Research

Love Your Data—And Let Others Love It, Too

Love your research data and let others love it, too
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[Lire en français]

The Projects initiative is a Digital Science endeavour. Projects is a desktop app that allows you to comprehensively organise and manage data you produce as research projects progress. The rationale behind Projects is that scientific data needs to be properly managed and preserved if we want it to be perennial. There’s indeed a worrisome trend showcasing that every year, the amount of research data being generated increases by 30%, and yet a massive 80% of scientific data is lost within two decades.

Projects and open science data-sharing platform figshare published an impressive and pretty telling infographic on science data preservation and chronic mismanagement [scroll down to see it]. What struck me looking at these numbers is neither the high-throughput data production nor the overall funds it requires – 1,5 trillion USD spent on R&D! – but the little to no information on public policies aimed at solving the problem.

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Nature Middle East’s weekly science dose (Oct 4 — Oct 10)

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Have you heard of reptiles that swim? Such animals used to exist back in the Late Cretaceous period (that is, 98–66 million years ago). Mosasaurs were discovered back in 1764; it quickly became clear that they were marine predators, but the debate still continues on how exactly they swam. A part of the scientific community argues they moved like snakes. Bringing robust analysis and proofs, a recent study demonstrates that Mosasaurs were skilled swimmers, achieving swim speed comparable to sharks.

On a different and more to-the-ground note, researchers have identified a better curative approach for acute leukaemia. The latter is the blood cancer that claims hundreds of lives every year. A comparison between more than 1,000 samples revealed that a drug treatment gives much better remission results. It thus improves survival rates than total body irradiation.

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[Announcement] OKCon Open & Citizen Science hackday: submissions

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I’ve already announced the OKCon ‘Open & Citizen Science satellite event’. As you may remember, we launched idea submissions several days ago. The detailed descriptions are below. You can vote for your favourite one and join us geeking out next Thursday, Sept 19. Don’t hesitate to get back to us either via Twitter (@MaliciaRogue, @stefankasberger) or via mail.

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Syria’s vanishing history

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[This was first published on Nature Middle East.]

The war in Syria is laying waste to ancient monuments and artefacts, while archaeologists and citizens scramble to protect what they can.

Syria’s rich cultural heritage, which stretches back to the beginnings of human history, is at risk as fighting ravages the country.

Gathering accurate information is a challenge, but despite the violence, archaeologists and citizens have been trying to document the destruction of historical sites in the wake of all international archaeological missions leaving Syria.

From Babylonians to Arabs and the Crusaders, numerous civilisations have left their mark on Syria. Six of the country’s sites appear on UNESCO’s World Heritage Sites list: Damascus, Aleppo, the Crac des Chevaliers, Palmyra, Bosra and the Ancient Villages in Northern Syria. Hundreds of monuments are on UNESCO’s Tentative List, and the national heritage register also boasts a wealth of treasures.

Since the unrest began in March 2011, the destruction of cultural sites has often been reported. The cause of damage ranges from shelling and gunfire to army occupation and bombing. Rampant looting and illegal developments on unguarded archaeological sites is also rife.

Syria’s Directorate-General of the Antiquities and Museums (DGAM) is the authority in charge of the maintaining, safeguarding and preserving the country’s heritage, but the ongoing conflict makes DGAM’s remit increasingly difficult.

Before the violence started, about 180 national and international archaeological missions were represented in Syria, but they all left the country in 2011.

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[Announcement] Open and Citizen Science in the heart of Europe

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Stefan Kasberger from OKFn Austria and myself are organizing this one-day workshop as an OKCon satellite event. Join us!

Thursday 19 September, 10:00 – 17:00 @ Centre Universitaire d’Informatique Université de Genève, Auditorium, Ground Floor

Coordinators: Stefan Kasberger (Open Knowledge Foundation Austria) and Rayna Stamboliyska (Open Knowledge Foundation France), in collaboration with Daniel Lombraña González (Citizen Cyberscience Center / Citizen Cyberlab) François Grey (Citizen Cyberscience Center / University of Geneva), Margaret Gold/ Brian Fuchs (Citizen Cyberlab / The Mobile Collective)

Hacking science makes us happy. If it makes you happy, too, then, this year’s Open Knowledge Conference is the place to be!

Indeed, OKCon 2013 is where an amazing bouquet of insights from Open and Citizen science will converge. But if you thought there would be only food for the brain, you were wrong. A satellite event will take place on 19 September aiming at giving space for everyone to actually get great things done.

