6 ms·

We need a GitHub of Science

246 points by marciovm123 16y ago

emilepetrone 16y ago
I tried to start a science network a few years ago, knowble.net, and I know this problem well. The main roadblock we faced was the "publish or perish" mentality. Luckily this mindset seems to be shifting & the idea of a 'GitHub of Science' is very powerful. Much more than a Science LinkedIn, which is what Knowble was. The main unanswered questions for this idea are 1) Funding & 2) Maintenance. Knowble was a for-profit venture, but should have been a non-profit organization. So where can you/someone get the funding to build & maintain the site? If you need a python hacker to help out - my email is emile.petrone (at) gmail.com
- nolite 16y ago
  Thought of starting a science network myself... mind if I email you? Want to know more about what your roadblocks
mariuskempe 16y ago
I agree (http://www.quora.com/What-online-tools-do-scientists-wish-existed-to-facilitate-their-work/answer/Marius-Kempe http://www.quora.com/What-online-tools-do-scientists-wish-ex...). Why don't we just start using GitHub itself to do this and go from there? The pain points will suggest ways that a real science-focused github could improve on GitHub itself.
- Ruudjah 16y ago
  The problem is currently GUI. There are no good GUI's to work with git. Windows and Mac OS X have some GUI tools scratching the surface of what's possible with git, but none come close in opening up the full possibilities of git. Linux has a few very alpha, specific (like showing branches) GUI tools. If we want non-programmers to use git, we need GUI's to instantly visualize the state, commands and other possibilities. No non-programmer is going to learn git using a CLI.
  - mcrider 16y ago
    Perhaps if it caught on enough. There are many people that had to learn LaTeX who were not programmers, which is IMHO not a trivial feat. Not that I'm disagreeing with you--But making git point-and-clickable doesn't strike me as being very simple.
  - alextp 16y ago
    I agree. I think that github is such a good tool to interact with git repos that if they made a version that can work locally (the main difference is explicitly dealing with the index and the current tree) I'd use it to manage git projects in a heartbeat.
Groxx 16y ago
>- GitHub's success is not just about openness, but also a prestige economy that rewards valuable content producers with credit and attention I don't think I can agree with that. GitHub's success, IMO, seems to be based almost entirely on its openness. It has turned contributing to open source software into a drop-dead easy task, which would never be found nor contributed to if they weren't open. And they keep making it easier. I've fixed a number of things with machines which don't have Git installed, simply because they have their on-site editor. Imagine if GitHub were behind a paywall. Do you think it would still be the success it is today? And, I may be weird, but I very rarely look at the names associated with commit histories. The code should speak for itself. The rest of it sounds about right, scientific publishing as a whole is massively backwards compared to GitHub, if you're looking at it from an "Open" perspective. But I think that a lot of that is that the researchers tend to be insular compared to the implementers (businesses guarding their IP aside - they're not really GitHub's target audience anyway). GitHub isn't used exclusively for comp-sci researchers to post their findings with code, it's more for people doing things with ideas others have contributed to. There are experiments on GitHub, absolutely. I have a few myself. But the main thing that GitHub has done is to make final products easy to find, modify, and contribute to. I have significant doubts that it would fit a research workflow smoothly, without becoming something else entirely.
- Ruudjah 16y ago
  John Resig started a project to generate resumes from the contributions at github. Regularly I see posts at HN/reddit/etc sites of users saying: "I build this and that, check it out!". Personally, a motivation (of a lot more motivations) is indeed prestige. Now I can show off my nice work. Sure, openness started it all: Linus shared his VCS, which in turn sparked Github, which in turn initiated thousands of developers to share their code. But openness really isn't the sole driver for people to share their code any more; more incentives, of which prestige is an important one, drive the popularity of github.
  - Groxx 16y ago
    >"I build this and that, check it out!" But people do that with other open source sites as well. Does GitHub provide this feature better than SourceForge or others? You still need to go to the user's page, they don't advertise it anywhere else. Do people go to GitHub to see information about person X, or project Y? And for the posts on social sites, are they more often about the creator or what they created?
deleted 16y ago
[deleted]
chanri 16y ago
Half of Github's success is because Git was so successful and easy to use. People started using Git first, and then Github came along and made things more social. There is no fundamental equivalent to Git in basic science or engineering research. Until you have something that is relatively popular and makes collaboration relatively easy to use, it will be difficult to have a "GitHub of Science".
