Talibangelical News - Evangelical Christians Now Control SCOTUS

On abortion, few Americans take an absolutist view| Pew Research Center

The much trumpeted impending SCOTUS ruling effectively striking down Roe vs Wade and so making abortion illegal in America unless specifically decriminalised at state level, is widely at odds with American public opinion, but largely in line with the views of white evangelical Christians, showing the degree to which entitled white evangelical Christianity, with Donald Trump's help, has subverted SCOTUS.

While 61% of Americans are in favour of legalised abortions, only 37% oppose it. SCOTUS is representing only a minority of American extremists while ignoring the views of the vast majority. On this issue, if no other, SCOTUS can be seen to represent only a minority of Americans, who nevertheless feel entitled to have their views predominating.

This Pew Research survey show that, of all the religious groups in the USA, only the White Evangelicals back a ban on abortion. 73% of white evangelicals say their almost universal opposition to abortion is shaped by their religion, while only 28% of white, non-evangelical Protestants say their views have a religious basis and 7% of non-affiliated cite religion as shaping their views.

Quantum Evolution - How A Quantum Fluctuation Can Cause Mutation

The Double Helix of DNA

Getty Images

Quantum mechanics could explain why DNA can spontaneously mutate | University of Surrey

Another of creationism’s central dogmas was unintentionally laid to rest by science yesterday, when three scientists from Surrey University's Leverhulme Quantum Biology Doctoral Training Centre, which includes the famous science broadcaster, Professor Jim Al-Khalili, published a paper which showed that DNA can spontaneously mutate due to nothing more than a random quantum fluctuation. Creationist dogma insists, with no evidence to support it and in spite of evidence to the contrary, that no new information can arise in the genome without violating the Second Law of Thermodynamics [sic]. Don't ask! It's based on some half-baked notion that information is like energy and can't be created, or rather, in creation world, can only be created by magic.

But, as the Surrey University team say in their open access Communications Physics paper:

Due to the significance of the quantum tunnelling even at biological temperatures, we find that the canonical and tautomeric forms of G-C inter-convert over timescales far shorter than biological ones and hence thermal equilibrium is rapidly reached. Furthermore, we find a large tautomeric occupation probability of 1.73 × 10−4, suggesting that such proton transfer may well play a far more important role in DNA mutation than has hitherto been suggested.

The Surrey University news release explains what that means:

Evolution News - How the Cephalopods Evolved

The Hawaiian bobtail squid (Euprymna scolopes) is a model system for studying animal-bacterial symbiosis.

Credit: Tom Kleindinst

Squid and Octopus Genome Studies Reveal How Cephalopods’ Unique Traits Evolved | Marine Biological Laboratory

The cephalopods - octopuses, squids and their relatives - are often cited by creationists as something that can't be explained by mainstream evolutionary theory because they, allegedly, have a unique genome. I have even known creationists claim they prove special creation because their favourite creator god created them as a different lifeform. Mind you, I have also known people committed to other wackadoodle notions, claim that they are 'alien' species that arrived on Earth in alien spaceships.

Of course, they are, like all other classes of organisms on Earth, the result of an evolutionary process and there is nothing about their genome that can't be explained in other than standard biogenetic terms. They have exactly the same genetic 'code' as all other life on Earth.

However, that's not to say they don't have some unique characteristics, as these latest papers in Nature Communication show.

As the University of Chicago, Marine Biological Laboratory news release accompanying the two papers explains:

Evolution News - How the Black Rat's Environment was Provided By Humans

Black rats, Rattus rattus

Source: Wikipedia by Kilesson - own work. CC BY-SA 3.0

how the black rat colonised Europe in the Roman and Medieval periods - News and events, University of York

An open access paper published in Nature Communications yesterday, will be understood by anyone with even a basic understanding of evolutionary biology as an example of evolution in progress, but will probably be waved aside by creationists because the subject of it, the black rat, Rattus rattus, didn't change into a cat or a dog or even a new species.

The paper records how the black rat colonised Europe on two separate occasions, separated by a dramatic decline and extinction in some areas. Each rise and fall in population and each wave of expansion was facilitated by patterns of human habitation and trade because the species had evolved to benefit from just those human activities as a commensal species on human civilisation.

We’ve long known that the spread of rats is linked to human events, and we suspected that Roman expansion brought them north into Europe.

But one remarkable result of our study is quite how much of a single event this seems to have been: all of our Roman rat bones from England to Serbia form a single group in genetic terms.

When rats reappear in the Medieval period we see a completely different genetic signature – but again all of our samples from England to Hungary to Finland all group together. We couldn’t have hoped for clearer evidence of repeated colonisation of Europe.

Our results show how human-commensal species like the black rat, animals which flourish around human settlements, can act as ideal proxies for human historical processes.

Dr David Orton, co-author
Department of Archaeology
University of York, York, UK.

The modern dominance of brown rats has obscured the fascinating history of black rats in Europe. Generating genetic signatures of these ancient black rats reveals how closely black rat and human population dynamics mirror each other.

Alexandra Jamieson, co-first author
Palaeogenomics & Bio-Archaeology Research Network
Research Laboratory for Archaeology and History of Art
University of Oxford, Oxford, UK

The study was conducted by a team led by scientists from the University of York along with colleagues from the University of Oxford and the Max Planck Institute, who conducted DNA analysis of archaeological remains. These showed that the rats expanded into Europe in two waves, each with a characteristic DNA signature, showing that they originated from two different populations.

This study is a great showcase of how the genetic background of human commensal species, like the black rat, could reflect historical or economic events. And more attention should be paid to these often neglected small animals.

