The Scientific Paper Is Obsolete. Here's What's Next. - The Atlantic


77 bookmarks. First posted by farley13 14 days ago.


Here’s what’s next. The scientific paper—the actual form of it—was one of the enabling inventions of modernity. Before it was developed in the 1600s, results were communicated privately in letters, ephemerally in lectures, or all at once in books. via Pocket
debates  interactive  management  python  wolfram 
2 days ago by kintopp
T he scientific paper—the actual form of it—was one of the enabling inventions of modernity. Before it was developed in the 1600s, results were communicated…
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3 days ago by indirect
It’s Apple v. Microsoft all over again, only this time Linux is winning
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3 days ago by miljko
T he scientific paper—the actual form of it—was one of the enabling inventions of modernity. Before it was developed in the 1600s, results were communicated…
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3 days ago by johnrclark
T he scientific paper—the actual form of it—was one of the enabling inventions of modernity. Before it was developed in the 1600s, results were communicated…
3 days ago by jkleske
The 1988 Forbes profile about him tried to get to the root of it: “In the words of Harry Woolf, the former director of the prestigious Institute for Advanced Study in [Princeton, New Jersey]—where Wolfram, at 23, was one of the youngest senior researchers ever—he has ‘a cultivated difficulty of character added to an intrinsic sense of loneliness, isolation, and uniqueness.’” But where Mathematica gets its powers from an army of Wolfram Research programmers, Python’s bare-bones core is supplemented by a massive library of extra features—for processing images, making music, building AIs, analyzing language, graphing data sets—built by a community of open-source contributors working for free. Instead of building a specialized, stand-alone application, let alone spending man-centuries on it, the IPython team—Pérez was now joined by Brian Granger, a physics professor at California Polytechnic State University at San Luis Obispo; and Min Ragan-Kelley, a Ph.D. student at UC Berkeley working in computational physics—built their notebooks as simple web pages. “I’m all in favor of there being a maniac in the middle.”A 1997 essay by Eric S. Raymond titled “The Cathedral and the Bazaar,” in some sense the founding document of the modern open-source movement, challenged the notion that complex software had to be built like a cathedral, “carefully crafted by individual wizards or small bands of mages working in splendid isolation.” Raymond’s experience as one of the stewards of the Linux k
4 days ago by sechilds
At every turn, IPython chose the way that was more inclusive, to the point where it’s no longer called “IPython”: The project rebranded itself as “Jupyter” in 2014 to recognize the fact that it was no longer just for Python. The Jupyter notebook, as it’s called, is like a Mathematica notebook but for any programming language. You can have a Python notebook, or a C notebook, or an R notebook, or Ruby, or Javascript, or Julia. Anyone can build support for their programming language in Jupyter. Today it supports more than 100 languages.

Theodore Gray, who developed the original Mathematica notebook interface, said that he once as an experiment tried to build support for other programming languages into it. “It never went anywhere,” he told me. “The company had no interest in supporting this. And also because when you have to support a lot of different languages, you can’t do it as deeply.”
mathematica  jupyper  python  science  research 
4 days ago by euler
“Scientific methods evolve now at the speed of software; the skill most in demand among physicists, biologists, chemists, geologists, even anthropologists and research psychologists, is facility with programming languages and “data science” packages. ” https://t.co/mrBC5TR0dD pic.twitter.com/sE8zlw7FJr

— Will Richardson (@willrich45) April 11, 2018
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7 days ago by willrichardson
I adore this piece about scientific papers becoming obselete. Computers! Drama! Big dumb personalities!
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8 days ago by robinrendle
a cultivated difficulty of character added to an intrinsic sense of loneliness, isolation, and uniqueness

