Using artificial intelligence to discover new treatments for superbugs

Machine learning is pointing researchers toward molecules that are structurally different from current antibiotics

Fabiola De Marchi


University of Padua

Antimicrobial resistance is an emerging threat to healthcare systems worldwide. As a consequence of the spread of drug-resistant bacteria, also called “superbugs,” medical treatments could become ineffective for an increasing number of people in the next years. To fix this huge problem, chemists are asked to find new effective antibiotics. 

Drug discovery is an expensive and time-consuming process during which pharmaceutical chemists look for new candidate molecules to interact with a particular target protein or pathway causing the disease. Chemists screen large libraries of thousands to millions of molecules, looking for compounds with specific biological effects and low toxicity. However, these screenings are not very efficient: if chemical libraries don’t include molecules with enough structural diversity, chemists will fail to discover antibiotics with molecular structures different from the ones already tested in laboratories or clinical trials. 

Now machine learning is flanking chemoinformatics through innovative deep neural network approaches to find new drugs. An example of how this approach works can be seen in a recent study by James Collins and coworkers at MIT. First, researchers trained a neural network model to predict growth inhibition of Escherichia coli using a set of 2335 diverse molecules; then, they applied the optimized neural network model to screen large chemical libraries with more than 107 million molecules. 

They ended up with a list of candidate molecules structurally different from known antibiotics, and ranked them based on their predicted biological activity. Among those candidates, they found that halicin, a compound under investigation as a treatment for diabetes, displayed high efficacy against E. coli and a large spectrum of pathogens such as Acinetobacter baumanii, at the top list of resistant bacteria which urgently requires new antibiotics.

Research groups are currently developing similar deep learning approaches to find new compounds that could fight the COVID-19 virus. This suggests how recent improvements in machine learning can assist chemists' work to speed up and lower the costs of the drug discovery process.

Glowing worms have less sex when the lights are on

Artificial lighting makes it harder for bioluminescent insects to find mates

Sara Zlotnik

Ecology & Evolutionary Biology

University of Florida

Human activities like deforestation and fossil fuel use are major drivers of biodiversity loss. But what about seemingly innocuous activities like turning the lights on at night? While most people who live in cities or suburbs are used to the effects of artificial lights, many wild animals that live alongside us are not so good at coping with this widespread form of pollution.

Ecologists in Finland recently published a study on the effects of artificial lights on mate attraction in a bioluminescent beetle species called the common glow-worm of Europe (Lampyris noctiluca). Female glow-worms use their bioluminescent abdomen to attract male mates, but this reproductive strategy only works at night, when the glowing signal is readily apparent. Artificial lights are making the night-time landscape much less dark in many places, which could reduce the glow-worms’ ability to find mates.

To test the effects of artificial lights on mate attraction, the researchers made fake female glow-worms and set up traps to capture any males that came in contact with them. Very few males approached female glow-worms that were just one meter from away from an artificial light, while they easily found the females that were over two meters away. So, mate attraction in these insects is seriously disrupted by artificial lights, but females might be able to compensate if they move further away from the light.

Unfortunately, the researchers ran another experiment and found that in the presence of an artificial light, female glow-worms are likely to not signal at all, or even hide, rather than to move further away. This unhelpful behavior is quite understandable considering that for most of the evolutionary history of these insects, artificial lighting did not exist.

The results of these experiments clearly demonstrate how detrimental night-time lighting can be for wild animals, especially nocturnal animals that use visual forms of communication such as bioluminescence.  And beyond these worms, artificial lights have also contributed to global firefly declines as well as the declines of many non-bioluminescent insects, such as moths, crickets, and mayflies.

What's really in your salmon? These scientists found out

Nutritional information isn't required on seafood packaging in North America

Salmon is enjoyed by people around the world for its range of nutritional benefits. However, purchasing Canadian salmon with high nutritional content and low levels of contaminants can be a shot in the dark because nutritional information is not required on seafood packaging in North America. 

Stephanie Colombo, an assistant professor of Aquaculture at Dalhousie University, wanted to determine the nutritional composition of different types of salmon available to Canadian consumers. No study has been done like this on Canadian salmon before, so her results provide a comparative baseline for future research.

Colombo’s team purchased six types of salmon fillets available in Canadian grocery stores to compare their nutritional information. They analyzed farmed Atlantic, farmed organic Atlantic, farmed organic Chinook, wild Chinook, wild Pacific pink and wild Sockeye. There are many misconceptions when it comes to choosing between wild and farmed salmon, with many consumers believing that farmed salmon is nutritionally inferior to wild salmon, and has more contaminants. The researchers analyzed the salmon's protein, fat, fatty acids, and mercury contents to determine if there is any truth behind these preconceptions. 

salmon up close

Photo by Sas Kia on Unsplash

Surprisingly, the study found that the biggest determinant of protein and fat content and mercury levels was the species of salmon the fillets came from, which is due to their different diets. They also found that factors like wild or farmed and organic or non-organic did not have a major impact on mercury levels in the tested salmon.

Wild Sockeye and wild Chinook fillets were the most nutrient-dense and had the highest omega-3 fatty acid content. However, for frequent consumers, the study suggested farmed Atlantic salmon as an affordable, nutrient-dense, low-mercury alternative to Sockeye or Chinook. Future research should consider the nutritional content of farmed salmon fed sustainable plant-based diets in comparison with traditional fish-based diets.

