What Open Source Shares With Science 115
An anonymous reader sends in a philosophical piece at ZDNet about the similarities between open source development and the scientific method. Here's an excerpt:
"The speed of progress is greatly enhanced by virtue of the fact the practitioners of Science publish not only results, but methodology, and techniques. In programmatic terms, this is equivalent to both the binary and the source code. This not only helps 'bootstrap' others into the field, to learn from the examples set, but makes it possible for others to verify or refute the results (or techniques) under investigation. In an almost guided-Darwinian evolutionary fashion, this makes the scientific process a powerful tool for the highlighting, analysis and possible culling of ideas and concepts; less useful ideas and hypothesEs die, and likely contenders come sharply into focus. Newton made his famous comment about 'standing on the shoulders of giants,' in part, to indicate that his contributions to human knowledge could not have been achieved solely. He needed the 'firmament' beneath him hypothesized, tested and confirmed by generations of scientists, philosophers and thinkers before him, over centuries."
Sadly, education is lagging behind once again. (Score:3, Insightful)
Why hasn't the scientific community produced open textbooks, free to re-print, photocopy and distribute (a la Creative Commons license)
Why is it hard for pioneering ideas like that of the state of California trying to open their school textbooks to be implemented?
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Re:Sadly, education is lagging behind once again. (Score:5, Interesting)
Computer Science and Computer Engineering classes have yet to implement significant group collaboration.
Or they go too far in the other direction. I distinctly remember one database class in my MS curriculum which had thirty people working together on a one-semester project, and it was a nightmare. At the time I was working as a DBA lead with a team of five people including myself, which was a pretty good number for our project, so I had a pretty decent idea of how things should work. Trying to get thirty CS students, only a couple of whom had any real industry experience, to work together on a single project in that length of time was just Not Going To Happen. I tried very hard to get the professor to break the class into a few groups and have each group work independently on the problem, but he wouldn't budge; he had a Grand Vision of what all these people working together would accomplish. The mythical man-month in action.
The result was pretty much what you'd expect. Three-quarters of the class slacked off, a quarter did all they could, and instead of a working project at the end of the semester we had a half-finished mess. A few of us strongly suspected hat what he really wanted was a polished product he could distribute under his own name, so this chaos may in fact have been a silver lining ... But the experience was of no real value to anyone in the end.
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Well, yeah, there is that. The students might have taken that lesson away (those of us who didn't already know it, anyway.) The prof? Honestly, I don't think he was capable of learning much.
In any case, it certainly didn't meet the stated goal of the course. You know, you can demonstrate that hitting yourself in the head with a hammer really hurts, but it's hard to say how much you learn from putting it to the test.
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This whole "meta-lessons" strikes me as a bit of a cop-out. A good teacher might occasional do a big "meta-lesson" drill in a constrained lad session. Get 30 people to fuck up a 3 hour lab, then tell them what they did wrong.
Getting 30 people to fuck up a semester of work, in the hopes that they "learn a lesson about teamwork" is outright incompetence.
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But the experience was of no real value to anyone in the end.
What do you mean, Mr. Informative?
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I meant exactly what I said. The students, whose goal was to learn more about databases, didn't get that. If the professor's goal was a class full of students who knew more about large database projects than they knew coming in, he didn't get that. If his goal was (as we suspected) a finished project he could clean up a bit and put his own name on, he didn't get that either. Nobody won.
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When they do that to us in (Chemical) Engineering they want us to produce a badly-managed and half-finished mess, the first time around anyway.
They consider it a Learning Experience. And that it is!
Your professor didn't go too far per se, it's just that he assumed that group work just happens. It's something you really have to learn. It doesn't surprise me to hear of academics behaving that way though.
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I've taken roughly the same class, and as part of the quarter that didn't slack off as much, I was pretty satisfied with the experience. The fact is, I don't think that those who slacked off would ever do that well on a proper programming team, and that class very quickly separated those who cared about their craft from those that didn't.
The point isn't to create a working project. The point is to get experience of what creating such a project feels like.
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Open source shares everything with everyone.
It is sort of like Ghandi, only it is written as 010001110110100001100001011011100110010001101001.
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There are useful failures, yeah. I'm not convinced this was one of them.
