How to support open-source software and stay sane – Nature

Illustration by The Project Twins

On 10 April, astrophysicists announced that they had captured the first ever image of a black hole. This was exhilarating news, but none of the giddy headlines mentioned that the image would have been impossible without open-source software. The image was created using Matplotlib, a Python library for graphing data, as well as other components of the open-source Python ecosystem. Just five days later, the US National Science Foundation (NSF) rejected a grant proposal to support that ecosystem, saying that the software lacked sufficient impact. It’s a familiar problem: open-source software is widely acknowledged as crucially important in science, yet it is funded non-sustainably.

The world’s strongest MRI machines are pushing human imaging to new limits – Nature

Image credit: Centre for Advanced Imaging, The University of Queensland

On a cold morning in Minneapolis last December, a man walked into a research centre to venture where only pigs had gone before: into the strongest magnetic resonance imaging (MRI) machine built to scan the human body. First, he changed into a hospital gown, and researchers made sure he had no metal on his body: no piercings, rings, metal implants or pacemakers. Any metal could be ripped out by the immensely powerful, 10.5-tesla magnet — weighing almost 3 times more than a Boeing 737 aeroplane and a full 50% more powerful than the strongest magnets approved for clinical use. “This is a window we’ve just never had in the intact human brain,” says Ravi Menon.

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.

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.

The nose knows how to kill MRSA – Nature


A new antibiotic was right under our noses—or rather, in them. Produced by a bacterium living in the human nose, the molecule kills the potentially deadly methicillin-resistant Staphylococcus aureus (MRSA) in mice and rats. When Andreas Peschel and his team stumbled upon lugdunin, they weren’t looking for a new antibiotic. They were studying S. aureus in its natural environment, the human nose. “If you want to keep the bacteria in check, you need to understand their lifestyle,” he says. “And to understand that, we also looked at its competitors.”

If you give a mouse a menstrual cycle – Nature


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.

Biological specimen troves get a reprieve

The bones of the goliath frog help scientists to study modern populations of this species, which is threatened by hunting. Marc Schlossman/Panos

The US National Science Foundation (NSF) has quietly reinstated its programme to support biological specimen collections that are important for studying disease, invasive species, climate change and conservation. Scientists had protested against the agency’s decision, announced in March, to suspend the programme pending an evaluation that is due later this year.

Read the full story in Nature.

Why Preprints in Physics, But Not Biology? – Undark

Scientific journal policies, along with differences in the history and culture of the disciplines, may play a role.

In a piece published in the New York Times last month, Amy Harmon wrote about “rogue” biologists publishing their research directly to the Web. But as Harmon noted, this kind of activity is hardly news for physicists, who have been publishing these so-called “preprints” — that is, research published digitally, prior to appearing in a formal, peer-reviewed journal — on the website since 1991.

Read the full story in Undark.