The two halves of a new compound team up to fight cancer

When combined, ruthenium and platinum do a better job at killing cancer cells than their individual parts

Cancer cells' ability to gain drug resistance makes them smarter than we think. To outsmart these rogue cells, some research groups are working to develop multi-action, multi-target cancer therapies. Molecules for such therapies are like Swiss-army knives that can change their reaction mechanisms depending on the job at hand. 

One recent molecule, made by researchers in France and Israel, is better than the sum of its parts. Made up of two metals — ruthenium and platinum — one half of the new molecule turns into a lethal cancer-killer when irradiated with light, and the other half kills cancerous cells just by gluing itself to them.

Photodynamic therapy is a medical procedure that uses light as a way of treating cancers and other skin diseases. Normally, a drug known as a photosensitizer is used in combination with the light therapy to increase the effectiveness of the treatment. Photosensitizers do this by absorbing lots of light and reacting to help make small molecules that can go on to destroy tumors. 

The new molecule for multi-action therapy works in two ways. The ruthenium center helps the solubility of the drug so it can reach the tumors and acts as a miniature antenna to gather as much light as possible there, much like a traditional photosensitizer. But rather than working alone, it transfers some of this light energy to the platinum half of the molecule, turning the platinum site into a highly efficient chemotherapy drug that can bind very tightly to DNA. By doing this, the platinum half of the molecule only reveals its identity as a highly effective chemotherapy drug when it is already at the site of the tumor, reducing unwanted side-effects and toxicity elsewhere in the body. By teaming up and working together, the ruthenium half of the molecule also helps to boost the anti-cancer activity of the platinum, helping it overcome issues with drug resistance.

A new scientific method plays tag to understand neutrinos

Neutrinos are subatomic particles that scientists have puzzled over for decades

Simone Eizagirre


University of Cambridge

An interdisciplinary collaboration of physicists, chemists, and materials scientists based at the University of the Basque Country (UPV-EHU) and the Donostia International Physics Centre has invented a new ultrasensitive molecular sensing technique to monitor a nuclear decay reaction. With it, the collaboration could solve a decadeslong mystery about the nature of neutrino particles and address some of the fundamental questions about our universe.

Neutrinos are subatomic particles that have no electrical charge and extremely small mass — some even think they could have no mass. Most particles of matter have a corresponding antiparticle, which has the same mass but opposite physical charges, but scientists have been puzzling for decades over whether neutrinos could be their own antiparticles.

One way to answer this question is by studying a process called “neutrinoless double beta decay.” In this rare type of nuclear decay, two neutrons from the nucleus of an atom turn into protons, emitting two electrons in the process. This can occur spontaneously in a particular isotope of xenon atoms (136-Xe), which undergo decay into barium ions. However, the process is so rare that observing it is very difficult and until now, scientists had not found a viable method of detecting individual barium ions.

In their results, published recently in Nature, the authors report a “tagging” method that could be used to detect barium ions that originate from this decay. They have designed a fluorescent molecule that can capture the barium ions to form a supramolecular complex. These molecules usually emit green light when excited with ultraviolet illumination, but the emission turns blue if the complexes have captured barium ions.

What is remarkable about this work is its truly interdisciplinary nature. It harnesses the expertise of synthetic chemists and materials scientists to develop an experimental technique that will be applied in a completely different field: particle physics. The success of this collaboration, involving researchers from nine different research institutes, shows how interdisciplinary science often leads to innovative and impactful solutions, as well as the value in bringing in new perspectives to our work.

During the pandemic, mid-day might be the safest time to play soccer

New research looks into how to keep sports leagues in play while minimizing COVID-19 spread

Francesco Zangari

Molecular Biology

University of Toronto

The COVID-19 pandemic has brought global sports to a halt and led to uncertainty of how leagues will complete the season in progress. While North American leagues like the MLB, NBA, and NHL have just started up again, time will tell how successful their COVID control plans are.

Nonetheless, soccer has resumed across Europe and a recent preprint by scientists at The Hebrew University of Jerusalem highlights how this restart can be made safer by simply scheduling matches strategically. 

The, researchers focused on the primary surfaces most contacted by soccer players. They began by taking grass and synthetic leather (as a proxy for the ball’s surface) and monitoring how long a virus very similar to SARS-CoV-2 survived on them at two time points when matches are frequently played: mid-day (1:00 PM, ~30 degrees Celsius) or nighttime (8:00 PM, ~22 degrees C). 

They saw a stark difference in virus survival. Surfaces exposed to mid-day conditions had little virus survival past 90 minutes, while nighttime exposed surfaces remained contaminated for 24 hours. They pointed to differences in heat and UV light as the potential mediators of virus inactivation. These findings suggest that organizers of European soccer leagues should schedule matches at mid-day for safety. 

Chewing pasta too much makes it less healthy

The latest pasta research shows that tiny bits of noodles lead to higher glucose levels

Josseline Ramos-Figueroa


University of Saskatchewan

Refrigerating dried or homemade pasta may be beneficial to health, but also may alter how pasta breaks down upon chewing.

When cooking every day becomes too impractical, many people resort to meal prepping. This can mean a constant cycle of refrigerating and reheating meals. In the case of pasta, this process actually might be be beneficial for your health.

Controlling glucose levels is critical to decreasing the risk of heart disease, diabetes, and obesity. Previous studies have shown that eating reheated pasta produced lower blood glucose levels than consuming freshly boiled pasta. Lower glucose levels were obtained because a new type of starch, called resistant starch, forms at cold temperatures. In our gut, enzymes break starch down into units of glucose. But for this resistant starch, degradation is slower, so less glucose forms. Do different types of pasta produce the same result? And does harsh or mild chewing affect starch degradation?