S. Wolfram is E. Yudkowsky if Yudkowsky actually were as intelligent and accomplished as he thinks.

[and Wolfram himself is such a gigantic ass that every article about his products and achievements ends up getting digressing on what an ass he is.]
science  publishing  tech  wolfram 
9 days ago by tkmharris
Here’s what’s next. The scientific paper—the actual form of it—was one of the enabling inventions of modernity. Before it was developed in the 1600s, results were communicated privately in letters, ephemerally in lectures, or all at once in books. via Pocket
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9 days ago by bschlagel
T he scientific paper—the actual form of it—was one of the enabling inventions of modernity. Before it was developed in the 1600s, results were communicated…
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10 days ago by joeywu02
Here’s what’s next. The scientific paper—the actual form of it—was one of the enabling inventions of modernity. Before it was developed in the 1600s, results were communicated privately in letters, ephemerally in lectures, or all at once in books. via Pocket
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10 days ago by joostw
Slow-paced & inefficient, can research journals adapt to keep up with the pace of change?
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10 days ago by mathewi
Slow-paced & inefficient, can research journals adapt to keep up with the pace of change?
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10 days ago by fkbarrett
“Elsevier hired me to do some consulting thing about ‘What would the future of scientific publishing look like?’” This was before the Mathematica notebook, but he gave them a spiel along the same lines. “A few years ago I was talking to some of their upper management again. I realized in this meeting, oh my gosh, I said exactly the same things 35 years ago!”
The paper announcing the first confirmed detection of gravitational waves was published in the traditional way, as a PDF, but with a supplemental IPython notebook. The notebook walks through the work that generated every figure in the paper. Anyone who wants to can run the code for themselves, tweaking parts of it as they see fit, playing with the calculations to get a better handle on how each one works. At a certain point in the notebook, it gets to the part where the signal that generated the gravitational waves is processed into sound, and this you can play in your browser, hearing for yourself what the scientists heard first, the bloop of two black holes colliding.
At every turn, IPython chose the way that was more inclusive, to the point where it’s no longer called “IPython”: The project rebranded itself as “Jupyter” in 2014 to recognize the fact that it was no longer just for Python. The Jupyter notebook, as it’s called, is like a Mathematica notebook but for any programming language.
When you improve the praxis of science, the dream is that you’ll improve its products, too. Leibniz’s notation, by making it easier to do calculus, expanded the space of what it was possible to think. The grand scientific challenges of our day are as often as not computational puzzles: How to integrate billions of base pairs of genomic data, and 10 times that amount of proteomic data, and historical patient data, and the results of pharmacological screens into a coherent account of how somebody got sick and what to do to make them better? How to make actionable an endless stream of new temperature and precipitation data, and oceanographic and volcanic and seismic data? How to build, and make sense of, a neuron-by-neuron map of a thinking brain? Equipping scientists with computational notebooks, or some evolved form of them, might bring their minds to a level with problems now out of reach.
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11 days ago by rauschen
T he scientific paper—the actual form of it—was one of the enabling inventions of modernity. Before it was developed in the 1600s, results were communicated…
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11 days ago by matttrent
The Scientific Paper Is Obsolete | T he scientific paper—the actual form of it—was one of the enabling inventions of modernity. Before it was developed in the 1600s, results were communicated… | https://ift.tt/2JmUaob | via Instapaper and IFTTT
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11 days ago by habi
The idea for IPython’s notebook interface came from Mathematica. Pérez admired the way that Mathematica notebooks encouraged an exploratory style. “You would sketch something out—because that’s how you reason about a problem, that’s how you understand a problem.” Computational notebooks, he said, “bring that idea of live narrative out ... You can think through the process, and you’re effectively using the computer, if you will, as a computational partner, and as a thinking partner.”

Instead of building a specialized, stand-alone application, let alone spending man-centuries on it, the IPython team—Pérez was now joined by Brian Granger, a physics professor at California Polytechnic State University at San Luis Obispo; and Min Ragan-Kelley, a Ph.D. student at UC Berkeley working in computational physics—built their notebooks as simple web pages. The interface is missing Mathematica’s Steve Jobsian polish, and its sophistication. But by latching itself to the web, IPython got what is essentially free labor: Any time Google, Apple, or a random programmer open-sourced a new plotting tool, or published better code for rendering math, the improvement would get rolled into IPython. “It has paid off handsomely,” Pérez said.

