Handful of Biologists Went Rogue and Published Directly to Internet

http://www.nytimes.com/2016/03/16/science/asap-bio-biologists-published-to-the-internet.html

by srikar • 10 years ago

492 169 10 years ago

batbomb4• 10 years ago

Why not just use arxiv.org?

cossatot2• 10 years ago

Probably because bioRxiv.org, where these folks submitted their work, will be more widely read by biologists than arxiv.org.

batbomb4• 10 years ago

biorxiv reeks of NIH (No pun intended)

Analemma_• 10 years ago

Does arXiv accept biology papers? I think they are exclusively math/physics/CS.

batbomb4• 10 years ago

It used to be only particle physics, then only physics, but my impression is they expand to fit whatever. I'm sure they wouldn't mind expanding, but probably some of it is they don't have experts/money to help out with some of the organizational things they typically do for a field.

plg• 10 years ago

computational biology, sure

jonchang• 10 years ago

arxiv only accepts computational biology papers. Compare the subject areas of biorxiv http://biorxiv.org/ and arxiv http://arxiv.org/archive/q-bio

batbomb4• 10 years ago

That's not necessarily an immutable fact of arxiv.org though, otherwise there wouldn't even be computational biology on there.

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

jessriedel11• 10 years ago

I heard from Paul Ginsparg that bioArxiv's original raison d'etre was to give biologists more assistance in producing professionally typeset documents since far fewer of them know LaTeX then physicists. This was going to be funded by a submission fee of ~$50. That idea was apparently nixed, so that the difference with the arXiv are now mostly cosmetic (with the notable exception that bioArxiv has commentary).

Fractionalization is generally undesirable, but it's plausible that bioArxiv can make tweaks that accelerate adoption among biologists compared to arXiv.

cossatot2• 10 years ago

Discoverability is a big part of it as well, at least at the user end. I find out about new papers from email alerts of subject matter and tables of contents of the new issue of the journals I keep up with. (Obviously when I need to look into a particular issue I use google scholar).

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.

gaur2• 10 years ago

to give biologists more assistance in producing professionally typeset documents

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.

dfraser992• 10 years ago

Information wants to be free, BITCH... But seriously, given the increasing "media savviness" of subsequent generations (from Baby Boomers who grew up with TV, to Gen Y for whom the Internet is a given), the general ability across the spectrum of humanity to synthesize disparate information sources and filter them, compare and contrast, decide what is 'truthy' vs actually true... is increasing. Given all the information scientists have to process... What if machine learning was applied to this problem? The role of traditional gatekeepers is breaking down. I see this is the publishing industry - lots of content, most of the self-published books are awful, but books like "Wool" are able to rise to the top.

At least I hope humanity is getting more sophisticated. What is the median of the age of Trump supporters and the one sigma std dev? That would be an interesting statistic.

blakesterz• 10 years ago

I was working in academia back in 2002 and I remember talking about this crazy open access thing, and blogs, and wikis, with the folks on the tenure committee then. I remember thinking how fast this tenure/publishing thing will change in the next few years. And here it is 13 years later and there's a headline about a HANDFUL of biologists going rouge and daring to publish a PREPRINT!? I know there's been quite a bit of progress, but I'm still surprised at just how little things have changed.

dave2000• 10 years ago

"HANDFUL of biologists going rouge"

Rouge? They're positively crimson, darling.

stuxnet794• 10 years ago

Why is everybody down-voting this? The unintentional double entendre is pretty hilarious :)

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.

michaelhoffman7• 10 years ago

3000 manuscripts posted to bioRxiv since 2013. More than a handful.

yitchelle• 10 years ago

The HANDFUL is referring to the number of biologist, not the number of manuscripts.

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

jackcosgrove2• 10 years ago

I know the "wisdom of crowds" is passe, but the continued success (all things considered) of Wikipedia and open source software really makes me question the value of quality gatekeepers. I know I'm biased because I work in software and the costs of mediocrity in this industry are less than in others, but I think we could speed up innovation and discovery if we opened up science and made it more publicly accessible and collaborative. At some point the gatekeepers are just protecting their turf and hold back progress.

agumonkey2• 10 years ago

Truth lies in between. We're not for faster AND lower quality, mostly for less absurd resistance in the flow of knowledge. Granted that in some domains, a paper stuck in a waiting queue means death for people. Let's hope this kicks discussion and adaptation.

jackcosgrove2• 10 years ago

I'm for faster and greater quantity, knowing that will reduce median quality and, I believe, increase average quality.

d0mine2• 10 years ago

The crucial difference is that an amateur can provide a meaningful contribution to an open-source software project while the same is unlikely in (modern) science.

