About 8000 years ago, i.e. around about the time Creationists believe the Universe was created, humans had already diversified in Eurasia into several major cultural groups, each with its distinct genome, having adapted to the local environment including local pathogens like viruses and bacteria.
Evidence from archaeology shows that farmers, complete with their domesticated livestock, were migrating into Western Europe and mixing with the indigenous hunter-gatherers.
Until now, it had been assumed that close proximity to their domestic livestock would have meant that the incoming farmers would have a more developed immune system, having evolved immunity to the pathogens carried by their livestock. The genes associated with this immune system would be expected to be favoured by natural selection so should account for the largest part of the genes of modern Europeans.
However, that view fails to take into account that the farmers were migrating into a new environment with new environmental selectors.
So, the evidence produced by researchers at the Francis Crick Institute's Ancient Genomics Laboratory have shown that in fact, modern Europeans have inherited only about half their immunity genes from the incoming farmers and the other half from the hunter-gatherers, showing that the hunter-gatherers' genes for immunity were selected equally by natural selection. This evidence comes from comparing the genomes of 677 individuals spanning Mesolithic and Neolithic Europe.br>
The conclusion then is that hunter-gatherers had evolved immunity genes in response to local conditions and that those local conditions then influenced which of their genes the incoming farmers retained and which indigenous genes were retained. In fact, it was increased diversity which was favoured by natural selection, not specific immunity to specific pathogens.
By contrast, the genes for (lack of) skin pigmentation that the farmers brought with them from Central Asia were retained differentially to give modern Europeans their pale skin, probably as an adaptation to lower vitamin D in the diet, since vitamin D is produced by the action of sunlight on skin.
A team of researchers at Virginia Tech has produced evidence of something that would, if they understood its implications, spread despondency throughout the Creationist cults. They have shown that there was a sharp increase by about 50% in the level of biologically available nitrogen in Earth's oceans, 800 million years ago, coincident with the rise of the eukaryotes.
So strongly is this increase associated with the rise of the eukaryotes that the clear implication is that this is what either triggered or at least facilitated this major evolutionary step and that it was the limited availability of biological nitrogen that delayed this change.
The eukaryotes went on to evolve into the multicellular organisms which are the dominant life forms on Earth today.
So, not only is this evidence that there were simple living organisms on Earth 799,990,000 years before Creationists believe the Universe was created, but that the evolution of modern life forms was dependent on environmental change.
The thing about an omniscience, omnipotent designer is that everything it designs should be perfect for the purpose for which it was designed. That means it should be maximally efficient, minimally complex and incapable of improvement.
This wouldn’t be true of something 'designed' by a natural, utilitarian process operating without a plan, of course, because even a suboptimal solution could be more successful than its predecessor, and that's the only test applied by the natural selection process.
The upshot is that, if the 'design' can be improved in any way, it can't have been designed by an omniscient, omnipotent designer.
So, if they understand it and can't dismiss it, Creationists should be acutely embarrassed by news that an international team of physicists, chemists and biologists, led by the University of Cambridge, UK, are close to doing just that with one of the fundamental processes necessary for almost all life on Earth - photosynthesis.
A whitespotted char caught by angling during the survey
In a fascinating experiment in Japan, two scientists from Hokkaido University
have shown a complex evolutionary relationship between parasitism and the
likelihood of a fish being caught by an angler. And, as always with scientific
evidence, it's not good news for Creationists.
No doubt though, they'll resort to their fall-back strategy of using their own
definition of 'evolution' (one 'kind' turning into another, unrelated 'kind', in
a single event), rather than the one science uses (change in allele frequency in
a population over time).
But this is no so much about the sheer malevolence of any designer that could
come up with parasites like this parasitic species of copepod which infects the
mouth and gills of fish. Instead, it is about how parasitism, prey and predators
are in a complex, dynamic evolutionary relationship which can only be understood
and explained by reference to the basics of the Theory of Evolution by Natural
Selection.
