16 ms·

Handful of Biologists Went Rogue and Published Directly to Internet

492 points by srikar 11y ago

batbomb 11y ago
Why not just use arxiv.org?
- cossatot 11y ago
  Probably because bioRxiv.org, where these folks submitted their work, will be more widely read by biologists than arxiv.org.
  - batbomb 11y ago
    biorxiv reeks of NIH (No pun intended)
    - knowaveragejoe 11y ago
      And that means?
      - TallGuyShort 11y ago
        NIH means "not invented here", referring to the tendency of some engineers to build their own tools from scratch rather than learn or adapt an off-the-shelf tool. Can't comment on the context as I'm not experienced with these different *xives.
        tosseraccount 11y ago
        National Institutes of Health provides a lot of the funding for biology and medical research.
        jessriedel 11y ago
        Hence "(no pun intended)".
- Analemma_ 11y ago
  Does arXiv accept biology papers? I think they are exclusively math/physics/CS.
  - batbomb 11y 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 11y ago
    computational biology, sure
- jonchang 11y ago
  arxiv only accepts computational biology papers. Compare the subject areas of biorxiv http://biorxiv.org/ http://biorxiv.org/ and arxiv http://arxiv.org/archive/q-bio http://arxiv.org/archive/q-bio
  - batbomb 11y 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.
- jessriedel 11y 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.
  - cossatot 11y 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.
dfraser992 11y 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 11y 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 11y ago
  "HANDFUL of biologists going rouge" Rouge? They're positively crimson, darling.
  - stuxnet79 11y 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.
- michaelhoffman 11y ago
  3000 manuscripts posted to bioRxiv since 2013. More than a handful.
  - yitchelle 11y 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.
jackcosgrove 11y 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.
- agumonkey 11y 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.
  - jackcosgrove 11y ago
    I'm for faster and greater quantity, knowing that will reduce median quality and, I believe, increase average quality.
  - deleted 11y ago
    [deleted]
- d0mine 11y 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.
  - nl 11y 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.
dekhn 11y 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.
- TheBiv 11y 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.
  - dekhn 11y 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.
    - TheBiv 11y ago
      Ah, awesome!! Makes complete sense! Thank you very much for unpacking it and all the best in your career in Biology! I am in tech now, but studied Biology at Texas A&M for undergrad so hearing the words in your response reminded me of the good ol' days!
timrpeterson 11y 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.
- michaelhoffman 11y 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 11y 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).
- nycticorax 11y 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 11y 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.)
    - nycticorax 11y ago
      How do you know this? One reason they're called "preprints" is that they haven't (necessarily) been peer-reviewed...
danieltillett 11y 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.
- stuxnet79 11y 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.
  - danieltillett 11y 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 11y 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.
- dnautics 11y 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.
  - jessriedel 11y 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.
  - michaelhoffman 11y ago
    It's a social problem, not a technical one. The main new features bioRxiv has are comments and digital object identifiers (DOIs).
pnathan 11y 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.
- Mz 11y 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.
  - pnathan 11y ago
    There's a concern there, but that doesn't promote understanding and trust, unfortunately. Elitism is a unpleasantly common accusation...
- dnautics 11y 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-there-are-too-many-patents-in-america/259725/ 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 http://notch.tumblr.com/post/27751395263/on-patents
slizard 11y 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 11y 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 11y 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 11y 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.
- jhbadger 11y 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.
  - michaelhoffman 11y ago
    Times have already changed. Many biology journals and publishers allow pre-prints. https://news.ycombinator.com/item?id=11293619 https://news.ycombinator.com/item?id=11293619
- chockablock 11y 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 11y 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 11y 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 11y 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
  - michaelhoffman 11y 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.
- Mz 11y 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 11y 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.
devy 11y 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 11y 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.
tevlon 11y 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 !
- stuxnet79 11y ago
  https://www.readcube.com/ https://www.readcube.com/ http://www.jove.com/ http://www.jove.com/
  - Blahah 11y 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.
    - jessriedel 11y ago
      Isn't that the idea? My impression is that it's a format introduced to help publishers like Nature introduce frictions to copying their content.
    - stuxnet79 11y ago
      Wasn't very impressed by it either, but clearly there are a few startups in this area.
- jessriedel 11y 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.
  - tevlon 11y ago
kusmi 11y 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 11y 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 11y 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 11y 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 11y ago
What about ODF? The Open Document Foundation has been separate from the content creation applications for a couple of years now.
return0 11y 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 11y ago
  HTML?
  - return0 11y ago
    Of course, i mean an easy way for researchers to write them.
p4wnc6 11y ago
This isn't that innovative. Creationists have been doing this for years.
- hutzlibu 11y ago
  But for different reasons ... nobody (serious) wants them. If they were in high demand, they would paywall themself, for sure.
mirimir 11y 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.
the_watcher 11y 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.
ylem 11y 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 11y ago
What's stopping them from writing in HTML with some standard CSS?
- pc2g4d 11y ago
  MathML's lack of support?
octatoan 11y 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 http://stacks.math.columbia.edu
yeukhon 11y 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 .... to 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.
lolidaisuki 11y ago
In the field of cryptography many people publish their papers on IACR ePrint archive[1]. I was rather surprised that it hadn't been mentioned on this thread. It would be really cool to see more fields start doing this in a wide scale. [1]: http://eprint.iacr.org/ http://eprint.iacr.org/

