Tuesday, 24 January 2023

Creationism in Crisis - How the Bible Narrative Misled 19th Century Palaeontologists

Creationism in Crisis

How the Bible Narrative Misled 19th Century Palaeontologists

Reconstruction of the ceremonial burial
Credit: Natalia Klimczak
© National Museum of Wales

Paviland Cave, Gower, South Wales
Paviland Cave (Goat’s Hole), Gower Peninsula
Red Lady of Paviland: the story of a 33,000 year-old-skeleton – and the calls for it to return to Wales

The significance of the discovery of human remains in a Welsh cave almost exactly 200 years ago to the day, on 18 January, 1823, was entirely missed because the Oxford University Palaeontologist, William Buckland, was also an Anglican priest who believed the Bible to be the inerrant word of a creator god and so literal history.

Today, this is something only believed by scientifically illiterate Creationists and those made too afraid by childhood indoctrination to question it or acknowledge the evidence to the contrary.

After changing his mind several times, Buckland concluded on scant evidence that the skeletal remains were that of a female prostitute who had drowned in the Biblical flood and whose body had got washed into the cave along with the other animal remains found there, because this was the only way he could think of to fit the facts into the Bible narrative.

In fact, the body is that of a man of about 25-28, who died about 33,000 years ago and so is the earliest example of a ceremonial burial in Western Europe. In taking the remains, together with the artifacts found with them, back to Oxford and failing to recognise their cultural significance to Wales, he so deprived Wales of a cultural icon.

The story of how the Bible, or rather the mistaken belief that the Bible is literal history, mislead 19th Century palaeontologists is told by Ffion Reynolds, Honorary Research Fellow, and Jacqui Mulville, Professor in Bioarchaeology and Head of Archaeology and Conservation, both of Cardiff University, in an article in The Conversation. The article is reprinted here under a Creative Commons license, reformatted for stylistic consistency.

Monday, 23 January 2023

Creationism in Crisis - Humans Carry Traces of Ancestral Species

Creationism in Crisis

Humans Carry Traces of Ancestral Species
A reconstruction of the permian synapsid
Dimetrodon grandis

Branchiostoma lanceolatum
Branchiostoma lanceolatum

We can still see these 5 traces of ancestor species in all human bodies today

Your genes haven't always been human. In fact most of them have spent far more time not being human than they have being human.

This is because you inherited them from your parents and their parents before them, going right back to before your ancestors were human; before they were mammals, before they were vertebrates, and even before they were multicellular organisms.

To quote from my book, What Makes You So Special? From the Big Bang To You:
You are the product of billions of passes through the sieve of selection and at every pass your gene-line passed the fitness test. Your genes are good at surviving; and you are unique in the history of the cosmos. The likelihood of you being alive at all is almost vanishingly small and yet here you are. Never before has anyone with your combination of genes, your collection of atoms and your history existed.

And you never will again.

Almost all your genes have spent much longer being something else than they have being human. Your ancestors were there when Europe and Africa split off from the Americas. They were there as small mammal-like reptiles when dinosaurs ruled the earth. They saw pterodactyls flying overhead. They survived the mass-extinction which ended the dinosaurs’ reign and they saw the birds and the bats grow wings and take to the air.

Your ancestors swam in the Cambrian seas and crawled out onto the land as early air-gulping fish destined to become four–legged animals with lungs. Your ancestors lived through the Carboniferous era when dense forests of tree ferns grew in steaming jungles where dragonflies with meter-wide wings flew. They saw the trees fall and form the piles of vegetation destined to be coal as the climate changed and the Carboniferous forests collapsed. They saw the first flowering plants as plants and insects formed their mutual-benefit society.

Your ancestors lived through the first great toxic waste disaster when the cyanobacteria produced oxygen and triggered a mass extinction; and they learned to turn it to their advantage by evolving aerobic respiration.

Your ancestors were bacteria; maybe they were archaea; they may have been the strange Ediacarans which were the earliest known multi-cellular organisms. In almost every one of your cells, in your genes, you carry a record of your evolution, of the entire human evolution story, and of a great deal of the evolution story of every other living thing.

Your journey through space and time has been an adventure of disasters, adaptation, survival and recovery, many, many times you will have been on the brink of extinction - the fate of 99% of all known ancient species - yet your ancestors survived and because they were good at surviving you are here and now.
In the following article, reprinted from The Conversation under a Creative Commons licence, Alice Clement, Research Associate in the College of Science and Engineering, Flinders University, Australia, identifies five key features we have inherited from remote ancestors. These are:
  1. Bipedal walking, including changes to our pelvis - inherited from archaic hominins.
  2. Openings in our skull, inherited from our synapsid ancestors, which includes relatives of the Dimetrodon.
  3. Five fingers and toes, inherited from our fish ancestors that first emerged onto land.
  4. Teeth, inherited from early jawed fish from the Silurian, about 14 million years ago.
  5. The spinal chord and vetebrae, inherited from early chordates which evolved a 'notocord', some 500 million years ago.
The original article has been reformatted for stylistic consistency.

Sunday, 22 January 2023

Malevolent Designer News - How Creationism's Divine Malevolence Capriciously Choses Random Victims

Malevolent Designer News

How Creationism's Divine Malevolence Capriciously choses Random Victims

Study reveals new genetic disorder that causes susceptibility to opportunistic infections | VUMC Reporter | Vanderbilt University

Creationists are obliged by the dogma of their cult to believe that nothing in genetics happens by chance, so everything about an individual’s genetic makeup is the deliberate creation of their putative designer. Indeed, this creator choses the exact sperm that will fertilise the ovum to produce the intended individual complete with the precise genetic makeup of that individual, including any mutations that arise in the creation of the sperm and ovum.

So it must come as something of a shock to creationists to discover that their putative creator appear to randomly create individuals with genes that predispose them to genetic defects and illnesses that mean they will inevitably suffer through no fault of their own, and apparently regardless of how they have lived their lives. In fact, since these are inherited at conception, the predisposition must be at the capricious will of the creator of it.

One such genetic condition was recently discovered by an international team of researchers co-led by immunogeneticist Rubén Martínez-Barricarte from Vanderbilt University Medical Center who have discovered a new genetic disorder that causes immunodeficiency and profound susceptibility to opportunistic infections including a life-threatening fungal pneumonia.
The consortium's finding is reported, open access, in Science Immunology.

