F Rosa Rubicondior: Parasitism
Showing posts with label Parasitism. Show all posts
Showing posts with label Parasitism. Show all posts

Monday 11 March 2024

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


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

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

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

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

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

But first, a little background on Wolbachia:

Saturday 9 March 2024

Creationism in Crisis - How Genomic Imprinting Evolved - Unintelligently


Revealing the evolutionary origin of genomic imprinting 
Caenorhabditis elegans

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

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

But the reason for genomic imprinting involves something even more embarrassing to any creationists who understand it - it probably evolved out of an arms race not between the organism and a foreign parasite but between the organism and one of its genes that had gone rogue and turned into a 'jumping' gene or 'selfish genetic element':
What exactly are 'selfish genetic elements' and what do they do? Selfish genetic elements are DNA sequences that have evolved to enhance their own transmission to the next generation, often at the expense of the organism's overall fitness. These elements can manipulate various cellular and reproductive processes to increase their own propagation within a population, sometimes even if it is detrimental to the host organism.

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

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

Selfish genetic elements can have significant implications for evolutionary processes, population genetics, and genome stability. They can influence patterns of genetic diversity, contribute to speciation, and even drive the evolution of complex biological systems. However, they can also pose challenges for organisms by causing genetic disorders or reducing overall reproductive success.
In the case of the nematode, Caenorhabditis elegans, this arms race has produced a truly bizarre result, and something only an unintelligent, mindless designer, or a malevolent designer, could come up with, known as toxic ascaris, or TAs:

Saturday 2 March 2024

Unintelligent Design - The Heath-Robinson Workaround For A Design Fault In The Immune System


The “switch” that keeps the immune system from attacking the body - EPFL

A Machine for Testing Golf Drivers - William Heath-Robinson
A characteristic of designs by creationism's putative intelligent designer, is the needless complexity which often arises because earlier solutions were suboptimal and either didn't work very well or tended to cause problems that needed to be mitigated with another layer of (often suboptimal) complexity.

This is also a characteristic of systems 'designed' by a mindless natural process with no power or mechanism for scrapping a suboptimal design and starting again and no ability to predict the future and design for problems which will arise later.

In fact, what creationists think is evidence of a supreme intelligence, more often seems to resemble the designs of the British cartoonist and eccentric designer, William Heath-Robinson, who was famous for his machines designed to solve every-day problem, which were invariably far more complex than they need have been, and which incorporated everyday objects such as umbrellas, full coal-scuttles for counter-weights, lengths of knotted string and stepladders balanced on upright pianos to give them enough height. Take away any of these unlikely components and the whole machine would fail, in an almost perfect metaphor for how evolution can exapt pre-exiting structures from other processes and structures for novel functions, to give the appearance of irreducible complexity.

And yet they work, or at least look as though they would if anyone ever made one.

An example of a Heath-Robinson machine in mammalian 'design' was revealed by a scientists working at the Swiss École polytechnique fédérale de Lausanne (EPFL), who have discovered how the body prevents the immune system from attacking itself.

But, as the very many auto-immune diseases show, this system is far from perfect and frequently fails, sometime with serious, even fatal, consequences.

But the whole immune system is only needed because something designed pathogens such as bacteria, viruses and other parasites, apparently to attack us and make us sick in the first place. Parasites are a source of conflict for creationists who have to believe both that the putative designer god is the only entity capable of designing living things, and that something else created parasites because their god wouldn't do such a thing, and both that their god is omnipotent, but powerless against that other designer.

So, what is this mechanism the EPFL researchers have discovered?

Their findings are the subject of an open access paper in Nature and is explained in an EPFL news release:

Friday 1 March 2024

Malevolent Designer News - How Creationism's Divine Malevolence Is Adapting The Avian Flu Virus to Kill Marine Mammals


Avian Influenza Virus Is Adapting to Spread to Marine Mammals | UC Davis

Elephant seals lie dead on a beach in Argentina following an outbreak of avian influenza in the region.
Photo: Maxi Jonas.
As an example of creationist double-think and intellectual bankruptcy, their attitude toward parasites like viruses is a classic:
  • "Only God is capable of designing organisms, so "Look at the trees!" and "What about irreducible complexity?"
  • "Something else created parasites like bacteria, worms and viruses, because God wouldn't do something like that!"

Simultaneously committing blasphemy and refuting their own argument from teleology!

I wonder then how that rarest of animals, the intellectually honest creationist copes with the news that the creator of the avian flu virus, H5N1, is in the process of adapting it to kill marine mammals such as elephant seals, just as it adapted the SARS-CoV-2 virus from a bat virus to one that could kill humans and cause economic collapse.

Evidence that it is doing so, if you believe viruses are created and don't evolve naturally, which dogma forbids a creationist from believing, comes in the form of a study by scientists from University of California, Davis, and the National Institute of Agricultural Technology (INTA) in Argentina. The study, the first genomic characterization of H5N1 in marine wildlife on the Atlantic shore of South America, is published in the journal Emerging Infectious Diseases and is described in a UC Davis news release:

Tuesday 27 February 2024

Malevolent Designer News - How Creationism's Favourite Sadist May Use Climate Change To Increase The Suffering In The World


Parasitic worms cause huge economic loss to farmers and can infest humans too.
Temperature, humidity may drive future transmission of parasitic worm infections | Penn State University

Creationists who believe nothing happens unless their invisible magic god wants it to have to have all manner of intellectual gymnastics to avoid giving it credit for all the nasty things to be found in nature, such as parasitic worms.

Their favourite strategy is the old trick of believing two mutually exclusive ideas simultaneously - that only their god is capable of designing living systems, so anything too complex for them to understand must have been created by it, whilst simultaneously believing that all pathogens are created by another entity, called 'Sin', no matter how complex or difficult to understand they may be.

