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:

Malevolent Designer News - How A Deadly Superbug Is 'Designed' To Make Us Sick

Staphylococcus aureus

CDC

Scanning electron micrograph of methicillin-resistant Staphylococcus aureus (MRSA) bacteria being engulfed by an immune cell known as a neutrophil.

Credit: National Institute of Allergy and Infectious Diseases, National Institutes of Health

Researchers discover genes behind antibiotic resistance in deadly superbug infections | Doherty Website

Scientists based at the Docherty Institute, Melbourne University, Victoria, Australia have discovered just how devious any designer of the deadly super bug, Staphylococcus aureus, also known as Golden staph, would need to have been to come up with such a clever way to make us sick and die.

Curiously, for people who purport to worship the putative designer of all living things, creationists would have us believe that the designer is just such a mendacious malevolence, rather than have us believe that a natural process such as evolution by natural selection is responsible for parasites and the way they evade our immune systems - also, so creationists claim, designed by the same designer, making it look like a bumbling incompetent amnesiac than a supremely intelligent deity.

First, a brief background on S. aureus and MRSA:

Creationism in Crisis - Even 'Artificial' Cells With a Minimal Genome Evolve Naturally

Electron micrographs of a cluster of minimal cells magnified 15,000 times.

Credit: Tom Deerinck and Mark Ellisman
University of California at San Diego.

Artificial cells demonstrate that "life finds a way": 2023 news: News: News & Events: Department of Biology: Indiana University Bloomington

It's turning out to be another terrible week for those few creationists capable, and willing, to read the science.

Here for example is a report on the work of a team led by evolutionary biologist, Professor Jay T. Lennon, of the Department of Biology in the College of Arts and Sciences at Indiana University. It shows a number of things that refute basic creationist dogmas:

• The team use a genetically engineered, stripped down version of the bacterium Mycoplasma mycoides, a parasitic organism that, in common with many parasites had lost genes in the course of its evolution as a dependent parasite in the gut of goats and similar animals, reducing its genome to just 901 genes. So here we have evolution by loss of information (something creationists claim can't happen because their dogma says loss of information is invariably detrimental) as the starting point of this research.
• The team then removed all but the essential genes needed to maintain a functional, reproducing cell, removing a further 45 percent of the genes, reducing the genome to just 493 genes, showing the massive amount of redundancy in a cell's genome - something that no intelligent designer would have designed, showing there was no intelligence in the design of M. mycoides. By comparison, a typical cell can contain 20,000 genes!
• The team then allowed the minimal cell to evolve for 300 days, or 2000 generations (equivalent to 40,000 years of human evolution). They found that even with a minimal genome and so fewer targets for mutation and selection to act on, the minimum cells evolved towards greater fitness, just as the TOE predicts.
• And of course, as with all biological research, there is the complete dependence on the TOE to understand and explain the results, with no hint of doubt in it's explanatory powers or any suggestion that the creationists superstition with its magic and unproven supernatural entity might offer a better explanation of the facts.

Here then is how the Indiana University news release describes the research:

Unintelligent Design - The Complex Lengths to Which Creationism's Idiot Designer Goes To Solve the Problems Its Incompetence Causes

Unintelligent Design

The Complex Lengths to Which Creationism's Idiot Designer Goes To Solve the Problems Its Incompetence Causes

Photo: Getty Images

Your baby’s gut is crawling with unknown viruses – University of Copenhagen

Human gut microbiome

Source

If you've bought into the Creation Cult's intelligent [sic] design notion, it's probably best to ignore articles like this that might cause you to doubt the competence of your putative designer, but you're probably used to ignoring evidence that refutes creationism or you wouldn't have fallen for the intelligent [sic] design hoax in the first place.

Nevertheless, it discoveries such as this by Danish Scientists led by Shiraz A. Shah, of Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark, together with colleagues from France and Canada, that highlight the way arms races can lead to ludicrous levels of complexity of which any even half-competent designer would be rightly ashamed.

It comes about because the human gut, especially that of babies, is an ideal, warm, moist, and nutrient-rich environment for micro-organisms, so is teeming with bacteria, protozoa, and viruses, some of which are harmless but some of which parasitize both the microbes and the human cells of the gut.

One incidental benefit that creationists will point to is that the presence of these organisms probably helps train the developing babies’ immune system so it is more effective in later life, so the presence of these organisms can be beneficial.

But hold on! What are they 'training the immune system' for? They are training it to protect us from the very bacteria that the supposedly intelligent designer designed to harm us. At least, since it is supposedly omniscient, it knew what its bacteria and viruses would do when it designed them, so we must assume it designed them for that purpose.

