User:Daniel Mietchen/Talks/Open Science Days 2014

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Open Science and Wikimedia

Warmup 1: Wikipedia[edit]

Warmup 2: show of hands[edit]

  • Number of people in the audience?
  • Who has ever written a research article that finally got published?
  • Who has ever written a research article that finally got published under an open license?
  • Who has ever reviewed a research article?
  • Who has ever signed their review of a research article?
  • Who has ever used research datasets or scientific software published by others?
  • Who has ever contributed to research datasets or scientific software published under an open license?
  • Who has ever got scooped?
  • Who has ever read a Wikipedia article (in any language)?
  • Who has ever contributed to a Wikipedia article (in any language)?

Warmup 3: Format[edit]

Vision: Open science[edit]

Sharing research with the world as soon as it is recorded. Now imagine this with open licenses and public version histories as the default setting. A grant proposal has been submitted to explore funding opportunities for open research.


What have others said on the topic?

I want publishers to publish my workflows. — Philip E. Bourne

...thinking outside the paper doesn't come naturally! --David De Roure

what I think we need in scholarship is the web, but editable — Peter Sefton

There is but one journal: The scientific literature. — Richard Gordon

Science is already a wiki if you look at it a certain way. It’s just a highly inefficient one — the incremental edits are made in papers instead of wikispace, and significant effort is expended to recapitulate existing knowledge in a paper in order to support the one to three new assertions made in any one paper. — John Wilbanks. Illustration: papers and wikispace.

What if everyone in the world were in your lab – a ‘hive mind’ of sorts, but composed of countless creative intellects rather than mindless worker ants, and one in which resources, reagents and effort could be shared, along with ideas, in a manner not dictated by institutional and geographical constraints? — Chris Patil and Vivian Siegel

Somewhere at the fringe of science, someone will start using wiki publishing for science publishing. — John Schmidt (2006)

Whenever danger exists of unnecessarily duplicating efforts to solve problems, ought not scientists try to discover whether the experiments have been performed elsewhere? Ought not all scientists be concerned about rapid publication and wide distribution of results, and even of experiments under way, so as to avoid waste? When a scientist in one field discovers evidence of methods which he cannot use but which may be useful in other fields, ought he not inform others about it? If a new and better technique has been discovered in one field, ought not scientists in other fields investigate its workability, or adaptability, in their fields? When a newly confirmed discovery in one field implies need for revising assumptions or conclusions in another field, do not scientists in the one field have a duty to publicize it and scientists in the other field a duty to hasten to inform themselves about it? — Archie J. Bahm

Better still, if you assert something said in another paper, sod the citation, transclude the relevant text, with a full electronic citation allowing you to verify it. — Christopher Gutteridge

The current Open Access model is provisioning for legacy genres and formats of scholarly communication. That's great for archival purposes, but this is not the next real destination for scholarly discourse. Why? Because consequential intellectual work takes place in myriad ways outside of traditional scholarly genres, that's why, and the digital realm is ready to capture, organize, value, and disseminate those other ways of generating knowledge. — Gideon Burton

The internet allows for a much more powerful system than the current journal system, much more powerful than even an open journal system.
Some things I'd like to see in a unified online open system
  • Hyperlinking between papers
  • Discussion threads for papers
  • Collaborative mark ups of papers, so that difficult papers can be communally dissected and fleshed out, or so that students can work through a paper and provide a mark up to ease the reading for other students
  • An ongoing wiki for every subfield, detailing current outstanding problems, papers to read to get up to speed, most recent progress, etc, as well as curating accepted knowledge. Wikis should also be able to be marked up by students, so that difficult material can be broken down and fleshed out for the sake of other students. — TheEzEzz

So, we had the idea that you do your systematic review before you do your research; you do your research, and then if you haven't changed much, you haven't really made a big impact, whereas if you've actually shifted things one way or the other and made it more precise then you have. — Elizabeth Wager

What I wonder is why professors don't curate [pages on] Wikipedia and add course materials and open access sections of textbooks, much of which they post online anyways. We aren't really seeing the potential that you would hope for with all of the Web 2.0 tools out there. We aren't seeing the academic community take advantage of them as much as other subsets of the community. — David Lipman

The Internet represents an opportunity to change this system, one which has created a 300-year-old, collective long-term memory, into something new and more efficient, perhaps adding in a current, collective short-term working memory at the same time. With new online tools, scientists could begin to share techniques, data and ideas online to the benefit of all parties, and the public at large. — Robert J. Simpson, paraphrasing Michael Nielsen

While scientists have gloried in the disruptive effect that the Web is having on publishers and libraries, with many fields strongly pushing open publication models, we are much more resistant to letting it be a disruptive force in the practice of our disciplines. — James Hendler

Technological revolutions are a privileged moment in which old customs and legitimations may be put under scrutiny. The world of academy should not risk at missing this opportunity to rethink about the fundamental aims and responsibilities of our profession. — Gloria Origgi

I’m feel­ing frus­trated. What else can you feel when the sys­tem is bro­ken, you know that sys­tem must change, but there is lit­tle incen­tive for those per­pet­u­at­ing the sys­tem to change it for the better. — Steven Bell

Wikipedia is probably the most robust Petri dish we have for actually studying the process of words and contributions, because it is auditable. — Peter Frishauf

How cool would it be to fork articles, a la Github. - Jason Priem

What can you do with what you know? — Dale Dougherty

Healthcare is one of the areas where open data will potentially take off soonest and have the biggest impact. — Tim O'Reilly

Reality today[edit]

Adélie penguins are identified and weighed each time they cross the automated weighbridge on their way to and from the sea. The data are recorded but not made public, not even in or alongside the "publication".
  • Two videos providing the basis for an article[2] but not published along with it.
A water droplet surviving an attempt to be cut by a knife. (view stats) A water droplet cut by a knife. (view stats)

Publishing to and from Wikipedia[edit]



Open Access Media Importer[edit]

An example of open science - from the original proposal to all outputs.


  1. ^ Lescroël, A. L.; Ballard, G.; Grémillet, D.; Authier, M.; Ainley, D. G. (2014). Descamps, Sébastien, ed. "Antarctic Climate Change: Extreme Events Disrupt Plastic Phenotypic Response in Adélie Penguins". PLoS ONE. 9 (1): e85291. doi:10.1371/journal.pone.0085291. PMC 3906005. PMID 24489657.
  2. ^ Yanashima, R.; García, A. A.; Aldridge, J.; Weiss, N.; Hayes, M. A.; Andrews, J. H. (2012). Docoslis, Aristides, ed. "Cutting a Drop of Water Pinned by Wire Loops Using a Superhydrophobic Surface and Knife". PLoS ONE. 7 (9): e45893. doi:10.1371/journal.pone.0045893. PMC 3454355. PMID 23029297.
  3. ^ Williams, J. T.; Carpenter, K. E.; Van Tassell, J. L.; Hoetjes, P.; Toller, W.; Etnoyer, P.; Smith, M. (2010). Gratwicke, Brian, ed. "Biodiversity Assessment of the Fishes of Saba Bank Atoll, Netherlands Antilles". PLoS ONE. 5 (5): e10676. doi:10.1371/journal.pone.0010676. PMC 2873961. PMID 20505760. CC0 full text media metadata
  4. ^ Mietchen, D.; Maloney, C.; and Moskopp, N. D. (2013) Inconsistent XML as a Barrier to Reuse of Open Access Content. Journal Article Tag Suite Conference (JATS-Con) Proceedings 2013.


This page forms part of a talk given on October 14, 2014 at the Open Science Days 2014 at the Harnack House in Berlin.