And of course, they are forbidden by dogma to believe in more than one creator and must believe, also by dogma, that that creator is omni-everything - omnibenevolent, omniscient and omnipotent - so they have to believe that whatever its designs do, they were designed to do it, and whatever the future may bring, they were aware of that whilst designing their creations.

What percentage of the surface of Earth is habitable to humans without special equipment? Approximately 29% of the Earth's surface is comprised of land, which is habitable to humans without special equipment. The remaining 71% is covered by water, primarily in the form of oceans, which generally require specialized equipment for prolonged habitation. Therefore, without considering other factors such as climate, terrain, and resources, roughly 29% of Earth's surface is habitable to humans without special equipment.
That means, creationists have no choice but to accept that the results of climate change were part of their designer creator's plan, as was the response of their creations to it. And one of those responses to climate change may be an increase in parasitic worms in parts of the world they have not been prevalent in before.

Many of these worms are, or have been, confined to the tropics and sub-tropical zones, and the northern and southern part of the world, where most advanced economies are based, have been relatively free from them. But, as Earth gets warmer, the 'habitable zone' for parasitic worms expands to incorporate more of the advanced economies, but the habitable zone for humans shrinks even further.

This is the prediction of a team of researchers from the Center for Infectious Disease Dynamics and Department of Biology, The Pennsylvania State University (PennState), Pennsylvania, USA, and Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milano, Italy, led by Professor Isabella Cattadori and Dr. Chiara Vanalli of PennState, who have just published their findings, open access, in the journal Ecology Letters. Their work is explained in a PennState news release:

Wednesday 24 January 2024

Malevolent Designer News - How Bacterial Pathogens Are Cleverly Designed to Invade Their Victim's Body


Functional model for Yen-Tc toxicity. Following ingestion of the Tc, it is likely that the surface-bound chitinases bind to and/or degrade the chitin-rich peritrophic membrane of the insect midgut. Cell surface recognition is likely facilitated by motifs within the A subunits prior to internalization. Similarities to the well characterized bacterial binary toxin systems (e.g., anthrax, cholera, diphtheria) suggest a mechanism involving receptor-mediated endocytosis followed by pore formation and translocation of the B and/or C components into the cytosol (I), although alternative mechanisms (e.g., II, III) cannot be ruled out.

Landsberg, MJ., Jones, SA., Rothnagel R., et al (2011)
24-01-18 | Max Planck Institute of Molecular Physiology

Imagine you're in charge of an invading army laying siege to your enemy's outer defences. How do you neutralise them?

One way would be to send a small group of soldiers, packed with high explosives and deadly toxins on a kamikaze mission into the defences, with instructions to detonate their explosives and so spread the toxins when inside to destroy the defences and kill the defenders. You could improve on that by removing any temptation the suicide bombers might have to not detonate their defences by automating the trigger to fire as soon as they encountered the defender.

That's exactly what a team at the Max Planck Institute for Molecular Physiology (MPI MOPH), Dortmund, Germany, have found bacteria use to gain access to their victim’s body and make their hosts sick and die. The team, led by Stefan Raunser, Director of MPI MOPH, have published their findings, open access, in Nature Microbiology. Their work is described in a MPI MOPH press release:

Sunday 21 January 2024

Creationism in Crisis - When Creationists Believe The Universe Was Being Made From Nothing, People Were Chewing Gum and Eating Trout, Deer And Nuts In Scandinavia


The plastelina casts for one of the chewing gums from Huseby Klev. The cast captures the teeth imprints from each side.
Photo: Verner Alexandersen.
Ancient chewing gum reveals stone age diet - Stockholm University

How could the Bible's authors possibly have known what people were doing in Scandinavia when they didn’t even know where Scandinavia was because they thought Earth was a small flat place with a dome over it to keep the water above the sky out, centred on the Middle East?

The answer is that they couldn't of course. Had they done so, they would have concocted much less parochial tales about the things they didn't understand and would have known that Earth was much older than the few thousand years they imagined.

But now we know much better than they did. For example, modern science is able to take the resin people were chewing on (probably to make glue from it) and analyse the DNA in it to see what they had been eating and what organisms they had living in their mouths. It turns out that just about the time when the Bible's authors were setting their creation tale, people in Scandinavia were eating trout, deer and hazelnuts, and suffering from pathogenic bacteria, oblivious of the creation allegedly going on far away in the Canaanite Hills.

Although creationists now tell us that pathogens and other parasites didn't exist before the supposed 'Fall' and must have been made since by a thing called 'Sin', there is no biblical support for this modern invention which has been hurriedly cobbled together to defend the alleged creator god from the charge of malevolence in the design of pathogens which do nothing other than make more copies of themselves and add to the suffering in the world.

Embarrassingly for those creationist apologists, the same study presents compelling evidence of commensal and pathogenic organisms in the mouths of these Scandinavians, just as there are today in modern humans, including bacteria that cause teeth to fall out.

How scientists discovered this is the subject of an open access paper in Scientific Reports and a news release from Stockholm University:

Monday 1 January 2024

Unintelligent Design - Another Ludicrously Complex Arms Race, This Time Between Plants And A Predatory Fungus


Discovery: plants use “trojan horse” to fight mold invasions | News Running epigenetics a close second for the most obvious evidence on unintelligent design in nature is the ubiquitous arms race; Arms races are a major component of evolutionary biology, easily understandable in terms of evolution by natural selection. One organism (call it Organism A) predates on, or parasitises another (call it Organism B); this creates an advantage for Organism B in avoiding being eaten of serving as the host of Organism A, so any functional defense mechanism is selected for by natural selection. This in turn creates an advantage for Organism A to evolve a mechanism for overcoming Organism B's defences, and so on until a state of equilibrium is achieved in which either one or the other organism is no longer able to evolve further.