He Yu, co-first author
Department of Archaeogenetics
Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany And School of Life Sciences
Peking University
Beijing, China

Archaeological black rat mandible.

Image credit: Ewan Chipping, University of York

The first wave occurred during the Roman Empire when the 'Pax Romana' created the stable conditions for population growth and trade with the black rat able to travel along trade routes and exploit human settlements, crops and refuse. With the collapse of the Roman Empire in the Early Middle Ages, the economy collapsed, the population fell, and along with it, the black rat population. This could have been precipitated by the 'Justinian Plague', an early form of the Black Death, caused by the bacterium, Yersinia pestis which killed about 20% of the population of Constantinople and affected the entire Mediterranean basin, Europe and the Near East.

The second wave came on the back of growth in long range trade in the Middle Ages and the growth of cities as centres of commerce. They have now declined again, this time probably because of competition from the closely related brown rat, Rattus norvegicus, which similarly evolved to be a commensal species on human civilisation, along with the house mouse, Mus musculus and is now the dominant rat in temperate Europe.

Copyright: © 2022 The authors. Published by Springer Nature, Ltd.
Open access

The team's paper was published open access yesterday in the journal Nature Communications:

Abstract

The distribution of the black rat (Rattus rattus) has been heavily influenced by its association with humans. The dispersal history of this non-native commensal rodent across Europe, however, remains poorly understood, and different introductions may have occurred during the Roman and medieval periods. Here, in order to reconstruct the population history of European black rats, we first generate a de novo genome assembly of the black rat. We then sequence 67 ancient and three modern black rat mitogenomes, and 36 ancient and three modern nuclear genomes from archaeological sites spanning the 1st-17th centuries CE in Europe and North Africa. Analyses of our newly reported sequences, together with published mitochondrial DNA sequences, confirm that black rats were introduced into the Mediterranean and Europe from Southwest Asia. Genomic analyses of the ancient rats reveal a population turnover in temperate Europe between the 6th and 10th centuries CE, coincident with an archaeologically attested decline in the black rat population. The near disappearance and re-emergence of black rats in Europe may have been the result of the breakdown of the Roman Empire, the First Plague Pandemic, and/or post-Roman climatic cooling.

A Population dynamics of the black rat (R. rattus), Asian house rat (R. tanezumi) and brown rat (R. norvegicus) estimated by PSMC, with 100 bootstrap replicates. B Demographic modelling of the divergence and migration among the black rat, Asian house rat and brown rat estimated by G-PhoCS. The values represent the average estimates of effective population sizes (in thousands), population divergence times (Mya) and the total migration rate through time. The 95% HPD range of all estimates are listed in Supplementary Data.

Yu, H., Jamieson, A., Hulme-Beaman, A. et al.
Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history.
Nat Commun 13, 2399 (2022). https://doi.org/10.1038/s41467-022-30009-z

Copyright: © 2022 The authors. Published by Springer Nature, Ltd.
Open access
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

What is probably lost on creationists with their child-like understanding of evolution where one species changes into another, often by giving birth to it, or by changing physically into it like one of their transformer toys, is that findings such as this example of co-evolution where one species' evolutionary path is dependent on that of another species with which it has formed an alliance, is an illustration of how evolution works. Species do not normally evolve significantly in isolation from the other organisms in their ecosystem but move into and occupy niches as and when these become available, often, as in the case of the black rat, created by another organism.

The first major step in this process was of course, the evolution of the black rat to be able to occupy the niche humans were creating in their buildings, food stores, refuse and trade routes. Then, as these developed in Europe the black rat expanded into this newly available range. When that collapsed, the rats lost their habitat and their population crashed along with the human economy. And so the black rat's evolutionary future became dependent on human civilisation and economic activity, to expand its range again as the economy in Europe recovered to its previous level under the Roman Empire, during the Middle Ages, only to lose out again when the brown rat expanded its range in response to the opportunities human civilisation had provided.

In other words, a very nice illustration of evolution in progress, albeit one which creationists wouldn’t recognise or understand because they have a simplistic understanding of what evolution is.

Evolution News - When Lizards and Snakes Evolved

The fossil of Jurassic lizard Eichstaettisaurus.

Image credit: Jorge Herrera Flores

May: Researchers discover overlooked lizards | News and features | University of Bristol

With so many science papers casually and unintentionally refuting creationism just by revealing the facts, most weeks are bad weeks for creationists and their cults, but this week has been worse than most and it's only half done!

On top of the news of how environmental changes have been shown to influence evolution, just as the Theory of Evolution explains, we now have a paper which sheds more light on the evolution of the squamates (i.e. cold-blooded vertebrates with scales - snakes and lizards) and which shows the scientists involved have no doubts about the TOE being the grand unifying theory in biology that makes best sense of the data.

A collared lizard posing on a rock in Colorado.

Pahcal123 under CC BY-SA 4.0 license

This paper by scientists from the Institut Català de Paleontologia Miquel Crusafont (ICP) and the University of Bristol, in the best traditions of science, challenges the previous consensus over just when this order radiated into its current diversity and pushes that back from the Cretaceous Era between 145.5 and 65.5 million years ago, into the Jurassic, between 201 and 145 million years ago. It had previously been assumed that the main period of evolutionary radiation had been part of the so-called Cretaceous Terrestrial Revolution, when many terrestrial tetrapod groups like mammals, lizards and birds, apparently underwent a great diversification, triggered by the rise of flowering plants.

However, the research team led by Dr Arnau Bolet, palaeontologist at the Institut Català de Paleontologia Miquel Crusafont and the University of Bristol, has shown that, although Jurassic squamate fossils are rare, it is possible to detect the more advanced features found in modern species in them, showing that the major phases of evolutionary diversification had occurred by then.