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The main problem here is, yes, people do learn by doing the exact same problems. Sometimes it's boring, like a quicksort; sometimes it's cool, like Ruby Koans [github.com], but at the very least, no one learns to program without learning Hello World.
Yes, at a certain point, it'd be cool to be doing new things, and sharing, and collaborating. But there is a reason the existing problems should be done, and sharing source code is pretty much like sharing an essay -- not good.
Re:Sadly, education is lagging behind once again. (Score:4, Insightful)
The main problem here is, yes, people do learn by doing the exact same problems.
Let me rephrase that: people as an individual learn by reinventing the wheel, if it's their first own wheel. People as a group learn by using the best known wheels to create new things.
The problem is, education is either going for a lot of different wheels, or forcing people with no wheels to invent a car.
^ That above is a +5 Insightful (Score:2)
I like your analogy. Forcing people with no wheels to invent a car. Clearly, concisely, and accurately depicts the nature of the problem-- Thank You!
I disagree that Open Source is like Science (Score:5, Interesting)
Are you sure? Because science is done by a handful of "qualified" people working in ivory towers. A cathedral staffed with priests, if you will.
Open Source, though, is more like a bazaar. Wild and eclectic, the bazaar atmosphere takes the best and worst of everything, stirs it together, and produces some of the finest things found anywhere. Everyone has a say and anyone can set up shop.
I'm no millionaire, but I'd say that Open Source is much more like a bazaar than a cathedral.
Re:I disagree that Open Source is like Science (Score:4, Insightful)
WRT both science and OSS, the cathedral and the bazaar are converging. In science, the number and the size of the "ivory towers" is growing all the time, and they're getting better about sharing information both between institutions and the world as a whole. In OSS, while it's true that anyone can jump in at any time, the most successful OSS projects generally center around a core development team which carefully vets contributions. As for your use of quotation marks around the word "qualified" ... while amateurs may sometimes make significant contributions in both science and software, the truth of the matter is that a formal education in the subject at hand makes it a lot more likely that your work will be good enough to be useful to the field.
Re:I disagree that Open Source is like Science (Score:5, Insightful)
Yes, yes, we all know about 'The Cathedral and the Bazaar', but your characterisation of science as a cathedral with priests is way out of line. The same spirit of taking what works and building on it is the foundation of scientific endeavour. There's no "one true way" or revered holy texts of science, only what works. When something is found to not work, it has to be changed or discarded...
You can try belittling qualifications, but getting qualified isn't some sort of indoctrination process (or at least it shouldn't be, granted it might resemble indoctrination in some places, but I submit that those places are turning out bad scientists, however qualified they are). As science advances, the necessary knowledge, experience and learning to make a meaningful contribution only grows, meaning people have to spend those years of study and specialisation, learning about what's gone before, to reach a point in a field where they can do something new.
Re:I disagree that Open Source is like Science (Score:5, Insightful)
What is this 'qualification' you speak of?
Granted, your odds of getting peer reviewed is quite small without the requisite sheepskins hanging on your office wall. But there's nothing in the rule book that says science can't be done in one's garage.
The nature of some science dictates the need for some rather exotic equipment. And my neighborhood has a covenant against building LHCs in one's garage. But it isn't unknown for amateurs to discover comets or other objects [wikipedia.org].
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Granted, your odds of getting peer reviewed is quite small without the requisite sheepskins hanging on your office wall. But there's nothing in the rule book that says science can't be done in one's garage.
Except for the laws about civilian's having/using high explosives.....
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He didn't men TV-"science" like Mythbusters. Besides: Laws are just paper. Without anyone to actually notice it, *and* complain about it, they are irrelevant. You can have as much explosives as you want, as long as nobody you don't trust and who isn't OK with it, sees them.
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Granted, your odds of getting peer reviewed is quite small without the requisite sheepskins hanging on your office wall.
Funny, no one has ever asked to see my degrees before reviewing a paper.
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What a grand lad you are! We know that, once in a blue moon, one of you proles accidentally shits out something valuable. We scientists might name it after you!
If you stare at the sky mindlessly for years, you might find a shiny. We scientists might name it after you! PS good luck finding something: there are thousands of lottery winners every year, but only a few people who spot new celestial objects. In addition, having your misspelled name in page 1113 of a stellar catalog is a lot les
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Science has changed man.