The paper announcing the first confirmed detection of gravitational waves was published in the traditional way, as a PDF, but with a supplemental IPython notebook. The notebook walks through the work that generated every figure in the paper. Anyone who wants to can run the code for themselves, tweaking parts of it as they see fit, playing with the calculations to get a better handle on how each one works. At a certain point in the notebook, it gets to the part where the signal that generated the gravitational waves is processed into sound, and this you can play in your browser, hearing for yourself what the scientists heard first, the bloop of two black holes colliding.
science  publishing  mathematica  python 
11 days ago by madamim
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.
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11 days ago by zryb
RT : adroitly connects 's Explorable Explanations, 's Mathematica, an…
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12 days ago by mshook
Ready to move to the next artefact to disseminate science... Let's all go to Jupyter
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12 days ago by shaneisley
adroitly connects 's Explorable Explanations, 's Mathematica, an…
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12 days ago by kleinsound
adroitly connects 's Explorable Explanations, 's Mathematica, an…
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12 days ago by grantpotter
Here’s what’s next. The scientific paper—the actual form of it—was one of the enabling inventions of modernity. Before it was developed in the 1600s, results were communicated privately in letters, ephemerally in lectures, or all at once in books. via Pocket
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12 days ago by archizoo
A very nice essay on the nature and format of the scientific manuscript:
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12 days ago by cdrago
RT : The Scientific Paper Is Obsolete
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12 days ago by freerange_inc
Jupyter Notebooks, apparently.
science  research  python  jupyter  mathematica  wolfram 
13 days ago by pw201
I think this is fairly flawed in a number of ways but the underlying point about sharing code/data is totally valid. Also, some of the content about papers being hard to understand is also a bit odd because it's not like they are aimed at a general audience.
science  publishing  papers  notebooks  mathematica 
13 days ago by mr_stru
Here’s what’s next. The scientific paper—the actual form of it—was one of the enabling inventions of modernity. Before it was developed in the 1600s, results were communicated privately in letters, ephemerally in lectures, or all at once in books.
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13 days ago by matus.tomlein
The Scientific Paper Is Obsolete via Instapaper https://ift.tt/2JmUaob
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13 days ago by stephenfrancoeur
The scientific paper is obsolete. predicts what will take its place:
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13 days ago by wlanderson
RT : The scientific paper is obsolete. predicts what will take its place:
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13 days ago by mtchl
I want to be enjoying this article, but gosh, it is difficult.
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13 days ago by jasonclark
T he scientific paper—the actual form of it—was one of the enabling inventions of modernity. Before it was developed in the 1600s, results were communicated…
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13 days ago by rogerhsueh
T he scientific paper—the actual form of it—was one of the enabling inventions of modernity. Before it was developed in the 1600s, results were communicated…
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13 days ago by toph
Notebook interface
science 
13 days ago by JustinW80
Here’s what’s next.
science 
13 days ago by vanadium
The scientific paper is obsolete. predicts what will take its place:
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13 days ago by rukku
Here’s what’s next. The scientific paper—the actual form of it—was one of the enabling inventions of modernity. Before it was developed in the 1600s, results were communicated privately in letters, ephemerally in lectures, or all at once in books. via Pocket
research  publishing  visualization  abstracts  computing 
13 days ago by dougleigh
Nice article about the value of Jupyter and Mathematica notebooks for science
science  publishing  jupyter  notebooks  mathematica  wolfram  via:metafilter 
13 days ago by nelson
Good article on the future of notebooks (Jupyter) for science
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13 days ago by ljegou
Honored to be in this piece by w re future of scientific pubs
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13 days ago by danbri