Malevolent Designer News - An Even Nastier Inbuilt Ability of the SARS-CoV-2 Virius Revealed

COVID is a 'smart virus' that can affect DNA – but that doesn't mean you can pass it on to your kids

Recent research has revealed just how sneaky the designer of the SARS-Cov-2 virus that caused COVID-19 would have had to have been, had there been any truth in the childish Creationists superstition that there is a magic intelligent [sic] designer who designs these things.

Like several other pathological viruses and bacteria, SARS-CoV-2 can manipulate out epigenetic system for its own advantage. Briefly, the epigenetic system is a complex process for turning off those genes that are not needed in the specialised cells of a multicellular organism.

In fact, the existence of this complex process is one of the strongest arguments against any intelligence being involved in evolution because it is only needed because the cells in a multicellular organism replicate in exactly the same way as a single-celled organism, even though only a fraction of the DNA will be needed in any specialised cell, whereas a single-celled organism needs its entire genome to function. No intelligent designer who understood the basic principles of good design would come up with such a complex system when it should not be beyond its wit to design a system where only those genes needed by the specialist cells were inherited by them. Utilitarian evolution, on the other hand, is quite capable of coming up with something so unintelligent.

What is Epigenetics? - CDC Genomics & Precision Health

Back to the discovery of what the SARS-CoV-2 virus is capable of:

The following article from The Conversation by Lara Herrero, Research Leader in Virology and Infectious Disease, Griffith University, Queensland, Australia, explains the research and its significance. It is reprinted here under a Creative Commons licence, reformatted for stylistic consistency. The original article cam be read here:

Creationism In Crisis - Ray Comfort's Deception Caught in a Venus Fly Traps

Ray 'Bananas' Comfort

Ray Comfort is an American multi-millionaire Televangelist, Creationist grifter who makes his money out of scientifically illiterate dupes in the Creationist cults, by posing as an expert scientist.

His latest piece of disinformation is his claim that the Venus flytrap, Dionaea muscipula, is an example of irreducible complexity because the trap mechanism could not have evolved. In the Creationist lexicon, ‘irreducible complexity’ is code for ‘the Christian god did it’, so the Bible is literal truth’.

Comfort has no qualifications in biology, or any science subject yet feels qualified to tell his marks that millions of working biomedical scientists have got things all wrong and he knows best. Posturing as an expert is a familiar Creationist tactic intended to deceive, or, as a Christian would put it, an example of bearing false witness. Nevertheless, he should be capable of even the most cursory of fact checking in the age of the Internet, but doesn't feel he needs to, as he knows his target marks never check what he says, so he'll probably get away with it. It’s the tactic of the snake oil salesman.

Had he bothered with fact-checking, however, he would have discovered the freely available scientific evidence that flatly contradicts and gives the lie to his claim. Not only is the evolutionary pathway of the Venus flytrap known, but it is a very nice example of Darwinian evolution.

But then Creationists cult leaders, like their members, have no interest in the truth. Their mission is to mislead those who eagerly send them money for disinformation that makes them feel important, with a special relationisp with the Creator of the Universe who made it all with them in mind.

And Comfort laughs all the way to the bank.

An earlier ploy by Comfort was to tell his followers that there is no gravity in space [sic], so this proves God wrote the Bible [sic]. A more famous one was to claim the banana is specially designed to fit in the hand as you eat it, knowing his cult won't understand the role of selective breeding in plant cultivation. As others have pointed out, it is equally well designed to fit in other orifices too.

How Creationists Lie To Us - Ray Comfort

Mind you, Comfort's own ignorance sometimes comes back to bite him, like the time he complained about the pain of an impacted wisdom tooth for which he needed surgery, not realising wisdom teeth and the problems we have with them is both evidence for evolution and against intelligent design, but then Comfort was blissfully ignorant of those things.