This can lead to some extreme adaptations such as the stupidly long neck and legs of the giraffe which is a response to acacia trees evolving longer trunks to place their leaves, flowers and seeds beyond the reach of giraffes. In the process, acacia trees need to produce masses of cellulose to build the trunk and pump water much higher against gravity than if they were low-growing bushes, and giraffes have to maintain a very high blood pressure to keep their brain supplied with oxygen while drinking water places them at risk of predation by lions because they can't stand up and raise their heads quickly or they will lose consciousness. And they need the additional complexity of special valves in their neck veins to maintain a high blood pressure to their brain.

Now, take away acacia trees (imagine a sudden virus that wipes them out) and the giraffe is no longer superbly adapted for its environment; instead, it is severely handicapped, and might even find feeding from an alternative source difficult.

Another arms race can be seen at the moment is where the SARS-CoV-2 virus is evolving new variants every few months in response to growing herd immunity in its hosts, the human population, due to vaccinations and sub-lethal infections. The virus is getting better at evading our antibodies for long enough for us to pass on the infection to someone else and is tending to be less lethal, so we survive to infect others, even being asymptomatic. Gradually the virus will evolve to become a relatively mild infection that most of us will catch as often as we catch the common cold, and only especially vulnerable people will be made seriously ill by it.

These are just two examples of hundreds of similar arms races in nature; there are even arms races between sexes of the same species as females evolve strategies to retain the ability to only mate with a male of her choice, while males evolve strategies to deprive her of that ability.

But how on Earth can this be explained in terms of design by a single designer, or, including the creationists fallback excuse for parasites, two designers - their supposedly omnipotent, omniscient god and 'Sin'? Would not an omnipotent, omniscient god know in advance what Sin's next response would be and create a design that it couldn't overcome, so an arms race never started in the first place? Or are we to believe that creationism’s god and this 'Sin' thing are equal in all things yet able to conceal their next move from something all-knowing, but powerless to stop its rival? In other words, neither omniscient nor omnipotent.

The notion of intelligent design is quite simply incompatible with the evidence of arms races, for which evolution provides a ready answer.

I have devoted the whole of chapter 3 to arms races in nature in my popular, illustrated book, The Unintelligent Designer: Refuting The Intelligent Design Hoax, but what it doesn't include is this recently discovered arms race between plants and a parasitic fungus, Botrytis cinerea, or gray mold.

Thursday 28 December 2023

Malevolent Design - How A Cat Poo Parasite Can Change Your Personality


Toxoplasma gondii is an obligate intracellular, parasitic protozoan that causes the disease toxoplasmosis. Diagram of Toxoplasma structure.
Image Credit: Designua / Shutterstock
Toxoplasma 'cat poo' parasite infects billions – so why is it so hard to study?

In my last blogpost, I described how the parasitic organism, cryptosporidium, is one of those 'irreducibly complex' organisms that creationists have been fooled by Michael J Behe into believing are proof of their putative creator god, because, so their ignorant intuition tells them, there can only be one intelligent designer capable of designing an irreducibly complex structure such as the bacterial flagellum or the apical complex structure that all members of the Apicomplex phylum characteristically possess.

Sadly for them, though, their reliance on this 'proof' of their god precludes them from arguing that these nasty little pathogens that appear to be designed to make us and other animals sick is the work of another intelligent creator, 'Sin', so the inescapable conclusion must be that their beloved creator god is designing these pathogens to make us sick and to increase the suffering in the world.

As though that wasn't bad enough, we now have another related parasite, also a member of the Apicomplex phylum, that on the face of it, seems to be an even more determined attempt to make us sick. It's a parasite that once you have it, you have it for life, and the evidence is that it manipulates your behaviour and changes your personality too. This then raises doubts about the idea of free will that is a central part of creationist superstition, and notions of 'Original Sin' (that thing that can supposedly create parasites too).

This organism is Toxoplasma gondii which is carried by about 25% of the world's people, so the chance of you or me or any of your friends and family having it is quite high.

Wednesday 27 December 2023

Malevolent Design - More Nastiness From The Pestilential Designer, Or God, As Creationists Call It


Infections from a diarrhoea-causing parasite are on the rise in the UK – but experts aren't quite sure why

Cryptosporidium is a eukaryote protozoan parasite which creationists dogma says must have been designed by their favourite designer because that is the only entity capable of designing complex organisms, including 'irreducibly complex' structures.

Embarrassingly for creationists who are hoping to be able to blame 'Sin' for them, they are hung out to dry on the same hook that Michael J. Behe hung them on with the flagellum of the pathological E. coli bacterium, which they now happily wave as 'proof' of their designer good. Protozoans of the Apicomplexa phylum, of which the cryptosporidia are species, all have the apical complex organelle which is essential for them to break into a cell in order to infect it.

The characteristic apical complex organelle of the Apicomplexa phylum
Cryptosporidia appear to have two functions: to increase the suffering in the world by causing gastrointestinal disorders, usually resulting in severe diarrhoea; and to make more copies of themselves to infect more people and animals and spread the suffering more widely. They have no known beneficial functions in respect of humans or their other host species.

The species Cryptosporidium hominis is an obligate parasite on humans, so, according to creationists superstition, must have infected one or two of the Ark survivors, assuming there were no more than two individuals of the species present. Either that, or, according to creationist mythology, it has been created in the last four thousand years, which rules out being created by 'Sin' as a result of 'The Fall', which would mean it predates creationism's genocidal flood.

First, some AI background by way of introduction to the subject:

Monday 25 December 2023

Malevolent Design - Parasitic Mistletoe - Unintelligent Design, Malevolent Creation Or Evolution?