zeynel1 16y ago
I believe it represents a demonstrably superior way of distributing validated knowledge than academic publishing. This is where he goes wrong. As he demonstrates up to that point, the purpose of publishing in the academia is not to "distribute knowledge" but to gain academic points. And academic citation is not the same as copying code. Academic physicists routinely cite papers without reading them. The reason is that academic physicists cite like lawyers; to establish and assert precedence. So I would add "legal" citation to "prestige" and "popular" type citations. http://arxiv.org/ftp/arxiv/papers/1012/1012.4871.pdf http://arxiv.org/ftp/arxiv/papers/1012/1012.4871.pdf
melling 16y ago
Perhaps not at the academic level, at least not initially, but drawing more people into science by making it easier to ask questions and get answers couldn't hurt. http://area51.stackexchange.com/categories/7/science http://area51.stackexchange.com/categories/7/science Someday there might be 1,000,000 well-defined science/math questions, along with great answers.
- ignifero 16y ago
  There are science sections in quora as well, but people tend to post too many general/popsci/naive questions.
VladRussian 16y ago
arXiv.org?
- zeynel1 16y ago
  Yes, why not? One reason may be prestige. As he explains in the paragraph "publish or perish" he would hire an applicant who published 1 article in Nature or Science as opposed to an applicant who has 100 papers in the arxiv but nothing published in the "prestigious" journals. It is interesting that he does not claim to read the articles and evaluate their merits on content; academia is all about prestige.
countersignaler 16y ago
http://science.io http://science.io was featured on HN recently. Not github, but at least a place to discuss and sift research.
wicknicks 16y ago
The biggest problem with CS academicians have been in their misinterpretation of computers. Its a very different field from traditional sciences like Physics, Chemistry etc.. In traditional sciences, we study the world, understand it and express those ideas formally. With computers, its upto one's imagination what they can do with it. We just get so lost in the depths of formalism, that we forget that hacking and exploration are what can break boundaries and enable people to make computers do what they could not. Funnily, academia harbours the most brilliant minds of CS, and barely produces usable software. Its people who identify problems, and provide software/ideas who actually get things moving. Github/Blogosphere etc allow such solutions to emerge more efficiently by allowing a lot of people to look at such solutions. In academia, a publication is taken as a end point for problem solving. There are no incentives to build real software or real systems. If computer science wants to make a difference, it must move away from its publish or perish culture.
- xyzzyz 16y ago
  Computer Science is not about building real software or real systems, as opposed to Software Engineering. Your comment strikes me as missing the whole point of CS. Maybe it is so because of misleading English name -- as someone said, Computer Science is not about computers, just like Astronomy is not about telescopes -- but what kind of person would call Astronomy a Telescope Science?
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thisrod 16y ago
The programs on Github were written by amateurs. Professionals can do better - compare Python, PHP and Gnuplot to Mozilla, Scheme, Haskell, Plan 9 and Mathematica. But evidently people can keep their day jobs and still write good programs. Science is different. The amateurs are called cranks, and a small community of professionals does the good stuff. (There are exceptions, but few.) The basic issue is who will pay their living expenses, and buy the million dollar machines that they work on. These days, almost all research money is spent by governments. They spend most of it rewarding people for publishing in prestigious journals. Scientists will keep packaging their research that way until someone starts buying it in a different package.
- stewbrew 16y ago
  You're mixing language definitions and implementations. You're comparing software that was created by big companies with software created by small teams or single developers. I think good commenters can do better. BTW you're implying governments are funding over-priced journals people outside of prestigious institutions cannot afford. Even though that's true it's not the way it should be.
- SoftwareMaven 16y ago
  Most of the interesting projects on Github were written by professionals and are far better quality than the average "professional" day-job application because it is a developer's passion and not constrained by business development. I do not believe open source solves all problems, but you dismiss the incredible value and quality of so much that I find it difficult to take the rest of the comment seriously. It sounds more like "People with credentials (whether scientists or professional programmers) are the only people who can produce quality work. I have credentials. I'm part of the elite who can do quality work."
