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Category Archives: Open Science
Paul Meier: Still Saving Millions of Lives
You may never have heard of Paul Meier, but perhaps I can convince you he is one of the 2oth century’s greatest heroes. As I write from my “shelter in place” from the violent COVID-19 pandemic, I’m seeing news stories … Continue reading
My input for the OSTP RFI on reproducibility
Until Sept 23 2014, the US Office of Science and Technology Policy in the Whitehouse was accepting comments on their “Strategy for American Innovation.” My submitted comments on one part of that RFI, section 11 follow (with minor corrections): “11) … Continue reading
Changes in the Research Process Must Come From the Scientific Community, not Federal Regulation
I wrote this piece as an invited policy article for a major journal but they declined to publish it. It’s still very much a draft and they made some suggestions, but since realistically I won’t be able to get back … Continue reading
Posted in Intellectual Property, Law, Open Data, Open Science, OSTP, Reproducible Research
5 Comments
Data access going the way of journal article access? Insist on open data
The discussion around open access to published scientific results, the Open Access movement, is well known. The primary cause of the current situation — journal publishers owning copyright on journal articles and therefore charging for access — stems from authors … Continue reading
Don’t expect computer scientists to be on top of every use that’s found for computers, including scientific investigation
Computational scientists need to understand and assert their computational needs, and see that they are met. I just read this excellent interview with Donald Knuth, inventor of TeX and the concept of literate programming, as well as author of the … Continue reading
Posted in Open Science, Reproducible Research, Uncategorized
3 Comments
The nature of science in 2051
Right now scientific questions are chosen for study in a largely autocratic way. Typically grants for research on particular questions come from federal funding agencies, and scientists competitively apply with the money going to the chosen researcher via a peer … Continue reading
Posted in Open Science, Reproducible Research, Statistics
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Regulatory steps toward open science and reproducibility: we need a science cloud
This past January Obama signed the America COMPETES Re-authorization Act. It contains two interesting sections that advance the notions of open data and the federal role in supporting online access to scientific archives: 103 and 104, which read in part: … Continue reading
Generalize clinicaltrials.gov and register research hypotheses before analysis
Stanley Young is Director of Bioinformatics at the National Institute for Statistical Sciences, and gave a talk in 2009 on problems in modern scientific research. For example: 1 in 20 NIH-funded studies actually replicates; closed data and opacity; model selection … Continue reading
Open peer review of science: a possibility
The Nature journal Molecular Systems Biology published an editorial “From Bench to Website” explaining their move to a transparent system of peer review. Anonymous referee reports, editorial decisions, and author responses are published alongside the final published paper. When this … Continue reading
Posted in Open Science, Peer Review, Reproducible Research, Technology
3 Comments
Science and Video: a roadmap
Once again I find myself in the position of having collected slides from talks, and having audio from the sessions. I need a simple way to pin these together so they form a coherent narrative and I need a common … Continue reading
Posted in Conferences, Open Science, Talks, Technology
10 Comments
My Symposium at the AAAS Annual Meeting: The Digitization of Science
Yesterday I held a symposium at the AAAS Annual Meeting in Washington DC, called “The Digitization of Science: Reproducibility and Interdisciplinary Knowledge Transfer,” that was intended to bring attention to how massive computation is changing the practice of science, particularly … Continue reading
Letter Re Software and Scientific Publications – Nature
Mark Gerstein and I penned a reaction to two pieces published in Nature News last October, “Publish your computer code: it is good enough,” by Nick Barnes and “Computational Science…. Error” by Zeeya Merali. Nature declined to publish our note … Continue reading
Open Data Dead on Arrival
In 1984 Karl Popper wrote a private letter to an inquirer he didn’t know, responding to enclosed interview questions. The response was subsequently published and in it he wrote, among other things, that: “Every intellectual has a very special responsibility. … Continue reading
Ars technica article on reproducibility in science
John Timmer wrote an excellent article called “Keeping computers from ending science’s reproducibility.” I’m quoted in it. Here’s an excellent follow up blog post by Grant Jacobs, “Reproducible Research and computational biology.”
Code Repository for Machine Learning: mloss.org
The folks at mloss.org — Machine Leaning Open Source Software — invited a blog post on my roundtable on data and code sharing, held at Yale Law School last November. mloss.org’s philosophy is stated as: “Open source tools have recently … Continue reading
Posted in Conferences, Open Science, Reproducible Research, Software
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Video from "The Great Climategate Debate" held at MIT December 10, 2009
This is an excellent panel discussion regarding the leaked East Anglia docs as well as standards in science and the meaning of the scientific method. It was recorded on Dec 10, 2009, and here’s the description from the MIT World … Continue reading
My answer to the Edge Annual Question 2010: How is the Internet Changing the Way You Think?
