There is a simple paradox at the heart of creationism that I have never even
seen an attempt to resolve. It all comes from two beliefs: there is only one
designer god capable of designing living organisms and that designer god designed
us complete with our immune system with which we can attempt to resist attack by
pathogens, and that pathogens are not the work of this design, but are the
result of 'genetic entropy' and 'devolution' since Adam & Eve let 'sin' into
the world. The fact that Michael J. Behe, who invented that excuse, has let slip
that ID Creationism is Bible literalism in a lab coat seems to be lost on his
followers who still dutifully insist that it is a scientific alternative to
evolution and should be taught in school science class (presumably now with the
tale of Adam & Eve taught as real history and 'sin' as a real force in
science).
The paradox is, did the designer god give Adam & Eve an immune system, or
did it design an upgrade when 'sin' allowed pathogens to exist? If the former,
it was anticipating and planning for the so-called 'fall'; if the latter, it
lacked foresight so is not omniscient.
But however creationists resolve this paradox they still have to explain why the
'intelligently designed' immune system doesn't work very well and why whatever is
designing pathogens seems to be able to overcome it.
The nonsense about 'sin', 'the fall', etc., is trivially easy to refute because
any improvement in a parasite's ability to parasitise its host can't possibly be
regarded as a devolution from some assumed initial perfection because an
improvement can't be worse that what it's an improvement on. The whole nonsense
of 'devolution' is biological gobbledygook, intelligently designed to appeal to
scientifically illiterate simpletons who want to fit the Bible superstition
somewhere in the reasoning without bothering too much about the logic or the
biology.
So, the paradox boils down to why an intelligent designer would be having an
arms race with itself so the parasites it creates can continue to parasitise the
victims it creates complete with their immune system it created to stop them.
Creationists normally flee in terror at the mere mention of arms races, which is
why you'll never see them discussed in the cult literature apart from where
pathogens are waved aside as 'caused by sin', blah, blah, blah...
So, it would be refreshing indeed to see a genuine attempt by an intelligent
design creationist try to give some rational explanation, and hopefully without
giving away the fact that ID creationism is merely Christian fundamentalism in
disguise, for the discovery by a new UC Davis Health study that shows how the
Salmonella bacteria, a major cause of food poisoning, can invade the gut even
when protective bacteria are present.
As an added embarrassment for creationists, Salmonella is closely related to Escherichia coli (E.coli) that they usually cite Michael J. Behe as 'proving' it must have been designed by their god because its flagellum is 'irreducibly complex'.
First a little AI background information about Salmonella, where it came from
and what it does to us:
If there is one thing designed to get creationists chanting 'Common Designer!' it's evidence of the same gene doing the same thing in lots of different organisms, no matter how distantly related they are.
But when that gene is needed because of a basic design blunder long ago in the evolution of multicellular organisms, that chant looks increasingly forlorn.
For example, scientists have just shown how SOX and POU genes isolated from a single-celled choanoflagellate can be used to convert a mouse cell to function as the stem cell to clone another mouse. The reason this works is because something needs to reset the epigenetic setting in specialised cells. In a multicellular organism like a mouse, this effectively means any cell produced after the first few cell divisions of the fertilised zygote.
But why would a single-celled organism like a choanoflagellate need to do that? The answer it that epigenetics originally evolved to make an organism more able to respond to environmental changes and stresses.
A cell of the ichthyosporean C. perkinsii showing distinct signs of polarity, with clear cortical localization of the nucleus before the first cleavage. Microtubules are shown in magenta, DNA in blue, and the nuclear envelope in yellow.
Scientists believe they may have cracked the chicken and egg 'problem' that creationists have been fooled into thinking is a killer problem for the Theory of Evolution. With their child-like understanding of evolution, creationists can't imagine how species emerge over time from earlier species by a process of evolution and think that their mythical magic creation without ancestors is actually what happens, or at least what evolutionary biologists think happens. So, they imagine explaining how the first chicken hatched from the first egg before there was a chicken to lay it, is an insurmountable problem.
In fact, of course there never was a first chicken just as there never was a first human, and eggs are simply a phase in the life cycle of, in this case, chickens, so hens' eggs are chickens just as much so as adult hens are. The ancestral species that the Southeast Asian jungle fowl evolved from had been laying eggs ever since they diverged from the egg-laying avian dinosaurs that had evolved from the egg-laying theropod dinosaurs, etc, etc, back to the egg-laying tunicates and chordates in the Cambrian and their egg-laying ancestors...
Schematic representation of how a C. pneumoniae cell infects a human cell. The bacterium injects the protein SemD (green) into the cell, which activates the cell protein N-WASP, which in turn initiates vesicle formation.
The problem of parasites for creationists is one that, despite the best efforts of apologists like Michael J Behe of the Deception Institute, just won't go away.
Sadly, Behe shot himself in the foot with his original claim to have proven 'intelligent [sic] design in living organisms with his choice of the bacterial flagellum in E. coli, where he persuaded his willing audience that these nasty little pathogens had been intelligently designed - and by unspoken assumption, designed by the locally-popular god.
Now creationists wave his 'proof' of design as evidence for their creator god because only their god is capable of creating living organisms.
But, with characteristic double-think, creationists also argue that their god is omnibenevolent, so something else must have created parasites like E. coli, and, courtesy again of Michael J. Behe, they cite 'Sin' causing 'genetic entropy' and the absurd idea of 'devolution' this supposedly causes, as the cause of parasites and pathogens (but not the bacterial flagellum, obviously!).
The problem with that notion is that they need to do their double-think trick one more time and believe that a trait with improves a pathogens ability to live and reproduce in its host makes it somehow less perfect that one without that trait. So, in the creationist's world, an improvement is a move away from perfection!
But, with a cult that appears to believe learning is a move away from the 'perfection' of pristine ignorance (from whence comes expertise in all aspects of science), that's probably not too difficult a feat of mental gymnastics for a creationist to perform.
This is the second paper today to show the apparent obsession creationism's putative designer has with creating viruses, if you believe that superstition.
The first paper dealt with the discovery that there are some 600 different viruses to be found on a used toothbrush and on the shower heads in US bathrooms; this one reports on a discovery that makes that finding pale into insignificance. It is the discovery, using the machine learning of AI, of 161,979 new viruses!
This is just tip of the iceberg as the authors say the method just scratches the surface of biodiversity and opens up a world of discovery with millions more to be discovered.