With our friends Daniel Lombraña González (Citizen Cyberscience Center / Citizen Cyberlab) François Grey (Citizen Cyberscience Center / University of Geneva), Margaret Gold/ Brian Fuchs (Citizen Cyberlab / The Mobile Collective), we have come up with a way allowing everyone to take part to this exciting day.

I have an idea!

We know you do. Hence, we have a dedicated form ready for you to submit a short description of what you are keen to work on. You can also indicate what additional competences you need in order to get your project done.

Idea submission will be running from today until 10 September. Every week, we will be updating everyone (through the Open Science mailing list) telling you about the new ideas submitted. In addition, a community call will be scheduled to discuss and narrow down these ideas so that they actually become feasible within one-day long hands-on sprint.

Working together

The idea of the satellite event is to geek out together. On 11 September, we will be publishing a poll with all ideas so that you can be able to vote for the project you want to work on on Day D. Voting will run until 18 September.

Do not forget to bring your favourite geeking gear (laptop, some flavour of mobile device or a fancy notebook in the perfect 1.0 fashion). We will have WiFi, cookies and fun!

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The workshop space can accommodate up to 45 people. To sign-up, express your interest in the topic and get in touch with the coordinators please write to openandcitizenscience@okcon.org.

Thoughts on Open Innovation: The Rebirth of the Citizen Scientist

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This is the section in a chapter I co-wrote and edited with friends from the Open Science group of the Open Knowledge Foundation. The chapter is part of the insightful discussion that the Open Forum Academy (OFA) initiated earlier this year, and I am very glad to have been part of it. The chapter, entitled “Bottom-Up Creation of Open Scientific Knowledge”, is part of OFA’s second book, “Thoughts on Open Innovation”. Enjoy the read!

🎧 Listen to this post:

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University of Geneva hosts Citizen Cyberscience on PLoS Blogs ‘CitizenSci’

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Citizen Cyberscience was at the honour at the University of Geneva on April 22-23, 2013. I wrote a brief sum-up on it for PLoS Blogs ‘Citizen Science’.

A short time ago, I attended a two-day Citizen Cyberscience workshop at the University of Geneva. As much as the USA and the UK are happy having a vibrant community of citizen scientists, such initiatives in many other European countries are still stuttering. A dedicated workshop in one such country was thus even more exciting. I was there not only because of my interest in the topic but also on behalf of my current position within the EU-funded Citizen Cyberlab’s Synthetic Biology section.

The goal of the workshop was both to get everyone updated on the latest developments of tools for actual citizen science doing and “to work in teams to design and implement a first prototype of a citizen cyberscience project”. The first day was dedicated to talks, and the second day – to hands-on activities. As I recently launched the ‘Open & Citizen Science’ workgroup at the Open Knowledge Foundation France, I am pretty much interested into concrete tools I can use to get people involved into actual projects. Thus, there were two talks of special interest for me: the presentations of Epicollect and Crowdcrafting.

[read more on PLoS Blogs]
[View the story “#CitizenCyberscience workshop in Geneva” on Storify]

Living on Mars

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[This op-ed was first published on Al-Jazeera English.]

“Touchdown confirmed. We are safe on Mars.”

It has been nearly nine months now that the Curiosity Rover touched down on Mars. Do not be fooled by its cockamamie drawing penchant: the Rover has identified traces of calcium (often associated with water), and a stream bed. Around Christmas 2012, the NASA team winnowed down rich in clay mudstone containing small amounts of carbon, oxygen, hydrogen, nitrogen, sulphur and phosphorus – the building blocks of life. The dizzying amount of data Curiosity has been sending is by all accounts changing our perceptions and the possibilities we envision.

The Curiosity Rover’s startling wander on Mars has energised burgeoning – and often private – space tourism endeavours. US millionaire Dennis Tito for instance thinks going to Mars is so simple that it just might work. His Inspiration Mars programme launched back in February 2013 aims at sending a couple of humans on a journey on January 5, 2018, as Mars and the Earth would align on this day which enables a no-fuss trajectory. They will return 501 days later having flown by, but not landed on, Mars. Albeit still scant details about the five-year development plan, NASA hailed “the adventurous spirit of […] citizen explorers”.

Bold minds have come up with Mars One, a non-profit/for-profit hybrid plan to send people settle a colony on Mars. Living on Mars thus does not seem to be a nut job any more. Mars Onewill train people – no specific skills required – for eight years prior to sending them in such a mission. Going to Mars seems within reach, and we are planning to send people to live there. The question is thus not when but how: how do you live on Mars?

