Numerous institutions have their postdoctoral fellows and administrators returning this week from the National Postdoctoral Association Annual Meeting (April 12-14) in Orlando, Florida.
The meeting was a perfect balance of career development sessions, interactive workshops, and opportunities for meaningful networking, with presentations including "Did They Really Just Say That?! Responding to Bias at Work", "NSF Postdoctoral Research Fellowships: Strategies for Success", and mealtime meetups for general or specific groups. The poster viewing session had us furiously scribbling down ideas to bring back to our respective campuses such as PENNView, a postdoctoral diversity initiative to expose Mid-Atlantic doctoral candidates to research at the University of Pennsylvania. Another poster by Ralph J. Hazlewood shared their successful methods for increasing postdoc engagement and attendance at Vanderbilt University. I know I speak for many attendees when I say I'm excited to share what I have learned and improve the postdoc experience! Hope to see y'all at the 2020 meeting in San Diego.
A new study has been spurring headlines recently, as scientists have shown restoration of cellular activity in post-mortem pig brains, hours after they have died.
This has prompted some irresponsible headlines suggesting that these brains were "kept alive", a conclusion the authors themselves did not make. Rather, the authors showed that they could restore the electrical and metabolic activity of some brain cells and promote dilation of blood vessels. But should we consider this "alive?"
The conversation about what counts as "alive" in a brain has been interesting. If we are to take this paper and consider electrical and metabolic activity in brain cells "live brains", we are forced to be consistent and conclude the same about cell culture and brain organoids, both of which can produce brain cells with electrical and metabolic activity.
I was delighted to learn about Werner's Nomenclature of Colours, a fascinating intersection of art and science. It's a book, first published in 1814, that orders, classifies, and names 110 colors and provides examples of where they can be found in the natural world.
The book is based on the work of the German geologist Abraham Gottlob Werner who, in his 1774 book Treatise on the External Characters of Fossils (), developed a nomenclature of colors so as to offer a standard with which to describe the visual characteristics of minerals. Clearly taken by the idea, some three decades later the Scottish painter of flowers Patrick Syme amended and extended Werner’s system. In addition to the mineral referent, for each of Werner’s colors Syme added an example from the animal and vegetable kingdom, as well as providing an actual patch of color on the page to accompany the words. While Werner found a suite of 79 tints enough for his geological purpose, now opened up to other realms of nature, Syme added 31 extra colors to bring the total to 110.
I love how this book dances back and forth between science and art. At the same time that it's trying to order and classify colors in a rigorous way, it's also making subjective associations between those colors and the natural world. I think it also tells a larger story about the close relationship between science and art, and how our ordered scientific knowledge emerges out of our subjective observations.
Sydney Brenner died yesterday. That's him on the right, standing next to James Watson at the Asilomar Conference, 1975. I don't want to write a proper eulogy, because they've been done (here's a good one). It'll do to say that he was a scientist of a stratospheric status. I sometimes thought about him when I was in grad school and kept being surprised that we were both working in science at the same time. It was like reminding myself that a myth wasn't myth at all but real flesh and blood, like someone casually remarking that there were dragons in the parking lot. He won a Nobel Prize in 2002, rightfully so, but it should've been his second. He was a fulcrum of 20th century biology, a peer of essentially every famous biologist of the '50s, like Rosalind Franklin and Watson and Crick.
A lot of the focus from Brenner's career has been on his introducing Caenorhabditis elegans, a cute little flatworm into the biologist's repertoire. (It's okay, usually people just say "see el-uh-gans".) It should! He won a Nobel Prize for it. C. elegans was a great idea -- they're easy to work with, you can store them in the freezer (something you can't do with fruit flies or mice, other neuroscientist favorites), and they have a very low, very specific number of neurons -- 302. No more, no less. That makes them easy to study, easy to grow and maintain, and easy to learn on. If you walk into a C. elegans lab you might be lucky enough to see a scientist sitting at a microscope, plucking their own hairs off their arm or their eyebrows to use as hooks to pick up tiny worms. This is absolutely true.
