Welcome to the March 2015 High Five here at Altmetric! In this blog post, my second for Altmetric, I’ll be leading you on a tour of the top 5 peer-reviewed scientific articles this month according to Altmetric’s scoring system. On a monthly basis from here on out, my High Five posts will examine a selection of the most popular research outputs Altmetric have seen attention for that month.
Paper #1. Reading Rats’ Minds
The faintest possibility of “mind-reading” struck a chord with readers who shared this study on Twitter this month.
“It sounds like the stuff of science fiction: researchers slice a brain into thin little sections and, just by measuring the properties of specific neurons, they can determine what an organism learned before it died. In fact, this sort of mind reading has become a reality. In work published today in Nature, researchers at Cold Spring Harbor Laboratory (CSHL) describe how postmortem brain slices can be “read” to determine how a rat was trained to behave in response to specific sounds. The work provides one of the first examples of how changes in the activity of individual neurons encode learning and memory in the brain.” – Cold Spring Harbor Laboratory, posted on psypost.org
EurekAlert! ran the headline “Scientists map memorable tunes in the rat brain: NIH-funded study helps understand how brain remembers everyday sensations.”
“For decades scientists have been trying to map memories in the brain,” said James Gnadt, Ph.D., a program director at the National Institute of Neurological Disorders and Stroke (NINDS), one of the NIH institutes that funded the study. “This study shows that scientists can begin to pinpoint the precise synapses where certain memories form and learning occurs.” – EurekAlert! press release
Writing for The Daily Beast, Charlotte Lytton reported that “Researchers have mapped rats’ memories, and humans could be next. Scientists may have cracked the code of memories by successfully tracing how they are imprinted on the brain. An experiment charted the nerve cell changes that occurred within rats’ brains as they made decisions—a process that could prove life changing if replicated in humans.”
Of course the actual study involved observing rat brain slices – not exactly a simple one-step removed from probing the formation of neural synapses in humans.
Shared by mostly members of the public, as well as other scientists, in the US and Europe, this study was largely mentioned on Twitter and in various news outlets.
Paper #2. A Computer That Teaches Itself Games
If the possibility of mind-reading catches readers’ attention, so does the possibility of machines teaching themselves to play video games – and then beating us humans in gameplay. In a study in Nature this month, researchers from Google DeepMind demonstrated the application of deep reinforcement learning in a computer system that “learned” how to play video games. The study was even the subject of Nature magazine’s cover graphic this month.
The study inspired a long list of news articles, popular science and tech magazine stories and blog posts this month.
Artificial intelligence bests humans at classic arcade games, by John Bohannon, Science
Google machine learns to master video games, by Rebecca Morelle, BBC.com
Google’s new AI plays Atari games as well as you can, or better, by Fancie Diep
“YOUR top score is about to be trounced. Google has developed artificial intelligence software capable of learning to play video games just by watching them.” – NewScientist
“Using a bio-inspired system architecture, scientists have created a single algorithm that is actually able to develop problem-solving skills when presented with challenges that can stump some humans. And then they immediately put it to use learning a set of classic video games.” – Shalini Saxena, Ars Technica
“You literally give it a new game, a new screen and it figures out after a few hours of game play what to do.” – Demis Hassabis, Google DeepMind, quote from BBC
“It’s definitely fun to see computers discover things that you didn’t figure out yourself.” – Vlad Mnih, DeepMind engineer, quote from Popular Science
But Paul Rodgers at Forbes offered some down-to-earth context for the performance of this new artificial intelligence.
“A computer that taught itself to play almost 50 video games including Space Invaders and Pong is being hailed as the pinnacle of artificial intelligence. But it is unlikely to spark the Terminator-like Armageddon predicted in recent months by technology entrepreneur Elon Musk (who provided early funding for the project) and physicist Stephen Hawking. Despite mastering more than half the classic Atari 2600 games, the program – deep Q-network (DQN), developed by DeepMind Technologies – struggled with more difficult challenges, such as, well, Pac-Man.” – Rodgers, Forbes.com
Writing in The Conversation (with his article also used for an IFLscience feature), Toby Walsh also offered limitations of this new artificial intelligence and future directions and challenges for deep learning. The DeepMind computer finds long-term planning in video games, like solving mazes, more difficult. This is because the system doesn’t have the ability to use long-term memories for decision making like humans do.
