Malevolent Designer News - How Creationism Divine Malevolence is Ahead of Medical Science

2022 News - Other SARS-CoV-2 Proteins are Important for Disease Severity, Aside from the Spike | University of Maryland School of Medicine

These must be such thrilling times for Creationists as almost every day scientists discover yet more evidence of the ingenuity of their putative divine malevolence in is design (and continuous redesign) of its SARS-CoV-2 virus that is still killing tens of thousands of people daily with COVID-19. Only recently it was announced that the equivalent of a jumbo jet full of people are being killed every day by it in the USA alone.

Daily Confirmed New Cases
(7-Day Moving Average)

Source: Johns Hopkins

To date (14 Oct. 2022) an estimated 624,161,610 people have been infected, of which 6,565,979 have died, 1,064,910 of those in the USA alone. Several countries are experiencing yet another wave of infections and there is reported to be an even more dangerous variant (BA.2.75.2) waiting in the wings.

And today’s piece of thrilling news for devotees of this putative pestilential sadist and habitual serial killer, is that it's not just the spike proteins that give the virus it's virulence, but another protein that the vaccines don't reach, but which can inhibit our immune response. The malevolent designer obviously anticipated medical science's response to the pandemic and built in a way round the defences medical science was going to give us, if you’ve fallen for the intelligent [sic] design hoax, that is..

What is interesting is that both BA.4 and BA.5 variants have the same genetic sequence for the spike protein. This means it’s the other genes, the non-spike protein genes, that seem to affect the way the virus copies itself and causes disease. So, mutations in these other accessory genes are what has allowed variants like BA.5 to outcompete the earlier versions of the virus.

Professor Matthew Frieman, PhD, co-lead author.
Alicia and Yaya Foundation Professor of Viral Pathogen Research
The Department of Microbiology & Immunology
University of Maryland School of Medicine, Baltimore, MD, USA.

The current predominant variant is the BA.5 subvariant of the Omicron variant. This has recently replaced the BA.4 subvariant by out-competing it for human resources. Both these variants are able to evade most of the antibodies our immune system raises after vaccination or following infection because the antibodies are produced against the spike proteins. This means vaccination and/or previous infection are less effective. However, both BA.4 and BA.5 have identical genes for the spike proteins so BA.5's advantage must come from somewhere other than those spike protein genes.

Creationism in Crisis - Another Bad Day for the Cult as Scientists Use the TOE to Understand Viral Diversity

Phylogenetic reconstruction of the global RNA virosphere

Source: Neri, Uri; Wolf, Yuri I. et al.(2022)
(CC BY-NC-ND 4.0)

NLM Researchers Build Understanding of the Virus Universe Using Metatranscriptome Mining

A large team of researchers from the National Library of Medicine (NLM) and collaborators from multiple institutions and the RNA Virus Discovery Consortium, have discovered new bacteriophage viruses including a variety of new clades that shed light on the evolution of viruses.

The most notable discovery is the dramatic increase in the number and diversity of viruses infecting bacteria that are shown to account for a much greater fraction of RNA viruses than we previously thought.

Dr. Eugene. V. Koonin, PhD, a co-author
National Center for Biotechnology Information
National Library of Medicine
National Institutes of Health, Bethesda, MD, USA

Despite the repeated claims of Creationist frauds, there is no sign of the Theory of Evolution being abandoned in favour of a bronze Age superstition involving magic, an unproven entity with no known modus operandum, and 'unknowable mysteries', the scientists interpret their findings using the TOE as the established scientific theory which best explains biodiversity, without the need for anything other than the operation of natural processes.

The study was conducted by data mining the results of 5,150 diverse metatranscriptomes which together contained the sequenced RNA of 2.5 million RNA viruses. The discoveries include viruses from several new taxons including two groups which constitute entirely new phyla.

The scientists have published their findings in the online journal Cell:

Declining Religion in USA - Latinos Are Leaving the Catholic Church

New poll finds 4 in 10 non-Catholic Latinos were once Catholic and left

Tucked away on page 15 of the NBC News/Telemundo National Survey report conducted over Sept. 17-26, 2022 by Hart Research Associates/Public Opinion Strategies, is a table that should spread despondency in the US Catholic Church, which had been pinning its hopes of avoiding the haemorrhage of members experience by other Christian churches in the USA, by the immigration of Hispanic people, assumed to be overwhelmingly Catholic.

Pale Blue Dot - Stunning Photos of Earth from Space

Beni River, Bolivia

These stunning satellite images look like abstract art – and they reveal much about our planet

As a change from exposing the dishonesty and gullibility of creationists and the cynically fraudulent false claims and blatant anti-science, politically-motivated propaganda of their cult leaders, I thought it would be good to see some amazing photographs of our beautiful home in the cosmos, the planet Earth, as seen from space.

This article by Emily Finch of Monash University, Australia, is reprinted from The Conversation's Photos from the Field series, under a Creative Commons license, reformatted for stylistic consistency. The original article can be read here:

Unintelligent Designer News - Another Design Without a Purpose

Two life stages of 'amphibious fungi'　Outside gut: on host excrement (left), Inside gut: yeast-like growth (right)

It Takes Guts: Fungus Living inside Cave Crickets Reveals Fungal Evolution Steps - University of Tsukuba

Design is what links creativity and innovation. It shapes ideas to become practical and attractive propositions for users or customers. Design may be described as creativity deployed to a specific end.

Sir George Cox - What is Design and Why It Matters

Complexity versus simplicity is a common design tradeoff. Complexity always has a cost. As such, complexity is ideally minimized for equivalent functionality and quality… Adding complexity without adding functionality or quality is known as needless complexity. Complexity can be exciting and it is possible to get involved in making technologies, communications or ideas complex for the sake of complexity. Generally, this is a mistake as complexity costs more to develop, support and use

John Spacy, Design Expert - Design: Complexity vs Simplicity.

It's clear from these definitions of good design that good, intelligent, design is practical and has to suit the specific needs of the user or client. In other words, the thing being designed must have a clear purpose. It should also be minimally complex and maximally simple.

But what of purpose in the design of living organisms?