It's astonishing to think about but Brenner should have already won a Nobel Prize by the time he actually got one for C. elegans. He was one of the last living members of the Phage Group, a collection of molecular biologists who used bacteriophages, viruses that infect bacteria, as models to discover the most basic fundamentals of genetics -- how DNA works, how proteins are made, and what the genetic code is. Earlier this week we published an article about Elisa Izaurralde, who worked out how messenger RNA (mRNA) gets distributed around the cell. Sydney Brenner invited the idea of mRNA more or less out of thin air. The idea is that mRNA acts as a temporary copy of the information encoded in DNA. A cell uses that copy to make a protein, instead of reading directly off of DNA. In the early 1960s there...wasn't much in the way of concrete evidence to support this idea. Brenner (and a few others, including Francis Crick) knew at the time that there was DNA, and there was protein, but there was something in the middle that was missing. They stuck RNA in the middle. Just like that.
*The Eighth Day of Creation: The Makers of the Revolution in Biology - Horace Freeland Judson
I've been thinking about a question for my fellow scientists lately: What's one paper that you always use to contextualize your work, that you wish you could share with everyone because you just think it's SO DARN COOL?
Mine is "Biodiversity hotspots for conservation priorities." I love this paper because the authors came up with the 25 places on earth with the highest concentrations of plant and animal species. They argue that in an era of very limited funding for protecting nature, focusing mainly on these regions will return the most bang for our conservation buck. And this paper is super relevant to my work because I study forests in the Tropical Andes, home to 45,000 plant species. Nearly half of these (~20,000) can only be found in this hotspot.
There are hotspots for animal enthusiasts, too! The island of Madagascar - home to multiple lemur species, the fossa, and the so-ugly-it's-almost-cute aye-aye - is a prime example. There are now 36 hotspots, with eleven new ones added in the past two decades. Scientists, nature lovers, world travelers: is your favorite place on the list? Shout out at me about your favorite papers and hotspots on Twitter and I'll share your replies!
Philosophers and researchers have long searched for estimates of pi, from approximations using the golden ratio to the famous fraction 22/7. One such estimate was accidentally discovered by French mathematician Georges-Louis Leclerc, Comte de Buffon – Buffon for short. He asked a simple question: Suppose a needle of a particular length is dropped onto a wooden floor with evenly spaced boards of the same width. What is the chance that the needle crosses a crack between the boards?
The angle of the needle determines how likely it is to have crossed the crack: with a smaller angle between the needle and the cracks, it is easier for the needle to land without crossing one. So, the solution to the “Needle Problem” relates the sine function to the needle’s angle, drawing a curve where the needle will always cross the crack. The area under this curve is compared to the rest of the area the needle could have landed, estimating the chance the needle crossed a crack. The resulting ratio relates the length of the needle, the distance between the needle and the crack, and pi – a simple shuffling of variables yields an estimate of pi.
Now, if you were to drop a needle on a wooden floor yourself, it would take you thousands of attempts before you could reasonably calculate pi. That's because the ratio mentioned above is in the case of infinite attempts – in the real world, we are limited to the number of times we can drop a needle. Researchers at the University of Illinois – Urbana-Champaign developed a simulation to virtually drop needles and estimate pi. On this Pi Day, try it out to see how close you can get to pi using Buffon’s Needle.
When I started studying to become a particle physicist, I noticed that π appeared not only in math courses, but also in almost every subject covered in each physics class. From the coil of a spring to the properties of light, pi shows up again and again, no matter what. To celebrate Pi Day, I want to take you on a brief quantum journey.
In the early 1900’s, quantum mechanics was arising as a way to explain the mysterious behavior of elementary particles, such as photons and electrons. That's when researchers came up with the concept of wave–particle duality, the idea that particles could behave as both indivisible pieces of matter and astonishingly, as waves. A fundamental fact of nature.
