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We need a GitHub of Science

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51–60 of 68 posts

Re: We need a GitHub of Science

#51

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 exp…

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?

Re: We need a GitHub of Science

#52
post #42

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…

I don't know much about expensive lab equipment, but if you follow the DIY world, or the open source world , or even indian/chinese innovators, you see people building physical stuff at fractions of the price of commercial stuff. A few example to illustrate my point: 1. Open farm tech - tractor and brick compressor and 1/3 to 1/10 of the commercial prices. they plan a whole set of manufacturing equipment at those red…

Also, as rapid prototyping picks up steam, this should also (eventually) help with sourcing equipment more cheaply. Lab on a chip (aka microfluidic tech) is a great example of Moore's law making it into labs.

Re: We need a GitHub of Science

#53

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…

Shoulders of giants and all that.

Re: We need a GitHub of Science

#54

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…

I used to think this as well. But if you think about things which are ridiculously expensive -- like cars or airplanes or Google's datacenters -- all of them got their start in someone's garage. After spending some time with the Open Wetware/DIYBio guys, I realized that no one (other than the DIYBio guys) has really spent time reducing the costs of the fundamental toolkit of the molecular biologist. Now they are star…

I agree that the DIYbio folks et al are incredibly exciting. But saying that those projects have to do with "building a Github of science" is putting the cart before the horse. To extend my metaphor for a moment, it's as if the engineers of 1963 had decided to popularize open source software by inventing and promoting Github, instead of inventing the personal computer and Ethernet first.

(As an aside, there are fascinating historical examples of people who did invent the web before inventing the personal computer, like this guy:

http://en.wikipedia.org/wiki/Paul_Otlet

Of course, he ended up as many of these slightly-too-early visionaries did: His work lost all its funding and he was kind of sad.)

Build the gel box and then worry about the social network. Or better yet, don't worry about the social network at all: These gel box users will network themselves, no problem. It would be a challenge to stop them from finding each other online.

Re: We need a GitHub of Science

#55
post #42

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…

I don't know much about expensive lab equipment, but if you follow the DIY world, or the open source world , or even indian/chinese innovators, you see people building physical stuff at fractions of the price of commercial stuff. A few example to illustrate my point: 1. Open farm tech - tractor and brick compressor and 1/3 to 1/10 of the commercial prices. they plan a whole set of manufacturing equipment at those red…

I now see a terrible flaw in my essay of last night: I took the cheap and easy rhetorical route of emphasizing the costs of the fanciest equipment. Whereas the thing that kills you in science budgeting is actually the mundane stuff that you need in vast quantities.

Perhaps I should have talked about something boring, like absolutely clean, absolutely sterile containers. There is nothing sexy about containers and pipettes, and they are individually cheap. But they add up. The most reliable technique is to just buy quantities of disposable ones. You can try to save money by using recyclable containers instead, by washing dishes a lot, but washing dishes by hand is expensive even if you don't do it very patiently and carefully. And you need to be really careful, because if you move your cell culture from dish to dish to dish ten times, and even one of those dishes is contaminated, guess what? Your experiment might now be contaminated. And for every Alexander Fleming (a lucky guy whose contaminated experiment turned out to be a Nobel-Prize-winning medical breakthrough) there are a thousand experiments that have to be discarded because the data isn't reliable.

But even that argument is misleading, because the most expensive ingredient in science is not even a material good. It's time. Science is about patience and consistency. Doing an experiment once is not science. Doing it one thousand times and getting absolutely consistent results -- that is science. The work of being a scientist is about carefully building and debugging a reliable sequence of steps ("grow, filter, sort, lyse, plate, stain, image"): A sequence that can be repeated over and over to obtain thousands of data points that are extremely self-consistent.

The reason why professional scientists use such expensive equipment is that the equipment is actually cheap compared to the cost of spending two years taking data that turn out to be full of errors because your tools weren't reliable. Too much random error and you won't see your data amid the noise; too much systematic error and you might eventually have to throw out 100% of your work and start over. Trust me: If you want to experience soul-crushing misery [1], work sixty hours a week taking data for two years, then set the data on fire because it's unsalvageable. I have seen this happen many times. It has happened to me. It happens all the time in science, but you can't afford to have it happen too often.

So, yeah, you can take pictures of earth from space for $200, but can you take the same picture one thousand times, under consistent lighting and from consistent altitude and position? Yeah, you can build an electron microscope in your basement, but will it keep working every day for five years while you take your data? How much maintenance will it require? How much time will you waste waiting for it to pump down every time you change samples, or tweaking the knobs for hours every time to get a usable picture? Will it spread thin layers of carbon on your electronics, or go through a six-month phase where it can't focus well enough to see your samples?

---

[1] Fortunately, the misery is temporary. If it isn't, you're just not cut out to be an experimental scientist. Science requires reserves of forward-looking optimism! So what if yesterday was hell? It was a learning experience that will make tomorrow better! ;)

Re: We need a GitHub of Science

#56

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 bu…

You may not want to believe it, but this is not an engineering challenge.

Re: We need a GitHub of Science

#58

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…

That is the kind of thinking that is holding life sciences back: lack of openness, obsession with centuries old journals etc. Starting in comp. Neuroscience, and coming from a physics background I was shocked by how little info neuroscientists share with each other. I cant even access most of the papers I need from home. There is no repository of data or even computational models (well there is modeldb) . There have been several attempts to make the life sciences more open on the web, but it's not working because there is no culture of openness. For cryin out loud, most of the journals don't even have an online comments section. Big, ambitious projects are missing (think LHC-scale), and the pioneers in these are private institutions like the Allen brain institute. Maybe it's not possible to make a github for science, but it's certainly possible for a high profile university to require its staff to publish in open access journals only. That would be a start

Re: We need a GitHub of Science

#59

Earlier quoted context omitted.

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…

Shoulders of giants and all that.

If I have seen further than others, it is only by standing on the shoulders of grants.

Re: We need a GitHub of Science

#60
post #14

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 Someday there might be 1,000,000 well-defined science/math questions, along with great answers.

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