And, if we accept that it designed bacteria to train our immune system, why did it then design the viruses that kill these beneficial bacteria?

But whatever it was thinking of, if 'thinking' is the appropriate term, the result is a baby’s gut teeming with more than 200 different families of virus, many of which were unknown prior to this study. The team's findings are published, open access, in the journal Nature Microbiology.

The research and its significance is explained in a University of Copenhagen news release:

Creationism in Crisis - What on Earth was the 'Designer' Thinking?

Creationism in Crisis

What on Earth was the 'Designer' Thinking?

Credit: Lenora Martinez-Nunez

The ‘Rapunzel’ virus: an evolutionary oddity

Figure 2
Intra- and inter-ring interactions. A The primary intra-ring interface between two subunits (green and cyan) within a ring. B Schematic quantifying interactions from a single subunit (α) to illustrate the extensive, cooperative network. Numbers and line widths (not lengths) correspond to quantification of the interactions between α and neighboring subunits as calculated by the PDBePISA server (Supplementary Tables 3 and 4). C Surface representation of two subunits reveals a ball and socket geometry between rings. A single subunit (orange) has two loops (Loop1 and Loop2) that fit into sockets (Socket1 - gray, and Socket2 - white) of a subunit in the ring below it (green). D Surface electrostatics of ring interfaces demonstrate an important role for electrostatics in inter-ring interactions.

Agnello, et. al., (2023), Journal of Biological Chemistry

Creationists would have us believe that there are two forms of life on Earth - that designed by their putative, omnibelevolent, omniscient, omnipotent god and that designed by some magical thing (or is it a process?) called 'sin'. For some mysterious reason, their supposedly omnipotent, omniscient god doesn't have enough power to overcome this 'sin' and is reduced to playing inevitable games with it such as indulging in arms races to defend its creation while 'sin' tries to harm it.

In addition, Creationists believe one of two things:

1. Their god didn't know when he created the mythical founder couple, Adam & Eve, that this would result in this 'sin' thing being created.
2. It did know, but created them anyway, presumably not understanding the consequences.

And of course they believe in the literal truth of the Bible where their god is reported as telling Isaiah that in fact he created evil.:

I form the light, and create darkness: I make peace, and create evil: I the Lord do all these things.

Isiah 47:7

And they also believe that their god created everything on Earth for his special creation, them of course, or more generally, all humans

Not for the first time, Creationism requires its dupes to believe two or more mutually exclusive things simultaneously.
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So, with that in mind, imagine being a Creationist and trying to understand what on Earth your magic god was trying to achieve when it created bacteria, then created the phage viruses to parasitise them, described in the research by a team from the Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester MA, USA.

Their research is published open access in the Journal of Biological Chemistry and described in the magazine for the American Society for Biochemistry and Molecular Biology (ASBMB). It describes a phage virus, P74-26, nicknamed the “Rapunzel bacteriophage”, with an extraordinarily long 'tail' which is capable of parasitising even extremophile bacteria that live in hot springs where temperatures can reach 170^oC. Neither these bacteria nor the phage virus appear to have any benefit to mankind.

The study was to determine the construction and function of the very long 'tail'.

The discovery was of something that the Creationist idol, Michael J Behe would undoubtedly proclaim as 'irreducibly complex', therefore proof that the locally popular god did it.

To make matters worse for Creationists, the study casually and unintentionally refutes one of the lies that their cult leaders fool them with - that the Theory of Evolution (TOE) is being increasingly rejected by mainstream biologists in favour of their childish, magical and supernatural explanation. The scientists who did the study are in no doubt that the 'tail' is a product of an evolutionary process and that the TOE is a perfect model for explaining and understanding the observed facts.

From the ASBMB magazine:

A recent study in the Journal of Biological Chemistry has revealed the secret behind an evolutionary marvel: a bacteriophage with an extremely long tail. This extraordinary tail is part of a bacteriophage that lives in inhospitable hot springs and preys on some of the toughest bacteria on the planet.

Bacteriophages are a group of viruses that infect and replicate in bacteria and are the most common and diverse things on Earth.

The bacteriophage P74-26 has a tail 10 times longer than most other phage tails and is nearly 1 micrometer long, about the width of some spider’s silk.

Angnello, et al.(2023) Journal of Biological Chemistry

Bacteriophages, or phages for short, are everywhere that bacteria are, including the dirt and water around you and in your own body’s microbial ecosystem as well.

Each phage tail is made up of many small building blocks that come together to form a long tube. Our research finds that these building blocks can change shape, or conformation, as they come together. This shape-changing behavior is important in allowing the building blocks to fit together and form the correct structure of the tail tube.