As the Bristol University press release accompanying the team's open access published paper in the online journal, eLife, explains:

Evolution News - How the Distribution of Alaska's Dinosaurs was Determined by Their Environment.

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Sedimentary deposits of the Prince Creek Formation are exposed in bluffs adjacent to the Colville River, on Alaska’s North Slope, in this July 2007 photograph. The sedimentary rocks represent prehistoric river channels, floodplains, lakes and ponds, and thin peat swamps.

Photo: Professor Paul J. McCarthy

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Sedimentary rocks of the Cantwell Formation, representing a prehistoric floodplain environment, are shown in this June 2017 photograph. Dinosaur tracks are visible at the base of the thick, upper sandstone bed.

Photo: Professor Paul J. Paul McCarthy

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Thick fossil soil in the Chignik Formation at Aniakchak Bay, southwest Alaska, is preserved beneath sandstone of a meandering river channel in this July 2021 photograph. Tree trunks that have turned to coal are visible at the top of the fossil soil in a few places.

Photo: Professor Paul J. Paul McCarthy

Precipitation helped drive distribution of Alaska dinosaurs | Geophysical Institute

It's been another terrible week for Creationists, especially those who have been deluded into the absurd notion that the Theory of Evolution is about to be replaced by their favourite childish superstition.

Following quickly on the heels of a paper by a team from Leipzig, Germany, showing that the evolution of plants was strongly influenced by major environmental changes caused by the extermination of large, herbivorous dinosaurs and the rise of large herbivorous mammals 25 million years later, exactly as the theory of Evolution predicts, we have news of another study, by scientists from the Geophysical Institute of the University of Alaska Fairbanks, USA, Southern Methodist University, Texas, USA, Hokkaido University, Japan and the University of Kansas, USA, showing how the distribution of dinosaurs was affected by the environment in which they lived, just as the TOE predicts.

Evolution News - How the Extinction of Large Dinosaurs affected the Evolution of Plants

Latania loddigesii palm fruits and leaves in Xishuangbanna Tropical Botanical Garden, China

Picture: Renske Onstein/iDiv

Dinosaur extinction changed plant evolution

A prediction of the Theory of Evolution is that a major change in a species' environment will result in evolutionary adaptation to that change. One such major change in the environment of plants was the sudden extinction of the large herbivorous dinosaurs, followed by a period of some 25 million years until the large herbivorous mammals had evolved. According to the TOE, then, we would expect to see these changes recorded in the genetic and fossil record of plants.

This is exactly what a research team led by the German Centre for Integrative Biodiversity Research (iDiv) and Leipzig University found when they examined the genetic and fossil records of palm trees, which they chose as a model system for the study. They were also able to show that the changes following the extinction of large, non-flying dinosaurs were so profound that they were only partially reversed by the evolution of large mammals such as elephants.

From the iDiv press release:

With the extinction of large, non-flying dinosaurs 66 million years ago, large herbivores were missing on Earth for the subsequent 25 million years. Since plants and herbivorous animals influence each other, the question arises whether, and how this very long absence and the later return of the so-called "megaherbivores" affected the evolution of the plant world.

We were thus able to refute the previous scientific assumption that the presence of large palm fruits depended exclusively on megaherbivores. We therefore assume that the lack of influence of large herbivores led to denser vegetations in which plants with larger seeds and fruits had an evolutionary advantage.

Defence traits without predators apparently no longer offered evolutionary advantages, however, they returned in most palm species when new megaherbivores evolved, in contrast to the changes in fruits, which persisted.

Dr Renske Onstein, first author
Evolution and Adaptation
German Centre for Integrative Biodiversity Research (iDiv)
Halle–Jena–Leipzig, Leipzig, Germany

To answer this question, a research team led by iDiv and Leipzig University analysed fossil and living palms today. Genetic analyses enabled the researchers to trace the evolutionary developments of plants during and after the absence of megaherbivores. Thus, they first confirmed the common scientific assumption that many palm species at the time of the dinosaurs bore large fruits and were covered with spines and thorns on their trunks and leaves.

However, the research team found that the "evolutionary speed" with which new palm species with small fruits arose during the megaherbivore gap decreased, whereas the evolutionary speed of those with large fruits remained almost constant. The size of the fruits themselves, however, also increased. So, there were palms with large fruits even after the extinction of the dinosaurs. Apparently, much smaller animals could also eat large fruits and spread the seeds with their excretions.

[…]

However, the defence traits of the plants; spines and thorns on leaves and stems, showed a different picture: the number of palm species with defence traits decreased during the megaherbivore gap.

With their work, the researchers shed new light on evolution and adaptation during one of the most enigmatic and unique periods in the history of plant evolution, during and after megaherbivore extinctions. Understanding how megaherbivore extinctions affected plant evolution in the past can also help predict future ecological developments. For example, the authors have noted the loss of traits during the megaherbivore gap. This loss can affect important ecosystem functions and processes, such as seed dispersal or herbivory. The ongoing extinction of large animals due to human hunting and climate change may thus also affect trait variation in plant communities and ecosystems today and in the foreseeable future.