Creationism's putative creator is nothing if not obsessive.
One of its obsessions appears to be designing ever-more exquisite ways to kill its creation as almost nothing in nature exists that doesn't have something that lives on or in it, often killing it in the process or at least weakening it in some way.
Its most visible obsession seems to be with designing beetles of which there are some 500,000 species with more being discovered almost daily. It's highly likely that there may be as many as a million different beetles in the world, many of which catch and devour other arthropods.
But it's in the field of virology that we find another obsession with designing variations on a general theme. Not only are there literally hundreds of thousands of viruses but every species has multiple variants - look at the number of different variants of the SARS-CoV-2 virus that have emerged since the initial wave of the COVID-19 pandemic!
The Bushveld Igneous Complex (BIC), South Africa. This picture shows a very famous outcrop where nearly horizontal black and white layers are observed. The BIC made of layers of igneous rock in a basin shape, formed over a period of about 1 million years, after which it seems to have barely changed.
In today's incidental rebuttal of creationist dogma, archaeologists have discovered living colonies of microbes sealed within cracks in 2-billion-year-old rocks from South Africa.
The microbes became sealed in the cracks by tightly-packed layers of clay so effectively creating sealed chambers from which nothing could escape and, more importantly, nothing could enter. They have survived over geological time by firstly having an extremely low metabolic rate, with a generation time measured in thousands, even millions of years, compared to surface-dwelling microbes with generation times in hours or minutes, and by utilising sulphates as their energy source.
What they demonstrate, apart from the fallacy of Earth only being made by magic 10,000 years ago, is that in a highly stable environment, a plentiful source of energy and the ability to recycle their dead with almost no loss of energy, there is no environmental pressure to evolve, so the microbes have remained virtually unchanged for hundreds of millions, even billions of years.
The human gut, like that of other mammals, birds and vertebrates in particular and the gut of many insects and worms, in fact any organism with a moth and an anus, is an ideal environment for a whole host of other organisms, most of which will have co-evolved with humans and have been with us since our ancestors were small insectivores, skulking in the dark of the night to avoid dinosaurs and predatory proto-birds.
They for a complex and dynamic ecosystem of competing and cooperating bacteria, viruses, fungi and protozoa which exists in a more or less stable balance of arms races, predation and symbiosis.
One of the clutch of science publications which casually and unintentionally refute creationism to be published today, comes in the form of a paper by a team from the University of Tokyo, Tohoku University and Kochi University, Japan, which describes a new method for analysing ancient microfossils, and so discovering more about how key processes evolved in early cellular life.
The purpose of this is to discover not whether (that is never in doubt) but the precise details of how and when these key processes evolved.
Although good hygiene and safe drinking water have most brought cholera under control in developed societies, it is still a major kill, especially of children, in poor and technologically under-developed countries.
It was a cholera outbreak of 1849 in Soho, London, the John Snow famously showed was statistically linked to drinking water from a well in Broad Steet, eventually persuading the authorities to remove the pump handle from the well, so ending the epidemic, that Snow conformed the Germ Theory of disease and founded modern epidemiology.
The cause was later shown to be a leaking septic tank which was contaminating the water in the well, and more remotely to a baby which caught cholera elsewhere whose nappy (diaper) was washed into the sewer, introducing the Vibrio cholerae into the septic tank.
I was born and brought up in North Oxfordshire in a rural community where, a generation earlier, cholera had been the single most common cause of death of children. A perusal of the parish burial registers shows regular patterns of epidemics causing a sudden increase in child deaths.
Even in technologically advanced countries, natural disasters such as earthquakes and floods, and man-made conflicts such as those currently in Gaza and Ukraine can destroy the infrastructure and quickly lead to conditions in which cholera can further devastate an already weakened population.
It would be an especially despicable malevolence that designed an organism to exploit people in those situation to ensure there was even more suffering, but those subscribing to the intelligent design hoax are unwittingly attributing exactly that to their putative designer god.
In the study, scientists performed a genetic analysis on the bones of 133 human individuals from late Neolithic megalithic graves near Warburg in North Rhine-Westphalia. The team discovered the genome of the bacterium Yersinia pestis in the bone samples of two independent individuals. Additionally, previously published genomic data from a bone sample of a Neolithic dog found in Ajvide (Sweden) suggested a potential infection route.
What was creationism's divine malevolence up to with one of its most successful pathogens with which if killed hundreds of millions and changes society - the Yersinia pestis bacterium which caused the waves of black death and plague that regularly spread across the world?
It seems to have been experimenting, possibly trying to either perfect its virulence or work out the best delivery system to ensure it got to and killed as many people as possible. Sometimes, entire villages were wiped out. Not far from where I currently live are a couple of former villages that disappeared during the black death - the village of Woodperry near Oxford is an example, surviving now only in the name 'Woodperry Road' and a farmhouse later built on the site.
But 5000 years ago, Y. pestis doesn't seem to have been anything like a virulent as it became in the 12th Century. According to a recent discovery, it was capable of killing the occasional neolithic farmer but not of becoming a major pandemic able to kill hundreds of thousands and depopulate vast areas.
So, what changed, and more to the point, which explanation would a creationist prefer; the one which blames their god or the one which attributes it to evolution, climate change and cultural changes in human society? One thing we can be sure of though is the Michael J. Behe's biologically nonsensical religious apologetic of 'genetic entropy', causing the bacterium to 'devolve' away from an assumed created perfection (as though that were remotely possible), can be ruled out, because whatever the changes were, it led to a massive increase in the number of Y. pestis organisms, so was indisputably beneficial to it - in other words, in classical terms, it evolved.
In a very nice example of how humans and their gut microbiome have co-evolved, researchers from the Wellcome Sanger Institute, University College London (UCL), and the University of Birmingham, have identified a bacterium that helps digest breast milk and protects the baby from harmful pathogens.
As an example of intelligent [sic] design, this comes as close to a Heath-Robinson solution to a problem of the designer's own making as it's possible to imagine.
No designer who designed a baby's digestive system so it is susceptible to the harmful pathogens that it also designed, and created the baby to feed on breast milk that is difficult to digest, then solved those problems by creating another bacterium to fight the pathogens and help digest the milk, and infecting the baby with it, doesn't deserve the adjective 'intelligent'. 'Bloody stupid' would be a more appropriate term.
It's almost exactly as though the designer of these systems is a mindless automaton, simply obeying the natural laws of chemistry and physics and working without a plan!