Mistletoe haustorium on a birth branch.
At a time of giving and receiving, our many Australian mistletoes do it too

Mistletoe is a hemiparasitic plant and obligate parasite on many different species of tree. It can kill a heavily infested tree. Although mistletoe is photosynthetic, so produces its own sugars, it is dependent on its host for water and the nutrients such as nitrates and other minerals that the host plant obtains from soil. There is no evidence that mistletoe gives anything back to the host in the form of sugars.

Mistletoes and similar parasitic plants obtain the nutrients from their host via a structure called a haustorium which infiltrates the host tissues and forms a close association with the vascular bundles.

But why would an intelligent designer create all the complexity needed for a parasitic lifestyle when it had supposedly designed other plants to obtain nutrients from the soil, and simply added another layer of complexity between the host's roots and the parasitic plant's tissues to achieve the same result? In fact, this is just another example of the needless complexity that characterises evolved systems and distinguishes them from intelligently designed systems, which are characteristically minimally complex.
And it hasn't just done it once! There are over 100 parasitic species of similar plants in Australia alone, which I'll come to next, but first, a little AI background on mistletoe:

Thursday 7 December 2023

Unintelligent Design News - How A Badly Designed Protein Causes Autoimmune Diseases


William Heath Robinson
Fungus-fighting protein key to overcoming autoimmune disease and cancer | Australian National University

The more you learn of creationism's putative intelligent [sic] designer, the more like William Heath Robinson it becomes.

The main difference is that, no matter how ramshakled they were, William Heath Robinsons inventions actually worked, even if they didn't produce the required result. The same can't be said for creationism's god's designs. They resemble piecemeal designs where each part is designed in isolation in response to a problem, often a problem somewhere else in the design, where near enough is good enough and there is no joined up thinking.

Rather like a William Heath Robinson machine, conbbled together from disparate parts, but where when a knotted piece of string breaks, instead of replacing it with a new piece of string or tying the broken ends together, like Heath Robinson would, a different, weaker sort of string is designed and tied across the broken ends, but then that keeps breaking too.

An example of this inept design was discovered recently and found to be the cause of autoimmune diseases such as iritable bowel syndrome (IBS), type 1 diabetes, eczema and other chronic disorders. The problem is with a protein called DECTIN-1 (also known as CLEC7A) which is producd by the immune system in response to fungal infections. Researchers at The Australian National University (ANU) have discovered that a mutated form of DECTIN-1 limits the production of T regulatory cells or so-called ‘guardian’ cells in the immune system.

Mutations arise, of course, because of another poor design - the process for replicating DNA, which is so prone to errors that another mechanism for repairing it is needed. However this is also prone to errors, the result of which means that many of our cells carry mutations, some of which cause cancers.

The research is publshed in Science Advances and ex[lained in an Australian Nationa University News release:

Wednesday 6 December 2023

Malevolent Designer News - How A Bacterium Is 'Intelligently Designed' To Turn Plants Into Zombies


The Life Cycle of a 26S Proteasome.

From Infamy to Ingenuity – Bacterial Hijack Mechanisms as Advanced Genetic Tools | John Innes Centre

Scientists working at the John Innes Centre, Norwich, Norfolk, UK., have worked out the sneaky way a bacterium converts an internal cell mechanism in plants to suit its own purpose at the expense of the host, in another example of how a parasite can zombify its host.

Creationists looking at this mechanism from the arrogant perspective that sees their own ignorant incredulity as scientific data, would conclude that it must be intelligently designed, but would then need to perform intellectual summersaults to explain why, even though their own putative creator god is the only supernatural entity capable of designing complex living organisms, something called 'Sin' also creates complex living organisms, so their omnipotent god is not responsible for parasites.

The parasitic Phytoplasma bacterium is transmitted by insects and causes diseases like Aster Yellows, significantly diminishing yields in leaf crops including oilseed rape, lettuce, carrots, grapevines, onions, and a variety of ornamental and vegetable crops worldwide. It is also responsible for the familiar 'witches' brooms' in trees in which the plant produces a proliferation of thin branches and leave.

How it does this is explained in an open access research paper in PNAS. It does it by hijacking the protein recycling function of a cell organelles, the 26S proteasome, so first a little AI background about the 26S proteasomes:

Unintelligent Design - Or Is It Malevolence? How Bacteria Are Designed to Exploit Our Mucus


Movement of mucus in the respiratory tract

Bacteria's mucus maneuvers: Study reveals how snot facilitates infection | Penn State University

The mucous membrane lining our respiratory system has evolved (or, according to creationists, been intelligently [sic] designed) to keep our respiratory system clean as we breathe in air containing particles of dirt, dust, pollen and bacteria. It does this by secreting mucus that traps the particles, then ciliated cells on the surface sweep them towards our pharynx to be swallowed and disposed of in our digestive system where the proteins in the mucous are recycled.

Other body cavities are lined by a mucous membrane that serves to protect and keep the cavity moist and lubricated.

But, in one of those research papers that creationists have to avoid reading, a team of researchers from Penn State University, have shown how bacteria have evolved (or been intelligently [sic] designed, according to creationists) to exploit the mucous, the better to infect us and make us sick, and the thicker the mucus, the better it is for these would-be pathogens.

Infections by bacteria, known medically as opportunist infections, especially in the nasal sinuses and lungs, are a frequent complication of viral infections such as a common cold or influenza. These opportunist infections can be more dangerous than the virus infections that facilitate them.

The team showed that bacteria find it easier to swim, swarm and form colonies in thick mucus than in thin, watery mucus and that this swarming probably helps protect them from the antibacterial enzymes in the mucus.

Their research is explained in a Penn State news release:

Creationism in Crisis - A Monster Virus Is A BIG Problem For Creationists


Pithovirus sibericum
Pithoviruses Are Invaded by Repeats That Contribute to Their Evolution and Divergence from Cedratviruses | Molecular Biology and Evolution | Oxford Academic

Regular readers with very long memories may remember how I wrote about something big and potentially nasty emerging from Siberian permafrost back in 2014.