figital 16y ago
We also need a GitHub of government / legislation.
mechanical_fish 16y ago
I'm a former biophysics postdoc myself. Now I work for an open-source software company. This post strikes me as charmingly naive. You have to love this guy. And yet any essay that discusses the incentive structure of science but doesn't use the word "grant" until the last sentence is beating around the bush. Follow the money, my friends. The publications are a side issue. To the extent that your count of top-tier publications matters when trying to get an academic job, it's because it's correlated with your ability to bring in money. (Money comes from peer review too, and what your peers want to read about is also what they want to fund.) What the hiring committees really want is grants. Grant money pays for labs and salaries. It pays for grad students and postdocs. And grant money literally buys prestige: Big projects come from big grants, and big grants require strong track records and a bunch of preliminary data, which in turn comes from smaller grants, or from the shared equipment that your neighbor bought with her grants. The fact that there aren't that many top-tier peer-reviewed journals is a side effect of the limited number of top scientists, and the number of scientists is limited by available resources, not by lack of knowledge or connections or education. I could literally pick up the phone and reach a dozen Ivy-educated postdocs who would be full-time scientists if they could afford it. Why can you find so much great software on Github? There are lots of reasons, but a fundamental one is: Moore's Law. Computer hardware has become so dirt cheap that you can be a programmer in your spare time. You can literally be a twelve-year-old kid with a $200 cast-off computer and yet do top-notch software work. If computers cost millions of dollars each, like they did in 1963, we wouldn't have Github. We'd have the drawer of a desk on the ninth floor of Tech Square. (After all, in the old days half the AI researchers in the world lived within a few miles of that drawer, and the others were just a phone call away.) That's how most advanced science works today: There's no need for more publishing infrastructure for scientific technique, because the available methods of getting the word out -- top journals, second-tier journals, email, the phone, bumping into people in the hallway at conferences -- scale well enough to meet the limited demand. Because just having the recipe for your very own scanning multiphoton microscope doesn't do you much good: You need a $150,000 laser, and a $200,000 microscope, and tens of thousands of dollars in lenses and filters and dyes, and a couple of trained optics experts to maintain the thing, and that's before you even have something to photograph. I wish there were a magical way to turn everyone's suburban basement into a cancer research lab, the way Github has turned everyone's couch into a potential CS research lab, but there's no magic bullet. A few technologies, like DNA sequencing, are sufficiently generic, useful, and automatable to be amenable to Moore's-Law-based solutions, so we probably will soon be able to (e.g.) drop leaves into the hopper of a $1000 box and get a readout of the tree's genetics. But something like cancer research is never going to be cheap. To study cancer you must first have a creature that has cancer. Mice are as cheap as those get, and mice are not cheap, especially if you know what the word mycoplasma means.
guygurari 16y ago
I'm a Ph.D. student working in theoretical high-energy physics. In this field we don't rely on peer-reviewed journals. Instead, when a researchers wants to "publish" a paper she uploads it to the arXiv, and the paper appears on the site within a day or two. The arXiv is open in the sense that almost anyone can publish there [1]. Researchers in the field catch up on new research by scanning the arXiv daily for interesting papers. No one I know reads peer-reviewed journals. I know that many papers are also published in journals, but I believe this is a formality that has more to do with obtaining grants and such than with actual communication within the community. As far as I know there's no reason to publish in a journal before you become a professor. The result is similar to the GitHub situation in many ways. Because there are no barriers to publishing, everyone makes up their own mind about which papers are interesting. If your work is relevant, others will build on it and cite you. They will discuss it in their group meeting, and so on. A scientist's reputation is then directly related to the quality of their work, as judged by the community, with no artificial barriers. This means that a self-respecting scientist would not publish a sub-par paper even though it's technicality possible to do so, because that would hurt her reputation. So it seems to me that the situation in high-energy physics is close to ideal, with respect to ease of publishing and the social aspect of reputation. Having said that, there are certainly aspects of GitHub that I would love to see adopted. For instance, when several researchers are writing a paper, generally no version control system is employed. Instead, at any point in time the draft is "locked" by one of the collaborators, and only that person can change it. Beyond the obvious inefficiency of this method, note that it is also difficult to track what changes were made in each lock cycle. I use diff for this purpose, but in my experience many scientists in the field aren't aware of such tools. So something that could really help is a simple way to collaborate on papers, just a basic source control system. Also, it must be possible to work on the paper in private within the collaboration, and only publish the end result. [1] The few barriers that exist are in place to keep out the crackpots, who reduce the signal-to-noise ratio and in that sense resemble spammers.
