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Archives de Tag: Open access

Thoughts on Open Innovation: The Rebirth of the Citizen Scientist

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.

 
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Publié par le 25 mai 2013 dans Research, Science

 

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The Future of Libraries, by OpenSite

This was first published on Open-Site.org.

The Future of Libraries

 
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Publié par le 5 février 2013 dans #dataviz, Open access, Open data

 

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[Special bookmark] Open Access and Open Data only

There were lot of very interesting things on the Web these last days on Open Access and Open Data. I would like to remind you that the very first Science 3.0 Blogging Contest starting on October 18 is dedicated to Open Access and will run parallel to the Open Access Week! I greatly invite you to take part, as a blogger, as a reader, as both! You will find below several links to make you feel even more eager than now October 18 comes.

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Publié par le 12 octobre 2010 dans Bookmark, Open access, Open data, Science

 

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Bookmark: Links to read, from here and there

I am currently spending my time reading papers. And user guides. The cliché of the lab rat is not applicable anymore. The cliché of the computer geek neither: I am hardly launching sudo aptitude update && sudo aptitude safe-upgrade on my Debian and this is it. The number of tabs in my browser is dangerously approaching 200 and this makes me nervous 🙂 So, here is a nice bunch of links:

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Publié par le 8 octobre 2010 dans Bookmark, Open access, Open data, Science

 

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Bookmark: Interesting opinion about Open Access journals

Open AccessA nice publication by Jocelyn Kaiser in Science titled « Free Journals Grow Amid Ongoing Debate » discusses the success of Open Access journals such as PLoS and BioMed Central ones and brings by some presumably controversial points.

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Publié par le 4 octobre 2010 dans Bookmark, Open access, Science

 

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Get involved: Making metrics that measure what matters

Cameron Neylon is inviting today everybody to join and take actively part in a poject to redefine bibliographic metrics. Creating this kind of system is essential for sharing knowledge and « there is an opportunity to connect technical expertise and data with the needs of funders, researchers, and perhaps even the mainstream media and government. ». The current proposal stands for a Barcamp day in UK followed by two-day hackfest. The proposal is available to view and edit as a GoogleDoc.

 
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Publié par le 24 septembre 2010 dans Open access, Open data, Science

 

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Bookmark: BMJ Open, accessible medical research

This is an open access journal launched very recently and focused on medical research. It aims at publishing not only full-text reports, but also pilot studies and pre-protocols. Moreover, all data will be published online and reviewers’ comments will figure alongside the main text. This initiative emphasizes the importance of transparency and data sharing in science. Support BMJ Open, submit your results there!

 
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Publié par le 23 septembre 2010 dans Bookmark, Open access, Open data, Science

 

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Bookmark: Videos from the Conference on Open Access Publishing are available

Just a quick link to the videos of the COASP (Conference on Open Access Scholarly Publishing) held from August 22 to August 24, 2010 in Prague (Czech Republic). Enjoy!

 
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Publié par le 21 septembre 2010 dans Bookmark, Open access, Science

 

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Bookmark: Conference on Open Access in Africa

Open AccessBioMed Central announced last week they will be hosting a 2-day conference on Open Access publishing at Kenyatta University (Nairobi, Kenia). It will take place from November 10 to November 11, 2010.

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Publié par le 21 septembre 2010 dans Bookmark, Open access, Science

 

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Bookmark: BioMed Central launches a new initiative to promote data sharing

Open AccessBMC Researcher Notes’ latest editorial titles A call for BMC Research Notes contributions promoting best practice in data standardization, sharing and publication. It announces a new initiative aiming at promoting best practice in sharing and publishing data, with a focus on standardized, re-useable formats. Thus, data from original research project described by precised Data Notes will be made publicly accessible and, along with, an example dataset will be included.

This great initiative is a new step towards open data and research reproducibility!

Read the original announcement from BMC.

 
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Publié par le 2 septembre 2010 dans Bookmark, Open access, Open data, Science

 

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Les premiers résultats de l’étude de publication à accès ouvert sont en ligne

Open Access - PLoSLa deuxième conférence internationale sur l’édition scientifique en libre accès a eu lieu à Prague entre le 22 et le 24 août 2010. Elle est organisée par OASPA (Open Access Scholarly Publishers Association). Les premiers résultats du projet Open Access y ont été présentés.

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Publié par le 29 août 2010 dans Open access, Open data, Science

 

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Bookmark: Bethesda statement on Open Access publishing

It can be read here. A translation in French is also available.

