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Seeing what the naked eye can’t − 4 essential reads on how scientists bring the microscopic world into plain sight

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Seeing what the naked eye can’t − 4 essential reads on how scientists bring the microscopic world into plain sight

This microscopy image shows the retina of a mouse, laid flat and made fluorescent.
Kenyoung Kim, Wonkyu Ju and Mark Ellisman/National Center for Microscopy and Imaging Research, University of California, San Diego via Flickr, CC BY-NC

Vivian Lam, The Conversation

The microscope is an iconic symbol of the life sciences – and for good reason. From the discovery of the existence of cells to the structure of DNA, microscopy has been a quintessential tool of the field, unlocking new dimensions of the living world not only for scientists but also for the general public.

For the life sciences, where understanding the function of a living thing often requires interpreting its form, imaging is vital to confirming theories and revealing what is yet unknown.

This selection of stories from The Conversation’s archive presents a few ways in which microscopy has contributed to different forms of scientific knowledge, including techniques that take visualization beyond sight altogether.

1. Seeing as identifying

Over the past few centuries, the microscope has undergone a gradual but significant evolution. Each advance has allowed researchers to see increasingly smaller and more fragile structures and biomolecules at increasingly higher resolution – from cells, to the structures within cells, to the structures within the structures within cells, down to atoms.

But there is still a resolution gap between the smallest and largest structures of the cell. Biophysicist Jeremy Berg drew an analogy to Google Maps: Though scientists could see the city as a whole and individual houses, they couldn’t make out the neighborhoods.

“Seeing these neighborhood-level details is essential to being able to understand how individual components work together in the environment of a cell,” he writes.

Scientists are working to bridge that resolution gap. Improvements to the 2014 Nobel Prize-winning superresolution microscopy, for example, have enhanced the study of lengthy processes like cell division by capturing images across a range of size and time scales simultaneously, bringing clarity to details traditional microscopes tend to blur.

Cryo-ET image of SARS-CoV-2
Cryo-electron tomography shows what molecules look like in high resolution – in this case, the virus that causes COVID-19.
Nanographics, CC BY-SA

Another technique, cryo-electron microscopy, or cryo-EM, won a Nobel Prize in 2017 for bringing even more complex, dynamic molecules into view by flash-freezing them. This creates a protective glasslike shell around samples as they’re bombarded by a beam of electrons to create their photo op. Cryo-ET, a specialized type of cryo-EM, can construct 3D images of molecular structures within their natural environments.

These techniques not only generate images at or near atomic resolution but also preserve the natural shape of difficult-to-capture biomolecules of interest. Researchers were able to use cryo-EM, for instance, to capture the elusive structure of the protein on the surface of the shape-shifting hepatitis C virus, providing key information for a future vaccine.

Further enhancements to science’s visual acuity will reveal more of the fine details of the building blocks of life.

“I anticipate seeing new theories on how we understand cells, moving from disorganized bags of molecules to intricately organized and dynamic systems,” writes Berg.

2. Seeing as scoping

Microscopy images are often framed as snapshots – circumscribed parts of a whole that have been magnified to reveal their hidden features. But nothing in an organism works in isolation. After discerning individual components, scientists are tasked with charting how they interact with each other in the macrosystem of the body. Figuring this out requires not only identifying every component that makes up a particular cell, tissue and organ but also placing them in relation to each other – in other words, making a map.

Researchers have been charting the brain by stitching together multiple snapshots like a photo mosaic. They use different techniques to label a specific cell type and then image the whole brain at high resolution. Layer by layer, each run-through creates an increasingly detailed and more complete model. Neuroscientist Yongsoo Kim likens the process to a satellite image of the brain. Combining millions of these photos allows researchers to zoom into the weeds and zoom out to a bird’s-eye view.

Stiched high-resolution microscopy image of mouse brain.
Zooming in on this image of a mouse brain reveals rectangular lines where images were stitched together, with each colored dot representing a specific brain cell type.
Yongsoo Kim, CC BY-NC-ND

But building a map of a city, however detailed, is not the same as understanding its rhythm and atmosphere. Likewise, knowing where every cell is located relative to each other doesn’t necessarily tell researchers how they function or interact. Just as important as charting out the landscape of an organ is coming up with a working theory of how it all fits together and performs as a whole. Right now, Kim notes, analysis lags behind technical advances in data collection.