The technical details of the study are outlined in the abstract to the team's paper, published recently in the Royal Society's journal, Proceeding of the Royal Society B:

Copyright: © 2022 The authors. Published by the Royal Society
Open access

Abstract

The Cretaceous–Palaeogene (K-Pg) extinction of the non-avian dinosaurs (66 Ma) led to a 25 million year gap of megaherbivores (>1000 kg) before the evolution of megaherbivorous mammals in the Late Eocene (40 Ma). The botanical consequences of this ‘Palaeocene megaherbivore gap’ (PMHG) remain poorly explored. We hypothesize that the absence of megaherbivores should result in changes in the diversification and trait evolution of associated plant lineages. We used phylogenetic time- and trait-dependent diversification models with palms (Arecaceae) and show that the PMHG was characterized by speciation slowdowns, decreased evolution of armature and increased evolution of megafaunal (≥4 cm) fruits. This suggests that the absence of browsing by megaherbivores during the PMHG may have led to a loss of defence traits, but the absence of megaherbivorous seed dispersers did not lead to a loss of megafaunal fruits. Instead, increases in PMHG fruit sizes may be explained by simultaneously rising temperatures, rainforest expansion, and the subsequent radiation of seed-dispersing birds and mammals. We show that the profound impact of the PMHG on plant diversification can be detected even with the overwriting of adaptations by the subsequent Late Eocene opening up of megaherbivore-associated ecological opportunities. Our study provides a quantitative, comparative framework to assess diversification and adaptation during one of the most enigmatic periods in angiosperm history.

Onstein, Renske E.; Kissling, W. Daniel; Linder, H. Peter (2022)
The megaherbivore gap after the non-avian dinosaur extinctions modified trait evolution and diversification of tropical palms
Proceedings of the Royal Society B: Biological Sciences, 289(1972); DOI: 10.1098/rspb.2021.2633

Copyright: © 2022 The authors. Published by the Royal Society
Open access
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

Again, we see a prediction of the TOE confirmed by observation and analysis, and again we see how the TOE is the foundation of modern biology and the only theory capable of making these predictions and explaining the observable facts. We also see the stupidity of any designer who would design large herbivores to eat plant seeds, then protects the seeds against being eaten by the large herbivores it designed to eat them. Then, apparently, had to redo those protective designs when it designed a new lot of large herbivores to eat the seeds, having exterminated the first lot 25 million years earlier.

Bible Blunder News - Scientists Find no Evidence for Noah's Flood in Southern England

Study Reveals Stonehenge Landscape Before The World-Famous Monument | University of Southampton

Why the site on Salisbury Plain in Wiltshire in southern England was chosen for the building of the massive stone circle remains a mystery as is the identity of the first builders, although there is now strong evidence that migrants to the area from Southwest Wales, dismantled a bluestone circle and brought it with them, to construct the first phase of the monument.

Now scientists at Southampton University have shown that 4000 years before that, i.e. about 9000 years ago, the area was "covered by open woodland, with meadow-like clearings, inhabited by grazing animals and hunter-gatherers".

The problem this raises for YECs of course, is that this evidence should have been obliterated during the mythical Noahic flood and replaced by a deposit of silt containing jumbled fossils from disconnected landmasses. Not only is that predicted layer of silt not there, but there is no evidence of any inundation in the intervening years, other than that expected periodically in a river flood plain; instead, the archaeological evidence in the geological column shows continuous habitation and a population of earlier mammals, the ancestors of modern domestic animals, such as aurochs, and a continuous series of animal and plant remains progressing from earlier to later forms.

As the University of Southampton news release explains:

Unintelligent Designer News - How Creationism's Designer Could Have Done Much Better

How a soil microbe could rev up artificial photosynthesis | SLAC National Accelerator Laboratory

Readers may recall that I wrote recently about how the process of photosynthesis, on which almost all life on Earth ultimately depends, involves an enzyme known as RuBisCo, and why it would be a major embarrassment to intelligent [sic] design creationists, if only they understood it. I also wrote about it in my popular book, The Unintelligent Designer: Refuting the Intelligent Design Hoax as an example of the sort of prolific waste that refutes the notion of intelligent design.

But it just got a lot worse for creationism because scientists have discovered that a soil bacterium, Kitasatospora setae has an enzyme which does the same job, only very much faster, which begs the question for intelligent [sic] design creationists, why didn't their putative intelligent designer give this enzyme to all photosynthesising organisms, so saving waste and making more efficient use of the available CO₂? Did it deliberately give them all a less efficient process?

The discovery was made by an international team of scientists from the Department of Energy’s SLAC National Accelerator Laboratory, Stanford University, USA, Max Planck Institute for Terrestrial Microbiology in Germany, DOE’s Joint Genome Institute (JGI) and the University of Concepción in Chile. They have published their findings, open access in the journal ACS Central Science, this week.

As the Stamford National Accelerator Laboratory (SLAC) news release explains:

Crisis? What Crisis? Scientists Work Out How Mitochondria Evolved

A white blood cell ingests rod-shaped bacteria (pink) in this micrograph. Legionella bacteria probably evolved to exploit this system about 2 billion years ago.

Ancestors of legionella bacteria infected cells two billion years ago | Press release - Uppsala University, Sweden

One of the mysteries of evolutionary biology was how and when complex (eukaryote) cells acquired mitochondria. Now scientists at Upsala University, Sweden, believe they have solved that problem.

They have discovered that, soon after eukaryotes began to feed on bacteria by phagocytosis (swallowing them whole and digesting them internally) the ancestors of legionella bacteria evolved the ability to exploit this system and live as parasites inside the cells, as early as two billion years ago.

They also believe they have solved one of the chicken-and-egg conundrums in evolutionary biology - which came first, phagocytosis, which requires energy to digest the phagocytosed organisms, or mitochondria, which supply the cell with energy. Some scientists believe that the cell would need mitochondria to supply enough energy for phagocytosis. However, this finding appears to show that phagocytosis was the process by which mitochondria were acquired. This of course, explains why eukaryotes soon evolved a symbiotic relationship from what almost certainly began as a host-parasite relationship. The benefits were so great.

The Upsala team published their findings, open access, in the journal Molecular Biology and Evolution last February.