The NASA does many things well, and the reason why is because it buries every problem in experts. Recently, the NASA used a crowd-sourced approach to better prepare the Mars Exploration Program. The NASA Space Apps Challenges make no exception: during a two-day (April 20-21) event held simultaneously in multiple cities across the world, experts from all backgrounds gathered to address a total of 50 challenges. These ranged from software to hardware and visualisation challenges, including robotics and citizen science platforms. Paris – where I live – also participated, and I was invited to lead the “Citizen Science” section.

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Retraction Watch suffers DMCA bugs*

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*Ok, trolling away, DMCA itself is a bug.

The background: Retraction Watch is one of the must-follow resources on the web for anyone who is interested in scientific publishing. The blog, maintained and nurtured by Ivan Oransky (Reuters health editor) and Adam Marcus (science journalist and managing editor of Anesthesiology News), is the place for keeping abreast of retractions and corrections in scientific and medical journals. Recently, the blog editors woke up to find out that 10 of the posts have been taken down.

What happened? Apparently, some firm from India copied these 10 posts — relating to Anil Potti, a cancer researcher whose career is imploding as 19 of his papers were already retracted, — then claimed them and filed a DMCA takedown notice. Consequently, the posts were pulled off by WordPress from Retraction Watch… and haven’t been restored thus far.

#ArsenicLife reviews leaked

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You certainly remember the allegedly revolutionary discovery of a bacterium using arsenic instead of phosphate to build its nucleic acids. Arsenic is a poison, and phosphate is mandatory for life. Thus, this alien, “the first known microorganism on Earth able to thrive and reproduce using the toxic chemical arsenic” as presented during the NASA HQs press conference, was supposed to be an alien constituting a paradigm shift, etc. — you remember the hype. The alien that wasn’t one as I already summed up critics shortly after the paper was published (ici en français). The story received an incredible media coverage as well as a huge number of comments from other fellow scientists. A few months after the paper was published in Science, follow-up studies revealed the bacterium does require phosphate — even though in small amounts — to be able to grow and sustain life.
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Science blogging in the Arab world (or the lack thereof)

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This was first posted at Nature Middle East blog ‘House of Wisdom’.

When I started browsing the web for science blogs from the Middle East and North Africa (MENA) region, I didn’t think it would be such an adventure. And for a quest, it was one.

I thus started entering keywords in the search engine. The outcome was disappointing: one or two blogs in English popped up. I thought it is because I was only searching in English, but French and Arabic searches did not harbour significantly more results. When I asked friends to point me out my wrongdoing, they just laughed and the comment invariably was: “dear, spare your efforts, there is no such thing like science blogging in the region.”

The blogging culture in the Arab world thus seems to mainly touch opinionated people with a say in politics and economy. There is nothing wrong with this. I’ll spare you a lecture on the importance of social media for changing the society we live in, this has been thoroughly discussed elsewhere. Loads of bits and ink have also been spilled to demonstrate the importance of science blogging. Given the paucity of science blogs in the Arab World, I guess a reminder is more than useful.

Why writing about science? Reason #1: scientists get to speak directly to the public. Reason #2: lay scientists or enthusiasts engage and keep up to date with developments in various scientific fields. Reason #3: open discussions on research topics are promoted among peers.

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World AIDS Day 2012: When Will We Live in an AIDS-free World?

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This was originally posted on FutureChallenges.com

HIV & AIDS. Image by the author (CC-by-SA 3.0)

HIV & AIDS. Click to view full size. Image by the author (CC-by-SA 3.0)

On Nov 20, the Joint United Nations Programme on HIV/AIDS (UNAIDS) Executive Director Michel Sidibé announced the main findings published in the latest AIDS report. Encouragingly, the number of adults and children worldwide acquiring HIV infection in 2011 was 20% lower than in 2001. Noticeably, AIDS-related deaths have decreased by ⅓ in Sub-Saharan Africa (the region which suffers AIDS the most) for the last six years. Are we reasonably close to the end of AIDS world over?

All this sounds definitely promising. Fewer people die from AIDS-related ailments, fewer babies are born with HIV. Our optimism, however, should not make us forget those 34 million world over living with HIV today. There are still nearly 7 million eligible for therapy but without access to it. Even more disturbing is to know that half of these 34 million are unaware they have HIV. These observations point to the urgent need to work for substantial reductions in HIV infections as well as for better care for those suffering AIDS already.