A Creationist Nightmare Plant - Malevolent Design AND Evolution by Loss of Genes and Complexity

Geosiris australiensis

Source: Grey & Lee (2017)

Geosiris is an early contender for Sexiest Plant of 2019

Readers may remember how I recently described one of the most important symbiotic relationships on Earth - that between trees and fungi - as a classic example of how cooperation can evolve by the interaction of 'selfish' genes with other genes in their environment.

Creationists looking at that same relationship will insist that it is evidence of intelligent [sic] design, without ever providing evidence that such a designer entity has ever existed, any plausible mechanism by which it could have arisen without a designer, or a single, authenticated example of it ever having made chemistry and/or physics do something they couldn’t do without it.

Nevertheless, despite these shortcomings of their superstition, which means it isn't even a theory in the scientific sense, it satisfies their desire for easy answers, conforms with what their mummy and daddy believed, and avoids all that tiresome learning. Their conclusion is, therefore, that it must be true because it passes their "What do I want to be true?" test.

This article then will spoil that smugly self-satisfying conclusion on at least three counts:

1. It shows any designer of this example to be a malevolent cheat who favours free-loading parasites.
2. It involves evolution by loss of genes - something Creationist dogma claims is impossible in the erroneous belief that loss of information and loss of complexity are always deleterious, even though they are commonplace in successful parasites.
3. It involves plate tectonics and an old Earth to explain how this example from Australia is related to species from Madagascar and the Comoro Islands.

The one crumb of comfort for Creationists is that it involves free-loading in a cooperative relationship - something they claim means cooperative behaviour can't evolved by 'selfish' genes because any such relationship will always degenerate due to selfish freeloaders always having an advantage. An argument that is manifestly untrue because so many cooperative relationships exist in nature and any examples such as this, of freeloading, are numerically small compared to the very many which work. The evolutionary explanation is relatively simple - freeloading will provoke resistance which will reduce the benefits of freeloading, whereas cooperation will always improve since both parties benefit.

Those Creationists who are afraid of even considering whether they could be wrong in case they upset an invisible, mind-reading, magic sky man, should probably stop reading now.

The following article by Elizabeth Joyce of James Cook University, Australia, reprinted from The Conversation under a Creative Commons license, reformatted for stylistic consistency, concerns a recently-discovered Australian parasitic plant that freeloads on the symbiotic relationship between fungi and plants by stealing the nutrients from the photosynthetic plant but giving nothing back. The original article can be read here:

Evolution News - Why Are There 'Living Fossils?'

The American horseshoe crab, Limulus polyphemus

From coelacanths to crinoids: these 9 'living fossils' haven't changed in millions of years

Here is a article that Creationists can use to make fools of themselves with by showing they don't understand the subject about which they consider themselves to be leading experts.

It is about the so-called 'living fossils' - species that have remained superficially unchanged for tens, even hundreds of millions of years. I say superficially because there is no way to know how much evolution has occurred because we don't have samples of the species' DNA from millions of years ago, so we only have the physical appearance to go by and a great deal of evolution happens in genes that control the physiology or soft tissue and birdsstructures, not in the hard body-parts that more easily fossilise.

The other thing that Creationists make fools of themselves with is their naive assumption that there must be some rule in the Theory of Evolution which says species evolve at a more or less constant rate, so remaining unchanged means the TOE is wrong, conveniently forgetting that the handful of 'living fossils' are dwarfed by the millions of species with evidence of evolutionary change in just a few million years, including all living and extinct mammals and birds.

In the following article, the first thing to note is that all the examples of 'living fossils' are marine creatures, most of which inhabit the deep ocean floor or even buried in it. Away from mid-ocean ridges and the subduction zones around the edges of land masses, this is one of the most stable environments on Earth.

Since the primary driver of evolution is environmental change and maladaptation, producing opportunities for environmental selectors to select for or against genetic variations, a stable environment and/or near perfect adaptation means there will be little or no pressure to evolve. This is not a fault with the theory but a confirmation of it, in that it predicts that environmental change will drive evolutionary change, so it follows that environmental stability will result in little or no evolutionary change.

Here then is a sample of these 'living fossils' in an article from The Conversation by Alice Clement, Research Associate in the College of Science and Engineering, Flinders University, Australia. It is reprinted here under a Creative Commons license, reformatted for stylistic consistency. The original article can be read here:

Malevolent Designer News - How the SARS-CoV-2 Virus is Getting Better at Making You Sick More Quickly

Data Source

Incubation Period of COVID-19 Caused by Unique SARS-CoV-2 Strains: A Systematic Review and Meta-analysis | Infectious Diseases | JAMA Network Open | JAMA Network

A meta-analysis by scientists from the School of Public Health, Peking University, Beijing, China and Vanke School of Public Health, Tsinghua University, Beijing, China, has revealed just how sneaky Creationism's favourite pestilential designer has been with it variants of the SARS-CoV-2 virus - if you subscribe to that childish Bronze Age superstition, that is.

This meta-analysis of 141 relevant articles shows that, as well as becoming more virulent and more easily transmitted from person to person, the variant had a progressively shortening incubation period.

This might seem counter-intuitive because a slow incubation period means that a carrier remains asymptomatic for longer and so is more likely to spread the infection without realising they are infected. However, a short incubation period before it starts destroying cells in earnest also means the virus gets established more quickly and produces lots of new virus particles to be shed into the environment much sooner, and often before the victim's immune system has had time to react to it.

So, there is a trade-off between long incubation and asymptomatic spread and the short incubation and the number of virus particles being shed. It seems the balance tipped towards shorter incubation.

The analysis showed that "the incubation periods of COVID-19 caused by the Alpha, Beta, Delta, and Omicron variants were 5.00, 4.50, 4.41, and 3.42 days, respectively."

Malevolent Designer News - Creationism's Divine Malevolence is all Set for a Major Comeback with COVID-19 AND Influenza

H3N2 virus.

Despite appearances H3N2 is not closely related to SARS-CoV-2 but simultaneous infection with both can be especially dangerous

Flu is set for a big comeback now COVID restrictions are lifted – here’s what you need to know

Creationism's malevolent designer is not one to be defeated easily, as we saw with its response to the anti-SARS-CoV-2 virus vaccines produced by medical science to help control the COVid-19 pandemic, where it came up with all manner of variant to get around the social distancing measures and the vaccines, and we're still not through it yet despite the political pressure to return to pre-pandemic ways.

