Tag Archives: Scientific

Millions of Borderlands 3 Players Are Now Collectively Listed as Contributors to a Peer Reviewed Scientific Paper – IGN

  1. Millions of Borderlands 3 Players Are Now Collectively Listed as Contributors to a Peer Reviewed Scientific Paper IGN
  2. Borderlands 3 community scores a big win for science: ‘These players have helped trace the evolutionary relationships of more than a million different kinds of bacteria that live in the human gut’ PC Gamer
  3. Improving microbial phylogeny with citizen science within a mass-market video game Nature.com
  4. Millions of Gamers Help Advance Microbiome Research Technology Networks
  5. Millions Of Borderlands 3 Players Have Helped Microbiome Research Forbes

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‘Scientific breakthrough’ leads to discovery of first antibiotic that kills drug-resistant bacteria in 50 years – New York Post

  1. ‘Scientific breakthrough’ leads to discovery of first antibiotic that kills drug-resistant bacteria in 50 years New York Post
  2. Experimental antibiotic kills deadly superbug, opens whole new class of drugs Ars Technica
  3. Novel antibiotic class shows promise against carbapenem-resistant Acinetobacter University of Minnesota Twin Cities
  4. Scientists Hail New Antibiotic That Can Kill Drug-Resistant Bacteria Good News Network
  5. New antibiotic zosurabalpin shows promise against drug-resistant bacteria – an expert explains how it works The Conversation

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Class switch towards spike protein-specific IgG4 antibodies after SARS-CoV-2 mRNA vaccination depends on prior infection history | Scientific Reports – Nature.com

  1. Class switch towards spike protein-specific IgG4 antibodies after SARS-CoV-2 mRNA vaccination depends on prior infection history | Scientific Reports Nature.com
  2. Exposure to lung-migrating helminth protects against murine SARS-CoV-2 infection through macrophage-dependent T cell activation Science
  3. Differences in SARS-CoV-2 specific humoral and cellular immune responses after contralateral and ipsilateral COVID-19 vaccination The Lancet
  4. Detection of different variants of SARS-CoV-2 RNA (genome) on inanimate surfaces in high-touch public environmental surfaces | Scientific Reports Nature.com
  5. Elevated binding and functional antibody responses to SARS-CoV-2 in infants versus mothers Nature.com
  6. View Full Coverage on Google News

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Family of Henrietta Lacks settles lawsuit against Thermo Fisher Scientific – The Associated Press

  1. Family of Henrietta Lacks settles lawsuit against Thermo Fisher Scientific The Associated Press
  2. Family of Henrietta Lacks Settles With Biotech Company That Used Her Cells The New York Times
  3. Henrietta Lacks’ family settles lawsuit after cells used for countless medical breakthroughs CBS News
  4. Henrietta Lacks’ family settles with company in lawsuit over ‘immortal’ cell line Maryland Daily Record
  5. The family of Henrietta Lacks, whose stolen cancer cells changed medicine, settles lawsuit Yahoo News
  6. View Full Coverage on Google News

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Post COVID-19 symptoms are common, also among young adults in the general population | Scientific Reports – Nature.com

  1. Post COVID-19 symptoms are common, also among young adults in the general population | Scientific Reports Nature.com
  2. Does previous antibiotic treatment affect COVID-19 severity? News-Medical.Net
  3. Individual-level precision diagnosis for coronavirus disease 2019 related severe outcome: an early study in New York | Scientific Reports Nature.com
  4. Self-reported long COVID symptoms not identified in diagnostic tests News-Medical.Net
  5. Long COVID prevalence and impact on quality of life 2 years after acute COVID-19 | Scientific Reports Nature.com
  6. View Full Coverage on Google News

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Is ‘The Last of Us’ Fungal Pandemic Possible? A Scientific Investigation

Back in 2019, Craig Mazin and HBO released Chernobyl, a masterful series dramatizing the 1986 nuclear reactor meltdown at the eponymous power plant. The TV show earned critical praise and a couple of Emmys but at CNET Science we were most interested in how closely Mazin and co. were able to stick to real-world science. Turns out, they did a good job.

Mazin’s next HBO outing is The Last of Us, based on the 2013 survival-horror video game of the same name. CNET’s own Sean Keane has described the show, which debuted on Sunday, as “the greatest video game adaptation ever made.”

The Last of Us imagines a world ravaged by a fungal apocalypse caused by a creepy, mind-controlling fungus known as Cordyceps. That fungus is real, so I’ve naturally been wondering just how likely a fungi apocalypse really is. 

The idea has been investigated in the context of the game many times, but HBO’s version of the Cordyceps brain infection is slightly different to the one game developer Naughty Dog first conjured in 2013. 

What follows is an investigation of the plausibility of a fungal pandemic, caused by a Cordyceps-like pathogen that changes human behavior. I’m going to assume you’re at least somewhat familiar with the story of Joel and Ellie, the two protagonists making their way across the ruins of a post-apocalyptic USA. I’m also going to say at the top that this is an examination of a fictional world, so there’s always wiggle room for the story to develop in unexpected ways.

This includes some light spoilers from episodes 2 and 3 of The Last of Us, so if you’re trying to keep your viewing experience spoiler-free, it’s time for you to bail. 

The real world inspiration for The Last of Us

You can blame David Attenborough and nature documentaries for the shambling, clicking horrors that haunt The Last of Us.