According to a news release by Bill Snyder of Vanderbilt University:

Evolution News - Neanderthals In France Unaffected by Climate Change

Evolution News

Neanderthals In France Unaffected by Climate Change
Artist's representation of Neanderthals hunting a mammouth

Spear in hand

Credit: Matteo De Stefano/MUSE, CC BY-SA
In the Neanderthal site of Combe-Grenal, France, hunting strategies were unaffected by changing climate: Hunted animals at Combe-Grenal consistently came from open tundra-like habitats -- ScienceDaily

In a very neat example of how much information can be obtained by forensic examination and deductive logic, a team of paleoarchaeologists have shown that because climate change, profound though it was at times, never changed the food or distribution of the animals they hunted, Neanderthals in France never needed to change their hunting strategies.

This conclusion was arrived at after examining the microwear on the surface of the teeth of the remains of hunted animals found at the Combe-Grenal site in France. This microwear showed that, during the few weeks before they were killed, they ate the same vegetation regardless of the climate on the European tundra as the climate fluctuated widely during the Middle Palaeolithic from around 150,000 to 45,000 years ago when Neanderthals intermittently occupied the site.

The scientists' findings are published open access in PLoS ONE.

According to information supplied by PLOS:

Biodiversity News - In The Chinese Year of the Rabbit, Several Related Species are Endangered

Biodiversity News

In The Chinese Year of the Rabbit, Several Related Species are Endangered
European brown hare, Lepus europaeus

European hare,
In the Year of the Rabbit, spare a thought for all these wonderful endangered bunny species

The once common European brown hare, Lepus europeaeus has declined by 80% in the UK in recent years, and, as the Chinese year of the Rabbit is about to begin, it's not the only threatened species of the order Lagomorpha, to which rabbits, hares and other related species belong.

In the following article, reprinted from The Conversation under a Creative Commons license, Emma Sherratt, Senior Research Fellow in Ecology & Evolutionary Biology, University of Adelaide, Australia, list just a few of the 108 lagomorphs, two-thirds of which were already threatened by climate change. Now the number endangered has risen from 13 to 16.

Her original article has been reformatted for stylistic consistency.

Friday, 20 January 2023

Evolution in Crisis - Wild Animals Are Evolving Faster Than Anybody Thought

Creationism in Crisis

Wild Animals Are Evolving Faster Than Anybody Thought
Eurasian blue tit, Cyanistes caeruleus

Great tit, Parus major
Great tit, Parus major, one of the species studied

Wild animals are evolving faster than anybody thought

In a paper published in Science last May, a team of research biologists led by Timothée Bonnet of the Australian National University presented evidence that should create consternation and anguish amongst Creationist frauds intent on convincing their cult members that the Theory of Evolution is somehow in crisis and being increasingly rejected by research biologists in favour of their childish origin myth. It reports the finding that evolution is proceeding even faster than anyone previously thought.

Of course, the definition they used for evolution is the standard scientific one of change in allele frequency over time, not the absurd Creationist notion that it means one species suddenly changing into another, or even organisms changing into humans via a few 'intermediate species'.

One of the studies, on great tits, was carried out just a stones throw from where I live, in Wytham Wood, near Oxford, one of the most intensively studied areas of woodland in the world, belonging as it does to Oxford University. The research and its significance were reported in an article in The Conversation written by lead author, Timothée Bonnet, researcher in evolutionary biology (DECRA fellow), Australian National University. The article is reprinted here under a Creative Commons licence. It is reformatted for stylistic consistency.

Creationism in Crisis - Watching Evolution Down Under

Creationism in Crisis
Watching Evolution Down Under

Could feral animals in Australia become distinct species? It's possible – and we're seeing some early signs

Australian feral domestic cat
Australian feral domestic cats are getting bigger
Evolution is defined as change in allele frequency in a population over time. It is not a single event but a slow process which often needs a long period of time to be observed. Speciation may be the incidental result of this process of change over time but it is not the purpose of it, nor is it required for evolution to be occurring.

It doesn't seem to matter to a Creationist that observable examples of evolution in progress, in other words, examples of observed change in allele frequency in the population over time, can be found throughout nature, because they will simply dismiss it by redefining evolution as the childish notion of a sudden change of one species into another. So, for example, evolutionary changes in Australian feral domestic cats will be dismissed as, "But they're still cats!"

In fact, feral domestic cats are not the only species that can be observed evolving in Australia where a combination of the founder effect, genetic drift and natural selection in the unique Australian environment are causing introduced species to diverge from their ancestral species. In the following article, Bill Bateman, Associate professor, Curtin University, Perth, Western Australia, describes a number of examples of observable evolutionary change.

Creationists who have been fooled into believing that evolution is a theory in crisis and biologists are abandoning it in favour of their childish superstition including magic and a supernatural entity should note the complete lack of any evidence for that idiotic notion. The article describes evolutionary changes and the causes of them which are entirely consistent with the scientific Theory of Evolution. No-where are magic or supernatural entities invoked to explain the observations.

The article is reprinted from The Conversation under a Creative Commons license, reformatted for stylistic consistency.

Monday, 16 January 2023

Creationism in Crisis - How Humans Evolved to Live in Cold Climates

Creationism in Crisis

How Humans Evolved to Live in Cold Climates
Most humans haven't evolved to cope with the cold, yet we dominate northern climates – here's why

Turku, Finland in Winter
Turku, Finland in Winter

Jarmo Piironem/Eyem/Getty Images
With the exception of only a few, relatively minor, changes to our genome, such as loss of skin pigmentation and changes to hair and eye colour, and the ingression of Neanderthal and Denisovan genes, non-African humans differ little from the first Homo sapiens to venture out of Africa, where they had evolved as a tropical species. Today, humans are the only Great Ape to live outside of the tropics.

And yet we have managed to live in northern climates with shorter days in winter and sub-zero temperatures in which the earliest members of our species would probably not survive a night without special measures.

With our physical and physiological makeup differing so little from our African forebears, what has enabled us to survive in these hostile conditions to which we were so mal adapted? The answer is that an additional layer of evolution is operating alongside genetic evolution - memetic, or cultural, evolution - so-called gene-meme co-evolution.