The equivalent of a jumbo jet full of people still dies from COVID-19 every day in the USA. Can you imagine the outcry if a real jumbo jet crashed killing everyone on board every day? How many people would continue to fly and demand the government stop whatever they're doing to prevent these crashes?

Now, though, with the sensible measures like social distances, wearing face coverings and regular hand cleansing with alcohol jells just about being ignored, Creationism's divine malevolence has the ground prepared for a double whammy.

A double whammy?

The same measures that were intended to mitigate the effects of the pandemic in 2020 and 2021 were also very effective against the influenza viruses that normally do the rounds in the winter months, with the result that the numbers dying or being made seriously ill during 2020 and 2021 were very significantly down on a normal year and the number of people being infected and building up their natural immunity also fell.

In addition, as complacency spreads and less people bother with COVID-19 boosters, what 'herd immunity' there was is also diminishing fast. A recent study in Barcelona showed that, even with a vaccine and having had an infection, most people's antibody level will be virtually undetectable in 12 months, unless boosted with further vaccinations.

Another recent study identified a new sub-strain of the SARS-CoV-2 omicron variant (BA.2.75.2) which can evade most of the antibodies provided by infection and vaccination. We don't know which new strain will produce the next wave, because it depends on several factors such as infectivity, incubation period and asymptomatic transmission, but BA.2.75.2 is a good candidate

Malevolent Design News - Is Creationism's Divine Malevolence Already Modifying the Monkeypox Virus?

The monkeypox virus is mutating. Are scientists worried?

The monkeypox virus (particles shown in this coloured image from a transmission electron microscope) is a DNA virus that readily detects and repairs small mutations in its genome, so it evolves more slowly than other pathogens.

Credit: National Institutes of Health/Science Photo Library

Researchers at the Minnesota Department of Health in St. Paul have discovered that the monkeypox virus is showing signs of some radical modifications to its DNA. Being a DNA virus, it has mechanisms for repairing 'mistakes' in its genome when it replicates, which means it evolves much more slowly than, say, the SARS-CoV-2 virus which is an RNA virus and can mutate quickly and frequently, as we are witnessing with the proliferation of new variants.

But the mutations discovered by the Minnesota team in the monkeypox virus appear to have escaped this repair mechanism and involve deletion of whole chunks of DNA and rearrangement of other parts. The discovery was made in the course of routine sequencing of the virus DNA from a patient with the disease, and was subsequently verified by Crystal Gigante, a microbiologist at the US Centers for Disease Control and Prevention in Atlanta, Georgia, who was called in to help with the investigation.

The good news is that the mutations so far don't involve the part of the DNA which codes for the protein which is the target of tecovirimat, an antiviral drug being tested for use against monkeypox in humans.

Biodiversity News - How Trees and Fungi Need Each Other and We Need Both

Pinus radiata and Amanita muscaria

The ancient, intimate relationship between trees and fungi, from fairy toadstools to technicolour mushrooms

One of the most important symbiotic relationships on the planet is that between trees and fungi, without which we would have no trees, no forests, no timber, less oxygen and according to climatologists, very different weather patterns.

We would also not have all the species that depend on trees and forests which support one of the most diverse biota on the planet.

Trees themselves are an example of unintelligent design, as I explain in my book, The Unintelligent Designer: Refuting the Intelligent Design Hoax because their trunks and branches are the result of a massively wasteful arms race, as each tree competes with its neighbours to get its leaves above the canopy and into the sunlight. The result is a massive waste of energy and resource to build a structure which would have been unnecessary, had the ancestors of today's trees all being intelligently designed to stay at ground level and not compete for resources.

As a result of this unnecessary and wasteful complexity, another layer of complexity in the form of this symbiotic relationship between trees and fungi, which makes this possible, has evolved. Without it, trees could not obtain the nutrients they need or pump the water the leaves need to the top of the structure. So, from the perspective of the notion of intelligent [sic] design, we have massive waste and needless complexity to solve problems of the designer’s own incompetent making. So this relationship between fungi and trees represents one of the most glaring examples of the lack of foresight, planning and intelligence in whatever the design process behind it was.

From an evolutionary perspective, however, there is no need to explain bad design since there is no design process, as any intelligent person would understand it, involved. The result put the evolution of life on Earth on a trajectory that resulted in what we see today, and on which thousands of species are now dependent having evolved specialisations fitting them to live and survive in those niches by a process of co-evolving co-dependency - a predictable consequence of the process of evolution by natural selection.

The symbiotic relationship is between the roots of trees and the fungal hyphae in the soil, known as mycorrhizas. It is a lovely example of how Richard Dawkin's 'selfish genes' will form mutually beneficial alliances with the genomes of two or more organisms behaving like a single genome, albeit stored in different cells, co-evolving an every closer relationship, not of wasteful competition but of the more efficient cooperation, because cooperation benefits both organisms.

Mycorrhizas - Australian National Arboretum.

In another of the The Conversation series, 'Photos from the Field', Doctor Gregory Moore of The University of Melbourne and Associate Professor Mark Brundrett of the School of Biological Sciences, The University of Western Australia, explain this relationship, its evolutionary origins and why it is so important to the ecology of the planet. The open access article is reproduced here under a Creative Commons licence, reformatted for stylistic consistency. The original article can be read here:

The ancient, intimate relationship between trees and fungi, from fairy toadstools to technicolour mushrooms

Cortinarius kula

Credit: Mark Brundrett, Author provided

Gregory Moore, The University of Melbourne and Mark Brundrett, The University of Western Australia

Environmental scientists see flora, fauna and phenomena the rest of us rarely do. In this series, we’ve invited them to share their unique photos from the field.

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You may be familiar with the red toadstool with white spots, which are often the homes of fairies in children’s stories. These toadstools are also a small part of grander magical story: they are striking examples of mycorrhizas.

Mycorrhizas (pronounced my-cor-rye-zas) is the name for fungi associated with the root systems of many plants including trees, shrubs, groundcovers and grasses. These relationships are mutually symbiotic, which means both members benefit.

Fungi have a deeply ancient evolutionary origin, and colonised land with the first plants around 500 million years ago to form these partnerships. We humans often underestimate their importance to the ecosystems that have shaped life on earth.

So let’s take a closer look at how this relationship works and why it’s so important for Australian ecosystems.