A wave can be thought of as a repeating oscillation. Picture a clock. Every 60 seconds, the hands complete a revolution and covers a 360 degree angle, or, in units of radians, 2π.
The period of the rotation would then be 60 seconds, and the angular frequency, corresponding to the angular displacement per unit time, would be 2π divided by 60 seconds. So, even if the clock’s hands are following a circular path, their movement can be described by a wave.
Elementary particles like electrons, photons, and quarks have all the properties of waves, like wavelengths and angular frequencies. It is natural to find the number pi in many equations within the quantum mechanics framework that describe the behavior of these particles.
The Heinsenberg uncertainty principle is a beautiful example of the consequences of the particles' wave-like nature. It essentially states the curious fact that we can't simultaneously measure both the position and velocity of a particle . The more accurate the measurement of either of the two variables is, the more uncertain the other one gets. In fact, exact position and velocity have no meaning at all in the quantum realm. Although the implications of this principle are extremely complex, the equation that describes it is a very simple one that depends, you guessed it, on π.
From the circumference of a circle to quantum mechanics, pi plays a crucial role in our understanding of nature.
Like many quantities in science, we can never determine the value of π exactly, but we can approximate it. You can even estimate π yourself with candy and a piece of paper.
Start by drawing a square. Let’s make it 8.5 inches long on each side so it fills up the width of a standard sheet of office paper. Now, draw a circle with a diameter of 8.5 inches within that square.
Now we need something to drop onto the drawing, like grains of rice or M&Ms. Begin by covering the square and circle with the objects and then count the number that are within the circle and the total number of objects. From this information, we can estimate the value of π. We can calculate the area of a circle with π r2, where r is the radius (the distance from the center of the circle to the outside). Based on how we drew the circle and square, the square will have a side length of 2r, so the area will be (2r)2 or 4r2.
Back to the M&Ms: to guess how many of the dropped candies will land inside the circle, we can calculate the ratio of the circle’s area to the square’s area: (π r2)/4r2 = π/4. When I tried this with 100 M&Ms, I found that 78 of them were inside the circle and 22 of them were outside the circle but inside the square. This means 78% of the total M&Ms landed in the circle. From our ratio calculations, we estimated that π/4 candies would land within the circle. Now, we can compare the fraction of the M&Ms that landed in the circle to the theoretical number to estimate π. Doing so, we find π/4 = 0.78 so π is about 3.12. The actual value of π is 3.14159265…. so our result isn’t a bad approximation. If we wanted to get a better estimate, we could use a lot more M&Ms and a much bigger drawing.
Of course, counting all the M&Ms takes a long time, so using more than a few hundred M&Ms isn’t practical. Instead of actually dropping M&Ms onto a square and circle, we could write a computer program to simulate dropping thousands or even millions of candies onto a circle and square and counting them up. The computer can “drop” and count a million M&Ms in a matter of seconds. When I tried this, I found that 785,389 of the 1 million simulated M&Ms landed within the circle, leading to an estimated value of 3.141556, which is even closer to the true value of pi than our estimate using only 100 M&Ms.
This is only one of many ways to approximate π. Nevertheless, this is a simple way to estimate π with just regular household materials.
We are excited to announce a new partnership with Two Photon, a small company that makes science art. In addition to creating enamel pins, jewelry, and other cool products, they also provide small grants for people starting new science communication projects.
As you probably know, members of the Massive consortium write two articles for publication during their training. These first two articles are unpaid, which is where Two Photon comes in! They'll be providing grants for a small group of prospective writers with little or no previous experience to participate in Massive's science writing training. Two Photon grantees, known as Photon Fellows, will be paid for their first two training articles, which will make it possible for them to participate without doing any unpaid work. If you're interested in being one of the writers supported by Two Photon, join our consortium! You can use the code TwoPhoton to waive the fee. Once you're in the consortium, you'll find links to the Photon Fellows interest form. We're really looking forward to the articles that come out of this partnership.