The 30,000-year-old monster in question was a form of giant virus then unknown to science, now named Pithoviruses sibericus. It came back to life when thawed. Since then, several other related pithoviruses have been discovered in soil and aquatic sources. Fortunately, all those discovered so far are parasitic only on one species of amoeba, Acanthamoeba castellanii and don't pose a threat to humans or multicellular life.

The question was, why are they so large, or more particularly, why do they have such a massive genome, including some genes normally found in complex cells. the Pithovirus species so far discovered have a genome of between 460 to 686 kb. Their genome, moreover, is similar to that of bacteria and archaea, in that it is DNA-based and forms a single circular 'chromosome'.

But it's not the fact that the first one was found in permafrost dating back 20,000 before 'Creation Week', difficult though that little inconvenience is for creationists; it is the account of how they acquired this massive genome that is the thing of nightmares for any creationists who understand the biology.

They acquired it by processes that give the lie to their basic dogma that new genetic information can't arise in a genome without 'God magic'.

A team of researchers have shown that they acquired new genetic information and such a massive genome by:
  1. Horizontal gene transfer (5% -7 %)
  2. Gene duplication (14% - 28%)
  3. Massive inversions of repeated sequences of DNA.
All these are familiar mutations in which the genome size is increased, and by which 'spare' copies of genes and novel sequences are free to mutate and give rise to new genes and new functions.

And this gives the lie to the ludicrous creationist dogma that no new information can arise by mutation because all mutations are deleterious. There is nothing deleterious in having a spare copy of a gene, nor in mutations in that spare copy, least of all if it gives a new function that increases fitness.

The researchers, from the Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix–Marseille University, Centre National de la Recherche Scientifique, Marseille, France were led by Matthieu Legendre. Their findings are published, open access, in Molecular Biology and Evolution:

Saturday 2 December 2023

Malevolent Design News - How 'Intelligently Designed' Pathogens Use The Tactics Of A Burglar To Make Us Sick



Pathogens use force to breach immune defenses, study finds: IU News

Creationists trying to defend their magic creator god argue that it didn't create pathogenic parasites and instead blame it on 'Sin'. Sadly for them, however, one of their leading cult gurus, Michael J. Behe, has pulled that rug from underneath them by writing a book in which he used the supposedly irreducibly complex flagellum of a common pathogen, Escherichia coli (E. coli) to argue that it must have been intelligently designed, (so God did it!). Behe's book, 'Darwin’s Black Box' is constantly being cited as 'proof' that the reputedly omniscience, omnipotent creator god of the Bible and Qur'an is real and creates things.

So, let's go with their 'proof of God' argument and assume therefore that pathogens are the intentional design of their putative designer god and were designed for the function they perform - making us sick, while producing more copies of themselves to make others sick too.

Now a team of researchers have shown the lengths this alleged designer god has gone to to continue making us sick and suffer. The team, led by Professor Yan Yu, of the College of Arts and Sciences’ Department of Chemistry, Indian University, Bloomington, IN, USA have shown that the intracellular pathogens like Toxoplasma, tuberculosis, malaria and chlamydia don't use subtlety to gain entry into the cell, probably because this would provoke an immune response as our immune system, allegedly designed by the same intelligent designer to protect us from the pathogens it designed to harm us, tried to fight back. Instead, they use brute force to break into the cell and once inside use the same force to break into a cell vacuole where they are protected by the internal cell membranes.

How the research team which included Professor Yan Yu's colleagues from Indiana University with Thomas K. Gaetjens and Steven M. Abel of the Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, USA, made this discovery is explained in an Indian University new release:

Tuesday 21 November 2023

Creationism in Crisis - Which Side Should a True-Believing Creationist Be On? The 'Designer' Who Designs Resistance Or The Scientists?


Diagram of the complex eukaryote, Plasmodium falciparum
New approaches in the fight against drug resistance in malaria | FAU Erlangen-Nürnberg

Despite asking creationists multiple times how they reconcile believing that their putative intelligent [sic] designer designs complex organisms, such as the parasite, Plasmodium falciparum which cause malaria, with their belief that this putative designer is the supposedly omnibenevolent god if the Bible and Qur'an, I can never get a rational answer.

Most often they resort to the fallback claim that parasites and the suffering they cause were not created by their putative intelligent designer, but by another designer they call 'Sin', which of course is nonsensical and borders on blasphemy because it denies the supremacy of their supposed designer god, and allows for another designer over whom their supposedly omnipotent god is powerless.

But, to their embarrassment, if they manage to do the joined-up thinking, their guru, Michael J. Behe - who has the status of a 'brilliant scientist' in creationist circles - wrote a book, The Edge of Evolution in which he argued (wrongly) that the development of anti-malarial drug resistance in Plasmodium falciparum must have been intelligently designed, using the 'big scary numbers' tactic of arguing that the likelihood of each of the five steps needed arising by chance was so small, that the chances of all five of them occurring in the right sequence is so infinitesimally small that it couldn't have happened by chance alone, so needed divine intervention.

The fact that he used bad biology and even worse maths, in effect assuming that all the mutations had to happen together in as single cell as a single event, instead of in parallel across the species gene pool, as was shown by microbiologist Kenneth R Miller, is by the by, since creationists generally treat anything Michael J Behe says as proven science, they are stuck with his claim that their god is responsible for anti-malarial drug resistance in the malaria parasite - which infects about 20 million people, mostly children annually, and kills 700,000 of them.

Creationists also believe, contrary to the claim that humans have free will, that their god has a plan for each of us, so presumably planned to have those people die of malaria, and that to oppose their god's divine plan in any way is to oppose their god.

