Machine learning gets a journal for interactive figures – Nature

Image: Goh, G. Why momentum really works. Distill (2017)

Sometimes it’s hard to understand someone else’s research through a static scientific paper. Across countless universities and companies, at whiteboards and cafeteria tables, you’ll find scientists in animated conversations explaining their research to one another, asking questions, playing around with each other’s data: in short, interacting. Across the internet in recent years, people have extended these explanations to include interactive graphics and code.

Now a web-only machine-learning journal called Distill aims to provide a formal home for these interactive graphical explanations.

Read the full story in Nature

Blockchains Won’t Fix the Problem with Genomics – NeoLife

Illustration by Igor Bastidas

This is shaping up to be the year of DNA for cryptocurrency. One startup after another is offering to pay you in bitcoin-like tokens for sharing your genetic data.

But it’s hard to see how using blockchains and cryptocurrencies will substantially increase demand for genome sequencing. That’s a vexing problem because too few genomes have been sequenced and analyzed to generate as many meaningful insights as scientists had hoped.

Read the full story in NeoLife.

Fixing gerrymandering with geometry – Tufts Now

Photo: Alonso Nichols/Tufts University

The esoteric world of pure math doesn’t usually play much of a role in promoting fairness in the U.S. political system, but Tufts mathematicians Moon Duchin and Mira Bernstein believe that needs to change. It is math, they say, that could help overcome gerrymandering—the practice of drawing legislative districts that favor one party, class or race.

Read the full story in Tufts Now.

How to build a human cell atlas – Nature

photo by Casey Atkins for Nature

Aviv Regev likes to work at the edge of what is possible. In 2011, the computational biologist was collaborating with molecular geneticist Joshua Levin to test a handful of methods for sequencing RNA. The scientists were aiming to push the technologies to the brink of failure and see which performed the best. They processed samples with degraded RNA or vanishingly small amounts of the molecule. Eventually, Levin pointed out that they were sequencing less RNA than appears in a single cell.

To Regev, that sounded like an opportunity. The cell is the basic unit of life and she had long been looking for ways to explore how complex networks of genes operate in individual cells, how those networks can differ and, ultimately, how diverse cell populations work together. The answers to such questions would reveal, in essence, how complex organisms such as humans are built.

Read the full story in Nature.

What will it take to 3-D print organs? – NeoLife

Sebastian Kaulitzki/Shutterstock; Scientific Reports

Every day in the U.S., about 22 people die waiting for an organ transplant. If scientists could 3-D print organs like kidneys, livers and hearts, all those lives could be saved. For years, people have been touting personalized organ printing as the future.

But despite decades of promising work in bioengineered bladders and other kinds of human tissue, we’re not close to having more complicated organs made from scratch. Harvard professor Jennifer Lewis, a leader in advanced 3-D printing of biological tissue, has only recently developed the ability to print part of a nephron, an individual unit of a kidney.

I asked Lewis what it will take to someday print a full kidney or a similarly complex organ.

Read the full story in NeoLife.

Take two placebos and call me in the morning – NeoLife

Illustration by Gabriel Alcala

When a new drug is being tested in a controlled clinical trial, half the patients get the real drug and half get a placebo, something harmless like a sugar pill or a saline injection. But patients on the placebo often improve anyway, and that’s because they expect that they’re getting the real drug, right? Well, no. Harvard professor Ted Kaptchuk’s research has exploded that explanation. Read the full story in NeoLife.

Fish fossil upends scientists’ view of jaw evolution – Nature

Dinghua Yang

A fossil fish found in Yunnan, China, has filled in a gaping hole in how researchers thought the vertebrate jaw evolved.

The 423-million-year-old specimen, dubbed Qilinyu rostrata, is part of an ancient group of armoured fish called placoderms. The fossil is the oldest ever found with a modern three-part jaw, which includes two bones in the upper jaw and one in the lower jaw. Researchers reported their find on 20 October in Science.

Read the full story in Nature.

Tasmanian devils show signs of resistance to devastating facial cancer – Nature

Jason Reed/Reuters

A contagious facial cancer that is almost always fatal has cut a wide swathe through the population of Tasmanian devils since 1996. The disease has reduced the devil population by 80%, and researchers have predicted that the cancer will drive the animals to extinction within decades. But a study published on 30 August in Nature Communications offers hope. Researchers have found that Tasmanian devils have developed some genetic resistance to the disease in just four to six generations.