You need years of intense studying even to understand the current state of the art in a chosen scientific field.

Experiments require more money too.

nl2• 10 years ago

As someone who has fallen into a transition from software engineering to science I think I can say this is mostly wrong.

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.

cooper12• 10 years ago

I disagree. There's no reason that properly educated and briefed volunteers can't do a lot of the same work. Just look at citizen scientists. [0] There have been studies that have shown them to be just as effective as experts. [1]

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

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

dekhn13• 10 years ago

When I first found out about the web, early 90's, and it was "obvious" that the role of the web was to expand scientific publishing. I expected that everybody would publish latex files (raw source, not PDFs) in computationally accessible formats, with raw data in easily parseable, semantic forms.

That didn't really happen as expected. In my own chosen field (biology) it happened much more slowly than I hoped- physics (with arxiv) was far better. However, just getting PDFs on biorxiv is only a small part of the long game. I did not appreciate the huge importance placed on publishing in high-profile journals has on one's career trajectory and how large a role that would play in slowing the transition to free publication and post-publication review.

The long game is to enable the vast existing resources, and the new resources, to be parsed semantically by artificial intelligence algorithms. We've already passed the point where individuals can understand the full literature in their chosen field and so eventually we will need AI just to make progress.

TheBiv2• 10 years ago

Can you unpack what is meant by "to be parsed semantically by artificial intelligence algorithms"?

I understand the words, but in this context it has me a bit confused as to what problem you see AI solving.

dekhn13• 10 years ago

I mean, if somebody includes the name of a gene in their text, the goal is to annotate (then use the annotation) the gene in the text of the paper. It's often nontrivial to extract the meaning from the text without having a full experiment human. A typical case would be a reference to a gene by name, where the paper authors really meant the transcript or the protein product.

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.

eitally• 10 years ago

What he/she is saying is that the pace of research & publishing is such that it's impossible for researchers & academics to stay current the only fashioned way (reading, writing and attending conferences). It would be beneficial to have an intelligent bot that could be trained to browse for content of interest as a mechanism to augment an individual human's capacity to do this manually.

Houshalter• 10 years ago

Someday I'd love to feed scientific papers into AI algorithms. Watson does that, and google is starting to. But the file formats are such a mess, especially with equations and figures.

imglorp• 10 years ago

it was "obvious" that the role of the web was to expand scientific publishing

Yeah especially considering the roles CERN and NCSA played. Things might be different if they had published there immediately instead of staying on their journals.

logicrook• 10 years ago

I expected that everybody would publish latex files (raw source, not PDFs) in computationally accessible formats, with raw data in easily parseable, semantic forms.

Do you realize that many researchers would be ashamed if others saw their latex code?

A friend worked for a journal, he kept a folder of the worst that he had ever seen, and could rant for hours one some gems. Including some papers that were beautifully typeset, about elegant combinatorics/type theory, and were coded on the latex equivalent of a spaceship cobbled with recycled plastic bottles, scraps and duct tape.

Do you imagine going through thousand lines macro tex file that grew over the years, when Latex is one of the worst mess ever, with conflicting packages, absurd syntactic 'features', and legacy crippling flaws that make debugging an horrible task?

Please, continue to compile your .tex.

soperj• 10 years ago

It would be much easier to get better if you could view other's latex code.

mentat• 10 years ago

Or, if published, we could develop tools to normalize the data and improve the state of the art.

jhbadger2• 10 years ago

Also, (experimental) biologists tend not to use TeX/LaTeX. Typically they use Microsoft Word and a proprietary citation manager like Endnote. Typesetting is seen as something the journal deals with, not the author.

agumonkey2• 10 years ago

Shame in 'science', I find that unbelievably absurd.

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

dekhn13• 10 years ago

I wasn't defending LaTeX; I don't use it any more.