Memetic evolution has taken us from the bands of hunter-gatherers huddled round a campfire and sheltering in caves and rock overhangs, to a modern urbanised, hi-tec species living in centrally heated buildings or dressing in warm clothing and entirely dependent on science and technology for our survival. Put us naked out in the open on a cold winter night and few of us would survive, let alone thrive, and survival without cloths and shelter would be impossible on the arctic tundra even in summer.

In the following article, reprinted from The Conversation, Laura Buck, Lecturer in Evolutionary Anthropology, and Kyoko Yamaguchi, Senior Lecturer in Human Genetics, both of Liverpool John Moores University, explain how we and our cousin species, the Neanderthals adapted to the very non-African conditions they found themselves in.

The article has been reformatted for stylistic consistency; the original can be read here.

Most humans haven’t evolved to cope with the cold, yet we dominate northern climates – here’s why

Humans have used technology to adapt to the cold.

Laura Buck, Liverpool John Moores University and Kyoko Yamaguchi, Liverpool John Moores University

Humans are a tropical species. We have lived in warm climates for most of our evolutionary history, which might explain why so many of us spend winter huddled under a blanket, clutching a hot water bottle and dreaming of summer.

Indeed all living apes are found in the tropics. The oldest known fossils from the human lineage (hominins) come from central and eastern Africa. The hominins who dispersed northwards into higher latitudes had to deal with, for the first time, freezing temperatures, shorter days that limited foraging time, snow that made hunting more difficult and icy wind chill that exacerbated heat loss from their bodies.

Given our limited adaptation to the cold, why is it that our species has come to dominate not only our warm ancestral lands but every part of the globe? The answer lies in our ability to developed intricate cultural solutions to the challenges of life.
Woman warming her hands with cat next to space heater
Many humans dread the cold of winter.
The earliest signs of hominins living in northern Europe are from Happisburgh in Norfolk, eastern England, where 900,000-year-old footprints and stone tools have been found. At that time, Happisburgh was dominated by coniferous forest with cold winters, similar to southern Scandinavia today. There is little evidence the Happisburgh hominins stayed at the site for long, which suggests they didn’t have time to adapt physically.

It’s still a bit of a mystery how these hominins survived the tough conditions that were so different from their ancestral African homelands. There are no caves in the region, nor evidence of shelters. Artefacts from Happisburgh are simple, suggesting no complex technology.

Evidence for deliberate campfires at this time is contentious. Tools for tailoring fitted, weather-proof clothes don’t appear in western Europe until almost 850,000 years later. Many animals migrate to avoid seasonal cold, but the Happisburgh hominins would have had to travel about 800km south to make a meaningful difference.

It’s hard to imagine hominins surviving those ancient Norfolk winters without fire or warm clothing. Yet the fact the hominins were so far north means they must have found a way to survive the cold, so who knows what archaeologists will find in the future.

The Boxgrove hunters

Sites from more recent settlements, such as Boxgrove in West Sussex, southern England, offer more clues about how ancient hominins survived northern climates. The Boxgrove site dates to nearly 500,000 years ago, when the climate deteriorated towards one of the coldest periods in human history.

There is good evidence these hominins hunted animals, from cut marks on bones, to a horse shoulder blade probably pierced by a wooden spear. These finds fit with studies of people who live as foragers today which show people in colder regions depend on animal prey more than their warm climate counterparts. Meat is rich in the calories and fats needed to weather the cold.

A fossilised hominin shin bone from Boxgrove is robust compared to living humans, suggesting it belonged to a tall, stocky hominin. Larger bodies with relatively short limbs reduce heat loss by minimising surface area.

The best silhouette for avoiding heat loss is a sphere, so animals and humans in cold climates get as close to that shape as possible. There is also clearer evidence for campfires by this period.

Cold climate specialists

The Neanderthals, who lived in Eurasia about 400,000-40,000 years ago, inhabited glacial climates . Compared to their predecessors in Africa, and to us, they had short, strong limbs, and wide, muscular bodies suited to producing and retaining heat.

Yet the Neanderthal protruding face and beaky nose are the opposite of what we might expect to be adaptive in an ice age. Like Japanese macaques living in cold areas and lab rats raised in cold conditions, living humans from cold climates tend to have relatively high, narrow noses and broad, flat cheekbones.

Computer modelling of ancient skeletons suggests Neanderthal noses were more efficient than those of earlier, warm-adapted species at conserving heat and moisture. It seems the internal structure is as important as overall nose size.
Musk ox standing in the snow.
Musk ox are well adapted for cold weather.
Even with their cold-adapted physique, Neanderthals were still hostage to their tropical ancestry. For example, they lacked the thick fur of other mammals in glacial Europe, such as woolly rhinos and musk oxen. Instead, Neanderthals developed complex culture to cope.

There is archaeological evidence they made clothes and shelters from animal skins. Evidence of cooking and use of fire to make birch pitch glue for the manufacture of tools show sophisticated Neanderthal control of fire.

More controversially, some archaeologists say early Neanderthal bones from the 400,000-year-old site of Sima de los Huesos in northern Spain show seasonal damage from slowing down their metabolisms to hibernate. The authors argue these bones show cycles of interrupted growth and healing.

Only a few species of primate hibernate such as some lemurs in Madagascar and the African lesser bushbaby, as well as the pygmy slow loris in norther Vietnam.
A lesser bushbaby seen feeding on tree resin on a safari at night in South Africa
Lesser bushbabies are one of the few primates that hibernate.
This might give you the idea that humans can hibernate too. But most species that hibernate have small bodies, with some exceptions like bears. Humans may be too big to hibernate.

Jack of all trades

The earliest fossils in the Homo sapiens lineage date from 300,000 years ago, from Morocco. But we didn’t spread out of Africa until about 60,000 years ago, colonising all parts of the globe. This makes us relative newcomers in most habitats we now inhabit. Over the intervening thousands of years, people living in freezing cold places have adapted biologically to their environment but on a small scale.

One well-known example of this adaptation is that in areas with low sunlight, Homo sapiens developed light skin tones, which are better at synthesising vitamin D. The genomes of living Inuit people from Greenland demonstrate physiological adaptation to a fat-rich marine diet, beneficial in the cold.