To find some answers, a group of researchers dug into two types of pasta: dried spaghetti and fresh homemade tagliatelle. And to simulate pasta particles produced upon chewing, they cut cooked pasta to two different sizes.

Results showed that cooled or reheated dry pasta only produced a small change in starch degradation than in freshly boiled pasta. However, with small-sized fresh pasta, the researchers saw a sharper decrease in starch degradation compared to dry pasta.

The researchers presume that the non-starch ingredients in pasta might point to additional factors for the formation of resistant starch. They also argued that the size of pasta particles formed during chewing may have greater effect than the process of cooling and reheating pasta. They proposed that industrial pasta production should consider pasta sizes and shapes that will naturally break into large pieces.

Jaime Chambers


Washington State University

Two wolves press their noses against a fence, scenting a tray of food on the other side. A rope dangles within their reach — a clue to the puzzle. If only one wolf pulls the rope, it comes loose and no one gets the food. But if they tug together, the snack will be theirs.

This might seem like a test of plain-old smarts. Put two good problem-solvers together, and they can figure it out. But according to a recent study published in Nature, the wolves’ bond with each other — rather than either individual’s intent or mental abilities — matters most. 

Wolves cooperate famously well. They coordinate to tackle large prey in the wild, and outperform dog duos in experiments requiring teamwork. But individual wolves’ cooperative abilities vary, and researchers at the University of Vienna’s Wolf Science Center wondered why.

To find out, they presented wolf pairs with three tasks designed to measure cooperation. In the rope test, each duo coordinated to get a meaty morsel. In the other two tests, wolves made choices with no reward to themselves. They pushed a touch screen to give their partner a reward (or not), and took turns pushing a buzzer that sometimes gave both a snack, and sometimes only their partner. 

 Researchers also measured each wolf’s individual traits, such as self-control, learning speed, persistence, and understanding of cause-and-effect. When it came to cooperating, these qualities didn’t matter so much. The wolves’ social bond most strongly shaped their success, not any particular individual quality. The more positive the prior relationship between two wolves, the better they performed on all three tasks.  

Scientists are still learning what drives cooperation in many species, but many hypothesize that “emotional bookkeeping” plays a role. When individuals share positive experiences, they tend to associate each other with positive emotions. A mental record of good vibes makes cooperation more likely, as an automatic first response. 

This study supports that idea. Wolves that feel good about each other cooperate better. The same has been found in humans, too — something to consider the next time you’re faced with a group project.

How mezcal bubbles can help us understand lava flows

The fluid mechanics of a good mezcal are complex

Adam Fortais


McMaster University

Mezcal is a classic Mexican spirit distilled from the agave plant. It can take your margaritas to the next level, but a new understanding of a traditional distillation technique used by mezcal producers could also provide insight into producing biofoams and better understanding lava flows.

When a mezcal producer wants to test the their product, they squirt a thin jet of the spirit into a vessel and observe the bubbles that result. If the bubbles pop quickly, that's not good; there is likely something wrong with the alcohol content. But if the bubbles survive 30 seconds or longer, they have a well-balanced spirit. And while this technique has been used for many years, exactly why it works has long been a mystery.

Bubbles on the surface of a liquid pop when the bubble "membrane" thins and becomes unstable. This happens to soap bubbles when gravity causes the fluid in the bubble to drain and thin. However, when a group of fluid mechanists studied mezcal bubbles, they found fluid flowed up, into the bubble. 

Alcohol has a lower surface tension than water, which means it evaporates and spreads more readily. So, when a mezcal bubble forms, the alcohol begins evaporating faster than the water. This increases the surface tension in the bubble compared to the rest of the liquid, and causes more high-alcohol fluid to flow up, into the bubble, thus slowing the thinning process.

The specifics involve viscosity and density of the fluid as well, but the researchers found that the effect was largely dependent on alcohol content. There was a narrow range of alcohol contents that maximized bubble lifetime; deviations above and below 50% drastically reduced how long bubbles lasted. 

The physics behind this process is useful for distilling alcohol, but the principals are transferable to all sorts of materials, like lava, biological materials, and soaps, just to name a few. The research team hopes this information will also be useful for better understanding some environmental, biological, and industrial processes. 

Farah Qaiser

Molecular Genetics

University of Toronto

In early June, a racist incident in Central Park sparked #BlackBirdersWeek: a week-long social media effort which celebrated and amplified the voices of Black nature enthusiasts. Since then, several social media movements have emerged to celebrate Black academics across a variety of disciplines, including #BlackInAstro (June 22 - 26), #BlackBotanistsWeek (July 6 - 11) and #BlackInAnimalBehaviour (July 23 - 27). 

#BlackInNeuro is in progress. Between July 27th and August 2nd, organizers have developed several activities to celebrate Black excellence in all things neuroscience, including panels and discussions on neuroracism, graduate school journeys, and more. Organizers have also asked for participants to share pop talks (a short one-minute introduction video) – never an easy task.

Instead of trying to capture all of these stories in words, here are some you should dive into and share.

Meet Mia Larrieu, an incoming PhD student who will be studying the behaviour of chickadees.

Wondering how many Black women have earned a PhD in astronomy in the US? Check out #BlackInAstro.

Learn about Taylor Harris’ journey into plants:

Why are campaigns like this important? 

Have you ever tried to explain your research in one minute, using accessible language? Here’s #BlackInNeuro co-organizer, Ti’Air Riggins, talking about microelectrode arrays (aka brain probes).

Since June, Black academics have been sharing their experiences in academia, from microaggressions to physical threats. Massive Science editor, Cassie Freund, spoke to #BlackInTheIvory co-founder, Dr. Shardé Davis, about this:

Additional campaigns along these lines are already being planned, with #BlackInChem set to take place between August 10-15th. And, importantly, a group of Black ecologists recently penned a comment in Nature’s Ecology & Evolution, calling for an acceptance of the “full expression of Black excellence in all its forms,” pointing out that these social media movements demonstrate the many forms of Black scholarship and community engagement, and should also be recognized in guidelines for tenure, promotion and hiring.

Despite the ADA, science often isn't accessible for disabled people

Laboratories and field work aren't set up for disabled scientists. They must be

Jennifer Keelan left her wheelchair at the bottom of the Capitol building steps. She was eight years old, the youngest person participating in the "Capitol Crawl." She stuffed a pamphlet into the pocket of her pinstripe jeans. She intended to hand it to a member of Congress, urging them to pass the Americans with Disabilities Act. As she dragged herself up the steps she exclaimed, "I'll take all night if I have to."

There was anger in her voice and it is an anger that I, and many other disabled scientists, can relate to.

The ADA prohibits discrimination against disabled people. Yet here we are, thirty years after its passage, and disabled scientists still don't have access to our work and learning spaces. And when we say we don't have access, we mean that quite literally. 

At UC Davis, there is an outdoor teaching area that may appear unremarkable to most. But it caught the eye of Megan Lynch, a Master's student in Horticulture and Agronomy. She took a picture and posted it on Twitter, asking able-bodied folks to #SpotTheAccessibilityFail, a hashtag she created. 

Uneven stones, a small step, a faded map - all barriers that prevent disabled people from using this space. "It was not designed with the idea that horticulture students at a public university would include disabled people,” Lynch said via email.

Administrations treat the ADA as if it is the gold standard for accessibility. But disabled people know that it mandates only the bare minimum and most campuses fail to meet it.  

Lynch isn't impressed. She has had trouble getting anyone at UC Davis to care about disability inclusion, even her union. So she founded UC Access Now, a campaign for universal design, accessibility, and inclusion for disabled people on the University of California campuses. 

This campaign is important. But as Lynch says, "It's hard enough to survive as a disabled student without adding on unpaid DEI work in the form of activism." It isn't the responsibility of disabled scientists to break down the barriers meant to exclude us.

"The assumption that no one with a disability could ever possibly do [horticulture and agronomy] is part of what keeps the field so inaccessible." Abled people refuse to change and that is why there are so few disabled people in science, Lynch said. And she is right. 

It's time to show up for disabled scientists. To fulfill the promise made to us thirty years ago. It's time for change.

You can follow UC Access Now on Twitter at @AccessUC and read their Demandifesto here.

[Ed: An earlier version of this  article misused the term "able-bodied" in the 8th paragraph. This has been replaced with the appropriate term, "abled." The distinction is important as there are some disabled people who are able-bodied.  Dan Samorodnitsky, Senior Editor]   

Wolbachia bacteria stop mosquitos from spreading viruses

You may have never heard of Wolbachia, but these bacteria could save us from dengue and malaria

Marnie Willman


University of Manitoba Bannatyne and National Microbiology Laboratory

The Aedes aegypti mosquito is one of the most notorious insects because of it can transmit tropical diseases such as dengue, yellow fever, malaria, and Zika virus. Climate change threatens to amplify their damage as increasing global temperatures enable the mosquitoes to survive in new geographical areas that were traditionally too cold. 

But, there is a glimmer of hope to this tale. It turns out, mosquitos have a natural emeny: Wolbachia. Wolbachia is a bacteria that infects over half of arthropod species, including A. aegypti. These bacteria can stop the viruses that mosquitos carry from being contagious, blocking transmission to humans. Little is known about how the Wolbachia can do this, and has become the subject of global research. 

In a paper published in Frontiers in Microbiology, Suzanne Ford and colleagues unravel some of the mystery behind Wolbachia "virus blocking.". Wolbachia introduced to A. aegypti mosquitoes was found to be stably-inherited by offspring, meaning that the bacteria was passed from mosquito parents to offspring, and that this blocked transmission of dengue, Zika, and chikungunya viruses.

This study also aimed to inspect the genetic inheritance of the bacterium and how blocking could be enhanced in a lab to make viral transmission from mosquitoes more ineffective. The researchers found a specific signaling pathway that resulted in resistance to dengue virus in mosquitoes. Mosquitoes that are resistant to the virus have faster cell replication in their midgut region than those who are susceptible. This study found Wolbachia bacteria enhanced this effect. These mosquitoes in turn do not acquire the dengue virus as easily, and as a result, they don't pass it to other animals, such as humans. 

This is an important step forward, because so little is known about how Wolbachia bacteria reduce transmission of tropical viral diseases. Imagine if Wolbachia-infected mosquitoes populated the globe, eliminating mosquito-borne viruses altogether!  

A new COVID-19 test uses CRISPR to detect the virus

The test returns results in just 40-70 minutes

Polychronis Fatouros

Synthetic Biology

Having tests that can quickly and accurately detect SARS-CoV-2 is of utmost  importance now that sports leagues are starting up again and parents are considering sending their children to school. 

Now, scientists from the Broad Institute at MIT have harnessed  the power of the versatile CRISPR system to rapidly and accurately detect the genetic material of the virus on the spot, without  sophisticated equipment of a research clinical lab. This is a major breakthrough, because it means that testing now can be deployed at far-reaching places miles away from medical infrastructure. 

This paper (currently posted as a pre-print) showcases the new test, which is aptly named STOPCovid. Upon contact with a sample, the CRISPR system searches for the genetic material of the virus. If present, it gets activated and runs rampant, snipping up RNA molecules. Once the RNAs are chopped up, they undergo a chemical reaction and give distinguishable signal on a strip of paper in just 40-70 minutes. 

Both the sensitivity and specificity of this test are very high and this is a crucial weapon in our arsenal against this virus. Time to test, test, test!  

Max Levy

Science and Health Journalism and Chemical Engineering

The latest Mars rover, Perseverance, launched today. The rover aims to land at Jezero Crater, on February 18th, 2021. This specific site was chosen because scientists believe it was once an enormous crater lake. Soil near the crater’s rim may contain minerals that preserve ancient microbial life. 

Jezero Crater

Jezero Crater, the Perseverance landing site


As with previous Mars missions, Perseverance is basically a state-of-the-art lab on four wheels.

The planetary Instrument for X-ray Lithochemistry, or PIXL, will beam X-rays at rocks to quickly profile the chemical elements within them. For scientists, understanding that chemistry helps piece together how Mars’ rock features formed, and whether microbes were involved. And another instrument, the Scanning Habitable Environments with Raman & Luminescence for Organics & Chemicals (SHERLOC) works by beaming UV light on soil and rocks to find minerals and carbon-rich organic molecules.

Another experiment launching with Perseverance getting a ton of attention is Ingenuity – the first controlled flight on another planet: a Mars helicopter. Ingenuity will test our ability to design aircrafts in otherworldly conditions – Mars’ atmosphere is thinner than Earth’s, so Ingenuity’s two four-foot blades will spin eight times faster than conventional helicopters. 

Over 10 million people signed up to send their names to Mars. The names are stenciled on chips onboard the rover, and "passengers" received souvenir boarding passes. Of course, no humans are onboard this time around.

But other experiments will test important technology for future human missions. One will monitor weather, and another make oxygen, an important step to enable round-trip visits.

Female capybaras control their own mating destinies

New research shows that they are more choosy about which males they mate with than previously thought

The long list of non-human species where females reign supreme when it comes to choosing a mate is getting a new entry: the capybara. Scientists have just discovered prevailing female choice in what was once thought to be a male-dominated mating system. 

The capybara, Hydrochoerus hydrochaeris, is a semiaquatic rodent that can weigh up to 200 lbs. It has long been known for its mating system that prioritizes male access to large groups of females (like a harem, of sorts) over female preference. This new finding upends what scientists previously thought.  

To figure this out, three researchers, led by biologist Miguel A Bedoya-Pérez, packed their bags and set out for Venezuela during the mating season. The three observed capybaras at Hato El Cedral, a massive cattle ranch found in the country's Llanos (huge grasslands that experience intermittent flooding). 

Due to the previously mentioned semiaquatic ecology of the capybara, the researchers couldn’t use traditional methods of capture to collect data on the capybaras. Instead, they chose the next best thing, riding horseback and lassoing the giant rodents.  

After tagging 26 individual capybaras, the team observed the groups. They watched female behavior very carefully over several months, noting when they were cooperative to mating advances and when they avoided them.

They found that females rejected dominant male capybaras' sexual advances just 1.8% of the time,  but rejected subordinate males 41.7% of the time. This discovery has shed the first rays of light on cryptic female choice in the capybara world. 

"Sizzling sticks of molecular dynamite" can cause Parkinson's from inside the body

When our body's repair mechanisms aren't working properly, these molecules roam free and wreak havoc

Adithi Ramakrishnan

Developmental Neuroscience

College of William and Mary

Parkinson’s disease (PD) affects 1 percent of the population over 65, and the question of how it develops still remains unanswered. One of the more recently studied risk factors for Parkinson’s comes from inside the body.

As we age, our genetic material is harmed by molecules called reactive oxygen species (ROS). Think of them as sizzling sticks of dynamite with a short fuse, latching onto strands of DNA and damaging them with a chemical reaction. One of the only ways to thwart their plot is with the body’s disaster response team: proteins that repair broken DNA before it causes any additional damage to our body. Mutations in these proteins mean that damaged DNA goes unfixed, and that ROS are free to wreak havoc on the brain and body — leading to neurodegenerative diseases like Parkinson’s.

A recent study looked at three different mutations in DNA repair proteins to see if these mutations were linked with a higher PD risk. The researchers isolated DNA from 97 Parkinson’s patients and 102 healthy controls to see if there was a relationship between the mutations they had and their health status. They found no relationship between two of the mutations and Parkinson’s, but a mutation in the XRCC1 gene made it two to three times more likely that a patient would have PD. The higher incidence of XRCC1 mutations in Parkinson’s patients compared to controls indicates that this mutation could be a risk factor for PD, and if studied further, could provide more information about how dysfunctional DNA repair can lead to brain damage and disease.

Parkinson’s has several potential risk factors, and many of them are extrinsic: cigarette smoke, heavy metal exposure, or pesticides. The study of DNA damage and repair reveals that PD risk factors can have a significant impact even at the molecular level. Understanding the deadly dance between ROS, DNA, and repair mechanisms may reveal more about how Parkinson’s gets its hooks into the brain and body.

A promising Alzheimer's treatment comes from the red maple tree

The red maple is the only known natural source of compounds called ginnalins

Josseline Ramos-Figueroa


University of Saskatchewan

If you've been to Canada or eastern North America, chances are you've seen a maple tree. And if you were there long enough, you might also have found out that there are several types of maple, one of which is the red maple.

It might not surprise you that the red maple is one of the commercial sources of maple syrup. What's more surprising is that scientists believe red maples' leaves might help treat Alzheimer’s disease (AD). 

Studies revealed that red maple’s leaves abound with polyphenols, compounds known for their health benefits, Including antioxidant and anti-inflammatory properties. When polyphenolic leaf extract from maples was analyzed, it contained ginnalin A, ginnalin B, and ginnalin C. The red maple is the only known natural source of these ginnalins to date.

Acer rubrum, the red maple

Clarissa Munger Badger / Public domain

Many studies have looked at ginnalins as anticancers. But in early January, Researchers published a study looking into the potential of ginnalin A to treat Alzheimer's. They did this because they realized that the molecular scaffold of ginnalin A and that of other polyphenols previously tested for AD treatment were similar. They thought that this structural resemblance might lead to similar performance.

In their study, ginnalin A stopped and reverse the aggregation of amyloid-beta (Aβ) proteins found in AD. Results also suggested that the potency of ginnalin A was even better than any other polyphenol investigated so far.

Had the red maple's leaves not been analyzed, we likely wouldn’t be talking about ginnalin A. That is the beauty of science: what we know today is built upon the past. While these results encourage more research on ginnalin A, we must wait for more studies to develop.

Have you been getting less sleep than usual? Check in with your gut!

A new study in fruit flies reveals lethal links between sleep deprivation and the gut

Samuel J Walker


Harvard Medical School and Beth Israel Deaconess Medical Center

The average person sleeps for about a third of their life. There must be something really important about sleeping - but just what is sleep good for?

One approach scientists take to understand why sleep is so important is to prevent animals sleeping for long periods of time. But this is challenging because sleep deprivation promotes “rebound sleep” – the powerful urge to sleep that hits you after an all-nighter. So, the authors of a recent study, published in the journal Cell, devised an ingenious method to bypass rebound sleep in fruit flies: they activated specific neurons in the flies' brains to keep them awake.

The researchers discovered that preventing these flies from sleeping by manipulating these neurons caused death after 10-15 days. Then they tackled the question of where in the body one might see changes or damage after 10 days of sleep deprivation? Surprisingly, they did not find any obvious changes in the brain. Instead, sleep deprivation caused a huge buildup of specific toxins, called “reactive oxygen species” (ROS) in the flies' guts. ROS are a normal byproduct of cell activity, but excessive ROS production causes cell damage. The scientists discovered damage throughout the flies' guts due to ROS accumulation.

Now they knew that sleep deprivation caused gut damage. But did it prematurely kill the flies? To test this, the researchers fed flies a variety of antioxidants, substances which protect against ROS. Adding these antioxidants to flies’ diets didn’t reduce sleep loss, but it did prevent the accumulation of ROS in the intestine. Crucially, it allowed flies to survive as long as they usually would despite the loss of sleep. In fact, by expressing enzymes that break down ROS just within cells of the gut, the authors were able to protect flies from death by sleep deprivation.

This study suggests that one essential function of sleep might be to prevent damage to the gut. How sleep loss causes ROS buildup remains unclear. But the authors show that similar damage occurs in the intestines of mice when they lose sleep – indicating that sleep may protect the guts of many species, not just flies. In the modern world, many of us live with chronic insufficient sleep, and it remains to be seen how this affects the health of our guts. But perhaps the next time your eyes start to droop, you will think of your gut and head to bed!

Monkeys can predict human behavior

The ability to perceive and understand how others might react to a situation is not unique to humans

Meredith Schmehl


Duke University

You’ve just finished cooking dinner when your roommate enters the kitchen. Suspecting that she doesn’t know the stove is still hot, you warn her before she gets too close.

We can often recognize the differences between what we know and what others know, allowing us to predict what others might think and do. Most humans demonstrate this ability by the age of four. But is this ability unique to humans, or could other animals also predict others’ beliefs?

In a recent study led by Isao Hasegawa, a physiologist at Niigata University School of Medicine in Japan, researchers tested whether a monkey could guess what a human believes. They tracked the monkey’s eyes to infer its expectations. When monkeys (and people) expect someone to take a particular action, they tend to look toward relevant objects or locations in the environment. Where a monkey looks can reveal what it expects someone else to do.

The researchers took advantage of this behavior while a monkey watched videos involving unexpected actions. In the videos, a human actor (the “opponent”) hides a toy under an overturned box in the presence of another actor (the “searcher”). The searcher then leaves the room. While the searcher is absent, the opponent moves the toy to a new hiding place under a second overturned box, and then removes the toy entirely while running away. Finally, the searcher returns to the room to retrieve the hidden toy. The searcher doesn’t know that the opponent has removed the toy. But the monkey, having seen the entire video, knows that the toy is gone.

The researchers wanted to know if the monkey would understand that the searcher’s beliefs differ from reality. They tracked the monkey’s eyes to determine where the monkey believed the searcher would look for the toy. If the monkey tended to look at the original hiding place, this would suggest that it understood the searcher’s false beliefs about the toy’s location. However, if the monkey tended to look at the second box or elsewhere in the scene, this would suggest that the monkey did not fully grasp that the searcher’s beliefs are different from its own.

They found that monkeys were likely to look at the first box, where the searcher believed the toy was still hidden, indicating that monkeys expected the searcher to look for the toy under that box. These results suggest that monkeys can understand others’ false beliefs and predict their actions accordingly, just like humans. Perhaps humans have more in common with other animals than we think.

Flip the light on and hide your cashmere — it's Moth Week

Join a popular new community science project

Olivia Box

Natural Resources and Forest Ecology

University of Vermont

This week the spotlight- or porch light- is on moths.

It's National Moth Week. And the main event, started by a non-profit began with a local moth night and has quickly grown into a large community science effort. Over 800 people have registered in over 50 different countries, which the organization reports is a record-breaker. With this many moth-er's, or people who search for moths, this year's Moth Week is sure to capture even a slice of the diversity of moths.

Moths, often overlooked nocturnal pollinators, are some of the most diverse species with estimates up to 160,000 different species. Moths are largely nocturnal, and the best way to see them is to turn on your light around dusk and watch them flock towards the light

They can camouflage to avoid predators like the great oak beauty, while others are showy like the rosy maple moth.

Moths are also bioindicators, which means they can tell scientists about the health of an ecosystem. More moths can mean there are more plant species, which generally indicates a healthy and diverse ecosystem. Many species, such as bats and birds, rely on moths for their food source as well. 

You have until July 26th to get "mothing", or moth-searching. Join a moth event and take a picture of your backyard moth and upload it to the Flickr site. Ready, set, MOTH!

Matthew Vandermeulen


University at Buffalo

With us all spending a lot of time at home recently, many have picked up new hobbies, like cooking and baking. This has led to some of us becoming friends with Saccharomyces cerevisiae, a single-celled fungus known as baker’s yeast. This new friend may be tiny, but baker’s yeast arguably contends with dogs for the title of man’s best friend. 

S. cerevisiae has been associated with human culture for thousands of years for its use in fermentation, a process used in making alcoholic beverages and baking. Biological research has progressed in many areas because this organism is so commonly used to understand cellular and molecular biology. For all that society uses S. cerevisiae, you have to wonder, where did the yeast come from?

Originally, researchers hypothesized its origin to be from China/Far East Asia after discovering wild yeast in primeval forests from that area. In a more recent study, researchers found more evidence supporting that origin story comparing the genome of the discovered wild yeast and known domesticated yeast.

The researchers compared 106 wild and 260 domesticated yeast strains by phylogenetic analysis, or comparing family trees based on DNA sequence. They saw evidence of reduced genetic diversity in the domesticated yeast compared to the wild lineages. This suggests a founder effect — when an entire population descends from only a few individuals of an original population. Finding this founder effect implies that originally yeast were domesticated in China/Far East Asia. After early domestication, the dispersal and diversification of those yeasts is hypothesized to have led to the massive global collection of all other domesticated strains that we use today. Further analysis with even more domesticated and wild yeast from all over the globe will help further support this hypothesis.

So the next time you’re in the kitchen with your new friend, let them know they have a place to call home.

Raj Rajeshwar Malinda

Cell Biology and Developmental Biology

We've probably all been flooded with information about COVID-19 transmission, and scientists are still learning details about how it is spread. One thing is for certain: the virus is transmitted through tiny droplets from people's mouths, expelled when they talk, cough, sing, and sneeze. This is why mask-wearing is so important. A recent, fascinating Twitter post by researcher Rich Davis at Providence Sacred Heart Medical Center drives the point home:

Davis demonstrated how many bacteria were spread onto culture plates by daily interactions with and without a mask. After 24 hours of incubation, the results showed that minimal bacterial colonies were produced when he wore a mask while talking, coughing, singing and sneezing, but this was not true when he performed those same actions without a mask. The culture plates were covered with bacteria, particularly those populated when Davis sneezed or coughed. Want to protect others from your exhalations, and the viruses and bacteria particles they carry? Properly wearing masks and social distancing can reduce the burden of infections. 

In some places, planting trees doesn't help store any more carbon

New research adds to evidence that simply planting trees won't stop climate change

Hannah Thomasy


University of Washington

All over the world, people are engaging in massive tree-planting campaigns to help stop climate change — but will it do any good? Previous research has emphasized that planting trees can’t be our only climate change mitigation strategy, but a new study from researchers at the University of Exeter paints an even bleaker picture.

Historically, scientists have believed that tress can slow climate change by sequestering carbon, removing it from the air and storing it in their wood. While the ability of trees to store carbon is helpful, ecologists say that it’s the carbon storage of the entire ecosystem is important too.

These ecologists measured stored carbon in a Northern Scotland ecosystem — both above and below ground — in experimental areas where trees had been planted either 12 or 39 years previously. They then compared this ecosystem to nearby control areas where the natural heather moorland had been left undisturbed.

Surprisingly, researchers found that plots with trees did not have greater ecosystem carbon storage than the undisturbed sections. Even though the trees themselves stored carbon, this was counter-acted by a decrease in the organic carbon present in the soils where the trees were growing.

This doesn’t mean that planting trees can’t be helpful in certain cases — reforesting areas that once had trees could have many benefits. But this study stresses that planting trees is not a one-size-fits-all solution and that it shouldn’t be done indiscriminately. In areas that haven’t historically had trees, or in places with large amounts of organic carbon present in the soil, planting trees might not be beneficial at all.

Can men be bisexual?


Dan Samorodnitsky

Senior Editor


But PNAS published a bad and stupid paper just to make sure.

Senior author, J. Michael Bailey, has a record of transphobia and terrible research practices, including using off-the-record conversations in studies. Steven Pinker, academia's enfant connard, who for some reason was allowed to be the paper's editor, has a history of supporting Bailey.

Anyway this is stupid and ludicrous. It's bad science to strip away social context from the questions you want to ask. It's straight up hateful to look at obviously common human behavior, test whether it exists, and treat it like a pathology. It's not for a laboratory scientist to say whether the way a human behaves is real. Take the very first sentence from the abstract as an example: 

The question whether some men have a bisexual orientation—that is, whether they are substantially sexually aroused and attracted to both sexes—has remained controversial among both scientists and laypersons.

That's not true at all! This is just making up out of thin air a reason to subject people to invasive and personal questioning. Why is getting a statistically significant erection the standard for whether something can be said to exist? Bisexual men exist because there are men who are bisexual.

Social scientist Dan Simpson said it best:

Imagine saying “the indium/gallium strain gauge I hooked up to this  man’s penis didn’t show consistent arousal as I Clockwork Orange’d him with gender-spanning porn, so male bisexuality does not exist”.

A new bird song has spread all over in North America

Nearly all the white-throated sparrows are singing a new tune

Amanda Rossillo

Evolutionary Anthropology

Duke University

Bird songs often create pleasant background noise for us humans. But for the birds, these songs are full of crucial information that helps them attract mates and mark their territory. While it’s not uncommon for individual birds to develop new endings to their songs, these changes are rarely picked up by other birds.

If you’ve ever spent time in North America, you’ve probably heard the male white-throated sparrow’s distinctive song, which sounds like Oh-my-sweet-Canada-Canada-Canada. In the last few decades, however, scientists have noticed that these birds are changing their tune.

Canadian ornithologists first noticed the change in the late 1990s while doing fieldwork in British Columbia, Canada. The new songs had a different beat, sounding instead like Oh-my-sweet-Cana-Cana-Cana-Canada. And it didn’t take long for this new trend to catch on.

In 2004, about half of the sparrows in Alberta were singing the new version of the song. But when the same area was sampled ten years later, every single sparrow sampled had made the switch. To get a sense of how the new version was spreading, the Canadian team turned to community science for help. They used recordings of 1,785 male sparrows across North America that were collected by the public through popular apps like eBird, as well as geolocators to track the birds’ seasonal migrations.

Rather than flying directly south to California as expected, the results showed that sparrows in western Canada were actually crossing the Rocky Mountains, heading as far east as Arkansas. This suggests that these birds bring the new version east during the winter, most likely teaching it to local younger males. As of 2019, the East Coast appears to be the last stronghold for the original song.

It’s still unclear why this new beat took off so quickly and comprehensively. It’s possible that an updated song serves keeps females interested, who may otherwise get bored of the same song after a while. Such a major change in the sparrow’s song highlights how strongly migration and breeding can influence bird behavior across vast geographical expanses.

An artificial intelligence algorithm designed to beat a video game takes on ecology and evolution

The algorithm Alphastar was originally developed to play Starcraft II

Ashley Marranzino

Marine Biology

University of Rhode Island

An artificial intelligence (AI) system programmed to play the popular online strategy game StarCraft II may be able to help scientists answer some pressing questions in the fields of ecology and evolutionary biology. 

The AI system, named AlphaStar, was originally designed to beat top-ranking StarCraft II players. After being fed data from millions of StarCraft II matches, AlphaStar had accumulated experience equivalent to 200 years of continually playing the game and was able to annihilate human opponents, outperforming 99.8% of ranked players. Now, scientists think the algorithm that made AlphaStar into an effective StarCraft II competitor may be able to help answer complicated ecological and evolutionary questions. 

StarCraft II requires players to strategically compete for access to habitats and resources in a way that mimics a number of ecological and evolutionary strategies. As players compete for a finite amount of resources, they make trade-offs between colonizing new habitats and competing with opponents. As the game progresses, players end up following strategies that mirror those exhibited in nature such as producing numerous, inexpensive materials versus a few expensive materials (R vs. K strategies), developing specialized traits (leading to resource partitioning), or escalating competition with opponents (evolutionary arms race, for example how predators and prey continually evolve traits and skills to beat each other). 

All of these scenarios simulate ecological and evolutionary scenarios, so by learning how to strategically play StarCraft II, AlphaStar inadvertently became well-versed in ecological and evolutionary theories. AlphaStar’s algorithm even usedd unconventional, aggressive, and sometimes apparently counter-intuitive strategies that allowed the AI system to manage resources more effectively and become a stronger competitor than the human players. 

While StarCraft II is arguably a simplified model of real ecosystem-level interactions, scientists think they could learn a lot from AlphaStar’s algorithm by changing the starting conditions of the game and seeing what strategies the AI system uses to gain competitive advantage in the landscape. If they are correct, this video game-playing AI system could help scientists predict how ecosystems respond to environmental changes or how personality (meaning how likely an animal is to take a risk) drives evolution. 

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