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The Scientific Paper is Obsolete (2018)

theatlantic.com

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Re: The Scientific Paper is Obsolete (2018)

#21

Post by chrisseaton »

rtkaratekid wrote: post #3
PhilipVinc wrote: post #2

Papers today are longer than ever and full of jargon and symbols. They depend on chains of computer programs that generate data, and clean up data, and plot data, and run statistical models on data. These programs tend to be both so sloppily written and so central to the results that it’s contributed to a replication crisis, or put another way, a failure of the paper to perform its most basic task: to report what you…

I think this almost every time I read the paper. It’s like Linus’ “show me the code.” I just want papers now to “show me the data and the code.” And include a discussion about why these results are important. I think it’s a great time for the scientific community to improve transparency on these fronts. Sincerely, someone who reads a lot of research but contributes none because I’m an amateur. Edit: when I say data,…

> I just want papers now to “show me the data and the code.”

But the code is secondary to the idea. The idea and the discussion around how it was arrived at and what it means is the key thing. The code is just there to implement it. You could code the same idea ten different ways.

Re: The Scientific Paper is Obsolete (2018)

#23

Post by fennecfoxen »

AshamedCaptain wrote: post #17
queuebert wrote: post #11

Earlier quoted context omitted.

I do share code that way, but the traditional ivory tower standards by which I am judged require "refereed journal publications" in high impact factor traditional journals. I'm trying to fight back against that, largely unsuccessfully. What would help me is to have the old geezers consider GitHub issues, PRs, and commits as a type of citation and to have a better way of tracking when my code gets used by others that…

> What would help me is to have the old geezers consider GitHub issues, PRs, and commits as a type of citation As a geezer myself I am imagining what this type of request would look like in less than 5 years from now. "What would help me is to have the old geezers consider Tiktok videos and replies as a type of citation" i.e. if you open this particular can of worms for a very restricted subset of users (not only pro…

Tiktok videos are primarily used for entertainment, rather unlike Jupyter notebooks and source code repositories. Surely you have a more serious objection.

Re: The Scientific Paper is Obsolete (2018)

#24

Post by someguydave »

netizen-936824 wrote: post #8
rtkaratekid wrote: post #3

Earlier quoted context omitted.

I think this almost every time I read the paper. It’s like Linus’ “show me the code.” I just want papers now to “show me the data and the code.” And include a discussion about why these results are important. I think it’s a great time for the scientific community to improve transparency on these fronts. Sincerely, someone who reads a lot of research but contributes none because I’m an amateur. Edit: when I say data,…

Raw data can be on the order of terabytes, not that it can't be shared but this is a real barrier when it comes to raw data

I guess we should stop trying because datasets are big

Re: The Scientific Paper is Obsolete (2018)

#25

Post by sam-2727 »

I think this is a great idea theoretically, but in reality for most papers I don't want to see the data/underlying code. While it would be great to publish data/code with the paper (in the field I've worked on the most, astronomy, most data is already published with the paper anyways), I don't want/need to look through a notebook with the underlying code of the paper in order to just read the intro/conclusions (and maybe one key methods section). Interactive figures are a great idea, but again, oftentimes I don't really care to interact with the figure, or fiddle stuff around, I just want to know why the paper is important and how I should use its conclusions. The two-column format of most papers is very useful for skimming. So instead I would argue notebooks shouldn't replace papers, but supplement them (as they sometimes do already, in fact, but perhaps journals could make it an actual requirement to create a supplementary notebook).

As the article mentions, scientific fields are gigantic nowadays, and skimming papers is critical when you're citing 100+ references in your paper.

Re: The Scientific Paper is Obsolete (2018)

#26

Post by LudwigNagasena »

chrisseaton wrote: post #21
rtkaratekid wrote: post #3

Earlier quoted context omitted.

I think this almost every time I read the paper. It’s like Linus’ “show me the code.” I just want papers now to “show me the data and the code.” And include a discussion about why these results are important. I think it’s a great time for the scientific community to improve transparency on these fronts. Sincerely, someone who reads a lot of research but contributes none because I’m an amateur. Edit: when I say data,…

> I just want papers now to “show me the data and the code.” But the code is secondary to the idea. The idea and the discussion around how it was arrived at and what it means is the key thing. The code is just there to implement it. You could code the same idea ten different ways.