Malevolent Designer News - How Improved Hygiene Defeated Creationism's Divine Malevolence

Prevalence rates of helminths through time.

Prevalence of Ascaris, Trichuris, Taenia and Diphyllobothrium latum for four different time periods (Roman [n = 94], Anglo-Saxon [n = 79], High/Late Medieval [n = 159], and Industrial era [n = 116]). The confidence intervals are calculated using the Wilson Score interval (95% confidence level). Example photomicrographs of parasite eggs from left to right: Ascaris, Trichuris, Taenia and Diphyllobothrium latum Scale bar: 20 μm.

Ancient skeletons reveal the history of worm parasites in Britain | Department of Zoology

Devotees of creationism's intelligent [sic] malevolence will be thrilled by the news that scientists from Oxford University have discovered how successful it was at creating parasitic worms to make the life of Britons from earlier times just a little more miserable. (We can be sure that this was its intention because an omniscient creator could not create something with unintended consequence.)

What they may find harder to explain though, is why it didn't anticipate the improvements in our understanding of biology and the need for good hygiene, that led to a diminution of the problem later on and, with a few notable exceptions such as in London, an almost complete elimination of the problem.

By examining remains from 464 human burials, from 17 sites, dating from the Bronze Age to the Industrial Revolution, a team led by researchers from the Departments of Biology and Archaeology, Oxford, University, Oxford, UK, showed that the problem of parasitic worms was at it's highest in Britain during the late Roman and Late Medieval periods. With improved hygiene, however, the problem began to diminish, although, since progress in hygiene was patchy in the Victorian era, the pattern of parasite infection varied markedly. In London, for example, it was as bad as that seen in the wordst affected areas today, whilst in other areas, it was almost non-existant.

As the OU Department of Zoology News release explains:

Evolution News - How New Genetic Material is Acquired by Horizontal Gene Transfer.

Transmission pathways of snake BovBs via parasites. The representatives of HTs of snake BovBs via parasites are shown. The thick and thin arrows show the direction of HT and the similarities of BovB sequences between taxa, respectively.

Horizontal gene transfer: Frogs have acquired DNA from snakes with the help of parasites | New Scientist

A repetitive theme in the creationism vs science 'debates' is that no new information can arise in a genome because of some vaguely understood, or rather completely misunderstood and misrepresented notion that there is an equivalence between information and energy, so it would violate the Second Law of Thermodynamics for new information to arise, apparently from nowhere.

Incidentally, I have never yet encountered a creationist who could explain what genetic information is, exactly or how it is subject to the laws of thermodynamics. For that matter, I have never encountered a creationist who could explain the Second Law of Thermodynamics, though I’ve encountered hundreds who cite it as though it supports them.

Of course, their claim ignores the common phenomenon of accidental gene duplication where additional copies of lengths of DNA are accidentally duplicated in the genome during mitosis or meiosis. It also ignores another, less common, method - horizontal gene transfer - where lengths of DNA from one species can be inserted into the genome of another, often unrelated species, giving it new genetic material, or at least a supply of new DNA which can be randomly mutated and eventually evolve into something useful.

Horizontal gene transfer was thought to have played a major part in the evolution of early, single-celled organism and is still common in bacteria which can swap pieces of their genome in the form of plasmids, or small loops of DNA. However, there is also, in multicellular organisms, a less common, though perhaps more common than is generally realised, method of horizontal gene transfer via a parasite such as a virus, possibly carried by an intermediate host parasite such as a tic or parasitic worm.

A retrovirus inserts the DNA template for its RNA into the host cell's genome (and so escapes detection by the immune system). Later, it will become active and produce RNA versions of itself from that embedded DNA and infect other cells and organisms. Sometimes, however, it will also convert chunks of the host's own DNA into its RNA and carry that to a new host, where it again inserts itself, together with the newly acquired DNA into the new host genome. If this is a cell in the organism's germline, then this will be passed on to future generations.

These genes can then become 'jumping genes', or retrotransposons, which replicate themselves and insert themselves in random parts of the genome, often creating multiple copies of themselves as they do so.

For example, more than 18 per cent of the cow genome is composed of a retrotransposon called Bovine-B (BovB) which originally came from a snake by horizontal gene transfer some 40-50 million years ago. About 10 years ago, Atsushi Kurabayashi at the Nagahama Institute of Bio-Science and Technology, Japan discovered that a Madagascan frog had a version of the BovB gene which was a 95% match for that found in cows.

Since then, Kurabayashi and his colleagues have analysed the DNA from 106 snake species, 149 frog species and 42 species of their shared parasites – like leeches and ticks. This has enabled them to chart the history of this retrotransposon as it jumped between species. They estimate that there have been 54 horizontal transfers between snakes and frogs between 85 and 1.3 million years ago. For some reason, Madagascar seems to be a hotspot for this transfer since it happened about 14 times in the last 50 million years and now 91% of the island's frogs carry the snake BovB gene. By contrast, over the same period, this seems to have happen only once in mainland Africa. The difference is probably due to the prevalence of certain parasites in Madagascar. Curiously, BovB doesn't appear to have any function in any animal.

US Protestant Pastors are Thinking of Quitting in Increasing Numbers as Congregations Dwindle and Trust Falls

Pastors Share Top Reasons They’ve Considered Quitting Ministry in the Past Year - Barna Group

Hard on the news from Gallop that their latest survey shows a steep and accelerating decline in membership of churches and other places of worship, comes news that there has been a sharp increase over the past year in the number of Protestant pastors seriously thinking of quitting.

42% of Protestant pastors have given serious consideration to quitting in the last year, compared to just 29% in 2021. Towards the end of 2021, Barna reported that this figure had reached 38%. This represents a 145% increase in absolute terms over the year and those who say they have given it consideration now far outnumber those who say they haven't.