So, again a question I can never get a rational response to, is what should a true-believing creationist support - the god whom they believe creates parasites like malaria as part of its divine plan, or the biomedical scientists who work to thwart that plan?

This is of course, the sort of dilemmas that creationists need to avoid rather than have people accept that parasites like Plasmodium falciparum are the result of a mindless, amoral evolutionary process.

By contrast, and devoid of the sort of muddle, holding mutually exclusive views simultaneously, and dilemmas that creationism, with its evidence-free superstitions, gets itself into, the scientific view, supported by evidence, is:

Sunday 12 November 2023

Malevolent Designer News - How Creationism's Favourite Pestilential Sadist is Fighting Back Against Medical Science


Anopheles stephensi, already reached Ghana
First evidence of how the Asian malaria mosquito is spreading drug-resistant malaria in Africa - Lancaster University

You can never write Creationism's favourite sadist off in its battle to keep on killing children with its special tool, malaria. Just when you think medical science has it on the run and it looks possible that we could eradicate malaria like we did its other plaything, smallpox, it performs another twist of the arms race and redesigns the plasmodium parasite or a mosquito vector so they can evade our best efforts to protect children. And, pulling out all the stops, in this case, it's done both.

That's if you subscribe to the childish myth of a magic invisible designer creating all living things of course.

For normal people with a thinking ability above that of a slow 10-year-old, however, what we are seeing is an example of evolution by natural selection in response to an environment in which there are anti-malarial drugs and insecticides that kill mosquitoes.
Fact:
According to the WHO, there were an estimated 247 million cases of malaria worldwide in 2021 with over 600,000 deaths, mostly in Africa. Children under 5 accounted for about 80% of all malaria deaths in the region.
Before creationists start trying to cover their embarrassment, and absolve their god of blame by citing something called 'Sin', which apparently changed from a verb to a noun, materialised as an entity capable of operating outside the control of their supposedly omnipotent god and began creating living things too, may I remind them of their intelligent [sic] design guru, Michael J Behe's contribution to this debate.

Behe wrote one of their sacred books, The Edge of Evolution in which he used faulty logic and bad maths to try to prove that malarial resistance in plasmodium falciparum was intelligently designed, in order to appeal to his largely scientifically illiterate and gullible target readership. His 'argument' was destroyed by biologist Kenneth Miller however, when he pointed out that Behe had assumed in his maths that several mutations had to occur in sequence in a single cell as a single event - something that no evolutionary biologist would ever suggest - an argument that appears to have gone way over the heads of Behe's adoring readership.

Behe's faulty logic was in presenting evolution as something so highly unlikely that no evolutionary biologist would offer it as the mechanism by which evolution happens, then base his maths on that faulty logic and, voila! dutifully show that it is so highly unlikely that it probably didn't happen - so God did it!

Apparently, if you start off with a mechanism for evolution that no biologist in their right mind would ever suggest, you can easily show that it couldn't happen. Creationists regard this as 'creation science'!

But, true to form, Behe has now saddled creationists with the problem of blaming 'Sin' for something that he says was created by their putative intelligent [sic] designer, but then believing two mutually exclusive things simultaneously has never been a problem for creationists.

And that makes it all the more difficult for creationists to wave aside the evidence of malevolent intent, if we stick to the creationist superstition for a moment, in the news published recently in Nature Medicine that an insecticide-resistant species of mosquito Anopheles stephensi, capable of spreading drug and diagnostic-resistant strains of Plasmodium falciparum, has spread from Asia to Africa via the Horn of Africa and has already caused a surge in cases of malaria in Ethiopia, and this species is spreading at a fast rate never before recorded for a mosquito, having already reached Ghana in Northwest Africa. The finding, by an international team which includes Dr Luigi Sedda, from the Lancaster Ecology and Epidemiology Group at Lancaster University Medical School, Lancaster, UK, is outlined in a news release from Lancaster University:
Research by Lancaster University has led to the discovery of the role played by the Asian malaria mosquito (Anopheles stephensi) in the spread of drug and diagnosis-resistant malaria in Africa. Malaria is caused by a parasite which is spread by the bite of blood-sucking mosquitoes. According to the WHO, there were an estimated 247 million cases of malaria worldwide in 2021 with over 600,000 deaths, mostly in Africa. Children under 5 accounted for about 80% of all malaria deaths in the region.

Following its first detection in Djibouti in 2012, the Asian malaria mosquito Anopheles stephensi spread to the Horn of Africa (Ethiopia, Sudan, Somalia, and Eritrea) and beyond (Yemen, Nigeria, Kenya, and Ghana) at a speed unknown before for similar species.

People in households/dormitories with An. stephensi positivity had a 270% higher risk of malaria infection than those in households/dormitories where An. stephensi was not detected.

In addition, two other biological threats for the control of malaria were identified: drug resistance and diagnostic resistance of the parasite.

Dr Luigi Sedda, from the Lancaster Ecology and Epidemiology Group at Lancaster Medical School, is a joint first author on the paper which is published in Nature Medicine.

This is a very important finding. The mosquito that has spread in the Horn of Africa from Asia drove a major urban malaria outbreak in Ethiopia. An. stephensi is posing important public health concerns due to the increase in geographical presence, the capacity to persist throughout the year and to resist current insecticides, and to transmit drug and diagnostic resistant parasites.

The epidemiological characteristics of An. stephensi driven malaria can challenge the expectations for the new malaria vaccines to reduce the burden of malaria disease and deaths in Africa, the continent that was already highly hit by malaria and where successes in malaria reduction are currently stalled.