At the end of every year editors at my favorite website The Edge ask intellectuals to answer a thought-provoking question. This year it was “How is the internet changing the way you think?†My answer is posted here: http://www.edge.org/q2010/q10_15.html#stodden
Post 3: The OSTP’s call for comments regarding Public Access Policies for Science and Technology Funding Agencies Across the Federal Government
The following comments were posted in response to the OSTP’s call as posted here: http://www.ostp.gov/galleries/default-file/RFI%20Final%20for%20FR.pdf. The first wave, comments posted here, asked for feedback on implementation issues. The second wave requested input on Features and Technology (our post is here). … Continue reading
Post 2: The OSTP’s call for comments regarding Public Access Policies for Science and Technology Funding Agencies Across the Federal Government
The following comments were posted in response to the second wave of the OSTP’s call as posted here: http://www.ostp.gov/galleries/default-file/RFI%20Final%20for%20FR.pdf. The first wave, comments posted here and on the OSTP site here (scroll to the second last comment), asked for feedback … Continue reading
Nathan Myhrvold advocates for Reproducible Research on CNN
On yesterday’s edition of Fareed Zakaria’s GPS on CNN former Microsoft CTO and current CEO of Intellectual Ventures Nathan Myhrvold said reproducible research is an important response for climate science in the wake of Climategate, the recent file leak from … Continue reading
The OSTP's call for comments regarding Public Access Policies for Science and Technology Funding Agencies Across the Federal Government
The following comments were posted in response to the OSTP’s call as posted here: http://www.ostp.gov/galleries/default-file/RFI%20Final%20for%20FR.pdf: Open access to our body of federally funded research, including not only published papers but also any supporting data and code, is imperative, not just … Continue reading
The Climate Modeling Leak: Code and Data Generating Published Results Must be Open and Facilitate Reproducibility
On November 20 documents including email and code spanning more than a decade were leaked from the Climatic Research Unit (CRU) at East Anglia University in the UK. The Leak Reveals a Failure of Reproducibility of Computational Results It appears … Continue reading
Software and Intellectual Lock-in in Science
In a recent discussion with a friend, a hypothesis occurred to me: that increased levels of computation in scientific research could cause greater intellectual lock-in to particular ideas. Examining how ideas change in scientific thinking isn’t new. Thomas Kuhn for … Continue reading
My Interview with ITConversations on Reproducible Research
On September 30, I was interviewed by Jon Udell from ITConversations.org in his Interviews with Innovators series, on Reproducibility of Computational Science. Here’s the blurb: “If you’re a writer, a musician, or an artist, you can use Creative Commons licenses … Continue reading
Optimal Information Disclosure Levels: Data.gov and "Taleb's Criticism"
I was listening to the audio recording of last Friday’s :Scientific Data for Evidence Based Policy and Decision Making symposium at the National Academies, and was struck by the earnest effort on the part of members of the Whitehouse to … Continue reading
What's New at Science Foo Camp 2009
SciFoo is a wonderful annual gathering of thinkers about science. It’s an unconference and people who choose to speak do so. Here’s my reaction to a couple of these talks. In Pete Worden’s discussion of modeling future climate change, I … Continue reading
Bill Gates to Development Researchers: Create and Share Statistics
I was recently in Doha, Qatar, presenting my research on global communication technology use and democratic tendency at ICTD09. I spoke right before the keynote, Bill Gates, whose main point was that when you engage in a goal-oriented activity, such … Continue reading
Wolfram|Alpha Demoed at Harvard: Limits on Human Understanding?
Yesterday Stephen Wolfram gave the first demo of Wolfram|Alpha, coming in May, what he modestly describes as a system to make our stock of human knowledge computable. It includes not just facts, but also our algorithmic knowledge. He says, “Given … Continue reading
Posted in Open Science, Reproducible Research, Statistics, Talks, Technology
2 Comments
Stuart Shieber and the Future of Open Access Publishing
Back in February Harvard adopted a mandate requiring its faculty member to make their research papers available within a year of publication. Stuart Shieber is a computer science professor at Harvard and responsible for proposing the policy. He has since … Continue reading
Justice Scalia: Populist
Justice Scalia (HLS 1960) is speaking at the inaugural Herbert W. Vaughan Lecture today at Harvard Law School. It’s packed – I arrived at 4pm for the 4:30 talk and joined the end of a long line…. then was immediately … Continue reading
Posted in Law, Open Science, Talks
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A2K3: Opening Scientific Research Requires Societal Change
In the A2K3 panel on Open Access to Science and Research, Eve Gray, from the Centre for Educational Technology, University of Cape Town, sees the Open Access movement as a real societal change. Accordingly she shows us a picture of … Continue reading
Legal Barriers to Open Science: my SciFoo talk
I had an amazing time participating at Science Foo Camp this year. This is a unique conference: there are 200 invitees comprising some of the most innovative thinkers about science today. Most are scientists but not all – there are … Continue reading
A2K3 Kaltura Award
I am honored and humbled to win the A2K3 Kaltura prize for best paper. Peter Suber posts about it here and gives the abstract. His post also includes a link to a draft of the paper, which can also be … Continue reading
A2K3: A World Trade Agreement for Knowledge?
Thiru Balasubramanian, Geneva Representative for Knowledge Ecology International presents a proposal (from a forthcoming paper by James Love and Manon Ress) for a WTO treaty on knowledge (so far all WTO agreements extend to private goods only). Since information is … Continue reading
Posted in A2K3, Conferences, Intellectual Property, Open Science
1 Comment
A2K3: Tim Hubbard on Open Science
In the first panel at A2K3 on the history, impact, and future of the global A2K movement, Tim Hubbard, a genetics researcher, laments that scientists tend to carry out their work in a closed way and thus very little data … Continue reading