Fishing has been practiced by humans for about 40,000 years, usually for food
but latterly for sport. The functional difference being that fish caught for
food are removed from the population as form of predation, whereas fish caught
for sport are quickly released back into the wild.
The scientists conducted an elegant experiment consisting of two surveys:
Figure 1. A new orchid species Spiranthes hachijoensis with
beautiful glasswork-like flowers found in a private garden.
(A) Inflorescence. (B) Close up of inflorescence. (C) Flower. Scale bars: 10
mm (A & B) and 5 mm (C) in the Tokyo Prefecture..
Photographs: Masayuki Ishibashi (A & C) and Kenji Suetsugu (B).
Science is always open to new information but it's not often to be found hiding
in plain sight, like this newly-discovered species of orchid. It was discovered
by scientists from Kobe University, Japan, growing in private gardens, parks and
even lawns and on balconies, on the Japanese island of Hachijo in the Tokyo
Prefecture. It has since been named Spiranthes hachijoensis.
The search suggests there may be other undiscovered, related species growing in
familiar places but overlooked because of the way they have speciates from a
common ancestor. In the case of S. hachijoensis speciation probably
occurred due to reproductive isolation because it flowers a month earlier than
the related taxon it grows alongside. As the Kobe University news release
explains, the genus Spiranthes on the Japanese mainland was once
considered to be a single species, S. australis, but closer examination
has revealed that there are several distinct species within the genus and there
may well be more:
P.T. Barnum, the 'Greatest Showman' and half-owner of Barnum & Bailey Circus reputedly said, "There's a sucker born every minute".
Sometimes though, especially reading the comments of Creationists and religious fundamentalist in the social media, that would seem to be on the conservative side, with tens, or even hundreds, of millions apparently believing in magic and evil demons; that evidence is forged; that scientists are all evil, mad and part of a vast conspiracy; that reality is an illusion, but not to them, and that inerrant knowledge just pops itself into their brain if they have an open mind, so the best expertise comes from pristine ignorance. I've even had a Creationist tell me that Jesus tells him what to believe, curiously, it always coincides with what Ken Ham tells him to believe.
So what is the psychology behind these wackadoodle fantasy beliefs, other than the acute manifestations of clinical psychosis?
Long before a clan of camel herders and traders along the western edge of Arabia were forced by tribal loyalty to follow a new, charismatic 'Prophet of Allah", and long before a tribe of Canaanite hill farmers in the hill of southern Syria adopted the god Yahweh from the local pantheon as their own, and created a mythical history to give them a unique identity and justify their land-theft, genocide and territorial expansion, scattered bands of early pastoralists had banded together to build hundreds of massive monuments for religious rituals in the Al-Nafūd Desert in the north of Arabia, close to the Western end of the 'fertile crescent'.
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Detail of north-west (preserved) interlocking cells of associated feature IDIHA-F-0011149.
The main (central) chamber of mustatil IDIHA-F-0011081 with three up-right stones (A-C). Flat stones in centre of image acted as support for primary up-right stone in the rear. The blocked doorway is visible in the left of the photo.
Horns found on a collapsed “bench” in Phase 4B. Left to right, large cattle horns/sheaths (#0043) and (#0033), goat horn sheath (#0047), goat (#0041), and cattle horn (#0040).
These structures were only discovered in 2016 by satellite imagery. Now known by the local people as Mustatil ('rectangles")., they were constructed some 7000 years ago, before the Pyramids of Egypt or Stonehenge in southern England and are probably the oldest man-made stone structures on Earth. The organisation and manpower required to build these structures suggests some unifying idea across a large area to give a commonality of purpose to scattered tribes, pointing to a single religion with maybe an accepted central religious authority associated with the site in northern Arabia where these structures were created.
They are also associated with elaborate rock-carvings of strange geometric shapes and patters, which were probably originally painted.
As with the Pyramids and the Bronze Age structures of Stonehenge and Silbury Hill, in Wiltshire, UK, they suggest an organised state with an economy strong enough to provide a surplus wealth and food production sufficient to finance these constructions and feed the workers.