Dr Luigi Sedda, co-first author
Lancaster Ecology and Epidemiology Group,
Lancaster Medical School, Lancaster University, Lancaster, UK.
A water storage facility in a village in Ethiopia, a structure targeted by Anopheles stephensi
The capacity of Anopheles stephensi to use manmade water storage containers which are abundant in rapidly expanding African urban settings, coupled with its unique ecology, behavioural plasticity and resistance to major insecticides, makes it unamenable to conventional mosquito control tools. This latest evidence can change the prospects of malaria control and elimination in the face of any future intervention that ignores the presence of this invasive species.

The study was led by the Armauer Hansen Research Institute in Ethiopia with the collaboration of Lancaster University (UK), the Adama Science and Technology University (Ethiopia); University of California, San Francisco (USA); The London School of Hygiene and Tropical Medicine (UK); Radboudumc University Medical Center (The Netherlands); U.S. President’s Malaria Initiative (USA) and the Federal Ministry of Health (Ethiopia).
Well, you have to hand it to creationism's divine malevolence! Faced with the prospect of losing one of its best tools for killing innocent children and greatly increasing the suffering in the world, it has hit back hard and fast with a newly redesigned super mosquito to spread its newly-redesigned malaria parasites.

Of course, that's if you don't accept that evolution by natural selection is quite capable of producing this sort of response to anti-mosquito insecticides and anti-malaria drugs by the well-known evolutionary process biologists know as an evolutionary arms race - the antithesis of intelligent design.

Creationism in Crisis - Scientists Create Evolutionary Arms Races In a Laboratory


A typical E. coli phage virus.
Bacteria-Virus Arms Race Provides Rare Window into Rapid and Complex Evolution

Creationists hate evolutionary arms races because they can't be sensibly explained in terms of intelligent design by a single omnipotent, omniscient designer and for a creationist, any other sort of designer(s) would be a serious blasphemy that would see them swiftly ejected from their cult and cast into outer darkness, socially speaking.

And yet evolutionary arms races are an integral part of evolution, probably accounting for more biodiversity than sex selection and environmental change. Evolutionary arms races are the inevitable result of the fact that living things eat other living things, either as parasite or as predators, so there are two ways an organism in a parasite-host or predator-prey relationship can gain an advantage over others of its species: it can either be a more successful parasite/predator or it can be better at avoiding being parasitised or eaten. Either scenario will lead to more offspring carrying the genes for greater success so they will increase in the species gene pool and the whole population will evolve in that direction, creating selection pressure on the other member of the relationship to respond appropriately.

This is all the result of natural selection at works, with no plan and no sentience needed.

It should not be beyond the wit of an average 10-year-old to comprehend that unless childhood brainwashing and theophobic psychosis has prevented rational thinking.

of course, in a natural setting, this all happens relatively slowly in small increments over time, so the evolutionary changes might not be observable for several generations.

So, a group of researchers from UC San Diego, Georgia Institute of Technology and Maryland University, have found a way to speed up the process in laboratory flasks by using small quantities of bacteria and the bacterial parasites, bacteriophage viruses, usually simply called phage viruses.

The news release from UC San Diego explains the research and its significance:

Friday 10 November 2023

Creationism in Crisis - Head Lice Bring More Lousy News For Creationists


Head lice hitched a ride on humans to the Americas at least twice
Male human head louse, Pediculus humanus capitis
According to the creationist favourite arguments - the argument from ignorant incredulity and the false dichotomy - anything which is complex, such as cells, multicellular organisms, cultural ethics, etc., must have been intelligently designed by their particular god by magic, because that is the only answer allowed. Evolution is ruled out by dogmas, as too hard to understand, by someone too lazy to learn biology and too afraid to consider being wrong.

So, following what passes for creationist logic, creationists should believe that the species-specific, obligate parasite, the head louse, Pediculus humanus capitis, must have been intelligently designed by the creationists' god.

Which begs the questions, why would an omnibenevolent designer:
  1. design an irritating parasite?
  2. design its DNA to look like head lice had co-evolved with humans over millions of years from a common ancestor with the louse, Pediculus schaeffi, that parasitises chimpanzees?
And, as with all host-specific, obligate parasites, like pubic lice, chlamydia, and other STDs, there is the little matter of who on the Ark, was host to them and how did they acquire them?

Of the three lice that can infest humans, the head louse, Pediculus humanus capitis, the closely-related body louse, P. h. humanus and the more distantly-related pubic louse, Phthiriasis pubis, all have their counterparts in our nearest great ape relatives, in the latter case, the gorilla, and all have genomes that map closely onto the evolutionary history of different human populations.

Humans inherited the ancestor of P. humanus when we diverged from the chimpanzees and, as we lost body hair, it became isolated to our head and facial hair. Later, when we started wearing clothes, our lice diverged into two sub-species, P. h. capitis and P. h. humanus (also called P. h. corporis) respectively. How we managed to acquire the sexually-transmitted pubic or crab louse, Phthiriasis pubis, from an ancestor of gorillas about 3.3 million years ago, is a matter for speculation.
What are the three species of lice that infest humans and what can they tell us about our evolutionary history and the history of different human populations? There are three species of lice that infest humans:
  1. Pediculus humanus capitis:This is the head louse, which infests the human scalp and hair.
  2. Pediculus humanus corporis:This is the body louse, which lives and lays its eggs on clothing and only feeds on the human body.
  3. Pthirus pubis:This is the pubic louse, which infests coarse body hair, especially in the genital area but can also be found in other coarse body hair.
These lice can provide insights into our evolutionary history and the history of different human populations through a field known as "phylogeography." Phylogeography involves studying the genetic variation within a species to understand its historical migration patterns and population dynamics. Lice are highly host-specific, meaning that they have evolved to live on and feed exclusively from humans. The divergence of head and body lice is thought to have occurred when humans began wearing clothing. The body louse adapted to live in clothing and only feeds on the human body when needed, while the head louse remained adapted to living in human hair. Research on the genetic diversity of human lice has contributed to our understanding of human evolution and migration. For example, studies have used genetic data from lice to estimate when humans started wearing clothing, which is linked to the migration out of Africa. The idea is that as humans migrated to different climates, the need for clothing increased, leading to the divergence of body lice from head lice. Additionally, the study of lice genetics has been used to investigate the timing and patterns of human migration and to trace the movement of human populations over time. This research helps scientists map out the historical interactions and separations of human populations, providing valuable information about the peopling of different regions of the world. In summary, the genetic diversity of human lice provides clues about our evolutionary history, including migration patterns, the development of cultural practices like clothing use, and the historical interactions among human populations.
Now, a group of scientists led by Marina Ascunce, of the United States Department of Agriculture’s Agricultural Research Service (USDA-ARS), together with colleagues, have used this knowledge to show that head lice came to America twice; once with the first wave of human migration from Siberia via the land bridge, Beringia, which was located between Siberia and Alaska, what is now the Bering Strait, when sea-levels were lower, and again with European colonists. They report these findings in a new study published on November 8 in the open-access journal PLOS ONE.