An intimate relationship

Fungi come in a beautiful diversity of shapes, sizes and colours. The following photos by my co-author Mark Brundrett are just a few examples of those growing in southwest Australia.

Mycorrhizas are not to be confused with fungi that decompose dead plant matter (saprophytes) or those that cause disease (pathogens).

The glowing ghost mushroom looks like it comes from a fungal netherworld

Saprophytes are fungi that recycle nutrients, and these can also be large and impressive. They can create tree hollows, which provide shelter for nesting birds and other animals such as possums.

The ethereal ghost fungus, for example, is a saprophyte. It famously glows green in the dark, and recycles nutrients in ecosystems by breaking down dead wood.

The bioluminescent ghost fungus growing on a tree stump.

Credit: Mark Brundrett, Author provided

The primary role of mycorrhizas, on the other hand, is to provide resources such as phosphorus and nitrogen to flowering plants. They also effectively increase the absorptive surface area of the plant’s root system, allowing plants to take up much-needed water and nutrients so they grow better and more quickly.

In return, the plants provide carbohydrates, a product of photosynthesis, which mycorrhizas require to grow.

The yellow navel fungus Lichenomphalia chromacea forms a protective crust on soils in association with lichen fungi and algae.

Credit: Mark Brundrett, Author provided

Cortinarius vinaceolamellatus is a beautiful fungus that supports the growth of of tall eucalyptus forests.

Credit: Mark Brundrett, Author provided

This saprophyte is a relative of the common mushroom sold in shops (a species of Agaricus). Australian fungi can be toxic so leave them where they grow.

Credit: Mark Brundrett, Author provided

There are five different types of mycorrhizas, and two of these are particularly important in Australian ecosystems. One type is called “ectomycorrhiza”, where fungi wrap their hyphae (long, very fine hair-like structures that contact the soil) around the plant roots underground but don’t penetrate the root cells.

The other, called “endomycorrhiza”, is where fungi grow into the plant root, penetrating and branching within the root cells to form what look like little, microscopic trees. This is about as intimate a relationship between different types of organisms as you can get!

Microscopic cross-sectional view of an ectomycorrhizal pine tree root about 0.5 millimetres wide. This revels a labyrinth of black stained fungus hyphae surrounding root cells to form a nutrient exchange zone.

Credit: Mark Brundrett, Author provided

Arbuscular mycorrhizas are tiny tree-like growths inside the root cell where materials are exchanged with the host plant.

Credit: Mark Brundrett, Author provided

Mushrooms as big as dinner plates

We often become aware of the presence of mycorrhizas only when conditions for reproduction are right, and a mushroom or toadstool emerges from the ground. Such conditions may only occur every five to ten years. For some species, there may be centuries between reproductive events.

For many of us, our experience with mycorrhizal fungi begins in very early childhood when we first catch sight of those spotty red and white toadstools, called the fly agaric or Amanita muscaria.

These fungi are often depicted in children’s book illustrations, such as Little Red Riding Hood, Jack and the Beanstalk, and a number of Enid Blyton’s tales. I recall conifers, such as pine trees, often growing nearby in the background of these pictures. This was no coincidence, Amanita muscaria forms mycorrhizal associations with many conifers, as well as oaks.

The fly agaric or Amanita muscaria is a striking fungus often seen in children’s books.

Credit: Mark Brundrett, Author provided

The fame of Amanita muscaria also arises from the hallucinogenic properties it sometimes has, but this fungus is most likely to have toxic consequences for those who eat it. It was also used as a natural insect killer.

Credit: Mark Brundrett, Author provided

The mycorrhizal fungi associated with eucalypts can be less showy, with many being 75-100 millimetres across and a creamy, light tan in colour. They quite often pop up in home gardens, frequently in lawns, where they’re very obvious and usually within 4 to 5 metres of a tree trunk.

Others are spectacular, including the bright purple, orange or green Cortinarius species shown in the photos below. In fact, the beauty and diversity of our fungi now supports a new ecotourism industry in Australia, particularly in Tasmania.

The bright green mushroom Cortinarius austroveneta is found in tall eucalypt forests.

Credit: Mark Brundrett, Author provided

Cortinarius erythrocephalus is another brilliantly coloured mycorrhizal forest mushroom.

Credit: Mark Brundrett, Author provided

Cortinarius rotundisporus, also known as the elegant blue webcap, can be found in southern Australia.

Credit: Mark Brundrett, Author provided

Some fungi are most impressive in the spring following bushfires, such as the abundant orange cup fungus shown below that stabilises ash beds.

How fungi's knack for networking boosts ecological recovery after bushfires

The orange cup fungus Anthrocobya muelleri is found briefly after severe fires.

Credit: Mark Brundrett, Author provided

Indeed, most plants form mycorrhizal associations. Those that don’t include plants from the common vegetable families Brassicaceae (think broccoli, cauliflower, kale) and Chenopodiaceae (spinach, beetroot, and quinoa). Neither do members of the Proteaceae family, such as native banksias and grevilleas. These plants invest in very complex roots rather than fungal associations.

This is a species of Ramaria, a mycorrhizal genus comprising approximately 200 species of coral fungi.

Credit: Mark Brundrett

Phlebopus marginatus is possibly Australia’s largest terrestrial mushroom, with one found in Victoria weighing in at 29 kilograms.

Credit: Mark Brundrett, Author provided

Who’s really in control?

Because we are so familiar with many of the plants in our environment, we are inclined to think it’s them that control their relationship with mycorrhizal fungi.

But it is possible mycorrhizal fungi exercise much more control. Or perhaps, the relationship is a perfect mutualistic symbiosis where partners share everything, including control, equally. We just don’t know yet.

5 ways fungi could change the world, from cleaning water to breaking down plastics

Members of the fungus kingdom work in synchrony with the plant kingdom to support all terrestrial life, including animals such as ourselves. We may not think about fungi very often, but we cannot survive without them.

One of the surprise elements of Douglas Adam’s Hitchhiker’s Guide to the Galaxy, was that the Earth and its inhabitants existed as part of an experiment designed and controlled by white laboratory mice.

I sometimes wonder if the fate of the Earth’s terrestrial ecosystems rests on mycorrhizal fungi. If so, perhaps we need to show them greater respect.