Unintelligently Designed Teeth Cause Ray Discomfort

Dionaea muscipula trap mechanism

By Mnolf - Own work, CC BY-SA 3.0, Link

Anyway, back to the Venus flytrap; the following is the result of a few minutes search on Google - something Comfort can rely on his dupes not doing. It reveals a fascinating story of gradual evolution of the 'snap-trap' mechanism, including repurposing pre-existing structure which originally had an unrelated function.

The evolution of carnivory in plants is a specialised form of foliar feeding where the plant derives nutrients through its leaves in addition to any it obtains through its roots. It generally occurs in conditions where the soil is deficient in nutrients, such as in acidic bogs where water soluble nutrients, especially nitrates, leach out of the soil. It is believed to have occurred independently six times in the angiosperms, based on extant species, and possibly more in carnivorous lineages now extinct.

But it's not the evolution of carnivory itself that Comfort is trying to fool his marks with, but the 'snap-trap' mechanism which captures the prey.

How does the Venus flytrap work? | University of Tasmania

As Comfort could have discovered in just a few minutes had he bothered to, the evolution of this mechanism probably occurred in a common ancestor of Dionaea and the closely related, Aldrovanda. Two studies in 2002 and 2003 and a further study in 2009, have shed light on how this occurred:

Unintelligent Design - Eels

Back in 2013, I wrote a blog about the European Eel for Creationist children, not realising then that all Creationists think like children, or at least all Creationists you are ever likely to encounter on the social media. It is a good introduction to an article about eels in The Conversation by Dr Kylie Soanes, a Postdoctoral Fellow in the School of Ecosystem and Forest Sciences, The University of Melbourne, Australia. My article was written in the days when intelligent [sic] design advocates were still hoping to get away with pretending ID was real science, not fundamentalist Christianity in disguise.

How The Eel Was Designed

The European Eel, Anguilla anguilla

The European Eel (Anguilla anguilla) is a wonderful example of how God, sorry, the Intelligent Designer works.

One day the Intelligent Designer decided to make a strange creature that looked like a snake, but which lived in water like a fish. He used gills like he had used for other fish so they could breathe in water and which He had decided not to use for some other animals which live in water, like seals, whales and turtles and He decided to include some small scales on their skin which don't seem to have any purpose because he designed them with a tough, slimy skin, but obviously these scales weren't there by accident.

But His most brilliant idea was how they were going to breed. He made it so they needed to spend many years living in rivers and lakes and places like paddy fields and even sewers to put on enough weight so they could go on a very long journey across the Atlantic all the way to the Sargasso Sea near America to lay their eggs, so the young eels have to travel all the way back to Europe again. This is obviously much more sensible than just laying their eggs in the rivers where they live, like most other fish do.

To make this journey, He designed eels so that, come the time for breeding, they strip their bodies down to the bare essentials - basically just the equipment for swimming, a large store of fat for the journey and a pair of gonads for reproducing. They have to take up to fifteen years getting fat enough before they do the journey and then they digest their own digestive system to make themselves lighter. This is obviously much better than needing to bother with eating on the journey through an ocean teeming with the sort of food they had been eating in the rivers they grew up in. As any experienced back-packer will tell you, it's obviously much better to be really big and fat before you start a long journey to save you having to bother eating on the way, and then doing away with your digestive system to make you lighter.

In fact, He brilliantly designed them to look like you would expect if they had once been sea-living at a time when their spawning ground was much closer to Europe but now someone had moved it all the way to America as though they were moving the sea bed around. The fact that very many of them don't survive the journey to the Sargasso Sea is all part of the plan obviously because this ensures that only those best at swimming to the Sargasso Sea get rewarded with breeding - and you can't say fairer than that.

He also made sure that they have no hope of ever returning once they've spawned because they can't eat and have used up all their fat, and He had another brilliant plan for them to go to all this trouble so most of their offspring would be eaten by other things on their journey back to Europe just as though their real purpose was to be food for other creatures.