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).

beambot• 10 years ago

HA! Not to mention unflattering comments in LaTeX or BibTeX files. You thought source code had expletives... yeah.

chriswarbo• 10 years ago

Do you realize that many researchers would be ashamed if others saw their latex code?

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.

slang800• 10 years ago

Do you realize that many researchers would be ashamed if others saw their latex code?

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

haberman• 10 years ago

I did not appreciate the huge importance placed on publishing in high-profile journals has on one's career trajectory

Who is it primarily that is concerned with such things? (Curious.)

Is it fellow academics? Or university administrators? Or government agencies that control grants?

Whoever it is, these are the people we need to work on, it seems.

dekhn13• 10 years ago

If you go the principal investigator route (professor or scientist at national lab), then your boss and granting agencies are the ones that care about your pubs. It's critical to obtaining tenure (if you don't, you're kicked out of the university) and grants.

dekhn13• 10 years ago

I should also mention that my graduate program (top-tier in its field) unofficially required all students to publish in a top-tier journal to be allowed to graduate with a PhD. It was unofficial, but enforced by all the professor/advisors. If you didn't publish in a high enough journal, you'd end up in 7-8th year with a long thesis and have to leave with a master's degree.

Fomite2• 10 years ago

"Is it fellow academics? Or university administrators? Or government agencies that control grants?"

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.

transcranial• 10 years ago

Might be interested to check out https://science.ai

return04• 10 years ago

Latex is a terrible format that most biologists will never learn. HTML is the one uber-standard, it was actually created for that.

scentoni• 10 years ago

Obviously you've never had to typeset non-trivial mathematical expressions.

timrpeterson• 10 years ago

Nobel prize winning scientists can go rogue. Until these same rogues hire incoming professors based on their own biorxiv papers this is a small advance.

This whole thing needs to start at the level of the funding agency, namely NIH. Publishing in a good journal is a prerequisite to getting a grant. Try getting an R01 on a Biorxiv paper. Not gonna happen.

michaelhoffman7• 10 years ago

Most of the pre-prints posted on bioRxiv are submitted and later accepted to a traditional journal. The authors get the best of both worlds—early dissemination of their results and still get the stamp of approval from traditional journals that many other institutions value.

chrisamiller• 10 years ago

This article is a little bit breathless. In the academic circles that I run (genomics, computational biology, cancer), bioArxiv is not "going rogue". It's becoming pretty common, and will continue to increase in popularity as the FUD surrounding preprints and high-impact journals begins to dissipate. i.e. Nature won't accept my paper if it's on bioArxiv! (Yes they will).

nycticorax3• 10 years ago

It's certainly fear, uncertainty, and doubt, but usually when people use the term "FUD' they mean to imply that the fear, uncertainty, and doubt are unfounded. But in this case, all three are justified. The article mentions that Nature and Science are open to papers that have been pre-published. But I believe that many biology journals still have a blanket policy of not considering papers that have been pre-published. If that's the case, the working scientist is highly motivated to not pre-publish, since it shuts the door to later (peer-reviewed) publication. Unless, of course, the scientist is 100% sure they can get it published in Science or Nature. And in practice one is almost never sure of this.

I'm always curious to know how physics, as a field, got over this and related humps. Was it just easier to get everyone on board because it's a smaller community? Were the journals not as savvy to the fact that pre-prints are not really in their interest?

KKKKkkkk1• 10 years ago

The journals don't really care about preprints. Most of their revenue comes from university subscriptions, and so long as they can claim that their paywalled versions of the papers are the final and official ones and the preprints are merely unedited drafts, there is no threat to that revenue stream. (Placating the journals is part of the reason why they're called preprints rather than just papers. On Arxiv, authors will often update their preprint even after the paper is accepted in a journal.)

michaelhoffman7• 10 years ago

Almost all the publishers I would consider publishing in now allow pre-prints. A partial list: Nature journals (not just Nature), AAAS (not just Science), PNAS, Springer, Cambridge University Press, Cold Spring Harbor Press, many Oxford University Press journals. Cell Press does not forbid it although they reserve right to make a case-by-case decision.

danieltillett2• 10 years ago

If I was an evil journal editor I would use the metrics on biorivx to accept or reject papers. This would make it easy to predict the future impact factor and help you game the impact factor of your journal.

stuxnet794• 10 years ago

This is actually very clever. With this we will just be moving the goal posts but at least it will prove to scientists that any notoriety acquired in the pre-print stage can lead to later career success.

danieltillett2• 10 years ago

It is actually quite hard to predict which papers will become hits and which become misses. If I look back over my own papers there were a few I knew were going to (minor) hits, but quite a few of the papers I thought would be of interest were ignored while others I thought were pretty minor attracted a lot of interest.