And yet, because they left no records, like the religion that inspired the building of Knossos in Minoan Create, we have no idea what that religion was or why it was able to inspire the creation of these structures for the rituals that were performed there, and why the people living there considered it necessary and worth all the effort!
Clearly, the god(s) (and it was probably a pantheon of gods, like the neighbouring Mesopotamians had later) had massive imaginary powers, giving the priesthood enormous powers of command and control, and elaborate rituals were considered necessary to appease or thank them. Yet we have no idea what those imaginary powers were, and whatever they were believed to have done, or not done in response to the rituals continued to be done or not done when the rituals ceased, their last believer died, and the monuments crumbled.
The First Law of Theodynamics:
Gods can be created out of nothing and will disappear without trace.
This is a phenomenon that has been repeated time and again throughout human history as religions have come and gone together with their imaginary gods. No one now mourns at the graveside of these old dead gods.
No-one believes in Mars, Ra, Wodan, Thor or Saturn, and no-one says the rituals that were once essential to keep the seasons coming and going, the crops growing or the Nile flooding, and yet the seasons continue to come and go, the crops grow and the Nile still floods at the right time.
The prayers and rituals that once influenced these old gods are no longer needed, and the natural occurrences that were once 'obviously' caused or created by them are now just as 'obviously' caused or created by different gods in response to different prayers and rituals. And they will still occur when the current batch of gods have been consigned to the graveyard of the gods along with all the others.
What started me thinking in that line, was a recent article concerning the Arabian monuments in The Conversation by Melissa Kennedy, and
Hugh Thomas, Lecturers in Archaeology at the University of Sydney. Their article is reprinted here under a Creative Commons licence, reformatted for stylistic consistency. The original can be read here
Enigmatic ruins across Arabia hosted ancient ritual sacrifices
A group of three mustatil and later Bronze Age funerary pendants on a rocky outcrop, southeast of AlUla County.
Source: AAKSA / The Royal Commission for AlUla, Author provided
Over the past five years, archaeologists have identified more than 1,600 monumental stone structures dotted across a swathe of Saudi Arabia larger than Italy. The purpose of these ancient stone buildings, dating back more than 7,000 years, has been a puzzle for researchers.
Our excavations and surveys reveal these were ritual structures, constructed by ancient herders and hunters who gathered to sacrifice animals to an unknown deity – perhaps in response to ancient climate change. The study is published in PLOS ONE today.
Desert discoveries
In the 1970s, the first archaeological surveys of northwest Saudi Arabia identified an ancient and mysterious rectangular structure. The sandstone walls of the structure were 95m long, and although it was determined to be unique, no further study of this unusual site was undertaken.
Over the following decades, airline passengers would see similar large “rectangles” dotted across the country. However, it was not until 2018 that one was excavated.
The main architectural features of a mustatil.
Credit: AAKSA / The Royal Commission for AlUla, Author provided
These structures are now known as mustatils (Arabic for rectangle). We have been studying them for the past five years as part of a larger archaeological study sponsored by the Saudi Royal Commission for AlUla.
The smallest mustatils are around 20m long, while the largest are over 600m. Previous work by our team determined that all mustatils follow a similar architectural plan. Two thick ends were connected by between two to five long walls, creating up to four courtyards.
Access to the mustatil was through a narrow entrance in the base. There would then have been a long walk, perhaps in the form of a procession, to the “head”, where the main ritual activity took place.
Previous studies determined that the mustatils are at least 7,000 years old, dating to the end of the Neolithic period.
Cattle remains
In 2019–2020, we undertook excavations at a mustatil site called IDIHA-0008222. The structure, made from unworked sandstone, measures 140m in length and 20m in width.
Excavations in the head of the mustatil revealed a semi-subterranean chamber. Within this chamber were three large, vertical stones. We have interpreted these as “betyls”, or sacred standing stones which represented unknown ancient deities.
The excavated mustatil at IDIHA-0008222.
Credit: AAKSA / The Royal Commission for AlUla, Author provided
Surrounding these stones were well-preserved cattle, goat, and gazelle horns. The horns are so well preserved that much of what we find is the horn sheath, made of keratin – the same substance as hair and nails. We found only the upper cranial elements of these animals: the teeth, skulls, and horns. This suggests a clear and specific choice of offerings.