As a high school pupil in Bulgaria, a friend and I had a youth NGO. We organized campaigns to teach our buddies that AIDS can happen to anyone. Once you’ve been through the very colourful moment of putting a condom on a banana to show how it is done in front of a crowd of high-on-hormones teens, you find it easy to read tedious reports and studies on trends in HIV/AIDS. And when you read a press release by the International AIDS Society (IAS) officially launching its Global Strategy “Towards an HIV Cure”, you just jump to the roof.

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Life performs computation much more than you’ve ever thought

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This post was first published on SciLogs.com ‘Beyond the Lab’

“The level of intelligence has been tremendously increased, because people are thinking and communicating in terms of screens, and not in lettered books. Much of the real action is taking place in what is called cyberspace. People have learned how to boot up, activate, and transmit their brains.

Essentially, there’s a universe inside your brain. The number of connections possible inside your brain is limitless. And as people have learned to have more managerial and direct creative access to their brains, they have also developed matrices or networks of people that communicate electronically. There are direct brain/computer link-ups. You can just jack yourself in and pilot your brain around in cyberspace-electronic space.” ― Timothy Leary, Chaos & Cyber Culture

This quote brings up thoroughly discussed concepts of “wired human interactions” and “globalized self,” all describing our relationship to the internet. The quote also highlights another perspective: the ultimate connection as showcased in cyberpunk culture through the “console cowboy” Case in the Neuromancer or the “game pods”, these outlets plugged through bio-ports in Cronenberg’s movie, Existenz. But if this sounded as daring science fiction 10 years ago, achieving this ‘ultimate connection’ now looks feasible in the near future. Research unveiling the hidden potential of DNA in terms of molecular computation has been ongoing for years, and its outcomes are more promising and mind-blowing than one might have imagined. I kindly invite you to join me in a dive into the exciting waters of DNA-based computers.
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No to Cuts: Secure EU Budget for Science

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[En français]

Since yesterday (22 November), the European Union holds a very important meeting: EU heads of states decide upon member states budgets. Naturally, EU budget for research is discussed during this meeting, and its amount for the next seven years is determined (re HORIZON 2020, the follow-up of FP7). Researchers have mobilized to have their voices heard as the European Commission proposes the minimal amount of 80 billion euros for HORIZON 2020 budget, opposing the 100 billion euros suggested by the European Parliament. As the initiative No Cuts on Research highlights it, “for the European Research Council (ERC) that means annual increases of about 6% which is just enough to allow the ERC to consolidate its funding activity and its mission to support European leadership in world class research. It will not be sufficient, though, to launch any new activities.” Fears persist, however, that these 80 billion euros melt down to much less.

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Bacon Fans United: The Pig Genome Sequenced

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This was initially published on Australian Science.

Breeding healthier and meatier piggies has been one of the many scientific challenges of the past decades; creating more reliable models to study human diseases is another. The swine disease model is indeed much better to use when studying human disorders than the (thus far) widely used murine models. Although pigs reproduce slower than mice and are more expensive to take care of, they are more similar to humans when it comes to anatomy and physiology. These common grounds have allowed the development of accurate swine models for diabetes, cystic fibrosis or retinitis pigmentosa (a cause of blindness). In its issue of 15 November, Nature published the fully sequenced and annotated pig genome. This is a major achievement, and will allow considerable progress to be made on both the yummy and the healthy fronts.

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The Genetic Fatality of What You Are

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This morning while checking my Twitter feed, I stumbled upon a tweet on the “internet addiction gene”. My reaction was: “Have pity. Please”. Thankfully, some people have had spare time to write and dismiss such a scientific breakthrough. It is perhaps a question of timing — all the very recent hysteria about how ENCODE unveiled the indispensability of “junk DNA” just got a bit on my nerves. I’ve written about this elsewhere, so would prefer to skip it here and focus on the ultimate honour for people like me (i.e., geneticists): identifying “the gene of [insert some word here]”.

Actually, I’m pretty committed to do all my best and discover no “gene of”. Before coming to the concrete reasons why, let me list the top ranking “gene of” below.

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Women in Science: Why So Few?

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[This piece was first published on FutureChallenges.org.]

When a  few years ago I first got interested in this topic, I obsessively read all I could about it. The oldest paper I found at that time was from 1965 and bore the title: “Women in Science: Why So Few?” Yes, it’s the same as the title of the current posting and no, this is not a simple coincidence: women are thin on the ground in science and technology.

