What Open Source Shares With Science

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."

Comments

Sadly, education is lagging behind once again.

[pm_rat_poison]

Sadly, education has yet to follow this trend. Computer Science and Computer Engineering classes have yet to implement significant group collaboration. And while the hack tenet of "something that has been done once shouldn't be done again" was a conceived by some bright students, educators still give identical tedious projects that have the students complete in isolated groups, many times of consisting by just. There has even been an instance of a student being threatened to fail a class because he posted the source code of his project. How can we expect future developers to collaborate when their education forces a way to work that is very alien to the open culture and resembles that of a proprietary company
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?

Re:Sadly, education is lagging behind once again.

[Daniel Dvorkin]

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.

Re:Sadly, education is lagging behind once again.

[Jurily]

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.

Re:Sadly, education is lagging behind once again.

[jabithew]

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.

I disagree that Open Source is like Science

[BadAnalogyGuy]

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

[Daniel Dvorkin]

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

[mpeskett]

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

[lbbros]

Street guys like us don't stand a chance nowadays.

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.

Re:I disagree that Open Source is like Science

[PPH]

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.

Re:I disagree that Open Source is like Science

[Anonymous Coward]

Funny, I know a biotech startup in an East L.A. warehouse. They got cash from Crest and are doing work on new ways of combating tooth decay by disrupting bacterial biofilms in the mouth. Sorry to burst your bubble, bud.

Re:I disagree that Open Source is like Science

[joocemann]

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.

Re:I disagree that Open Source is like Science

[simcop2387]

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.....

Re:I disagree that Open Source is like Science

[binarylarry]

That's like saying no one can do professional software development out of their home office because they don't have mainframe.

Re:I disagree that Open Source is like Science

[jabithew]

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.

Re:I disagree that Open Source is like Science

[ceoyoyo]

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.

Re:I disagree that Open Source is like Science

[BitHive]

There's "nothing in the rule book" in that the laws of physics don't preclude it but an education sure isn't an impediment! I am amused by the way you trivialize years of disciplined study and forging connections within a field as some kind of rain dance and equate discovering something (which anyone can do with some luck and equipment) to characterizing it in a form that expands the boundaries of scientific understanding (aka research). Why is it so hard for slashdot readers to accept that there are other technical disciplines and epistemic traditions that deserve respect and on the whole do in fact know something autodidact programmers don't?

Standing on the shoulders of giants

[Anonymous Coward]

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

[SoVeryTired]

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.

Science is not open

[presidenteloco]

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.

Re:Science is not open

[Paul Fernhout]

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
"Studies of social movements in the United States also show that the necessary social disruption has to be created through the principled use of strategic nonviolence. Any form of violence, whether property damage or physical battles with opponents and police, will turn off the great majority of Americans and bring down overwhelming police and military repression."

Re:Science is not open

[Daniel Dvorkin]

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 trend -- if your area of interest is, say, inorganic chemistry, it may be a lot harder to get past the barriers.

Re:Science is not open

[Metasquares]

Many authors who feel as you do go ahead and post their papers on their websites for all to view anyway once they're published. Google Scholar now indexes them too. I agree completely on the journals, but in the meantime, you can always try finding papers this way.

Re:Science is not open

[SoVeryTired]

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 to run. The peer review process would also need to change considerably if we moved to a truly open system. While I agree thet you may have a point, I don't think it's quite as cut-and-dried as you make it out to be.

Re:Science is not open

[c0d3g33k]

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.

So that would make

[Paaskonijn]

proprietary software the equivalent of intelligent design?

That doesn't quite sound right to me...

What open source shared with chocolate

[anyaristow]

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?

[Anonymous Coward]

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.

This is an intersting argument...

[meburke]

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.

open source = non-privatized science

[panthroman]

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!

Re:open source = non-privatized science

[Chris Mattern]

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 gene in vivo, anyways? No gene therapy done so far has worked on silencing a gene, only introducing a new one, and even *that's* been highly experimental and has had some nasty setbacks. And so on. Honestly, I'd think that you'd have an excellent chance of challenging that patent on the basis of utility: it doesn't *do* anything useful, at least not in and of itself.

Verily and forsooth

[Runaway1956]

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

[b4upoo]

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.

The Scientific Ethics of Open Source

[Anonymous Coward]

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? The answer is simple: it's not. Closed-source is actually scientifically unethical.