Why does science have to be published in articles in the first place? Isn't it more fruitful to have a peer-reviewed, citable, machine-readable database of scientific findings? We are no longer in the 1700s and there is too much redundant information in published papers anyway.
Articles are good for getting into a field you are not familiar with, especially when that field is obscure and lacks good textbooks.
The real problem is that we are continuing to support an industry that contributes nothing at all to the publication of scientific papers. We simply do not need publishers of any kind, regardless of open access, because we have a substantially better way to distribute articles: the Internet. Sure, we need archives of articles, but that is what university libraries are for. Sure, bandwidth is needed for distribution, but that is where P2P systems like BitTorrent come in (imagine a monthly torrent of peer reviewed articles for each field). The rest is already being organized without the assistance of publishers.
I was just thinking on the same lines. I work in the humanities and even if the article form remains, there is the possibility to radically rethink the journal model. The journal model is too closely tied to assumptions about print and distribution channels that no longer hold much value.
Science is still a very creative (i.e. non systematic) process. To create new "scientific findings" you need new insights. These insights typically come from publications/conferences/discussions with other researchers rather than big machine readable datasets.
Most research articles I read can be boiled down to a paragraph of substance, with the rest of the space filled with introductions and things we already know. Agree about conferences etc. but I don't see how articles create discussion, since most journals do not even have comment sections, and even those that do, rarely have any comments. Articles are an arcane notion used to gauge researcher's output, until something new and more efficient comes along.
Obviously this depends on the quality of an article, but there is more to the "extra bits" (i.e. that which is not plain data) than mere fluff. If you are very familiar with a topic (i.e have a PhD in precisely that area), the extra bits are not of much interest, though the methodology might be.
If you have some passing familiarity, then the introduction and discussion can help you a lot in understanding the implications proposed for the data. Most biomedical experimentation takes place in the context of considerable amount of uncertainty, e.g. relevance of the model used for human disease, etc, and more, as described in the article you linked to, so it does help many readers to have some kind of context.
The lack of discussion in biomedical articles is likely due to a fear of reprisals.
Depends a bit on the area. You can machine-code results if the field is extremely static in its conceptual and epistemic framework, so it's just a matter of slotting new things in place. Some "industrial-style" science does work like that. But large areas don't.
Most of the articles I read have the majority of the actual research going on in the text, not in whatever the "results" might nominally be. For example, a programming language paper might prove a few theorems about type-soundness, but it's rare that a new type-soundness theorem is really want you want out of the paper; that's just supporting apparatus. What's more interesting is the design discussion, motivation for why this feature was introduced and how it relates to previous features, explanation of how it was implemented, discussion of variants and future work, etc.
The "Open Data" movement is in fact underway. But adaption will be even slower there. When you look at the mess of formats and proprietary tools trying to lock you in in science, it becomes clear why that is. And there's a tendency in science to come up with ridiculously complex incompatible data models. First because Of the academic virtue of understanding it and second because nobody wants to fit a study to a data model but rather the other way around.
this sort of open data the poster one above suggested will always be problematic because the temptation will be to do meta-studies where you cross-compare datasets from experiments that 'look alike' while stripping context. It plays to a 'science is objective' fetishism, when in reality context is always subjective and context matters, deeply.
Presenting data as separate units in a publication serves the purpose of requiring actual cogitation and consideration before using the data. In a sense, all data are proprietary, and attempts to de-proprietarization of it is a mistaken endeavor. This is not to say that we shouldn't try to reproduce results, but we should be careful to acknowledge that the context is always different.
The function of research journals is to disseminate recent findings. In biology and medicine, it takes a while for a piece of published research to become accepted, as such recent findings are usually only of interest to other researchers. When something becomes accepted it enters text books and the like. Between the original papers and text books lie scholarly reviews and online databases.
Some examples: For individual genes, the established canon can usually be found online at places like Online Mendelian Inheritance in Man (OMIM) [0]. Furthermore, a lot of genetic data is now made available through what might be called "aggregators", such as Ensembl [1], which provides both a free web interface to explore genetic variation and also allows downloading of primary data. Similar resources exist for other types of data.