The code is there to show that the idea is worth the discussion around.

Re: The Scientific Paper is Obsolete (2018)

#27

Post by Mezzie »

queuebert wrote: post #11
robotresearcher wrote: post #6

Earlier quoted context omitted.

Do you do so? If not, why not?

I do share code that way, but the traditional ivory tower standards by which I am judged require "refereed journal publications" in high impact factor traditional journals. I'm trying to fight back against that, largely unsuccessfully. What would help me is to have the old geezers consider GitHub issues, PRs, and commits as a type of citation and to have a better way of tracking when my code gets used by others that…

> I also think citations of your work that find errors or correct things should count as a negative citation.

Strong disagree. Given how much influence colleagues can have over one another's career prospects, how petty academic disagreements can get, admin focus on metrics like citation count, and how it's easier to prove someone else wrong than to do your own original work (both have value, one is just easier), it would end up with people ONLY publishing 'negative citations' (or at least the proportion would skyrocket). I think that would be bad for science and also REALLY bad for the public's ability to value and understand science.

> Thus the references at the end of the paper should be split into two sections: stuff that was right and stuff that was wrong.

This, on the other hand, is brilliant and I love it and want to reform all the citation styles to accommodate it.

Re: The Scientific Paper is Obsolete (2018)

#28

Post by convolvatron »

d110af5ccf wrote: post #9
queuebert wrote: post #4

As a practicing scientist, I firmly believe the world would be much better off if we simply published version-controlled Jupyter notebooks on a free site, such as GitHub or ArXiv.

> As a practicing scientist > version-controlled Jupyter notebooks That's awfully field specific. It probably wouldn't work for most of STEM. Even for ML I shudder to imagine trying to make sense of the inevitable monstrosities. Writing a paper is part of the thinking process. It forces the author to sit down and work through things in an orderly manner and they're still often difficult to read. I'm definitely in fav…

I'm pretty sure all of us have the experience of cramming most of the paper into the two weeks before the deadline. Expecting someone to firm up their presentation without the risk of finalizing something half-assed is ... too much to ask for mere mortals.

Re: The Scientific Paper is Obsolete (2018)

#29

Post by fxtentacle »

chrisseaton wrote: post #21
rtkaratekid wrote: post #3

Earlier quoted context omitted.

I think this almost every time I read the paper. It’s like Linus’ “show me the code.” I just want papers now to “show me the data and the code.” And include a discussion about why these results are important. I think it’s a great time for the scientific community to improve transparency on these fronts. Sincerely, someone who reads a lot of research but contributes none because I’m an amateur. Edit: when I say data,…

> I just want papers now to “show me the data and the code.” But the code is secondary to the idea. The idea and the discussion around how it was arrived at and what it means is the key thing. The code is just there to implement it. You could code the same idea ten different ways.

Yes but chances are it only appears to work because the analysis code has bugs. So first i want to check the code and that it works before i put effort into understanding the idea.

Re: The Scientific Paper is Obsolete (2018)

#30

Post by Mezzie »

d110af5ccf wrote: post #16
queuebert wrote: post #11

Earlier quoted context omitted.

I do share code that way, but the traditional ivory tower standards by which I am judged require "refereed journal publications" in high impact factor traditional journals. I'm trying to fight back against that, largely unsuccessfully. What would help me is to have the old geezers consider GitHub issues, PRs, and commits as a type of citation and to have a better way of tracking when my code gets used by others that…

> the references at the end of the paper should be split into two sections: stuff that was right and stuff that was wrong I've seen stuff like this said before but I don't think it would work. Most citations are mixed in my experience. A few objections, a bunch of stuff you aren't commenting on, and some things you're building on. Or you agree with the raw data but completely disagree with the interpretation. Others…

Yes. We should record all of this, and turn them into easily browsable graphs/hypertext to easily assemble sets of papers to read/look into. At the very least things like 'background reading', 'further reading', 'supporting evidence' and 'addressed arguments' would be useful.

'We' meaning the librarians and archivists. You guys actually researching have more than enough to do.

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