The researchers have completed the largest study of UK baby microbiomes to date, carrying out whole genome sequencing to analyse stool samples from 1,288 healthy infants, all under one month old from the UK Baby Biome Study1.1.
Not content with the suffering that gum disease and dental caries cause, creationism's divine malevolence used at least one of the pathogens behind those problems to increase suffering a little more by aggrevating rhuematoid arthritis.
That's the inevitable conclusion honest creationist, who rejects the notion of evolution in which pathogenic parasites evolve naturally without intent, malevolent, benign or indifferent, should be drawing from the evidence from a Tokyo Medical and Dental University team of researchers led by Tokuju Okano and Toshihiko Suzuki of the Department of Bacterial Pathogenesis recently published in the International Journal of Oral Science.
This is not the first instance of creationism's divine malevolence multi-tasking its pathogens: in 2017 a team of researchers from The Chinese University of Hong Kong found a link between five oral bacteria, Peptostreptococcus stomatis, Streptococcus anginosus, Parvimonas micra, Slackia exigua and Dialister pneumosintes and the incidence of stomach and eosphageal cancer.
The oral bacterium which has been found to be aggrevating rheumatoid arthritis is Aggregatibacter actinomycetemcomitans.
One of the lines of attack against the science of evolutionary biology is the lie that Richard Dawkins was advocating selfishness with his seminal book, The Selfish Gene, so 'proving' that rejection of the Christian god as the explanation for biodiversity is because 'Evolutionists' just want to sin.
It is, of course, like other creationist attacks on science, utterly devoid of any factual basis and reflects badly both on those who seek to fool their target dupes with it and on their dupes who eagerly believe them in order to justify a pretense of moral superiority.
In fact, natural selection and differential success of different alleles within a selective environment is devoid of any moral contents because it is devoid of intelligent input and genes are passive in the process. In Dawkin’s analogy, the result is as though genes behave selfishly, not that they make moral decisions or have the ability to choose which environmental selectors act on them.
One of the predictable outcomes of this gene-centred approach is that in a competition, the result which suits all competitors is cooperation since in a cooperative alliance, all the genes are winners, just as with a human group, a cooperative group is invariably more successful than a group of competing individuals in perpetual conflict.
Most cells, either single-celled organisms like bacteria or the eukaryote cells of multicellular organisms, reproduce by simple division into two daughter cells. Under favourable conditions, this means a cell can produce a population of descendants that grows exponentially 1 → 2 → 4 → 8 → 16 → 32→64 … etc. (population = 2n; where n= the number of generations)
But the trick a bacterium, Corynebacterium matruchotii, that is only found in the human mouth uses is to divide into multiple new cells at each generation. For example, assuming it splits into 10 daughter cell at each generation, its growth rate from a single founder cell will be 1 → 10 → 100 → 1000 → 10,000 → 100,000 → 1,000,000 … etc., (population = 10n). But scientists have found it can do better than that, producing up to 14 new cells at each generation.
In 6 generations in favourable conditions, Corynebacterium matruchotii can produce 1 million or more offspring, against an 'ordinary' bacteria's 64, so rapidly out-pacing any other bacteria. C. matruchotii is an essential component of the plaque that quickly develops on teeth. It appears to have no other known function.
In some ways, C. matruchotii behaves more like fungal hyphae, growing at the tip to produce a long thin filament. It is this filament that then simply splits up into small sections, each of which becomes a new cell.
The filamentous bacteria C. matruchotii splitting into multiple cells at once, a rare kind of cell division called multiple fission.
Credit: Scott Chimileski, MBL
In 2020 a team of researchers showed how plaque is a highly structured and organised colony of different microorganisms which almost seems to be designed to allow Streptococcus mutans to get on with its job of dissolving the tooth enamel and causing caries. Creationists dogma insists that anything with a complex, organised structure must be intelligently designed because, so they assert, complexity and order can’t arise from disorder without intelligent intervention.
This latest discovery shows how the beginnings of this organised colony are established very quickly.
Tell a creationists that humans and chimpanzees have 98% of their genomes in common, and they'll tell you this doesn't prove common origins or 'macro-evolution', but show them evidence that two bacteria have evolved from a common ancestor because they have 80% of their genome in common and they'll tell you this doesn't mean they've evolved because they are both still 'bacteria kind'.
So, why doesn't 98% commonality mean humans and chimpanzees are both still 'ape kind'?
But the evidence that the two bacteria, Mycobacterium tuberculosis, and the newly-discovered M. spongiae is compelling, and gives a clue as to the origins of M. tuberculosis, one of the most deadly pathogenic bacteria, possibly from marine origins.
Immunofluorescence staining of human gastric cells grown in a microplate and infected with Chlamydia trachomatis. Blue: cell nuclei, green: C. trachomatis, grey: actin.
Image: Pargev Hovhannisyan / Universität Würzburg
Chlamydia doesn’t always cause symptoms, but when it does, these are some of the most common.
Chlamydia is a sexually-transmitted bacterial infection in which the bacteria are passed to a new victim during sexual intercourse. It caused few or no symptoms to begin with - usually nothing worse than mild itching - but if left untreated it can cause infertility and sometimes cancer. Fortunately, it can be treated successfully with antibiotics.
However, it is not unusual for people who have been successfully treated to develop a new infection with exactly the same strain as the previous infection, suggesting that the bacteria had somehow survived the antibiotic treatment although symptoms had disappeared, and traces of the bacteria had gone.
Researchers have now shown that chlamydia can take up residence in the gut where it can survive for some considerable time and develop increasing resistance to antibiotics with each course of treatment. The mechanism of this increasing resistance is a classic example of evolution as the antibiotic acts as an environmental selector which removes the non-resistant bacteria from the population gene pool, leaving the resistant form to become dominant in the gene pool.
Mono Lake, located east of the Sierra Nevada, just outside Yosemite National Park. Dotted with tufa formations, the lake’s salty water is laced with arsenic and cyanide, but is home to unique flies and brine shrimp as well as choanoflagellates.
Nicole King.
To be fair to them, the simple pastoralists from the ignorant and fearful infancy of out species who invented the creation myths that got included in the Bible, later decreed to be the inerrant word of a creator god and therefore deemed to be real science and history, could have known nothing of Mono Lake in Present day California and even less about the microscopic organisms about the size of a dust grain known now as choanoflagellates because, quite simply they lacked the technology to be able to see them - which is also why neither cells nor micro-organisms are mentioned nor even hinted at, anywhere in the Bible.
