it is that it needs training and until that's complete, it will treat all manner of things as parasites, including the food babies eat - and that could result in food allergies that would make life miserable!

But rather than do the simple thing and design the immune system to be able to tell the difference between food and harmful parasites, creationism's version of William Heath-Robinson went for one of the most bizarre solutions you can imagine. Rather like William Heath-Robinson's solution to an every-day problem, it co-opted things in the baby's environment to perform functions they were never intended to perform, like an upright piano being used to stand a step-ladder on to give it enough height, or a stick and some string being used to mend a broken spoke in a wheel, creationism's designer co-opted some of the bacteria that live in a baby's gut.

How it did this is explained in a free access paper in Science Immunology by a team of researchers from the Department of Pediatrics at Weill Cornell Medicine, led by Assistant Professor Dr. Melody Zeng of the Gale and Ira Drukier Institute for Children's Research. Their work is described in a Weill Cornel Medicine news item:

An artist’s interpretation of the newly identified aetosaur Garzapelta muelleri

Márcio L. Castro.

Tanks of the Triassic: New Crocodile Ancestor Identified | Jackson School of Geosciences | The University of Texas at Austin

In that very long period of Earth's history, long before creationism's god decided to create a small flat planet with a dome over it, and before even the dinosaurs rose to pre-eminence, another group of reptiles had evolved into armour-plated tank-like creatures with thick body-plates and fringes of curved spikes to deter predators. Some of these were later to evolve into the modern crocodiles.

Now three researchers from the University of Texas at Austin have identified a new species that lived 215 million years ago in the Triassic. The newly-identified species was found on a museum shelf where it had been since its discovery in Garza County in northwest Texas, some 30 years ago by the palaeontologist, Bill Mueller. The researchers have named the new species in his honor, as Garzapelta muelleri (Pelta = plate).

Religion News - People Who Believe Absurdities Will Commit Atrocities!

Why Religions Seem to Involve Outlandish Beliefs | Psychology Today

It's axiomatic that people who can believe absurdities can be persuaded to commit atrocities.

One only need look at the history of just about every world religion to know that is especially true of people who hold to religious beliefs, yet most religious people will look at other religions and wonder how on Earth they can believe that nonsense, while having no understanding why others who look at their beliefs have the same thoughts.

How many devout Christians, for example, would find nothing strange in the belief that the sun was swallowed each evening by the goddess Isis, who then gave birth to it every morning or that ancient Celtic chiefs physically mated with the Earth goddess at Tara to unite the Irish people with the land they lived on?

Yet those same Christians have no difficulty believing that the blood sacrifice of an innocent person can atone for collective 'sins' inherited from ancient ancestors or that the dismembered bodies of ancient holy men can somehow persuade a god to change his perfect plans for their better one, or an omniscient, omnibenevolent god needs to be told about a wrong and why if should be righted, or a mind-reading god needs to be told their thoughts.

And a Moslem who believes the founder of their religion split the moon in half and flew to Heaven on a magic flying creature finds it incomprehensible that saying prayers to a painting of an ancient holy man or priest can change the direction of the universe, or that the prohibition on 'graven images' doesn't apply to gold-covered icons or depictions of a god nailed to a stick, worn by people who believe tiny images of a blood sacrifice or miniature instrument of torture worn around their neck protects them from evil spirits?

There are even people who believe the sun can be made to perform strange maneuvers in the sky while no-one else on Earth noticed it and without Earth itself needing to suddenly change its speed and direction of rotation or orbital path round the sun. Even the leaders of a major branch of Christianity, with a whole panel of expert scientific advisors, believe that really happened and continue to send people to Fatima where it is alleged to have happened - just one of the many equally implausible and evidence-free beliefs orthodox Catholics needs to hold.

Even coeliac suffering Catholics can believe a piece of wafer, when the right spells are cast over it, miraculously becomes the body of a dead god to be consumed in a cannibalistic ritual, while knowing they need to avoid eating it to avoid the consequences of gluten intolerance! That's a condition of belonging to a cultural group called 'Catholics'.

How Science Works - Checking, Rechecking and Questioning What We Think We Know. The Only Certainty Is That There Are No Certainties

New research suggests that our universe has no dark matter | About us

A leading theoretical physicist has questioned whether dark matter really exists.

Dark Matter is a placeholder for what appears to be mass without substance which suffuses the universe, observable only by the gravity it exerts and thought by mainstream cosmologists to account for 27% of the matter in the universe with 'ordinary' matter making up just 5%. The rest - 68% - being composed of dark energy, another placeholder for something theory says should be there to account for the expansion of the universe, but which we don't have a model for in the standard model of particles and related fields.

I don't pretend to understand this stuff, but I'll post it here by way of a rebuttal of creationist claims that scientists devise experiments to try to prove preconceptions and that peer-review is just to ensure conformity to scientific orthodoxy.