So, to answer your question, there are indeed a number of bioinformaticians who are trying to do exactly what you propose, some sources have become "aggregators of aggregators", for example Bioinformatic Harvester [3].
Science needs a short format that is frozen in a certain point (not very far at the life of the text). If you want to change something, great, but those two requirements are very important.
People would also benefit from a large changing body that reflects out current knowledge. But that was impossible until very recently, so every initiative on that line is new. Anyway, that second body can not replace the short frozen format.
If those descriptions makes you think about version control software, well, there are already a lot of comments talking about it.
As that lack of enthusiasm demonstrates, the fundamental force driving the speed of the move towards full open access is what researchers — and research funders — want. Eisen says that although PLoS has become a success story — publishing 26,000 papers last year — it didn't catalyse the industry to change in the way that he had hoped. “I didn't expect publishers to give up their profits, but my frustration lies primarily with leaders of the science community for not recognizing that open access is a perfectly viable way to do publishing,” he says.
Among the reasons that a scientist may have against embracing open access publishing is perhaps being Editor in Chief or Associate Editor of a prestigious journal. That is just a line in a scholar's CV, but sometimes it counts. I would happily do without that line, but I'm sure many, young and old, would not.
Building prestige in an open-access publication is slow, and the transition might be slow by design.
Agreed. Yet my field (Operations Research) has seen four or five new journals born in the past 10 years, all of relatively high level. Most often they were born as an initiative of one or more scholars in the field, who convinced a publisher that the journal would receive submissions.
So there is room for new challengers. However, now these scholars treat this journal as their precious pet project, would like everyone to submit articles to it and are (understandably) unwilling to embark in another, open-access initiative.
It really depends on who the editors/founders are; e.g. the JMLR was automatically prestigious when founded by leaders of the ML community, forcing the previous crown bearer to become open access itself.
It can happen quickly given the right circumstances. In machine learning, the editors of Machine Learning resigned en masse and set up the open-access Journal of Machine Learning Research, which became the top ML journal quite soon after being launched: http://jmlr.org/
The old ML journal is still prestigious as well, but there's now an open-access alternative that's at least as good and probably somewhat better.
The main obstacle to dethroning commercial journals, as I see it, is the reputation they've built up over the decades. They're simply prestigious by default because of lock-in.
There are now ways of running an online reputational community, e.g. StackExchange, but they rely on a willingness to do things a different way. The more conservative members of the academic community aren't likely to shift their approaches, especially when they don't already participate in forums or academic blogging. They don't directly feel the pain of expensive subscriptions, either. So the academic publishers - the old order - can continue to rely on their deeply entrenched position as the arbiters of research quality - even though this quality is created by the unpaid academics who sit on the editorial committees.
(In fact, the publishers even sell this as a value that their journals provide - reputation - when it isn't an intrinsic value, but one that accrued to them while there was no feasible alternative. That value has now lost its underlying basis, but it persists because of inertia, and they're merely extracting rent from their ownership of the journals' brands, now.)
The solution, to my mind, has to be multifold:
1) Spread the dangerous idea that science should be accessible to all and free from paywalls, such that in all polite circles it should be a matter of course to believe so;
2) Build a very simple-to-use, cross-journal meta-database and community - preferably open-source - that collects papers from all open journals and aggregates upvotes, citations and prestige/rankings, and help it gain wide, career-influencing acceptance like Github enjoys now (maybe the arXiv could be evolved and adapted to fill this role?);
3) Get buy-in from senior decisionmakers and thought leaders in various academic fields by offering them a chance to shape the system.
This won't happen without the joint efforts of leading academics (like Sir Timothy Gowers), skilled technologists, UX designers, and government funders. Most of us on HN know how we could build a technical solution that fills these needs - we might even volunteer our time toward it - but we need marketers and advocates who can sell this system to the people who matter (who currently don't see the need to upset the current system). The reputational advantage enjoyed by commercial publishers won't be overcome simply with engineering.
(If anyone knows of open-source projects to this end, or about the arXiv's plans, please share them.)
probably more subversive to drop arXiv''s existing content into an instance of GitHub and conform the user interface to the existing arXiv U/I. Or, actually, just keep the colors and stick with Github's UI.
Github UI? Before forcing everything to look like github, please, please, remember the term "user experience research". Github UI has major issues and they keep improving. If every open website has a github UI, that's gon to be like seeing every website running default bootstrap interface. No.
Changes will be slow, but imho, definite. The oldies might have inertia but I think that people under the age of thirty (having grown up with arXiv and the like) much prefer open-access publishing. Cue for Max Planck's quote:
_"A scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die and a new generation grows up that is familiar with it."_
That said, we need to take initiative and step up to be the change we want to see.
Good post. The way I see it, journals have traditionally provided three core features: publishing, quality control (via peer review), and reputation (via exclusivity). The publishing aspect is basically solved -- just post your article to the arXiv.
The obstacle is the other two -- quality control and (in particular) reputation. What we need, and what you've more or less described, is an independent peer-review/evaluation platform where contributors can build & show-off reputation.
The good news is there is a lot of activity around this now. My startup Publons.com is one of many ventures trying things in this area: PubPeer, Peerage of Science, The Winnower, Libreapp.org, peerevaluation.org...
some conflicts of interest are viewed as obvious. If I publish a journal article with my affiliation being Genentech, I don't have to state that my work is owned by Genentech. If I am employed at UCSF and list my affiliation there, but hold significant equity in a spin-off that is commercializing the published technology, then that's when I declare a conflict.
Everyone knows Nature is not an open access journal. Putting a sentence that states that at the end of a news article written by their staff is pointless.
> some conflicts of interest are viewed as obvious. If I publish a journal article with my affiliation being Genentech, I don't have to state that my work is owned by Genentech.
That's simply NOT true...Nature's guidelines on declaring financial interests (http://www.nature.com/nature/journal/v412/n6849/full/412751a...) say that these include "Employment", defined as "Recent (that is, while engaged in the research project), present or anticipated employment by any organization that may gain or lose financially through publication of the paper."
Nature is covering this for one reason only: they stand to gain.
28 comments
[ 2.8 ms ] story [ 62.3 ms ] threadThe real problem is that we are continuing to support an industry that contributes nothing at all to the publication of scientific papers. We simply do not need publishers of any kind, regardless of open access, because we have a substantially better way to distribute articles: the Internet. Sure, we need archives of articles, but that is what university libraries are for. Sure, bandwidth is needed for distribution, but that is where P2P systems like BitTorrent come in (imagine a monthly torrent of peer reviewed articles for each field). The rest is already being organized without the assistance of publishers.
Ps. http://www.cell.com/neuron/retrieve/pii/S089662731300648X
If you have some passing familiarity, then the introduction and discussion can help you a lot in understanding the implications proposed for the data. Most biomedical experimentation takes place in the context of considerable amount of uncertainty, e.g. relevance of the model used for human disease, etc, and more, as described in the article you linked to, so it does help many readers to have some kind of context.
The lack of discussion in biomedical articles is likely due to a fear of reprisals.
Most of the articles I read have the majority of the actual research going on in the text, not in whatever the "results" might nominally be. For example, a programming language paper might prove a few theorems about type-soundness, but it's rare that a new type-soundness theorem is really want you want out of the paper; that's just supporting apparatus. What's more interesting is the design discussion, motivation for why this feature was introduced and how it relates to previous features, explanation of how it was implemented, discussion of variants and future work, etc.
Presenting data as separate units in a publication serves the purpose of requiring actual cogitation and consideration before using the data. In a sense, all data are proprietary, and attempts to de-proprietarization of it is a mistaken endeavor. This is not to say that we shouldn't try to reproduce results, but we should be careful to acknowledge that the context is always different.
Some examples: For individual genes, the established canon can usually be found online at places like Online Mendelian Inheritance in Man (OMIM) [0]. Furthermore, a lot of genetic data is now made available through what might be called "aggregators", such as Ensembl [1], which provides both a free web interface to explore genetic variation and also allows downloading of primary data. Similar resources exist for other types of data.
So, to answer your question, there are indeed a number of bioinformaticians who are trying to do exactly what you propose, some sources have become "aggregators of aggregators", for example Bioinformatic Harvester [3].