More direct evidence comes from DNA from a single 4,000-year-old permafrost-preserved hair from Greenland. The hair hints at genetic changes that led to stocky body shape that maximised heat production and retention, like the hominin we only have one shin bone from the Boxgrove site.

Our tropical legacy means we would still be unable to live in cold places without developing ways of coping with the temperatures. Take, for example, the traditional Inuit parka, which provides better insulation than the modern Canadian army winter uniform.

This human ability to adapt behaviourally was crucial to our evolutionary success. Even compared to other primates, humans show less physical climatic adaptation. Behavioural adaptation is quicker and more flexible than biological adaptation. Humans are the ultimate adapters, thriving in nearly every possible ecological niche. The Conversation
Laura Buck, Lecturer in Evolutionary Anthropology, Liverpool John Moores University and Kyoko Yamaguchi, Senior Lecturer in Human Genetics, Liverpool John Moores University

Published by The Conversation.
Open access. (CC BY 4.0)
It's hardly worth mentioning really, but there is no sign at all that the scientists think the Theory of Evolution is not fit for purpose anymore and are about to abandon it in favour of one involving magic and unproven supernatural entities. In fact, the TOE is fundamental even to our understanding of how human cultures developed and why, with a large enough brain and the ability to learn and pass on information, humans are no longer dependent on purely genetic evolution to adapt to change and exploit new opportunities.

What differentiates us from our archaic forebears is not so much our genes but our evolved cultures. The astonishing thing is that some people who live in and benefit from our evolved cultures continue to insist there is no such thing as evolution.

Sunday, 15 January 2023

Creationism in Crisis - How Our Immune Systems Have Evolved Over the Last 10,000 Years

Creationism in Crisis

How Our Immune Systems Have Evolved Over the Last 10,000 Years
Using paleogenomics to elucidate 10,000 years of immune system evolution | Institut Pasteur
Explanatory diagram
Explanatory diagram.
© Gaspard Kerner, Institut Pasteur
By analysing the genomes of more than 2,800 individuals who lived in Europe over the last 10,000 years, scientists at the Institut Pasteur, Université Paris Cité, the CNRS and the Collège de France, in collaboration with the Imagine Institute and The Rockefeller University, USA, have traced how the European human immune system has evolved over that period. The increase in frequency of most of the mutations that are advantageous in defending against pathogens were dated to after the Bronze Age, 4,500 years ago.

The scientists also observed that most of the mutations conferring a higher risk of developing inflammatory disorders have become more frequent over the past 10,000 years, suggesting that there is an evolutionary trade-off between greater immunity and greater risk of auto-immune, inflammatory disorders.

This trade-off, is, of course, something that we would not expect to see if the immune system had been improved by an intelligent designer, unless the designer malevolently intended us to suffer from auto-immune conditions.

The evolutionary explanation for this is simply that most of the benefit of a strong immune system manifests in childhood and early adulthood, before the individual has been exposed to environmental pathogens and built up a library of antibodies, and before they have had chance to produce offspring, when selection pressures are thus higher, whereas most of the detriment of auto-immune inflammatory conditions tends to occur in later life, after the individual has reproduced, when the selection pressure is thus much lower.

The research has just been published open access in the journal Cell Genomics.

The research and its significance are explained in a news release from the Institut Pasteur:

Creationism in Crisis - Perto Rican Lizards Evolving

Urban Lizards Share Genomic Markers Not Found in Forest-Dwellers
Puerto Rican crested anole, Anolis cristatellus
Puerto Rican crested anole, Anolis cristatellus
Photo credit: Kristin Winchell
Unlike creationism which, because it depends on magic and unproven, unfalsifiable magic supernatural entities, is incapable of making falsifiable predictions, the Theory of Evolution by Natural Selection (TOE) predicts that, from the same starting point, the same environmental changes will produce the same or very similar phenotypic changes, such as that recently reported for populations of lizards in Puerto Rico.

A paper recently published in Proceedings of the National Academy of Science (PNAS), reports on a case of parallel evolution between populations of the Puerto Rican crested anole, Anolis cristatellus, where unconnected populations in urban areas have evolved very similar adaptations to an urban environment compared to those living in a forest environment. The paper reports the findings of a team of researchers led by assistant professor of biology, Kristin Winchell, of New York University (NYU), NY, USA.

The NYU news release explains the research and its significance:

Saturday, 14 January 2023

Trumpanzee News - What Causes People to Fall For Conspiracy Theories?

Bullying, power and control: why people believe in conspiracy theories and how to respond
QAnon conspiracists in the failed insurrection
A supporter of President Donald Trump, seen wearing a QAnon shirt, is confronted by Capitol Police officers outside the Senate Chamber during the invasion of the U.S. Capitol
Credit: AP Photo/Manuel Balce Ceneta
It's probably hard for rationl people to understand why some people fall for such ludicrous conspiracy theories as the QAnon hoax that Donald Trump was fighting the Satanic cannibalistic paedophile ring led by Hillary Clinton and Barak Obama that is secretly running the 'deep state', or that the 2020 election was stolen (apparently without leaving a trace of evidence that would stand up in court). The same fruit loops have also been convinced that the odious liar, crook, serial adulterer, and incompetent narcissist, Trump was send by God to fight Satan and that God had told various self-appointed 'prophets' that Trump would win by a landslide in 2020, so he must have done really.

As it became more and more apparent just how badly Trump lost, being the only presidential candidate in American political history to lose the popular vote twice and that Joe Biden had won it by a record margin, so the conspiracy theories became more and more lurid.

So why do some credulous fools fall for these unlikely theories, usually involving vast secret conspiracies such as the entire scientific community together with all their technical and administrative staff and everyone involved in publishing scientific books, periodicals and papers, or senior military leaders and heads of government of even hostile states, together with their advisors and civil service?

In the following article, reprinted from The Conversation under a Creative Commons license, Daniel Jolley, Assistant Professor in Social Psychology, University of Nottingham, UK and Anthony, Lantian, Associate Professor in Psychology, Université Paris Nanterre – Université Paris Lumières, France, explain the psychology and the social causes of this gullibility and readiness to believe the patently absurd. The article, the original of which can be read here, is reformatted for stylistic consistence.