Further analysis suggests the bulk of these remains belonged to male animals and the cattle were aged between 2 and 12 years. Their slaughter would have formed a significant proportion of a community’s wealth, indicating these were high-value offerings.
Human remains
Current evidence suggests that the mustatils were in use between 5300 and 4900 BCE, a time when Arabia was green and humid. However, within a few generations, the ancient inhabitants of Saudi Arabia began to reuse these structures, this time to bury human body parts.
At IDIHA-0008222, a small structure had been built next to the mustatil. Inside were a partial foot, five vertebrae and several long bones.
Their placement suggests soft tissue was still present when they were buried. Forensic anthropologists were able to determine that the remains likely belonged to an individual aged between 30 and 40 years.
Our work at other mustatils has revealed similar deposits of human remains. Were these remains buried in attempt to claim ownership of the structure or some form of later ritual? These questions remain to be answered.
Pointing to water
The mustatils are changing how we view the Neolithic period not just in Arabia but across the Middle East. The sheer size of these structures and the amount of work involved in their construction suggests that multiple communities came together to create them, most probably as a form of group bonding.
Moreover, their widespread distribution across Saudi Arabia suggests the existence of a shared religious belief, one held over a vast and un-paralleled geographic distance. Currently, fewer than ten mustatils have been excavated, so our understanding of these structures is still in its infancy.
Mustatil locations in Saudi Arabia, with the location of site IDIHA-0008222 marked in red.
Credit: Esri, Maxar, Earthstar Geographics, the GIS User Community, USGS, NOAA / AAKSA / The Royal Commission for AlUla, Author provided
The key question to be answered is “why were they built?” A survey trip by our team may have, in part, solved this mystery.
While recording these structures after rain, we noted that almost all mustatils pointed towards areas that held water. Perhaps the mustatils were constructed and the animals offered to the god or gods to ensure the continuation of the rains and the fertility of the land.
The possibility remains that the mustatils were built in response to a changing climate, as the region became increasingly arid like it is today.
Two mustatil in Khaybar County pointing to standing water after rain.
Credit: AAKSA / The Royal Commission for AlUla, Author provided
Our study of the mustatils is ongoing. Our new project at the University of Sydney is focused on understanding why these monumental structures and others were built and what brought about their end.
We hope future excavations and analyses will reveal further insights into the life and death of the mustatils and the people who built them.
Melissa Kennedy, Lecturer in Archaeology, University of Sydney and Hugh Thomas, Lecturer in Archaeology, University of Sydney
Since the 1970s, monumental stone structures now called mustatil have been documented across Saudi Arabia. However, it was not until 2017 that the first intensive and systematic study of this structure type was undertaken, although this study could not determine the precise function of these features. Recent excavations in AlUla have now determined that these structures fulfilled a ritual purpose, with specifically selected elements of both wild and domestic taxa deposited around a betyl. This paper outlines the results of the University of Western Australia’s work at site IDIHA-0008222, a 140 m long mustatil (IDIHA-F-0011081), located 55 km east of AlUla. Work at this site sheds new and important light on the cult, herding and ‘pilgrimage’ in the Late Neolithic of north-west Arabia, with the site revealing one of the earliest chronometrically dated betyls in the Arabian Peninsula and some of the earliest evidence for domestic cattle in northern Arabia.