“Incredibly rich, high-resolution brain mapping presents a great opportunity for neuroscientists to deeply ponder what this new data says about how the brain works,” Kim writes. “Though there are still many unknowns about the brain, these new tools and techniques could help bring them to light.”

3. Seeing as recognizing

Every improvement in technology brings a parallel improvement in the data it collects, both in quality and in quantity. But that data is only useful insofar as researchers are able to analyze it – high granularity isn’t helpful if those details aren’t appreciable, and high output isn’t beneficial if it’s too overwhelming to organize.

Automated microscopes, for example, have made it possible to take time-lapse images of cells, resulting in massive amounts of data that require manual sifting. Neuroscientist Jeremy Linsley and his team encountered this dilemma in their own work on neurodegenerative disease. They’ve been relying on an army of interns to scour hundreds of thousands of images of neurons and tally each death – a slow and expensive process.

Microscopy images showing rat neurons before and after treatment with glutamate; the neurons are colored green when alive and yellow when dead
These images show living neurons colored green and dead neurons colored yellow.
Jeremy Linsley, CC BY-NC-ND

So they turned to artificial intelligence. Researchers can train an AI model to recognize specific patterns by feeding it many sample images, pointing out structures of interest and extrapolating the algorithm to new contexts. Linsley and his team developed a model to distinguish between living and dead neurons with greater speed and accuracy than people trained to do the same task.

They also opened the black box of the model to figure out how it was finding dead cells, revealing new signals of neuron death that researchers previously weren’t aware of because they weren’t obvious to the human eye.

“By taking out human guesswork, (AI models) increase the reproducibility and speed of research and can help researchers discover new phenomena in images that they would otherwise not have been able to easily recognize,” writes Linsley.

4. Seeing as appreciating

Even before they had the instruments to zoom in on samples, researchers had a tool in their arsenal to study the living world that they still use today: art.

Illustration of cells in a cork from Robert Hooke's Micrographia
This illustration from Robert Hooke’s ‘Micrographia’ shows the structure of cells in a cork.
Robert Hooke/National Library of Wales via Wikimedia Commons

Centuries ago, scientists and artists examined plants, animals and anatomy through illustration. Sketches of unfamiliar species in their natural environments aided in their classification, and drawings of the human body advanced study of its structure and function. With the help of the printing press, these artistic renderings – which later included the view under the lenses of early microscopes – popularized scientific knowledge about the natural world.

Though hand drawings have since given way to advanced imaging techniques and computer models, the legacy of communicating science through art continues. Scientific publications and BioArt competitions highlight laboratory images and videos to share the awe and wonder of studying the natural world with the general public. Using visualizations in classrooms and art museums can also promote science literacy by giving students a chance to look through the eye of the microscope as a scientist would.

Biologist and BioArt Awards judge Chris Curran believes that making visible the processes and concepts of science can grant a greater depth of understanding of the natural world necessary to being an informed citizen.

“That those images and videos are often beautiful is an added benefit,” she writes.

This video of cells migrating in a zebra fish embryo won first place in the 2022 Nikon Small World in Motion Competition.

And the abstract qualities of science can be made tangible in ways that don’t involve sight. Proteins, for instance, can be translated into music by mapping their physical properties into sound: amino acids turn into notes, while structural loops become tempos and motifs. Computational biologists Peng Zhang and Yuzong Chen enhanced the musicality of these mapping techniques by basing them on different music styles, such as that of Chopin. Consequently, a protein that prevents cancer formation, p53, sounds toccata-like, and the protein that binds to the hormone and neurotransmitter oxytocin flutters with recurring motifs.

Framing scientific images as art often requires no more than a change in perspective. And uncovering the poetry of science, many researchers would agree, can help reveal the artistry of life.The Conversation

Vivian Lam, Associate Health and Biomedicine Editor, The Conversation

This article is republished from The Conversation under a Creative Commons license. Read the original article.