Then, in a brilliant final move, the Intelligent Designer had the brilliant idea of designing a parasitic nematode worm which used to live only in a Japanese relative of the European eel but which He has now changed slightly so it now infects 80-100% of European eels, making it difficult for them to use the swim-bladders he had given them to make swimming easier, so the European eel is now an endangered species, as the number of young reaching Europe from the Sargasso Sea is down to a mere 2% of its former numbers in some places. But then who wants a lot of those ghastly slimy eels around, eh?

You have to hand it to God the Intelligent designer when He can come up with designs like that, don't you. Obviously, nothing like that could be produced by a mindless, natural, undirected, purposeless process like that silly Charles Darwin invented.

Now for Dr. Soanes' article, reprinted here under a Creative Commons license, reformatted for stylistic consistency. The original article can be read here:

Creationism In Crisis - How Hominins Spread from Central Asia Hundreds of Thousands of Years Before Creationists Believe Earth Was Created

Central Asia Identified as a Key Region for Human Ancestors | Cleveland Museum of Natural History

Fig 1. The study region.
A map of Central Asia derived by the authors using data for annual precipitation (Worldclim [14]), surface water [15], and rivers (Hydrosheds [16]). The study region (encircled with black line) is shown with the region of Caspian catchment (enclosed with red line). Key mountain ranges, deserts, and bodies of water are labeled. The location of Amir Timur Cave that hosted stalagmite S-12-4 analyzed in this study is shown as red circle.

Source

According to new research findings published in PLOS ONE, central Asia around the Aral Sea, East of the Caspian Sea, was the probable point from which early hominins spread across Eurasia, having migrated north out of Africa and settled in the now semi-arid steppes which were then periodically suitable for human habitation.

The study was conducted by a team led by Dr. Emma Finestone, Assistant Curator of Human Origins at the Cleveland Museum of Natural History and Research Affiliate of the Max Planck Institute for the Science of Human History and which included Dr. Paul Breeze and Professor Nick Drake from Kings College London, Professor Sebastian Breitenbach from Northumbria University Newcastle, Professor Farhod Maksudov from the Uzbekistan Academy of the Sciences, and Professor Michael Petraglia from Griffith University in Queensland, Australia.

The team presents compelling evidence that this now arid area of Central Asia had periods when local climate change meant it was suitable for hominin occupation and that the record of flint tools patterns coincides with the evidence of this climate change obtained from stalactites in local caves.

According to a news release by Cleveland Museum of Natural History:

Creationism in Crisis - How New DNA Functions Can Evolve With No Change in the Amount of Genetic Information

Butterfly wing patterns emerge from ancient “junk” DNA | Cornell Chronicle

Wings of the painted lady butterfly, Vanessa cardui, modified by deletion of non-coding DNA sequence.

Credit: Anyi Mazo-Vargas

This may come as a shock to devoted followers of the Creationist cult, but not to those leading Creationist frauds who specialise in misleading their credulous followers and understand full well that what they claim is designed to mislead and misinform, but scientists working at Cornell University have discovered that non-coding DNA modified from former 'junk' DNA, has a regulatory influence on how the genes which control the markings and colours on some butterflies wings express.

Creations have been conditioned to believe that there is no such thing as junk DNA since it all codes for something and that any change in function must involve an increase in the amount of genetic information (because a loss of information is always deleterious). Junk DNA is of course an embarrassment for Creationists as it belies the notion of intelligent design, and |Creationist dogma now says any mutation is detrimental because it moves the organism further away from the assumed initial perfection of magic creation, the ‘sin’ of ‘The Fall’ having caused ‘genetic entropy’.

Anyone working in the field of genetics will know both these beliefs are nonsense and not supported by the evidence because there are countless examples of advantageous mutations involving a simple substitution in a DNA codon where the number of codons remains the same, yet the meaning of the information changes. There are also countless examples of junk DNA which can be removed without loss of function, because even if the DNA in question is transcribed into messenger RNA (mRNA), it does not result in an active protein being produced.