Unintelligent, Malevolent Design News - How a Pathological Fungus has Been 'Designed' to Bypass a Plant's Defences That Were 'Designed' to Protect It.

A newly discovered protein helps the fungus that causes white mould stem rot in sunflowers and more than 600 other plant species bypass the plants' defences.

Newly Discovered Protein in Fungus Bypasses Plant Defenses : USDA ARS

Scientists working for the Agricultural Research Service (ARS) of the US Department of Agriculture (USDA) have discovered how a fungus can invading and kill plants, despite the fact that plants have defences in place supposedly for preventing exactly that sort of attack by parasitic fungi.

And, of course, being an observation of reality, their finding utterly refutes the childish notion of intelligent design creationism.

First consider this:

If you were intelligent and tasked to design living organisms, would you design an organism (say Organism B) that lived parasitically on other organisms that you had designed earlier (say, Organism A)? If you did, would you then treat Organism B as a problem and give Organism A a system for resisting Organism B, making it harder for Organism B to live?

And, if you did something that idiotic, would you then treat your protection for Organism A as another problem and modify Organism B so it could still parasitise Organism A by evading the defences you gave it?

Well, if you are Creationism's supposedly intelligent [sic] designer, that it exactly what you would do.

US Religious Affiliation News - Accelerating Decline in Church Membership to Below 50%.

U.S. Church Membership Falls Below Majority for First Time.

According to the latest Gallop survey, religious affiliation and church membership is declining at an accelerating rate in the USA and the religiously unaffiliated are now in the majority, with affiliates to the various religions falling below 50% for the first time since Gallup began polling in 1937!

In the 60 years between 1940 and 2000, this figure declined only 3% from 73 to 70%, a figure that, given the distribution of values over the period from about 66% to 76% probably represents a steady figure of about 70%, subject to random sampling error.

The significant decline began at the turn of the millennium, falling 9%age points from 70 to 61% in the first 10 years, 6%age points in the next 5 years and a full 8%age points in the last 5 years, an annual rate of decline of 0.9, 1.2 and 1.6 percentage points, respectively. In Gallop's survey, religious affiliation means self-identifying as belonging to a church, synagogue or mosque. In Gallop's words:

Gallup asks Americans a battery of questions on their religious attitudes and practices twice each year. The following analysis of declines in church membership relies on three-year aggregates from 1998-2000 (when church membership averaged 69%), 2008-2010 (62%), and 2018-2020 (49%). The aggregates allow for reliable estimates by subgroup, with each three-year period consisting of data from more than 6,000 U.S. adults.

Although not the same thing, there is a close correlation between not having a religious preference and having no religion. The decline in church membership is probably a function of the decline in religious preference. Since the turn of the millennium, the percentage of Americans who do not self-identify with any religion has grown from 8% to 21%; a 162.5% increase in absolute numbers.

Americans are quickly losing faith in faith!

Not only that, but opinions appear to be firming up with the, perhaps surprising, figure for those who, while having no religious preference are nevertheless members of a church, synagogue or mosque, falling from 10% in 1998-2000 to just 4% in 2018-2020.

Given the nearly perfect alignment between not having a religious preference and not belonging to a church, the 13-percentage-point increase in no religious affiliation since 1998-2000 appears to account for more than half of the 20-point decline in church membership over the same time. Most of the rest of the drop can be attributed to a decline in formal church membership among Americans who do have a religious preference. Between 1998 and 2000, an average of 73% of religious Americans belonged to a church, synagogue or mosque. Over the past three years, the average has fallen to 60%.

As has been noted before, there is a marked difference between generations in the degree of affiliation to and membership of, a religion, with the youngest group being the least religious and the most inclined to reject religion, with 'Millennials' (born between 1981 and 1996) only about half as likely to be members of a church, synagogue or mosque as 'Traditionalists' (born before 1946) at 36% and 66% respectively. 'Baby boomers' (born between 1946 and 1964) and 'Generation X' (born between 1965 and 1980) are 58% and 50% respectively.

The two major trends driving the drop in church membership -- more adults with no religious preference and falling rates of church membership among people who do have a religion -- are apparent in each of the generations over time. Since the turn of the century, there has been a near doubling in the percentage of traditionalists (from 4% to 7%), baby boomers (from 7% to 13%) and Gen Xers (11% to 20%) with no religious affiliation.

Religions are suffering the double-whammy of declining religious beliefs per se, and declining church membership amongst those who do admit to holding religious beliefs.

Currently, 31% of millennials have no religious affiliation, which is up from 22% a decade ago. Similarly, 33% of the portion of Generation Z that has reached adulthood have no religious preference. Also, each generation has seen a decline in church membership among those who do affiliate with a specific religion. These declines have ranged between six and eight points over the past two decades for traditionalists, baby boomers and Generation X who identify with a religious faith. In just the past 10 years, the share of religious millennials who are church members has declined from 63% to 50%.

As the final two charts show, the result is always the same, differing only in magnitude and then not by a great deal. No matter how the data is sliced up, every demographic has shown a marked and accelerating decline in church membership, even amongst the conservatives and republicans amongst whom are to be found the Evangelical Christian fundamentalists, who on the US political stage, have tended to be the loudest and most vociferous, so much so that to us from outside the USA, America sometimes seems to be a nation of loopy religious extremists.

Over this period too, the Catholics have had sexual abuse scandal after sexual abuse scandal with even the most senior US Catholic cleric being sacked and defrocked and diocese after diocese declaring bankruptcy to avoid paying the very large compensation and reparation bills. Scandals of sexual and financial impropriety have even engulfed the Vatican with the former pope standing accused of complicity in child abuse scandals and their coverup, in his former German archdiocese of Munich, and making deliberately misleading and inaccurate statements to the enquiry into the abuses.