Besides, the HTML coding is the sort of challenge I enjoy.

In fact, science is about continued reassessment and revision with names made not by confirming preconceptions but by overthrowing established consensus or exposing flaws in it which require further investigation. The leading theoretical physicist is Professor Rajendra Gupta of the Faculty of Science, University of Ottawa, Canada, who has just published a paper in The Astrophysical Journal. He has also authored an earlier paper which he believes shows the Universe to be about twice as old as the mainstream consensus believes it to be, so he can hardly be described as subscribing to some establishment orthodoxy. His work is explained in a University of Ottawa News release:

Why Religious People Find Atheism and Science Hard To Understand - Study Shows Atheists Are Generally More Intelligent Than Religious People

Why Are Religious People (Generally) Less Intelligent? | Psychology Today

One of the frustrating things about trying to debate with religious people in the social media, especially fundamentalists and creationists, is that they seem to have difficulty understanding simple logic such as the idea that the only reason for belief is evidence or the fact that lots of people believe something doesn't affect the truth of the belief.

There is also the impression (actually, it’s more than an impression, it seems to be a characteristic) that they think ignored evidence can be disregarded, so they will never read an article showing their beliefs to be wrong.

They generally seem more easily fooled by, for example, believing that an internet source supports them, when it is almost a rule that a link to a science paper provided by a fundamentalist will always say the opposite to what they claim it says, or that the ridiculous parody of science they've been fed by a creationist disinformation site such as AnswersInGenesis.com that no sane person would believe, is actually what real scientists believe. They have simply swallowed a lie and didn't see any need to check.

So, why do so many fundamentalists come across as limited in their ability to assimilate information and use it as the basis for opinions, other than an arrogant assumption that their beliefs must be true because they believe them, so no evidence is required and any contradictory evidence can be dismissed out of hand as 'wrong' or 'lies' or part of a giant conspiracy, and why do so many creationists came across as having the thinking ability of a toddler with a teleological view of the universe where even elementary particles are sentient and need to be told how to behave and which rules they must obey?

A meta-analysis of 63 earlier studies showed a statistically significant negative correlation between IQ and religiosity.

Creationism in Crisis - From Where Did The Bible's Authors Get The Idea That Humans Are Materially Different To Other Animals? And Why Were They Wrong?

Greek vase decoration - Dionysus and three figures.(Gods created in human image)

Friday essay: from political bees to talking pigs – how ancient thinkers saw the human-animal divide

It's a fundamental part of the Abrahamic religions and other religions that there is something materially different to humans, above and beyond the sort of difference that distinguishes one species from another. Biologically, of course, this is nonsense as any study of comparative anatomy and physiology will show. Humans are just another mammal, albeit with some highly evolved abilities that other species lack such as language, the ability to invent narrative, etc. The differences, as with the differences between any pair of related taxons is quantitative, not qualitative.

So, from where did religions and, especially the Abrahamic religions - Judaism, Christianity and Islam - get the idea of human exceptionalism from and why did they need to invent narratives to explain it, usually in terms of a special creation or a special closeness to gods - even a familial relationship or at least created in their image like children to their parents? In fact, as we will see, it’s much more likely that gods were created by humans in their image.

In the following article, reprinted from The Conversation, Professor Julia Kindt, Department of Classics and Ancient History, University of Sydney, SNW, Australia, explains the ideas origins in Ancient Greece and why it is wrong. Her article has been reformatted for stylistic purposes:

Archaeopteryx

Credit: Dotted Yeti/Shutterstock

A brief guide to birdwatching in the age of dinosaurs

What would it have been like to go bird-watching in that very long period of pre-'Creation Week' history just before a cataclysmic meteor strike cause the extinction of almost all the dinosaurs, 66 million years before creationists believe their god created a small, flat planet with a dome over it in the Middle-east?

At that time, Earth had a large population of dinosaurs, some of which were later to become modern birds which evolved to fill the vacated niches formerly occupied by the dinosaurs, while another survivor, a small rat-like early mammal, the descendant of mammal-like reptiles radiated into modern mammals.

For a period, these early birds, the avian dinosaurs which had evolved from the bipedal theropod dinosaurs, formed two major groups - the ornithuromorphs and the enantiornithine.

Creationism in Crisis - Rice Paddy Snakes In Thailand Diversified About 2.5 Million Years Before 'Creation Week'

Hypsiscopus murphyi sensu

Photo: Bryan Stuart

Rice paddy snake diversification was driven by geological and environmental factors in Thailand, molecular data suggests | KU News

In one of those far-away places that the simple-minded authors of the story in Genesis about a small flat Earth with a dome over it being magicked up out of nothing in the Middle East, 10,000 years ago, could never have guessed existed, and some 2.5 million years before they though Earth existed, major environmental changes were driving the diversification of a species of snake into several descendant species, just as the Theory of Evolution predicts.