- chancho 16y ago
  "In this field we don't rely on peer-reviewed journals...papers are also published in journals, but I believe this is a formality that has more to do with obtaining grants and such than with actual communication within the community." So peer reviewed journals are only important for grants, but your community doesn't rely on peer reviewed journals. Do you not rely on grants? Who funds your work? Do you all work for free, in your spare time?
erikpukinskis 16y ago
Good ideas, but I disagree that you need a Bill Gates to make it happen. The way this will happen is a grad student hacker who is avoiding working on his thesis will start coding it, and then create a kickstarter asking for support to spend the summer working on it. If she's a credible engineer, she'll get the support easily, and every subsequent kickstarter grant will also be fulfilled and it'll get built. If you build it (right) they will come.
- apl 16y ago
  You may not want to believe it, but this is not an engineering challenge.
mbreese 16y ago
One issue I see is what branch of science are we talking about? Physics largely seems to have this figured out via arXiv.org, but funding for molecular / biology / medical research is heavily dependent upon publication record. I'm not sure about Computer Science. But my point is when one says "Science" needs X or Y for "Science", no one is speaking the same language. These comments are enough evidence of this. Some have already mentioned arXiv.org, and others Science.io which seems to be specifically targeted at CS. When you add medical research, the needs for these branches is vastly different.
sunir 16y ago
My goal for http://bibdex.com http://bibdex.com is to be this. I based the software on a wiki (original name was Bibwiki). The idea was to build lit reviews on topics that you could reuse and share with colleagues privately or publicly with the world. I realized after starting that scientific communication is more complex, or at least it tries to be for various reasons. I could use help learning what people want from such a system. I am keen on feedback or insights to drive my development. Please, if you are interested, you can reach me at sunir at bibdex com.
diamondhead 16y ago
I think we need a github of any kind of information.
ignifero 16y ago
Do you think something like http://pubcentral.net http://pubcentral.net could be useful in that direction?
gsiener 16y ago
I just met the brains behind Opani (http://opani.com http://opani.com) last night and they are a huge step in this direction.
- etree 15y ago
  Opani is actually a huge step in the right direction. I think Marcio's post is fantastic. I would in fact add an additional idea to it. In addition to the open prestige inherent in GitHub, there is also the fact that one's work is vetted by a community. It becomes very difficult if not impossible to publish crap and claim that it is quality. In science this is not the case. The peer review system is supposed to protect us against that. However, my understanding is that a surprising percentage of research in top ten journals can't be reproduced either because key details about implementation are missing or because it is actually not reproducible. A GitHub for science could also meaningfully move the ball forward in making science reproducible as it should be easy to wrap ones scripts in a specification of an "environment" that can be readily setup, deployed, and run. A lot of work would be required to develop corollaries for non-computational scientific domains, but it would be a hugely valuable effort as discussed in the general reproducible research community (http://reproducibleresearch.net/ http://reproducibleresearch.net/).
juretriglav 16y ago
Yes we do. Not just a replica of it with different content though, but a separate product tailored to the needs (and wishes) of science, sharing only some of the core ideas of GitHub. Sometimes I wonder if I should welcome the surfacing of ideas that have a large overlap with my own, or be anxious knowing that my lead has possibly been somewhat reduced.
serichsen 15y ago
The most pressing problem of our modern information society is the abundance of crap. The service peer-review provides is the filtering of crap, so that not everyone has to do that by himself. This makes science possible, as not everyone can be a master of all trades. Publication without review is called "journalism". As a side note, I believe that Elsevier has acquired an extreme market dominance in the scientific publishing sector and is abusing it in alarming ways.