 
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Publié par le 1 août 2010 dans Open access, Science

 

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Bookmark: The third reviewer

Il s’agit d’un forum pour scientifiques où ils peuvent commenter des papiers récemment publiés. Un peu comme un Journal club. Pour l’instant, le thème ayant le plus d’articles est Neurosciences, mais la Microbiologie commence à arriver aussi.
Le (très) mauvais point : les articles non open access ne présentent que les abstracts (résumés). Donc, si on n’a pas accès au journal, c’est loupé pour lire le tout.

À voir ici.

 
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Publié par le 1 août 2010 dans Bookmark, Open access, Science

 

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Journal club: Tracking marsupial evolution using archaic genomic retroposon insertions

The phylogenetic relationships between two orders of marsupials have been intesively debated. Authors benefited from recent sequencing projects which provided two marsupial genomes: this of the South American opossum (Monodelphis domestica)and the one of a kangaroo, the Australian tammar wallaby (Macropus eugenii). Retroposons are suitable and homoplasy-free markers: their insertion sites are random; parallel insertions or exact excisions are very rare. Thus, if one finds a retroposon in the homologous genomic loci of both species this indicates a common ancestry; on the contrary: if the marker is missing in one of the species, it means prior divergence.Moreover, one retroposon can insert into another: this situation is called transposition into transposition. These nested mobile elements insertions provide precious information about the relative times during which given retroposon families integrated into genomes: young elements can insert into older ones, but the reciprocal is impossible.

After complete screening of the opposum and kangaroo genomes, authors found ~8,000 and ~4,000 nested retroposon insertions, respectively. Then, the frequencies and time scales of SINEs (Short INterspersed Elements) were calculated (using TinT software) and 3 groups identified:

  1. SINEs specific to the lineage leading to opossum => phylogenetically informative markers present in the opossum lineage;
  2. SINEs specific to the lineage leading to kangaroo => phylogenetically informative markers present in the kangaroo lineage;
  3. SINEs active in both species => phylogenetically informative markers present in both lineages .

Also, ~220,000 genomic loci containing retroposons were detected using three different strategies. After screening and experimental confirmation, a total of ~440 marsupial sequences were aligned and analyzed to reveal 53 informative markers. Ten of those confirmed again the monophyly of marsupials. The other 43 phylogenetically informative retroposon markers provide significant support for most of the basal splits within marsupials.

Phylogenetic tree of marsupials derived from retroposon data.

Phylogenetic tree of marsupials derived from retroposon data.

Authors did not find any loci containing elements present in opossum plus Paucituberculata but absent in kangaroo, which would have supported the alternative of a close relationship between Didelphimorphia and Paucituberculata. They screened for markers that would support the alternative hypothesis of Paucituberculata being the sister to all marsupials: experimental verification showed that all of the putative elements were also present in the order Paucituberculata (Rhyncholestes), thus supporting the monophyly of marsupials, but not the basal divergence.

Furthermore, 13 of the original 53 markers were present in the South American Microbiotheria and the 4 Australasian orders but not in either Didelphimorphia or Paucituberculata: this significantly supports the monophyly of Australidelphia. The branch separating Australidelphia from Didelphimorphia and Paucituberculata is one of the strongest supported as well. Nevertheless, poor fossil record from South America, Antarctica, and Australia does not allow to assess Australidelphian early realtionships and biogeography.

Two competing hypotheses exist regarding Microbiotheria: the latter are either excluded from the Australasian order (based on nuclear protein-coding genes) or embeded into it (completely or partially based on mitochondrial data). No reliable marsupial phylogeny is established up to now. In the present study, authors provide evidence for 4 independent diagnostic retroposon insertions which allow to place Microbiotheria within South America marsupials. Thus, authors propose the new name Euaustralidelphia for the monophyletic grouping of the four Australasian orders Notoryctemorphia, Dasyuromorphia, Peramelemorphia, and Diprotodontia. In total, 18 out of the initial 53 retroposon markers provide significant support for the monophyly of each of the five multi-species marsupial orders.

Authors conclude: « the retroposon marker system identified a clear separation between the South American and Australasian marsupials. Thus, the current findings support a simple paleobiogeographic hypothesis, indicating only a single effective migration from South America to Australia, which is remarkable given that South America, Antarctica, and Australia were connected in the South Gondwanan continent for a considerable time. »

ResearchBlogging.org
Nilsson MA, Churakov G, Sommer M, Tran NV, Zemann A, Brosius J, & Schmitz J (2010). Tracking marsupial evolution using archaic genomic retroposon insertions. PLoS biology, 8 (7) PMID: 20668664

 
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Publié par le 29 juillet 2010 dans Science

 

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