Gregory Moore, Doctor of Botany, The University of Melbourne and Mark Brundrett, Adjunct Associate Professor, School of Biological Sciences, The University of Western Australia

Published by The Conversation.
Open access. (CC BY 4.0)

Biodiversity News - Australia's Exotic Invertebrates

Mating Repsimus scarab beetles

Credit: Nick Porch

Photos from the field: zooming in on Australia’s hidden world of exquisite mites, snails and beetles | The Conversation

Most people will be familiar with Australia's unique set of mega- (and not so mega) fauna such as kangaroos, wallabies, koalas, dingoes, wombats, marsupial mice, and of course the egg-laying monotremes, the platypus and the echidna or spiny ant-eater, but how many people are aware of the equally unique and often bizarre array of invertebrates, apart from the dangerous spiders, that is?

In this article in The Conversation, 'Photos from the Field' series, from January 2021 Nick Porch, Senior Lecturer in Environmental Earth Science, Deakin University, Australia, shares some photographs of a small sample of the several hundred thousand uniquely Australian organisms, most of which will be almost completely unknown, even to Australians.

Creationists might like to ignore the bits about 150 million years, Gondwana and allusions to plate tectonics, in the explanation for why Australian bugs tend to be more closely related to South American bugs than those from New Zealand. Evidence of evolution on an old Earth will probably upset them.

The article is reprinted here under a Creative commons licence, reformatted for stylistic consistence. The original can be read here:

Malevolent Designer News - Has Creatonism's Divine Malevolence Lost the Plot?

Yellow-legged frogs killed by chytrid fungus in Sixty Lakes Basin area of the Sierra Nevada, California, USA

Photo credit: Joel Sartore/Natural History Museum.

A deadly disease has driven 7 Australian frogs to extinction – but this endangered frog is fighting back

I've written several times both in this blog and in my popular, illustrated book, The Malevolent Designer: Why Nature's God is not Good, about the deadly fungus, Batrachochytrium dendrobatidis, that is decimating the world population of amphibians, especially frogs.

As a piece of intelligent [sic] design, taking a previously harmless soil fungus and modifying to kill frogs, is about as good an example of the sheer nasty malevolence of any designer that could do such a thing as you could wish for.

Yet Creationists continue to insist only their favourite designer god could do such a thing, because evolution isn't capable of doing it. For some unexplained reason, chemistry and physics need magic to make them work.

God Hates Frogs

But now the news from Australia, is that frogs may be staging something of a fight back by developing resistance to it - again something that Creationists will insist must have been done by the same malevolent designer that designed the fungus to kill frogs in the first place.

Or that's to sort of bizarre belief system Creationists dupes have been fooled into.

As always though, the facts of biological science offer a more rational explanation. Here for example is a report by Matthijs Hollanders and David Newell of Southern Cross University, Australia, which gives evidence of this fightback. It is reprinted from The Conversation, reformatted for stylistic consistence, under a Creative Commons licence. The original article can be read here:

Creationism in Crisis - Transitional Forms in Recent Human Evolution

Comparing the Boxgrove and Atapuerca (Sima de los Huesos) human fossils: Do they represent distinct paleodemes? - Journal of Human Evolution

Figure 1. A) Location map and B) chronology of key European Middle Pleistocene hominin samples relative to the benthic foraminiferal oxygen isotopic stratigraphy (Lisiecki and Raymo, 2005).

One of the difficulties with palaeontology is fitting individual fossils into a taxonomic system that was designed for classifying contemporaneous organisms. This difficulty is inevitable given that species change over time as they evolve so it is not a flaw in the theory but a confirmation of it, rather like the problem of deciding exactly where one colour changes into another in a rainbow is not a flaw in the theory of why sunlight can be split into different colours but a confirmation of the theory.

Where do the colours change?

Just such a problem was illustrated by a paper published recently by a team of paleoanthropologists from England and Spain, led by Lucile Crété of the Centre for Human Evolution Research (CHER), The Natural History Museum, London, UK.

The team set out to decide whether hominin fossils from Boxgrove in West Sussex, England were of the same paleodeme as those found at the Sima de los Huesos (Pit of Bones) at Atapuerca, Castile and León, Spain.

Creationism in Crisis - The Evolutionary Origins of Nitrogen Fixation by Prokaryotes

Origin and Evolution of Nitrogen Fixation in Prokaryotes | Molecular Biology and Evolution | Oxford Academic

Despite ludicrous claims by Creationist frauds and their dupes that the Theory of Evolution (TOE) is about to be abandoned by mainstream biomedical science and replaced by an evidence-free Bronze Age superstition involving magic, the TOE continues to be the fundamental principle of biology and the framework which explains what can be observed, without the need for magic and unknowable mysteries.

Take for example the question of the origin of nitrogen fixation.

Nitrogen is essential for all biological organisms, being an integral part of all proteins, yet, despite the abundance of molecular nitrogen (N₂) in the atmosphere at about 78%, no eukaryote organisms can extract it directly. The problem is that N₂ is a very stable molecule with a triple bond between the two atoms, so, to be biologically active, it needs to be converted to ammonia (NH₃) which takes an enormous amount of energy and sixteen molecules of ATP. A significant proportion of ammonia comes from lightning strikes which convert a molecule of N₂ and three molecules of water (H₂O) into two molecules of NH₃ and a molecule of ozone (O₃)

N₂ + 3H₂O → 2NH₃ + O₃

But by far the most significant source of biological nitrogen is 'nitrogen fixation' by bacteria living often in symbiosis with plants. One example is nitrogen fixation by prokaryote bacteria is the relationship between rhizobia bacteria (Rhizobiaceae, α-Proteobacteria) which live in nodules in the roots of plants of the legume family. Other free-living nitrogen-fixing bacteria contribute to soil and marine nitrogen when the nitrogen in their bodies is released when they die.

Nitrogen Fixation by Legumes (Guide A-129) - New Mexico State University

The question for evolutionary biology was where and when did this ability to fix nitrogen originate? The prevailing consensus was that it originated in archaea and was acquired by bacteria by horizontal gene transfer. That consensus has now been challenged by a team of researchers from National Chung Hsing University and Academia Sinica, Taiwan, in an open access paper which argues that the process arose in bacteria first and was acquired by archaea later.