Malevolent Designer News - Creationism's Divine Malevolence is Getting Better At Killing People

The 'kraken' COVID variant XBB.1.5 is rising quickly in the US – here's what it could mean for the UK
Credit: peterschreiber.media/Shutterstock

As is entirely predictable from the Theory of Evolution, the SARS-CoV-2 virus that has caused the ongoing COVID-19 pandemic, has mutated to produce an even more infectious version - a subvariant of the Omicron variant, given the variant name XBB.1.5 and nicknames 'kraken', under the suggested new protocol of naming significant variants after Greek mythological creatures instead of letters of the Greek alphabet..

This appears to have originated in the USA where a large number of people have resisted getting vaccinated due to the politically-motivated antivaxx campaign by the far right supporters of failed president, Donald Trump,. Trump declared the pandemic to be a hoax and COVID-19 to be a mild illness, early on in the pandemic, when he was out of his depth and panicking over how to cope with the emergency. Having acted out of spite and motivated by racism and a desire to expunge his achievements, Trump had stupidly dismantled the contingencies for just such a pandemic put in place by his hated African-American predecessor, Barak Obama.

Inhibited from doing so by his narcissistic personality disorder, Trump was then unable to admit he got it wrong and his cronies in the Repugnican Party and the evangelical white Christian sects set about campaigning against any measures to mitigate the effects of the pandemic, including establishing the QAnon cult to promulgate disinformation.

The upshot is a high degree of vaccine scepticism in the USA with a significant majority being vaccinated - a recipe for producing lots of new variants in the unvaccinated population which will then find a niche in the vaccinated population, if they can evade the antibodies.

But is this variant anything to be overly concerned about?

In the following article, reprinted from The Conversation under a Creative Commons licence, Dr. Grace C Roberts, a research fellow in virology at the University of Leeds, assesses the risks from this new variant for the world in general and the UK in particular. The article has been reformatted for stylistic consistency. The original can be read here.

The ‘kraken’ COVID variant XBB.1.5 is rising quickly in the US – here’s what it could mean for the UK

Grace C Roberts, University of Leeds

The heavily mutated omicron variant of SARS-CoV-2, the virus that causes COVID-19, was first detected in late 2021.

Due to the many mutations in the spike protein (a protein on the surface of SARS-CoV-2 that allows the virus to attach to our cells) omicron was able to quickly become the dominant SARS-CoV-2 variant. These mutations allowed it to bind to respiratory cells more tightly than previous variants, rendering it more infectious.

Owing to the dominance of omicron, thanks to these mutations, the past several months have seen the emergence of many subvariants of omicron (scientists have identified more than 650 to date).

The latest variant to worry health professionals and virologists alike is XBB.1.5, nicknamed “kraken” by a group of scientists that has been naming new variants after mythological creatures to make the virus’ evolution more accessible to the public. Here’s what we know about it.

XBB.1.5 is a derivative of the XBB variant of omicron. XBB was never designated as a variant of concern by the World Health Organization because data shows that, while XBB’s mutations enable it to evade our immune systems better than previous omicron subvariants, it doesn’t appear to be causing an increase in infection rates.

In addition to the mutations that XBB.1 has, XBB.1.5 also carries a mutation called S486P in the spike protein region. Preliminary laboratory studies, yet to be peer-reviewed, have shown that, similar to XBB.1, XBB.1.5 is less sensitive to antibodies acquired from vaccination than previous variants XBB and BQ1.1. So it’s very good at evading our immune response.

The same preprint showed that XBB.1.5 was able to bind to ACE2 (the receptor the virus uses to infect our cells) more strongly than these earlier variants. This is the characteristic that made the original omicron variant so infectious and so dominant.
Having first been detected in October 2022 in the US, XBB.1.5 has spread rapidly in the country and is now responsible for around 28% of all new infections. Elsewhere, XBB.1.5 has been detected in at least 23 countries, including the UK. But according to the most recent data, it accounts for only 4% of COVID infections in England.

Given what we’re seeing in the US, it’s likely that XBB.1.5 will become the dominant strain in the UK and Europe in time. But as there are always differences in populations (for example, vaccination rates and social behaviour) it’s hard to predict exactly how things will play out.
A woman at a bus station wearing a mask.
XBB.1.5 is rife in the US, but not in the UK and Europe at this stage.
So should we be worried?

Though some of XBB.1.5’s characteristics are concerning, the real-world infection data is not showing an overall increase in infections or deaths globally or in the US (where XBB.1.5. is rife) at present.

It’s too early to tell whether infections from XBB.1.5 are more severe than previous variants, however experts agree that there is no evidence at this stage that it poses any higher risk than variants that have come before it.

Experts also agree that vaccination will continue to protect against serious disease and death from XBB.1.5.
With a new variant, there’s always the risk it will affect clinically vulnerable people more severely. Older people and those with conditions that affect their immune systems mount weaker responses to COVID vaccines, so are less protected than the “healthy” population. This means variants that spread more easily or can better evade our immune system may be more likely to infect these people if they’re exposed.

So, while COVID continues to circulate, it’s best to take extra precautions when meeting vulnerable people such as wearing a mask, washing your hands thoroughly, ventilating the space that you are in (or even meeting outdoors), and not meeting them at all if you are ill.

The Conversation Grace C Roberts, Research Fellow in Virology, University of Leeds

Published by The Conversation.
Open access. (CC BY 4.0)
It almost goes without saying that for a Creationists to claim intelligent [sic] design at work with these new variants is a tacit admission that their beloved creator god is malevolently designing ways to ensure its virus continues to make people sick and die and to disrupt economies indiscriminately across the world. That Creationists prefer us to have this view of their god rather than accept the science of evolution by mutation and natural selection betrays a hidden political agenda behind Creationism that requites people to distrust science and be misinformed about it.

This is, of course, the stated aim of the Discovery Insitute's failed Wedge Strategy.

Thursday, 12 January 2023

Creationism in Crisis - Improving on the "Intelligent Designer's" Designs

Rice Breeding Breakthrough to Feed Billions | UC Davis
Rice field in Bangall, India
A rice field in Bengal, India. Rice is a staple crop for billions of people, but it has proved difficult to bring high-yield hybrid rice strainers to farmers. UC Davis scientists have developed a method to propagate hybrid rice as cloned seeds, reducing costs for growers and allowing them to save improved seed from season to season.