Back in the 19th century, anyone could just set up shop. All you needed was a collection of flasks of bubbling liquid, and a Van Der Graph generator.
Now days it's all big industrial labs with huge ventilation systems, and men in white coats who even have googles. The frontiers of human knowledge is out of reach to all of us who don't have a billion dollar particle accelerator.
Street guys like us don't stand a chance nowadays.
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Depends on what science you do. For my own work, I can use a desktop PC with decent specifications, if I'm willing to wait a while for the results to come out.
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Van Der Graph generator.
I am not familiar with this graph.
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While making a whooshing sound?
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That's like saying no one can do professional software development out of their home office because they don't have mainframe.
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The frontiers of human knowledge is out of reach to all of us who don't have a billion dollar particle accelerator.
This shows that you lack imagination. There are frontiers that are still open.
For example in Astronomy, you can use nothing more than binoculars or a telescope - not the cheapest tools but well within reach - to contribute to variable star research just by regularly observing stars and using precise methods to determine their brightness by comparing them to other stars. Amateurs are needed for this sort of work because even with computerised surveys there are limitations to what the equipment can do. (Compu
Re:I disagree that Open Source is like Science (Score:5, Insightful)
You are wrong. Anyone can practice science --- follow the scientific method and you are a scientist.... The problem is whether you've established a history of valid application of that method and if your demonstrates that integrity upon review for publication.
The ivory towers you pretend to exist are only a figment of your imagination and/or ignorance.
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The ivory towers you pretend to exist are only a figment of your imagination and/or ignorance.
I'd go one further; I'd say the ivory towers exist more in OSS. If you can't program, you can't really contribute. Sure you can bug test betas and so on, which I do, but I can't write in C++, so I can't go and fix random bits that are broken or submit patches, though I'd dearly like to.
It's easier to pick up a basic understanding of the scientific method than to understand programming without education.
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"but I can't write in C++"
You can substitute any computer language in place of C++ in that statement and I still wouldn't believe it. Programming isn't that hard, it's just that some people value other things more so they don't put enough effort in to learn it. Sure, to be a programming "God" (if there is such a thing) may not be in the cards for you, but you could learn to be competent.
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He said can't, and he acknowledged that he hadn't put in the work. He was just saying that it required more training than the training required to become a scientist.
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An exact bug description that nails the source of the problem can be so helpful to the maintainer that fixing it will be trivial, and done right away. All you have to do then is bug people in IRC :-]
Extra functionality is hard to get, I agree with you.
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It's would be harder to get a high publication count as a non-professional, but if you did an interesting experiment it should be reasonably easy to publish. But publication count should only be an issue if you are in the ivory tower to begin with.
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First off, there's no need for the scare quotes. Academic science is done by a range of individuals. At the high end we've got professors and staff scientists who have decades of relevant experience. They're qualified to lead research groups and/or provide detailed technical expertise. A rung down you've got postdocs with 10-15 years of experience and then graduate st
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On the other hand, in science the typical model is that some careless graduate student messes up an experiment in such a way as to give unexpected (and therefore interesting results). A couple other members of the lab try to replicate the experiment with ambiguous results but the principle investigator (PI) is desperate for any interesting looking results at all that can be used in a grant application so the PI goes ahead and applies for a grant on the basis of the messed up results. Because the PI is working at a major research university the messed up results are given the benefit of the doubt and grant gets awarded to the PI. By the time the grant money becomes available (typically a year or two after the initial careless experiment), it is clear to most people in the lab that the entire research premise of the (typically five year) grant is bogus. But the PI is essentially required by the grant to hire someone to do the research and, anyway, the PI is typically so far removed from the actual research ((instead doing administrative stuff) that the PI is the last to know that the original results were bogus. So, anyway, some starry-eyed young post-doc gets hired on to spend five years of his life working on a research premise that is already known by pretty much everyone else in the lab (except the PI) to be totally bogus.
Thats... specific... You seem to be using your specific experience in one field of science to condemm the grant system for all fields of science.
If the PI is that clueless, then there's going to be trouble no matter how structured the grant is.
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I get the joke, but right now you're modded interesting so you get a serious reply.
