Handful of Biologists Went Rogue and Published Directly to Internet

I really don't get this argument; I see it come up regarding open data for reproducibility too. TeX/LaTeX source is just an extra piece of metadata which might help someone out in a few years time. That's nothing to feel ashamed of, and it's certainly less shameful than not providing the code. If the code allows flaws in the research to be exposed, that's either something to be proud of, or (if it was intentional) it's not the code that's shameful.

My own LaTeX is mostly an inconsistent mixture of copypasta from stackexchange. That doesn't mean I'm ashamed of it, and it's all in public Git repos at http://chriswarbo.net/git if any human or bot actually cares to look.

Speaking of which, the commit histories of those Git repositories aren't very good either. Lots of commit messages like "Fixes", or "Oops, typo in last commit", with multiple changes bundled into single commits, atomic changes spread across multiple commits, etc. But, in the same way as my LaTeX source, it's better than having no commit history, which would be the case if I set myself higher standards.

Of course, I can follow higher standards, but that's when I'm paid to and/or when collaboration is important. For personal stuff, I'd rather invest the time I save interacting with Git on writing more tests, or refactoring, etc.

I am certainly aware that many scientists don't want to publish their code out of embarrassment. It was a surprise to me, but I've heard that feedback.

I investigated various alternatives after I found LaTeX too arcane, including DocBook. It's still not entirely clear what solution exists to the collection of problems I have (want to semantically mark up my paper, want it to display nicely regardless of screen, etc).

About the 2nd part, may I rephrase it as PDFs are the docker of publication .. (Adobe would probably be very proud of that).

The exact same think could be said about HTML, but that hasn't stopped people...

The semantic parsing part is an annotation process. AI algorithms are required to make accurate annotations - a huge amount of context is required.

So if authors instead marked up their papers such that each mentioned entity's semantic meaning was obvious, it would make it much easier to AI that scans all papers and generates hypotheses.

Yes.

Fellow Academics: The people who will be discussing your tenure case, writing letters of support, nominating you for prizes, etc.

University Administrators: The people who are the final word in your tenure case, and who do things like evaluate how well your department/college/etc. is performing.

Grants: Be they your fellow academics in the form of reviewers, program officers, etc., the prestige of your publications will likely matter to them.

Publications are the unit of currency in academia at the moment, and the incentive and evaluation structures at almost every step are oriented around that. Going your own way is a laudable step, perhaps, but largely the luxury of established researchers who have already had their prestige publications, or those willing to take the potential hit to their careers for the principled stand.

However, compared to the number of potential biologists or manuscripts that could be published, it is just a HANDFUL.

But to stay on topic, I'd say that the impact of blogs and wikis have been felt, it is just up to the gatekeepers, the powers-that-be to accept this as relevant. Like somebody said here, "publications" and Nature/Science papers shouldn't be nearly as influential (wrt career trajectory) as they were in 1986.

It seems to me that any given field of "science" isn't any harder than dropping into a new area of software engineering. There's a lot to learn, sure, but there's a lot to do as well and there are areas where an complete rank amateur can make significant contributions.

It's still true that every day I discover something I have no idea at all about. But it seems that this is fairly normal in science - people know a lot about a single specialized area and not much outside it.

[0]: https://en.wikipedia.org/wiki/Citizen_science

[1]: http://journals.plos.org/plosone/article?id=10.1371/journal....

edit: clarification

The only wrinkle to this is that citations in more popular venues are more likely to be seen and re-cited.

I have no words for my disgust at the lack of honesty that scooping would demonstrate.

I have never once found a paper of particular relevance to my research (geology/geophysics) on arXiv. I haven't looked very many times, but after striking out several times, why keep trying?

If there was a geoRxiv then I would probably browse it more regularly because the chances of me finding something relevant would be much higher.

For that reason, and another, I kind of disagree that fragmentation (or fractionalization) is undesirable. The second reason, which is not unrelated, is that–at least with peer-reviewed journals–the quality of the work in field- or subfield-specific venues is often far higher than in the sort of pan-scientific journals like Science or Nature. I think a lot of it has to do with the quality of the reviewing/editing, but a lot of it is that the papers have to be written for and justified to a wider audience that wants to be wowed and doesn't know the background well enough to evaluate the science for its own sake.

If I write a paper and send it to Tectonophysics, I know that the readership will understand what I'm doing and why, and I will write the paper accordingly. If I write the paper for Nature, then I have describe and justify the how and why to a wide range of people from my peers to journalists for phys.org and the NYT. Sometimes that's fine: If I find out that the Seattle fault is loaded and ready to pop, the press, policy makers and citizens need to know. But if I find out that the stress field on the Seattle fault is largely determined by the topography near the fault and that has some persistent influence on how an earthquake rupture propagates on the fault (but doesn't necessarily change the seismic hazard) then I don't need to go through the rigmarole of explaining and justifying any of that to anyone who isn't intrinsically interested, and maybe more importantly, I don't have to explain (i.e. gloss over) the subtleties, ambiguities and caveats of the work to an audience that lacks the relevant background. This simply allows me to write a more clear and more honest paper.

This brings up a tangent that is relevant to the broader topic of self-publication: You always need to write to a specific audience, and with a journal you know who that audience is. With a blog or a website, you don't necessarily. That may be fine but it can trip a lot of people up, and make the writing much worse.

So why does it seem like Greider's paper received none of that assistance? It's typeset in double-spaced Arial. Both double-spacing and Arial are immediate indications of unprofessional typesetting.

It's probably more likely due to a lack of demand. There's only about 4k articles on all of biorxiv in any case.

https://news.ycombinator.com/item?id=11293619

But on the flipside, the TeX document will often be ugly no matter how you are reading it, and the author can't easily apply tweaks for aesthetics or readability--many try, hence the TeX markup horrorshow.

One area I have never understood (apart from editor laziness) is letting the authors write the article title and abstract. So many great papers are overlooked because the authors wrote a boring or misleading title or abstract.