What are choanoflagellates and how do they relate to other organisms?
Choanoflagellates are a group of free-living, single-celled organisms that are considered to be the closest living relatives of animals (metazoans). They are part of the clade Opisthokonta, which also includes fungi, animals, and some protists. Here’s a closer look at what choanoflagellates are and their relationship to other organisms:
Characteristics of Choanoflagellates
Structure: Choanoflagellates are characterized by a distinctive cell structure. Each cell has a single flagellum, which is a whip-like structure used for movement, surrounded by a collar of microvilli (tiny, finger-like projections). The flagellum beats, drawing water through the collar, which traps bacteria and other small particles for the choanoflagellate to feed on.
Habitat: These organisms are commonly found in aquatic environments, including both freshwater and marine ecosystems.
Lifestyle: Choanoflagellates can exist as single cells, but some species form colonies. Their colonial forms are of particular interest because they offer insights into the possible evolutionary steps that led to multicellularity in animals.
Relationship to Other Organisms
Closest Relatives to Animals: Genetic and molecular studies have shown that choanoflagellates are the closest living relatives to animals. This means that they share a common ancestor with animals, which is believed to have lived over 600 million years ago.
Evolutionary Significance: The relationship between choanoflagellates and animals is crucial for understanding the origin of multicellularity. It is thought that the transition from single-celled to multicellular organisms may have occurred through mechanisms similar to those seen in choanoflagellate colonies. The study of choanoflagellates helps scientists understand the early evolution of animals and the development of complex tissues and organs.
Shared Genes: Choanoflagellates possess many genes that are also found in animals, including those involved in cell adhesion, signaling, and extracellular matrix formation. These genes are essential for the development and maintenance of multicellular structures in animals, suggesting that the genetic toolkit required for multicellularity was already present in the last common ancestor of choanoflagellates and animals.
In summary, choanoflagellates are not only fascinating in their own right as unique protists, but they also play a key role in understanding the evolutionary steps that led to the rise of the animal kingdom.
And, being unaware of the history of life on a planet that they thought was only a few thousand years old and had been created out of nothing by magic with all the animals and plants fully formed, they could never in a million years, have guessed how multicellular animals evolved several hundred million years ago out of colonies of single-celled organisms.
And, of course, it's the yawning chasm between what the Bible's authors believed and what we now know, that tells us the Bible can't be the work of an omniscient creator god.
But of course, there are still a few (shrinking) gaps in what we know too. For example, although we have the genetic and structural evidence that multicellular organisms evolved out of single-celled organisms, we don't yet know the precise details, which is why a team of researchers from University of California, Berkeley have been studying a little-known choanoflagellates found in Mono Lake, near the Sierra Nevada, California. choanoflagellates are known to form colonies of organisms so can help shed some light on how related organisms originally got together to form simple multicellular organisms.
An additional discovery of this research was how these colonies incorporate a bacterial biome in a process analogous to the way most multicellular animals have associated biomes like out gut biome, for example.
The Berkely team's work is the subject of an open access paper in the American Society for Microbiology (ASM) journal mBio. It is also explained in a University of California Berkely news release:
Creature the size of a dust grain found hiding in California’s Mono LakeColonies of these choanoflagellates — members of a group considered to be the closest living relatives of all animals — have their own unique microbiomes.
Mono Lake in the Eastern Sierra Nevada is known for its towering tufa formations, abundant brine shrimp and black clouds of alkali flies uniquely adapted to the salty, arsenic- and cyanide-laced water.
University of California, Berkeley, researchers have now found another unusual creature lurking in the lake’s briny shallows — one that could tell scientists about the origin of animals more than 650 million years ago.
The organism is a choanoflagellate, a microscopic, single-celled form of life that can divide and develop into multicellular colonies in a way that’s similar to how animal embryos form. It’s not a type of animal, however, but a member of a sister group to all animals. And as animals’ closest living relative, the choanoflagellate is a crucial model for the leap from one-celled to multicellular life.
Surprisingly, it harbors its own microbiome, making it the first choanoflagellate known to establish a stable physical relationship with bacteria, instead of solely eating them. As such, it’s one of the simplest organisms known to have a microbiome.
Very little is known about choanoflagellates, and there are interesting biological phenomena that we can only gain insight into if we understand their ecology.
Professor Nicole King, senior author
Professor of molecular and cell biology
Howard Hughes Medical Institute and Department of Molecular and Cell Biology
University of California, Berkeley, California, USA.
Globular colonies of the choanoflagellate B. monosierra seen under a microscope. As indicated by the 50-micron scale bar, these colonies are at the limit of what’s visible to the naked eye.
Alain Garcia De Las Bayonas, Nicole King lab.
Typically visible only through a microscope, choanoflagellates are often ignored by aquatic biologists, who instead focus on macroscopic animals, photosynthetic algae or bacteria. But their biology and lifestyle can give insight into creatures that existed in the oceans before animals evolved and that eventually gave rise to animals. This species in particular could shed light on the origin of interactions between animals and bacteria that led to the human microbiome.
Animals evolved in oceans that were filled with bacteria. If you think about the tree of life, all organisms that are alive now are related to each other through evolutionary time. So if we study organisms that are alive today, then we can reconstruct what happened in the past.
Professor Nicole King.
King and her UC Berkeley colleagues described the organism — which they named Barroeca monosierra, after the lake — in a paper published online Aug. 14 in the journal mBio.
A beautiful colony
Nearly 10 years ago, then-UC Berkeley graduate student Daniel Richter came back from a climbing trip in the Eastern Sierra Nevada with a vial of Mono Lake water he’d casually collected along the way. Under the microscope, it was alive with choanoflagellates. Aside from brine shrimp, alkali flies and various species of nematode, few other forms of life have been reported to live in the inhospitable waters of the lake.
The newly named species Barroeca monosierra discovered in Mono Lake. Colonies of these organisms consist of numerous identical cells (cyan), each with flagella (green) that allow them to propel themselves through the water. This choanoflagellate colony hosts its own microbiome (red), something never before seen in these organisms. The extracellular matrix with which the bacteria interact is shown in white.
Video credit: Davis Laundon and Pawel Burkhardt, Sars Centre, Norway; Kent McDonald and Nicole King, UC Berkeley.
