Nature Genetics iCOGS collection

This week Nature Genetics published a Focus issue on cancer risk, including findings from the COGS (Collaborative Oncological Gene-environment Study) consortium, published as 13 coordinated papers in this Nature Genetics iCOGS collection:

At Nature Genetics, we give voice to leading efforts to understand the genetic basis of disease.  Over the past six years, we have seen mass surveys of genetic variants across the human genome, called genome-wide association studies, yield key insights into hundreds of common diseases.

Today, we’re proud to see how COGS, extending this approach to oncology, has doubled the number of genetic regions implicated in breast, ovarian and prostate cancers.  As such, these 13 papers represent a milestone in our understanding of these common cancers, and exemplify what’s needed in such discovery efforts.

Some of the overall findings from the collection can be found in this blog post. Continue reading →

How to write an editorial (in tweets)

This week Nature Chemistry published an editorial describing how they have used Twitter over the past 4 years. The piece was written as a series of tweets which the team then shared on Twitter on Wednesday. How and why did they put it together?

The version that was handed over to our production team consisted of a title, standfirst, Wordle, and 42 tweets in the main body of the article. It turned out to be 22 lines too long. Ouch. Look at the picture of the proof to see what needed to be done to cut it down to size. 4-line tweets were cut to 3 and a couple of tweets were removed completely. Click through to the larger version of the image to see exactly what changes were made. And it was on the second page so you can’t see it, but #overlyhonestmethods had to be cut from the hashtag tweet (it didn’t play nice with line breaks).

The ’42′ ending still works; one tweet for the title, one for the standfirst and 40 for the main text (you could argue that the original version was actually 44 tweets and the published one is genuinely 42 tweets in total). We still had problems with orphans and widowsin the pdf version, so we shifted some of the tweets around. If you compare the proof to the published version (and you care that much) you can figure out what was moved where. Yes, it’s somewhat bizarre that an Editorial about how we use a web 2.0 tool is dictated — to some extent — by old-fashioned typesetting issues, but there you go.

Stuart Cantrill explains more in the The Sceptical Chymist Blog. You can also follow Nature Chemistry on Twitter, they are @NatureChemistry. Continue reading →

Crime and punishment: From the neuroscience of freewill to legal reform

This week’s Soapbox Science guest post is by Mark Stokes, a senior research scientist at the Oxford Centre for Human Brain Activity, University of Oxford. He looks at whether it’s possible that a brain tumour could cause a person to commit mass murder. He recalls the story of Charles Whitman as a case study:

Charles Whitman – Source: Wikimedia commons

On August 1^st 1966, Charles Whitman ascended the Tower of the University of Texas Austin and opened fire on innocent bystanders, having already killed his wife and mother. In his apparent suicide note, he wrote:

“I do not really understand myself these days. I am supposed to be an average reasonable and intelligent young man. However, lately (I cannot recall when it started) I have been a victim of many unusual and irrational thoughts”.

He suspected that there was something wrong with his brain, and indeed subsequent autopsy revealed an extremely aggressive tumour that was impinging on brain tissue.

Mark’s post ties in with Brain Awareness Week and March’s SpotOn NYC (#SoNYC) event on “Communication and the Brain.”

Over on the SpotOn NYC blog you will also find a collection of related blog posts with contributions from Mo Costandi, Vaughan Bell and The Neurocritic and others.

Tackling Mental Illness In Africa

Traditional Medicine

In another post to tie in with March’s SpotOn NYC event, Scitable’s blogger Khalil A. Cassimally looks at mental illness in Africa:

In October last year, Human Rights Watch released a damning report which documented the inhumane treatment of Ghanaian sufferers of mental illnesses. In a country where an estimated three million people live with mental disabilities, the report describes the overcrowding and unsanitary conditions of three public psychiatric hospitals. The report also sheds light on so-called spiritual healing centers, presided by independent faith healers. Nearly all patients in the eight centers inspected were chained to trees by their ankles and left to sleep, urinate, defecate and bathe in that same spot. Some of the patients had been chained as such for five months. Some of the patients were less than 10 years old.

Learn more about these issues in Khalil’s post. 

From tumours to tapeworms

On the map: Taenia solium
SHUTTERSTOCK

Yevgeniy Grigoryev explains in the Spoonful of Medicine Blog, commonly used cancer drugs could be repurposed to help eliminate tapeworm infections:

A team led by Matthew Berriman, a geneticist who studies parasites at the Welcome Trust Sanger Institute in Hinxton, UK, sequenced the genomes of three human-infective tapeworm species as well as a fourth tapeworm that lives in the intestines of rats and mice. Their analysis, published online today of Nature found that among more than 1,000 gene products that are predicted to be druggable in the parasite responsible for echinococcosis—a disease that affects an estimated 2–3 million people worldwide—more than 200 already have existing therapies (many in the oncology space) that block them.