How DOES DeepMind learn to win? Neuroecology blog author Adam Calhoun has insights here.
This study was shared more by scientists and science communicators on Twitter than our first top five paper of the month.
Paper #3. An Incredibly Young Mammoth Black Hole
Our next “High Five” paper attracted international news and social media attention. Published in Nature by Wu and colleagues, the study describes the discovery of a particularly large “ultraluminous quasar” (powered by a super-massive black hole).
“Astronomers have identified a mammoth black hole weighing as much as 12 billion suns. It’s not the biggest black hole ever found, but it’s astonishingly young. The giant appears to have swelled to its enormous size only 875 million years after the big bang, when the universe was just 6 percent of its current age. That’s a surprise, astronomers report Wednesday in the journal Nature, because giant black holes are thought to grow relatively slowly by vacuuming up gas and even stars that venture too close.” – Michael D. Lemonick, National Geographic
“How can a quasar so luminous, and a black hole so massive, form so early in the history of the Universe, at an era soon after the earliest stars and galaxies have just emerged? And what is the relationship between this monster black hole and its surrounding environment, including its host galaxy?” – Xiaohui Fan, study co-author, quoted by Duncan Geere on Wired.co.uk
A massive black hole that is unexpectedly big and unexpectedly young – what is more shareworthy? It’s a perfect fit with the news value for unexpectedness and “wow” factor. Read more about the discovery at Science News, Science.com, NewScientist and Nature.com.
“Wu and his colleagues spotted the black hole using the Lijiang Telescope in Yunnan, China. The object appeared as a bright, red, point-like source. The brightness and spectrum of its light revealed it to be an ancient quasar: a large black hole that occupies the centre of a galaxy and causes interstellar gas to overheat and shine brighter than any star as it spirals into the hole’s gravitational sink.” – Davide Castelvecchi, Nature.com
Paper #4. Ice Cream’s Hidden Ingredient Makes Mice Sick
The next High Five paper of the month is a prime example of “science news you can use.” It is certainly useful for me, as an atopic individual prone to chronic allergies and asthma. It hit a chord online, according to Altmetric social media share numbers, with members of the public, scientists, healthcare professionals and science bloggers alike.
Publishing in Nature magazine this month, Benoit Chassaing and colleagues reported that at relatively low concentrations of two commonly used dietary emulsifiers, wild-type mice demonstrated induced low-grade inflammation and obesity/metabolic syndrome. The effects were more pronounced in mice predisposed to gut inflammation disorders (like inflammatory bowel disease).
“Common additives in ice cream, margarine, packaged bread and many processed foods may promote the inflammatory bowel diseases ulcerative colitis and Crohn’s disease as well as a group of obesity-related conditions, scientists said on Wednesday. The researchers focused on emulsifiers, chemicals added to many food products to improve texture and extend shelf life. In mouse experiments, they found emulsifiers can change the species composition of gut bacteria and induce intestinal inflammation.” – Will Dunham, Reuters
“Food additives may keep snacks fresh and tasty looking, but they can wreak havoc on the gut. These additives disrupt the intestine’s protection from bacteria and boost inflammation in mice, scientists report online February 25 in Nature. The new research “underscores the fact that a lot of things we eat … may not be as safe as we think they are,” says Eugene Chang, a gastroenterologist at the University of Chicago.” – Science News magazine
“Food additives that are commonly used to thicken and stabilize processed foods may disrupt the bacterial makeup of the gut, causing health problems, a new study in animals suggests. In the study, mice that were fed two chemicals that are commonly added to foods gained weight, had altered blood sugar and developed intestinal problems. The chemicals were “emulsifying agents,” chemicals that hold together mixtures that include both fat and water, which would otherwise separate.” – Discovery news
Many articles offered readers lists of foods that contain emulsifiers, including typically ice cream, condiments, candy and bread that stays soft due to dough softeners.