It was just packed full of these big, beautiful colonies of choanoflagellates. I mean, they were the biggest ones we’d ever seen.
Professor Nicole King.
The colonies of what seemed to be close to 100 identical choanoflagellate cells formed a hollow sphere that twirled and spun as each individual cell kicked its flagella.
One of the things that’s interesting about them is that these colonies have a shape similar to the blastula — a hollow ball of cells that forms early in animal development. We wanted to learn more about it.
Professor Nicole King.
At the time, however, King was occupied with other species of choanos, as she calls them, so the Mono Lake choanos languished in the freezer until some students revived and stained them to look at their unusual, doughnut-shaped chromosomes. Surprisingly, there was also DNA inside the hollow colony where there should have been no cells. After further investigation, graduate student Kayley Hake determined that they were bacteria.
A colony of choanoflagellates stained to show its features. Cyan indicates DNA — the doughnut-shaped DNA of the choanoflagellate cells and a cloud of bacterial DNA inside the colony — while flagella are white and microscopic hairs (villi) on each cell are red.
Kayley Hake, Nicole King lab
The bacteria were a huge surprise. That just was fascinating.
Professor Nicole King.
Hake also detected connective structures, called extracellular matrix, inside the spherical colony that were secreted by the choanos.
Only then did it occur to Hake and King that these might not be the remains of bacteria the choanos ate, but bacteria living and grazing on stuff secreted by the colony.
No one had ever described a choanoflagellate with a stable physical interaction with bacteria. In our prior studies, we found that choanos responded to small bacterial molecules that were floating through the water, or [that] the choanos were eating the bacteria, but there was no case where they were doing anything that could potentially be a symbiosis. Or in this case, a microbiome.
Professor Nicole King.
King teamed up with Jill Banfield, a pioneer in metagenomics and a UC Berkeley professor of environmental science, policy and management and of earth and planetary science, to determine which bacterial species were in the water and inside the choanos. Metagenomics involves sequencing all the DNA in an environmental sample to reconstruct the genomes of the organisms living there.
After Banfield’s lab identified the microbes in Mono Lake water, Hake created DNA probes to determine which ones were also inside the choanos. The bacterial populations were not identical, King said, so evidently some bacteria survive better than others inside the oxygen-starved lumen of the choanoflagellate colony. Hake determined that they were not there accidentally; they were growing and dividing. Perhaps they were escaping the toxic environment of the lake, King mused, or maybe the choanos were farming the bacteria to eat them.
Much of this is speculation, she admits. Future experiments should uncover how the bacteria interact with the choanoflagellates. Past work in her lab has already shown that bacteria act like an aphrodisiac to stimulate mating in choanoflagellates, and that bacteria can stimulate single-celled choanos to aggregate into colonies.
For her, the Mono Lake choanoflagellate will become another model system in which to study evolution, just like the choanos that live in splash pools on the island of Curaçao in the Caribbean — her main focus at the moment — and the choanos in pools at the North and South Poles. It might be a challenge to get more samples from Mono Lake, however. On a recent visit, only six of 100 samples contained these energetic microorganisms.
I think there’s a great deal more that needs to be done on the microbial life of Mono Lake, because it really underpins everything else about the ecosystem,. I’m excited about B. monosierra as a new model for studying interactions between eukaryotes and bacteria. And I hope it tells us something about evolution. But even if it doesn’t, I think it’s a fascinating phenomenon.
Professor Nicole King.
In addition to King, Banfield, Hake and Richter, UC Berkeley co-authors of the paper include former doctoral student Patrick West, electron microscopist Kent McDonald and postdoctoral fellows Josean Reyes-Rivera and Alain Garcia De Las Bayonas. The work is supported by HHMI and the National Science Foundation.
ABSTRACT
As the closest living relatives of animals, choanoflagellates offer insights into the ancestry of animal cell physiology. Here, we report the isolation and characterization of a colonial choanoflagellate from Mono Lake, California. The choanoflagellate forms large spherical colonies that are an order of magnitude larger than those formed by the closely related choanoflagellate Salpingoeca rosetta. In cultures maintained in the laboratory, the lumen of the spherical colony is filled with a branched network of extracellular matrix and colonized by bacteria, including diverse Gammaproteobacteria and Alphaproteobacteria. We propose to erect Barroeca monosierra gen. nov., sp. nov. Hake, Burkhardt, Richter, and King to accommodate this extremophile choanoflagellate. The physical association between bacteria and B. monosierra in culture presents a new experimental model for investigating interactions among bacteria and eukaryotes. Future work will investigate the nature of these interactions in wild populations and the mechanisms underpinning the colonization of B. monosierra spheres by bacteria.
IMPORTANCE
The diversity of organisms that live in the extreme environment of Mono Lake (California, USA) is limited. We sought to investigate whether the closest living relatives of animals, the choanoflagellates, exist in Mono Lake, a hypersaline, alkaline, arsenic-rich environment. We repeatedly isolated members of a new species of choanoflagellate, which we have named Barroeca monosierra. Characterization of B. monosierra revealed that it forms large spherical colonies containing diverse co-isolated bacteria, providing an opportunity to investigate mechanisms underlying physical associations between eukaryotes and bacteria.
OBSERVATION
A newly identified choanoflagellate species forms large spherical colonies
Choanoflagellates are the closest living relatives of animals and, as such, provide insights into the origin of key features of animal biology (1, 2). Over five sampling trips to Mono Lake, California (Fig. 1A; Table S1), we collected single-celled choanoflagellates and large spherical choanoflagellate colonies, many of which were seemingly hollow (Fig. 1B). In colonies and single cells, each cell bore the diagnostic collar complex observed in other choanoflagellates: an apical flagellum surrounded by a collar of microvilli (1, 2). In the spherical colonies, each cell was oriented with the basal pole of the cell body facing inwards and the apical flagellum facing out (Fig. 1B). We know of no prior reports of choanoflagellates having been isolated and cultured from any hypersaline alkaline lake, including Mono Lake.