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.

reporter• 10 years ago

I just uploaded three articles in the last two weeks to BioRxiv. The papers were previously just sitting in review. I have already received several emails thanking and informing me that my work is influencing the manuscripts they are writing - more citations. Overall the experience has been an extremely positive experience for me. I don't really see any downsides. So excited for the revolution.

dnautics2• 10 years ago

the amazing thing is that arXiv has always had a "quantitative bio" section, and I guess it took a sea change for this to be come a thing in bio.

jessriedel11• 10 years ago

At least originally, I believe bioArxiv's raison d'etre was to give biologists more assistance in producing professionally typeset documents (since far fewer of them know LaTeX then physicists). Not sure that's still true.

michaelhoffman7• 10 years ago

It's a social problem, not a technical one. The main new features bioRxiv has are comments and digital object identifiers (DOIs).

pnathan3• 10 years ago

I talk with a doctoral candidate in Chemistry regularly about the different paper cultures. It's amazing how different different disciplines are... her accounts of Chemistry is that (I synthesize) they are extremely locked down and research is very much aimed towards granting patents. Knowledge sharing to the broader chemistry community does not appear to be a key goal.

It was a huge shock to me, coming from CS: knowledge sharing has such a high value in our community.

Mz2• 10 years ago

I think another issue wrt biology in particular is that there is a great deal of fear about what laymen might do with the info. I have a genetic disorder and have spent 15 years getting myself healthier. Good faith efforts to share what I have learned along the way consistently result in shit shows and ugly personal attacks. I share a lot less these days.

On the one hand, I have sympathy for the very real concerns people have about bad (potentially harmful) health information going out. On the other hand, I think the primary reason it is dangerous to begin with is a lack of a culture of vigorous discussion. It is only dangerous if it cannot be thoroughly hashed out. Unfortunately, it seems there is no place where that can happen.

pnathan3• 10 years ago

There's a concern there, but that doesn't promote understanding and trust, unfortunately. Elitism is a unpleasantly common accusation...

dnautics2• 10 years ago

consider though that that culture is heavily influenced by the pharma industry (where many PhDs will wind up with productive jobs). Over and over again, the mantra (e.g. [0] [1]) is that "pharma is the one place where IP makes sense", even among IP skeptics.

[0] Richard Posner ("pharmaceuticals are the poster child for the patent system.... Most industries could get along fine without patent protection.") http://www.theatlantic.com/business/archive/2012/07/why-ther...

[1] Notch "I would personally prefer it to have those be government funded (like with CERN or NASA) and patent free as opposed to what’s happening with medicine, but I do understand why some people thin[k] patents are good in these areas." http://notch.tumblr.com/post/27751395263/on-patents

analog31• 10 years ago

A grad student is really exposed to being "scooped," i.e., to having their project taken up, finished, and published by somebody else. There are even professors who are notorious for this.

chockablock2• 10 years ago

Or more commonly, someone who was already working in the area will rush to publish their own work to avoid being scooped themselves.

pnathan3• 10 years ago

A grad student is really exposed to being "scooped," i.e., to having their project taken up, finished, and published by somebody else. There are even professors who are notorious for this.

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

slizard• 10 years ago

While this is nice in that it sets the example (and provides publicity to bioarxiv) it's not a couple of Nobel laureates that post one out of dozen(s) of papers/year published that will make the real difference.

The system is aged and inefficient (some would even argue it's rotten) and IMO comprehensive changes are needed. Like racial or gender discrimination can't be addressed without changing the social rules people live by, the current academic system that's rather elitist, non-inclusive, discriminatory, often more biased and less fair than many think needs to change substantially.