In the case of butterfly wing patterns, however, the controlling DNA doesn't even code mRNA. The researchers found that it acts like switches that can turn on or off a basic ground plan of markings, turning up some patterns and down others. In this way, evolutionary change can be rapid with small changes to this non-coding, regulatory DNA.

As the Cornell Chronical explains:

Creationism in Crisis - How Evolution Correlated with Changing Atmospheric Oxygen Levels

Dynamic oxygen levels may have accelerated animal evolution  | University of Leeds

Credit: Dr Emily. G. Mitchell – University of Cambridge.

An essential part of the Theory of Evolution is that environmental change should be reflected in evolutionary change in taxons because a changing environment is the main driver of evolution. So, if the TOE was wrong and Creationism was a better explanation for biodiversity, we would expect to see no connection between major environmental change and evolutionary change. Indeed, if Bible literalist Creationism were correct, we would not expect to see any evidence of major environmental change even, since this evidence-free superstition is that a magic deity created everything as it is today.

And yet, a research team at the University of Leeds supported by the Universities of Lyon, Exeter and UCL, has found evidence that early animals evolved on Earth in response to wildly fluctuating atmospheric oxygen levels, and in particular during the period following the 'Great Oxidation Event' which occurred some 2 billion years ago when the cyanobacteria evolved photosynthesis and began polluting the atmosphere with the process's waste product, oxygen.
In between, that and the third step about 200 million years ago when atmospheric oxygen reached todays level, there was a second step during the 500 million-year long Neoproterozoic Era which began about 1 billion years ago. Until now, what happened during that period when early forms of animals appear in the fossil record, was something of a mystery. It was during this era that the earliest multicellular life forms, Ediacaran biota, made their appearance.

As the Leeds University News release explains:

Creationism in Crisis - How The 'Designer' of Photosynthesis Tried to Improve It's Mistake and Failed Again

Back to the future of photosynthesis | Max-Planck-Gesellschaft

A 3d cartoon depiction of the activated RuBisCO from spinach in open form with active site accessible. The active site Lys175 residues are marked in pink, and a close-up of the residue is provided to the right for one of the monomers composing the enzyme.

Credit: Ericlin1337 - Own work CC BY-SA 4.0, Link

Evolution, of course, doesn't have an intelligent designer because it's a purely natural, non-sentient process involving nothing more that the operation of chemistry and physics in a selective environment. However, Creationists insist that nothing happens without god-magic and the involvement of a sentient directing entity, even though the existence of such an entity has never been demonstrated or explained, and there are no authenticated accounts of it ever making anything happen that couldn't have happened without it.

So, let’s look at the evolution of photosynthesis and especially the essential enzyme RuBisCo and the implications of recent research by a team from the Max-Planck-Institute for Terrestrial Microbiology in Marburg, Germany in collaboration with scientists from the University of Singapore.

Order From Chaos in Space - Science Exlains it

An alien magastructure?
Surely there must be an intelligence behind such an ordered structure! Read on!

Left: false-colour JWST/MIRI Imager observations of WR 140 taken with the F770W, F1500W and F2100W filters that correspond to blue, green and red, respectively. Eight symmetric diffraction spikes are seen around the saturated core of WR 140 (at the origin) that exhibit bluer colours than the dust emission. Right: JWST/MIRI MRS spectral data cube images of WR 140 from Channel 2 at 8.01 μm taken at two different positions that cover the central binary and shell 1 (Offset 1, top) and shells 1 and 2 (Offset 2, bottom) shown in a square-root stretch. The central binary and bright dust emission features are labelled in the MRS data cube images.