We used a technique called cryo-electron microscopy, which is a huge microscope that allows us to take thousands of images and short movies at a very high magnification. By taking lots of pictures of the phage’s tail tubes and stacking them together, we were able to figure out exactly how the building blocks fit together.

Bacteriophages are gaining ever-growing interest as an alternative to antibiotics for treating bacterial infections. By studying phage assembly, we can better understand how these viruses interact with bacteria, which could lead to the development of more effective phage-based therapies. … I believe that studying unique, interesting things can lead to findings and applications that we can’t even yet imagine.

Emily Agnello, first author
Department of Biochemistry and Molecular Biotechnology
University of Massachusetts Chan Medical School
Worcester, MA, USA.

Unlike many of the viruses that infect humans and animals that contain only one compartment, phages consist of a tail attached to a spiky, prismlike protein shell that contains their DNA.

Phage tails, like hairstyles, vary in length and style; some are long and bouncy while others are short and stiff. While most phages have short, microscopic tails, the “Rapunzel bacteriophage” P74-26 has a tail 10 times longer than most and is nearly 1 micrometer long, about the width of some spider’s silk. The “Rapunzel” moniker is derived from the fairy tale in which a girl with extremely long hair was locked in a tower by an evil witch.

Brian Kelch, an associate professor of biochemistry and molecular biotechnology at UMass Chan who supervised the work, described P74-26 as having a “monster of a tail.”

transmission electron micrograph of multiple bacteriophages attached to a bacterial cell wall; the magnification is approximately 200,000.

Professor Graham Beards, (Wikimedia Commons)

Compared with most phages, P74-26 uses half the number of building blocks to form stacking rings that make up the tail.

Phage tails are important for puncturing bacteria, which are coated in a dense, viscous substance. P74-26’s long tail allows it to invade and infect the toughest bacteria. Not only does P74-26 have an extremely long tail, but it is also the most stable phage, allowing it to exist in and infect bacteria that live in hot springs that can reach over 170° F. Researchers have been studying P74-26 to find out why and how it can exist in such extreme environments.

To work with a phage that thrives in such high temperatures, Agnello had to adjust the conditions of her experiments to coax the phage tail to assemble itself in a test tube. Kelch said Agnello created a system with which she could induce rapid tail self-assembly.

I like to think about these phage building blocks as kind of like Legos. The Lego has studs on one side and the holes or sockets on the other. Imagine a Lego where the sockets start off closed. But as you start to build with the Legos, the sockets begin to open up to allow the studs on other Legos to build a larger assembly. This movement is an important way that these phage building blocks self-regulate their assembly.

We think what has happened is that some ancient virus fused its building blocks into one protein. Imagine two small Lego bricks are fused into one large brick with no seams. This long tail is built with larger, sturdier building blocks. We think that could be stabilizing the tail at high temperatures.

Brian A. Kelch, corresponding author
Department of Biochemistry and Molecular Biotechnology
University of Massachusetts Chan Medical School
Worcester, MA, USA

The researchers used high-power imaging techniques as well as computer simulations and found that the building blocks of the tail lean on each other to stabilize themselves.

They found P74-26 uses a “ball and socket” mechanism to sturdy itself. In addition, the tail is formed from vertically stacking rings of molecules that make a hollow canal.

Kelch pointed out that, compared with most phages, P74-26 uses half the number of building blocks to form stacking rings that make up the tail.

The researchers now plan to use genetic manipulation to alter the length of the phage tail and see how that changes its behavior.

Phages occupy almost every corner of the globe and are important to a variety of industries like healthcare, environmental conservation and food safety. In fact, long-tailed phages like P74-26 have been used in preliminary clinical trials to treat certain bacterial infections.

Copyright: © 2023 The authors.
Published by Elsevier Inc. Open access. (CC BY 4.0)

More technical detail is given in the teams open access paper in the Journal of Biological Chemistry:

Abstract

Tail tube assembly is an essential step in the lifecycle of long-tailed bacteriophages. Limited structural and biophysical information has impeded an understanding of assembly and stability of their long, flexible tail tubes. The hyperthermophilic phage P74-26 is particularly intriguing as it has the longest tail of any known virus (nearly 1 μm) and is the most thermostable known phage. Here, we use structures of the P74-26 tail tube along with an in vitro system for studying tube assembly kinetics to propose the first molecular model for the tail tube assembly of long-tailed phages. Our high resolution cryo-EM structure provides insight into how the P74-26 phage assembles through flexible loops that fit into neighboring rings through tight “ball-and-socket”-like interactions. Guided by this structure, and in combination with mutational, light scattering, and molecular dynamics simulations data, we propose a model for the assembly of conserved tube-like structures across phage and other entities possessing Tail Tube-like proteins. We propose that formation of a full ring promotes the adoption of a tube elongation-competent conformation among the flexible loops and their corresponding sockets, which is further stabilized by an adjacent ring. Tail assembly is controlled by the cooperative interaction of dynamic intra- and inter-ring contacts. Given the structural conservation among tail tube proteins and tail-like structures, our model can explain the mechanism of high-fidelity assembly of long, stable tubes.