Getty Images

A paper published a couple of weeks ago should have been a major embarrassment to Creationists who believe the Bible tale that a perfect, supremely intelligent designer designed all the plants and animals of the world for mankind.

If that were the case, why have a team of scientists at UC Davis managed to improve the rice plant - a basic staple in the diet of many people.

In fact, of course, the rice plant, like all human crops and just about every domestic animal, has been improved immeasurably in the few tens of thousands of years since humans transitioned from hunter-gatherers to cattle-herders and farmers.

(341-270 BCE)
Is God willing to prevent evil, but not able? Then he is not omnipotent. Is he able, but not willing? Then he is malevolent. Is he both able and willing? Then whence cometh evil? Is he neither able nor willing? Then why call him God?
If they had been intelligently designed, especially by an omniscient, omnipotent god, they would be perfectly fit for purpose already with no room for improvement. The fact that they aren't, should suggest to Creationists that there is a problem with their notion, since there was self-evidently no omniscient, omnipotent intelligence involved.

Human domestic animals and cultivated crops have been produced by selective breeding, and now genetic engineering, from the wild types that evolved without a plan and fitted only for maximising the number in the next generation. Nothing, and no-one bred wild rice, wild cattle, wild corn or wild sheep for human consumption or ease of harvest and storage. We did that from whatever starting point the natural processes of evolution had provided.

To anyone who understand it, it presents what amounts to the Epicurus Paradox all over again. The research and its significance is explained in an article by Andy Fell in UC Davis News:

Monday, 9 January 2023

Creationism in Crisis - Common Origins of Modern and Neanderthal Humans

Human and Neanderthal brains have a surprising 'youthful' quality in common, new research finds.
Neanderthal man
A picture taken on September 6, 2021, shows the reconstruction of the face of the oldest Neanderthal found in the Netherlands, nicknamed Krijn, on display at the National Museum of Antiquities in Leiden.
Bart Maat/ANP/AFP Via Getty Images
The idea of common origins of related species is a fundamental part of the Theory of Evolution, supported by both countless examples of nested hierarchies and the science of cladistics.

Creationists need to resort to unproven claims of common design, to explain the same or closely similar structures and processes being found in related species. In contrast to the scientific explanation of observable evidence of natural processes with no plan, no intent and no magical mysteries, Creationists need to invoke an unproven, unexplained and unfalsifiable magic supernatural entity, claiming this to be the better of the two for no other reason than that their mummy and daddy believed it and it makes them feel special.

Just such an example of the evidence of common origins has recently been published in Nature Ecology & Evolution which shows that both modern Homo sapiens and Neanderthals had the same rapid evolution of the organisation of the brain that is believed to be responsible for high levels of cognitive ability.

The fact that this is present in two closely related species is highly suggestive that it was present at least in their last common ancestor. It also suggests that Neanderthals had a level of cognitive ability on a par with modern humans.

The research and its significance is the subject of an article in The Conversation by three of the researchers, Professor Stephen Wroe, University of New England, Armidale, NSW, Australia; Dr. Gabriele Sansalone, Institute of Marine Sciences, National Research Council, Messina, Italy, and Professor Pasquale Raia, Department of Earth Sciences, Environment and Resources, Università degli Studi di Napoli Federico II, Monte Sant’Angelo, Naples, Italy. That article is reprinted here under a Creative Commons license, reformatted for stylistic consistency. The original article can be read here.

Human and Neanderthal brains have a surprising ‘youthful’ quality in common, new research finds

Neanderthal skull.
Credit: Petr Student/Shutterstock

Stephen Wroe, University of New England; Gabriele Sansalone, Institute of Marine Sciences, and Pasquale Raia, University of Naples Federico II

Many believe our particularly large brain is what makes us human – but is there more to it? The brain’s shape, as well as the shapes of its component parts (lobes) may also be important.

Results of a study we published today in Nature Ecology & Evolution show that the way the different parts of the human brain evolved separates us from our primate relatives. In a sense, our brains never grow up. We share this “Peter Pan syndrome” with only one other primate – the Neanderthals.

Our findings provide insight into what makes us human, but also further narrow any distinction between ourselves and our extinct, heavy-browed cousins.

Tracking the evolution of the brain

Mammalian brains have four distinct regions or lobes, each with particular functions. The frontal lobe is associated with reasoning and abstract thought, the temporal lobe with preserving memory, the occipital lobe with vision, and the parietal lobe helps to integrate sensory inputs.
A colourful diagram of the human brain, showing frontal lobes at the front and occipital lobe at the back
The four main parts of the brain form the cerebral cortex.
Credit: The Conversation, CC BY-ND
We investigated whether the brain’s lobes evolved independently of each other, or whether evolutionary change in any one lobe appears to be necessarily tied to changes in others – that is, evidence the evolution of the lobes is “integrated”.

In particular, we wanted to know how human brains might differ from other primates in this respect.

One way to address this question is to look at how the different lobes have changed over time among different species, measuring how much shape change in each lobe correlates with shape change in others.

Alternatively, we can measure the degree to which the brain’s lobes are integrated with each other as an animal grows through different stages of its life cycle.

Does a shape change in one part of the growing brain correlate with change in other parts? This can be informative because evolutionary steps can often be retraced through an animal’s development. A common example is the brief appearance of gill slits in early human embryos, reflecting the fact we can trace our evolution back to fish.

We used both methods. Our first analysis included 3D brain models of hundreds of living and fossil primates (monkeys and apes, as well as humans and our close fossil relatives). This allowed us to map brain evolution over time.

Our other digital brain data set consisted of living ape species and humans at different growth stages, allowing us to chart integration of the brain’s parts in different species as they mature. Our brain models were based on CT scans of skulls. By digitally filling the brain cavities, you can get a good approximation of the brain’s shape.

A surprising result

The results of our analyses surprised us. Tracking change over deep time across dozens of primate species, we found humans had particularly high levels of brain integration, especially between the parietal and frontal lobes.

But we also found we’re not unique. Integration between these lobes was similarly high in Neanderthals too.

Looking at changes in shape through growth revealed that in apes, such as the chimpanzee, integration between the brain’s lobes is comparable to that of humans until they reach adolescence.