Such change will be aided by important people setting examples (and often going back to their old ways). However more substantial change is needed on multiple levels, most importantly: academic leaders and funding agencies (run by the former) need to stop looking at who's who and how many Nature/Science/insert-your-fancy-journal papers does the person have. For instance, the culture of applying for grant money with work that's half done to maximize one's chances needs to stop and so should the over-emphasis of impressive and positive results.

Additionally, publishers exploiting everyone need to die out and as long as these researchers "go rogue" with a single paper (rather than for instance committing to publish 100% preprints and >75% open access), not much will change.

nickbauman• 10 years ago

Uh ... isn't this what Tim Berners-Lee meant when he created the world wide web was that scientists do this exactly? It's like he handed a machine gun to us cavemen scientists 25 years ago and we've been collectively clubbing him in the head with it ever since.

zem• 10 years ago

can someone explain this bit:

If university libraries drop their costly journal subscriptions in favor of free preprints, journals may well withdraw permission to use them

withdraw permission to do what exactly, and enforced how?

damontal• 10 years ago

preprints are free but when they are added to an issue of a journal, that issue might not be free. so journal X agrees to free preprints (rough drafts) and then charges for the actual issue. if the library drops subscription to the journal, maybe the journal/society/publisher pulls the library's permission to use the preprints.

jhbadger2• 10 years ago

Withdraw permission to publish an article in their journal that has already been distributed as a preprint. Many journals in biology do that now -- they consider it publishing an article twice, which is a big no no ("self plagiarism"). This is beginning to change and hopefully preprints will be accepted in biology as they are in other fields.

michaelhoffman7• 10 years ago

Times have already changed. Many biology journals and publishers allow pre-prints.

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

chockablock2• 10 years ago

It's little appreciated, but journals are in competition with each other for good papers, too. Editors at top journals are out at conferences trying to find the next submissions and handing out business cards. Nature editors are pissed when a hot paper goes to Science instead (savvy PIs exploit this dynamic). In this kind of 'market', a publisher who unilaterally rejects preprinted papers is putting themselves out of the running for those papers.

hwang89• 10 years ago

What's the best way to support and reward these researchers? Something we can do in the next five minutes while they have the reader's attention.

adrianN• 10 years ago

Write a paper that cites them and get it published in Nature. Papers and citations in high-impact journals are what gets scientists a job, grants, and tenure.

shawn-furyan• 10 years ago

It's hard to tell whether this is a joke with a lot of truth, a genuine sideways takedown of the effort being reported in the article, a cynic's lament, or just a straightforward answer to the question of what would be the most helpful (if not most accessible) action for these authors. In any case I find it a tremendously compelling comment. It evokes a lot in a very small footprint.

edit: clarification

michaelhoffman7• 10 years ago

Papers in prestigious journals matter, but the location of a citation does not really matter. As long as the source is included in whatever you're using to count citations (usually Google Scholar, Scopus, or Web of Science), a citation in Nature is no more valuable than one in PLOS ONE.

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

Mz2• 10 years ago

Retweet? Post their papers to discussion forums, such as HN or others? If you read it and understand it, email them or tweet and give feedback? Simply comment somewhere to let them know you applaud this?

toufka• 10 years ago

This is good advice worth more than us here might expect. A bit of chatter about a paper is worth a whole lot. In a specialized field, getting 2 or 3 comments back after publication is 'a lot'. Doubling that to 5 or 6 interesting comments doubles the feedback and interest.

Yen• 10 years ago

The thing I'd want to see most of all? An experiment confirming or refuting the result of a posted paper, and the results of that experiment posted as a pre-print within ~3 months.

I.e., actually getting real science done fast, taking advantage of how the long journal process was bypassed.

noelsusman• 10 years ago

Nothing of real importance, but I'm sure they would appreciate a nice email.

devy• 10 years ago

Is it just me who think that this NYT title reflects the negative view of releasing research results in preprints by using the phrase "went rogue"?

Speeding up the knowledge sharing and to solve more problems more quickly is a good thing IMMO. As the same article pointed out, Physicists has been releasing research results in preprints since 1990s.

valleyer• 10 years ago

I agree it's a terrible title, but I think the "went rogue" reflects more the NYT's attempt to conjure up a BuzzFeedy title than anything else.

tevlon2• 10 years ago

Does somebody know why we are still using pdfs for papers ? I know a lot of people that are trying to parse PDF files and it is an awful process.