492 points by srikar 11y ago

batbomb 11y ago

Why not just use arxiv.org?

cossatot 11y ago
Probably because bioRxiv.org, where these folks submitted their work, will be more widely read by biologists than arxiv.org.
- batbomb 11y ago
  biorxiv reeks of NIH (No pun intended)
  - knowaveragejoe 11y ago
    And that means?
    - TallGuyShort 11y ago
      NIH means "not invented here", referring to the tendency of some engineers to build their own tools from scratch rather than learn or adapt an off-the-shelf tool. Can't comment on the context as I'm not experienced with these different *xives.
      - tosseraccount 11y ago
        National Institutes of Health provides a lot of the funding for biology and medical research.
        jessriedel 11y ago
        Hence "(no pun intended)".
Analemma_ 11y ago
Does arXiv accept biology papers? I think they are exclusively math/physics/CS.
- batbomb 11y 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 11y ago
  computational biology, sure
jonchang 11y ago
arxiv only accepts computational biology papers. Compare the subject areas of biorxiv http://biorxiv.org/ http://biorxiv.org/ and arxiv http://arxiv.org/archive/q-bio http://arxiv.org/archive/q-bio
- batbomb 11y 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.
jessriedel 11y 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.
- cossatot 11y 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.

dfraser992 11y 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 11y 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 11y ago
"HANDFUL of biologists going rouge" Rouge? They're positively crimson, darling.
- stuxnet79 11y 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.
michaelhoffman 11y ago
3000 manuscripts posted to bioRxiv since 2013. More than a handful.
- yitchelle 11y 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.

jackcosgrove 11y 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.

agumonkey 11y 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.
- jackcosgrove 11y ago
  I'm for faster and greater quantity, knowing that will reduce median quality and, I believe, increase average quality.
- deleted 11y ago
  [deleted]
d0mine 11y 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.
- nl 11y 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.

dekhn 11y 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.

TheBiv 11y 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.
- dekhn 11y 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.
  - TheBiv 11y ago
    Ah, awesome!! Makes complete sense! Thank you very much for unpacking it and all the best in your career in Biology! I am in tech now, but studied Biology at Texas A&M for undergrad so hearing the words in your response reminded me of the good ol' days!

timrpeterson 11y 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.

michaelhoffman 11y 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 11y 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).

nycticorax 11y 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 11y 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.)
  - nycticorax 11y ago
    How do you know this? One reason they're called "preprints" is that they haven't (necessarily) been peer-reviewed...

danieltillett 11y 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.

stuxnet79 11y 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.
- danieltillett 11y 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 11y 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.

dnautics 11y 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.
- jessriedel 11y 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.
- michaelhoffman 11y ago
  It's a social problem, not a technical one. The main new features bioRxiv has are comments and digital object identifiers (DOIs).

pnathan 11y 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.

Mz 11y 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.
- pnathan 11y ago
  There's a concern there, but that doesn't promote understanding and trust, unfortunately. Elitism is a unpleasantly common accusation...
dnautics 11y 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-there-are-too-many-patents-in-america/259725/ 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 http://notch.tumblr.com/post/27751395263/on-patents

slizard 11y 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 11y 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 11y 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 11y 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.
jhbadger 11y 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.
- michaelhoffman 11y ago
  Times have already changed. Many biology journals and publishers allow pre-prints. https://news.ycombinator.com/item?id=11293619 https://news.ycombinator.com/item?id=11293619
chockablock 11y 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 11y 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 11y 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 11y 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
- michaelhoffman 11y 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.
Mz 11y 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 11y 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.

devy 11y 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 11y 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.

tevlon 11y 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 !

stuxnet79 11y ago
https://www.readcube.com/ https://www.readcube.com/ http://www.jove.com/ http://www.jove.com/
- Blahah 11y 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.
  - jessriedel 11y ago
    Isn't that the idea? My impression is that it's a format introduced to help publishers like Nature introduce frictions to copying their content.
  - stuxnet79 11y ago
    Wasn't very impressed by it either, but clearly there are a few startups in this area.
jessriedel 11y 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.
- tevlon 11y ago

kusmi 11y 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 11y 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 11y 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 11y 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 11y ago

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

return0 11y 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 11y ago
HTML?
- return0 11y ago
  Of course, i mean an easy way for researchers to write them.

p4wnc6 11y ago

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

hutzlibu 11y ago
But for different reasons ... nobody (serious) wants them. If they were in high demand, they would paywall themself, for sure.

mirimir 11y 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.

the_watcher 11y 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.

ylem 11y 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 11y ago

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

pc2g4d 11y ago
MathML's lack of support?

octatoan 11y 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 http://stacks.math.columbia.edu

yeukhon 11y 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 .... to 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.

lolidaisuki 11y ago

In the field of cryptography many people publish their papers on IACR ePrint archive[1]. I was rather surprised that it hadn't been mentioned on this thread. It would be really cool to see more fields start doing this in a wide scale. [1]: http://eprint.iacr.org/ http://eprint.iacr.org/