Fig 1
Fig 1 A colonial choanoflagellate isolated from Mono Lake. (A) Choanoflagellates were collected from three sampling sites (asterisks) near the shore of Mono Lake, California (modified from a map in the public domain, formatted as USGS Imagery Only; https://www.usgs.gov/volcanoes/long-valley-caldera) (B) B. monosierra forms large colonies (differential interference contrast image). Scale bar = 50 µm. (C) B. monosierra (shown in bold) is a craspedid choanoflagellate closely related to S. rosetta and Microstomoeca roanoka. Phylogeny based on sequences of three genes: 18S rRNA, EFL, and HSP90. Metazoa (seven species) were collapsed to save space. Bayesian posterior probabilities are indicated above each internal branch, and maximum likelihood bootstrap values are below. (A “—” value indicates a bifurcation lacking support or not present in one of the two reconstructions.) Also see Fig. S1C for further phylogenetic analyses. (D and E) Two colonies from the ML2.1G culture (Fig. S1, Box2) reveal the extremes of the B. monosierra colony size range (D, 58 µm diameter; E, 19 µm diameter; scale bar = 20 µm). In B. monosierra colonies, each cell is oriented with its apical flagellum (white; labeled with anti-tubulin antibody) and the apical collar of microvilli (red; stained with phalloidin) pointing out. Nuclei (cyan) were visualized with the DNA-stain Hoechst 33342. (F) Colonies of B. monosierra span from 10 µm in diameter, a size comparable to that of small S. rosetta colonies, to 120 µm, over an order of magnitude larger. The diameters of B. monosierra and S. rosetta colonies were plotted as a violin plot; the median is indicated as a thick black line. Diameters of the colonies in panels D and E are indicated as colored bars behind the violin plot (D, red bar; E, blue bar).
Fig 2
Fig 2 Bacteria reside in the lumina of B. monosierra colonies. (A and A′) The center of a B. monosierra colony from culture ML2.1G (Fig. S1, Box 2), shown as a maximum intensity projection (A) and optical z-section (A′), contains DNA (revealed by Hoechst 33342 staining; cyan). Apical flagella were labeled with anti-tubulin antibody (white); microvilli were stained with phalloidin (red). Hoechst 33342 staining (cyan) revealed the spherical choanoflagellate nuclei along the colony perimeter and an amorphous cloud of DNA sitting within the central cavity formed by the monolayer of choanoflagellate cells. (B, B’’ and B′) A thin section through a B. monosierra colony, imaged by transmission electron microscopy (TEM), revealed the presence of small cells in the central cavity. (B′) Inset (box from panel B) reveals that the interior cells are each surrounded by a cell wall. (C, C’’, C’’’, and C″′′) The small cells inside B. monosierra colonies (grown from cultures ML2.1E/ML2.1EC) are bacteria, as revealed by hybridization with a broad-spectrum 16S rRNA probe (C, green) and a probe targeting Gammaproteobacteria (C′, red). Choanoflagellate nuclei and bacterial nucleoids were revealed by staining with Hoechst (C″, cyan). (C″′) Merge of panels C, C′, and C″. Scale bar for all = 5 µm. (D, D’ and D″) 3D reconstruction of a 70-cell B. monosierra colony from transmission electron micrographs of serial ultrathin sections revealed that the bacteria are closely associated with and wrapped around the extracellular matrix (ECM) inside the colony. (D) Whole colony view. (D′) Cut-away view of colony center. False colors indicate cell bodies (cyan), microvilli (orange), flagella (green), bacteria (red), ECM (white), intercellular bridges (yellow; see also Fig. S5), and filopodia (purple). (D″) Reducing the opacity of the choanoflagellate cell renderings revealed the presence of bacteria positioned between the lateral surfaces of choanoflagellate cells (brackets; see also Fig. S7). (E) Representative B. monosierra colony from an environmental sample shown as an average intensity projection (planes 17–27 from 1-µm optical sections). Choanoflagellate nuclei and bacterial nucleoids (examples indicated by arrowheads) were revealed by staining with Hoechst (cyan). To allow visualization of the much smaller bacterial nucleoids, the imaging of the choanoflagellate nuclei was saturated. Concanavalin A staining (magenta) revealed the branched extracellular matrix. (F and G) Optical sections 19 and 24, respectively, of the B. monosierra colony shown in panel E. (F′ and G′) Higher magnification Hoechst-stained DNA from the boxed regions in F and G, highlighting the resident bacteria (examples indicated by arrowheads). Scale bars in panels E–G = 10 μm.
This discovery shows a plausible route to multicellularity from a related single-celled eukaryote organism and offers an explanation for the early stages of embryo development where a single-cell zygote gives rise early on to a hollow gastrula. This could have formed in an ancestral multicellular metazoan as somewhere for a symbiotic colony of bacteria to reside and provide nutrients in return for protection. It also offers a plausible explanation for our commensal, symbiotic microbiome in our gut which has its embryonic origins in the hollow gastrula.
Creationists might also like to ignore the fact that the research team believe they are explaining a fundamental step in the evolution of multicellularity 650 million years ago, and have found no need to abandon science and the scientific method and turn to creationism with its magic and unproven entities for a more rational explanation of the facts.
And of course, as with 99.9975% of all history, this stage in the evolution of multicellular life happened in that long, pre-'Creation Week', period of Earth's history.
A comparison of immune proteins called viperins from Asgard archaea (left) and from a group of more complex life that includes humans, called eukaryotes (right). The three-dimensional shapes (a.k.a. structures) are strikingly similar, suggesting they also function similarly.
Multicellular organisms are collections of specialised eukaryote cells, which are themselves collections of prokaryote cells that have been around for several billion years before getting together to form more complex cells.
And those prokaryote cells - bacteria and archaea - had had to cope with viruses which arose as soon as there were replicating assemblages of DNA for them to parasitize and co-opt the replication mechanism to make more copies of themselves.
The result was one of the first evolutionary arms races as the prokaryotes evolved ways to prevent themselves being parasitised and viruses evolved ways to overcome the microbes defences.
And, or course, the later eukaryote, complex cells that were to form the multicellular organisms inherited these antiviral defences and carried on the arms race with viruses, so it makes sense to find some of the remnants of these microbial defences, probably modified, inside our own cells, and forming a first line of defences.
This is a simple prediction of the Theory of Evolution and the resulting descent with modification from a common ancestor from billions of years ago.
What information do you have on the anti-viral proteins, Asgard Viperin and Eukaryote Viperin?