[0] www.ncbi.nlm.nih.gov/omim
[1] www.ensembl.org/index.html
[3] en.wikipedia.org/wiki/Bioinformatic_Harvester
People would also benefit from a large changing body that reflects out current knowledge. But that was impossible until very recently, so every initiative on that line is new. Anyway, that second body can not replace the short frozen format.
If those descriptions makes you think about version control software, well, there are already a lot of comments talking about it.
Among the reasons that a scientist may have against embracing open access publishing is perhaps being Editor in Chief or Associate Editor of a prestigious journal. That is just a line in a scholar's CV, but sometimes it counts. I would happily do without that line, but I'm sure many, young and old, would not.
Building prestige in an open-access publication is slow, and the transition might be slow by design.
So there is room for new challengers. However, now these scholars treat this journal as their precious pet project, would like everyone to submit articles to it and are (understandably) unwilling to embark in another, open-access initiative.
[edit: clarity]
The old ML journal is still prestigious as well, but there's now an open-access alternative that's at least as good and probably somewhat better.
There are now ways of running an online reputational community, e.g. StackExchange, but they rely on a willingness to do things a different way. The more conservative members of the academic community aren't likely to shift their approaches, especially when they don't already participate in forums or academic blogging. They don't directly feel the pain of expensive subscriptions, either. So the academic publishers - the old order - can continue to rely on their deeply entrenched position as the arbiters of research quality - even though this quality is created by the unpaid academics who sit on the editorial committees.
(In fact, the publishers even sell this as a value that their journals provide - reputation - when it isn't an intrinsic value, but one that accrued to them while there was no feasible alternative. That value has now lost its underlying basis, but it persists because of inertia, and they're merely extracting rent from their ownership of the journals' brands, now.)
The solution, to my mind, has to be multifold:
1) Spread the dangerous idea that science should be accessible to all and free from paywalls, such that in all polite circles it should be a matter of course to believe so;
2) Build a very simple-to-use, cross-journal meta-database and community - preferably open-source - that collects papers from all open journals and aggregates upvotes, citations and prestige/rankings, and help it gain wide, career-influencing acceptance like Github enjoys now (maybe the arXiv could be evolved and adapted to fill this role?);
3) Get buy-in from senior decisionmakers and thought leaders in various academic fields by offering them a chance to shape the system.
This won't happen without the joint efforts of leading academics (like Sir Timothy Gowers), skilled technologists, UX designers, and government funders. Most of us on HN know how we could build a technical solution that fills these needs - we might even volunteer our time toward it - but we need marketers and advocates who can sell this system to the people who matter (who currently don't see the need to upset the current system). The reputational advantage enjoyed by commercial publishers won't be overcome simply with engineering.
(If anyone knows of open-source projects to this end, or about the arXiv's plans, please share them.)
_"A scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die and a new generation grows up that is familiar with it."_
That said, we need to take initiative and step up to be the change we want to see.
TagTeam, being developed at Harvard by Peter Suber and co is one effort in that direction. https://osc.hul.harvard.edu/liblab/proj/enhanced-social-tagg... and https://github.com/berkmancenter/tagteam
I'm curious to see whether Mozilla Science Lab is taking any initiative in this regard; so far they've focused on other aspects.
The obstacle is the other two -- quality control and (in particular) reputation. What we need, and what you've more or less described, is an independent peer-review/evaluation platform where contributors can build & show-off reputation.
The good news is there is a lot of activity around this now. My startup Publons.com is one of many ventures trying things in this area: PubPeer, Peerage of Science, The Winnower, Libreapp.org, peerevaluation.org...
Everyone knows Nature is not an open access journal. Putting a sentence that states that at the end of a news article written by their staff is pointless.
That's simply NOT true...Nature's guidelines on declaring financial interests (http://www.nature.com/nature/journal/v412/n6849/full/412751a...) say that these include "Employment", defined as "Recent (that is, while engaged in the research project), present or anticipated employment by any organization that may gain or lose financially through publication of the paper."
Nature is covering this for one reason only: they stand to gain.