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We need a GitHub of Science

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21–30 of 68 posts

Re: We need a GitHub of Science

#21
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.

Re: We need a GitHub of Science

#23
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.

Re: We need a GitHub of Science

#24
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.

Re: We need a GitHub of Science

#25

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 pub…

Do you need exclusive access to your very own scanning multiphoton microscope? Seems like laboratory virtualization would go hand in hand with open source science.

Re: We need a GitHub of Science

#26
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.

Re: We need a GitHub of Science

#27

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 pub…

Do you need exclusive access to your very own scanning multiphoton microscope? Seems like laboratory virtualization would go hand in hand with open source science.

You may not need exclusive access to one, which is why a lot of institutions setup "centers" for this type of work (center for visualization, for example). Then multiple people can share the equipment and cost - if you can recruit people with a similar research focus. So, you may not need one exclusively, but you do need one locally available.

Re: We need a GitHub of Science

#28

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 pub…

Thanks for the love =).

I agree about funding being an ulterior motive for a hiring committee to look at publication history. In my defense, I brought it about 2/3 of the way through with:

"We need trusted ways to quantify just how useful that API and associated code are to the scientific community, which can be listed on a scientist's profile and utilized by committees making hiring and funding decisions."

Science is constrained by resources, like everything else, but that doesn't mean scientists shouldn't try to optimize what can be done with the resources available.

Also, you imply that good science requires your own experimental data - and bearing associated costs - but that's only true when experimentalists aren't incentivized to share their data.

Re: We need a GitHub of Science

#29
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.

Re: We need a GitHub of Science

#30

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 pub…

Do you need exclusive access to your very own scanning multiphoton microscope? Seems like laboratory virtualization would go hand in hand with open source science.

You can share them. Many labs do. Indeed, most of these things are probably shared in one way or another.

And you're correct: The trick to encouraging open source science is not to focus on the social networking tech -- that will be ready when you need it -- but to first attack the problem of doing quality lab work on the cheap. That's where the bottleneck is.

The biggest problem with shared facilities is the tragedy of the commons. In engineering -- or machining or woodworking or cooking, for that matter -- you quickly learn the importance of having your own tools. It only takes seconds to ruin a good tool. It only takes seconds to contaminate your cell culture, or your neighbor's cell culture, or an entire room full of your department's laboratory mice.

And mailing your samples off to a distant "virtual" lab is fine if you're studying disposable samples, or inorganic samples, or samples that have been permanently fixed and preserved on a glass slide. But living cells ship poorly even when you're allowed to ship them at all, and animals ship even more poorly than that. So often you've got to live next door to the equipment you're trying to share, and that's still expensive.

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