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In Disney’s ‘Moana,’ the characters navigate using the stars, just like real Polynesian explorers − an astronomer explains how these methods work

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theconversation.com – Christopher Palma, Teaching Professor, Department of Astronomy & Astrophysics, Penn State – 2024-12-20 07:17:00

Wayfarers around the world have used the stars to navigate the sea.
Wirestock/iStock via Getty Images Plus

Christopher Palma, Penn State

If you have visited an island like one of the Hawaiian Islands, Tahiti or Easter Island, also known as Rapa Nui, you may have noticed how small these land masses appear against the vast Pacific Ocean. If you’re on Hawaii, the nearest island to you is more than 1,000 miles (1,600 kilometers) away, and the coast of the continental United States is more than 2,000 miles (3,200 kilometers) away. To say these islands are secluded is an understatement.

For me, watching the movie “Moana” in 2016 was eye-opening. I knew that Polynesian people traveled between a number of Pacific islands, but seeing Moana set sail on a canoe made me realize exactly how small those boats are compared with what must have seemed like an endless ocean. Yet our fictional hero went on this journey anyway, like the countless real-life Polynesian voyagers upon which she is based.

Oceania as shown from the ISS
Islands in Polynesia can be thousands of miles apart.
NASA

As an astronomer, I have been teaching college students and visitors to our planetarium how to find stars in our sky for more than 20 years. As part of teaching appreciation for the beauty of the sky and the stars, I want to help people understand that if you know the stars well, you can never get lost.

U.S. Navy veterans learned the stars in their navigation courses, and European cultures used the stars to navigate, but the techniques of Polynesian wayfinding shown in Moana brought these ideas to a very wide audience.

The movie Moana gave me a new hook – pun not intended – for my planetarium shows and lessons on how to locate objects in the night sky. With “Moana 2” out now, I am excited to see even more astronomy on the big screen and to figure out how I can build new lessons using the ideas in the movie.

The North Star

Have you ever found the North Star, Polaris, in your sky? I try to spot it every time I am out observing, and I teach visitors at my shows to use the “pointer stars” in the bowl of the Big Dipper to find it. These two stars in the Big Dipper point you directly to Polaris.

If you are facing Polaris, then you know you are facing north. Polaris is special because it is almost directly above Earth’s North Pole, and so everyone north of the equator can see it year-round in exactly the same spot in their sky.

It’s a key star for navigation because if you measure its height above your horizon, that tells you how far you are north of Earth’s equator. For the large number of people who live near 40 degrees north of the equator, you will see Polaris about 40 degrees above your horizon.

If you live in northern Canada, Polaris will appear higher in your sky, and if you live closer to the equator, Polaris will appear closer to the horizon. The other stars and constellations come and go with the seasons, though, so what you see opposite Polaris in the sky will change every month.

Look for the Big Dipper to find the North Star, Polaris.

You can use all of the stars to navigate, but to do that you need to know where to find them on every night of the year and at every hour of the night. So, navigating with stars other than Polaris is more complicated to learn.

Maui’s fishhook

At the end of June, around 11 p.m., a bright red star might catch your eye if you look directly opposite from Polaris. This is the star Antares, and it is the brightest star in the constellation Scorpius, the Scorpion.

If you are a “Moana” fan like me and the others in my family, though, you may know this group of stars by a different name – Maui’s fishhook.

If you are in the Northern Hemisphere, Scorpius may not fully appear above your horizon, but if you are on a Polynesian island, you should see all of the constellation rising in the southeast, hitting its highest point in the sky when it is due south, and setting in the southwest.

Astronomers and navigators can measure latitude using the height of the stars, which Maui and Moana did in the movie using their hands as measuring tools.

The easiest way to do this is to figure out how high Polaris is above your horizon. If you can’t see it at all, you must be south of the equator, but if you see Polaris 5 degrees (the width of three fingers at arm’s length) or 10 degrees above your horizon (the width of your full fist held at arm’s length), then you are 5 degrees or 10 degrees north of the equator.

The other stars, like those in Maui’s fishhook, will appear to rise, set and hit their highest point at different locations in the sky depending on where you are on the Earth.

Polynesian navigators memorized where these stars would appear in the sky from the different islands they sailed between, and so by looking for those stars in the sky at night, they could determine which direction to sail and for how long to travel across the ocean.

Today, most people just pull out their phones and use the built-in GPS as a guide. Ever since “Moana” was in theaters, I see a completely different reaction to my planetarium talks about using the stars for navigation. By accurately showing how Polynesian navigators used the stars to sail across the ocean, Moana helps even those of us who have never sailed at night to understand the methods of celestial navigation.

The first “Moana” movie came out when my son was 3 years old, and he took an instant liking to the songs, the story and the scenery. There are many jokes about parents who dread having to watch a child’s favorite over and over again, but in my case, I fell in love with the movie too.

Since then, I have wanted to thank the storytellers who made this movie for being so careful to show the astronomy of navigation correctly. I also appreciated that they showed how Polynesian voyagers used the stars and other clues, such as ocean currents, to sail across the huge Pacific Ocean and land safely on a very small island thousands of miles from their home.The Conversation

Christopher Palma, Teaching Professor, Department of Astronomy & Astrophysics, Penn State

This article is republished from The Conversation under a Creative Commons license. Read the original article.

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Listening for the right radio signals could be an effective way to track small drones

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theconversation.com – Iain Boyd, Director of the Center for National Security Initiatives and Professor of Aerospace Engineering Sciences, University of Colorado Boulder – 2024-12-17 17:28:00

Small drones can be hard to track at night.
Kevin Carter/Getty Images

Iain Boyd, University of Colorado Boulder

The recent spate of unidentified drone sightings in the U.S., including some near sensitive locations such as airports and military installations, has caused significant public concern.

Some of this recent increase in activity may be related to a September 2023 change in U.S. Federal Aviation Administration regulations that now allow drone operators to fly at night. But most of the sightings are likely airplanes or helicopters rather than drones.

The inability of the U.S. government to definitively identify the aircraft in the recent incidents, however, has some people wondering, why can’t they?

I am an engineer who studies defense systems. I see radio frequency sensors as a promising approach to detecting, tracking and identifying drones, not least because drone detectors based on the technology are already available. But I also see challenges to using the detectors to comprehensively spot drones flying over American communities.

How drones are controlled

Operators communicate with drones from a distance using radio frequency signals. Radio frequency signals are widely used in everyday life such as in garage door openers, car key fobs and, of course, radios. Because the radio spectrum is used for so many different purposes, it is carefully regulated by the Federal Communications Commission.

Drone communications are only allowed in narrow bands around specific frequencies such as at 5 gigahertz. Each make and model of a drone uses unique communication protocols coded within the radio frequency signals to interpret instructions from an operator and to send data back to them. In this way, a drone pilot can instruct the drone to execute a flight maneuver, and the drone can inform the pilot where it is and how fast it is flying.

Identifying drones by radio signals

Radio frequency sensors can listen in to the well-known drone frequencies to detect communication protocols that are specific to each particular drone model. In a sense, these radio frequency signals represent a unique fingerprint of each type of drone.

In the best-case scenario, authorities can use the radio frequency signals to determine the drone’s location, range, speed and flight direction. These radio frequency devices are called passive sensors because they simply listen out for and receive signals without taking any active steps. The typical range limit for detecting signals is about 3 miles (4.8 kilometers) from the source.

These sensors do not represent advanced technology, and they are readily available. So, why haven’t authorities made wider use of them?

Drones were all the buzz in the Northeast at the end of 2024.

Challenges to using radio frequency sensors

While the monitoring of radio frequency signals is a promising approach to detecting and identifying drones, there are several challenges to doing so.

First, it’s only possible for a sensor to obtain detailed information on drones that the sensor knows the communication protocols for. Getting sensors that can detect a wide range of drones will require coordination between all drone manufacturers and some central registration entity.

In the absence of information that makes it possible to decode the radio frequency signals, all that can be inferred about a drone is a rough idea of its location and direction. This situation can be improved by deploying multiple sensors and coordinating their information.

Second, the detection approach works best in “quiet” radio frequency environments where there are no buildings, machinery or people. It’s not easy to confidently attribute the unique source of a radio frequency signal in urban settings and other cluttered environments. Radio frequency signals bounce off all solid surfaces, making it difficult to be sure where the original signal came from. Again, the use of multiple sensors around a particular location, and careful placement of those sensors, can help to alleviate this issue.

Third, a major part of the concern over the inability to detect and identify drones is that they may be operated by criminals or terrorists. If drone operators with malicious intent know that an area targeted for a drone operation is being monitored by radio frequency sensors, they may develop effective countermeasures. For example, they may use signal frequencies that lie outside the FCC-regulated parameters, and communication protocols that have not been registered. An even more effective countermeasure is to preprogram the flight path of a drone to completely avoid the use of any radio frequency communications between the operator and the drone.

Finally, widespread deployment of radio frequency sensors for tracking drones would be logistically complicated and financially expensive. There are likely thousands of locations in the U.S. alone that might require protection from hostile drone attacks. The cost of deploying a fully effective drone detection system would be significant.

There are other means of detecting drones, including radar systems and networks of acoustic sensors, which listen for the unique sounds drones generate. But radar systems are relatively expensive, and acoustic drone detection is a new technology.

The way forward

It was almost guaranteed that at some point the problem of unidentified drones would arise. People are operating drones more and more in regions of the airspace that have previously been very sparsely populated.

Perhaps the recent concerns over drone sightings are a wake-up call. The airspace is only going to become much more congested in the coming years as more consumers buy drones, drones are used for more commercial purposes, and air-taxis come into use. There’s only so much that drone detection technologies can do, and it might become necessary for the FAA to tighten regulation of the nation’s airspace by, for example, requiring drone operators to submit detailed flight plans.

In the meantime, don’t be too quick to assume those blinking lights you see in the night sky are drones.The Conversation

Iain Boyd, Director of the Center for National Security Initiatives and Professor of Aerospace Engineering Sciences, University of Colorado Boulder

This article is republished from The Conversation under a Creative Commons license. Read the original article.

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Vaccine misinformation distorts science – a biochemist explains how RFK Jr. and his lawyer’s claims threaten public health

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theconversation.com – Mark R. O’Brian, Professor and Chair of Biochemistry, University at Buffalo – 2024-12-17 07:01:00

Many fatal childhood illnesses can be prevented with vaccination.
Westend61/Getty Images

Mark R. O’Brian, University at Buffalo

Vaccinations provide significant protection for the public against infectious diseases and substantially reduce health care costs. Therefore, it is noteworthy that President-elect Donald Trump wants Robert F. Kennedy Jr., a leading critic of childhood vaccination, to be secretary of Health and Human Services.

Doctors, scientists and public health researchers have expressed concerns that Kennedy would turn his views into policies that could undermine public health. As a case in point, news reports have highlighted how Kennedy’s lawyer, Aaron Siri, has in recent years petitioned the Food and Drug Administration to withdraw or suspend approval of numerous vaccines over alleged safety concerns.

I am a biochemist and molecular biologist studying the roles microbes play in health and disease. I also teach medical students and am interested in how the public understands science.

Here are some facts about vaccines that Kennedy and Siri get wrong:

Vaccines are effective and safe

Public health data from 1974 to the present conclude that vaccines have saved at least 154 million lives worldwide over the past 50 years. Vaccines are also continually monitored for safety in the U.S.

Nevertheless, the false claim that vaccines cause autism persists despite study after study of large populations throughout the world showing no causal link between them.

Claims about the dangers of vaccines often come from misrepresenting scientific research papers. In an interview with podcaster Joe Rogan, Kennedy incorrectly cited studies allegedly showing vaccines cause massive brain inflammation in laboratory monkeys, and that the hepatitis B vaccine increases autism rates in children by over 1,000-fold compared with unvaccinated kids. Those studies make no such claims.

In the same interview, Kennedy also made the unusual claim that a 2002 vaccine study included a control group of children 6 months of age and younger who were fed mercury-contaminated tuna sandwiches. No sandwiches are mentioned in that study.

Similarly, Siri filed a petition in 2022 to withdraw approval of a polio vaccine based on alleged safety concerns. The vaccine in question is made from an inactivated form of the polio virus, which is safer than the previously used live attenuated vaccine. The inactivated vaccine is made from polio virus cultured in the Vero cell line, a type of cell that researchers have been safely using for various medical applications since 1962. While the petition uses provocative language comparing this cell line to cancer cells, it does not claim that it causes cancer.

Gloved hands of clinician placing band-aid on child's arm, a syringe and vaccine vial beside them
Vaccines are continuously monitored for safety before and long after they’re made available to the general public.
Elena Zaretskaya/Moment via Getty Images

Vaccines undergo the same approval process as other drugs

Clinical trials for vaccines and other drugs are blinded, randomized and placebo-controlled studies. For a vaccine trial, this means that participants are randomly divided into one group that receives the vaccine and a second group that receives a placebo saline solution. The researchers carrying out the study, and sometimes the participants themselves, do not know who has received the vaccine or the placebo until the study has finished. This eliminates bias.

Results are published in the public domain. For example, vaccine trial data for COVID-19, human papilloma virus, rotavirus and hepatitis B are available for anyone to access.

Aluminum adjuvants help boost immunity

Kennedy is co-counsel with a law firm that is suing the pharmaceutical company Merck based in part on the unfounded assertion that the aluminum in one of its vaccines causes neurological disease. Aluminum is added to many vaccines as an adjuvant to strengthen the body’s immune response to the vaccine, thereby enhancing the body’s defense against the targeted microbe.

The law firm’s claim is based on a 2020 report showing that brain tissue from some patients with Alzheimer’s disease, autism and multiple sclerosis have elevated levels of aluminum. The authors of that study do not assert that vaccines are the source of the aluminum, and vaccines are unlikely to be the culprit.

Notably, the brain samples analyzed in that study were from 47- to 105-year-old patients. Most people are exposed to aluminum primarily through their diets, and aluminum is eliminated from the body within days. Therefore, aluminum exposure from childhood vaccines is not expected to persist in those patients.

Ironically, Kennedy’s lawyer, Siri, wants the FDA to withdraw some vaccines for containing less aluminum than stated by the manufacturer.

Vaccine manufacturers are liable for injury or death

Kennedy’s lawsuit against Merck contradicts his insistence that vaccine manufacturers are fully immune from litigation.

His claim is based on an incorrect interpretation of the National Vaccine Injury Compensation Program, or VICP. The VICP is a no-fault federal program created to reduce frivolous lawsuits against vaccine manufacturers, which threaten to cause vaccine shortages and a resurgence of vaccine-preventable disease.

A person claiming injury from a vaccine can petition the U.S. Court of Federal Claims through the VICP for monetary compensation. If the VICP petition is denied, the claimant can then sue the vaccine manufacturer.

Gloved hand picking up vaccine vial among a tray of vaccine vials
Drug manufacturers are liable for any vaccine-related death or injury.
Andreas Ren Photography Germany/Image Source via Getty Images

The majority of cases resolved under the VICP end in a negotiated settlement between parties without establishing that a vaccine was the cause of the claimed injury. Kennedy and his law firm have incorrectly used the payouts under the VICP to assert that vaccines are unsafe.

The VICP gets the vaccine manufacturer off the hook only if it has complied with all requirements of the Federal Food, Drug and Cosmetic Act and exercised due care. It does not protect the vaccine maker from claims of fraud or withholding information regarding the safety or efficacy of the vaccine during its development or after approval.

Good nutrition and sanitation are not substitutes for vaccination

Kennedy asserts that populations with adequate nutrition do not need vaccines to avoid infectious diseases. While it is clear that improvements in nutrition, sanitation, water treatment, food safety and public health measures have played important roles in reducing deaths and severe complications from infectious diseases, these factors do not eliminate the need for vaccines.

After World War II, the U.S. was a wealthy nation with substantial health-related infrastructure. Yet, Americans reported an average of 1 million cases per year of now-preventable infectious diseases.

Vaccines introduced or expanded in the 1950s and 1960s against diseases like diphtheria, pertussis, tetanus, measles, polio, mumps, rubella and Haemophilus influenza B have resulted in the near or complete eradication of those diseases.

It’s easy to forget why many infectious diseases are rarely encountered today: The success of vaccines does not always tell its own story. RFK Jr.’s potential ascent to the role of secretary of Health and Human Services will offer up ample opportunities to retell this story and counter misinformation.

This is an updated version of an article originally published on July 26, 2024.The Conversation

Mark R. O’Brian, Professor and Chair of Biochemistry, University at Buffalo

This article is republished from The Conversation under a Creative Commons license. Read the original article.

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