If those simple-minded Bronze Age pastoralists had known about it and understood its significance in terms of the history of life on Earth and the dynamic geology of the planet, just imagine how different their imaginative tale would have been! As it was, they had to do their best with what little knowledge and understanding they had.

The snake in question was the Rice Paddy snake, otherwise known as a mud snake, and the far-away place was Thailand where the rise of the Khorat Plateau caused environmental changes that resulted in the evolutionary diversification of the Hypsiscopus genus.

The team of researchers from various American and Southeast Asian Universities, who have shown this link between environmental change and evolutionary radiation in a genus was led by Dr. Justin Bernstein, of the University of Kansas Center for Genomics. Their findings are published open access in Scientific Reports and are explained in a Kansas University news release:

A theropod track lies in rock near the west bank of the Kukpowruk River.

Photo: Anthony Fiorillo

Alaska dinosaur tracks reveal a lush, wet environment | Geophysical Institute

About 100 million yearsd before creationism's god decided to create a small flat planet with a dome over it to keep the water about its sky out, there were dinosaurs living in what is now northern Alaska. The problem for creationists is that the people who wrote their favourite creation myths were ignorant both of dinosaurs and Alaska so had no idea their tales needed to include something about them, which is why everything they wrote about either happened within a day or two's walk if the Canaanite Hills or were plagiarized from nearby cultures.

Now a team of paleontologists and archaeologists have discovered fossilised dinosaur footprints and the remains of plants in the Nanushuk Formation that show the climate there was warmer and wetter than today, at a time when species were migrating over the landbridge between Siberia in Asia and North America.

Unlike the Paluxy hoax, which had creationists fooled for the best part of a decade, there were no human footprints (hand-carved or otherwise) associated with these dinosaur tracks.

Because creationists will try to falsify the aging of the Nanshuk Formation, claiming the method must have been flawed to such an extent that if made 10,000 years or less look like 100 million years, here is actually how the dating was done - it’s; those dreaded zircons in volcanic deposits again, plus stratigraphy based on index fossils found in rocks of known age:

Do you have any information on the Nanushuk Formation in northern Alaska and how its age was estimated? The Nanushuk Formation is a geological formation located in northern Alaska, particularly in the North Slope region. It is primarily composed of sandstone, siltstone, and shale, and it contains significant oil and gas reserves. The formation is of great interest to geologists and petroleum geologists due to its hydrocarbon potential.

The age of the Nanushuk Formation has been estimated through various methods, including biostratigraphy and radiometric dating of volcanic ash layers within the formation. Biostratigraphy involves the study of fossil assemblages found within the rocks to determine their relative ages. By comparing the fossils present in the Nanushuk Formation to those found in other formations with well-established ages, geologists can infer the approximate age of the Nanushuk Formation.

Additionally, radiometric dating techniques, such as radiocarbon dating or uranium-lead dating, can be used to determine the absolute ages of specific minerals or volcanic ash layers within the formation. These methods rely on the decay of radioactive isotopes within the rocks to estimate the time since their formation.

Through a combination of these techniques, geologists have estimated that the Nanushuk Formation was deposited during the Late Cretaceous period, approximately 70 to 80 million years ago. However, the precise age estimates may vary depending on the specific location within the formation and the methods used for dating.

The team, led by Dr. Anthony R. Fiorillo of the New Mexico Museum of Natural History & Science, Albuquerque, USA and including Professor Paul McCarthy of University of Alaska Fairbanks (UAF) College of Natural Science and Mathematics, have published their findings open access in the journal Geosciences. It is explained in a UAF news item:

How Science Works - Giraffes - A single Pan-African Species Or Several Distinct Species?

Reticulated giraffe, Buffalo Springs, Kenya. Photo: Mogens Trolle

Photo: Mogens Trolle

Gene flow in giraffes and what it means for their conservation – Department of Biology - University of Copenhagen

In an evolutionary picture that resembles that of humans, giraffes appear to have speciated, or partially speciates at different times and in different parts of their range, then hybridized, before splitting again with regular gene-flow between the groups.

Similarly, though over a greater range, humans seems to have partially speciated into isolated populations in Africa before coming together again and spreading to Eurasia as Homo erectus which then split into Neanderthals, Denisovans and possibly others before meeting up with H. sapiens coming out of Africa in a second wave, to interbreed with the Eurasian species. The result is genetically distinct populations with evidence of ancient hybridization and gene flow.

Because conservation efforts tend to be directed at the species level, it is important for giraffe conservation to determine whether there is a single pan-African species with local sub-species or whether there are four or more species, each with a smaller population and therefore more vulnerable to habitat destruction and extinction.

To try to resolve this issue, as part of the African Wildlife Genomics research framework led by research groups at the Department of Biology at the University of Copenhagen, scientist carried out an extensive genome analysis to establish whether the different populations have been genetically isolated for long enough to be regarded as distinct species, even though, in captivity, they freely interbreed.