Where is the graveyard of dead gods? What lingering mourner waters their mounds? There was a day when Jupiter was the king of the gods, and any man who doubted his puissance was ipso facto a barbarian and an ignoramus. But where in all the world is there a man who worships Jupiter today? And what of Huitzilopochtli? In one year—and it is no more than five hundred years ago—fifty thousand youths and maidens were slain in sacrifice to him. Today, if he is remembered at all, it is only by some vagrant savage in the depths of the Mexican forest. Huitzilopochtli, like many other gods, had no human father; his mother was a virtuous widow; he was born of an apparently innocent flirtation that she carried on with the sun. When he frowned, his father, the sun, stood still. When he roared with rage, earthquakes engulfed whole cities. When he thirsted he was watered with ten thousand gallons of human blood. But today Huitzilopochtli is as magnificently forgotten as Alien G. Thurman. Once the peer of Allah, Buddha and Wotan, he is now the peer of General Coxey, Richmond P. Hobson, Nan Patterson, Alton B. Parker, Adelina Patti, General Weyler, and Tom Sharkey…
But they have company in oblivion: the hell of dead gods is as crowded as the Presbyterian hell for babies. Damona is there, and Esus, and Drunemeton, and Silvana, and Dervones, and Adsalluta, and Deva, and Belisama, and Axona, and Vintios, and Taranuous, and Sulis, and Cocidius, and Adsmerius, and Dumiatis, and Caletos, and Moccus, and Ollovidius, and Albiorix, and Leucitius, and Vitucadrus, and Ogmios, and Uxellimus, and Borvo, and Grannos, and Mogons. All mighty gods in their day, worshiped by millions, full of demands and impositions, able to bind and loose—all gods of the first class, not dilettanti. Men labored for generations to build vast temples to them—temples with stones as large as hay-wagons. The business of interpreting their whims occupied thousands of priests, wizards, archdeacons, evangelists, haruspices, bishops, archbishops. To doubt them was to die, usually at the stake. Armies took to the field to defend them against infidels: villages were burned, women and children were butchered, cattle were driven off. Yet in the end they all withered and died, and today there is none so poor to do them reverence. Worse, the very tombs in which they lie are lost, and so even a respectful stranger is debarred from paying them the slightest and politest homage.
Apart from having to design the virus to overcome the defences it designed to protect us from the viruses it creates to harm up, if you follow me, it then has to continually modify its design to overcome the defences human medical science devises, such as vaccines (which only work because we have those defences in the first place, no matter how inadequate). It is as though Creationism's supposedly omniscient, omnipotent designer doesn't have a clue about the future and can only respond when it happens.
And, like a true amnesiac, it seems to forget entirely what it designed yesterday, and why it designed it, so it ends up in a pointless and wasteful arms race with itself; continually designing solutions today to the solutions it designed yesterday which it now thinks are new problems to be solved.
And now we learn from a study by researchers at Sweden's Karolinska Institutet that infection by one of its earlier designs, the OC43 corona virus which causes the common cold, produces antibodies that give some protection against its SARS-CoV-2 coronavirus!
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:
Their god didn't know when he created the mythical founder couple, Adam & Eve, that this would result in this 'sin' thing being created.
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. g a
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 170oC. 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.
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
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.
South Polar skua, Stercorarius maccormicki, with nest
According to a survey published, open access, yesterday in the Cell Press journal, Current Biology almost the entire breeding population of three seabirds failed to breed on important breeding grounds in Antarctica, due to unseasonably high snowfall in the Antarctic 'Summer' (December 2020-January 2022) when breeding normally takes place. The unusual weather is almost certainly due to man-made climate change.
The researchers found not a single nest of the South Polar skua, and only a handful of the nests of the Antarctic petrel, Thalassoica antarctica, and Snow petrel, Pagodroma nivea, on the main breeding ground of Dronning Maud Land (Queen Maud Land) in the Norwegian-administered sector of Antarctica.
The Ludicrous Complexity of Arms Races Between Parasites and Hosts
Researchers from Penn Vet observed, for the first time, an intestinal pyogranuloma, formed in response to Yersinia infection. The organized grouping of cells includes monocytes (in green), neutrophils (in magenta), and Yersinia
bacteria (in white), and depends on monocytes to form and to control infection, the team found.
Image: The Brodsky Laboratory
Peyer's Patches - organized lymphoid nodules commonly found in the small intestines.
Hard though it is to imagine any intelligent adult holding to such beliefs, Creationists believe that parasites were intelligently designed to make us sick and the same designer gave us an immune system to help stop parasites doing what it designed them to do. It then indulged in a pointless arms race with itself to try to make sure both parasites and our immune system did what they were designed to do.