Alien megastructures? Cosmic thumbprint? What's behind a James Webb telescope photo that had even astronomers stumped

One of the Creationist cult's articles of faith is the demonstrably false assertion that you can't get order from chaos, although how they imagine raindrops form, or even more subtly, how an internal combustion engine works without the operation of the gas laws which are emergent laws from the chaotic mass action of gas molecules, is anyone's guess.

A moment's thought should tell them that, with a directional force involved, there can be no such thing as true randomness in nature. One such force is of course gravity which turns a cloud of randomly distributed gas particles into an ordered sun and maybe a planetary system. Another example is the process of natural selection which gives a non-random progress towards assorted genes in a species from the random occurrence of genetic mutations.

And here is yet another example of structure emerging naturally from chaotic dust particles in an article from The Conversation by Professor Peter Tuthill, an Astrophysicist at the University of Sydney, NSW, Australia. The article is reproduced here under a Creative Commons license, reformatted for stylistic consistency. The force in this instance is the complex pattern of gravity generated by two stars in elliptical orbit around each other in a binary system and the intense solar winds each gives off which drives regular pulses of dust from their surfaces.

The original article can be read here:

Unintelligent Design - The Daft Design for Bioluminescence in a Squid

Symbiotic Organs: Extreme Intimacy with the Microbial World | TS Digest | The Scientist

Hawaiian bobtail squid, Euprymna scolopes

Imagine for a moment that you are an intelligent designer, and your task is to provide a squid with bioluminescence - something you've done hundreds, even thousands of times in other species by giving them special enzymes and substances called phosphors. What would you do?

Well, if you’ve got any sense, you would adapt one of the hundreds of tried and tested processes you used in other species, wouldn't you? That would be the intelligent thing to do and would mean minimal complexity and maximal simplicity - two of the hall marks of good design (actually two sides of the same coin since you can't have one without the other).

But not if you're Yahweh, the creator god of the Creationist cults - the one they call an intelligent designer - a misnomer, as we shall see.

Creationism in Crisis - Darwin's Finches Provide More Evidence for Speciation by Evolution

Widespread variation of inherited retroviruses among Darwin’s finches - Uppsala University, Sweden

A total of 293 Darwin’s finch samples representing 18 species, 4 hybrids and 2 outgroup species (Loxigilla noctis and Tiaris bicolor) from 16 islands^6,9,10,11 were included in the study. Island names are indicated above finch species, hybrids and their respective sampling sizes. Finch species abbreviations: Big Bird lineage (Geospiza fortis x Geospiza conirostris), C. fus (Certhidea fusca), C. hel (Camarhynchus heliobates), C. pal (Camarhynchus pallidus), C. par (Camarhynchus parvulus), C. pau (Camarhynchus pauper), C. psi (Camarhynchus psittacula), C. oli (Certhidea olivacea), G. acu (Geospiza acutirostris), G. con (Geospiza conirostris), G. dif (Geospiza difficilis), G. for (Geospiza fortis), G. ful (Geospiza fuliginosa), G. mag (Geospiza magnirostris), G. pro (Geospiza propinqua), G. sca (Geospiza scandens), G. sep (Geospiza septentrionalis), Hybrid ff (Hybrid G. fortis x G. fuliginosa), Hybrid ffs (Hybrid G. fortis x G. fuliginosa x G. scandens), Hybrid fs (Hybrid G. fuliginosa x G. scandens), L. noc (Loxigilla noctis), T. bic (Tiaris bicolor), P. cra (Platyspiza crassirostris), P. ino (Pinaroloxias inornata).

This is the sort of research that should send any dedicated Creationist into a rage, and frantically scouring their armoury of techniques for coping with cognitive dissonance, if only they understood enough of the subject to realise its implications.

It's an account of how Darwin's finches were used as the basis for showing how the Theory of Evolution can explain the presence and differences in the remnants of ancient retroviruses in the genome of those finches that inspired Charles Darwin to formulate the Theory of Evolution all those years ago.

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:

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?

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 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.

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 - 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.

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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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