246 points by marciovm123 16y ago

I tried to start a science network a few years ago, knowble.net, and I know this problem well. The main roadblock we faced was the "publish or perish" mentality. Luckily this mindset seems to be shifting & the idea of a 'GitHub of Science' is very powerful. Much more than a Science LinkedIn, which is what Knowble was. The main unanswered questions for this idea are 1) Funding & 2) Maintenance. Knowble was a for-profit venture, but should have been a non-profit organization. So where can you/someone get the funding to build & maintain the site? If you need a python hacker to help out - my email is emile.petrone (at) gmail.com

nolite 16y ago
Thought of starting a science network myself... mind if I email you? Want to know more about what your roadblocks

mariuskempe 16y ago

I agree (http://www.quora.com/What-online-tools-do-scientists-wish-existed-to-facilitate-their-work/answer/Marius-Kempe http://www.quora.com/What-online-tools-do-scientists-wish-ex...). Why don't we just start using GitHub itself to do this and go from there? The pain points will suggest ways that a real science-focused github could improve on GitHub itself.

Ruudjah 16y ago
The problem is currently GUI. There are no good GUI's to work with git. Windows and Mac OS X have some GUI tools scratching the surface of what's possible with git, but none come close in opening up the full possibilities of git. Linux has a few very alpha, specific (like showing branches) GUI tools. If we want non-programmers to use git, we need GUI's to instantly visualize the state, commands and other possibilities. No non-programmer is going to learn git using a CLI.
- mcrider 16y ago
  Perhaps if it caught on enough. There are many people that had to learn LaTeX who were not programmers, which is IMHO not a trivial feat. Not that I'm disagreeing with you--But making git point-and-clickable doesn't strike me as being very simple.
- alextp 16y ago
  I agree. I think that github is such a good tool to interact with git repos that if they made a version that can work locally (the main difference is explicitly dealing with the index and the current tree) I'd use it to manage git projects in a heartbeat.

Groxx 16y ago

>- GitHub's success is not just about openness, but also a prestige economy that rewards valuable content producers with credit and attention I don't think I can agree with that. GitHub's success, IMO, seems to be based almost entirely on its openness. It has turned contributing to open source software into a drop-dead easy task, which would never be found nor contributed to if they weren't open. And they keep making it easier. I've fixed a number of things with machines which don't have Git installed, simply because they have their on-site editor. Imagine if GitHub were behind a paywall. Do you think it would still be the success it is today? And, I may be weird, but I very rarely look at the names associated with commit histories. The code should speak for itself. The rest of it sounds about right, scientific publishing as a whole is massively backwards compared to GitHub, if you're looking at it from an "Open" perspective. But I think that a lot of that is that the researchers tend to be insular compared to the implementers (businesses guarding their IP aside - they're not really GitHub's target audience anyway). GitHub isn't used exclusively for comp-sci researchers to post their findings with code, it's more for people doing things with ideas others have contributed to. There are experiments on GitHub, absolutely. I have a few myself. But the main thing that GitHub has done is to make final products easy to find, modify, and contribute to. I have significant doubts that it would fit a research workflow smoothly, without becoming something else entirely.

Ruudjah 16y ago
John Resig started a project to generate resumes from the contributions at github. Regularly I see posts at HN/reddit/etc sites of users saying: "I build this and that, check it out!". Personally, a motivation (of a lot more motivations) is indeed prestige. Now I can show off my nice work. Sure, openness started it all: Linus shared his VCS, which in turn sparked Github, which in turn initiated thousands of developers to share their code. But openness really isn't the sole driver for people to share their code any more; more incentives, of which prestige is an important one, drive the popularity of github.
- Groxx 16y ago
  >"I build this and that, check it out!" But people do that with other open source sites as well. Does GitHub provide this feature better than SourceForge or others? You still need to go to the user's page, they don't advertise it anywhere else. Do people go to GitHub to see information about person X, or project Y? And for the posts on social sites, are they more often about the creator or what they created?