The evidence is in the form of an in-depth analysis of the >30,000 prokaryotic genomes that have so far been sequenced, to test the two competing hypotheses. This analysis produced nested hierarchies, in which the nitrogen-fixing archaea were nested inside the bacterial clades, and the fact that the majority of archaea use the bacterial Mo (molybdenum) transporter (ModABC) and not the archaeal Mo transporter (WtpABC). In other words, the majority of archaea use the bacterial process, not the archaeal process.

These observations, of course, only make any sense as the result of an evolutionary process. Certainly, there is no evidence of intelligent design here. After all, why design two different methods to achieve the same result. Also, why not designs eukaryotes to fix nitrogen directly by giving them the same processes used in bacteria and archaea, or one less demanding of energy, instead of opting for the much more complex system of symbiosis and dependence on dead bacteria releasing their fixed nitrogen?

In evolutionary terms of course, there was no evolutionary pressure on eukaryotes to evolve independent nitrogen fixation because bacteria and archaea were already abundant when the first eukaryotes and the first multicellular organisms arose, so biological nitrogen was not in short supply. That situation did not apply in the early evolution of the prokaryotes, for whom nitrogen would have been in very short supply, so the expenditure of energy in the process of fixing atmospheric nitrogen was cost-effective.

The resulting eukaryote plant life evolved to fit the environment in which they were evolving. The additional energy needed by an independent nitrogen fixing metabolic process would have made any evolution in that direction, deleterious, so it never evolved. For the legumes, it proved advantageous with little additional resource, to have nitrogen fixing bacteria living symbiotically in their roots.

An example there of how the process of evolution by natural selection results in a compromise solution which tends to provide the greatest benefit for the least cost.

Copyright: © 2022 The authors.
Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. Open access. (CC BY-NC 4.0)

The Taiwan team's paper is published open access in the Oxford Academic journal, Molecular Biology and Evolution:

Abstract

The origin of nitrogen fixation is an important issue in evolutionary biology. While nitrogen is required by all living organisms, only a small fraction of bacteria and archaea can fix nitrogen. The prevailing view is that nitrogen fixation first evolved in archaea and was later transferred to bacteria. However, nitrogen-fixing (Nif) bacteria are far larger in number and far more diverse in ecological niches than Nif archaea. We, therefore, propose the bacteria-first hypothesis, which postulates that nitrogen fixation first evolved in bacteria and was later transferred to archaea. As >30,000 prokaryotic genomes have been sequenced, we conduct an in-depth comparison of the two hypotheses. We first identify the six genes involved in nitrogen fixation in all sequenced prokaryotic genomes and then reconstruct phylogenetic trees using the six Nif proteins individually or in combination. In each of these trees, the earliest lineages are bacterial Nif protein sequences and in the oldest clade (group) the archaeal sequences are all nested inside bacterial sequences, suggesting that the Nif proteins first evolved in bacteria. The bacteria-first hypothesis is further supported by the observation that the majority of Nif archaea carry the major bacterial Mo (molybdenum) transporter (ModABC) rather than the archaeal Mo transporter (WtpABC). Moreover, in our phylogeny of all available ModA and WtpA protein sequences, the earliest lineages are bacterial sequences while archaeal sequences are nested inside bacterial sequences. Furthermore, the bacteria-first hypothesis is supported by available isotopic data. In conclusion, our study strongly supports the bacteria-first hypothesis.

Hong-Wei Pi, Jinn-Jy Lin, Chi-An Chen, Po-Hsiang Wang, Yin-Ru Chiang, Chieh-Chen Huang, Chiu-Chung Young, Wen-Hsiung Li,
Origin and Evolution of Nitrogen Fixation in Prokaryotes, Molecular Biology and Evolution, 39(9), September 2022, msac181, DOI: 10.1093/molbev/msac181

Copyright: © 2022 The authors.
Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. Open access
Reprinted under a Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)

Creationism in Crisis - How Our Extended Genome of Micro-Organisms Killed Rivals For Land During the European Imperial Expansion

A Tongan Village

Photo: State Library of New South Wales

New data reveals severe impact of European contact with Pacific islands - CHL - ANU

In his Pulitzer Prize-winning book, Guns, Germs and Steel, Professor Jared Diamond, makes the point that it was not just superior technology (guns and steel) that enabled European imperialists to colonise much of the undeveloped world, but also our armoury of lethal germs that we unwittingly took with us.

Our germs, many of which are derived from related varieties in our domestic cattle, had being living with us for thousands of years in Europe where the population had developed a degree of natural resistance. However, when we came into contact with people who had lived, for example, on remote Pacific Islands, these people had little or no natural immunity, so diseases like measles and mumps were lethal and spread quickly, going ahead of us like a fifth column, working in secret to kill or severely weaken the indigenous population, making it easy to take control through force of arms.

This is an example of a sudden environmental change giving a big advantage to one group and being severely detrimental to a rival group. In evolutionary terms, this could be one reason why we have failed to develop complete resistance to our commensal and sometime pathogenic microbes and viruses; as we evolved, it was advantageous to us to have this invisible 'fifth column' to help us take over new territory. It's a classic example of how genes can form alliances and don't even need to belong to the same species, just so long as both benefit from the alliance.

Now two researchers from the Australian National University (ANU) School of Culture, History & Language, PhD candidate Phillip Parton and Professor Geoffrey Clark, have shown that this devastation of the population on Pacific islands was even worse than previously thought, with the population of the island of Tongatapu in the kingdom of Tonga being reduced to just 10,000 in 50 years, from 50-60,000 when Europeans first landed.

Their work, published in the Journal of Archaeological Science, indicates population declines were a lot larger than previously thought.

As the ANU news release explains:

Creationism In Crisis - Another 'God-Filled' Gap Just Got a Lot Smaller

Molecular dynamic simulation of ADP and acetyl phosphate

Aaron Halpern, UCL (CC-BY 4.0)

What is perhaps the favourite of all Creationism's 'God-filled' gaps - abiogenesis - just go a lot smaller with the news today that Nick Lane and colleagues of University College, London, UK, have shown how ATP became the universal energy currency used by all living organisms, so adding another layer to our understanding of how the earliest self-sufficient, self-replicating organisms arose from pre-existing molecules.