Spiking genomic databases with misinformation could protect patient privacy – Nature

Nature

Large genomic databases are indispensable for scientists looking for genetic variations associated with diseases. But they come with privacy risks for people who contribute their DNA. To address those concerns, a system developed by Bonnie Berger and Sean Simmons, computer scientists at MIT, masks the donor’s identity by adding a small amount of noise, or random variation, to the results it returns on a user’s query.

If you give a mouse a menstrual cycle – Nature

fotandy/Getty

Mice are a mainstay of biomedical research laboratories. But the rodents are poor models for studying women’s reproductive health, because they don’t menstruate. Now researchers at Monash University in Clayton, Australia, say that they have found a rodent that defies this conventional wisdom: the spiny mouse (Acomys cahirinus). If the finding holds up, the animal could one day be used to research women’s menstruation-related health conditions.

Power of positive thinking skews mindfulness studies – Nature

Lucy Nicholson/REUTERS

There’s a little too much wishful thinking about mindfulness, and it is skewing how researchers report their studies of the technique.

Researchers at McGill University analysed 124 published trials of mindfulness as a mental-health treatment, and found that scientists reported positive findings 60% more often than is statistically likely. The team also examined another 21 trials that were registered with databases such as ClinicalTrials.gov; of these, 62% were unpublished 30 months after they finished. The findings hint that negative results are going unpublished.

Read the full story in Nature.

Why People Turn to Lemurs and Other Endangered Animals for Dinner in Madagascar – Smithsonian

Image credit: Thomas Marent/Minden Pictures/Corbis

Madagascar is home to many unique and threatened mammals, such as lemurs and small hedgehog-like creatures called tenrecs. Most people wouldn’t think of consuming one of these animals, but for many in Madagascar, bushmeat is on the menu. Scientists assumed that people turned to wild meat just to survive, but two new studies that examine the entire supply chain for this meat have found that consumption of wild mammals in Madagascar is common and far more open a practice than anyone had suspected.Read the full article in Smithsonian.

Biological specimen troves threatened by funding pause – Nature

Image credit: Marc Schlossman/Panos

The cabinets of the Field Museum in Chicago hold a collection of eggs that led to one of the most famous conservation discoveries of the twentieth century: that the pesticide DDT was causing widespread nesting failures in birds of prey.

But such specimen troves — which are used to identify species, track diseases and study climate change — have lost a valuable means of support. Last week, the US National Science Foundation (NSF) announced that it would indefinitely suspend a programme that provides funding to maintain biological research collections.

Read the full article in Nature.

Conor Walsh | Innovators Under 35 – MIT Technology Review

Walsh with his soft robotic exosuit.

This robotics researcher might have something in just your size.

Most robotics labs don’t contain sewing machines. But there’s a room full of them in Conor Walsh’s lab, along with three full-time textile experts and a wall of fabrics in neat plastic bins. There’s a rack that looks as if it belongs in a sporting goods store, with a row of what could be some new kind of running shorts in an array of sizes.

For Walsh, a robot is not necessarily a rigid metal machine. He’s working on robots that are soft, lightweight, and flexible so people can wear them to enhance their abilities.

Read the full profile in MIT Technology Review.

Should babies have their genomes sequenced? – MIT Technology Review

Illustration by Sophia Foster-Dimino

The BabySeq project in Boston has begun collecting data to quantify the risks and benefits of DNA sequencing at birth.

The central question for this project is what will come of giving genomic information to parents and their baby’s doctor. Will doctors order more tests and interventions? Will those tests and interventions make babies healthier? Or will they just waste money, or even end up doing more harm than good?

Read the full article in MIT Technology Review.

Parents beat clinicians at detecting autism signs in infants – Spectrum News

Image: Compassionate Eye Foundation/Getty Images

Parents who have one child with an autism diagnosis can more accurately spot signs of the condition in their younger child at 12 months of age than clinicians can, according to a new study1. The advantage fades by 18 months of age, however.

The findings suggest that surveying knowledgeable parents could move up the date of autism diagnosis, enabling therapy to begin sooner.

Read the full story in Spectrum News