The useful contributors to open source are not only highly skilled but they're also much fewer in number than contributors to science. If you want to contribute to science you can pretty much show up at a lab with half a brain, say you'd like to work for free, and you'll probably get your name on a paper after a bit.
Heh (Score:2)
Standing on the shoulders of giants (Score:4, Interesting)
Yay for factual errors!
Newtons comment with regards to 'standing on the shoulders of giants' was actually just a jab at Robert Hooke (the two eminent Physicists hated each other, with the phrase originating in a letter Newton sent to Hooke).
However, Hooke was of significantly smaller stature than Newton, so by 'standing on the shoulders of giants' Newton was telling Hooke that he had learning nothing from him.
Although a fantastic scientist Newton was a very poor example of a human being, he was rude, offensive and incredibly stuck up.
Re:Standing on the shoulders of giants (Score:4, Interesting)
Hooke was a bit of a bastard himself. He claimed to have reviewed Newton's theory of colour, which was perfectly correct. In fact, Hooke just trashed it in favour of his own theory. This rejection made Newton extremely reluctant to publish any of his other ideas, which may have set science back thirty years.
With this in mind, perhaps the jab wasn't all that unjustified.
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But, as Richard Feynman points out in Q.E.D., Isaac Newton was correct with his corpuscular theory of light.
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First, the sentence itself is much older and gets attributed to Bernard of Chartes (died around 1124).
Second, using Isaac Newton as an example for a scientist is complicated, because at this time, there wasn't a scientific method. Isaac Newton for instance was very interested in Alchimy and Astrology and even calculated (like Bishop James Ussher) the age of the earth according to the bible. In some way this was a hobby to many of the scholars at the time, even Johannes Kepler published his findings.
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Alright, but did Newton have any bad characteristics?
Science is not open (Score:5, Insightful)
As long as scientific results and techniques are hidden in very expensive privately-run journals and conference proceedings,
it cannot in any sense be considered open in the same sense as open-source or "fsf-free" software.
I would like to pursue scientific research as an amateur, but am prevented from doing so.
And this problem doesn't apply only to me, but to countless fully qualified scientists whose institutions cannot
afford the knowledge.
Science badly needs a Bastille day.
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Not to mention university and community-college libraries, which are usually happy to grant access to interested members of the community. Other than inconvenience (a nominal fee, traveling to/from libraries, etc.), access to traditional journals aren't really an impediment to the motivated amateur scientist.
That said, online access to any research results paid for by public funds is what today's society should expect and demand nowadays.
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That was an interesting insight, to question how open science really is in practice, based on the practical difficulty of accessing information, even now.
By the way, on the Bastille day part, just a reminder from:
"Social Movements and Strategic Nonviolence"
http://sociology.ucsc.edu/whorulesamerica/change/science_nonviolence.html [ucsc.edu]
"Studies of social movements in the United States also show that the necessary social disruption has to be created through the principled use of strateg
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Are you sure? Go to a public university library. lots of bound journal. where i live all you need is a drivers license to prove you pay in state taxes to support the local Uni. Often times you can get access to some online journals. And text books.
Take one class and you can join professional societies for student fees and get access to online publications. Sometimes you need a prof to write a letter but if you take a class and are on good terms with them they'll do it if you show keen interest.
Here's a real
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Go to a public university library.
Sure, that's only a $20 for train and bus tickets, and four hours of my time. Not much more overhead than clicking a link to a pdf file.
Don't underestimate the difference between free and "costs money". And don't underestimate the time it takes to get to your nearest university.
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Some libraries will *mail* you books or if you have a local mobile library will deliver it.
Every dedicated scientist I have ever met spent years as and underpaid grad student, working week ends, holidays etc. 10 - 12 hour days. Sometimes getting frost bite or getting tropical diseases.
It's a matter of priorities.
Are you dedicated or a dilettante? Would rather do science or sit on the couch playing video games? Spend vacation in Vegas or doing field work in Guatemala?