At this point, integration rapidly falls away in the apes, but continues well into adulthood in humans.
A chart mapping brain integration in evolution
Left: a chart shows the degree of integration between the brain’s lobes, with cooler colours indicating higher integration. Right: translucent skulls of a human, Neanderthal, chimp and gorilla, showing the digitally reconstructed brains within.

Credit: Gabriele Sansalone and Marina Melchionna, Author provided
Neanderthals were sophisticated people

So what does this all mean? Our result suggest what distinguishes us from other primates is not just that our brains are bigger. The evolution of the different parts of our brain is more deeply integrated, and, unlike any other living primate, we retain this right through into adult life.

A greater capacity for learning is typically associated with juvenile life stages. We suggest this Peter Pan syndrome played a powerful role in the evolution of human intelligence.
There’s another important implication. It’s increasingly clear that Neanderthals, long characterised as brutish dullards, were adaptable, capable and sophisticated people.

Archaeological findings continue to mount support for their development of sophisticated technologies, from the earliest known evidence of string, to the manufacture of tar. Neanderthal cave art shows they indulged in complex symbolic thought.

Us and them

Our results further blur any dividing line between us and them. This said, many remain convinced some innately superior intellectual quality gave us humans a competitive advantage, allowing us to drive our “inferior” cousins to extinction.

There are many reasons why one group of people may dominate, or even eradicate others. Early Western scientists sought to identify cranial features linked to their own “greater intelligence” to explain world domination by Europeans. Of course, we now know skull shape had nothing to do with it.

We humans may ourselves have come perilously close to extinction 70,000 years ago.

If so, it’s not because we weren’t smart. If we had gone extinct, perhaps the descendants of Neanderthals would today be scratching their heads, trying to figure out just how their “superior” brains gave them the edge.
The Conversation
Stephen Wroe, Professor, University of New England; Gabriele Sansalone, PostDoc fellow, Institute of Marine Sciences, and Pasquale Raia, Professor of Paleontology and Paleoecology, University of Naples Federico II

Published by The Conversation.
Open access. (CC BY 4.0)
In the abstract to their paper in Nature Ecology & Evolution the researchers say:

There is controversy around the mechanisms that guided the change in brain shape during the evolution of modern humans. It has long been held that different cortical areas evolved independently from each other to develop their unique functional specializations. However, some recent studies suggest that high integration between different cortical areas could facilitate the emergence of equally extreme, highly specialized brain functions. Here, we analyse the evolution of brain shape in primates using three-dimensional geometric morphometrics of endocasts. We aim to determine, firstly, whether modern humans present unique developmental patterns of covariation between brain cortical areas; and secondly, whether hominins experienced unusually high rates of evolution in brain covariation as compared to other primates. On the basis of analyses including modern humans and other extant great apes at different developmental stages, we first demonstrate that, unlike our closest living relatives, Homo sapiens retain high levels of covariation between cortical areas into adulthood. Among the other great apes, high levels of covariation are only found in immature individuals. Secondly, at the macro-evolutionary level, our analysis of 400 endocasts, representing 148 extant primate species and 6 fossil hominins, shows that strong covariation between different areas of the brain in H. sapiens and Homo neanderthalensis evolved under distinctly higher evolutionary rates than in any other primate, suggesting that natural selection favoured a greatly integrated brain in both species. These results hold when extinct species are excluded and allometric effects are accounted for. Our findings demonstrate that high covariation in the brain may have played a critical role in the evolution of unique cognitive capacities and complex behaviours in both modern humans and Neanderthals.

Creationists, of course, are used to the facts not supporting their beliefs and have developed all manner of coping mechanisms, so little bit of evidence such as this are unlikely to win many over to the intellectual rigours of science as a route to the truth of the world we live in. Theirs is a puny little god who can be seriously damaged by a whiff of doubt and so appreciates the self-sacrifice of intellectual dishonesty, just so long as its followers never consider changing their minds or contemplating the possibility of being wrong, for that would put the income stream of the cult leaders at risk.

Saturday, 7 January 2023

Creationism in Crisis - A Double Whammy From Salmonella

New role of small RNAs in Salmonella infections uncovered | Carl R. Woese Institute for Genomic Biology
Pathogenic Salmonella bacteria.
Image Credit: nobeastsofierce / Shutterstock
A paper published last month in the American Society for Microbiology's Journal of Bacteriology would be a double embarrassment for Creationists if they were capable of understanding its implications.

The authors, a research team led by Cari Vanderpool and Sabrina Abdulla of the Carl R. Woese Institute for Genomic Biology (IGB) and the Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA, have shown how the virulence of the pathogenic bacteria, Salmonella, is controlled.

The bad news for Creationists is that:
  • It shows that if this system was designed by an intelligent entity, that entity intended to make people sick, because that's what it does.
  • It involved control of a system known as the type III secretory system, which is related to and very similar to the Type II secretory system that biologists believe was the evolutionary ancestor of the bacterial flagella that Creationist dogma insists was intelligently designed because it couldn't have evolved.
According to News-Medical.net:

Friday, 6 January 2023

Malevolent Designer News - Getting Better At Killing Salamanders With 'Jumping Genes'

A fire salamander.
Credit: Jaime Bosch.
Research news - ‘Jumping genes’ help fungus kill salamanders - University of Exeter

Creationist mode:

Embarrassingly for Creationists, when their divine malevolence wanted to improve the ability of one of its pathogens to kill salamanders, it used a method that Creationists deny exists. It increased the amount of genetic information, not by magic like creationists believe genetic information gets created, but by using one of the methods evolutionary biologists know creates new genetic information naturally, without magic or supernatural entities - so-called 'jumping genes'.

'Jumping genes' or transposons, are pieces of DNA that have the ability to copy and paste themselves into new parts of the DNA, often carrying genes with them. In so doing they add new information into the genome and replicate any genes they carry with them. These copies of genes can them mutate without loss of function because the originals still exist, or as in the case of this fungal pathogen, they can augment the activity (and the virulence) of the original gene.

The fungal pathogen is Batrachochytrium salamandrivorans (Bsal) which infects the skin of salamanders, killing them. This is of course an example of beneficial mutations (from Bsal’s point of view), since Bsal produces more copies of itself the more salamanders it can infect.