deleted 16y ago

[deleted]

chanri 16y ago

Half of Github's success is because Git was so successful and easy to use. People started using Git first, and then Github came along and made things more social. There is no fundamental equivalent to Git in basic science or engineering research. Until you have something that is relatively popular and makes collaboration relatively easy to use, it will be difficult to have a "GitHub of Science".

zeynel1 16y ago

I believe it represents a demonstrably superior way of distributing validated knowledge than academic publishing. This is where he goes wrong. As he demonstrates up to that point, the purpose of publishing in the academia is not to "distribute knowledge" but to gain academic points. And academic citation is not the same as copying code. Academic physicists routinely cite papers without reading them. The reason is that academic physicists cite like lawyers; to establish and assert precedence. So I would add "legal" citation to "prestige" and "popular" type citations. http://arxiv.org/ftp/arxiv/papers/1012/1012.4871.pdf http://arxiv.org/ftp/arxiv/papers/1012/1012.4871.pdf

melling 16y ago

Perhaps not at the academic level, at least not initially, but drawing more people into science by making it easier to ask questions and get answers couldn't hurt. http://area51.stackexchange.com/categories/7/science http://area51.stackexchange.com/categories/7/science Someday there might be 1,000,000 well-defined science/math questions, along with great answers.

ignifero 16y ago
There are science sections in quora as well, but people tend to post too many general/popsci/naive questions.

VladRussian 16y ago

arXiv.org?

zeynel1 16y ago
Yes, why not? One reason may be prestige. As he explains in the paragraph "publish or perish" he would hire an applicant who published 1 article in Nature or Science as opposed to an applicant who has 100 papers in the arxiv but nothing published in the "prestigious" journals. It is interesting that he does not claim to read the articles and evaluate their merits on content; academia is all about prestige.

countersignaler 16y ago

http://science.io http://science.io was featured on HN recently. Not github, but at least a place to discuss and sift research.

wicknicks 16y ago

The biggest problem with CS academicians have been in their misinterpretation of computers. Its a very different field from traditional sciences like Physics, Chemistry etc.. In traditional sciences, we study the world, understand it and express those ideas formally. With computers, its upto one's imagination what they can do with it. We just get so lost in the depths of formalism, that we forget that hacking and exploration are what can break boundaries and enable people to make computers do what they could not. Funnily, academia harbours the most brilliant minds of CS, and barely produces usable software. Its people who identify problems, and provide software/ideas who actually get things moving. Github/Blogosphere etc allow such solutions to emerge more efficiently by allowing a lot of people to look at such solutions. In academia, a publication is taken as a end point for problem solving. There are no incentives to build real software or real systems. If computer science wants to make a difference, it must move away from its publish or perish culture.

xyzzyz 16y ago
Computer Science is not about building real software or real systems, as opposed to Software Engineering. Your comment strikes me as missing the whole point of CS. Maybe it is so because of misleading English name -- as someone said, Computer Science is not about computers, just like Astronomy is not about telescopes -- but what kind of person would call Astronomy a Telescope Science?

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thisrod 16y ago

The programs on Github were written by amateurs. Professionals can do better - compare Python, PHP and Gnuplot to Mozilla, Scheme, Haskell, Plan 9 and Mathematica. But evidently people can keep their day jobs and still write good programs. Science is different. The amateurs are called cranks, and a small community of professionals does the good stuff. (There are exceptions, but few.) The basic issue is who will pay their living expenses, and buy the million dollar machines that they work on. These days, almost all research money is spent by governments. They spend most of it rewarding people for publishing in prestigious journals. Scientists will keep packaging their research that way until someone starts buying it in a different package.

stewbrew 16y ago
You're mixing language definitions and implementations. You're comparing software that was created by big companies with software created by small teams or single developers. I think good commenters can do better. BTW you're implying governments are funding over-priced journals people outside of prestigious institutions cannot afford. Even though that's true it's not the way it should be.
SoftwareMaven 16y ago
Most of the interesting projects on Github were written by professionals and are far better quality than the average "professional" day-job application because it is a developer's passion and not constrained by business development. I do not believe open source solves all problems, but you dismiss the incredible value and quality of so much that I find it difficult to take the rest of the comment seriously. It sounds more like "People with credentials (whether scientists or professional programmers) are the only people who can produce quality work. I have credentials. I'm part of the elite who can do quality work."

figital 16y ago

We also need a GitHub of government / legislation.

mechanical_fish 16y ago

I'm a former biophysics postdoc myself. Now I work for an open-source software company. This post strikes me as charmingly naive. You have to love this guy. And yet any essay that discusses the incentive structure of science but doesn't use the word "grant" until the last sentence is beating around the bush. Follow the money, my friends. The publications are a side issue. To the extent that your count of top-tier publications matters when trying to get an academic job, it's because it's correlated with your ability to bring in money. (Money comes from peer review too, and what your peers want to read about is also what they want to fund.) What the hiring committees really want is grants. Grant money pays for labs and salaries. It pays for grad students and postdocs. And grant money literally buys prestige: Big projects come from big grants, and big grants require strong track records and a bunch of preliminary data, which in turn comes from smaller grants, or from the shared equipment that your neighbor bought with her grants. The fact that there aren't that many top-tier peer-reviewed journals is a side effect of the limited number of top scientists, and the number of scientists is limited by available resources, not by lack of knowledge or connections or education. I could literally pick up the phone and reach a dozen Ivy-educated postdocs who would be full-time scientists if they could afford it. Why can you find so much great software on Github? There are lots of reasons, but a fundamental one is: Moore's Law. Computer hardware has become so dirt cheap that you can be a programmer in your spare time. You can literally be a twelve-year-old kid with a $200 cast-off computer and yet do top-notch software work. If computers cost millions of dollars each, like they did in 1963, we wouldn't have Github. We'd have the drawer of a desk on the ninth floor of Tech Square. (After all, in the old days half the AI researchers in the world lived within a few miles of that drawer, and the others were just a phone call away.) That's how most advanced science works today: There's no need for more publishing infrastructure for scientific technique, because the available methods of getting the word out -- top journals, second-tier journals, email, the phone, bumping into people in the hallway at conferences -- scale well enough to meet the limited demand. Because just having the recipe for your very own scanning multiphoton microscope doesn't do you much good: You need a $150,000 laser, and a $200,000 microscope, and tens of thousands of dollars in lenses and filters and dyes, and a couple of trained optics experts to maintain the thing, and that's before you even have something to photograph. I wish there were a magical way to turn everyone's suburban basement into a cancer research lab, the way Github has turned everyone's couch into a potential CS research lab, but there's no magic bullet. A few technologies, like DNA sequencing, are sufficiently generic, useful, and automatable to be amenable to Moore's-Law-based solutions, so we probably will soon be able to (e.g.) drop leaves into the hopper of a $1000 box and get a readout of the tree's genetics. But something like cancer research is never going to be cheap. To study cancer you must first have a creature that has cancer. Mice are as cheap as those get, and mice are not cheap, especially if you know what the word mycoplasma means.

guygurari 16y ago

I'm a Ph.D. student working in theoretical high-energy physics. In this field we don't rely on peer-reviewed journals. Instead, when a researchers wants to "publish" a paper she uploads it to the arXiv, and the paper appears on the site within a day or two. The arXiv is open in the sense that almost anyone can publish there [1]. Researchers in the field catch up on new research by scanning the arXiv daily for interesting papers. No one I know reads peer-reviewed journals. I know that many papers are also published in journals, but I believe this is a formality that has more to do with obtaining grants and such than with actual communication within the community. As far as I know there's no reason to publish in a journal before you become a professor. The result is similar to the GitHub situation in many ways. Because there are no barriers to publishing, everyone makes up their own mind about which papers are interesting. If your work is relevant, others will build on it and cite you. They will discuss it in their group meeting, and so on. A scientist's reputation is then directly related to the quality of their work, as judged by the community, with no artificial barriers. This means that a self-respecting scientist would not publish a sub-par paper even though it's technicality possible to do so, because that would hurt her reputation. So it seems to me that the situation in high-energy physics is close to ideal, with respect to ease of publishing and the social aspect of reputation. Having said that, there are certainly aspects of GitHub that I would love to see adopted. For instance, when several researchers are writing a paper, generally no version control system is employed. Instead, at any point in time the draft is "locked" by one of the collaborators, and only that person can change it. Beyond the obvious inefficiency of this method, note that it is also difficult to track what changes were made in each lock cycle. I use diff for this purpose, but in my experience many scientists in the field aren't aware of such tools. So something that could really help is a simple way to collaborate on papers, just a basic source control system. Also, it must be possible to work on the paper in private within the collaboration, and only publish the end result. [1] The few barriers that exist are in place to keep out the crackpots, who reduce the signal-to-noise ratio and in that sense resemble spammers.