Asgard Viperin and Eukaryote Viperin are both antiviral proteins that play crucial roles in the innate immune response, particularly in targeting and neutralizing viral infections. They belong to a broader family of proteins called Viperin (virus inhibitory protein, endoplasmic reticulum-associated, interferon-inducible). Viperin is a well-known antiviral protein that is highly conserved across various species, including archaea, bacteria, and eukaryotes. Here's a breakdown of what is known about Asgard Viperin and Eukaryote Viperin:
Asgard Viperin
Origin: Asgard Viperin is derived from the Asgard archaea, a group of microorganisms that are thought to be closely related to the last common ancestor of archaea and eukaryotes. These archaea were discovered in deep-sea hydrothermal vent environments and are considered important in studying the evolution of complex life forms.
Function: Asgard Viperin has been identified as an antiviral protein that provides insights into the ancient mechanisms of immune defense. Its function is similar to that of Viperin in eukaryotes, where it inhibits viral replication by targeting viral components or the cellular machinery viruses depend on for replication.
Structure and Mechanism: Like other Viperins, Asgard Viperin is likely to have a radical SAM (S-adenosylmethionine) domain, which is critical for its antiviral activity. This domain allows the protein to produce a reactive radical species, which can interfere with viral processes, such as the synthesis of nucleotides that viruses require for replication.
Evolutionary Significance: The discovery of Asgard Viperin highlights the ancient origins of antiviral defense mechanisms. It suggests that the strategies used by modern eukaryotic cells to combat viruses may have deep evolutionary roots.
Eukaryote Viperin
Origin: Eukaryote Viperin is found in eukaryotic organisms, including humans. It is one of the interferon-stimulated genes (ISGs) that are upregulated in response to viral infection. This protein is highly conserved across various species, from simple eukaryotes like algae to complex organisms like mammals.
Function: In eukaryotes, Viperin is a key player in the innate immune response. It exerts its antiviral effects through multiple mechanisms, depending on the type of virus. For example:
Inhibition of Viral Replication: Viperin can interfere with the replication of viruses by altering lipid metabolism or disrupting the assembly of viral particles.
Interaction with Cellular Machinery: It can inhibit viral RNA polymerase, thereby preventing the replication of RNA viruses.
Modulation of Immune Response: Viperin can enhance the production of other antiviral molecules and modulate the signaling pathways involved in the immune response.
Mechanism of Action: The radical SAM domain is crucial for the antiviral activity of Viperin in eukaryotes. This domain facilitates the formation of a radical species that can interfere with the function of viral proteins or the host cell machinery that viruses exploit.
Clinical Relevance: Understanding the role of Viperin in the immune response has significant implications for developing antiviral therapies. Since Viperin is involved in the response to a wide range of viruses, enhancing its activity could be a potential strategy for treating viral infections.
Comparative Insights
The study of Asgard and Eukaryote Viperin provides valuable insights into the evolution of antiviral defense mechanisms. The presence of similar antiviral proteins in both archaea and eukaryotes suggests that these defense strategies are ancient and have been conserved throughout evolution.
While both Asgard and Eukaryote Viperin share functional similarities, their specific roles and mechanisms may differ due to the differences in their cellular environments and the types of viruses they encounter.
Research Significance
The discovery and study of Asgard Viperin contribute to our understanding of the origin of eukaryotic cells and their immune systems. It also opens up new avenues for research into the evolution of antiviral defenses and the development of new antiviral strategies based on ancient mechanisms.
Understanding these proteins, particularly in the context of their evolutionary history and their function in modern organisms, is crucial for advancing our knowledge of immune responses and the development of antiviral therapies.
And this is precisely what researchers in the College of Natural Science at The University of Texas at Austin have found. They have shown that the proteins Asgard Viperin from the Asgard archaea and the Eukaryote viperin, possessed by eukaryotes including humans are structurally (and functionally) very similar.
Next Time You Beat a Virus, Thank Your Microbial AncestorsTwo of our key defenses against viruses have persisted for billions of years, arising before complex life.
When you get infected with a virus, some of the first weapons your body deploys to fight it were passed down to us from our microbial ancestors billions of years ago. According to new research from The University of Texas at Austin, two key elements of our innate immune system came from a group of microbes called Asgard archaea.
Specifically, viperins and argonautes, two proteins that are known to play important roles in the immune systems of all complex life — from insects to plants to humans — came from the Asgard archaea. Versions of these defense proteins are also present in bacteria, but the versions in complex life forms are most closely related to those in Asgard archaea, according to the new scientific study published in the journal Nature Communications.
This research bolsters the idea that all complex life, called eukaryotes, arose from a symbiotic relationship between bacteria and Asgard archaea.
It adds more support to the fact that the Asgards are our microbial ancestors. It says that not only did eukaryotes get all these rich structural proteins that we’ve seen before in Asgards, now it’s saying that even some of the defense systems in eukaryotes came from Asgards.
Associate Professor Brett J. Baker, senior author
Associate professor of integrative biology and marine science
Department of Integrative Biology
University of Texas at Austin, Austin, TX, USA.
The researchers identified for the first time a large arsenal of defense systems in archaea that were previously known only in bacteria.
When viperins detect foreign DNA, which might indicate a dangerous virus, they edit the DNA so that the cell can no longer make copies of the DNA, which stops the virus from spreading. When argonautes detect foreign DNA, they chop it up, also halting the virus. Additionally, in more complex organisms, argonautes can block the virus from making proteins in a process called RNA silencing.
Viral infections are one of the evolutionary pressures that we have had since life began, and it is critical to always have some sort of defense. When bacteria and archaea discovered tools that worked, they were passed down and are still part of our first line of defense.
Assistant Professor Pedro Leão, lead author
Department of Microbiology - RIBES
Radboud University, Nijmegen, The Netherlands.
The researchers compared proteins involved in immunity across the tree of life and found many closely related ones. Then they used an AI tool called ColabFold to predict whether ones that had similar amino acid sequences also had similar three-dimensional shapes (aka structures). (It’s the shape of a protein that determines how it functions.) This showed that variations of the viperin protein probably maintained the same structure and function across the tree of life. They then created a kind of family tree, or phylogeny, of these sister amino acid sequences and structures that showed evolutionary relationships.
A family tree of immune proteins called viperins from different organisms. Versions of viperin found in complex life forms, called eukaryotes (green), fit within the group of viperins from Asgard archaea (purple).
Credit: University of Texas at Austin.
Finally, the researchers took viperins from Asgard archaea genomes, cloned them into bacteria (so the bacteria would express the proteins), challenged the bacteria with viruses, and showed that Asgard viperins do in fact provide some protection to the modified bacteria. They survived better than bacteria without the immune proteins.
