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Category Archives: Scientific Method
Why Distinguishing Experiential and Inferential Computational Knowledge is Important
Scientific communities are grappling with assessing knowledge derived from computational processes: interpretability of machine learning models; generalizability of data science claims; verifiability of computational science. There are two broad categories of “knowing” at play here that distinguish approaches to understanding … Continue reading
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
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
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
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.”
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