Tuesday, August 25, 2020

The Scientific Paper is Obsolete. Here's what's Next ...


Well ... Not quite.

This article, wiritten by James Somers, came out in The Atlantic in April 2018, but I only just recently ran across it via PocketWorthy.

I thought it was a fascinating read, considering a big part of our bread-and-butter as health science librarians is still journal articles.    The mode may have shifted to digital formats but they are still flat 1-dimensional articles, standard pdfs.  But they could be so much more ...

Back to Somer's article:  

"This is, of course, the whole problem of scientific communication in a nutshell: Scientific results today are as often as not found with the help of computers. That’s because the ideas are complex, dynamic, hard to grab ahold of in your mind’s eye. And yet by far the most popular tool we have for communicating these results is the PDF—literally a simulation of a piece of paper. Maybe we can do better."

He introduces us to software called Wolfram Computational Notebooks (Mathematica) and makes a case for the next thing after journal articles being computational essays that are interactive and dynamic, allowing the reader to "read it and run it:"  

The idea is that a “paper” of this sort would [be dynamic ...]—interactive diagrams interleaved within the text—with the added benefit that all the code generating those diagrams, and the data behind them, would be right there for the reader to see and play with. “Frankly, when you do something that is a nice clean Wolfram-language thing in a notebook, there’s no [BS] there. It is what it is, it does what it does. You don’t get to fudge your data,” Wolfram says.

To write a paper in a Mathematica notebook is to reveal your results and methods at the same time; the published paper and the work that begot it. Which shouldn’t just make it easier for readers to understand what you did—it should make it easier for them to replicate it (or not). With millions of scientists worldwide producing incremental contributions, the only way to have those contributions add up to something significant is if others can reliably build on them. “That’s what having science presented as computational essays can achieve,” Wolfram said.

It sounds like Mathematica hasn't quite been adopted like the open source option has ...  Jupyter is an open source version of computational notebooks.  Somers compared the two computational notebooks thus:  Wolfram's uses the quintissential cathedral approach vs Jupyter's open source bazaar approach.  Wolfram's is the proprietary software, carefully constructed, and Jupyter is wide open and freely available and adaptable.

So far, pdfs are still the standard format for publishing.  Journals don't seem to be requiring computational essays as supplemental data along with article submissions -- or are they?

This sounds absolutely fascinating to me. Are any HSL Librarians using this software?  Either Wolfram's or Jupyter?  Is it available at your institutions?  Are you helping researchers manage their data with this type of software?  Have you seen any of these computational essays?  [They give an example in the article, but I wasn't able to get much out of it ...]  Where are they stored and published?  How are they made available?  Is NLM using these computational essays in the biomedical field?  I'm curious to know more ...

What's your experience with computational essays?  

Should I ask MLA for a CE class on them so we can all learn more?

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