Nevertheless, the decline in membership of the Catholic church (-18%), while being double that of the Protestant churches (9%), it is within the normal range of decline for other demographics. The highest rates of decline (25%) are to be found in Democrat-leaning voters and residents in the Eastern United States (presumably East Coast, New England). The protestant churches show the smallest decline at 9%. This possibly reflects the fact that evangelical, Republican-voting, Americans tend also to be white Protestant.

Perhaps surprisingly, given that earlier polls tended to show that religiosity was declining faster in American men than women, this polls show a reversal of that trend, with a steeper decline for women (20%) than for men (18%). American women are making up for their earlier tardiness in abandoning religious institutions.

Just as a bit of fun, if the rate of decline over the last 5 years is maintained and projected into the future, let alone continues to accelerate at the rate its's been accelerating since 2000, membership of religious establishments in the USA should be in single percentage points within the next 15-20 years and should be a mere footnote in history by the middle of the 21st century.

What seems to be happening is what Europe and the rest of the industrial world experience since 1945 - the decline in religiosity proceedes exponentially as first a few, then more and finally very many people abandoned religion as Atheism and non-affiliation first became thinkable, then acceptable, and now the norm as we realised that we did not need the church involved in our daily lives and as the church reacted by becoming even more reactionary and condemning of an increasingly Humanist society, freed from the straight-jacket imposed by dubious religious 'morality' with its support for intolerance, division, hate and bigotry.

Hopefully, in the USA, the support given to the odious and deplorable Donald Trump by the Christian churches has opened the eyes of many Americans to the hypocritical, misogynistic, racist, self-serving and socially divisive nature of fundamentalist Christianity in the USA where, more than perhaps anywhere else in the developed world:

Religion provides excuses for people who need excuses.

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Evolution News - The Evolution of the Dingo

Dingo on the Nullarbor Plain, Australia

By Henry Whitehead - Original photograph, CC BY-SA 3.0

An international team, led by scientists from Australia and including scientists from the USA, Denmark and Germany, has generated high quality genomes of the dingo, the German shepherd and basenji domestic dogs, and compared them to the genomes of the Greenland wolf and other domestic dogs, to discover exactly where in the evolutionary tree of dogs, the dingo split off from other dogs.

Dingoes have existed in Australia, in isolation from other dogs, for tens of thousands of years, and appear to have split off early in the domestication of dogs from their wolf ancestors. They still carry some of the characteristic genes of wolves, which have been modified in domestic dogs. For example, domestic dogs have multiple copies of a gene (amylase 2B) for digesting starch, while wolves and dingoes only have a single copy. A recently evolved trait in domestic dogs is the ability to raise their eyebrows as a non-verbal communication with humans. This ability is absent from wolves and domestic dogs.

But the question of whether dingoes are descended from feral domestic dogs taken to Australia by the first human migrants or are descended from an ancestral species to the domestic dog has still not been settled.

The team have published their findings, open access, in the journal Science Advances, and, unusual for a scientific publication, two of the team, have also written an open access article describing their work, in The Conversation

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Creationism's Demon

The Keeper at the Gate of Creationists' Perception

Creationism's Demon, or Morton's Demon to give it its correct name, was discovered by Glenn Morton, a former YEC, who, when he graduated as a geologist and began to do some serious scientific research, not only realised the data did not support the notion of a young Earth but actually falsified it. If he was going to earn his living as a professional geologist, he needed to abandon creationism and use real science.

Trying to understand how he had been deluding himself, he realised there was an explanation already in the form of a psychological devise, which was analogous to an idea invented by James Clark Maxwell in 1867 (Maxwell's Demon) to explain how the 2nd Law of Thermodynamics could theoretically be violated. This psychological devise he called Morton's Demon.

In Morton's own words (reproduced in full as a copyright condition):

Evolution News - How Our Gut Biota May Be Dictating What We Eat.

Got food cravings? What’s living in your gut may be responsible | University of Pittsburgh

In a fascinating example of the kind of thing that co-evolution can produce, scientist at Pittsburg University believe they have shown how the gut biota of mice could be controlling the mouse's cravings for particular foods.

If this holds true for humans, it could mean that our gut biota could be telling us what they want us to eat, based not on our nutritional needs, but on theirs. We have, of course, been evolving along with our gut organisms since the first multicellular organisms evolved the first alimentary cannal, and possibly even earlier. More recently, it has proved possible to track the dispersion out of Africa and across the globe by subtle differences in the strains of organisms in our gut biota.

In other words, evolution has had plenty of time to evolve suptle relationships between us and our internal biota and, biologically speaking, we have not been evolving as a single species but as a collony, so any species in the colony could be influencing the evolution of the colony as a whole.

That evolutionary relationship was behind the research by the Pittsburgh Scientists, Assistant professor, Kevin Kohl and Doctor Brian Trevelline, as the Pittsburgh University new release explains:

Evolution News - Yet Another of the 'Missing' Transitional Form

Artist’s reconstruction of the feathered pterosaur Tupandactylus, showing the feather types along the bottom of the headcrest: dark monofilaments and lighter-coloured branched feathers.

Copyright © Bob Nicholls

News and Views | University College Cork

It's difficult to keep track of all these 'non-existent' transitional fossils. Like London buses, you can wait for ages, then several will turn up together. One can't help but wonder how creationist find the time to ignore all of them.

Here for instance is one recently discovered fossil showing the transition from dinosaur to bird feathers, complete with evidence of pigmentation, showing that colour was important for display, even in these pterosaurs.