The potential for new pharmacological interventions doesn’t end there. You can find out more in Yevgeniy’s post. 

Fight for clinical data ‘needs to go global’

More needs to be done at the global level to ensure that researchers release all relevant data from clinical trials. Daniel Cressey explains in the News Blog:

High on the agenda at today’s opening evidence session in an inquiry by Parliament’s Science and Technology Select Committee is whether pharmaceutical companies withhold data that might paint their drugs in a bad light, a subject that is attracting increasing attention in Europe and elsewhere in the world.

“We are eroding belief in medicines because people can’t trust the results that are published,” said Keith Bragman, president of the Faculty of Pharmaceutical Medicine.

Fiona Godlee, editor in chief of the BMJ – which has published a number of articles attacking drug companies for lack openness on clinical trial data, notably regarding access to data on Roche’s Tamiflu – said, “We recognise it’s a problem across the research enterprise.”

Continue to Daniel’s post to find out more.

Students launch popular science magazine

Mohammed Yahia reveals in the House of Wisdom Blog, there are only a few really good initiatives to engage the public with science in the Arab World, such as FameLab or Stars of Science. However, a group of students who are passionate about science decided to take their interest a step further and launch the first student popular science magazine in Egypt:

The magazine, which they are calling The Vector, will start by covering research on and off the GUC campus in a format accessible to anyone interested in science. It will also cover research happening internationally, with articles that span both physical and biological sciences.

“With a heritage of poor science curricula in terms of content, approach and presentation  simply speaking the world ‘science’ is sufficient to invoke a string of dull memories to the average Egyptian,” says Youssef George, the editor-in-chief of the new magazine. To counter this, he suggests the written word will not be enough. “In a community in which most individuals gather information from audio-visuals, it is inevitable to go for that at a later phase.”

The magazine will start as an online publication, launching its first issue next May. However, the students hope to have a monthly print edition by September 2013.

More information on The Vector, in Mohammed’s post.

To Get Twitter Followers, Be Nice and Be Useful

In his latest post, SciLogs blogger Matt Shipman looks at a forthcoming paper that examines factors related to getting Twitter followers:

The researchers found that tweets, or Twitter messages, containing positive sentiments (e.g., “This study is really interesting”) are positively associated with gaining followers. It’s not a huge boost, but it’s there. By the same token, tweets with negative sentiments (e.g., “This study is a waste of time”) are negatively associated with gaining followers. The impact here is a little more pronounced.

The researchers hypothesize that this is because Twitter is a platform where users are usually connected by weak social ties – they don’t know each other very well. And, as the paper says, “negative sentiment from strangers may be unpleasant or uncomfortable for a potential new follower to see.”

Matt encourages readers to  take a look at the paper.

Women’s Work

This week, a special issue of Nature looks at how science remains institutionally sexist. The issue considers the gender gap and what’s being done to bridge it. At November’s SpotOn London conference, we looked at some of these issues with a session dedicated to women in science and in the run-up to the talk we hosted a collection of blog posts on the SpotOn site:

Why female scientists should blog

To Blog or Not to Blog

Athene Donald, Professor of Experimental Physics at the University of Cambridge looks at the challenges of using social media and blogging as a way to overcome the frequent invisibility of women in science:

… If you start a blog, what then? How do you get a readership? Do you have to do that dreadful thing ‘self-promote’ in order to make sure people read it and is that anathema for many would-be bloggers (as for women in other instances as I discussed here)? ….I found it painful to self-promote at the outset, but I have more or less got inured to doing so through Twitter. But as recent experiences showed me, there is more to it than just that, and support from friends is vital in keeping fighting the good fight.

You can find a summary of the other featured posts, divided by topic, here. Continue reading →

Why We Need Science Communication

In this week’s Soapbox Science guest post, science illustrator Emily Coren shares a list of valuable resources for science communicators:

I’ve attended several meetings this past year and when I talk with other science communicators, there are certain sources that keep coming up in conversation. I’d like to share with you some of the resources that describe and inform the theory and practice of science communication and have helped shape my perception of the work that I do.  I’m amazed at how new this information is to many of my peers in both science and science communication and I hope you will find the references as interesting and helpful as I did.

Why We Need Science Communication

• The Public Understanding of Science, The Royal Society, London 1985.

A comprehensive treatise on why science communication is important to society. It makes recommendations for what we can do as a society to improve our understanding of, and engagement with, science.  Continue reading →

This week’s guest blogger on Soapbox Science is Alan Alda: actor, director, writer, and founding member of the Center for Communicating Science at Stony Brook University. He talks about his lifelong interest in communicating science and opening up these channels to encourage children:

We launched The Flame Challenge through the Center for Communicating Science, which I had helped found at Stony Brook University, and it immediately caught the imagination of people from all over the world. Hundreds of entries came in from scientists in 31 countries and were judged by 6,000 kids from across the globe. This year, the Flame Challenge is sponsored by both the AAAS and the American Chemical Society.

