## There's physics behind shifting tombstones that has nothing to do with ghosts

We're sorry to say

Science Education

University of Illinois at Chicago

Ed: All this week Massive is marking Halloween with stories of scary, witchy, and downright ghastly stories from nature

If you walk around an old cemetery, you might notice tombstones that have sunk into the dirt, tilted to the side, or even appeared to move across the ground since they (and their owners) were first placed. This is because these gravemarkers are heavy and the dirt under our feet is often unstable over long time periods. The tread marks left behind have inspired spooky urban legends.

Unfortunately for those that love ghost stories, there’s a scientific explanation behind the phenomenon of moving tombstones. It’s  got the wonderfully spooky name of "downhill creep" (or soil creep), and also explains natural phenomena such as bending trees on a hillside or depressions in mountainsides.

There is even a physics formula that explains downhill creep. Called diffusional sediment flux, this is calculated as the product of hill-slope and a value called the diffusion constant. Those values multiplied together yields the speed at which a given tombstone (or any physical object on a hill) moves over time. In addition to just modeling tombstone movement, this formula has also recently been used to calculate how erosion rates change with precipitation

So if we calculated this value for the average tombstone on a hill, it is pretty clear that it will always be gently moving, tombstone owner beneath be damned.

Share an interesting science story or tell a short one of your own

## Think mosquitoes only drink blood? Think again.

Mosquitoes also drink nectar, serving as pollinators for certain types of orchids

When we think of mosquitoes, we usually think of itchy bites and diseases like malaria or Zika. While they do feed on human and animal blood, mosquitoes are much like many other insects — they also use the sugar in nectar for energy for reproduction, movement, and survival.

A study by researchers at the University of Washington has identified the floral cues — or unique scents that attract different pollinator species — that influence mosquito visitation to a flower. The lab found that a specific scent produced by Platanthera obtusata, the blunt-leaved bog orchid, attracts the Aedes mosquito. Scientists observed the feeding behavior of mosquitoes on orchid flowers, and analyzed the compounds of the orchid's scent using mass spectrometry — a process which can identify chemical compounds based on the molecule's mass and chemical structure.

Mosquitoes feed on a wide variety of flowering plants, and in some cases even perform pollination while in search of nectar sources in the depths of flowers for sugar feeding.

The Platanthera orchids produced a distinct pattern of specific compounds, which are recognized and used by mosquitoes to distinguish between Platanthera and other species of orchids. The scent profile of Platanthera orchids and other mosquito-pollinated flowers were similar, taking science a step toward understanding why mosquitoes are more likely to pollinate one species over another.

By understanding the olfactory cues used by insects like mosquitoes, researchers can better understand the impact that smell has on the allure of mosquito prey, such as humans. Manipulation of mosquito senses serves a large role in mosquito bite prevention, and will play an important role in our future goal to eradicate mosquito-borne diseases.

## Iron concentrations in teenagers' brains can be linked to their cognitive abilities

Also, women reach peak iron concentration in their brains earlier than men

Neuroscience

Medical College of Wisconsin

You might have heard of iron deficiency anemia. Iron is the central element in hemoglobin, the oxygen-carrying protein of our blood. Having low concentrations of iron can lead to not having a proper circulation of oxygen, which usually translates to feeling tired or weak. However, there is also iron stored in tissues, including the brain. There, it helps with the cell’s production of energy, with the formation of myelin (i.e. white matter), and it is used by different enzymes that produce neurotransmitters.

Much like everything brain-related, the concentration of tissue iron in the central nervous system needs to stay in a perfect balance. Too much iron might lead to an increased chance of neurodegeneration, too little iron might cause irreversible changes in brain chemistry. But what was previously unknown was whether teenagers were particularly susceptible to iron deficiency, as much as babies and children can be. A group of scientists from the University of Pennsylvania has now shown that there is a correlation between brain tissue iron during adolescence with cognitive abilities.

Bart Larsen and their colleagues analyzed brain scans of 922 humans (8-26 years old). Using a technique called R2* relaxometry, they were able to quantify the concentration of iron in the brain by magnetic resonance. This concentration, especially in a brain region called basal ganglia increased over time in all samples. However, there were some observed sex differences, with women's brains reaching a peak of iron concentration earlier. By doing a battery of neurocognitive tests, the researchers found that there was a correlation between how much iron was being accumulated over time with a person's cognitive performance.

Although only a correlation, studies like this are important in finding how different external factors affect our development. Worth pointing out: iron deficiency is still a problem in the US affecting 15% of women and 3% of men. With this new study, we are more aware of the importance of iron in the normal brain development of teenagers.

## On #WorldPangolinDay, we celebrate this roly-poly scaly anteater, one of the world's most trafficked mammals

But celebrations are marred by the recent suggestion that pangolins may be the SARS-CoV-2 carrier

Neuroscience

University of Sussex

Today is the World Pangolin Day. This day is celebrated each year, on the third Saturday of February, to raise awareness about pangolins. But this year, the ninth World Pangolin Day might have a different focus, given that a link has recently been suggested between pangolins and the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which originated in Wuhan, China. However, we cannot blame the spread of this coronavirus on the pangolin, even if they do turn out to be the carriers.

Pangolins are mammals ranging in size from about a foot to over three feet. There are eight species of pangolin in the world, all covered in scales made of keratin, the protein that also makes up our hair and nails. They eat insects, including ants and termites, which has earned them the name scaly anteater.

Sadly, pangolins face the risk of extinction in the wild, mainly caused by humans trafficking pangolins for their meat and their scales. In fact, they are among the most trafficked wild mammals in the world.

If pangolins do carry the SARS-CoV-2, which has not yet been conclusively proven, the spread was likely only possible due to this trafficking. Generally speaking, pangolins like to keep to themselves and are mostly nocturnal, so they do not often come into contact with humans naturally, unless we go out looking for them.