It's as though the creator is some hate-filled but incompetent, schizophrenic amnesiac, intent on harming us one day and protecting us the next, but not remembering what it was trying to do yesterday and treating its solutions to problems yesterday as problems to be solved today, and no real idea about the basic principles of design.
Now researchers at the University of Pennsylvania School of Veterinary Medicine (Penn Vet) have discovered how this arms race has resulted in a continuous battle in or intestines between our immune system and bacteria if the Yersina genus which includes the plague organism, Y. pestis.
The setting for creationism's putative designer's ludicrous battle with itself is the host's intestines where the Yersinia organisms, which are designed to overcome the body's first line of defences, set up colonies in the lymph system. The lymph system's purpose is to protect us from these sorts of infections but the pathogens have been designed to use the system against us!
The body's response is to then try to seal in these colonies with a collection of immune cells to form a granuloma, sustained by monocytes.
The problem is this solution doesn't always work as designed and the granulomas break down when the monocytes fail to sustain them. The infection can ten enter the blood stream and cause serious illness.
The research and its significance is described in a news release from Penn Vet:
Yersinia bacteria cause a variety of human and animal diseases, the most notorious being the plague, caused by Yersinia pestis. A relative, Yersinia pseudotuberculosis, causes gastrointestinal illness and is less deadly, but naturally infects both mice and humans, making it a useful model for studying its interactions with the immune system.
These two pathogens, as well as a third close cousin, Y. enterocolitica, which affects swine and can cause food-borne illness if people consume infected meat, have many traits in common, particularly their knack for interfering with the immune system’s ability to respond to infection.
The plague pathogen is blood-borne and transmitted by infected fleas. Infection with the other two depends on ingestion. Yet the focus of much of the work in the field had been on interactions of Yersinia with lymphoid tissues, rather than the intestine. A new study of Y. pseudotuberculosis led by a team from Penn’s School of Veterinary Medicine and published in Nature Microbiology demonstrates that, in response to infection, the host immune system forms small, walled-off lesions in the intestines called granulomas. It’s the first time these organized collections of immune cells have been found in the intestines in response to Yersinia infections.
The team went on to show that monocytes, a type of immune cell, sustain these granulomas. Without them, the granulomas deteriorated, allowing the mice to be overtaken by Yersinia.
Our data reveal a previously unappreciated site where Yersinia can colonize and the immune system is engaged. These granulomas form in order to control the bacterial infection in the intestines. And we show that if they don’t form or fail to be maintained, the bacteria are able to overcome the control of the immune system and cause greater systemic infection.
In all three Yersinia infections, a hallmark is that they colonize lymphoid tissues and are able to escape immune control and replicate, cause disease, and spread.
Because it’s an orally acquired pathogen, we were interested in how the bacteria behaved in the intestines. Daniel [Sorobetea, first-author] made this initial observation that, following Yersinia pseudotuberculosis infection, there were macroscopically visible lesions all along the length of the gut that had never been described before.
We hypothesize that it’s a general role for the monocytes in other tissues as well.
Previous to this study we knew of Peyer’s patches to be the primary site where the body interacts with the outside environment through the mucosal tissue of the intestines.
These therapies have caused an explosion of excitement in the cancer field, the idea of reinvigorating the immune system. Conceptually we can also think about how to coax the immune system to be reinvigorated to attack pathogens in these settings of chronic infection as well.
Professor Igor E. Brodsky, senior author
Robert R. Marshak Professor and chair of the Department of Pathobiology
University of Pennsylvania School of Veterinary Medicine.
Pennsylvania, USA.
The findings have implications for developing new therapies that leverage the host immune system, Brodsky says. A drug that harnessed the power of immune cells to not only keep Yersinia in check but to overcome its defenses, they say, could potentially eliminate the pathogen altogether.