“The ingredients that lend a smooth, stable consistency to ice cream, chocolate bars, and other packaged snacks may promote certain chronic inflammatory diseases. That’s the claim of a new study, which finds increases in metabolic disease and intestinal inflammation in mice fed two common emulsifiers used in processed food. The authors are a long way from confirming similar effects in humans, but they suggest that these ingredients cause damage by disrupting the barrier between the immune system and the microbiome—the collection of microbes that inhabit our bodies. [The research] group is now preparing a more ambitious study that compares the microbiomes of people who completely avoid emulsifiers for several weeks with those on a standard Western diet.” – Science
I wouldn’t mind partaking in that study myself! Which further goes to show that this research resonated with people on an everyday level, as we all wonder whether our diets are keeping us healthy or keeping us sick.
Ed Yong also covered the Nature study for his National Geographic blog Not Exactly Rocket Science. Yong does a fantastic job laying out how the experiments were conducted and what the implications are for humans – and what we don’t know yet. The FDA is still maintaining its position that it “does not have sufficient evidence to alter its previous conclusion that polysorbate 80 and carboxymethyl cellulose [the emulsifiers under study in the Nature paper] are considered safe under their intended conditions of use in food.”
“We’re certainly eating less processed food since we’ve been doing this work. It took a lot of effort, but we did find one type of ice-cream in the supermarket that’s emulsifier-free.” – Study author Andrew Gewirtz, quoted in Not Exactly Rocket Science
Paper #5. Tiny Color-Shifting Crystals are the Chameleon’s Secret
The last study on our list is my personal favorite: Photonic crystals cause active colour change in chameleons, published open access in Nature Communications.
In this new study, researchers identify the source of chameleons rapid color change, and it isn’t pigments. It’s tiny crystals of guanine, or nanocrystals. Unexpected? Quite!
The secret ingedient is…crystals? By Sarah Hird, Nothing in Biology Makes Sense
The secret to how chameleons change color: Nanocrystals, by Neel Patel, Wired.com
Chameleons don’t change colour, they use smart mirrors, by Andy Coghlan, NewScientist
“For a long time, scientists thought the color change—which only occurs in males—was controlled by pigment-containing organelles. But it turns out the mechanism actually has more in common with physics and nanomaterials than with biology: It’s driven by a set of tiny crystals embedded in the reptiles’ skin.” – Neel Patel, Wired.com
“Milinkovitch and his colleagues have demonstrated the presence of two layers of light-reflecting cells in the chameleon’s skin, a superficial layer with a regular lattice of guanine crystals in the cytoplasm and a deeper layer with a less organised array of larger crystals. The chameleon’s optical wizardry results from subtle shifts in the orientation of crystals in the upper layer and the combined effect that both layers have on light.” – Henry Nicholls, The Guardian
Above are electron microscope images of the superficial layer of nanocrystals in chameleon’s skin. Crystal orientation in the relaxed state of the chameleon (left) is tighter and more triangular than the crystal orientation when the chameleon is excited (right). The scale bar is 200 nanometers. For comparison, a strand of human hair is around 80,000 to 100,000 nanometers wide, depending on how course your hair is.
By changing the spacing between these nanocrystals, the chameleons can alter which wavelengths of light their skin absorbs and reflects. – Bethany Halford, C&EN
“One nanometer is about as long as your fingernail grows in one second.” – Nano.gov
In other words, the nanocyrstals that create the chameleons color-shifting skin are tiny – really tiny.
“These [chameleon] colors are generated without pigments, via a physical phenomenon of optical interference. They result from interactions between certain wavelengths and nanoscopic structures, such as tiny crystals present in the skin of the reptiles.” – Michel Milinkovitch, professor at the Department of Genetics and Evolution at UNIGE, via Nanowerk article. Source: University de Geneve
In another research study this month, a group of researchers actually created a color-changing film that mimics the chameleon’s skin. Christie Wilcox has a great blog post about that here.
Chameleons are known for their vibrant color changes. While the old wives’ tale that they change color to match their surroundings isn’t true, they are capable of remarkable shifts in hue, a trait which has fascinated scientists for years. – Christie Wilcox, Science Sushi
Not only was this study a chance to share colorful pictures (it helps that the figures in the paper are reusable under a Creative Commons license), it was a chance to share a bit of nano science underlying a familiar biological color-change phenomenon, which apparently we didn’t know the underlying cause of until now. I’m not surprised this study made quite the rounds in the media and on social media this month!