As always, the process evicts Creationism's shrinking little god because it is explained using just the natural laws of chemistry and physics acting on pre-existing molecules, with no place for magic or supernatural powers.

The mystery was, how the system for producing ATP could have evolved when the process used by cells today is a multi-step process which itself utilises ATP at six different points. Clearly, there must have been a simpler process for creating ATP early on in the evolution of living organisms and, because of it's universality, this was almost certainly in a common ancestor to all forms of life.

In prokaryote cells such as bacteria, the process occurs in the cell itself but in eukaryote cells the process takes place in the mitochondria - the descendants of bacteria originally incorporated into other prokaryote cells to give rise to the eukaryotes.

What is ATP and how is it synthesised? Wikipedia - Adenosine triphosphate

As explained in information provided ahead of publication by PLoS Biology:

Creationism in Crisis - Evolutionary Palaeontologist, Svante Pääbo, Wins Nobel Prize for Medicine

Svante Pääbo

Sweden's Pääbo wins Nobel Medicine Prize for sequencing Neanderthal DNA

This is the sort of news that the leading frauds in the Creationist cults must be dreading, if they still have an hope of convincing their dupes that the Theory of Evolution is a theory in crisis, about to be overthrown and replaced by religious superstition. It is the news that leading evolutionary palaeontologist and geneticist, Professor Svante Pääbo, director of the Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany has been awarded a Nobel Prize for his work in the field of human evolution.

Far from being a theory in crisis, the Theory of Evolution is very much mainstream biomedical science, to the extent that the work Pääbo and his team are doing is central to our understanding of our recent history and how we relate to the archaic hominins that were our direct ancestors and the direct ancestors of other species of the Homo genus.

One of Pääbo's first major contributions to evolutionary biology was in sequencing Neanderthal genomes, then discovering that modern non-African Homo sapiens have at various times in recent history, had a significant ingression of Neanderthal DNA due to interbreeding between the two species. This horizontal gene transfer meant anatomically modern hominins acquired genes that had evolved in Neanderthals over a period of some 250,000 years, giving us significant adaptations to the cold, cloudy northern climates in Eurasia. Today, modern non-African humans have 2-4% Neanderthal DNA, most of it acquired about 40,000-60,000 years ago when the two species co-existed in Eurasia.

Human Evolution - Sex With Neanderthals
So What Did The Neanderthals Ever Do For Us?
More Evidence For a Human Ring Species
Evolution News - Women with Neanderthal Genes are More Fertile
Ancient Teeth Show Human Roots

Pääbo and his team then succeeded in sequencing the genome of a previously unknown hominin from a finger bone found in the Denisova Cave in Siberia and showed that this was a third distinct species of hominin, the Denisovans, who coexisted with Neanderthals, with whom they interbred extensively, and with H. sapiens with whom they also interbred. This led to the discovery that south East Asian and Melanesian people today have a significant proportion of Denisovan DNA, indicating frequent interbreeding as Homo sapiens spread out of Africa across central, southern and south-eastern Asia and into Indonesia, New Guinea and Australia.

There is also a mysterious fourth hominin whose DNA has been found in Neanderthals and some Homo sapiens. Neanderthals and Denisovans were the descendants of an earlier migration out of Africa of an archaic hominin, probably H. erectus. H. sapiens are almost certainly the descendants of those H. erectus who stayed in Africa.
What this tells us is that for much of recent human history, we have co-existed with several other hominin species whose evolutionary divergence from us and each other was not sufficiently advanced to prevent interbreeding, probably because for most of the 250,000 years that Neanderthals had lived in Eurasia, during which the ancestors of H. sapiens lived in Africa, interbreeding was a rare event so there was no evolutionary pressure to either reintegrate into a single species or to establish barriers to hybridization.

Having said that, though, there is a recent explanation for the disappearance of Neanderthals which suggests that they were never exterminated but simply merged into the growing population of H. sapiens which quickly outnumbered them, to the extent that there is now more Neanderthal DNA in the world than there ever was prior to 40,000 years ago.

Human Evolution News - We have More Neanderthal DNA Now Than They Ever Had

When Homo sapiens came out of Africa, the period of co-existence was too short for barriers to hybridization to evolve, so for much of our recent history, the Homo complex of species behaved very much like a ring species of incompletely speciated regionals species and subspecies.

Ring species

Creationist frauds now have the task of explaining to their credulous dupes why, if the TOE is a theory in crisis, one of its main exponents, whose work only makes any sense in the context of evolving hominin species, has been awarded the most prestigious prize in science - a Nobel Prize. We can now expect a proliferation of childish conspiracy theories as they seek to cope with the cognitive dissonance.

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Malevolent Designer News - How Creationism's Divine Malevolence Gives us Dementia

Viral infections including COVID are among the important causes of dementia – one more reason to consider vaccination

What is not generally recognised is the role of viruses, such as SARS-CoV-2 which caused COVID-19, have in causing dementia. Now recent research has shown that 'Long Covid' is emerging as one ot the most important causes of dementia.

Now, with many countries discontinuing the policy of isolating people with COVID-19 and allowing them to continue to work and mix socially, the virus is becoming endemic in the population, so the long-term effects, such as dementia are going to increase.

The following article by Professor John Donne Potter of the Research Centre for Hauora and Health, Massey University, New Zealand, reproduced from The Conversation under a Creative Commons open access licence, reformatted for stylistic consistency, highlights the role of viruses in dementia. The original article can be read here.

Viral infections including COVID are among the important causes of dementia – one more reason to consider vaccination

Credit: Sven Hoppe/picture alliance via Getty Images

John Donne Potter, Massey University

With more of us living into old age than at any other time, dementia is increasing steadily worldwide, with major individual, family, societal and economic consequences.

Treatment remains largely ineffective and aspects of the underlying pathophysiology are still unclear. But there is good evidence that neurodegenerative diseases – and their manifestation as dementia – are not an inevitable consequence of ageing.

Many causes of dementia, including viral infections, are preventable.

COVID and other viral infections are centrally involved in insults to the brain and subsequent neurodegeneration. COVID-positive outpatients have a more than three-fold higher risk of Alzheimer’s and more than two-fold higher risk of Parkinson’s disease.

A study of almost three million found risks of psychiatric disorders following COVID infection returned to baseline after one to two months. But other disorders, including “brain fog” and dementia, were still higher than among controls two years later.