The world is full of people who go to coc
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It depends on the field, really. In bioinformatics, we're lucky enough to have (a) a growing number of open access journals, as another poster mentioned, and (b) a number of enormous public access databases with raw data available to anyone who wants to use it. In biology and medicine in general, the NIH public access policy is designed to ensure that the finished product (i.e. journal articles) doesn't stay locked up forever. But I understand that bioinformatics is kind of at the leading edge of this tr
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A bioinformatician myself as well, I'd say that it depends. Some databases are really gold mines for analyses, others (I'm looking at you, Gene Expression Omnibus) contain data that's not as useful as it could be because it's poorly annotated. This is IMO a side effect of the dreaded "Publish or perish" syndrome: in order to publish your findings, you need to have them available in a public resource, but n
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Well, yeah, the annotation often sucks, and I do wish GEO would enforce better annotation standards. Part of the problem in this specific domain, I think, is that MIAME is, to put it politely, a rather open-ended standard. If we had more structured annotation standards, both human- and machine-readable, and the databases strictly enforced these standards for submissions, we'd all be a lot better off. A number of people I work with are working on exactly this problem, and listening to them complain I get
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That's what stuff like ISA-TAB and MAGE-TAB are supposed to solve, but the implementations outside the organizations that mandated them (EBI in this case) are lacking, if present at all.
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Any authors who want people to read their papers post them on their websites for all to view. Doing CS research last term, only a handful of the researchers directed people to a journal to read their work. Most are concerned with their own prestige, not with the journal.
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I can't speak for other disciplines, but Mathematics is quite open. While most journals do not publish their papers, most decent academics have PDFs of their publications on their website, or on ArXiV. It's rarely a problem to find what you're looking for, even without a university subscription to a selection of journals.
Amateur research is extremely difficult to conduct productively these days, since all the low-hanging fruit has been picked. Most experiments need teams of people and highly expensive labs
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I don't think open access is anywhere near open enough yet, even in mathematics. As regards 1), the moving wall in publishing actually prevents amateurs to know where the interest lies until several years after the low hanging fruit were picked by the professionals. Moreover, project
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I agree with what you're saying here, but this is likely a product of the way our current world works, where privatization is necessary for capitalism.
Science, afaik, has no interest in exclusivity -- but what you're seeing is a product of necessity within the framework of existence that we are in.
Don't worry, though. The world is already too small for hoarding and privatization. Blood will continue to spill for resources until we decide to die and stop making babies, or restructure our approach to life i
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What, the MIB keep showing up at your house and flashing your memory away?
They don't you say?
Then nothing is keeping you from performing research on your own time in your place except yourself.
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Nonsense. Go to a library.
Open source software is hidden away behind very expensive Internet connections and hardware requirements. Certainly more expensive than a library card, if you even need that.
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As long as scientific results and techniques are hidden in very expensive privately-run journals and conference proceedings, it cannot in any sense be considered open in the same sense as open-source or "fsf-free" software.
Those "expensive privately-run journals" are available to the public, though. Really, how much good is the source code if you don't have an "expensive, privately-owned machine" to compile it on, and how many internet cafes or public libraries have computers equipped with development software or allow users to install their own?
The real cost of entry into science isn't the subscription fees for journals, it's the time required to catch up on the current state of affairs. I mean, unless you actually speci
So that would make (Score:4, Funny)
That doesn't quite sound right to me...
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No, that would make proprietary software the equivalent of fundamentalist churches. Intelligent design itself is not in competition with the scientific method.
Sounds right to me... (Score:2)
The theory of Intelligent Design has a lot of holes.
So does proprietary software.
What open source shared with chocolate (Score:3, Funny)
Open source is like a box of chocolates. I'm not sure why...I just wanted to say that. It's what I thought of when I read the story.
How bout Scientists share their sourcecode? (Score:2, Insightful)
People would be surprised how much software is developed under grant from the gov and is NOT open source. Some institutions like Cal Tech refuse to release their source code or even license it under an open source license that lets them retain copyright.
In an almost guided-Darwinian evolutionary ... (Score:2)
crickets.
Yeah, like part of what I posted. (Score:2)
http://slashdot.org/comments.pl?sid=1259963&cid=28244145&art_pos=9 [slashdot.org]
I think I posted it before but I can't find it off hand.
Manufacturing and engineering often closed too... (Score:2)
I wrote on that here: ...
"Society of Manufacturing Engineers (SME) Licensing issues"
http://groups.google.com/group/openmanufacturing/msg/da82d9fd52265dbc?hl=en [google.com]
"So basically, SME is using post-scarcity charitable dollars and tax
exemptions to finance the creation and distribution of artificial scarcity
of manufacturing information, which otherwise they could put up for free for
all on their website.