The results were a little surprising but highlight the difficulty in determining whether speciation has occurred within a population where differentiation is still in progress and few barriers to hybridisation have arisen. The problem is compounded by the fact that there is not a fixed definition of species, although biologists understand what the term means in a given context.

I've previously written blog posts about this problem, using the Eurasian crows as an example - an article incidentally which was recommended reading for Scottish biology students doing their 'Highers'.

The researchers have published their findings open access in the online Cell Press journal, Current Biology and explain it in a news item from the University of Copenhagen Biology Department:

Malevolent Design - How The Malaria Parasite is 'Designed' To Evolve And Outwit Medical Science

The malaria parasite generates genetic diversity using an evolutionary ‘copy-paste’ tactic | EMBL

Devotees of creationism’s divine malevolence would be conflicted by this news if they understood it, because it shows the creative genius of any intelligent designer who could come up with this system, but, it looks like it did so (if you believe it couldn't happen naturally) by setting up an evolutionary process that creationists are obliged by dogma to believe doesn't work.

The news is that the organisms that causes malaria, Plasmodium falciparum, is 'designed' to quickly find a way to overcome the anti-malarial drugs medical science has developed to cure people suffering from it and to prevent others from getting malaria, by evolving very quickly.

The discovery was by researchers at European Molecular Biology Laboratory's (EMBL’s) European Bioinformatics Institute who have identified a mechanism of ‘copy-paste’ genetics that increases the genetic diversity of the parasite at accelerated time scales. This helps solve a long-standing mystery regarding why the parasite displays hotspots of genetic diversity in an otherwise unremarkable genetic landscape. Copy-paste' is a way of doing something creationists insist is impossible without the aid of god-magic of increasing the genetic information in a genome and making it available for evolution by mutation and selection without any loss of function in the original copied genes.

The team have recently published their finding in the open access journal PLOS Biology and describe it in an EMBL news item:

Acinetobacter baumannii seen under a scanning electron-microscope

Escherichia coli

What makes a pathogen antibiotic-resistant? | Sanford Burnham Prebys

One of todays examples of the stupidity of creationism is something of a novelty. Usually, by applying the central tenets of creationism, any putative designer of living things like parasites either appears malevolent (and sometime it has to be said, malevolent at a near genius level in the ways it finds to make us and other animals sick) or it looks incompetent in that its 'solutions' are often to problems of its own making and more often than not to solutions it designed for one side of an arms race which it now trets as problems for the other side.

But today's example can only be described as an example of incompetent malevolennce, as creationism's putative designer, faced with the same 'problem' of medical science developing antibiotics effective against two different species of pathogen, set about designign two completely different 'solutions' to this problem. - Talk about re-inventing the wheel!

The pathogens are: Escherichia coli and Acinetobacter baumannii.

Creationists will probably be familiar with Escherichia coli (E. coli) because they believe their guru, Michael J Behe, 'proved' their god exists by claiming (falsely) that E. coli's flagellum must have been intelligently designed because he didn't know it evolved out of a pre-exiting structure and couldn't think how else it could have evolved. But then such is the standard of creationist apologetics!

What Behe had unwitting done was destroy the traditional excuse creationists use to explain pathogens like E. coli by blaming them on another 'designer' called 'Sin' which somehow creates living organisms although the creationit designer god is the only entitiy capable of designing livign things, so any example of 'intelligent design, real or imaginary, if 'proof' of this designer god's existance.

So, what creationists are now left with is an E.coli with a flegellum designed by their god to make it better at making us sick, and now resitant to antibiotics to help it win against medical science trying to prevent it makign us sick!

But what creationists are less likely to be familiar with is the pathogen, Acinetobacter baumannii, so here is a little background:

Unintelligent Design - RuBisCO Is Slowly Evolving - And Becoming Even More Embarrassing For Any Creationist Who Understands It

Photo by Kumiko SHIMIZU on Unsplash

The world’s most prolific CO₂-fixing enzyme is slowly getting better | University of Oxford

The world’s worst enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase, or RuBisCo as it is known, has featured in these blog posts several times and it described in my book, The Unintelligent Designer: Refuting the Intelligent Design Hoax as an example of the lack of intelligence in biological systems, and, as such, why it would be a major embarrassment to creationists - if they understood it.

Briefly, RuBisCo is one of the most ancient enzymes known and became an essential component of photosynthesis early on in the history of life on Earth when the first cyanobacteria evolved the ability to use the energy from sunlight to fix the carbon in atmospheric carbon dioxide (CO₂) to build the sugar glucose. Eventually, these photosynthesising cyanobacteria became incorporated into plant cells as the chloroplasts to produce the green plants at the base of most food chains. Because it is so inefficient, it quickly became probably the most abundant enzyme on Earth, making up with quantity what it lacked in quality.