A novel battlefield
Y. pestis, Y. pseudotuberculosis, and Y. enterocolitica share a keen ability to evade immune detection.
Earlier studies had shown that Yersinia prompted the formation of granulomas in the lymph nodes and spleen but had never observed them in the intestines until Daniel Sorobetea, a research fellow in Brodsky’s group, took a closer look at the intestines of mice infected with Y. pseudotuberculosis.
The research team, including Sorobetea and later Rina Matsuda, a doctoral student in the lab, saw that these same lesions were present when mice were infected with Y. enterocolitica, forming within five days after an infection.
A biopsy of the intestinal tissues confirmed that the lesions were a type of granuloma, known as a pyogranuloma, composed of a variety of immune cells, including monocytes and neutrophils, another type of white blood cell that is part of the body's front line in fighting bacteria and viruses.
Granulomas form in other diseases that involve chronic infection, including tuberculosis, for which Y. pseudotuberculosis is named. Somewhat paradoxically, these granulomas—while key in controlling infection by walling off the infectious agent—also sustain a population of the pathogen within those walls.
The team wanted to understand how these granulomas were both formed and maintained, working with mice lacking monocytes as well as animals treated with an antibody that depletes monocytes. In the animals lacking monocytes “these granulomas, with their distinct architecture, wouldn’t form,” Brodsky says.
Instead, a more disorganized and necrotic abscess developed, neutrophils failed to be activated, and the mice were less able to control the invading bacteria. These animals experienced higher levels of bacteria in their intestines and succumbed to their infections.
Groundwork for the future
The researchers believe the monocytes are responsible for recruiting neutrophils to the site of infection and thus launching the formation of the granuloma, helping to control the bacteria. This leading role for monocytes may exist beyond the intestines, the researchers believe.
But the discoveries also point to the intestines as a key site of engagement between the immune system and Yersinia.
Peyer’s patches are small areas of lymphoid tissue present in the intestines that serve to regulate the microbiome and fend off infection.
In future work, Brodsky and colleagues hope to continue to piece together the mechanism by which monocytes and neutrophils contain the bacteria, an effort they’re pursing in collaboration with Sunny Shin’s lab in the Perelman School of Medicine’s microbiology department.
A deeper understanding of the molecular pathways that regulate this immune response could one day offer inroads into host-directed immune therapies, by which a drug could tip the scales in favor of the host immune system, unleashing its might to fully eradicate the bacteria rather than simply corralling them in granulomas.
Abstract
Granulomas are organized immune cell aggregates formed in response to chronic infection or antigen persistence. The bacterial pathogen Yersinia pseudotuberculosis (Yp) blocks innate inflammatory signalling and immune defence, inducing neutrophil-rich pyogranulomas (PGs) within lymphoid tissues. Here we uncover that Yp also triggers PG formation within the murine intestinal mucosa. Mice lacking circulating monocytes fail to form defined PGs, have defects in neutrophil activation and succumb to Yp infection. Yersinia lacking virulence factors that target actin polymerization to block phagocytosis and reactive oxygen burst do not induce PGs, indicating that intestinal PGs form in response to Yp disruption of cytoskeletal dynamics. Notably, mutation of the virulence factor YopH restores PG formation and control of Yp in mice lacking circulating monocytes, demonstrating that monocytes override YopH-dependent blockade of innate immune defence. This work reveals an unappreciated site of Yersinia intestinal invasion and defines host and pathogen drivers of intestinal granuloma formation.
Sorobetea, Daniel; Matsuda, Rina; Peterson, Stefan T.; Grayczyk, James P.; Rao, Indira; Krespan, Elise; Lanza, Matthew; Assenmacher, Charles-Antoine; Mack, Matthias; Beiting, Daniel P.; Radaelli, Enrico; Brodsky, Igor E.
Inflammatory monocytes promote granuloma control of Yersinia infection Nature Microbiology (2023); DOI: 10.1038/s41564-023-01338-6
I doubt that any Creationist would have the courage to read this far, but this offer is open to any who do: Please explain how this system can be regarded as the work of an omnibenevolent, omniscience, intelligent designer and not the work of either an incompetent malevolence or the result of amoral, utilitarian natural processes operating without a plan.