The new study analysed the DNA of 274 human lice from 25 geographic sites around the world. This analysis revealed the existence of two genetically isolated clusters of lice that only rarely interbred. Cluster I had a worldwide distribution, while cluster II was found in Europe and the Americas. There is also a population found in the Americas which appears to be the result of a mixture between lice descended from populations that arrived with the First People carrying cluster I lice and those descended from European (cluster II) lice, which were brought over during the colonization of the Americas.

The researchers also identified a population of lice in Central America which shows a close genetic with lice in Asia. This is consistent with the idea that people from East Asia migrated to North America and became the first Native Americans. These people then spread south into Central America, where modern louse populations today still retain a genetic signature from their distant Asian ancestors.

Abstract The human louse, Pediculus humanus, is an obligate blood-sucking ectoparasite that has coevolved with humans for millennia. Given the intimate relationship between this parasite and the human host, the study of human lice has the potential to shed light on aspects of human evolution that are difficult to interpret using other biological evidence. In this study, we analyzed the genetic variation in 274 human lice from 25 geographic sites around the world by using nuclear microsatellite loci and female-inherited mitochondrial DNA sequences. Nuclear genetic diversity analysis revealed the presence of two distinct genetic clusters I and II, which are subdivided into subclusters: Ia-Ib and IIa-IIb, respectively. Among these samples, we observed the presence of the two most common louse mitochondrial haplogroups: A and B that were found in both nuclear Clusters I and II. Evidence of nuclear admixture was uncommon (12%) and was predominate in the New World potentially mirroring the history of colonization in the Americas. These findings were supported by novel DIYABC simulations that were built using both host and parasite data to define parameters and models suggesting that admixture between cI and cII was very recent. This pattern could also be the result of a reproductive barrier between these two nuclear genetic clusters. In addition to providing new evolutionary knowledge about this human parasite, our study could guide the development of new analyses in other host-parasite systems.
Fig 1. Humans and lice.
The map shows the geographic distribution of the modern human head lice included in this study using green dots. Archeological findings of human lice are shown with the figure of a human louse on the map with the corresponding estimated dates from: [3, 5, 6, 21, 22]. In addition, the map reflects the approximate locations of hominin fossil remains and their proposed distribution based on: [2338]. Each hominin is color coded as follows: Neanderthal (Blue), Denisovan (Black), and Anatomical Modern Humans (Orange).

The outline map was downloaded from Wikimedia: Map author: Maulucioni (https://commons.wikimedia.org/wiki/File:World_map_with_the_Americas_on_the_right.png).
This file is licensed under the Creative Commons Attribution-Share Alike 4.0 International license. https://creativecommons.org/licenses/by-sa/4.0/legalcode.

Fig 5. Proposed global co-migration of human lice and humans.
Top: Map depicting the collection sites of the human lice included in this study. The color of each circle corresponds to the majority nuclear genetic cluster to which sampled individuals were assigned. Sites with admixed lice are indicated with patterned circles including colors of the two major genetic clusters at that site. The proposed migrations of anatomically modern humans out of Africa into Europe, Asia and the Americas, as well as the more recent European colonization of the New World are indicated with thick grey arrows. Hypothetical human louse co-migrations are indicated with orange and blue arrows. At the bottom, the STRUCTURE plot from Fig 3A corresponding to the assignment of 274 lice from 25 geographical sites at K = 4 (Table 1) is shown.

The outline map was downloaded from Wikimedia: Map author: Maulucioni (https://commons.wikimedia.org/wiki/File:World_map_with_the_Americas_on_the_right.png).
This file is licensed under the Creative Commons Attribution-Share Alike 4.0 International license. https://creativecommons.org/licenses/by-sa/4.0/legalcode.


As the author point out, analysis of the DNA of host-specific obligate parasites such as lice can help fill in gaps in the fossil record because their evolution is closely linked to their host's evolution, patterns of migration and , in our case, to cultural changes such as wearing cloths. Again, in the case of humans, a clear pattern emerges which maps exactly onto other evidence of migration, isolation and remixing, confirming the value of DNA analysis in this respect. There is a clear line of migration out of Africa into Asia and from Asia into the Americas with the earliest human migrants. The lice Europeans inherited, had been partially isolated in the European Peninsula with their hosts, or possible had evolved with Neanderthals who then passed them on the modern humans, were the able to remix with the Asian/American variety from the 15th century onwards.

So what creationists need to explain, as well as why their putative designer went to the trouble of designing an obligate parasite to live on us, is why it then gave them DNA that looked like they had evolved over millions of years, share a ecommon ancestor with those of chimpanzees and reflected our pattern of migration out of Africa and across the world over a period of several tens of thousands of years.
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