Creationist mode:

The discovery of these jumping genes and their role in increasing the virulence of Bsal was made by a team of scientists led by the MRC Centre for Medical Mycology at Exeter University, Devon, UK. Their findings as published, open access, in Proceeding of the National Academy of Science (PNAS).

The Exeter University news release gives the details:
A fungus that infects salamanders contains multiple copies of the same “jumping genes”, scientists have discovered.

Jumping genes, called transposons, can “copy and paste” themselves and impact the organism.

Most organisms have some repeated parts of their DNA, some of which are jumping genes, but this can be harmful – and mechanisms exist to prevent or limit this.

However, the new study – led by the MRC Centre for Medical Mycology at the University of Exeter – finds a possible evolutionary advantage of these jumping genes in a fungus called Batrachochytrium salamandrivorans (Bsal).

Not only did they find different versions of these jumping genes repeated multiple times in Bsal’s genome – but the gene in question appears to have duplicated another group of genes that play a role in how severely it affects infected fire salamanders.

Bsal and related fungal species infect amphibians worldwide, and have been responsible for more than 90 extinctions. Bsal infects the skin of salamanders and newts and causes severe wounds.

It emerged in Asia, where many newts and salamanders have some tolerance, but it has spread to Europe and is causing European salamander populations to decline.

Using new sequencing technologies, we found that Bsal has undergone a genome expansion compared to related species – that is to say, it now has a bigger genome with more genes and also more of these ‘jumping gene’ transposons.

If you think of an organism’s genome as a blueprint, transposons are like having many identical pages, and sometimes, during the process of copying and pasting, other parts of the book are also copied.

It appears that this copying and pasting caused by repetitive jumping gene transposons has also amplified some skin-destroying genes. Having more of these skin-destruction genes allow the fungus to destroy the skin of salamanders more quickly, making it more deadly.

Theresa Wacker, first author.
Medical Research Council Centre for Medical Mycology
University of Exeter, Exeter, UK.

Most organisms have a few jumping gene transposons. In humans, they typically make up less than 1% of the genome, and we have controlling mechanisms to prevent this from rising.

In Bsal, repeated jumping genes make up about 19% of the genome. Transposon jumping genes can interfere with regular gene function and cause problems for the organism – but for Bsal this seems to be outweighed by the advantages.

This kind of gene repetition is probably more widespread in nature than we currently realise.

If, as appears to be the case, it confers an evolutionary advantage for the pathogen by making it more virulent, it’s not clear why this isn’t much more common.

Dr. Rhys A Farrer, lead author.
Medical Research Council Centre for Medical Mycology
University of Exeter, Exeter, UK
The new study found the ability of jumping gene transposons to copy and paste themselves contributed significantly to this expansion. The team are now doing further research.

Senior author Dr Rhys Farrer said repetitive DNA, including jumping genes, is sometimes referred to as “junk” DNA.

The study’s finding shed new light on the evolution of a major amphibian disease, and Dr Farrer called it a “paradigm shift” in terms of identifying repetitive genome content as a driving force behind its pathobiology.
Copyright: © 2023 The authors.
Published by PNAS. Open access. (CC BY 4.0)
The team's findings can be read in the journal PNAS:

Batrachochytrium salamandrivorans (Bsal) and its closest relative B. dendrobatidis (Bd) are fungal pathogens that threaten amphibians globally. Pathogenicity in vertebrates by species of Batrachochytrium is thought to have emerged from nonpathogenic and saprobic relatives over millions of years through gene expansions of secreted proteolytic enzymes families. Using deep nanopore sequencing and comparative genomics, we discover that Batrachochytrium genomes have undergone a repeat-driven expansion characterized by flanking repetitive elements enriched around pathogenicity genes, genes with signatures of positive selection, and genes upregulated during infection. These genomic features are the hallmarks of two-speed genomes that have to date only been described in plant pathogens. These discoveries shed new light on the evolution of fungal pathogens of vertebrates driving global declines and extinctions.


The origins and evolution of virulence in amphibian-infecting chytrids Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal) are largely unknown. Here, we use deep nanopore sequencing of Bsal and comparative genomics against 21 high-quality genome assemblies that span the fungal Chytridiomycota. We discover that Bsal has the most repeat-rich genome of the Chytridiomycota, comprising 40.9% repetitive elements; this genome has expanded to more than 3× the length of its conspecific Bd, with autonomous and fully functional LTR/Gypsy elements contributing significantly to the expansion. The M36 metalloprotease virulence factors are highly expanded (n = 177) in Bsal, most of which (53%) are flanked by transposable elements, suggesting they have a repeat-associated expansion. We find enrichment upstream of M36 metalloprotease genes of three novel repeat families belonging to the repeat superfamily of LINEs that are implicated with gene copy number variations. Additionally, Bsal has a highly compartmentalized genome architecture, with virulence factors enriched in gene-sparse/repeat-rich compartments, while core conserved genes are enriched in gene-rich/repeat-poor compartments. Genes upregulated during infection are primarily found in the gene-sparse/repeat-rich compartment in both Bd and Bsal. Furthermore, genes with signatures of positive selection in Bd are enriched in repeat-rich regions, suggesting these regions are a cradle for the evolution of chytrid pathogenicity. These are the hallmarks of two-speed genome evolution, and this study provides evidence of two-speed genomes in an animal pathogen, shedding light on the evolution of fungal pathogens of vertebrates driving global declines and extinctions.

Of special note for Creationists:
  • If this is intelligent design, the designer can't be regarded as benevolent, since the purpose of the fungus, and then of the modifications the team found, appears to be to make salamanders suffer and die.
  • The mechanism of the mutations is one which biologists already recognise as one of the methods by which information can increase in a genome.
  • This is an example of a beneficial (to the fungus) mutation since, by increasing its virulence, it is increasing the number of copies of the duplicated genes in the genome of the next generation compared to the normal compliment of genes.
  • The scientists are entirely dependent on the Theory of Evolution to explain why this mutation has increased and spread in the species genome. There is no suggestion in their findings that magic creation is a better explanation.
All in all then, a paper that Creationists will wish had never been published and which they are almost certain never mention inside their cult's echo chambers if they want to remain members.
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