But, evolution, unlike good intelligent design, is a one-way, utilitarian process in which whatever works better than preceded it will be retained and will provide the next basis for further evolution, because evolution has no mechanism to scrap a bad design and start again as any backward step will inevitably be worse, so will be quickly eliminated.

Tell me all about RuBisCo and why it's so inefficient. RuBisCo, or ribulose-1,5-bisphosphate carboxylase/oxygenase, is an enzyme crucial for the process of carbon fixation in plants, algae, and some bacteria. It catalyzes the first major step of the Calvin cycle, which is the primary pathway for carbon dioxide fixation in photosynthesis. Despite its importance, RuBisCo is often considered inefficient for several reasons:

Malevolent Design - How a Bacterium Carries a Virus That Selectively Kills Male Insects And Only Allows Infected Females To Breed

How does a virus hijack insect sperm to control disease vectors and pests? | Penn State University

Wolbachia are a genus of bacteria that form a symbiotic relationship with about 50% of arthropod species, including insects and spiders but they can also manipulate the species for their own ends (in terms of breeding success). They are aided in this by a virus which is incorporated in their genome which has been shown to join forces with Wolbachia to ensure their own reproductive success in the form of females infected with the virus-bearing Wolbachia.

So completely have Wolbachia integrated with insects that one species of fruit fly has the entire Wolbachia genome incorporated into its own genome, making it, biologically, both bacterium and fruit fly.

One way Wolbachia ensure their own survival at the expense of the species of insect they infect is by making the sperm and egg incompatible if the female is not also a carrier of the right species of Wolbachia. And, to be on the safe side, two proteins produced by the virus break the sperm's DNA so any resulting embryo will be defective and will fail to develop. This ensures that only the females carrying the infection can breed, so increasing the Wolbachia and its virus in the gene pool.

The team who discovered this nasty little virus and how it acts selfishly, was co-led by Professor Seth R. Bordenstein, of the One Health Microbiome Center at Pennsylvania State University. They have published their findings in Science and described it in a Penn State News item.

But first, a little background on Wolbachia:

Unintelligent Design - How Epigenetic Settings Are Passed To Daughter Cells - Even William Heath Robinson Would Be Impressed

Cracking Epigenetic Inheritance: HKU Biologists Discovered the Secrets of How Gene Traits are Passed on - Press Releases - Media - HKU

It all started when single-celled organisms started to form colonies of like-minded individuals. The easiest way to do it was for the two daughter cells of a dividing cell to stick together instead of going their own way. They in turn would have had more daughter cells until they formed large clump of cells, but, unless the cells began to perform distinct functions, there was no advantage to forming clumps like that instead of each cell going its own way and fending for itself. Fortunately, there were no large predators around, otherwise a clump of cells would have made a tasty snack and the whole idea would have been abandoned as too risky by half, and we would be stuck now with a world of single-celled organisms and nothing else.

However, with the trial and error which characterises biological development, some of the cells in the clump began to perform specialist functions. For example, as the clump got larger, specialist cells would have been needed to exchange gasses with the environment or the cells at the centre would have been deprived of oxygen and their waste in the form of carbon dioxide would have accumulated because diffusing across a large mass of cells would be too slow to keep up with production and the supply of oxygen would be too slow to keep up with the demand. The same thing applied to getting nutrients into the center of the clump.

So, the clumps which had specialist cells fared better in the competition for resources than those which were just undifferentiated clumps. In fact, the clumps with specialised cells would probably have eaten the undifferentiated clumps and become predators. And with predators there was pressure for increased specialisation for movement, ingestion and excretion, for more efficient respiration and for reproduction. And predation also produced pressure for more motility, for senses like sight and smell and maybe hearing and as the organisms became more complex so they needed nervous systems to coordinate their activities and process and respond to the stimuli their senses were receiving from their environment and some would have evolved defensive armour such as scales and spikes and hard shells and internal structures like cartilage and bone to give their bodies shape and form and to make their swimming apparatus stiffer and more powerful.

But what they never managed to do was find a different way to produce all the different specialist cells by a different method to that used by their single-celled ancestors, so every cell in their body had the full genome whether they needed it or not, and more often than not, they didn't need most of it. A bone cell doesn't need to do what a nerve cell does, and a nerve cell doesn't need to do what a muscle cell does, and neither muscle nor nerve cells need to make bone, and what else needs to make elbow skin other than an elbow skin cell, except perhaps a scrotum skin cell? Yet they all have the genes for doing everything any one cell needs to do.

So, cue creationism's intelligent [sic] designer who has been designing and modifying all these different clumps of specialised cells but who, for some reason, seems incapable of recognising that its designs are heading for disaster unless it can think up a way to make sure each specialised cell has only the genes it needs. For reasons which no creationist apologist has ever managed to explain, their putative designer always behaves as though it can't undo a bad design and start again but is compelled to try to make the best of what it has muddled through with so far. In every way, creationism’s 'intelligent [sic] designer' behaves just like a mindless process operating without a plan, handicapped by acute amnesia, and constantly surprising itself with a new problem it designed just yesterday.

Just like the eccentric British designer and cartoonist, William Heath Robinson, no solution to a problem can be too complex even if it creates a new problem for which another overly complex solution has to be found. Unlikely objects, designed for a completely different purpose, will be pressed into service; a stepladder will be balanced precariously on top of a piano and an umbrella will be used to push a button when prodded by a sink plunger swinging on a length of knotted string. A labour-saving device for peeling potatoes will take half a dozen, intense and serious-looking men to operate it and peeling the potatoes will take considerably longer than had each man been given a potato peeler and left to get on with it. Eggs will be fried in a frying pan held over a candle lit by a match rubbed against a matchbox which swings into action when released by a lever when the scuttle-full of coal, or the boulder suspended on knotted string, lands on it.

Haven't had COVID yet? It could be more than just luck

There are some scary questions for creationists at the end of this article. They follow on naturally from what's being discussed, so creationists should probably avoid reading too far, unless they have a responsible adult with them.

This article from The Conversation is from May 2022, when we were into the second year of the COVID-19 pandemic and most vulnerable people had had the two-step vaccinations and many would have had the spring booster. At that point neither me nor my partner had had COVID-19, which we put down to rigorously following the recommendations regarding mask-wearing, social distancing, hand washing, etc. and had tried to reduce our vulnerability to the sever forms of it by losing about 3 stone in weight and, in my case, getting my blood pressure under control with medication. We also tried to ensure our immune systems were healthy by taking vitamin D3, vitamin C, zinc and iron supplements.

In the early days of the pandemic, even before the official restrictions on social contact, we had observed the basic rules of hygiene and everyone who came into the house used hand-cleanser at the front door. I had even managed to obtain a supply of face-masks and plastic gloves online, which we wore at all times outside the house. Every package that was delivered to the house was left for several hours before we touched it, and all our weekly shopping was delivered or bought with click and collect. Delivered bags were left for four hours before unpacking. And we took weekly tests just in case we had it asymptomatically. All that might seem a little over the top now, but we were vindicated as events were to prove.

We put the fact that we hadn't caught it by mid-2022 down to our preventative measures, not to luck or genetics - a view that was vindicated last year when we both came back from a two-week vacation in France with a mild form of COVID-19, despite having had all the boosters on offer. We probably picked it up in a crowded airport or on the plane, where all the social distancing measures had been forgotten and even face masks were no longer worn. We both felt like we had a mild case of flu for a couple of days and after a week we were testing negative. Had we contracted it in Spring 2020, the outcome would probably have been very different as we had no immunity, and both had three of the risk-factors - overweight, high BP and over 70. In addition, my partner had had a mastectomy and was receiving treatment for breast cancer.

One reason you can't ever be sure that you won't catch COVID-19 is because the virus keeps mutating to produce new variants so, even if you were fortunate enough to have natural or acquired immunity to the variants so far, it is quite possible that the next or subsequent variants will have evolved a way round it. The following chart from the UK NHS, shows the rise and fall of the main variants over the course of the pandemic:

Source: NHS UKHSA Date Dashboard

But still, a few people managed to stay free from the virus. In the following article, reprinted from The Conversation under a Creative Commons license, Lindsay Broadbent, Research Fellow, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, explains why. Her article has been reformatted for stylistic consistency:

Creationism in Crisis - Geobiologists Discover The Cause of Earth's First Mass Extinctions Event - 550 Million Years Before 'Creation Week'

Impressions of the Ediacaran fossils Dickinsonia (at center) with the smaller anchor shaped Parvancorina (left) in sandstone of the Ediacara Member from the Nilpena Ediacara National Park in South Australia.

Photo: Scott Evans.

Geobiologists shine new light on Earth’s first known mass extinction event 550 million years ago | VTx | Virginia Tech

A big problem for Creationists, especially those who believe the Bible was written by an infallible creator god, so think Earth is just a few thousand years old, is that science keeps finding evidence that Earth is billions of years old, and finding fossils of the life-forms that were around then.

As though that wasn't refutation enough, a team of scientists from Virginia Tech have now explained the mass extinction that wiped out most of these early life forms several billion years ago - giving the lie that they were intelligently designed by a god with the ability of foresight. Such a god would have known about the future mass extinctions and either prevented it, designed his creations to survive it or at least waited till it was safe to create things. Creating things to go extinct is not the act of an intelligent or sane creator.

This mass extinction appears not to have been a sudden event, such as that that resulted in the extinction of the non-avian dinosaurs and large marine reptile predators, but to have occurred in two phases that resulted in a loss of about 80% of species and separated by about 10 million years.

But before creationists get over-excited, this does not mean all the Ediacarans were extinct at the Cambrian 'explosion' so the Cambrian biota had no ancestors. It means that there were still about 20% of the Ediacaran biota to evolve over the 6 million years of the Cambrian 'explosion' into the Cambrian biota.

The Ediacaran mass extinction was probably caused by falling Oxygen levels as Ediacarans that had evolved large mass to surface-area ratios suffered from a loss of oxygen more so than those which had retained a smaller mass to surface area ratio.

How this mass extinction was identified and related to changes in global oxygen levels was the subject of an open access paper in PNAS and a Virginal Tech News item:

Cliffs of the Hangman Sandstone Formation, where many of the fossils were found.

Credit: Neil Davies

Earth’s earliest forest revealed in Somerset fossils

Archaeologists have found what are believed to be the remains of the earliest forest so far discovered in Devonian sandstone rocks dated to 390 million years ago, which makes them 4 million years older than the previous record found in New York State, and means they were living almost 390 million years before creationism's 'Creation Week' when their god decided to create a small flat planet with a dome over it, centered on the Middle East.

The fossils were discovered in coastal cliffs near Minehead, Dorset, England in what is known as the Eifelian Hangman Sandstone Formation and consist of primitive trees which were ancestral to today's trees but looked more like palm trees. The discovery is the subject of a paper in the Journal of the Geological Society and a news release from the University of Cambridge, UK.

First a little about this rock formation:

Creationism in Crisis - How Genomic Imprinting Evolved - Unintelligently

Revealing the evolutionary origin of genomic imprinting 

Caenorhabditis elegans

Genomic imprinting is the process by which genes are suppressed by epigenetic settings that differ depending on whether the genes come from the father or the mother in a sexually-reproducing species.

This is an example of the sort of Heath Robinson machine which a natural, mindless evolutionary process can and does produce and which distinguishes evolved systems from intelligently designed processes. It comes from the fact that multicellular organism uses the same method to replicate their cells as their single-celled ancestors used, yet only need a small selection of the genes depending on how specialised the particular cells are.

But the reason for genomic imprinting involves something even more embarrassing to any creationists who understand it - it probably evolved out of an arms race not between the organism and a foreign parasite but between the organism and one of its genes that had gone rogue and turned into a 'jumping' gene or 'selfish genetic element':

What exactly are 'selfish genetic elements' and what do they do? Selfish genetic elements are DNA sequences that have evolved to enhance their own transmission to the next generation, often at the expense of the organism's overall fitness. These elements can manipulate various cellular and reproductive processes to increase their own propagation within a population, sometimes even if it is detrimental to the host organism.

One well-known example of selfish genetic elements is transposable elements, also known as jumping genes. These DNA sequences have the ability to move or copy themselves within the genome, potentially disrupting genes or regulatory sequences in the process. While transposable elements can sometimes contribute to genetic variation and evolution, they can also cause harmful mutations or genomic instability.

Another example of selfish genetic elements is meiotic drive elements. These elements bias their own transmission during meiosis, the process by which gametes (sperm and eggs) are formed. Meiotic drive can result in the preferential transmission of one allele (variant of a gene) over another, leading to distortions in genetic inheritance patterns within a population.

Selfish genetic elements can have significant implications for evolutionary processes, population genetics, and genome stability. They can influence patterns of genetic diversity, contribute to speciation, and even drive the evolution of complex biological systems. However, they can also pose challenges for organisms by causing genetic disorders or reducing overall reproductive success.

In the case of the nematode, Caenorhabditis elegans, this arms race has produced a truly bizarre result, and something only an unintelligent, mindless designer, or a malevolent designer, could come up with, known as toxic ascaris, or TAs:

Creationism in Crisis - Like Humans, Bumblebees Learn Through Social Interaction And May Have Cumulative Culture

Buff-tailed Bumblebee, Bombus terrestris

Source: Wikipedia.

Bees master complex tasks through social interaction - Queen Mary University of London

A sacred Tenet of creationism is that we humans are a special creation by the creator of the universe who made everything just for us. They point to the many 'unique' traits and abilities of humans as evidence of this - the ability to teach and learn, to form cultures, even walking upright are frequently cited as examples. It's also a sacred Tenet of creationism that anything which might refute the sacred tenets of creationism must be ignore, hand-waved aside or misrepresented but never, ever acknowledged for what it is - a refutation of creationism.

So, we can expect one or more of those tactics for handling the cognitive dissonance that news that bumble bees can teach and learn and so have at least the basis for forming cumulative cultures. The news itself comes in the form of an open access research paper in Nature by a team Led by Dr Alice Bridges and Lars Chittka, Professor of Sensory and Behavioural Ecology at Queen Mary University of London.

