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

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Brought to you first at the Nature Middle East’s ‘House of Wisdom’ blog.

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 and it became clear quite quickly that they were actually 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 actually 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 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 and improves survival rates than total body irradiation. Continue reading

[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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[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 CyberlabFrançois 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!

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!

The rebirth of the citizen scientist

In the recent decade, the term ‘citizen science’ has emerged to define public involvement in genuine research projects. Synonym labels such as ‘crowd-sourced science,’ or ‘networked science’ actually represent a new make-up for an old idea: back in 1982, science theoretician Feyerabend advocated the “democratization of science.” Going more decades backwards in time, Thomas Jefferson used to envision weather stations operated by volunteers as a means for people to be informed and educated thus engaging into self-governance, a dynamics that is currently happening for real.

This Jeffersonian idea illustrates one of the basic and most crucial issues with science as it is currently performed (i.e., through research within official institutions): its isolation. Contrastingly, citizen science operates – by design – free of the constraints inherent to such strongly formalized places. Citizen science thus not only relocates science, but it also fosters its growth in the mainstream of society. Non-professionals join professionals, thus co-creating knowledge that makes science an integral part of our daily lives and shared human culture.

Numerous examples can be quoted, each bringing its unique colour and shape to the picturesque landscape of citizen science: from birdwatchers illustrating how times of nesting shift as a consequence of climate change to disaster management, from mapping roadkill accidents to producing one’s fluorescent yoghurt at home. These projects illustrate a shift in public engagement in science: from citizens being solely data collectors to data analysts, visualisers and generators of new hypotheses. The hacker and DIY movements have widely contributed to the emergence of a true citizen science, i.e. one that fully explores human curiosity in a non-professional context.

Citizen science is in its infancy yet its popularity grows exponentially as the concept is modular enough to reach the humanities and social sciences (HSS), generally overlooked by both professionals from the so-called “hard” sciences, and citizens. HSS are studies of human nature at large. They encounter the same issues as the “hard” sciences: popularization and communication, policy questions, and a wide range of ethical concerns. Additionally and similarly, HSS have particular theoretical traditions, methodological orientations, and critical interests. The recent surge of citizen science, greatly assisted by information and communication technologies, thus allows reconsideration of the somewhat artificial categorizations of science domains and naturally involves trans- and interdisciplinarity in scientific practise.

These considerations indicate that one does not need a ten-person lab, multimillion-dollar grants and caffeine-intoxicated PhDs in order to perform brilliant science. Citizen systems of participation aimed at collective problem-solving bring, however, two crucial questions: Is citizen science capable of producing reliable data? What guarantees do we have that it is ethical science?

Engaging huge numbers of citizens in a research project means that massive input is generated. Indeed, volunteers already collect data for scientific projects: how reliable is this? Two decades ago, the USA introduced an amendment prohibiting volunteer-collected data to be used in the US National Biological Survey. In the case of a community-based bird species diversity survey, the estimated number of birds correlated with the changes in numbers of observers. Such examples contribute to a stigma associated with citizen science data, which is sometimes labelled ‘incompetent’ or ‘biased.’ In a recent piece, John Gollan argues the opposite: “a growing body of literature shows that data collected by citizens are comparable to those of professional scientists.” Although data-integrity issues can occur, Gollan highlights an important message: “it’s just a matter of honing in on those particular issues and addressing them if necessary. This can be through training to improve skill sets or calibrating data where possible.”

The second question that springs to mind when opening scientific practice to non-professionals is ethics. Many have voiced concerns about dubious ethical frameworks in various citizen science projects. The project that caused recent kerfuffle was uBiome, a project to sequence human genome entirely supported through crowdfunding. Indeed, research ethics are not something to play with: thus, every project dealing with human subjects requires the review and approval of an independent committee – generally referred to as Institutional Review Board (IRB) – prior to its start. The uBiome citizen science project was thoroughly criticized for seeking IRB review of their protocols only after the crowdfunding campaign was completed. A similarly strict review framework is de rigueur when a research project involves animal subjects. In a recent piece for Scientific American, professional scientist and citizen science advocate Caren Cooper called for community answers to ethical questions as the boundary between hobby practitioners and citizen scientists is too blurry to be defined, and so are the cases in which participants need to be invited to follow official ethics protocols. As also exemplified by numerous reactions from open and citizen science enthusiasts, IRB approval can be a hurdle for citizen scientists.

Cooper’s call-out to the community of both professional and citizen scientists does echo a widely shared concern: is there someone – and if so, who? – to provide oversight of DIYbio/citizen science practices? By design, both professional and citizen scientists need to urgently address this particular and foundational issue. None of us can continue standing passive when a threat is posed to citizen science. It fosters our common culture of curiosity and bridges gaps between people whose personal aims and leisure-time activities converge on a desire to advance research and improve human welfare and communities.

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.

Petitioning Obama: Build a Death Star!

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This is my #LulzOfDaDay 🙂 Background: the Obama administration provides a web platform — We the People, — for citizens to send a petition to the President, and “if a petition gets enough support, White House staff will review it, ensure it’s sent to the appropriate policy experts, and issue an official response.” Among the most popular petitions, you can find one calling for free access to scientific publications arising from taxpayer-funded research or the one asking for the removal of District Attorney Ortiz for overreach in Aaron Swartz case.

Star Wars Cookies, by Betsy Weber on Flickr (CC-by 2.0)

Star Wars Cookies, by Betsy Weber on Flickr (CC-by 2.0)

And here comes one of the most important petitions to Obama ever: “Secure resources and funding, and begin construction of a Death Star by 2016.” Launched on Nov 14, 2012 it has gathered nearly 35,000 signatures thus far. The rationale:

By focusing our defense resources into a space-superiority platform and weapon system such as a Death Star, the government can spur job creation in the fields of construction, engineering, space exploration, and more, and strengthen our national defense.

This makes you laugh? Come on, don’t go medieval on this concerned citizen. The Obama administration took his demand into consideration as it “shares your desire for job creation and a strong national defense.” Unfortunately, a Death Star isn’t on the horizon:

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#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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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!

The EMBO Meeting 2011 Continue reading

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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