The discovery was made by An international team of palaeontologists led by Dr Aude Cincotta and Prof. Maria McNamara from University College Cork (UCC), Ireland and Dr Pascal Godefroit from the Royal Belgian Institute of Natural Sciences, together with colleagues from Belgium and Brazil.

The discovery was made when the team examined the 115 million year old fossilized headcrest of the pterosaur, Tupandactylus imperator, from north-eastern Brazil.

The news item from University College, Cork, give the detils:

Covidiot Antivaxxer News - Study Shows That Covid-19 Can Cause Dementia

COVID-19 Pneumonia Increases Dementia Risk - MU School of Medicine

There are two ways of looking at the latest findings concerning the long-term effects of severe COVID-19.

• If you are a creationist, you could marvel at the inventive genius of any intelligent designer who could design such a thing as the SARS-CoV-2 virus that causes COVID-19 just to increase the suffering in the world
• If you are a caring and compassionate person, you can appreciate how this findings makes it imperative that as many people as possible are vaccinated and boosted in order to reduce the likelihood of someone else catching the disease and to help make the pandemic a thing of the past.

The finding, by researchers from the University of Missouri School of Medicine and MU Health Care shows that there is a significantly increased risk of developing dementia following a case of COVID-29-induced pneumonia, severe enough to requiring hospitalization.

The risk of new onset dementia was more common in COVID-19 pneumonia patients over the age of 70 in our study.

The type of dementia seen in survivors of COVID-19 infection mainly affects memory, ability to perform everyday tasks and self-regulation. Language and awareness of time and location remained relatively preserved.

The findings suggest a role for screening for cognitive deficits among COVID-19 survivors. If there is evidence of impairment during screening and if the patient continues to report cognitive symptoms, a referral for comprehensive assessment may be necessary.

Professor Adnan I. Qureshi, MD. Professor of clinical neurology
MU School of Medicine.

For the study, the researchers analysed the records of 1.4 billion medical encounters prior to July 31, 2021. They selected patients hospitalized with pneumonia for more than 24 hours. Among 10,403 patients with COVID-19 pneumonia, 312 (3%) developed new onset dementia after recovering, compared to 263 (2.5%) of the 10,403 patients with other types of pneumonia diagnosed with dementia. This represents a 20% increase in the risk of dementia following COVID-19 pneumonia.

The study was only of new onset dementia. The median time interval between infection and dementia diagnosis was 182 days for COVID-19 patients. The study only included new onset dementia associated with hospital admission during a short follow-up period. Dr Qureshi said a more detailed study, conducted over a longer time may help to determine the reasons why COVID-19 is linked to dementia.
The authors give more details in the abstract to their open access paper published in the journal Open Forum Infectious Diseases:

Abstract

Background
Case series without control groups suggest that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection may result in cognitive deficits and dementia in the postinfectious period.

Methods
Adult pneumonia patients with SARS-CoV-2 infection (index hospitalization) and age-, gender-, and race/ethnicity-matched contemporary control pneumonia patients without SARS-CoV-2 infection were identified from 110 healthcare facilities in United States. The risk of new diagnosis of dementia following >30 days after the index hospitalization event without any previous history of dementia was identified using logistic regression analysis to adjust for potential confounders.

Results
Among 10 403 patients with pneumonia associated with SARS-CoV-2 infection, 312 patients (3% [95% confidence interval {CI}, 2.7%–3.4%]) developed new-onset dementia over a median period of 182 days (quartile 1 = 113 days, quartile 3 = 277 days). After adjustment for age, gender, race/ethnicity, hypertension, diabetes mellitus, hyperlipidemia, nicotine dependence/tobacco use, alcohol use/abuse, atrial fibrillation, previous stroke, and congestive heart failure, the risk of new-onset dementia was significantly higher with pneumonia associated with SARS-CoV-2 infection compared with pneumonia unrelated to SARS-CoV-2 infection (odds ratio [OR], 1.3 [95% CI, 1.1–1.5]). The association remained significant after further adjustment for occurrence of stroke, septic shock, and intubation/mechanical ventilation during index hospitalization (OR, 1.3 [95% CI, 1.1–1.5]).

Conclusions
Approximately 3% of patients with pneumonia associated with SARS-CoV-2 infection developed new-onset dementia, which was significantly higher than the rate seen with other pneumonias.

Qureshi, Adnan I; Baskett, William I; Huang, Wei; Naqvi, S Hasan; Shyu, Chi-Ren
New-Onset Dementia Among Survivors of Pneumonia Associated With Severe Acute Respiratory Syndrome Coronavirus 2 Infection
Open Forum Infectious Diseases, Volume 9, Issue 4, April 2022, ofac115, doi: 10.1093/ofid/ofac115

Copyright: © 2022 The authors. Published by Oxford University Press on behalf of Infectious Diseases Society of America.
Open access
Reprinted under a Creative Commons Attribution-NonCommercial-NoDerivs licence (CC BY-NC-ND 4.0)

The findings from this study, with the findings in the study which was the subject of my last blog post which showed the efficacy of the vaccines in children, give a very clear message to anyone with a sense of social responsibility, which I appreciate tends not to include evangelical creationists and members of extremist right-wing antivaxxer cults, is that vaccinations work and should be encouraged, if we are ever to put an end to this pandemic and to reduce the suffering it has wrecked worldwide.

Probably what evangelical creationists hate most about the vaccines is that they represent a considerable triumph of science over what they believe to be the creation of their god, visited on mankind for disagreeing with evangelical creationists.

Don't be a Covidiot!
Get vaccinated or get boosted, Now!

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