“I think that given the difficulty in monitoring the populations of all pangolin species, it is difficult to ascertain how well they are doing,” says Daniel Ingram, a researcher from the University of Stirling. The different species have different lifestyles — some live in trees, while others are ground-dwelling — which means that scientists need to develop different methods to monitor them.

“Understanding the behaviour of wild pangolins better could play a role in pangolin conservation, as it could help improve monitoring methods and help us understand how pangolins respond to human disturbances,” says Ingram.

And it seems like this is even more important if pangolins do turn out to be the SARS-CoV-2 carrier.

## Scientists analyze centuries-old DNA to investigate French revolutionary's mysterious skin condition

Was scabies, syphilis or atopic eczema the reason why Jean-Paul Marat was in the bath when he was assassinated?

Molecular Genetics

University of Toronto

Jean-Paul Marat (1743-1793) was a French journalist, politician, physician, and scientist during the French Revolution, who was assassinated while taking a medicinal bath for his worsening skin condition. While the manner of Marat's death is obvious, the cause of his worsening health in his final years has remained a mystery, with doctors hypothesizing that conditions such as scabies, syphilis or atopic eczema may have been to blame. Now, scientists have analyzed DNA from his blood stains to shed some light on this issue.

During his life, Marat was a French revolutionary who advocated for the rights of the sans-culottes (the poorest members of society), but also served as a court doctor, published findings on fire, electricity, and light, and wrote a regular periodical, titled L'Ami du peuple (The Friend of the People). At the time of his assassination, Marat was annotating two L'Ami du peuple issues in his bath. These blood-stained issues (made of old cellulose paper) were later donated to the Département des Estampes, Bibliothèque National de France, offering a rare opportunity for scientists to use DNA sequencing to posthumously diagnose infections in a historical figure.

In this study, Toni de-Dois and their fellow researchers took two non-destructive forensic swabs — one of a blood stain, and a second from an area of L'Ami du peuple with no blood stains for comparison. Following DNA extraction and sequencing, the researchers compared the two swab samples to account for any contamination that may have occurred in the last 200 years or so, before carrying out a number of analyses to better understand Marat's health at the time of his death.

Instead, researchers found DNA fragments matching Malassezia restricta, which is a fungal pathogen that causes seborrheic dermatitis (a chronic form of eczema). They also noted the presence of DNA fragments matching Cutibacterium acnes (although common, it is linked to acne) and Staphylococcus aureus (often detected in atopic dermatitis, though found in low quantities in Marat).

So what does this all mean?

Although de-Dois and their fellow researchers were unable to reach a specific diagnosis, they do provide evidence that Marat was suffering from an advanced fungal infection, likely seborrheic dermatitis, with additional bacterial infections. This study also happens to be one of the first to leverage DNA sequencing technology to diagnose infections in historical figures.

To find the exact answer to the mystery Marat's worsening health, researchers will need to analyze more of the DNA found on Marat's preserved possessions — with the potential to apply this analysis to additional historical figures.

Our writers' recommendations for books about health, including pain, teeth, sex, and mental health

We asked consortium members what they are reading, and wow, they really came through! Here are a few of the health-related books they recommend. Just so you know,  Massive may collect a percentage of sales from the links on this page.

### The Mystery of the Exploding Teeth: And Other Curiosities from the History of Medicine, by Thomas Moore

Buy the book: Amazon, Independent Bookstores

I think it goes without saying that I was drawn to the book because of the title. The book does a great job of explaining medical mishaps in an accessible and fun, but respectful, way. I can’t help but draw parallels between some of the historically-used remedies (e.g., wine enemas) and what some people do now (e.g., coffee enemas) - Monica Javidnia

### The Collected Schizophrenias by Esmé Weijun Wang

Buy the book: Independent Bookstores, Amazon

In her essay collection, Esmé Wang describes her journey being diagnosed with bipolar disorder and subsequently after with schizoaffective disorder. I really enjoyed that the essays explored different aspects of the disease that I was unaware of such as involuntary hospitalization, mental illness stigma, and the history of the disease itself. While I was reading the essays, it became apparent how courageous the author is to share her life experiences and I think these essays will shed light on the disease and the stigma that surrounds it. - Felicia Davatolhagh

### Doing Harm: The Truth About How Bad Medicine and Lazy Science Leave Women Dismissed, Misdiagnosed, and Sick by Maya Dusenbery

Buy the book: Amazon, Independent Bookstores

Inspired by her own difficult experience with getting a diagnosis of rheumatoid arthritis, Dusenbery presents a really compelling look at gender bias in medicine that left me frustrated with the status quo. She covers the origins and outcomes of this bias, including historical medical practices (ugh, “hysteria”), basic biomedical research, the inclusion (well, lack of) women and minority communities in clinical trials, and interactions with clinicians. I hope this inspires people in the biomedical community to do better. - Rachel Stewart

### Books about science and sex

I'm currently reading Bonk: The Curious Coupling Of Science And Sex by Mary Roach, after I have read The Technology of Orgasm: “Hysteria,” the Vibrator, and Women’s Sexual Satisfaction by Rachel Maines. I am thinking of writing a book review on these two books! - Crystal Chan

## The science behind Nike's Vaporfly shoes

World Athletics has put limits on the types of shoes that marathoners can wear to prevent sponsored athletes from having unfair advantages

Chemical Biology

Dana-Farber Cancer Institute

On January 31st, World Athletics released new technical rules officially qualifying what a 'legal' running shoe is. A host of brands, led by Nike with its Vaporfly series, have forced the hand of the regulatory agency by developing shoes containing new types of lightweight foam and shock-absorbing carbon plates that function like springs. These types of shoes have been proven in studies to improve running economy over conventional marathon racing shoes.

Because Nike has led the development of these shoes, their sponsored runners have enjoyed a relative advantage over their competitors dating back to the 2016 Olympic Trials, where 4th place finisher (Sketchers-sponsored) Kara Goucher compared the Vaporfly shoes to a doping advantage. Distance-running scientists weighed in on the resulting kerfuffle, proposing limits on sole height to future-proof the stacking of carbon plates resulting in bigger and bigger springs.