This research highlights the integral role cellular defenses must have played from the beginning of both prokaryotic and eukaryotic life. It also inspires questions about how our modern understanding of eukaryotic immunity can benefit from unraveling some of its most ancient origins.
Emily Aguilar-Pine, co-author
Department of Integrative Biology
University of Texas at Austin, Austin, TX, USA.
It’s undeniable at this point that Asgard archaea contributed a lot to the complexity that we see in eukaryotes today, so why wouldn’t they also be involved in the origin of the immune system? We have strong evidence now that this is true.
Assistant Professor Pedro Leão
Other authors, all from UT, are Mary Little, Kathryn Appler, Daphne Sahaya, Kathryn Currie, Ilya Finkelstein and Valerie De Anda.
This work was supported by the Simons and Moore foundations (via the Moore-Simons Project on the Origin of the Eukaryotic Cell) and The Welch Foundation.
Abstract
Dozens of new antiviral systems have been recently characterized in bacteria. Some of these systems are present in eukaryotes and appear to have originated in prokaryotes, but little is known about these defense mechanisms in archaea. Here, we explore the diversity and distribution of defense systems in archaea and identify 2610 complete systems in Asgardarchaeota, a group of archaea related to eukaryotes. The Asgard defense systems comprise 89 unique systems, including argonaute, NLR, Mokosh, viperin, Lassamu, and CBASS. Asgard viperin and argonaute proteins have structural homology to eukaryotic proteins, and phylogenetic analyses suggest that eukaryotic viperin proteins were derived from Asgard viperins. We show that Asgard viperins display anti-phage activity when heterologously expressed in bacteria. Eukaryotic and bacterial argonaute proteins appear to have originated in Asgardarchaeota, and Asgard argonaute proteins have argonaute-PIWI domains, key components of eukaryotic RNA interference systems. Our results support that Asgardarchaeota played important roles in the origin of antiviral defense systems in eukaryotes.
Introduction
Organisms across the tree of life contain complex defense systems (DS) to battle viral infections1,2,3. Over the past decade, dozens of new DS have been identified and characterized in bacteria, sparking a debate about a potential link between these systems and the origins of innate immune mechanisms in eukaryotes. More recently, protein components of bacterial NLR (Nucleotide-binding domain leucine-rich repeat), CBASS (Cyclic oligonucleotide-based antiphage signaling system), viperins (virus-inhibitory protein, endoplasmic reticulum-associated, interferon (IFN)-inducible), argonautes, and other DS have been shown to exhibit homology with proteins involved in the eukaryotic immune system4. Most of the research on prokaryotic defense systems has focused on bacteria, with archaea representing <3% of the genomes in these studies5,6,7. Thus, very little is known about the diversity or evolution of these systems in archaea.
Recently, diverse novel genomes have been obtained belonging to the archaea most closely related to eukaryotes, commonly referred to as “Asgard” archaea, the phylum Asgardarchaeota8. In addition to being sister lineages to eukaryotes, these archaea also contain an array of genes that are hallmarks of complex cellular life involved in signal processing, transcription, and translocations, among other processes9. The Asgard archaea are descendants of the ancestral host that gave rise to eukaryotic life. One newly described order, the Hodarchaeales (within the Heimdallarchaeia class), shared a common ancestor with eukaryotes8. Here, we characterize defense systems in archaea and show that Asgard archaea have a broad array of these DS. We also show that Asgards contributed to the origins of innate immune mechanisms in eukaryotes.
Fig. 2: Evolutionary history and anti-phage activity of Asgard viperins.
A Phylogenetic analysis of viperins. Viperins phylogeny revealed ancestral links of eVip (eukaryotic viperin) with asVip (asgard viperin) (nodes marked in red), particularly those within the Heimdallarchaeia class (including Kariarchaeaceae (2), Heimdallarchaeaceae (3) and Hodarchaeales (5)). The size of the dots on the nodes is proportional to bootstrap values ranging between 60 and 100. B Structure-based homology of viperins. Consistent with the sequence homology-based phylogenetic tree, the eVip structure appears to have been inherited from asVip (red node). The darker green color represents reference sequences predicted experimentally. The size of the dots at the center of the nodes is proportional to bootstrap values ranging between 50 and 100. C Superposition of an eVip structure, predicted by X-ray diffraction (green), and the structural models of an asVip, archaeal viperin (arVip), and bacterial viperin (from left to right). The yellow color in the models emphasizes the high conservation of the viperin catalytic site across the tree of life. The information regarding bacteria, archaea, asgard archaea and eukaryotes in panels (A–C) are represented by the pink, blue, purple and green color respectively. D Anti-T7 phage activity of asVip in E. coli. Nine asVip (asVip 26,11,20,25,16,12,17,23,8) exhibited anti-viral activity as indicated by the p-values (*p < 0.05; **p < 0.01). E Anti-T7 phage activity of asVip after codon optimization for their expression in E. coli. One asVip from a Hodarchaeales organism provided protection against viral infection (asVip 19). The center line of each box plot denotes the median; the box contains the 25th to 75th percentiles. Black whiskers mark the 5th and 95th percentiles. pVip34 is a prokaryotic viperin selected as a positive control from Bernheim et al.13. Each experimental condition includes, on average, 53 plaques pooled from three biological replicates. A two-tailed t-test was used to calculate statistical significance in figures (E, D).
Fig. 3: Evolutionary history of Asgard argonaute proteins.
A Phylogeny of long type argonaute proteins from archaea, bacteria, and eukaryotes with cyclases as outgroup (grey). B Structure-based homology of argonautes. C Structural alignment of asAgo5 and 4OLA (eAgo) MID and PIWI domains (left), and the graphic model of the corresponding alignments (right). Salmon regions on the alignment highlight strong conservation (low RMDS values). Red amino acids in the structural alignment, and their respective models represent the 4OLA conserved functional residues in MID and PIWI. The information regarding bacteria, archaea, asgard archaea and eukaryotes are represented by the pink, blue, purple and green color respectively. The size of the dots on the nodes is proportional to bootstrap values ranging between 70 and 100.
A highly-conserved antiviral protein across all eukaryote cells speaks loudly of common ancestry. The fact that a very similar protein is found in an "Asgard" archaea is strongly supportive of the theory that the fist eukaryote cells were alliances of bacteria and archaea and that the "Asgard" archaea contributed antiviral protection on this early eukaryote, showing common ancestry extending back beyond the first eukaryotes.