chancho 16y ago
"In this field we don't rely on peer-reviewed journals...papers are also published in journals, but I believe this is a formality that has more to do with obtaining grants and such than with actual communication within the community." So peer reviewed journals are only important for grants, but your community doesn't rely on peer reviewed journals. Do you not rely on grants? Who funds your work? Do you all work for free, in your spare time?

erikpukinskis 16y ago

Good ideas, but I disagree that you need a Bill Gates to make it happen. The way this will happen is a grad student hacker who is avoiding working on his thesis will start coding it, and then create a kickstarter asking for support to spend the summer working on it. If she's a credible engineer, she'll get the support easily, and every subsequent kickstarter grant will also be fulfilled and it'll get built. If you build it (right) they will come.

apl 16y ago
You may not want to believe it, but this is not an engineering challenge.

mbreese 16y ago

One issue I see is what branch of science are we talking about? Physics largely seems to have this figured out via arXiv.org, but funding for molecular / biology / medical research is heavily dependent upon publication record. I'm not sure about Computer Science. But my point is when one says "Science" needs X or Y for "Science", no one is speaking the same language. These comments are enough evidence of this. Some have already mentioned arXiv.org, and others Science.io which seems to be specifically targeted at CS. When you add medical research, the needs for these branches is vastly different.

sunir 16y ago

My goal for http://bibdex.com http://bibdex.com is to be this. I based the software on a wiki (original name was Bibwiki). The idea was to build lit reviews on topics that you could reuse and share with colleagues privately or publicly with the world. I realized after starting that scientific communication is more complex, or at least it tries to be for various reasons. I could use help learning what people want from such a system. I am keen on feedback or insights to drive my development. Please, if you are interested, you can reach me at sunir at bibdex com.

diamondhead 16y ago

I think we need a github of any kind of information.

ignifero 16y ago

Do you think something like http://pubcentral.net http://pubcentral.net could be useful in that direction?

gsiener 16y ago

I just met the brains behind Opani (http://opani.com http://opani.com) last night and they are a huge step in this direction.

etree 15y ago
Opani is actually a huge step in the right direction. I think Marcio's post is fantastic. I would in fact add an additional idea to it. In addition to the open prestige inherent in GitHub, there is also the fact that one's work is vetted by a community. It becomes very difficult if not impossible to publish crap and claim that it is quality. In science this is not the case. The peer review system is supposed to protect us against that. However, my understanding is that a surprising percentage of research in top ten journals can't be reproduced either because key details about implementation are missing or because it is actually not reproducible. A GitHub for science could also meaningfully move the ball forward in making science reproducible as it should be easy to wrap ones scripts in a specification of an "environment" that can be readily setup, deployed, and run. A lot of work would be required to develop corollaries for non-computational scientific domains, but it would be a hugely valuable effort as discussed in the general reproducible research community (http://reproducibleresearch.net/ http://reproducibleresearch.net/).

juretriglav 16y ago

Yes we do. Not just a replica of it with different content though, but a separate product tailored to the needs (and wishes) of science, sharing only some of the core ideas of GitHub. Sometimes I wonder if I should welcome the surfacing of ideas that have a large overlap with my own, or be anxious knowing that my lead has possibly been somewhat reduced.

serichsen 15y ago

The most pressing problem of our modern information society is the abundance of crap. The service peer-review provides is the filtering of crap, so that not everyone has to do that by himself. This makes science possible, as not everyone can be a master of all trades. Publication without review is called "journalism". As a side note, I believe that Elsevier has acquired an extreme market dominance in the scientific publishing sector and is abusing it in alarming ways.