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[Brevia] Open Letter to the European Commission on Socio-economic Sciences & Humanities research

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In the proposal for next EC Framework Programme — Horizon 2020, — no funding for research in the social sciences and humanities is mentioned. If you support the idea of maintaining specific research funding for the social sciences and humanities (as it is the case under FP7), you are kindly invited to sign the open letter to the European Commission

Please forward this invitation to sign to others.

The EMBO Meeting blogging coverage

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I think you will all be interested in finding more about the many and various topics that were approached during The EMBO Meeting 2011. That is why I hereafter link to the other certified bloggers’ pages 🙂 In case you want to refresh your memory about some of the topics I shortly wrote about during The EMBO Meeting 2010, I link them below as well. Enjoy!

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The EMBO Meeting Day 0: Career Advancement Day

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The EMBO Meeting 2011As I told you earlier, I was selected as certified blogger for The EMBO Meeting 🙂 This was really cool even though I had to travel a lot right afterwards and am now ill: definitely, when you come back from a place where it is 38°C every day to ~23°C, you feel the difference! But anyway: blogging about the conference makes me feel better 😉 Here is thus a short overview of the Day 0.

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To PhD or not to PhD?

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I believe PhD fellows are wrongly thought to be students. I argue that, given our responsibilities, PhDs are early career researchers.

Ok, so here is some quick thought. The other day, I received a nice mail from a Nature Staff member asking me whether I’d like to take part in a blogging initiative they had about PhD. I accepted with great pleasure: this is an excellent opportunity to talk about important things and to reach a huge amount of people. Whether they would agree with what I say or not is secondary. Nobody asked for. To me, the crucial thing was to tell about what people can live through their years as a PhD. My answers are here.

This is not all. Nature has a dedicated issue on PhDs this week.

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Fellowships for divesity studies at CERN

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I saw this announcement and thought it might be of interest for people.

CERN  Graduate Fellowship position / Diversity studies at CERN

In keeping with its international and increasingly global character, the European Organization for Nuclear Research (CERN) has recently appointed a Diversity Officer to develop and implement a policy that will promote awareness and adherence to diversity, one of the established values of the Organisation.

In support of this new initiative, a position is now open to postgraduates in the framework of the CERN Fellowship Programme.
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Journal club and more

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So, as you may have noticed, I am a bit absent these days. Indeed, it is currently a lot of stuff to be completed, so I don’t have the time to write postings. But I’ll be back soon 😉 In the meantime, here are some papers and various blog postings I managed to read somehow:

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Bookmark: A parallel universe to be described soon

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I have to go to Journal Club now immediately, but the piece of news was just marvelously tempting to bookmark for later reading. So, here is what Reuters reports: “Physicists probing the origins of the cosmos hope that next year they will turn up the first proofs of the existence of concepts long dear to science-fiction writers such as hidden worlds and extra dimensions.” You can read the whole story here. Amazing!

 

Bookmark: NSF announces Wiki for Advancing Digitization of Biological Collection (ADBC)

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“The Emerging Frontiers office in the Directorate for Biological Sciences at the National Science Foundation recognizes the need to facilitate communication among diverse principal investigators, especially for new, highly collaborative programs such as Advancing Digitization of Biological Collections (ADBC)”, announces the NSF in The Dear Colleague Letter. They decided to use a wiki: you can access it here. Great initiative!

Boom boom boom, you knock me out right off of my feet…

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I really like this song! For those who do not know (shame on you!), it is John Lee Hoocker, one of the best bluesmen ever. I could keep on talking about blues, but my guess is it is far better to let you listen to it 🙂 So, let me go into something close to this song: turning Drosophila males’ heads. Indeed, a study published in the very last BMC Genomics shows that fruitfly males are under the spell: gene expression profiles in their heads are altered because of mating. Boom boom boom…

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When Tyrannosaurus rex had for breakfast… another Tyrannosaurus rex

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This post was chosen as an Editor's Selection for ResearchBlogging.org

(This was first published at The Urban Times)

In a study published in the online journal PLoS ONE yesterday, researchers show evidence for cannibalistic behaviour in Tyrannosaurus rex. Indeed, the king of the dinosaurs not only fed on other dinos but also on fellow T. rex, say the researchers after identifying bite marks on giants’ bones.

Tyrannosaurus rex was a quite amazing being: 42 ft in length, 13 ft tall at the hips and up to 7 tones in weight, with his two small but strong forelimbs and a running speed of 18km/h. It lived during the Late Cretaceous (which is between 67 and 65 millions of years ago), prior to the extension event. It was one of the few carnivorous species and is believed to have been preying upon hadrosaurs and ceratopsians; some experts have suggested it was primarily a scavenger.

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