In a must-watch episode on jungles in the 2006 BBC series Planet Earth, Attenborough and his documentary team encounter various behavior-manipulating fungi, including one that parasitizes carpenter ants: Ophiocordyceps. In the clip, which has been viewed on YouTube over 10 million times, the camera lingers on an ant with its jaws wrapped around a tree branch. A ghostly violin plays as Attenborough narrates the scene.

“Like something out of science fiction, the fruiting body of Cordyceps erupts from the ant’s head,” he says. 

The Planet Earth scene inspired Bruce Straley and Neil Druckmann, the director and creative director respectively, on 2013’s The Last of Us. In a GamesBeat interview after the game’s release, Druckmann mentions “ripping off” the documentary and Straley says that zombie ants were the “jumping off point” for the game. And the game does hew closely to its real-world source material.

The life cycle of Ophiocordyceps is gruesome but beautiful. Ants that come into contact with Ophiocordyceps spores on the jungle floor become infected. The fungus slips inside the ant’s body and begins to replicate. It takes up residence in particular regions, like the brain and muscle, releasing chemical compounds to manipulate behavior of the ant. The ant is directed to the underside of a leaf, high above the ground, and bites into it. Its jaw locks around the leaf thanks to some clever fungal compounds and it stays there until the fruiting body erupts from its head. Eventually it bursts open and releases more spores to the ground.

The process is highly specific. One species of Ophiocordyceps typically infects and zombifies just one species of ant. This specificity extends to the way the fungus takes over the mind of its host. A 2014 paper explored the ant-fungus relationship, finding that Ophiocordyceps had evolved a particular set of compounds to influence behavior of one species of ant, but those same compounds did not alter the behavior of different ant species (though the fungus will still often kill those ants).

Our real-world understanding of the fungus has also changed since The Last of Us was released in 2013.

The Planet Earth documentary was released in 2006. At the time, the ant-infecting parasite was, scientifically, known as Cordyceps unilateralis. In 2007, many of the Cordyceps fungi that parasitize insects, including ants but also things like caterpillars and spiders, were reclassified into a different family of fungi — Ophiocordyceps. While The Last of Us uses these two words interchangeably, they are now classed as different genera of fungi and scientists still use Cordyceps as a kind of generic name for all the species.

The Last of Us timeline

The pandemic’s origins are not revealed in the video game beyond a few stray newspaper clippings and notes, which seem to point to a South American origin. HBO’s adaptation dives a little further into the backstory, specifically in episodes 2 and 3. This gives us a little more to work with in terms of real world plausibility.

Here’s the timeline, as we understand it.

On the morning of Sept. 23, 2003, a woman working at a flour and grain factory on the western side of Jakarta was bitten by an unknown human being. She became violent, attacked four coworkers, biting three of them, before being locked in a bathroom and shot in the skull.

The three coworkers who were bitten were executed a few hours later. Fourteen coworkers could not be located.

A day later, on Sept. 24, 2003, two police officers in Jakarta, Indonesia walk into a restaurant and interrupt Ibu Ratna, a professor of mycology at the University of Indonesia, as she’s eating lunch. They take her to a laboratory at the Ministry of Health where she looks down a microscope and identifies a fungus: Ophiocordyceps. 

(Depending on the species Ratna saw, the fungus would have likely been classed as a Cordyceps in 2003… a potential plot hole or pedantry?)

Ratna asks why it’s been stained with chlorazol — which is commonly used to identify fungal elements from human hair, nails or other specimens. “Cordyceps cannot survive in humans,” she tells the police officer. She then examines the corpse of the woman who worked at the flour and grain factory. She cuts open the bite wound on the woman’s leg and rummages around in her mouth, discovering the corpse has been colonized by Ophiocordyceps.

After making her discovery, she makes a recommendation: The officer should bomb the city and everyone in it. 

On Sept. 26, 2003, the outbreak hits the US. This is dubbed Outbreak Day. In Austin, Texas, the first indications of trouble are obvious as ambulances screech through the city at around 3:15 p.m. 

In the early hours of Sept. 27, the outbreak reaches critical mass and the streets become chaotic. Planes are crashing into the ground. Highways out of Austin become blocked by the military. Members of the public have, against the advice of the emergency broadcast system, fled their homes. 

By Monday, Sept. 29, Joel explains to Ellie, “everything was gone.”

In The Last of Us, humanity tries to pick itself up two decades after a mutant Cordyceps fungus kickstarts a pandemic.

HBO

So, could it happen?

The short answer is: It’s improbable. The longer answer? Maybe, but with a ton of caveats

There are two key plot devices that underpin the fungal pandemic in the TV version of The Last of Us — climate change and how the fungi reproduce.

The Last of Us sets up its first season with an interview segment that takes place in 1968. Two fictional researchers are discussing pandemics on a talk show. One of them, Dr. Neumann, says he’s not scared of bacteria or viruses kickstarting a pandemic, unlike the other guest. What scares him most is fungi. Mostly because they don’t just kill the host, but take it over. 

The audience laughs (and after the past three years, you might too). Then 35 years later in the fictional world, that’s exactly what happens.

In the real world, scientists have often wondered why insects, plants and amphibians are so susceptible to fungal diseases. Research has shown that regulating body temperature, or homeothermy, is a great barrier against fungal infection. Fungi thrive in cooler environments and that’s why they’re potent enemies of insects, amphibians and plants. It also means they’re not as big a danger to hot-blooded animals, like ourselves. Fungi also have to be able to absorb human tissue, which they mostly struggle to do, and even if they manage to invade us, they still have to contend with a robust human immune system.

Humans can be infected by fungi, though. Candida, a yeast which causes thrush, is a potent species. A multidrug-resistant species, Candida auris, is of major concern in hospitals. There are also molds, which cause athlete’s foot and ringworm. Sometimes, these fungi evade our defenses, especially those of us with compromised immune systems. 

“The one thing you have to remember with fungal infections is that they predominantly infect people with an underlying condition,” Julianne Djordjevic, an associate professor at the University of Sydney who studies fungal infection of humans, tells CNET.

Things are changing, though. The world, ours and the one in The Last of Us, is heating up. “What if, for instance, the world were to get slightly warmer?” the fictional Dr. Neumann asks in the premiere. Higher temperatures could see fungi slowly adapt and evolve to withstand the types of heat they might experience inside a human body. Some scientists believe this is why Candida infections might be on the rise. 

Another species known as Ophiocordyceps sinensis, found on the Tibetan plateau, provides a potential counter. The species has long been used in Chinese medicine and some of the compounds it creates have been studied for their anti-cancer properties. However, in 2018, mycologists showed climate change — in addition to overharvesting — was leading to a decline in the species. The Himalayas are particularly vulnerable as the world warms and, at least for this species, adaptation and evolution aren’t keeping pace. Perhaps we’re warming the world too quickly for fungi to adapt.

Spores and tendrils

But how does Cordyceps spread? And so fast? As an ascomycetes, or sac fungi, the Ophiocordyceps that inhabit Earth’s temperate jungles propagate and survive through spores. It’s part of their life cycle: infect an ant, take it over, create a fruiting body, release the spores, start again.

HBO’s adaptation makes one huge change from the video game: spores aren’t the way Cordyceps moves between people. Mazin has said this is mostly because spores would mean everybody would have to wear a mask all the time (I’m not sure that’s particularly true but it would be pretty clunky in a TV show). Nevertheless, the adaptation replaces spores with “tendrils” and bites from infected people, two things we haven’t seen as infectious agents in the real world. They’re also affected by proximity. Whereas spores can travel hundreds of miles, tendrils and bites need close contact.

That’s the toughest part of this pandemic to square, but The Last of Us tries to provide a creative solution as to how society collapsed. 

In the video game, Joel and Ellie sometimes don gas masks in areas of dense Cordyceps spores.

Naughty Dog

Early in the series, as Joel and Ellie are wandering through the wreckage of civilization, Joel briefly touches on the accepted narrative of the pandemic’s origins: Cordyceps mutated. Then the fungi got into the food supply — things like bread, sugar and cereal all carried the mutated strain — and that food supply was shuttled around the globe. 

There is precedent for this kind of thing. The Great Famine, which ravaged Ireland in the 1840s and 1850s, was caused by an organism similar to a fungus, known as Phytophthora infestans, destroying potato crops. Though it didn’t directly infect and kill (or “mind control”) humans, it shows we’re at least susceptible to fungi in ways that aren’t getting much attention.

But the tendrils are still a problem for plausibility, even if their advantages for infected organization are partially explained in an early episode.

“The fungus also grows underground,” Tess, another survivor who partners with Joel, explains to Ellie in an early episode. “Long fibers like wires, some of them stretching over a mile. You step on a patch of Cordyceps in one place and you can wake a dozen infected from somewhere else.” This connection could alert infected to uninfected and make it near impossible to avoid them, but in the early stages of the pandemic it would take some extremely inept government responses to truly take off.

Maybe not so unlikely, given what we know about the most recent pandemics.

However, this change would require a major evolutionary deviation for Ophiocordyceps. Provided the Cordyceps that Ibu Ratna sees down her microscope and the Cordyceps in the real world are fundamentally the same, it would mean the fungus has fundamentally changed on a genetic level to something entirely alien. It would also be unusual for those fungi to then be in food crops unless those crops are highly contaminated with ants or spiders or moths. 

Overcoming these challenges we still have to get to a place where the fungus can control the behavior of a human being. While fungal compounds can alter the human mind (think LSD, for instance, which was isolated from a rye fungus), the specific compounds required to make humans more aggressive and help spread the infection would require a miraculous evolutionary leap for Ophiocordyceps.

There’s just a lot of challenges for a mutated fungus to overcome. Perhaps these will be explained in a second season.

Whenever I see an insect with Ophiocordyceps stalks protruding from its exoskeleton I think, damn… Nature is metal.

Kevin Schafer/Getty Images

Should we worry about fungal pandemics?

Pretty much every major crop that humanity depends on is threatened by a fungal pathogen. Rice, wheat and maize represent the biggest and most important source of calories for the human population. If a fungal pandemic were to rip through the crop supply… well, it might not be as frightening as the bitey, mind controlled “zombies” of The Last of Us, but it could be devastating in a different way.

What’s concerning researchers today is the rise of fungi which are resistant to antifungal drugs. According to a paper published in the journal Science in 2018, crop-destroying fungi accounts for about one fifth of perennial yield losses. They write that “[t]o avoid a global collapse in our ability to control fungal infections,” we need to promote the discovery of new antifungal drugs and ensure our current use of pesticides and chemicals don’t give rise to more worrisome strains. 

Another consideration? A dual pandemic — one that lowers the immunity of humans to such a point that pathogenic fungi can take hold.

Consider COVID-19. During the height of the pandemic, patients with COVID-19 were sometimes presenting with fungal diseases. Researchers investigated cases of “mucormycosis,” which is caused by black fungus, in 18 countries in 2022, writing that it’s an understudied and poorly understood complication of severe COVID-19. It seemed to affect males more than females and was predisposed to those with diabetes, an underlying condition that can affect immunity.

While it’s one of the freakiest apocalypse scenarios and makes good fodder for sci-fi TV, Cordyceps is unlikely to reduce humanity’s numbers by the billion. But the enemy is out there and we should be prepared. Right now, we’re not.

Updated Jan. 18: Closed captions make it clear the doctor at the beginning of the show is Dr. Neuman, not Dr. Newman. We’ve changed the spelling in this piece.   

Read original article here

Could ‘The Last of Us’ Fungal Pandemic Actually Happen? A Scientific Investigation

Back in 2019, Craig Mazin and HBO released Chernobyl, a masterful series dramatizing the 1986 nuclear reactor meltdown at the eponymous power plant. The TV show earned critical praise and a couple of Emmys but at CNET Science we were most interested in how closely Mazin and co. were able to stick to real world science. Turns out, they did a good job.

Mazin’s next HBO outing is The Last of Us, based on the 2013 survival-horror video game of the same name. CNET’s own Sean Keane has described the show, which debuted on Sunday, as “the greatest video game adaptation ever made.” 

The Last of Us imagines a world ravaged by a fungal apocalypse caused by a creepy, mind-controlling fungus known as Cordyceps. That fungus is real, so I’ve naturally been wondering just how likely a fungi apocalypse really is. 

The idea has been investigated in the context of the game many times, but HBO’s version of the Cordyceps brain infection is slightly different to the one Naughty Dog first conjured in 2013. 

What follows is an investigation of the plausibility of a fungal pandemic, caused by a Cordyceps-like pathogen that changes human behavior. I’m going to assume you’re at least somewhat familiar with the story of Joel and Ellie, the two protagonists making their way across the ruins of a post-apocalyptic USA. I’m also going to say at the top that this is an examination of a fictional world, so there’s always wiggle room for the story to develop in unexpected ways.

This includes some light spoilers from episodes 2 and 3 of The Last of Us, so if you’re trying to keep your viewing experience spoiler-free, it’s time for you to bail. 

The real world inspiration for The Last of Us

You can blame David Attenborough and nature documentaries for the shambling, clicking horrors that haunt The Last of Us.

In a must-watch episode on jungles in the 2006 BBC series Planet Earth, Attenborough and his documentary team encounter various behavior-manipulating fungi, including one that parasitizes carpenter ants: Ophiocordyceps. In the clip, which has been viewed on YouTube over 10 million times, the camera lingers on an ant with its jaws wrapped around a tree branch. A ghostly violin plays as Attenborough narrates the scene.

“Like something out of science fiction, the fruiting body of Cordyceps erupts from the ant’s head,” he says. 

The Planet Earth scene inspired Bruce Straley and Neil Druckmann, the director and creative director respectively, on 2013’s The Last of Us. In a GamesBeat interview after the game’s release, Druckmann mentions “ripping off” the documentary and Straley says that zombie ants were the “jumping off point” for the game. And the game does hew closely to its real-world source material.

The life cycle of Ophiocordyceps is gruesome but beautiful. Ants that come into contact with Ophiocordyceps spores on the jungle floor become infected. The fungus slips inside the ant’s body and begins to replicate. It takes up residence in particular regions, like the brain and muscle, releasing chemical compounds to manipulate behavior of the ant. The ant is directed to the underside of a leaf, high above the ground, and bites into it. Its jaw locks around the leaf thanks to some clever fungal compounds and it stays there until the fruiting body erupts from its head. Eventually it bursts open and releases more spores to the ground.

The process is highly specific. One species of Ophiocordyceps typically infects and zombifies just one species of ant. This specificity extends to the way the fungus takes over the mind of its host. A 2014 paper explored the ant-fungus relationship, finding that Ophiocordyceps had evolved a particular set of compounds to influence behavior of one species of ant, but those same compounds did not alter the behavior of different ant species (though the fungus will still often kill those ants).

Our real-world understanding of the fungus has also changed since The Last of Us was released in 2013.

The Planet Earth documentary was released in 2006. At the time, the ant-infecting parasite was, scientifically, known as Cordyceps unilateralis. In 2007, many of the Cordyceps fungi that parasitize insects, including ants but also things like caterpillars and spiders, were reclassified into a different family of fungi — Ophiocordyceps. While The Last of Us uses these two words interchangeably, they are now classed as different genera of fungi and scientists still use Cordyceps as a kind of generic name for all the species.

The Last of Us timeline

The pandemic’s origins are not revealed in the video game beyond a few stray newspaper clippings and notes, which seem to point to a South American origin. HBO’s adaptation dives a little further into the backstory, specifically in episodes 2 and 3. This gives us a little more to work with in terms of real world plausibility.

Here’s the timeline, as we understand it.

On the morning of Sept. 23, 2003, a woman working at a flour and grain factory on the western side of Jakarta was bitten by an unknown human being. She became violent, attacked four coworkers, biting three of them, before being locked in a bathroom and shot in the skull.

The three coworkers who were bitten were executed a few hours later. Fourteen coworkers could not be located.

A day later, on Sept. 24, 2003, two police officers in Jakarta, Indonesia walk into a restaurant and interrupt Ibu Ratna, a professor of mycology at the University of Indonesia, as she’s eating lunch. They take her to a laboratory at the Ministry of Health where she looks down a microscope and identifies a fungus: Ophiocordyceps. 

(Depending on the species Ratna saw, the fungus would have likely been classed as a Cordyceps in 2003… a potential plot hole or pedantry?)

Ratna asks why it’s been stained with chlorazol — which is commonly used to identify fungal elements from human hair, nails or other specimens. “Cordyceps cannot survive in humans,” she tells the police officer. She then examines the corpse of the woman who worked at the flour and grain factory. She cuts open the bite wound on the woman’s leg and rummages around in her mouth, discovering the corpse has been colonized by Ophiocordyceps.

After making her discovery, she makes a recommendation: The officer should bomb the city and everyone in it. 

On Sept. 26, 2003, the outbreak hits the US. This is dubbed Outbreak Day. In Austin, Texas, the first indications of trouble are obvious as ambulances screech through the city at around 3:15 p.m. 

In the early hours of Sept. 27, the outbreak reaches critical mass and the streets become chaotic. Planes are crashing into the ground. Highways out of Austin become blocked by the military. Members of the public have, against the advice of the emergency broadcast system, fled their homes. 

By Monday, Sept. 29, Joel explains to Ellie, “everything was gone.”

In The Last of Us, humanity tries to pick itself up two decades after a mutant Cordyceps fungus kickstarts a pandemic.

HBO

So, could it happen?

The short answer is: It’s improbable. The longer answer? Maybe, but with a ton of caveats

There are two key plot devices that underpin the fungal pandemic in the TV version of The Last of Us — climate change and how the fungi reproduce.

The Last of Us sets up its first season with an interview segment that takes place in 1968. Two fictional researchers are discussing pandemics on a talk show. One of them, Dr. Newman, says he’s not scared of bacteria or viruses kickstarting a pandemic, unlike the other guest. What scares him most is fungi. Mostly because they don’t just kill the host, but take it over. 

The audience laughs (and after the past three years, you might too). Then 35 years later in the fictional world, that’s exactly what happens.

In the real world, scientists have often wondered why insects, plants and amphibians are so susceptible to fungal diseases. Research has shown that regulating body temperature, or homeothermy, is a great barrier against fungal infection. Fungi thrive in cooler environments and that’s why they’re potent enemies of insects, amphibians and plants. It also means they’re not as big a danger to hot-blooded animals, like ourselves. Fungi also have to be able to absorb human tissue, which they mostly struggle to do, and even if they manage to invade us, they still have to contend with a robust human immune system.

Humans can be infected by fungi, though. Candida, a yeast which causes thrush, is a potent species. A multidrug-resistant species, Candida auris, is of major concern in hospitals. There are also molds, which cause athlete’s foot and ringworm. Sometimes, these fungi evade our defenses, especially those of us with compromised immune systems. 

“The one thing you have to remember with fungal infections is that they predominantly infect people with an underlying condition,” Julianne Djordjevic, an associate professor at the University of Sydney who studies fungal infection of humans, tells CNET.

Things are changing, though. The world, ours and the one in The Last of Us, is heating up. “What if, for instance, the world were to get slightly warmer?” the fictional Dr. Newman asks in the premiere. Higher temperatures could see fungi slowly adapt and evolve to withstand the types of heat they might experience inside a human body. Some scientists believe this is why Candida infections might be on the rise. 

Another species known as Ophiocordyceps sinensis, found on the Tibetan plateau, provides a potential counter. The species has long been used in Chinese medicine and some of the compounds it creates have been studied for their anti-cancer properties. However, in 2018, mycologists showed climate change — in addition to overharvesting — was leading to a decline in the species. The Himalayas are particularly vulnerable as the world warms and, at least for this species, adaptation and evolution isn’t keeping pace. Perhaps we’re warming the world too quickly for fungi to adapt.

Spores and tendrils

But how does Cordyceps spread? And so fast? As an ascomycetes, or sac fungi, the Ophiocordyceps that inhabit Earth’s temperate jungles propagate and survive through spores. It’s part of their life cycle: Infect an ant, take it over, create a fruiting body, release the spores, start again.

HBO’s adaptation makes one huge change from the video game: spores aren’t the way Cordyceps moves between people. Mazin has said this is mostly because spores would mean everybody would have to wear a mask all the time (I’m not sure that’s particularly true but it would be pretty clunky in a TV show). Nevertheless, the adaptation replaces spores with “tendrils” and bites from infected people, two things we haven’t seen as infectious agents in the real world. They’re also affected by proximity. Whereas spores can travel hundreds of miles, tendrils and bites need close contact.

That’s the toughest part of this pandemic to square, but The Last of Us tries to provide a creative solution as to how society collapsed. 

In the video game, Joel and Ellie sometimes don gas masks in areas of dense Cordyceps spores.

Naughty Dog

Early in the series, as Joel and Ellie are wandering through the wreckage of civilization, Joel briefly touches on the accepted narrative of the pandemic’s origins: Cordyceps mutated. Then the fungi got into the food supply — things like bread, sugar and cereal all carried the mutated strain — and that food supply was shuttled around the globe. 

There is precedent for this kind of thing. The Great Famine, which ravaged Ireland in the 1840s and 1850s, was caused by an organism similar to a fungus known as Phytophthora infestans destroying potato crops. Though it didn’t directly infect and kill (or “mind control”) humans, it shows we’re at least susceptible to fungi in ways that aren’t getting much attention.

But the tendrils are still a problem for plausibility, even if their advantages for infected organization are partially explained in an early episode.

“The fungus also grows underground,” Tess, another survivor who partners with Joel, explains to Ellie in an early episode. “Long fibers like wires, some of them stretching over a mile. You step on a patch of Cordyceps in one place and you can wake a dozen infected from somewhere else.” This connection could alert infected to uninfected and make it near impossible to avoid them, but in the early stages of the pandemic it would take some extremely inept government responses to truly take off.

Maybe not so unlikely, given what we know about the most recent pandemics.

However, this change would require a major evolutionary deviation for Ophiocordyceps. Provided the Cordyceps that Ibu Ratna sees down her microscope and the Cordyceps in the real world are fundamentally the same, it would mean the fungus has fundamentally changed on a genetic level to something entirely alien. It would also be unusual for those fungi to then be in food crops unless those crops are highly contaminated with ants or spiders or moths. 

Overcoming these challenges we still have to get to a place where the fungus can control the behavior of a human being. While fungal compounds can alter the human mind (think LSD, for instance, which was isolated from a rye fungus), the specific compounds required to make humans more aggressive and help spread the infection would require a miraculous evolutionary leap for Ophiocordyceps.

There’s just a lot of challenges for a mutated fungus to overcome. Perhaps these will be explained in a second season.

Whenever I see an insect with Ophiocordyceps stalks protruding from its exoskeleton I think, damn… Nature is metal.

Kevin Schafer/Getty

Should we worry about fungal pandemics?

Pretty much every major crop that humanity depends on is threatened by a fungal pathogen. Rice, wheat and maize represent the biggest and most important source of calories for the human population. If a fungal pandemic were to rip through the crop supply… well, it might not be as frightening as the bitey, mind controlled “zombies” of The Last of Us, but it could be devastating in a different way.

What’s concerning researchers today is the rise of fungi which are resistant to antifungal drugs. According to a paper published in the journal Science in 2018, crop-destroying fungi accounts for about one fifth of perennial yield losses. They write that “[t]o avoid a global collapse in our ability to control fungal infections,” we need to promote the discovery of new antifungal drugs and ensure our current use of pesticides and chemicals don’t give rise to more worrisome strains. 

Another consideration? A dual pandemic — one that lowers the immunity of humans to such a point that pathogenic fungi can take hold.

Consider COVID-19. During the height of the pandemic, patients with COVID-19 were sometimes presenting with fungal diseases. Researchers investigated cases of “mucormycosis,” which is caused by black fungus, in 18 countries in 2022, writing that it’s an understudied and poorly understood complication of severe COVID-19. It seemed to affect males more than females and was predisposed to those with diabetes, an underlying condition that can affect immunity.

While it’s one of the freakiest apocalypse scenarios and makes good fodder for Sci-Fi TV, Cordyceps is unlikely to reduce humanity’s numbers by the billion. But the enemy is out there and we should be prepared. Right now, we’re not.  

Read original article here

Are we living in the last days of the Scientific Age?

There are reasons to be skeptical of the paper in Nature, and scientists writing in response have been quick to point them out. First, the authors aren’t scientists in the common sense; they have doctorates in business management, not biology. Second, the data they used wasn’t polling of those in the fields, but a survey of patent filings. 

This has promoted criticism along the lines that the paper is more about the lack of new ideas busting open new areas for business, than in truly assessing changes to the underlying science. However, the actual data seems compelling, and the impact could hardly be higher.

We find that papers and patents are increasingly less likely to break with the past in ways that push science and technology in new directions. This pattern holds universally across fields and is robust across multiple different citation- and text-based metrics. Subsequently, we link this decline in disruptiveness to a narrowing in the use of previous knowledge, allowing us to reconcile the patterns we observe with the ‘shoulders of giants’ view. We find that the observed declines are unlikely to be driven by changes in the quality of published science, citation practices or field-specific factors. Overall, our results suggest that slowing rates of disruption may reflect a fundamental shift in the nature of science and technology.

The bulk of the paper is related to how they determined “disruptiveness” of papers and patent filings (which is where many of those offended by the idea find traction in disputing the overall theme), but the thrust of the conclusion is this: The number of publications has increased, many of those papers are very high quality, some remain disruptive, but many only confirm the status quo. Or at best, they offer new insight that leads to little potential for either scientific or economic impact.

This has immediately caused many publications covering the story to go in one of two directions. First, there’s doom mode (if not DOOM mode), expressing concerns that the well of new ideas may be running dry and that we’re genuinely running out of new things to discover. This is sometimes followed by pondering which STEM fields will die first. 

The second response usually starts with the phrase “in the late 19th century” before explaining how relativity and quantum mechanics upset the Newtonian apple cart. The last time we were convinced we knew everything, goes this line of reasoning, it turned out we really knew next to nothing. 

To this second idea, the only possible response is: Boy, I wish! Nothing excites a scientist, any scientist, more than results that don’t fit the prediction. For decades now, thousands of researchers have worked diligently to poke holes in the standard model of particle physics, the limits of relativity, and the fundamental frustrations inherent in quantum. However, each time a potential deviation from the predictions of the models appears, subsequent research only seems to serve to discover flaws, not in the basic theories, but with the previous paper. We are definitely living in an age where some of the predictions made a century ago have been tested to apparent equation … and stubbornly turned upright again and again. 

There are, of course, some well-known holes remaining. Wedding quantum to relativity remains elusive, even though schemes for making it work on (unvetted) paper are never in short supply. On a large, cosmological scale, making the visible universe obey our equations requires the belief that the vast majority of everything exists as invisible matter and inexplicable energy. These are giant Fudge Factors of the first water, and it seems just as likely that Dark Energy and Dark Matter will be written out of existence by some future insight into the math as it does that either will be “discovered” in a meaningful way. However, some of the most appealing theories that might offer fresh insights, often stitched together by thousands of scientists working over multiple decades, keep failing to hold up to real-world testing (i.e., supersymmetry and string theory).

There’s an important precursor to this paper that many media seem to have omitted from this discussion, and that’s the 1996 book, The End of Science, by science journalist John Horgan. Horgan is a prolific author and columnist for Scientific American, whose interview subjects included a list of scientists who might be seen as the most disruptive crew of the last three generations, from E.O. Wilson and Roger Penrose to Richard Dawkins, Stephen Jay Gould, and Stephen Hawking. Horgan has talked to them all, and hundreds of others.

Horgan’s book was a surprise bestseller (any time a science book makes the bestseller list, it’s a surprise), but there was a hard cadre of both scientists and science journalists who took umbrage at the book’s core idea: We should expect fewer, and less important, scientific discoveries as time goes on.

The reasoning behind this was simple. In the beginning, everything was available to discover. Scientists could make a discovery about the scale of the Earth with an upright stick. They could learn about the speed of sound by watching someone chop wood. However, with each passing year, as the big book of facts became more stuffed with learning, the difficulty of making fundamental new discoveries increases. In the 19th century, the electron was discovered by one guy using equipment that might have been found in a high school science lab (or the basement of a wealthy naturalist). To close out the particle zoo with the Higgs Boson took an international effort with an over $4 billion collider.

Seriously, how hard is it to believe that the easy stuff has been picked clean, and the discoveries that remain will come at an increasing cost? It seems entirely reasonable. But it was the next step that left a painful lump in many throats: What happens when the cost of a new discovery becomes so high that it simply is not achieved? Horgan saw that day if not already at hand, the certainly right around the corner. Horgan meshed this with a disquieting reminder of something that echoes the discussion between God and Job: If there are any rules by which the universe operates, there is no guarantee that we evolved apes can comprehend those rules in a meaningful way.

… given the limits constraining further research, science will be hard-pressed to make any truly profound additions to the knowledge it has already generated. Further research may yield no more great revelations or revolutions but only incremental returns.

There’s an extremely uncomfortable agreement between this conclusion from Horgan and the overview of the paper published in Nature. Or at least, in the way that paper is being presented in most of the media. However, that’s not a very accurate description of what’s actually hiding at the end of the patents and papers review.

Because while the number of revolutionary papers being published may have declined as a percentage of the total, and the impact of new research may even be somewhat fading as a whole, there is still a healthy vein of disruption in what’s being published today.

… the stability we observe in the sheer number of disruptive papers and patents suggests that science and technology do not appear to have reached the end of the ‘endless frontier.’ 

The implications of this go beyond just breathing a sigh of relief over finding new features in the iPhone 15. It may not be obvious, but the fundamental scientific theories that undergird our view of the universe remain open to attack. And that’s a good thing.



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More Scientific Images Should Go This Hard

I read a lot of press releases about new scientific papers for my job. Sometimes the art that accompanies them is funny, such as this unapologetically fuchsia rendering of the microscopic creature Saccorhytus. Sometimes they are evocative of a past world, such as this reconstruction of a 100-million-year-old crab. Sometimes these images are ambitious infographics or unsettling acts of Photoshop. Ostensibly, the purpose of these images is the same—to invite people to click on a story about something new we have discovered about the world.

On Thursday, scrolling through press releases, I saw an image that stopped me in my tracks. On one level, it was a photograph of a Nile crocodile rising from the water with half of an ungulate known as an impala dangling from its teeth. But it was also an artistic collage of rendered molecules, charts, and three neon lines streaked through the water where the crocodile had just made its kill. These visual details were so striking that, in my first viewing of the image, I nearly missed the half-swallowed impala, its delicate carcass one part of an image that contained multitudes. It was as if the crocodile had teleported to the 1990s to hunt amid the famous teal carpet of the Portland International Airport. Sure, I wanted to click. But the image also did what great art is supposed to do: It made me think. I wanted it on a t-shirt.

I saw the image on a site called Phys.org, which aggregates science and technology news. It accompanied a press release, “Study clarifies mystery of crocodilian hemoglobin,” which spotlighted the results of a new study in the journal Current Biology published by a group of scientists including Jay F. Storz, an evolutionary biologist at the University of Nebraska-Lincoln. The press release was written by Scott Schrage, a science writer at the university. But who had created the image? When I found the image on the University of Nebraska’s newsroom—Nebraska Today—I saw the image credit: “Shutterstock / Current Biology / Scott Schrage | University Communication and Marketing.” Scott Schrage! Writer and artist. I needed to talk to him.

Schrage, who has been writing about the university’s research for about seven years, is responsible not just writing about the scientific papers that come out of the university, but also for finding images to accompany them. Sometimes this secondary task is easy, a matter of sending Storz and a colleague to pose with penguins at the Omaha Zoo to promote a new paper on the evolution of penguin hemoglobin. (Storz is really into hemoglobin. His team made headlines for capturing the highest-dwelling mammal, the yellow-rumped leaf-eared mouse, which lives at heights above 22,000 feet, where there is just about 44 percent of the oxygen available at sea level.) But there won’t always be a penguin or yellow-rumped leaf-eared mouse nearby for a photoshoot, meaning Schrage has had to innovate.

“As you’re wading through these giant seas of text in like a 15- or 20-page paper, there are these beautiful little islands of visual engagement,” Schrage told me, referring to the charts or renderings often included in a paper. “They’re sort of delving into some technicalities that are beyond the scope of the story that I’m planning to write, but they’re just so, you know, pretty,” he said. So Schrage began experimenting, creating images that combined a paper’s visual components along with stock photography.

Storz told Schrage he had always been interested in footage of crocodiles found in nature documentaries: seeing the big reptiles lurk below the surface, thrash out of the water, and drag their prey underwater to drown them. This style of hunting meant the reptiles would have to hold their breath for an extraordinary amount of time, even more than an hour. Crocodiles can do this because they evolved a specialized way of regulating their hemoglobin, a “slow-release mechanism that allows crocodilians to efficiently exploit their onboard oxygen stores,” Storz told Schrage for the press release. (To learn more about the new research, you should definitely read Schrage’s story, which is much more thorough and nuanced than this one.)

Schrage began looking for stock photos of crocodiles ambushing their prey in the water. “This particular image I just thought was incredibly captivating,” he said. “It’s obviously like, deadly serious. But it’s also kind of cartoonish.” The dangling legs of the impala reminded him of Tom and Jerry cartoons, how a tail dangling from Tom’s mouth might have been the only hint that Jerry was in trouble.

The stripes came next. “I felt like I needed something to frame the croc,” Schrage said, adding that he arranged the stripes to be reminiscent of an evolutionary tree. He turned to a color palette of the ’90s. The teal stripe came first—reminiscent of the colors of the Charlotte Hornets, he noted—and then an orange creamsicle, and then a fuchsia stripe at the bottom. Schrage often tries to include the University of Nebraska-Lincoln’s customary red in images, but he worried, in the context of a watery hunt, blood red might be too on the nose. Besides, a crocodile’s hunt isn’t necessarily a bloodbath. “It’s drowning, it’s doing its death roll in its prey,” Schrage said. “More or less, especially with prey like an impala, it’s just swallowing it.”

Schrage overlaid the image with figures from the study: some charts and renderings of resurrected hemoglobin from the ancient ancestors of crocodiles. He also included an actual phylogenetic tree from the paper in the bottom-left corner. “As I was looking at these, I was thinking, OK, these kind of look like childlike, really rudimentary representations of crocodile teeth,” Schrage said. “So I was like, OK, let’s include that element as well.”

All combined, these elements make for a thoroughly unforgettable scientific image. When I asked Schrage if he considered himself a maximalist, he demurred. Institutional writing often comes with guidelines, many editors, and many eyes that want a say in what’s published. “But when I pull together an image like this, I let my flag fly a little bit,” he said. “When it comes to this, I do have more freedom.”

Schrage said he feels lucky to cover this kind of research. Reconstructing hemoglobins that are hundreds of millions of years old almost almost seems like science fiction, he said. And I feel lucky to encounter Schrage’s work and this particular image, which feels like a science communication hallucination—an image that made me gasp, my own, humble hemoglobin scurrying throughout my bloodstream.

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Rate of scientific breakthroughs slowing over time: Study

The measurement of gravitational waves was deemed a “disruptive” recent breakthrough by the researchers.

The rate of ground-breaking scientific discoveries and technological innovation is slowing down despite an ever-growing amount of knowledge, according to an analysis released Wednesday of millions of research papers and patents.

While previous research has shown downturns in individual disciplines, the study is the first that “emphatically, convincingly documents this decline of disruptiveness across all major fields of science and technology,” lead author Michael Park told AFP.

Park, a doctoral student at the University of Minnesota’s Carlson School of Management, called disruptive discoveries those that “break away from existing ideas” and “push the whole scientific field into new territory.”

The researchers gave a “disruptiveness score” to 45 million scientific papers dating from 1945 to 2010, and to 3.9 million US-based patents from 1976 to 2010.

From the start of those time ranges, research papers and patents have been increasingly likely to consolidate or build upon previous knowledge, according to results published in the journal Nature.

The ranking was based on how the papers were cited in other studies five years after publication, assuming that the more disruptive the research was, the less its predecessors would be cited.

The biggest decrease in disruptive research came in physical sciences such as physics and chemistry.

“The nature of research is shifting” as incremental innovations become more common, senior study author Russell Funk said.

Burden of knowledge

One theory for the decline is that all the “low-hanging fruit” of science has already been plucked.

If that were the case, disruptiveness in various scientific fields would have fallen at different speeds, Park said.

But instead “the declines are pretty consistent in their speeds and timing across all major fields,” Park said, indicating that the low-hanging fruit theory is not likely to be the culprit.

Instead, the researchers pointed to what has been dubbed “the burden of research,” which suggests there is now so much that scientists must learn to master a particular field they have little time left to push boundaries.

This causes scientists and inventors to “focus on a narrow slice of the existing knowledge, leading them to just come up with something more consolidating rather than disruptive,” Park said.

Another reason could be that “there’s increasing pressure in academia to publish, publish, publish, because that’s the metric that academics are assessed on,” he added.

The researchers called on universities and funding agencies to focus more on quality, rather than quantity, and consider full subsidies for year-long sabbaticals to allow academics to read and think more deeply.

“We’re not getting any less innovative as a species,” Park emphasized, pointing to recent breakthroughs such as the use of mRNA technology in COVID-19 vaccines, or the measurement of gravity waves in 2015.

Jerome Lamy, a historian and expert in the sociology of science at France’s CNRS research agency, who was not involved in the research, said it showed that “ultra-specialization” and the pressure to publish had increased over the years.

He blamed a global trend of academics being “forced to slice up their papers” to increase their number of publications, saying it had led to “a dulling of research.”

More information:
Michael Park et al, Papers and patents are becoming less disruptive over time, Nature (2023). DOI: 10.1038/s41586-022-05543-x

© 2023 AFP

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Rate of scientific breakthroughs slowing over time: Study (2023, January 4)
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