The team showed that a complex, two-step task, which needed to be performed to receive a reward in the form of a sweet liquid could be learned by bees who were allowed to watch a trained 'demonstrator' perform the task. The bees not only learned how to perform the steps involved but that there was a reward to be had for doing so.

The 'demonstrators' had previously been trained by giving intermediate rewards as each stage was completed successfully, which were eventually withdrawn, leaving only the final reward. The experiment and its significance are explained in a Queen Mary University news release:

Unintelligent Design - New Species Of Deep-Ocean Worm - But What Is It For, Exactly?

New Deep-Sea Worm Discovered at Methane Seep off Costa Rica | Scripps Institution of Oceanography

Fig 1. Pectinereis strickrotti gen. nov., sp. nov. in life.

A, B, D. Several epitokous males swimming near methane seeps of Mound 12 (~1,000 m depth) of the Costa Rica margin and videoed via the submersible DSV Alvin. A. A frame grab from a video taken on Alvin dive 4503 on Feb. 4, 2009. B and D. Frame grabs from video taken on Alvin dive 4987 on Nov. 2, 2018. C. A fragment of an atokous infaunal female was collected at the same depth and locality via sediment pushcore on Alvin dive 4984 on Oct. 30, 2018. A white egg ~350 μm in diameter is visible on the exterior. Scalebar 1 mm. E. An epitokous male swimming near methane seeps of Parrita Scar (~1,000 m depth) of the Costa Rica margin. The specimen was initially caught via slurp with the ROV SuBastian (dive S0218, Jan. 11, 2019) but escaped.

Images A, B, D, courtesy of Woods Hole Oceanographic Institute. E, courtesy of Schmidt Ocean Institute.

One of the hallmarks of good intelligent design is that the designed object must be designed for a purpose. No intelligent designer is going to waste time making something that doesn't have any use. Even a decorative use is a function. As the designer William Morris said, "Have nothing in your house that you do not know to be useful, or believe to be beautiful.", but creationism's designer seems to just design things for the sake of it - half a million different beetles, for example. And now we have the example of a deep-ocean worm that appears to have no other purpose than to make more deep-ocean worms.

It's almost exactly like these different organisms are being designed by a mindless, natural process without a plan and no sense of purpose!

According to creationist superstitions in Genesis, every living thing on Earth was created for the benefit of mankind, and, incidentally, named by Adam (as though Adam would have had enough time to name every living species!). So, a challenge to creationists is to tell us what these deep-ocean worms are for in terms of their utility value for humans, and how did Adam dive that deep to name them?

Its discovery if the subject of an open access paper in PLOS ONE and is described in a Scripps Institute for Oceanography news release:

Creationism in Crisis - Evolution of Porcini Fungus

A tale of terroir: Porcinis evolved to the local environment – @theU

This illustration is a little misleading because mycelia are often much larger than any of their mushrooms that appear on the surface of the soil or tree stumps. Fungi can grow up to a half a mile of the thread-like hyphae a day. In fact, the largest known organism on the planet is the Humongous Fungus (Armillaria ostoyae) in The Malheur National Forest, Oregon, measuring 2,385 acres (3.72 square miles) in area. It is estimated to be between 1900 and 8650 years old.

Photo credit: FoodPrint.org

The edible porcine fungus (Boletus edulis) also known as the boletus or penny bun is highly prized culinary delicacy throughout much of Europe. However, there is something strange about it evolution, especially in North America, according to a new report in the journal New Phytologist.

Creationists should note here that the scientists who produced the report see this 'problem' entirely within the Theory of Evolution by Natural Selection (TOE). The strangeness is not a problem for the theory but an example of how a fundamental principle of the theory - environmental selection - operates in North America.

The 'problem' is that while Boletus edulis exists in North America as a number of different varieties and genetically distinct populations, probably caused not so much by geographical isolation as environmental adaptation, albeit with regular ingress from surrounding populations, In Eurasia, a single genetic lineage dominates from Spain to Georgia to Scandinavia, so the interesting question is why does is the species genetically continuous in Eurasia but fragmented in North America; what is the difference between the two landmasses that causes this difference.

The Eurasian and North American populations are believed to have become separated during a period of climatic change and the onset of glaciation, 1.62–2.66 years ago. Attempts to segregate populations of Boletus edulis into distinct species based on phenotype have foundered on the genetic evidence, illustrating how small genetic differences can give large phenotypic differences and how a species in the process of speciating passes through a stage at which the diverging populations have not diverged sufficiently to qualify as new taxons because the practice of taxonomy tries to fit a continuous process into a series of distinct events.

The 'problem' is the subject of a free access paper in the journal New Phytologist by Keaton Tremble and Bryn T. M. Dentinger from Utah University, Utah, USA. together with J. I. Hoffman from Bielefeld University, Germany, and was described in a University of Utah press release:

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