We're also stocking a few Two Photon items in the Massive Science Shop! Check out the purple brain pins, Scientist necklaces, flask pins, and Science is for Everyone pins (click the giant brain picture below). And don't forget to pre-order a science tarot deck soon! All the proceeds from our shop go back into supporting our mission.
Massive and Two Photon have a lot in common: we both have small teams that appreciate science and art equally and believe science is for everyone. Thanks for supporting both of us!
We've spent the last few months getting our Kickstarter rewards shipping out to backers and prepping our tarot cards for production. Now that we've figured out the basics of order fulfillment—and let me tell you, international shipping is like opening twenty cans of worms—we're excited to take the next step forward and open the Massive Science Shop.
The first things we're putting up for sale are the Kickstarter rewards that weren't claimed by our backers. If you missed backing our campaign back in October, this is your second (and last!) chance to get one of our limited edition Women of Science Tarot Decks. We're only making 500, and over half have already been claimed by our backers. Make sure to pre-order yours before they're all gone.
In addition, we've got a regular edition of our tarot card deck, our sticker packs, and our postcard set up for sale right now. We'll put up our Women of Science posters for sale once they're ready.
Finally, all of this wouldn't be possible without the incredible support of our Kickstarter backers. They proved that people really want to see more imaginative representations of science exist in the world. Their support has not only helped us not just bring this one project into existence, but also helped us lay the groundwork to continue realizing new projects like it in the future. To all of our backers: thank you!
Helia Bravo Hollis was a plant researcher in Mexico, one of few women working in biology in the 1930s. Two species of plants, Ariocarpus bravoanus and Opuntia bravoana, were named to honor her.
She died in 2001, just before her 100th birthday. I'm a huge fan of hers because Latina women are underrepresented in the history of science and because I love desert plants. Also, mid-century field clothes were pretty cool. She did all her fieldwork in a skirt!
Hamilton was a software engineer before the position was even existed—in fact, she's the one who coined the term. She was one of the first people who distinguished software engineering as a legitimate field worthy of respect.
In the 1960s, she led the team that developed the in-flight software for the Apollo missions. Her team's hand-written software played a critical role in landing the astronauts of Apollo 11 on the moon, one of the first times a computer was trusted with the real-time execution of a mission-critical task.
Poly- and perfluoroalkyl substances (PFAs) repel both oil and water. So, as Anna Robuck wrote last fall:
"...PFASs are everywhere: fire-fighting foams, nonstick cookware like Teflon, stain-resistant carpet, water-resistant clothing, food packaging, compostable plates, some cosmetics, and other consumer products that repel oil, grease, or water."
They're ubiquitous, and because of that, they end up in our bodies. Now, the European Food Safety Authority says that humans can tolerate approximately...*pulls out adding machine*....99.9% of what they've been exposed to in the past.
In respone to this news, Robuck shared her thoughts:
"Ugh. Add this to the very-recent news that the US will refuse to set drinking water limits for these compounds.
My family lives near DuPont HQ, and some back of the envelope calculations suggest they (we) are drinking the weekly limit suggested in your link over the course of about three hours."
My favorite part of the science I do is field work. I fell in love with the study of geology because of all the field trips my classes took to mountains, road-side outcrops, and sand dunes on Lake Michigan, and the time spent wading in rivers and lakes. I never imagined, though, that I would spend my graduate studies crawling around underground in caves! I had been in so-called "show caves", like Mammoth Caves in Kentucky. But, they didn't prepare me for the thrill (and scariness) of crawling and climbing through the remote and unmodified caves central to my fieldwork.