It appears that World Athletics agrees: they've ruled that no more prototypes are allowed in competition; shoes must have a maximum sole height of 40 millimeters; and they may have no more than a single carbon plate. Those rules allow runners to wear Nike's popular Vaporfly 4% and Next% (pictured) shoes, but it appeared they would ban their Alphafly shoe, last year's prototype worn by both Eliud Kipchoge (1:59:40) and Brigid Kosgei  (2:14:04) when they shattered record marathon times in Vienna and Chicago. However, upon official measurement the Alphafly just barely cleared the height limitation at 39.5 millimeters.

Shoe brands will continue to innovate with new materials and designs, but whether they manufacture exclusively within those limits from a commercial aspect remains to be seen: is there a market for shoes that may not be competition-legal, but that could allow amateur athletes to reach the performance levels of more gifted athletes? That is a question that science cannot answer.

## You can mimic the physics happening on the surface of the Sun in your kitchen

As the plasma on the Sun's surface heats and cools, it forms cells the size of Texas

The images of the Sun recently obtained by the Daniel K. Inouye Telescope are stunning, but you don’t need a 4.24-meter telescope to see the physics first-hand.

Plasma heats within the Sun, becomes less dense, then rises to the Sun's surface. Once there, it cools, gets dense, and sinks again. The gorgeous “caramel popcorn” appearance is a result of the plasma becoming ordered into cells the size of Texas. The edges of these cells are defined by dark lines of sinking plasma. This is described by Rayleigh-Benard convection, which tells how the size of these regions depend on the properties like the temperature, density, and viscosity of the plasma, and how heat transfers through it.

The same sort of convection that happens in your kitchen. You can observe this effect by mixing food coloring and dish soap, then placing it in a pan on the stove. Of course, your convection cells will be a bit smaller than those on the surface of the Sun!

## Coffee baristas were right all along — grinding coffee finer doesn't always produce a stronger cup of espresso coffee

Scientists use mathematical modelling and experiments to prep the perfect cup of espresso

New research on the physics of espresso has generated a caffeine buzz in the news, but as a hipster, physicist, and a coffee snob, I feel obligated to contextualize these results.

As my fellow coffee lovers may know, espresso is made by forcing water through a bed of coffee particles, which extracts chemicals like caffeine and sugars. Smaller particles and higher pressures usually mean higher extraction and stronger cups, but experienced baristas know that grinding coffee finer doesn’t always produce a stronger cup. Baristas have proposed empirical solutions, but only now have scientists, in collaboration with the coffee community, succeeded in quantifying this effect.

With a mathematical model backed by experiments, researchers finally confirmed the theory that baristas have held for years; that high pressure (often achieved by adding more or finer grounds) and irregular particle size can cause flow channels to form, resulting in uneven wetting of the coffee, and ultimately making a weaker, less tasty brew.

Researchers hope this model helps make coffee more delicious with less waste — and the success of this work demonstrates the importance for clear science communication as fruitful collaborations can often be found outside academia.

## Wasps are parasitizing caterpillars less often under climate change

Changing interactions could lead to a decline in important ecosystem services like pest control

Biology

University at Buffalo

Assessing the impacts of climate change is essential for scientists who want to understand ecosystem dynamics. However, until recently, relatively few studies have linked climate variability to species interactions.

Researchers used data from 22 years of sampling at the La Selva Biological Research Station in Costa Rica to generate statistical models that measure changes in insect species diversity and richness and make future predictions. (Richness is a measurement of how many species are in a given area; diversity takes into account how many species there are as well as the number of individuals of each species.) Researchers looked at two types of insects: caterpillars and parasitoids. Parasitoids are a type of insect whose larvae live as parasites (usually in other insects) that eventually kill their hosts. These types of insects offer an important ecosystem service through species interactions by preventing outbreaks of herbivorous insects (like caterpillars) that can damage wild plant populations or crops in areas of agriculture.

The researchers found that species richness and diversity has declined in both caterpillars and parasitoids. Results suggest that these declines are partly driven by climate change and weather anomalies such as extreme precipitation and episodes of warmer than average temperatures, which have been occurring at an increasing rate at La Selva. Alongside the decreases in diversity and species richness, there has been a decrease in the interaction richness between caterpillars and parasitoids. A reduction in parasitism means that there is less biological control over herbivorous caterpillar outbreaks, which decreases ecosystem stability. By extrapolating the data for the next 100 years, this study predicts there will be a 30% drop in parasitism (compared to the 6.6% drop seen over the 22 year study period). These findings support the hypothesis that climate change is contributing to insect species declines. Further research is needed to explore the impacts of declining species interactions.

## Children with musical education gain greater self-control

Ability to delay gratification may help explain the benefits of musical training

Neuroscience and Molecular Biology

Johns Hopkins University

Playing a musical instrument requires a battery of unique skills, including being able to quickly and accurately assess incoming sounds, fine motor skills, and the coordination of behavior and feedback from one’s errors and mistakes. Receiving musical education at a young age has been shown to increase spatial-temporal skills. Musicians must often inhibit attention from one hand to focus on the movement of the other; this is called inhibitory control.

Inhibitory control is not a new idea; in fact, this concept is taught in most Psychology 101 lectures, using an example called the marshmallow test. In this famous experiment, an experimenter would place a marshmallow in front of a child and tell her to wait 15 minutes during the experimenter’s absence. The child was promised a second marshmallow if she had the willpower to wait. Those who waited and chose the delayed gratification tended to have better academic performance as adolescents.

A recent longitudinal study brings new light to this old topic. The results revealed children in their third year of musical training chose delayed gratification significantly more often than children in sports programs or those not participating in extracurricular activities. A previous study from the same research group showed that music students also had differences in brain activation (measured with fMRI) compared to students who were not involved in music or sports. During tasks that required cognitive control, the music students had increased activation of the inferior frontal gyrus (attentional demand and inhibition), anterior cingulate cortex (emotional control), and insula (self-awareness).

## The mice most scientists use to study Alzheimer's aren't accurate

A new Nature study shows that human and mouse brains with Alzheimer’s disease look and function differently

Biochemistry, Microbiology, and Chemical Biology

Rensselaer Polytechnic Institute

Scientists often conduct the first stage of drug trials in mouse models, including mice genetically engineered to develop Alzheimer’s disease. However, the accuracy of mice as a representation of human biology is being challenged daily, including by the authors of this Nature Medicine study in early January 2020.

Led by medical researchers at Washington University in St. Louis, the study shows that the most common Alzheimer’s disease (AD) mouse model, 5XFAD, has an entirely different genetic response to one of AD’s pathological hallmarks – amyloid-beta. In AD, specific neuron proteins are broken into two fragments, called amyloid-beta 40 and 42. These fragments clump together into non-functional masses – the protein version of tumor cells – that form even larger plaques that destroy neuron connections and inhibit brain function.

However, when analyzing brain cells, like microglia and astrocytes, the mouse cells had entirely different genetic responses to amyloid-b than human cells. Certain genes and proteins were under-expressed in AD-mice microglia and over-expressed in AD-human microglia, compared to normal brains. In addition, astrocyte cell differentiation was only mildly affected by AD in mice, but severely mutated in AD-human brains, leading to the formation of 6 different types of impaired astrocytes.

The study is one of many contributing to the growing discussion of how accurate Alzheimer’s disease mouse models are and why, if they do not closely match to the human AD disease state, we should continue using them.

## "Insect destroyer" fungus uses tiny, squishy cannons to fire spores

Scientists are studying this fungus for use as a more environmentally-friendly insecticide

Developmental Biology

RIKEN Center for Biosystems Dynamics Research

You may have heard of “zombie ants” — insects that are infected with a fungal pathogen that can control their behavior, coercing them into climbing to a high location to better spread fungal spores before meeting their end. But did you know that another species of pathogenic fungus, Entomophthora muscae or “insect destroyer,” could be harnessed by humans to act as a more environmentally friendly insecticide? Although we’ve known for decades that the insect destroyer fungus can infect flies, including the common housefly, we lacked the laboratory tools necessary to actually study the fungus-fly interaction in much detail.

Researchers at the University of California, Berkeley have identified a particular variety of this fungus that can infect the commonly-used fruit fly model organism, Drosophila melanogaster. This means that all of the tools we’ve accrued over the last century to study D. melanogaster in the lab can now be applied to its interaction with the fungus, making it much easier to learn how pathogens like the insect destroyer infect their host and control their behavior.

Scientists are also investigating the fungus itself, especially the ways that the fungus spreads its spores, which is a key part of how the fungus is able to infect new victims. Scientists found that E. muscae spores are shot out from cannon-like structures on the dead, infected flies at roughly 10m/s or 22mph — very fast in the world of fungal spores. This even inspired a follow-up study by biophysicists in Denmark that specifically examined the physics of spore ejection. The scientists created tiny, squishy cannons made of silicone that they could load with 3D-printed projectiles and fire with pressurized liquid, mimicking the actual ejection system used by the insect destroyer fungus. It turns out there’s a very specific canon and spore size that maximizes ejection speed and distance, increasing the chances of further fly infection.

## Coronavirus update: widespread diagnostic testing, bioRxiv, and two public health futures

Feb. 5th: 28 countries have confirmed cases

Microbial Disease Epidemiology

Yale University

The outbreak of a new coronavirus is a global public health emergency that has spread to at least 28 countries so far. There's a lot of news and it can be hard to make heads or tails of it all. It's a little overwhelming. Here are a few key updates that we think you should know about.

A diagnostic test has been authorized for use at public health labs across the U.S.

Until now, samples from suspected cases of the new coronavirus — dubbed "2019-nCoV acute respiratory disease” (where "n" stands for "novel" and "CoV" for "coronavirus") — had to be shipped to Centers for Disease Control and Prevention (CDC) labs. In an announcement on Tuesday, the Food and Drug Administration issued an emergency use authorization to fast-track the diagnostic test and permit its use at any CDC-qualified public health laboratory. The test itself converts specific regions of coronavirus's RNA genome into DNA, makes many copies of it using a process called amplification, and then tests it for the presence of these amplified bits with a glowing dye. Scientists hope that the availability of the test will prevent backlogs and enable the preventative measures that come with a real-time diagnosis.

Preprint repositories are spreading information, and misinformation

Preprint servers like bioRxiv have allowed scientists to share their research faster than ever before by giving papers a place to be read and shared before the peer review process. For perhaps the first time, we are now seeing how these repositories are helping and hurting in a public health response. Data sharing, through for forums like virological.org and the GISAID Initiative, have allowed researchers to sequence and start analyzing the coronavirus at unprecedented speed. At the same time, some scientists worry that publishing (and publicizing) before peer review is placing quantity over quality in this outbreak.

One preprint has already been withdrawn following widespread criticism, and bioRxiv has put up a banner on top of every page, cautioning viewers that the research posted there has not gone through peer review.

Two futures for 2019-nCoV

In one of my epidemiology classes this week, we split up into groups and underwent a coronavirus-themed crisis management case study. This is obviously just a simulation, but by day 21, the virus was everywhere and we had to transition from containment to mitigation.

I was struck by a recent article in STAT, which lays out two scenarios of what a future with endemic 2019-nCoV might look like:

One possibility adds this virus to the already four endemic human coronaviruses, which cause common cold and are a lower concern than something like the seasonal flu. Another possibility is a seasonal cycle in which coronavirus transmission dips during summer months due to their intolerance of higher heats and humidity.

We’ll keep checking in with these short roundups, so stay tuned.

## Yeah, one fish, two fish, but can fish actually count?

Studying zebrafish could help us unravel the neural circuitry underlying numerical skills

Neuroscience and Behavior

National Centre for Biological Sciences, India

Understanding and using quantitative information is important for animals to compete for resources, protect themselves from predators, get access to territories and for reproductive benefits. Certain species also exhibit an awareness of numerosity, or being able to differentiate between groups of varying numbers, at fine scales. While humans rely on a symbolic sense of numerosity (we have symbols and names for counts), animals depend on non-symbolic representations of numbers. Although they use this information for their survival, does this mean they are really counting?

Researchers from the lab of Giorgio Vallortigara have shown that zebrafish do in fact use ordinal counting in order to get to a “reward." Ordinal counting keeps track of a position (as in, the second door out of seven), as opposed to cardinal counting, which tracks an amount ("there are seven doors"). Zebrafish were trained to exit an arena with seven identical exits in a corridor, using only the second exit. This was done by blocking the other exits with a clear sheet of plastic. On the other side of the corridor was a reward of food and other fish. If the fish swam towards other exits, they did not receive any reward. But what happens when all doors are up for ‘swims’?

Post training, the fish were tested by decreasing the length of the corridor, decreasing the distance between exits, or increasing the number of exits. In the first two experiments, they chose the second exit with a frequency greater than random chance, indicating that they were in fact “counting” to choose which exit to use.

In the last experiment, along with choosing the second exit significantly more than the others, they also chose the second-to-last exit (second from the other end of the corridor) more than chance level. The higher numbers seemed to "confuse" the fish. In such contexts, the fish switched to using spatial feedback, along with ordinal information, to increase their chances of getting lunch with their pals.

Although evidence of numerical skills has been reported in birds, amphibians, mammals and even insects, studying it in a well-established model system like zebrafish opens up avenues to decode the mechanisms underlying this behaviour.

## Forget the Large Hadron Collider: fundamental particles ride plasma waves into high-speed collisions

If built, EuPRAXIA will be the world's first high energy plasma-based accelerator

Physical Chemistry

University of York

What comes to mind when you hear the words particle accelerator

Here's what I think, in the order of the thoughts that show up in my mind: giant metal ducts, Higgs boson, The Big Bang Theory and the CERN. I bet you got some of these as well (if not all of them), and here is why.

The Large Hadron Collider (LHC), at CERN in Geneva, is the very same particle accelerator where the Higgs boson was first observed. With a circumference of 27 kilometres, the LHC is the one of the largest machines in the world. It is even common knowledge as it has made headlines, and even been mentioned in The Big Bang Theory more than once.

However, did you know that approximately 30,000 particle accelerators exist today with many different functions? Not all of them are utilized for fundamental physics like the LHC — in fact only around 1% are. Instead, many of the smaller accelerators are used for cancer therapy, semiconductor manufacturing, or the production and identification of radioisotopes. In each case, the acceleration mechanism (which uses oscillating radio frequencies) requires large dimensions, coupled with high construction and maintenance costs, creating a limit on the use of such particle accelerators.

Instead, researchers in Europe are attempting to come up with a solution to bypass particle accelerators by using a plasma-based mechanism that should generate 1000 more acceleration potential per length.

Enter the European Plasma Research Accelerator with eXcellence, or EuPRAXIA for short.

EuPRAXIA plans to use the electric-field gradients, which are created in a pulse's wake, to accelerate particles to high energy levels while travelling over very short distances. It will require smaller, more compact and cost-effective machines.

Currently, plasma-based particle accelerators are still undergoing a proof-of-concept phase at multiple institutions, including CERN. If built, EuPRAXIA will be the world's first high energy plasma-based accelerator. In a recent conceptual design report, presented by over 40 institutes who are collaborating on this project, the authors state:

“EuPRAXIA is designed to be the required stepping stone to possible future plasma-based facilities… [it] should be fully functioning in the next 8-10 years.”

The idea is to build a facility — that also external operators could use — where the many intriguing potentials of particle accelerators will be explored, such that, maybe one day, giant metal ducts will not be the first thing that comes to mind.

## Why we shouldn't write off nuclear power

Despite radiation fears, changing to nuclear power could prevent millions of air pollution-associated deaths

Environmental Science

Oregon State University

After the "scare" near a Canadian nuclear power plant on January 12 which accidently sent a warning text to residents, many people are wondering about nuclear power. Is it safe?

In fact, nuclear power is one of the safest forms of power in terms of health burdens like air pollution. Even when you look at the larger picture of "death rate," nuclear energy is the third safest technology — behind only hydroelectricity and wind. In fact, in one study, it was estimated that the use of nuclear power has prevented about 1.84 million air pollution-related deaths. It has also been estimated, by the same study, that if nuclear power replaces fossil fuels, an additional 420,000 - 7.04 million future air pollution deaths could be prevented.

And that's just the tip of the iceberg. Nuclear power is one of the most efficient energy systems we have access to — while natural gas or coal power plants operate at full power about 50% of the time, nuclear power plants operate at full power 92.3% of the time.

Now, many people are rightfully concerned about radiation (radioactivity is nothing to joke about). But, believe it or not, nuclear power plants release LESS radiation into the environment than coal power plants. That's right! In fact, the waste by-product produced by one coal power plant (known as fly ash), carries 100 times more radioactivity into the environment than the shielded waste produced by a comparable nuclear power plant.

Now, of course, nuclear power isn't without its drawbacks — the problem of what to do with spent fuel is one of them, and past nuclear disasters may weigh heavily on people's minds. But to write off nuclear power as inherently unsafe or not worth pursuing, overlooks the many advantages it has when compared to coal burning, which has serious consequences in terms of air and water pollution as well as greenhouse gas emissions.

## Fish use "blood-doping" to survive in icy water

To keep their blood from becoming too thick, cold-water fish release blood cells from the spleen only when needed

Neuroscience

University of Sussex

Being a fish in the Antarctic is hard. The bald notothen, a fish that hunts for prey under the ice in Antarctica, has come up with all kinds of tricks to be able to survive in the freezing waters. Like many fish that live in cold waters, the bald notothen has a kind of antifreeze protein in its blood, which prevents it  from freezing. However, this strategy comes at a cost. The antifreeze in combination with the cold temperature causes the blood to become viscous.

“Due to this increased blood viscosity, the heart must work much harder,” explains Jeroen Brijs, lead author of a new study on bald notothen. In the long term, this could cause significant problems for the fish, but they’ve come up with a solution: their spleens are able to take up red blood cells. This reduces the number of these cells in the blood, so the blood becomes less viscous.

But they need to use this technique carefully, because red blood cells are needed to transport oxygen, which the fish need to be active. Without the red blood cells, they are effectively anemic and unable to hunt or feed. The fish have solved this problem by using a dynamic strategy: they release the red blood cells when they need to be active, and take them up in times of rest. This tactic has made them extremely successful in the cold waters.

They are not the only fish that use this technique. “Although the blood boosting strategy of bald notothens is not unique within the notothenioids, the magnitude of the strategy in bald notothens is by far the greatest,” says Brijs. What the bald notothen does is effectively the same as blood doping in athletes, but the fish are much better at it. Athletes can only increase their oxygen carrying capacity by about 5-25 percent. The bald notothens can increase their ability to carry oxygen by as much as 207 percent.

In order to be successful in extreme environments, fish have evolved many strategies to survive and thrive. For many fish, blood doping might be the key to living in the cold seas.

## Don't believe the conspiracy theories you hear about coronavirus and HIV

Especially if you work for the New York Times

The new coronavirus is scary, and lots of information is flying around in the pandemic. But please, don't believe everything you read, even if it came from scientists. Before panicking about news, wait for real, actual confirmation (and peer review) from scientists outside of a Twitter scrum.

Case in point, today a group of scientists based in India took the genome sequences of Wuhan coronavirus, did some armchair analysis (literally, all the work they did could be done from a desk in about an hour) which they shared in a pre-print (i.e. this hasn't gone through peer-review by other scientists yet), and found that it had similarities to the genome of...HIV.

Update, February 2nd: The paper has been withdrawn, following widespread criticism, like the kind below.

If you're a soup-brained Twitter user like me, you might have seen this sensational, zombie movie-ass tweet about the pre-print by Anand Ranganathan, a molecular biologist and author with 200k+ followers:

This prompted a blizzard of apocalyptic world building in the mentions, including a boost from prominent not-a-biologist New York Times opinion columnist Ross Douthat, who has about 160k followers:

The gist of the story is this: the Wuhan coronavirus (2019-nCoV) appears to have four additions to its genome that similar viruses, like SARS and MERS, are lacking. These additions are either identical or extremely similar to parts of the HIV genome. The authors go on to speculate that this may be why the coronavirus is spreading so quickly, and also that something sinister may be afoot:

"This uncanny similarity of novel inserts in [Wuhan coronavirus] to [HIV] is unlikely to be fortuitous."

They don't elaborate on what that means, but the Twitter interpretation is that someone engineered coronavirus with parts of HIV, to make it...I don't know. Infect better? It's unclear.

I double checked whether it was true that HIV and coronavirus have similarities. I took the four additional sequences (the "novel inserts") they found in the coronavirus genome and I looked to see if, as they said, it was similar to HIV. The truth is while these sequences do pop up in HIV,  they also pop up in tons of other viruses. There's no reason to immediately suspect a nefarious fusion of HIV and coronavirus.

Sequence one out of four is indeed found in both Wuhan coronavirus and HIV. The same sequence also appears in a virus that infects Streptococcus (spherical bacteria), a rat virus, and an "acute bee paralysis virus."

I did the same analysis on sequence two. Once again, HIV and the Wuhan coronavirus appear together, but also a mouse herpes virus, a rat cytomegalovirus (the virus that causes mononucleosis, popularly known as mono or the 'kissing disease'), and a virus that infects sweet potatoes.

The stories for the other two sequences are the same. Those sequences appear in benign viruses like Peach-associated luteovirus (a plant virus), Bovine papillomavirus type 9 (the cow version of HPV), and Leptopilina boulardi Toti-like virus (a virus that infects wasps).

So the facts are that Wuhan coronavirus may have some new additions to it, but they're common bits and pieces found in tons of viruses — not just HIV — and there's no proof that they even have anything to do with how the Wuhan coronavirus behaves.

And there's definitely no proof that they were put there on purpose.

## Algae are eating microplastics. From there, they can climb up the food chain to us

Freshwater microbes can absorb components of microplastics before getting eaten by other creatures

Biogeochemistry

University of Michigan

Microplastics have been making splashy headlines for years now and there's news: scientists used special carbon-containing polymers to track how microplastic moves through the aquatic biosphere. Plastics are very resistant to degradation in natural environments; knowing where they end up and how they're incorporated into food webs matters for human health. What starts out in algae can eventually end up in us.

To track how some microplastic moves through aquatic food webs, scientists in Finland and Austria turned to the molecular scale. They altered molecules of polyethelene (a common compound in plastics) to contain carbon-13, which they could use to trace those molecules later on. By measuring that tracer compound in the cell membranes of algae and zooplankton (aquatic microorganisms), they were able to see that carbon being incorporated into the organisms. As the zooplankton consumed the algae, the carbon went with them.

This is a step above how you might have seen plastic pollution before — a fish's stomach full of bits of bags and pieces of bottles. These microorganisms are actually repurposing the molecules in plastic, which increases the odds that other compounds in plastic could work their way up the food chain, too.

## We can't have a future with quantum computers without quantum mechanics

Scientists are building physical platforms for memory, computation, and networking — all things we need for quantum computing to be possible

A future with quantum computers and quantum networks requires a diverse set of technical tools. Like the classical computers we use every day, we need physical platforms for memory, computation, and networking. Unlike classical computers, however, these platforms need to be quantum-mechanical (read: very small and very cold).

The verdict is still out on which physical platforms will work best for quantum computing, but scientists are making breakthroughs on the more promising ones. Just this year, a group in the UK coupled a single ion (charged atom) to a very strong light field for the first time. They achieved what atomic physicists call the “strong coupling regime,” where the ion is more likely to interact with the light field than to lose energy and information to the rest of its environment.

These physicists achieved the strong coupling regime by putting the trapped ion in an optical cavity: two mirrors facing each other that trap light for a number of round-trip reflections. The smaller the volume between these mirrors, the stronger the coupling between the light and the ion. By using optical fibers as mirrors, they were able to make this volume very small.

Light-ion coupling is exactly the sort of effect that will allow scientists to create quantum networks. To send quantum information between quantum computers, we can send photons with specific quantum states through optical fibers. However, optical fibers aren't perfect — photons lose information as they travel large distances.

By putting a strongly-coupled ion in an optical cavity at each of these nodes, we can transfer quantum states from an incoming photon to the ion and back to a new photon to send on its way. The advances in this paper increased the efficiency of an important step in this procedure (heralded entanglement) by a factor of 1,900 compared with previous iterations.

With a total efficiency of only 1.7%, however, there's still a lot of work to be done before the age of practical quantum networks.

## My cat's coat is mostly white with dark tabby patches. What's going on?

A researcher uses a tweetorial to figure out the underlying genetics for their cat's coat

Neuroscience

University of Sussex

Have you ever wondered why your cat’s coat looks the way it does? Wonder no longer! Earlier this month, Emily Summerbell, a PhD student at Emory University, tweeted a ‘tweetorial’ on cat coat genetics. I used it to figure out the underlying genetics for my own cat’s coat.

This is my cat ‘Little Excuse’ (because when he’s sleeping on your lap, you’ve got an excuse to not get up).

Excuse has a short coat, which is controlled by the FGF5 gene. Short hair (L) is the dominant trait, meaning that if one out of two copies, or alleles, of the gene encodes for short hair, the cat will end up with short hair. Excuse is either homozygous, meaning he has two short hair alleles (LL), or heterozygous, meaning he has one short hair, and one long hair allele (Ll).

Though Excuse is for the majority white (we’ll get back to that later), he generally has dark-colored fur. This is encoded by the TYRP1 gene, for which the black allele is dominant. If he would have the allele for orange hair, this would override the black color, so the lack of any orange means that he has the recessive allele for the orange gene.

Back to the white fur. White fur is caused by the KIT gene, but it is not all-or-nothing. As you can see, Excuse is more than 50% white, which indicates that he is probably homozygous for the dominant white gene (SS).

Lastly, although it’s not clearly visible in this picture, Excuse’s dark patches have a tabby pattern to them. This is caused by the agouti and tabby genes, where the agouti gene determines whether a cat has a solid color coat, and the tabby gene determines the exact pattern.

Emily goes into much more detail in her Twitter thread, explaining colorpoint coat patterns, cats with diluted colors and more. If you are wondering why your cat looks the way it does, this thread will tell you all you need to know.

But in the meantime, what colour is your cat's coat — and do you know why?

## Rapid analysis shows that the 2019-nCoV coronavirus resembles viruses from bats

Another publication suggests that this coronavirus enters cells in a similar manner to SARS

Molecular Genetics

University of Toronto

The 2019 novel coronavirus (2019-nCoV) outbreak has sparked a speedy response, with scientists, physicians, and front-line healthcare professionals analyzing data in real-time in order to share findings and call out misinformation. Today, The Lancet published two new peer-reviewed studies: one which found that the new coronavirus is genetically distinct from human SARS and MERS, related viruses which caused their own outbreaks, and a second which reports clinical observations of 99 individuals with 2019-nCoV.

The first cases of the coronavirus outbreak were reported in late December 2019. In this new study, Nanshan Chen and colleagues analyzed available clinical, demographic, and laboratory data for 99 confirmed coronavirus cases at the Wuhan Jinyintan Hospital between Jan 1 to Jan 20, 2020, with clinical outcomes followed until 25th January.

Chen and colleagues reported that the average age of the 99 individuals with 2019-nCoV is around 55.5 years, where 51 have additional chronic conditions, including cardiovascular and cerebrovascular (blood flow to the brain) diseases. Clinical features of the 2019-nCoV include a fever, cough, shortness of breath, headaches, and a sore throat. 17 individuals went on to develop acute respiratory distress syndrome, resulting in death by multiple organ failure in 11 individuals. However, it is important to note here that most of the 2019-nCoV cases were treated with antivirals (75 individuals), antibiotics (70) and oxygen therapy (75), with promising prognoses, where 31 individuals were discharged as of 25th January.

Based on this sample, the study suggests that the 2019 coronavirus is more likely to affect older men already living with chronic conditions – but as this study only includes 99 individuals with confirmed cases, it may not present a complete picture of the outbreak. As of right now, there are over 6,000 confirmed coronavirus cases reported, where a total of 126 individuals have recovered, and 133 have died.

In a second Lancet study, Roujian Lu and their fellow colleagues carried out DNA sequencing on samples, obtained from either a throat swab or bronchoalveolar lavage fluids, from eight individuals who had visited the Huanan seafood market in Wuhan, China, and one individual who stayed in a hotel near the market. Upon sequencing the coronavirus’s genome, the researchers carried out phylogenetic analysis to narrow down the virus’s likely evolutionary origin, and homology modelling to explore the virus’ receptor-binding properties.

Lu and their fellow colleagues found that the 2019-nCoV genome sequences obtained from the nine patients were very similar (>99.98% similarity). Upon comparing the genome to other coronaviruses (like SARS), the researchers found that the 2019-nCoV is more closely related (~87% similarity) to two bat-derived SARS-like coronaviruses, but does not have as high genetic similarity to known human-infecting coronaviruses, including the SARS-CoV (~79%) or Middle Eastern Respiratory Syndrome (MERS) CoV (~50%).

The study also found that the 2019-nCoV has a similar receptor-binding structure like that of SARS-CoV, though there are small differences in certain areas. This suggests that like the SARS-CoV, the 2019-nCoV may use the same receptor (called ACE2) to enter cells, though confirmation is still needed.

Finally, phylogenetic analysis found that the 2019-nCoV belongs to the Betacoronavirus family – the same category that bat-derived coronaviruses fall into – suggesting that bats may indeed be the 2019-nCoV reservoir. However, the researchers note that most bat species are hibernating in late December, and that no bats were being sold at the Huanan seafood market, suggesting that while bats may be the initial host, there may have been a secondary animal species which transmitted the 2019-nCoV between bats and humans.

It’s clear that we can expect new findings from the research community in the coming days as scientists attempt to narrow down the source of the 2019-nCoV.

## Mini-brains are stressed out and not as reliable for disease modelling as scientists thought previously

Scientists compare cortical organoids to a developing human brain and spot key differences

Neuroscience

University of Pennsylvania

You may have heard of organoids (probably here on Massive Science) and how they are the next big thing in science, especially when it comes to studying the brain. Sure, cerebral organoids are pretty cool. They're formed when stem cells self-assemble into 3D structures that recapitulate brain development, making organoids a good model to study development as well as disease. But now, on top of the ethical debates brought on by these organoids, new research out today suggests that they may not be as reliable as the field thinks.

A new study published in Nature thoroughly characterized lab-grown organoids (developed from human cortical cells) by looking at which genes they expressed and compared them with a developing human brain. They found that, compared to the creation of very specific cell types seen in normal developing human brain, organoids had broader cell types. What seems to be missing is the cell sub-type specification. Imagine a tree that grew a generic "fruit" rather than a specific thing like an “orange” or an "apple."

The organoids also seemed to be more "stressed out" than their normal counterparts. Cellular stress markers that had previously been associated with blocking development of those specific cell types were over-activated in the organoids, but not in the human developing brain. Interestingly, transplanting the organoids into mouse brains blocked the increased cellular stress, and also increased cell type specification in the organoids.

Although this may seem as an unfortunate turn of events, it does not mean that all organoids should be disregarded, but rather that scientists should be more wary when drawing conclusions. As statistician George Box famously said, “All models are wrong, but some are useful.” Knowing these limitations, the field must think carefully about the questions they want to answer using the organoid as a model.

## Scientists built a 4D map of cell division

Cell division involves around 600 different proteins — it could take five or so years to study a single protein

Developmental Biology

RIKEN Center for Biosystems Dynamics Research

Studying biology at a molecular level is often really hard.

Biological processes require the coordinated efforts of hundreds of proteins — the molecular machines encoded by our genetic material. Each protein needs to engage in a particular interaction or reaction at a very specific place and time. It’s complicated.

For example, mitosis, the process by which a cell divides into two, involves around 600 different proteins! Trying to sort out where each needs to be at a given time, in what quantity, and why, is an arduous task.

Thanks to a new technique developed by scientists at the European Molecular Biology Laboratory (EMBL), which combines a quantitative microscopy method with various computational analyses, our job just got a little easier.

This method can produce a 4D (that’s 3D plus time!) map of every single protein involved in a given process, and is first being applied to mitosis. Here's an example:

You can check out the resulting computer model, called the Mitotic Cell Atlas, now — simply choose any combination of proteins from those available (so far) in a drop-down menu to see how they interact at every stage of mitosis.

It’s still going to take several years to gather data for all of the roughly 600 proteins involved in mitosis, but it’s a huge step forward for efficiently analyzing protein dynamics.

Even better, this technique can be applied to many fundamental biological processes, which will certainly aid our understanding of how these processes go wrong in human disease and in other organisms. For example, scientists are already considering building a Plant Cell Atlas. Goodbye snapshots, hello movies!

## You can add almost anything to improve graphene's function, even bird poop

For several years, researchers have been excitedly looking for the best dopant — before realizing that anything can improve graphene's electrocatalytic rate

Molecular Engineering and Materials Science

University of Chicago

Electrochemistry is the study of how chemical reactions generate electricity and conversely, how zapping solutions can trigger chemical reactions. Graphene, a mere sheet of carbon atoms, is known to be an excellent catalyst of electrochemical reactions as it can conduct electricity and has a large surface area to host reacting molecules. Furthermore, introducing dopants —  impurities that can alter a material's physical properties — into graphene can boost its electrocatalytic activity. For several years, the research community has been excitedly looking for the best dopant that could lead to the greatest electrocatalytic improvement in graphene.

It was one of those promising, success story-filled research areas, where newer and more complex dopants would give rise to ever-improving electrocatalytic rates — until scientists realized that almost anything will improve the electrocatalytic rate of graphene

These researchers laced graphene with guano, a low-tech fertilizer made of bird poop with usage dating back to the Incan empire. Compared to clean graphene, bird-poop laden graphene facilitated a higher rate of electrochemical reactions, typified by the oxygen reduction reaction (the reaction of dissolved oxygen) and the hydrogen evolution reaction (the breakdown of water).

The reason for this enhanced electrocatalytic ability is that bird poop contains a hodgepodge of elements, including metals such as cobalt, manganese, and nickel. Basically, the more impurities graphene contains, the better its electrocatalytic reactivity overall. Call it quantity over quality.

In the paper, the authors lament the pursuit for the ideal graphene dopant, admitting such endeavors are “meaningless” and “never-ending”, and at one point, say:

"One may exaggerate only a little by saying that if we spit on graphene it becomes a better electrocatalyst."

According to the researchers, at least in the context of electrocatalysis, we don’t have to worry about “[making graphene] great again.”