But, as popular as the challenge became, I don’t think we realized what a tough task it would be to explain a flame in a few words. (I didn’t know, for instance, that Michael Faraday had taken several lectures to do it. And that was without getting into modern physics.) In spite of the difficulty, though, we got some wonderful answers. The winning entry was a spectacular animated video.

You can watch the video in Alan’s post. This post was also featured in a blogging series building up to February’s SpotOn NYC (#SoNYC) event, hosted in association with the American Museum of Natural History as part of Social Media Week.  The panel’s focus was on Telling Stories with Scientists, examining the various ways of communicating scientific research. You can read all of the blog posts featured in the series here and follow the conversation using #smwScience and #SoNYC hashtags. Continue reading →

Let’s Find Out What Science Outreach Can Accomplish

This week’s Soapbox Science post is by Matt Shipman, he explains why outreach is important and how we can go about improving our efforts:

… scientists need funding agencies, academic department heads, grant reviewers and others in positions of authority to recognize the value of science outreach efforts. But scientists don’t have a body of data, quantitative analyses and peer-reviewed publications that can be used to define that value. There are a few isolated studies out there (e.g. linking news coverage to journal citations, or measuring the benefits of outreach at zoos), but not enough to support a robust argument in favor of science outreach.

The solution to this quandary is fairly clear. We need physical and life scientists who engage in outreach to partner with social scientists and do three things:

A) develop methodologies for collecting data and subjecting them to quantitative analysis

B) use those methods to conduct impact studies in conjunction with outreach projects

C) publish their findings.

Do you agree with Matt’s solutions? Share your suggestions in the growing comment thread.  Continue reading →

Antarctic researchers find life in subglacial lake

Quirin Schiermeier reveals in the News Blog that Lake Whillans, a small body of water huddled in eternal darkness beneath 800-metre-thick Antarctic ice, seems to harbour life:

Researchers with the US Antarctic expedition team WISSARD who accessed the lake on 28 January report that they have found microbes in samples of lake water and sediment — but what kind of known or novel organisms those might be has yet to be determined.

The bottom of subglacial Lake Whillans{credit}ALBERTO BEHAR, JPL/ASU{/credit}

If the reported preliminary findings hold up, it is the first time that life has been discovered in a subglacial lake.

How the bacteria produce and metabolize energy in an environment probably deprived of oxygen and nutrients is unclear. Team members speculate that the organisms might live on energy extracted from minerals in surrounding rocks — a survival strategy also used by certain bacteria found in gold mines.

Antarctica’s hidden lakes, sealed for probably millions of years, mark one of the utmost frontiers for life on Earth.  Many scientists think the lakes and what dwells in them will provide hints about which forms of life might exist on other planets or moons — for example on Jupiter’s moon Europa, which is thought to host a large sub-surface ocean.

You can find out more about this discovery in Quirin’s post. 

Crowdsourced coders

Computer coders are helping scientists to deal with the deluge of data pouring out of research labs. Ewen Callaway elaborates in the News Blog:

IMAGE VIA SLWORKING2 UNDER CREATIVE COMMONS

 A contest to write software to analyse immune-system genes garnered more than 100 entries, including many that vastly outperformed existing programs.

The US$6,000 contest was launched by researchers at Harvard Medical School and Harvard Business School, both in Boston, Massachusetts. TopCoder.com, a community of more than 400,000 coders who compete in programming competitions, hosted the contest. The results are described in a letter published today in Nature Biotechnology.

The challenge was to analyse the genes involved in the production of antibodies and immune-system sentinels called T-cell receptors. These genes are formed from dozens of modular DNA segments located throughout the genome, and they can be mixed and matched to yield trillions of unique proteins, each capable of recognizing a different pathogen or foreign molecule.

The post also considers the limits associated with crowdsourcing and the problems dealing with personal data. Continue reading →

{credit}TSHA/SHUTTERSTOCK{/credit}

Nature‘s Careers section is pleased to announce their latest international competition to select five young scientist columnists for 2013. All currently enrolled science graduate students and working postdocs are eligible. You can find out more in the Nature Jobs blog:

Over the course of the year, each columnist will write at least one column to be published in Nature, and will be encouraged to pitch more. Columnists will also be asked to write two or more Blog entries for the Naturejobs blog, charting their ups and downs through the year and describing how their experiences have shaped their future career choices.

You can see some examples of columns from past winners in the blog post. Continue reading →