My fieldwork in caves consists of cave monitoring, where we frequently visit the caves and measure their CO2 levels and temperature, and collect water from inside the cave to analyze back in our lab. We monitor the caves in the modern climate system, so we can better understand what they might be able tell us about past climate. The cave pictured here is Waipuna Cave in New Zealand's North Island, where we have cave deposits that serve as climate archives for the past 30,000 years. I've learned to love caves for both the awesome science they allow me to do, and their beauty. How can I not be inspired?
We asked our community whether or not the partial shutdown of the federal government, which has stretched into its second month, was having an impact on their research. One of our members is a former USDA researcher and helped illustrate the consequences of the shutdown on the government's scientific research. They asked to remain anonymous, citing limits on unauthorized statements imposed on scientists by the administration.
When it comes to agriculture research conducted by the USDA, they told us how a shutdown means the living things are not getting regular care. Plant research is often seasonal and so certain experiments need to be done at set seasonal times. If the few personnel allowed on station aren't capable of watering everything. Plants and insect colonies which aren't cared for could die. As a result, year-long projects could be irreparably lost.
Volcanoes of New Zealand are important figures in Māori (New Zealand's indigenous people) culture. When European exploration of New Zealand began in the early 1700's many places and landmarks were renamed, replacing their original Māori names. One such name change was Mount Taranaki, a volcano central in Māori legends with other mountains in the Tongariro National Park. Taranaki was renamed Mount Egmont by a Dutch explorer in 1770, and was taken by the British Crown in 1865. In 1986, Mount Taranaki (then Mount Egmont) was officially renamed "Mount Egmont or Mount Taranki" by the Lands Minister at the time, although the New Zealand Geographic Board had unanimously voted to return its name to Mount Taranaki months prior. In December 2017, eight iwi (people or nations of New Zealand) Taranaki officially signed an agreement with the Crown to begin the process of giving Mount Taranaki legal personality, meaning Mount Taranaki would have legal ownership over itself. Upon legalization, Taranaki will join Te Urewera and the Whanganui River, both of which have had legal identity since 2014.
Dr. Jiankiu He, a scientist in China claims to have edited the genome of two human embryos, which were then implanted and given birth to by their mother as twins, dubbed Lulu and Nana.
Dr. He says he edited the CCR5 gene, in order to provide the embryos with resistance to HIV infection. Jiankiu He says he did this because the father of the twins carried HIV. A version of CCR5 (CCR5-Δ32), mainly found in Northern European genomes, is known to confer immunity to certain variants of HIV.
Based on Dr. He’s presentation at the 2nd International Summit on Human Gene Editing this week, one of the two embryos did not have all its cells edited, as a result it is not clear that this baby will have resistance to HIV. The other embryo has only a single-copy of CCR5 edited (humans have two copies of all genes), and the resulting edited gene is not yet known to confer resistance to HIV. It is possible that neither of the two babies will have resistance to HIV. It would certainly be unethical to test this!
There are other ways, such as sperm washing during IVF, to prevent HIV transmission from father to off-spring.
Dr. He also detected an “off-target” edit, i.e. another region of the genome that was edited by the CRISPR technology used. He suggested that this was unlikely to result in any adverse medical outcomes.
He’s experiment was performed in secrecy. His former employer has denied involvement in the trial.
The informed consent form used by Dr. He appears to be misleading in terms of the risks involved.
Dr. He claims to have followed the recommendations of the US National Academies report on human gene-editing. However, his trial doesn’t seem to have followed several of these recommendations (highlighted below) and may yet ignore others.
Dr. He says he’s in the process of submitting a scientific manuscript for publication.
His experiment drew immediate criticism in China, with over a hundred scientists signing a letter decrying his work as unethical.
What we don’t yet know:
The role of He’s collaborator, Michael Deem, a professor of bioengineering at Rice University in the US.
There are media reports of a PR firm hired by He, but there’s no clarity about the role of this firm.
As of now it is still unclear which research institutions, which medical doctors, and which hospitals were involved in this project.