If somebody is looking for an idea for a new venture, this is a problem, yet to be solved !

stuxnet794• 10 years ago

https://www.readcube.com/

http://www.jove.com/

Blahah• 10 years ago

readcube is a spectacular somersault in the wrong direction. It is so much worse than a PDF - it actively fights me when I try to extract information.

jessriedel11• 10 years ago

We are using PDFs because they have universal adoption and, importantly, they reliably produce the same document everywhere. Most alternatives you might think of will give variable results on different machines.

There definitely needs to be something that makes it easier to parse and otherwise interact with a PDF. But, for network-effect reasons, it's probably easier to introduce a parseable overlay for PDFs than to replace the format wholesale.

tevlon2• 10 years ago

i disagree. While i agree, that PDFs are there and they will stay for a long time. The problem can be easily solved by journals. They make you use of their own LaTeX templates. It would be very easy to just force the submitters to add the LaTeX together with the pdf. Sometimes the easy solution is too obvious, i guess

jandrese• 10 years ago

There is a tug of war taking place here. TeX is nice because the documents are formatted for whatever your reading situation happens to be. PDF is formatted for exactly one situation, the A4 sheet you targeted.

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.

kusmi• 10 years ago

So it was put online without peer review? Papers can always be submitted by the author to PMC using NIHMS if the journal doesn't do it. However the paper must go through a journal because they arbitrate the peer review.

cs702• 10 years ago

When a mainstream publication like the New York Times has a positive article about Nobel-prize-winning scientists bypassing the choke-hold of established journals by directly publishing preprints online, you know it's the beginning of the end for the old, bureaucratic way of publishing scientific research.

Awesome.

excalibur• 10 years ago

But when the same article is exclusively citing Twitter as a source, it's far closer to the end of the end of their publication's integrity.

larakerns• 10 years ago

This needs to happen in more scientific fields, like a field-specific consensus publishing platform. Everyone agrees to publish their research to benefit everyone else.

cmurf• 10 years ago

What about ODF? The Open Document Foundation has been separate from the content creation applications for a couple of years now.

return04• 10 years ago

That is great (or, to be honest, it's way past time for this, this shouldn't be news). But we need to go beyond that. The PDF format is a relic. We need a platform where scientists can directly edit their articles. Figures should be replaced by interactive visualizations where possible. This would solve the problem of data availability and allow other researchers to have direct access to the data shown in a plot.

CroCroCro• 10 years ago

HTML?

return04• 10 years ago

Of course, i mean an easy way for researchers to write them.

p4wnc63• 10 years ago

This isn't that innovative. Creationists have been doing this for years.

hutzlibu3• 10 years ago

But for different reasons ... nobody (serious) wants them. If they were in high demand, they would paywall themself, for sure.

the_watcher• 10 years ago

The concerns over "peer review" seem ridiculous to me. The peers who would review it would still have access, and it would open it up to exponentially more people.

mirimir• 10 years ago

Even cooler, I think, are "working papers". In my arguably limited experience, this seems to be popular mostly in economics. As I understand it, authors are soliciting comment from peers, and thinking becomes long-term collaborative. It's a conversation, not a paper. Maybe scientific research can become even more open and collaborative, using the GitHub model or whatever.

ylem• 10 years ago

I'm a physicist and we routinely publish on the arxiv. I hope the chemists are next (a number of chemistry journals ban preprints)!!!

z3t4• 10 years ago

What's stopping them from writing in HTML with some standard CSS?

pc2g4d• 10 years ago

MathML's lack of support?

octatoan• 10 years ago

There's a massive project going on in math using GitHub to write an open-source algebraic geometry textbook.

http://stacks.math.columbia.edu

yeukhon• 10 years ago

Total off topic, but here is an anecdote I heard from a professor when he was explaining about review process. One reviewer argued to change

    Figure 5. The statistics ....

    Figure (5) The statistics ....

because the reviewer liked () format better, although (IMO) the new format is so ugly.

Another reviewer saw the comment and had a really nasty debate. The paper was published with the original format nonetheless.

Handful of Biologists Went Rogue and Published Directly to Internet

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