To be blunt, I feel it is unethical for a tax-exempt non-profit to withhold
17000 pap
This is an intersting argument... (Score:4, Interesting)
By argument, I mean in the logical sense, such as a "claim" bolstered by "proof, information, and example". (I'm trying to separate the /. process of somebody posting something and someone else immediately disagreeing. But, Hey, I'm not trying to start an argument here about slashdot postings...)
So, I wonder if this argument has been used in the patent "process vs. product" or "software patent" courts. It seems to me that patents are generally awarded to the "products of Science" rather than the science itself. If code processes, algorithms, and concepts are Science, then patents should only be awarded to the "products of Science" such as individual chips or other hardware that utilizes the software and not the software itself. This argument could help clarify the boundaries of the patentable domain.
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Congrats, from my point of view this is a really insightful way to argue against these patents. I'll use this logic when talking about the subject from now on to help stir debate.
open source = non-privatized science (Score:5, Insightful)
Software, like science, produces a non-rival public good. (Nonrival means it is not consumed when somebody uses it.) But there are private research companies just like there are private software companies.
I used to work in a publicly-funded virology lab studying Hepatitis C Virus (HCV). My biggest result was finding this particular human gene that HCV required in order to infect a person. If you took liver tissue, knocked out that gene, and tried to infect it with HCV... no infection. Has anyone seen this before? Nothing in the scientific literature, but we found a dusty old patent from a company that had clearly found this connection years earlier, but never published it or followed it up. The company was likely hedging its bets in case it wanted to follow up later. HCV kills tens of thousands of people a year (liver cancer). Just makes me so frustrated.
Most people are already familiar with negative market externalities like pollution or overfishing. Science and software both exemplify positive externalities, which are just as problematic in free market capitalism. If only there were a clear way to internalize externalities!
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Jeebus fricking cloister! Are companies actually allowed to be this evil?!??!!?
Re-motherfucking-lution now, please!
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(... I was so upset over how much evil the system allows, that I forgot a "vo" in there.)
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Please note: this is not a cure for Hepatitis C that these people are sitting on. It's only a lead, that with ten years work, *might* lead to a cure, or might not. You can stop infections in a test tube if you silence this gene. Okay. What if silencing that gene turns out to be fatal when you do it in living human body? What if silencing that gene doesn't help prevent that infection at all in the human body (a lot of things that work in vitro don't work in vivo)? And how are you going to silence the g
Let me think (Score:1)
Of course open source is like science.. (Score:2)
Programs are written in formal languages. Every program is an explicit mathemathical expression.
Hide the code, and your are invalidating the expression, just like showing a math result without stating the formula. That's not science, at all.
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Hiding the source code is just giving you the result in a language that is not to your liking (machine code).
Verily and forsooth (Score:4, Funny)
This article should be covered up, cast out, smothered, and wiped off the face of the intartubes. Somewhere in the Book of Gates, it must surely be written that Open Source is the work of the Devils, and that all who are contaminated by such heresy shall surely be cast into the lake of BSOD.
All who seek after the ways of wisdom are surely aware that both science and programming are best accomplished in secretive enclaves, and pursued by the holy clerics of Corporate America. Surely, in the pursuit of wisdom, lesser beings shall be confused and damned by their communistic, socialistic methods. No good can come of the curiosity of the little man.
Keep the science in the cathedrals, and keep the coding in Microsoft labs.
Thus speaketh the Gates.
All hail the great EULA!!
It's Time To Open Source Education (Score:4, Insightful)
Why not free up the educational system and put K1 right up through the Ph.D. level of education as free, open source, tools available in towns as well as on the net. Education is simply a form of information. Let's get the for money players out of the loop.
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The Scientific Ethics of Open Source (Score:2, Insightful)
I think it's important to note that open source is important for scientific ethics. As scientists, we are required to disclose everything about what we do - the methods, the errors, the methodologies - just as the article points out. If we don't, we are breaking a code of behavior that exists for the integrity and reliability of the field. How is it justifiable to go and hide that behind the shield of proprietary software in the DAQ or analysis just because somebody like SPSS wants to shut out competition?