The funding for the trial is still unclear. It appears to have been funded through He’s personal funds as well as funding from the Shenzhen Science and Technology Innovation Commission according to the clinical trial registration in China. The commission however has claimed to have never funded this project.
Documents showing ethics approval from the Shenzhen HOME Women’s and Children’s Hospital appeared on social media. However the hospital seems to have lodged a complaint suggesting this form was forged. We need to learn more about the ethics and approvals pipeline followed by He.
Dr. He has pledged to follow up with the health of the babies for the first 18 years of their life, however there is no information about who would be involved in this effort, nor what kind of tests this will involve, or how the results would be reported.
We do not yet know if the edits on the genome of the two babies will have any adverse effects. Some scientists have suggested that the method He used to screen the embryos for off-targets were insufficient. We will just have to wait and hope the babies do not suffer due to the editing.
Researchers from MIT have flown a plane powered by an ‘ion drive’ for the first time. The drive uses high powered electrodes to ionise and accelerate air particles, creating an ‘ionic wind’. This wind drove a 5m wide craft across a sports hall. Unlike the ion drives which have powered space craft for decades, this new drive uses air as its accelerant. The researchers say it could power silent drones.
Check out this video featuring Steven Barrett, the researcher who led the team:
This first flight made it about as far as the Wright brothers' first flight at Kitty Hawk. While it seems infeasible for passenger flights, it does have the potential to create a new class of small, silent, and clean drone aircraft.
In the US, food regulation is split in two. As they put it, the Food and Drug Administration (FDA) regulates most "food or food additives" in the US, including the production, packaging, labeling, and sale of food besides meat and poultry. Meat and poultry are regulated by the US Department of Agriculture (USDA). The USDA regulates the production, slaughter, and sale of all meat and meat products. These agency's joint decision on cell-based meats will treat these new products as different things at different points along the process of turning cells into meat.
The FDA will oversee the growth and production of cells. At harvest time, when the cells are collected to be turned into meat, regulation will transfer to the USDA. The decision can be seen as a win for the companies that make cell based meat, which advocated for a similar set up in a letter to the White House in August.
“In 1983, the U.S. Environmental Protection Agency declared the Bunker Hill Mine and smelter complex the nation’s second-largest Superfund site. The agency has been a presence in the valley ever since. Today, after 35 years and almost $900 million in cleanup costs, Bunker Hill’s tailings heap still oozes 400 pounds of toxic metals a day into the South Fork of the Coeur d’Alene River. Tundra swans still flap and stagger in the marshes. After picking up more mine waste downstream, the river dumps almost 400 tons of lead and 700 tons of zinc into Lake Coeur d’Alene every year.”
Our microbiome, the collective genomes of the microbes that live inside our digestive systems, has been linked to multiple facets of our health, from cancer to depression and everything in between. However, before you go recommending one probiotic over another, you might want to read ahead.
Large studies have revealed significant variation between the gut microbiome of both healthy individuals and those with health conditions, making it hard to identify associations between the gut microbiome and a person’s health. However, thanks to two recent studies (one in Amsterdam and one in Guangdong, China), the reasons for this variation are now clearer. The two studies showed that both ethnicity and geography are key factors in determining the gut microbiome. It gets even more complicated: most of the current knowledge about the connections between the microbiome and health come from studies of European and North American populations.
This new research highlights the importance of being careful when applying data about the gut microbiome to different groups of people: clearly, one size does not fit all. However, researchers still don’t know why differences in the gut microbiome are associated with ethnicity and geography. We’ll need to untangle the influence of genetics, cultural norms, and diet if we want to develop personalized microbiome-based treatments.
Purple sea urchins are eating all the kelp in California. But in Pittsburgh, hundreds of miles from the ocean, we order them in the mail.
They arrive wrapped in wet newspaper with pieces of seaweed to snack on. We keep them in tanks, next to some sea star buddies, and study how they grow skeletons. When we're done, we bleach them (the university considers them a biohazard) and save them as extremely fragile decorations.