🚨I wrote about “brain fog”—one of the most common & disabling symptoms of long COVID (and many other pre-pandemic conditions), and one of the most misunderstood.

Here’s what brain fog actually is, and what it’s like to live with it. 1/ https://t.co/Gq8iylgfBr

— Ed Yong is on sabbatical (@edyong209) September 12, 2022

Among more than six million adults older than 65, individuals with COVID were at a 70% higher risk than the uninfected for a new diagnosis of Alzheimer’s disease within a year of testing positive for COVID.

More than 150,000 people with COVID and 11 million controls have been involved in a study of long-term consequences of acute COVID infection. A year after infection, there was an overall 40% higher risk (an additional 71 cases per 1000 people) of neurologic disorders, including memory problems (80% higher risk) and Alzheimer’s disease (two-fold higher risk). These risks were elevated even among those not hospitalised for acute COVID.

These 12 things can reduce your dementia risk – but many Australians don't know them all

SARS-CoV-2, the virus that causes COVID, can invade brain tissue. Other viruses can also cause direct damage to the brain. A study of almost two million people showed the risk of Alzheimer’s was markedly lower in those who had been vaccinated against influenza.

The cost of dementia

Dementia is characterised by progressively deteriorating cognitive function. This involves memory, thinking, orientation, comprehension, language and judgement, often accompanied by changes in mood and emotional control.

It is one of the major causes of disability among older people. Worldwide prevalence exceeds 55 million and there are almost ten million new cases annually. It is the seventh leading cause of death. In 2019, the estimated global cost of dementia was US$1.3 trillion and rising.

The best known form of dementia – Alzheimer’s – was first described in 1907. Dementia is generally described as developing in three stages:

• impairment of memory, losing track of time and becoming lost in familiar places
• further deterioration of memory with forgetfulness of names and recent events, becoming confused at home, losing communication skills and personal care habits, repeated questioning, wandering
• increased difficulty walking, progressing to inactivity, marked memory loss, involving failure to recognise relatives and friends, disorientation in time and place, changes in behaviour, including lack of personal care and emergence of aggression.

Omicron-specific vaccines may give slightly better COVID protection – but getting boosted promptly is the best bet

Treatments largely unsuccessful

There are no cures and no resounding treatment successes. Management involves support for patients and carers to optimise physical activity, stimulate memory and treat accompanying physical or mental illness.

Dementia has a disproportionate impact on women, who account for 65% of dementia deaths and provide 70% of carer hours.

We may know less about the pathology of dementia than we imagined: some key data are under scrutiny for possible inappropriate manipulation.

Alzheimer's theory undermined by accusations of manipulated data – but does not bring dementia research to its knees

But we do know about many of the causes of dementia and therefore about prevention. In addition to viral infections, there are at least four other contributing causes: cardiovascular disease, type 2 diabetes (especially if untreated), traumatic brain injury and alcohol.

The brain has its own immune system – cells called microglia. These play a role in brain development, account for 5-10% of brain mass and become activated by damage and loss of function. They are also implicated in Alzheimer’s and their inflammation has been shown to be central to its pathology.

Dementia is preventable

In the absence of effective treatment, prevention is an important goal. The association with viral infections means we should pay careful attention to vaccine availability and uptake (for influenza, COVID and any future variants) and place greater emphasis on combatting misinformation regarding vaccines.

The association with atherosclerosis and stroke, as well as diabetes, supports primary prevention that involves healthier diets (plant-based diets low in salt and saturated fats), physical activity and weight control.

Alcohol consumption is a major problem globally. We have allowed high intake to be normalised and talk about no more than two glasses per day as though that is innocuous. Despite the myth of some beneficial aspects of alcohol, the safest intake is zero drinks per week.

My article speaks about a study that showed that people who chronically consume alcohol and become unconscious because of it, their chances of having dementia increase 10 fold. https://t.co/0DOFf9X5Zx @mrcopsych

— Hannah (@Hannah46221416) September 29, 2022

This requires a complete national rethink around the availability and acceptability of alcohol as well as assistance with alcohol addiction and treatment of alcohol-related disorders.

Traumatic brain injury is associated with sport and, more importantly, falls and car crashes. It is recognised as a global priority and there is increasing awareness of the preventability of falls among older people. The management of head injuries is being ramped up in contact sports.

However, data on the impact of best management of the initial injury on subsequent risk of dementia are lacking and risk remains elevated even 30 years after the initial trauma.

The evidence that dementia has preventable causes, including viral infection, should better inform policy and our own behaviour.

John Donne Potter, Professor, Research Centre for Hauora and Health, Massey University

Published by The Conversation.
Open access. (CC BY 4.0)

It seems then, that if you've fallen for the intelligent [sic] design hoax, you must now accept that the malevolent designer who designed the SARS-CoV-2 virus intended it to cause dementia in those who survived the initial attack. Unless, of course, you believe that it is a stupid designer who doesn't know what the organisms it is designing will do and is incapable of correcting its designs when it realises the consequences of what it’s done, if it has any concerns for those consequences. If the latter, you believe the designer has all the characteristics of a mindless natural process without a plan, exactly like evolution by natural selection.

Malevolent Designer News - How Ticks Are Designed to Make Us Sick

European tick, Ixodes ricinus

Study demonstrates for the first time that ticks weaken skin's immune response

Creationism's divine malevolence is nothing if not a fanatical perfectionist for whom no detail is too small in its quest to find ways to make its creation sick - or so you must believe if you've fallen for the intelligent [sic] design hoax.

Here for example is a paper in which the scientists have shown how well-designed ticks are for passing on infections to its victims, including humans and our livestock. The scientists found that tick saliva contains a powerful immuno-suppressant the prevent the body from reacting to the nasty little organisms it injects along with its saliva when it takes a meal. This also solves the mystery of why ticks are such powerful disease vectors. It almost seems they were designed for it.

The team of scientists led by led by Georg Stary (MedUni Vienna's Department of Dermatology, CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases) in collaboration with the research group of Hannes Stockinger (Center for Pathophysiology, Infectiology and Immunology at MedUni Vienna) have published their paper, open access, in the Journal of Clinical Investigation.

The Medical University of Vienna news release, explains the research and its significance: