Gain-of-function mutation research may help predict the next pandemic — or, critics argue, cause one.
This article was originally published on our sister site, Freethink.
"I was intrigued," says Ron Fouchier, in his rich, Dutch-accented English, "in how little things could kill large animals and humans."
It's late evening in Rotterdam as darkness slowly drapes our Skype conversation.
This fascination led the silver-haired virologist to venture into controversial gain-of-function mutation research — work by scientists that adds abilities to pathogens, including experiments that focus on SARS and MERS, the coronavirus cousins of the COVID-19 agent.
If we are to avoid another influenza pandemic, we will need to understand the kinds of flu viruses that could cause it. Gain-of-function mutation research can help us with that, says Fouchier, by telling us what kind of mutations might allow a virus to jump across species or evolve into more virulent strains. It could help us prepare and, in doing so, save lives.
Many of his scientific peers, however, disagree; they say his experiments are not worth the risks they pose to society.
A virus and a firestorm
The Dutch virologist, based at Erasmus Medical Center in Rotterdam, caused a firestorm of controversy about a decade ago, when he and Yoshihiro Kawaoka at the University of Wisconsin-Madison announced that they had successfully mutated H5N1, a strain of bird flu, to pass through the air between ferrets, in two separate experiments. Ferrets are considered the best flu models because their respiratory systems react to the flu much like humans.
The mutations that gave the virus its ability to be airborne transmissible are gain-of-function (GOF) mutations. GOF research is when scientists purposefully cause mutations that give viruses new abilities in an attempt to better understand the pathogen. In Fouchier's experiments, they wanted to see if it could be made airborne transmissible so that they could catch potentially dangerous strains early and develop new treatments and vaccines ahead of time.
The problem is: their mutated H5N1 could also cause a pandemic if it ever left the lab. In Science magazine, Fouchier himself called it "probably one of the most dangerous viruses you can make."
Just three special traits
Recreated 1918 influenza virionsCredit: Cynthia Goldsmith / CDC / Dr. Terrence Tumpey / Public domain via Wikipedia
For H5N1, Fouchier identified five mutations that could cause three special traits needed to trigger an avian flu to become airborne in mammals. Those traits are (1) the ability to attach to cells of the throat and nose, (2) the ability to survive the colder temperatures found in those places, and (3) the ability to survive in adverse environments.
A minimum of three mutations may be all that's needed for a virus in the wild to make the leap through the air in mammals. If it does, it could spread. Fast.
Fouchier calculates the odds of this happening to be fairly low, for any given virus. Each mutation has the potential to cripple the virus on its own. They need to be perfectly aligned for the flu to jump. But these mutations can — and do — happen.
"In 2013, a new virus popped up in China," says Fouchier. "H7N9."
H7N9 is another kind of avian flu, like H5N1. The CDC considers it the most likely flu strain to cause a pandemic. In the human outbreaks that occurred between 2013 and 2015, it killed a staggering 39% of known cases; if H7N9 were to have all five of the gain-of-function mutations Fouchier had identified in his work with H5N1, it could make COVID-19 look like a kitten in comparison.
H7N9 had three of those mutations in 2013.
Gain-of-function mutation: creating our fears to (possibly) prevent them
Flu viruses are basically eight pieces of RNA wrapped up in a ball. To create the gain-of-function mutations, the research used a DNA template for each piece, called a plasmid. Making a single mutation in the plasmid is easy, Fouchier says, and it's commonly done in genetics labs.
If you insert all eight plasmids into a mammalian cell, they hijack the cell's machinery to create flu virus RNA.
"Now you can start to assemble a new virus particle in that cell," Fouchier says.
One infected cell is enough to grow many new virus particles — from one to a thousand to a million; viruses are replication machines. And because they mutate so readily during their replication, the new viruses have to be checked to make sure it only has the mutations the lab caused.
The virus then goes into the ferrets, passing through them to generate new viruses until, on the 10th generation, it infected ferrets through the air. By analyzing the virus's genes in each generation, they can figure out what exact five mutations lead to H5N1 bird flu being airborne between ferrets.
And, potentially, people.
"This work should never have been done"
The potential for the modified H5N1 strain to cause a human pandemic if it ever slipped out of containment has sparked sharp criticism and no shortage of controversy. Rutgers molecular biologist Richard Ebright summed up the far end of the opposition when he told Science that the research "should never have been done."
"When I first heard about the experiments that make highly pathogenic avian influenza transmissible," says Philip Dormitzer, vice president and chief scientific officer of viral vaccines at Pfizer, "I was interested in the science but concerned about the risks of both the viruses themselves and of the consequences of the reaction to the experiments."
In 2014, in response to researchers' fears and some lab incidents, the federal government imposed a moratorium on all GOF research, freezing the work.
Some scientists believe gain-of-function mutation experiments could be extremely valuable in understanding the potential risks we face from wild influenza strains, but only if they are done right. Dormitzer says that a careful and thoughtful examination of the issue could lead to processes that make gain-of-function mutation research with viruses safer.
But in the meantime, the moratorium stifled some research into influenzas — and coronaviruses.
The National Academy of Science whipped up some new guidelines, and in December of 2017, the call went out: GOF studies could apply to be funded again. A panel formed by Health and Human Services (HHS) would review applications and make the decision of which studies to fund.
As of right now, only Kawaoka and Fouchier's studies have been approved, getting the green light last winter. They are resuming where they left off.
Pandora's locks: how to contain gain-of-function flu
Here's the thing: the work is indeed potentially dangerous. But there are layers upon layers of safety measures at both Fouchier's and Kawaoka's labs.
"You really need to think about it like an onion," says Rebecca Moritz of the University of Wisconsin-Madison. Moritz is the select agent responsible for Kawaoka's lab. Her job is to ensure that all safety standards are met and that protocols are created and drilled; basically, she's there to prevent viruses from escaping. And this virus has some extra-special considerations.
The specific H5N1 strain Kawaoka's lab uses is on a list called the Federal Select Agent Program. Pathogens on this list need to meet special safety considerations. The GOF experiments have even more stringent guidelines because the research is deemed "dual-use research of concern."
There was debate over whether Fouchier and Kawaoka's work should even be published.
"Dual-use research of concern is legitimate research that could potentially be used for nefarious purposes," Moritz says. At one time, there was debate over whether Fouchier and Kawaoka's work should even be published.
While the insights they found would help scientists, they could also be used to create bioweapons. The papers had to pass through a review by the U.S. National Science Board for Biosecurity, but they were eventually published.
Intentional biowarfare and terrorism aside, the gain-of-function mutation flu must be contained even from accidents. At Wisconsin, that begins with the building itself. The labs are specially designed to be able to contain pathogens (BSL-3 agricultural, for you Inside Baseball types).
They are essentially an airtight cement bunker, negatively pressurized so that air will only flow into the lab in case of any breach — keeping the viruses pushed in. And all air in and out of the lap passes through multiple HEPA filters.
Inside the lab, researchers wear special protective equipment, including respirators. Anyone coming or going into the lab must go through an intricate dance involving stripping and putting on various articles of clothing and passing through showers and decontamination.
And the most dangerous parts of the experiment are performed inside primary containment. For example, a biocontainment cabinet, which acts like an extra high-security box, inside the already highly-secure lab (kind of like the radiation glove box Homer Simpson is working in during the opening credits).
"Many people behind the institution are working to make sure this research can be done safely and securely." — REBECCA MORITZ
The Federal Select Agent program can come and inspect you at any time with no warning, Moritz says. At the bare minimum, the whole thing gets shaken down every three years.
There are numerous potential dangers — a vial of virus gets dropped; a needle prick; a ferret bite — but Moritz is confident that the safety measures and guidelines will prevent any catastrophe.
"The institution and many people behind the institution are working to make sure this research can be done safely and securely," Moritz says.
No human harm has come of the work yet, but the potential for it is real.
"Nature will continue to do this"
They were dead on the beaches.
In the spring of 2014, another type of bird flu, H10N7, swept through the harbor seal population of northern Europe. Starting in Sweden, the virus moved south and west, across Denmark, Germany, and the Netherlands. It is estimated that 10% of the entire seal population was killed.
The virus's evolution could be tracked through time and space, Fouchier says, as it progressed down the coast. Natural selection pushed through gain-of-function mutations in the seals, similarly to how H5N1 evolved to better jump between ferrets in his lab — his lab which, at the time, was shuttered.
"We did our work in the lab," Fouchier says, with a high level of safety and security. "But the same thing was happening on the beach here in the Netherlands. And so you can tell me to stop doing this research, but nature will continue to do this day in, day out."
Critics argue that the knowledge gained from the experiments is either non-existent or not worth the risk; Fouchier argues that GOF experiments are the only way to learn crucial information on what makes a flu virus a pandemic candidate.
"If these three traits could be caused by hundreds of combinations of five mutations, then that increases the risk of these things happening in nature immensely," Fouchier says.
"With something as crucial as flu, we need to investigate everything that we can," Fouchier says, hoping to find "a new Achilles' heel of the flu that we can use to stop the impact of it."
How a controversial study on psychic powers caused a revolution in psychology research.
Among the scientific studies that came out in the past decade, perhaps none were more controversial than the 2011 paper by the American psychologist Dr. Daryl Bem. He proved an explosive notion, that precognition, the ability to see future events, is actually real, setting off a period of soul-searching among psychologists that still persists to this day. How could an eminent Cornell University professor come to such a conclusion, which is so squarely outside mainstream science and props up parapsychology? Could his experiments, which seemed to follow accepted procedures and sound methods in coming up with this unexpected proof, be replicated?
The paper, "Feeling the Future: Experimental Evidence for Anomalous Retroactive Influences on Cognition and Affect," reported on nine experiments involving over 1,000 participants, with eight of them successfully showing that a person's responses could be influenced by stimulating events that happened after the responses were already made and recorded.
This possibility strongly supported the notion of precognition, where individuals seem to gain information or energy transfer that no physical or biological process we know of says they should have. Such phenomena, which also include telepathy and clairvoyance or remote viewing, are collectively known as "psi".
The experiments that seemed to prove Bem's thesis ranged in their approach. Some of the stimuli used were erotic in nature, with an early experiment consisting of having research subjects (Cornell undergrads) looking at a pair of curtains on a computer. They were supposed to guess which one had a hidden pornographic image, with the correct answer being randomly chosen after the student made their decision. Interestingly, students performed slightly better than simple guessing would have produced, with 53 percent choosing the correct location of the image.
Another experiment had students examining sets of words that they would then have to type out. Somehow, the students did better at first remembering words they would type out later. It's as if having the second opportunity to practice and remember words had benefits that went backwards in time.
Cognitive neuroscience professor Chris Chambers, one of Bem's critics (and there were many), called the conclusion of the paper "ridiculous." And yet, "this is really interesting because if a paper like this that's doing everything normally and properly can end up producing a ridiculous conclusion, then how many other papers that use those exact same methods that didn't reach ridiculous conclusions are similarly flawed?" Chambers wondered in an interview.
What Could ESP Mean?
Bem said that he chose to conduct experiments that were easy enough to be replicated by others. In a 2010 press release by Cornell, he pointed out that "I designed the experiments to be persuasive, simple and transparent enough to encourage them to try replicating these experiments for themselves."
He offered free packages with detailed instruction manuals on how to conduct such experiments, along with the requisite computer software for running the sessions and analyzing the data. He knew this work would face extreme scrutiny and encouraged other psychologists to get these results on their own. And that's exactly what they tried to do.
A 2010 study carried out by the University of California–Berkeley business school professor Leif Nelson and Carnegie Mellon's professor Jeff Galak used an online version of Bem's word-recall experiment and failed to come up with the same outcome from a sample group of over 100 people. Bem's argument against this approach was that trying to establish ESP online was not going to work.
Other studies, like the 2011 paper led by Eric-Jan Wagenmakers, a research methodologist at the University of Amsterdam, also couldn't replicate Bem's finds and took issue with the statistical analyses he employed, saying the psychologist overstated his evidence.
But there were studies that seemed to have replicated what Bem found. In fact, Bem's team published a meta-analysis in 2015 of 90 experiments from 33 different labs in 14 countries, which involved 12,406 participants. Analyzing the results, Bem demonstrated statistical support across all the studies for his conclusions on the existence of ESP, writing that there is "decisive evidence."
Of course, the decisiveness of this evidence is still in the eye of the beholder. In fact, psychologist Jonathan Schooler from the University of California–Santa Barbara, who was one of the original peer reviewers for Bem's work, supports the notion that the bias and even the psychic abilities of the experimenter may have a lot to do with the possible success of psi studies.
"If it's possible that consciousness influences reality and is sensitive to reality in ways that we don't currently understand, then this might be part of the scientific process itself," said Schooler. "Parapsychological factors may play out in the science of doing this research."
Psychology toolbox: How to use skepticism | Derren Brown
In an interview with Slate, Bem acknowledged the firestorm of reactions his research has caused. "The critics said that I put psychologists in an uncomfortable position and that they'd have to revise their views of the physical world or their views on research practice," he shared. "I think both are true. I still believe in psi, but I also think that methods in the field need to be cleaned up."
Indeed, the publication of Bem's paper prompted a call to replicate not just his study but psychology studies in general. After all, if an outlandish result is achieved, it's worth verifying if it can be repeated. Otherwise, the study could have errors and its result could simply be a fluke rather than any scientific discovery. A group of 270 scientists from 17 countries attempted replicating 100 studies from the year 2008, found in peer-reviewed psychology journals with solid reputations.
Their goal was to repeat all 100 experiments exactly as carried out by the original scientists. Unfortunately, and quite strikingly, only 36 percent of the replications managed to get the same results as the initial studies. To put it another way, 64 percent of the studies analyzed were potentially wrong, or at the very least misleadingly or insufficiently presented.
If so many studies could not be replicated, what did that mean for the whole field of psychology? New standards for psychology research were implemented. Researchers now commonly use the process of "pre-registration," whereby they write up how they would conduct the study and what their hypotheses might be, before they carry out the experiments. This limits their ability to manipulate data and report positive results before they are found.
Additionally, hundreds of scientific journals now publish "registered" reports that explain whether they would accept or reject submitted studies before they are undertaken. This makes the decision to publish papers focus on their methodology more than some sensational results.
As far as parapsychology and Bem's research, it is clear that extraordinary claims require extraordinary proof and it's safe to say the disputed nature of the studies that seemed to support ESP and similar phenomena have not made a real dent on the consensus scientific opinions. More reproducible work with much wider samples and unchallengeable statistical approaches must be done for such dramatic claims as precognition (which would break the second law of thermodynamics among other things in our accepted reality) to be taken more seriously.
Check out Dr. Daryl Bem's study here, published in the Journal of Personality and Social Psychology.
Certain water beetles can escape from frogs after being consumed.
- A Japanese scientist shows that some beetles can wiggle out of frog's butts after being eaten whole.
- The research suggests the beetle can get out in as little as 7 minutes.
- Most of the beetles swallowed in the experiment survived with no complications after being excreted.
In what is perhaps one of the weirdest experiments ever that comes from the category of "why did anyone need to know this?" scientists have proven that the Regimbartia attenuata beetle can climb out of a frog's butt after being eaten.
The research was carried out by Kobe University ecologist Shinji Sugiura. His team found that the majority of beetles swallowed by black-spotted pond frogs (Pelophylax nigromaculatus) used in their experiment managed to escape about 6 hours after and were perfectly fine.
"Here, I report active escape of the aquatic beetle R. attenuata from the vents of five frog species via the digestive tract," writes Sugiura in a new paper, adding "although adult beetles were easily eaten by frogs, 90 percent of swallowed beetles were excreted within six hours after being eaten and, surprisingly, were still alive."
One bug even got out in as little as 7 minutes.
Sugiura also tried putting wax on the legs of some of the beetles, preventing them from moving. These ones were not able to make it out alive, taking from 38 to 150 hours to be digested.
Naturally, as anyone would upon encountering such a story, you're wondering where's the video. Thankfully, the scientists recorded the proceedings:
The Regimbartia attenuata beetle can be found in the tropics, especially as pests in fish hatcheries. It's not the only kind of creature that can survive being swallowed. A recent study showed that snake eels are able to burrow out of the stomachs of fish using their sharp tails, only to become stuck, die, and be mummified in the gut cavity. Scientists are calling the beetle's ability the first documented "active prey escape." Usually, such travelers through the digestive tract have particular adaptations that make it possible for them to withstand extreme pH and lack of oxygen. The researchers think the beetle's trick is in inducing the frog to open a so-called "vent" controlled by the sphincter muscle.
"Individuals were always excreted head first from the frog vent, suggesting that R. attenuata stimulates the hind gut, urging the frog to defecate," explains Sugiura.
For more information, check out the study published in Current Biology.
Researchers find an unusual property of a bacteria that can breathe in metal.
- Scientists discover Shewanella oneidensis bacterium can "breathe in" certain metals and compounds.
- The bacteria produces a material that can be used to transfer electrons.
- Applications of the finding range from medical devices to new generation of sensors.
Researchers discovered an unusual property of a bacteria that can "breathe" in some metal and sulfur compounds and create materials that can improve electronics, energy storage, and medical devices.
Specifically, the anaerobic Shewanella oneidensis bacterium can produce molybdenum disulfide, a material that can transfer electronics as well as graphene, explains the press release from Rensselaer Polytechnic Institute, whose team of engineers carried out the research.
Engineering professor Shayla Sawyer thinks their accomplishment "has some serious potential" once the scientists fully investigate the process involved and learn to control it.
One of the possible applications of this finding could be in developing a new generation of nutrient sensors to be used on lakes and other bodies of water to examine the health of their ecosystems. A bacterial biofilm, a collective of the microorganisms, could track excess nutrients in real-time, helping address harmful algae growth and other water issues.
Postdoctorate researcher James Rees, who led the study, commented on the implications of their work:
"We find bacteria that are adapted to specific geochemical or biochemical environments can create, in some cases, very interesting and novel materials," Rees shared. "We are trying to bring that into the electrical engineering world."
What's unusual about Shewanella oneidensis is that it can create nanowires for transferring electrons, a fact that "lends itself to connecting to electronic devices that have already been made," Sawyer elaborated, calling it "the interface between the living world and the manmade world that is fascinating."
Check out the new study, which also involved Yuri Gorby as the paper's third author, in Biointerphases.
Olive oil leads to the discovery of a law that applies to atoms, superconductors, and even high energy physics.
- Physicists at the Dutch research institute AMOLF used olive oil in an experiment on light phase transitions.
- The scientists found that light would behave the same way in atoms, superconductors, and high energy physics.
- The discovery can lead to applications in new computing and sensing systems.
The dressing in your salad might redefine science if you look carefully enough. Researchers in the Netherlands used a drop of olive oil to discover a new universal law of phase transitions.
The research was carried out by the Interacting Photons group of the AMOLF institute, which focuses on fundamental physics. The experiment involved dropping olive oil into an optical cavity system of photons bouncing back and forth between two mirrors. It was set up to explore how light goes through phase transitions the way it would in boiling water, for example.
What's fascinating, this system had "memory" in how the oil made photons interact with themselves, as the group leader Said Rodriguez explained. "We created a system with memory by placing a drop of olive oil inside the cavity", said Rodriguez. "The oil mediates effective photon-photon interactions, which we can see by measuring the transmission of laser light through this cavity."
The research team, which also included Rodriguez's PhD students Zou Geng and Kevin Peters, increased and decreased the distances between the mirrors at different speeds and noted how light transmitted through the cavity was affected. They saw that the direction in which the mirrors moved influenced how much light got through the cavity, finding that "the transmission of light through the cavity is non-linear." This behavior of light, called hysteresis, is present in the phase transitions of boiling water or magnetic materials.
The scientists also increased the speed with which the oil-filled cavity opened and closed, observing that under such conditions the hysteresis was not always present. This allowed them to extrapolate a universal law. "The equations that describe how light behaves in our oil-filled cavity are similar to those describing collections of atoms, superconductors and even high energy physics," elaborated Rodriguez, adding: "Therefore, the universal behavior we discovered is likely to be observed in such systems as well."
An optical cavity formed by two mirrors used in the experiment. Light going through the cavity bounces between the mirrors until leaving to where the transmission is measured. The scientists filled this cavity with olive oil and moved the mirrors at varying speeds.
Credit: Henk-Jan Boluijt (AMOLF)
The researchers think their discovery may have potential applications in computing or sensing systems.
Check out their new study in Physical Review Letters.