Agnello, Emily; Pajak, Joshua; Liu, Xingchen; Kelch, Brian A.
Conformational dynamics control assembly of an extremely long bacteriophage tail tube
Journal of Biological Chemistry; (2023). DOI: 10.1016/j.jbc.2023.103021

Copyright: © 2023 The authors.
Published by Elsevier Inc. Open access
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

So, from a Creationist point of view, a massively complex solution to the problem of how to get through the defences of a bacterium that was designed to protect it from viruses in order to kill bacteria that, because they inhabit such extreme conditions, are or complete indifference to humans, being neither harmful nor harmless.

Creationists also argue that bacteria and viruses were created by 'sin' in some unexplained magical process, so this 'sin' thing is designing parasites to attack the parasites it creates!

It takes some special mental gymnastics to believe these organisms and the relationships between them are the result of an intelligent design process and not the result of a mindless, utilitarian natural process in which neither magic nor magicians was involved.

Malevolent Designer News - Bathing in Other People's Microbe Broth

Malevolent Designer News

Bathing in Other People's Microbe Broth!

"The more people in the Jacuzzi, the higher the levels of faeces and sweat shed into the water"

Faeces, urine and sweat – just how gross are hot tubs? A microbiologist explains

If there is anything Creationism's intelligent [sic] designer is notable for, it's never missing an opportunity to make more people sick with its specially designed pathological parasites. Take for example, the simple pleasure of sharing a Jacuzzi with friends and neighbours.

Of course, if it’s anything like the miserable old pleasure-hating deity of the Christian Bible or the Qur’an, the malevolent designer probably hates the idea of semi-naked people having fun in a hot tub together, drinking wine and maybe even touching one another. I'm reliably informed that Australians even make love in them!

We've often discussed the possibility of a Jacuzzi in our back garden, especially as we have nice neighbours who would undoubtedly join us in one with a glass or two of wine if invited. There are few things more relaxing than sparkling white wine and the tickle of bubbles rising up underneath you, especially on a balmy summer evening.

However, having read the following article by Primrose Freestone, Senior Lecturer in Clinical Microbiology, University of Leicester, I think I'll forego that pleasure in favour of sun loungers around a fire pit.

The article is reprinted from The Conversation under a Creative Commons licence, reformatted for stylistic consistence. The original can be read here.

Malevolent Designer News - Where Creationism's Favourite Sadist Released the Black Death on Humanity

Origins of the Black Death identified | Max-Planck-Gesellschaft

View of the Tian Shan mountains.
Studying ancient plague genomes, researchers traced the origins of the Black Death to Central Asia, close to Lake Issyk Kul, in what is now Kyrgyzstan.

© Lyazzat Musralina

The Black Death was one of Creationism's divine malevolence's earlier attempt to kill millions of people, and it was spectacularly successful, reducing the population of Eurasia by up to 60% between 1346 and 1353, and wiping out some villages completely - that is, of course, if you buy into the intelligent [sic] design hoax that says complex organism must have been designed because evolution doesn't happen, and even if it does, it can't account for complexity [sic].

The Black Death, which theologians at the time were in no doubt was some form of divine retribution - for whatever they said it was for. The shock of it to devout European Christian culture caused all sorts of obscure sects to arise, like the flagellants, who walked about beating themselves with whips. The obvious fact that praying to dead ancestors called saints and begging them to intercede with God and put a stop to the plague, wasn't working, coupled with a widespread belief that it was the routine debauchery and corruption within the Catholic Church that had resulted in divine retribution, eventually led to a fundamental reassessment of how people saw their relationship with God, culminating in the Protestant Reformation.

The pandemic was caused by the organism Yersinia pestis and a large team of researchers, including scientists from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, the University of Tübingen, Germany, and the University of Stirling, Scotland, UK have worked out exactly where it started, something that has long been a mystery. They did this by studying the genome of ancient samples of Y. pestis

From the Max Planck-Gesellschaft news release: