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Open v. Closed Source-Climate Change Research

timothy posted more than 9 years ago | from the it's-only-a-model dept.

Software 443

theidocles writes "The ongoing debate over the 'hockey stick' climate graph has an interesting side note. McKitrick & McIntyre (M&M), the critics, have published their complete source code and it's written using the well-known R statistics package (covered by the GPL). Mann, Bradley & Hughes, the defenders, described their algorithm but have only released part of their source code, and refuse to divulge the rest, which really makes it look like they have some errors/omissions to hide (they did publish the data they used). There's an issue of open source vs closed source as well as how much publicly-funded researchers should be required to disclose - should they be allowed to generate 'closed-source' solutions at the taxpayers' expense?"

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Short answer, no. (3, Insightful)

maotx (765127) | more than 9 years ago | (#12010677)

should they be allowed to generate 'closed-source' solutions at the taxpayers' expense?

No. I paid for it I want to see it. How else will we know if it works the way they say it works?

Re:Short answer, no. (0, Flamebait)

TedCheshireAcad (311748) | more than 9 years ago | (#12010733)

By this logic, then shouldn't you, the taxpayer, have a right to dictate how money, say, with Medicare, is spent?

You're footing the bill, shouldn't you have the right to say which doctors will be seen, and which medications will be prescribed? I realize that there is a government agency that plays this role, but when has anyone on slashdot ever trusted the government to make a decision for them?

Re:Short answer, no. (4, Insightful)

FuzzieNorn (203503) | more than 9 years ago | (#12010757)

No. By that logic, the taxpayer should be able to see information about how the selection of doctors is made, and which prescriptions should be prescribed, and generally how Medicare money is spent.

Re:Short answer, no. (1)

PyWiz (865118) | more than 9 years ago | (#12010898)

Should taxpayers be able to see information on secret military projects as well?

Re:Short answer, no. (1)

varmittang (849469) | more than 9 years ago | (#12010931)

Actually, we can. Just not the black ops projects that work on some high tech stuff that can be used for our protection. Other than that, you can see how much they spent on tanks, or airplanes. Just remember, this is outside the government spending, so since they want to use my money for none government things, then I should see what they produce.

Re:Short answer, no. (4, Insightful)

Glock27 (446276) | more than 9 years ago | (#12011065)

Should taxpayers be able to see information on secret military projects as well?

Not when the secret is current, and espionage is a concern. This is of course the current state of affairs.

Once the secret is no longer of military importance, all information that can be released should be released. In general that's what happens - note the wealth of information available on the WWII atomic weapon program for instance.

Re:Short answer, no. (1, Insightful)

Anonymous Coward | more than 9 years ago | (#12010744)

I didn't RTFA, but the other outfit probably regards its software as a core asset that it uses for a number of projects, including some that might be for private clients. This is a common consulting model. One compromise would be to share the source (ala Microsoft) with the government and whatever third party observers the government brings in.

As for opening the source, small consulting firms are generally worried that a couple partners (let's say a rainmaker and an academic guy) might take off and set up shop across the street. That could happen in any case, but with a software asset at least you have a barrier to entry. If the code is GPL you could get hosed. OTOH if you do open the source you can advertise that fact and possibly use it as a competitive advantage, as these people have done. So if I were in their position I'm not sure what I'd do.

Re:Short answer, no. (2, Insightful)

WyerByter (727074) | more than 9 years ago | (#12010915)

The code is their core asset, as they make their money putting forward and supporting the claim that global warming is occuring. (And they have the hockey stick to prove it.) If their code was opened the flaws suggested by M&M would become apparent, if they existed, as well as indications as to whether the errors were due to oversight, sloppy math or scientific bias. If any errors are found their livelyhoods as well as their cherished cause could tumble down around them. So much for peer review.

Re:Short answer, no. (1)

Cytlid (95255) | more than 9 years ago | (#12010778)

Hmm... isn't the government one of Microsoft's biggest customers? Do they pay them with taxpayer money? Are taxpayers then allowed to "see" source of products from Microsoft?

It's always bugged me that our elected officials hand our money to any vendor they'd like, but then on the flipside, one could argue, that's why they're elected officials.

Re:Short answer, no. (2, Insightful)

pianoman113 (204449) | more than 9 years ago | (#12011064)

An important difference is that the Microsoft tools the government uses are just tools. They were not developed with taxpayer money.
The government buys licenses for Microsoft Windows, Office, etc. just like it buys toilet paper or doorknobs.

Re:Short answer, no. (0)

Anonymous Coward | more than 9 years ago | (#12010796)

How about me here in Canada? I DID NOT pay for it, but if it's open sourced, I get to see it, use it, expand on it, etc.
On one hand, I do see the whole "information wants to be free" argument, ESPECIALLY when applied to science, but an other country's taxpayers paid for it, should I get a free ride?

Re:Short answer, no. (0, Troll)

tdemark (512406) | more than 9 years ago | (#12010815)

This should be an interesting discussion... three classic Slashdot knee-jerk reaction topics all pitted against each other:

  • Open source vs. Closed Source
    • Pro Open source: modded up
    • Pro Closed Source: modded down

  • Global warming

    • Global warming is occurring/imminent: modded up
    • No global warming: modded down

  • Publically funded research

    • Results must be published: modded up
    • Results kept private: modded down



Let's get ready to rumble!

- Tony

Re:Short answer, no. (2, Insightful)

ilikejam (762039) | more than 9 years ago | (#12010847)

Wasn't this sort of thing the whole reason the BSD license came about?

OT reply to sig (1)

shreevatsa (845645) | more than 9 years ago | (#12010992)

I have to usually do C-x C-s C-x k RET.
Have you set it up so it doesn't ask? Can you tell me how? I would like to know.

It's not science (1, Interesting)

Anonymous Coward | more than 9 years ago | (#12011056)

The scientific method:

1. Observe and describe a phenomena
2. Formulate an hypothesis
3. Use hypothesis to predict something
4. Independently verify those predictions

Step four requires, of course, that experiments can be corroborated, which implies that they can be duplicated. That is of course impossible if the tools employed are not shared.

The only scientific result that should be given any regard is that produced by real scientists doing real science. Pay no attention to the man behind the curtain.

Re:Short answer, no. (0)

woginuk (866628) | more than 9 years ago | (#12011073)

No. I paid for it I want to see it. How else will we know if it works the way they say it works?

Apart from that, if I have paid for it, it belongs to me. Why should somebody else have ownership rights over it and any subsequent profits/income deriving from it? Seems like robbery to me.

How much is enough? (5, Insightful)

mfh (56) | more than 9 years ago | (#12010679)

how much publicly-funded researchers should be required to disclose

All of it, baby. We're paying for it -- we should have the right to:

a) Know what you're spending our money on
b) Have the right to make it better ourselves
c) Learn of security flaws early so we can correct them

Especially when there is some doubt [slashdot.org] about the nature of the results in the closed source model from Mann et al.

Re:How much is enough? (1)

liquidpele (663430) | more than 9 years ago | (#12010724)

well... depends.
If a govt agency makes something, I agree 100%...
If the govt gives grants to another institution, I think the institution should not have to give everything away unless specified before hand.

Re:How much is enough? (-1, Offtopic)

ghoti (60903) | more than 9 years ago | (#12010880)

From your sig:
they called it "San Diego", which of course in German means "a whale's vagina".
Where did you hear that? "San Diego" doesn't mean anything in German, and doesn't even sound close to anything ...

Re:How much is enough? (-1)

Anonymous Coward | more than 9 years ago | (#12010903)

See movie: "The legend of Ron Burgundy"

Re:How much is enough? (-1, Offtopic)

Taladar (717494) | more than 9 years ago | (#12011068)

Even with the source in the (invisible to most) AC reply it still looks stupid to everything speaking german. I would suggest a sig change.

Re:How much is enough? (0)

Anonymous Coward | more than 9 years ago | (#12010831)

I think you are missing the point here. Security flaws in scientific computing are not really much of a problem. What _is_ a problem is the reproducibility of the results and the ability to check all of the methods used (fudge factors, kludges, plain errors). Making it better yourself sounds good but making it better generally requires a good understanding of the problem you're modeling. Making these program open source will not give the general public the ability to verify the climate change models, but it will give their colleagues the chance to do so. Using open source programs should really be a prerequisite for getting your model published. Sadly, this it tends to be the exception rather than the rule.

Re:How much is enough? (0)

Anonymous Coward | more than 9 years ago | (#12010857)

I think he was generalizing the Open Source vs. Closed Source model in general... not just for science. Fraud detection is a security feature of Open Source if you ask me.

Re:How much is enough? (4, Interesting)

R.Caley (126968) | more than 9 years ago | (#12010865)

We're paying for it

Of course, often you will only be paying for part of it. It is common for research to come out of a combination of `projects' funded from different sources.

What should happen if, for instance, a drug company funds a project into developing statistical theory and signal analysis and so on to improve analysis of early candidate drug screening data, and then the researchers use the prototype implementation in a publicly funded project they are involved in on climate data and find something significant?

Or what happens for part-state, part-commercially funded projects?

I think one thing which could be done is to give companies a (bigger) tax break on money put into research (internal or when they give grants) if they sign up to give out not only all the data, but things like source of programs and detailed design of prototypes and experimental setups.

Another thing would be to set up some kind of peer review process and then treat published source as a publication for the researcher. If your peers sign off to say that you have produced and documented the code to the level where it is a useful resource for other researchers, then it should count towards departmental and personal evaluations just as a journal article would. The formalised review process is important -- the average bit of lashed-together-to-get-the-data research code is more equivalent to a scribbled note on a whiteboard than to a journal article.

Perhaps all that is needed is an online journal set up and run as a properly organised accademic journal, but specialising in publishing code. Imagine an infrastructure not a million miles away from sourceforge, but with a peer review process to decide what gets counted as a release.

Re:How much is enough? (1)

kenthorvath (225950) | more than 9 years ago | (#12010866)

Funny how that argument looks if the research is being done by the NSA....

Re:How much is enough? (0)

Anonymous Coward | more than 9 years ago | (#12010910)

Research, not data mining and surveillance, smartass.

Re:How much is enough? (1)

PyWiz (865118) | more than 9 years ago | (#12010916)

Again, there are a LOT of things the government does with your money that you don't get to see, and for good reason. Military research, CIA/FBI operations, undercover cops, etc. You don't get the _details_ about all these things, you just know that your money is going to them. In this case, you know the money is going to research but as for the details of that research, you are kept in the dark, and possibly for good reason.

Re:How much is enough? (0)

Anonymous Coward | more than 9 years ago | (#12010942)

Yes, all of that special weather research. You never know when a terrorist could use that against us. /sarcasm

Re:How much is enough? (0)

Anonymous Coward | more than 9 years ago | (#12011027)

Good luck with your FOIA request on missile design.

It should be called argh! (5, Funny)

Anonymous Coward | more than 9 years ago | (#12010686)

I hate projects with names like R. I used R a while back, and it's a great program, but try searching for "R" plugins on Google. Not fun.

Re:It should be called argh! (0, Offtopic)

the_womble (580291) | more than 9 years ago | (#12010690)

Have you tried a google search for "r statistics"? Guesss what comes top?

Re:It should be called argh! (0)

Anonymous Coward | more than 9 years ago | (#12010706)

Um, the project page comes up, not a lot of help. I already have the damn program, I'm looking for 3rd party plugins etc.

CRAN is your friend (1, Informative)

Anonymous Coward | more than 9 years ago | (#12010808)

http://cran.r-project.org/
However, the name still sucks.

Re:It should be called argh! (0)

Anonymous Coward | more than 9 years ago | (#12010827)

R packages (i.e third party plugins) are available from CRAN http://cran.r-project.org/ [r-project.org] . There might be some packages on other web sites, but these are the ones that have passed the QA tests.

Re:It should be called argh! (1)

djmurdoch (306849) | more than 9 years ago | (#12011008)

R calls them "packages", not "plugins". If you search for "R plugins" you find a lot of non-R stuff, but if you search for "R packages" you find what you're looking for.

Re:It should be called argh! (3, Funny)

Anonymous Coward | more than 9 years ago | (#12010826)

Searching for LaTeX, on the other hand...

Re:It should be called argh! (0)

Anonymous Coward | more than 9 years ago | (#12010837)

I hate writing in R, mostly because of the functional style. It was fun when I found R because I hadn't known that there were any large projects like that around, especially ones that don't cost #{matlab.cost}.

Legal (1, Funny)

Anonymous Coward | more than 9 years ago | (#12010873)

This is actually an interesting legal debate. How would you register a trademark on the letter R?

R®????

Fake Science can easily be proved with Fake Data (-1, Troll)

Anonymous Coward | more than 9 years ago | (#12010694)

The Bush Science Team America has made an amazing discovery:
Fake Science can be easily proven with Fake Data.

The algorithms are the least important things (0, Troll)

Dancin_Santa (265275) | more than 9 years ago | (#12010702)

The most important thing is the data. You can even use something simple like the Excel (or Gnumeric) spreadsheet "best fit" plotting algorithm to the data, if you've got it.

But from all the stuff I've seen, there are always huge gaps where they are either assuming much lower average temperatures or are leaving the data out altogether and relying on a very short recent timespan to extrapolate into the future.

While I think that they are full of shit, for the most part, I do admit that having multiple tornados tear apart LA and a giant deep-freeze kill off all the Scots would be pretty cool.

I don't think Open vs. Closed source politics (2, Insightful)

BannedfrompostingAC (799263) | more than 9 years ago | (#12010711)

is in the interest of the science in this case.

Taxpayer funded whitewashes (2, Interesting)

BenBenBen (249969) | more than 9 years ago | (#12010713)

You might want to ask to see the model behind the CIA data [flight800.org] which proved conclusively that a 747, deprived of its forward fuselage, can convince over 600 witnesses that said 747 was shot down by a SAM.

Re:Taxpayer funded whitewashes (0)

Anonymous Coward | more than 9 years ago | (#12010860)

You need to work on your English. That sentence was unreadable.

Re:Taxpayer funded whitewashes (0)

Anonymous Coward | more than 9 years ago | (#12010966)

can convince over 600 witnesses

The link you provided says 96 witnesses.

Show me the RAW data. (3, Insightful)

Anonymous Coward | more than 9 years ago | (#12010730)

The problem with most of these studies is that they refuse to release the raw data.

A lot of times they select subsets of the data and then normalize or otherwise massage the data.

Thanks ... but no thanks !!!

The debate (2, Insightful)

Mr_Silver (213637) | more than 9 years ago | (#12010735)

So there is a debate going on? If that is the case, a link to where it is going on so we can see the arguments would be nice.

For all we know, there could be a very valid reason why they haven't released all of it. I'm not sure what that reason could be, but given that we don't have anything to go on, we're stuck to just guessing.

Re:The debate (3, Informative)

syphax (189065) | more than 9 years ago | (#12010806)

The debate is well-documented (by the Mann team, at least) here [realclimate.org] , here [realclimate.org] , here [realclimate.org] .

Re:The debate (3, Informative)

syphax (189065) | more than 9 years ago | (#12010820)

Looks like M&M have a blog [climateaudit.org] too...

Re:The debate (2, Informative)

ifoxtrot (529292) | more than 9 years ago | (#12010908)

The BBC also has an article that recounts the controversy here [bbc.co.uk] .

Expected Slashdot answer (1)

erroneus (253617) | more than 9 years ago | (#12010737)

...and I agree with it -- of course anything paid for by public funding should show a return on public interest. It seems way too obvious.

What isn't quite so obvious is employers owning works of an employee. It seems obvious that it should be restricted to stuff that is currently job related and developed on company time, but we all know of scenarios where companies reach too far. So without looking too deeply, I wonder if the other side considers some aspects of their work not relevant to that which was sponsored by public funds. If, for example, the project was intended to deliver data and software tools were developed along the way to achieving that goal, who owns the software tool?

Re:Expected Slashdot answer (0)

Anonymous Coward | more than 9 years ago | (#12010890)

Why allow non individuals to have IP in the first place? I'd much rather have a baseball card like resume for the shareholders to trade, lol.
I have a SW engineer that comes with 23 ideas and has a 137 productivity average I'll trade for that stack of unopened rookies...

Re:Expected Slashdot answer (1)

Sique (173459) | more than 9 years ago | (#12010929)


What isn't quite so obvious is employers owning works of an employee.


That's correct under English Common Law. But at least the "open sourc" group is from the Netherlands, and they work under the maximes of the Berne Convention. In German Law (43 UrhG) it states explicitely:

43 Urheber in Arbeits- oder Dienstverhältnissen

Die Vorschriften dieses Unterabschnitts sind auch anzuwenden, wenn der Urheber das Werk in Erfüllung seiner Verpflichtungen aus einem Arbeits- oder Dienstverhältnis geschaffen hat, soweit sich aus dem Inhalt oder dem Wesen des Arbeits- oder Dienstverhältnisses nichts anderes ergibt.


(which translates to: The rules of this paragraph are also valid, if the Author has created the Work in fulfillment of his duties from a employment or service contract, except if the type of the employment or service dictate otherwise.)

The exceptions are pointing at duties to keep a secret (if you are for instance a lawyer writing something for your client, you are not allowed to publish your essay at will) or or to publish your results for everyone to read (if you are writing the exact words for a law ;) ) or similar. They don't refer to any clauses in a contract.

It is still possible to make a contract about a future work (40), where you can give exclusive rights to your employer, but you still retain the Urheberschaft (the Authorship), which can't be sold or otherwise given to someone else. You even have the right after two years to regain the rights back if your employer doesn't use his rights or makes only partly use of your work (41, you could call it the Abandonware Clause).

But the Hockey Stick is True! (-1, Flamebait)

wiredog (43288) | more than 9 years ago | (#12010740)

It has to be! It supports the Global Warming Theory! Anything that supports global warming is true, and anyone who talks about the opponents of the theory maybe doing something more correctly than the supporters is a neo-con radical supporter of Dubya!

It's sad to see Slashdot becoming a supporter of the Republican Orthodoxy.

Almost as sad as seeing the ad hominem attacks that some greens use against anyone who questions their orthodoxy...

Re:But the Hockey Stick is True! (5, Insightful)

BenBenBen (249969) | more than 9 years ago | (#12010833)

That Global Warming is a manmade, real phenomona is accepted by 99.9% of scientists in the fields involved. To trot out the "only a theory", "some experts dispute" etc routine is like getting the Flat Earth Society involved every time someone talks about circumnavigation. "Heads in the sand" is going to be on our culture's gravestone when the next lot of intelligent life evolves here and starts wondering why parts of Nevada are 10,000 times the normal radiation level.

Re:But the Hockey Stick is True! (1)

FatRatBastard (7583) | more than 9 years ago | (#12010884)

The same could be said about the theory of a flat earth. At some point 99.9% of the experts were pretty damn sure of that too. The problem is science isn't done by consensus. Its done by proving hypothesis.

The problem is nutters on the Green side equate people saying "you still haven't proven it" with people meaning "it doesn't exist." Is global warming real and a problem? Very well may be. As shown in the original posting, however, there is still a way to go before anyone can say its proven.

Re:But the Hockey Stick is True! (2, Insightful)

hankwang (413283) | more than 9 years ago | (#12010969)

The same could be said about the theory of a flat earth. At some point 99.9% of the experts were pretty damn sure of that too.

Actually, 99% of the well-educated people today incorrectly believe that 99.9% of the scientists in the middle ages believed in the concept of a flat earth.

The has been a generally accepted notion that the earth is round [wikipedia.org] since the 1st century A.D.. Disputes have only been about (1) whether the sun revolves around the earth or the other way around, and (2) what the radius of the earth is.

Re:But the Hockey Stick is True! (1)

provolt (54870) | more than 9 years ago | (#12010892)

But Mr. Gallileo, the theory that the sun revolves around the earth is accepted by 99.9% of all scientistis in the fields involved.

Re:But the Hockey Stick is True! (1)

goldspider (445116) | more than 9 years ago | (#12010923)

So you want us to cut down on greenhouse gas emissions, but you also bemoan nuclear power?

So what exactly is YOUR solution? Nuclear is a perfectly viable solution until we come up with something better. At the very least, it's far cleaner than burning coal for our energy.

Re:But the Hockey Stick is True! (1)

caseydk (203763) | more than 9 years ago | (#12010936)

If the models and data are accurate, then release them to public scrutiny.

*If* the information is as bullet proof as you say, then they have nothing to be concerned about. Since only one side has done this, only one side is opening itself up to peer review.

This is the equivalent to SCO saying "you have our code!", not producing any evidence to demonstrate this, and then IBM delivering truckloads of evidence to the contrary.

Man-made and natural (1)

L.Bob.Rife (844620) | more than 9 years ago | (#12010950)

We know that the earth IS getting warmer. And we know that it goes through natural cycles of climate change. We know that people affect the climate in SOME way, but the debate too often focuses on how much is caused by man, and how much is natural, as if natural warming is somehow better.

The point so many global warming critics ignore is that whether it is a natural phenonema or not, doesn't change the danger. The amount of crops that can be grown worldwide will shrink for every degree the planet goes up, until evolution kicks in.

Just a few degrees globally can literally end up causing the starvation of millions of people.

Re:But the Hockey Stick is True! (2, Informative)

grqb (410789) | more than 9 years ago | (#12010863)

I think that the argument though is that the hockey stick has happened before in the past. I mean, the earth naturally warms and naturally cools, there has been global warming before the advent of fossil fuels.



This is the big problem for people trying to fight the critics. For me though it's easy. The CO2 levels in the atmosphere have never been as high as they are now (at about 370ppm) and they're expected to increase up to 700ppm if we finish off the oil (which may be in 70 years or longer). But the point is, even if global warming is/is not happening, having over 370ppm of CO2 in the atmosphere is just not good! Here's a pretty good summary of the global warming argumnts [thewatt.com] .

No brainer... (5, Insightful)

wileynet (779280) | more than 9 years ago | (#12010751)

Science, like government, should be transparent. The public should be able to see and evaluate every part. Any science, or government, that hides it's implementation is inherently suspect to corruption.
Closed science is half a step from religion. You are expected to have faith in the researcher's methodologies, analysis, assumptions, and motives. Sorry, but good science does not rely on faith.

Re:No brainer... (1)

DaHat (247651) | more than 9 years ago | (#12010823)

The fallacy of your argument is the assumption that the public will review the work, the same goes for OSS, just because the code is open doesn't mean people are going to examine it in depth enough to find all of the flaws.

Re:No brainer... (3, Interesting)

dpilot (134227) | more than 9 years ago | (#12010981)

It's not necessary that a large number of people in the public review the work. It's only necessary that SOME people in the public review it, and that those be self-selected people.

I run quite a selection of software on my machines, and to be honest, I've never done a security review of ANY of it. To be equally honest, I'm not really competent to do a security review of the code, though with effort I could well become so. But by and large, I pay attention to OSS community discussions, and know that others who appear to be competent have review that software. Note that I use the term "appear to be competent," since I have no personal knowledge of their qualifications. However, when enough people who "appear to be competent" reach a concensus, either:
1: They're all incompetent in the same way.
2: They're all email aliases of the same guy hunched over the keyboard in his parents' basement.
3: They're the techno-incarnation of the Club of Rome, bent on World Dominatino.
4: They're a variety of informed backgrounds and opinions who have come to a rough concensus.
I submit that 4 is most likely. 1 is possible, given that there are common misconceptions, but the larger the group, the less likely 1 becomes. 2 and 3 are just plain for the tin-foil hat club.

I argue that the work needs to be open for the self-selection of reviewers. If the reviewers are selected by the authors, no matter how hard they try to find 'fair and neutral' parties or even antagonists, something will be missed.

Re:No brainer... (2, Insightful)

provolt (54870) | more than 9 years ago | (#12010912)

Closed science is half a step from religion.


But to many in the environmental movement it is a religion. Orthodox Environmentalism is just as strict as any other orthodox religion, and just as faith-based and close to new ideas.

Re:No brainer... (0)

Anonymous Coward | more than 9 years ago | (#12010958)

The public has absolutely no chance of understanding scientific research.

I'm sure what you meant to say was that the science should be open to other scientists to review. This is the basis of peer review. Obviously, climate research requires a small modification in the amount of information published with papers.

For interest's sake, crystallographic data of protein structures underwent a similar review in Biochemistry a few years ago. It used to be enough to include only the most basic data, and keep most of the information secret - now, if you want to publish a paper, you must have the full details available for review by other scientists within a certain time period. (Can't remember the full details sorry; I'm a biochemist, but not a crystallographer...)

It is only a small revision in the peer review process for this field that requires modification - it doesn't require huge efforts to make databases that the public can access. The people who can understand the information will know how to access it anyway.

Just because it's code it should be open? (3, Interesting)

asciiRider (154712) | more than 9 years ago | (#12010752)

The pharmaceutical industry receives huge subsidies from us - they don't produce "open" drugs - why should this be any different? I know it's apples and oranges - but one should be really careful about the idea of withholding funds from -good- research just because of licensing issues. Lesser of two evils? Would we rather have -no- research?

complicated...

Re:Just because it's code it should be open? (2, Informative)

climb_no_fear (572210) | more than 9 years ago | (#12010814)

I work for a pharma company. When we publish, we have to publish the structure of the compound used. You or a skilled chemist could cook it up and reproduce my work. That makes it science. Even if it's patented, you can do this under the freedom to research clause.

Re:Just because it's code it should be open? (3, Insightful)

mccalli (323026) | more than 9 years ago | (#12010838)

The pharmaceutical industry receives huge subsidies from us - they don't produce "open" drugs - why should this be any different?

It shouldn't. But of course there are two ways to resolve this inconsistency:

  1. Allow publically funded closed-source climate models
  2. Require drug companies to open up that amount of research was was carried out using public funds.

Option 2 please.

Cheers,
Ian

Re:Just because it's code it should be open? (1)

TheRaven64 (641858) | more than 9 years ago | (#12010944)

Speaking from my ivory tower (which is actually a nice glass fronted building overlooking the sea - which is much more fun when it's not raining than it is today) in academia, I feel strongly that the research community should justify its existence by releasing full results. The number of times I've come across papers which basically say `look at us! We did something clever! Be impressed!' without actually giving enough details of what they did to reproduce it is sickening. Society funds academics for two purposes:
  1. To keep us out of trouble.
  2. So that society can benefit from our research.
And research that is publicly funded should be fully published under a license as close to public domain as possible. Something like the BSD license (requiring credit and with a legal disclaimer) is probably ideal. If you want to keep your research secret then go and work in industry, and put up with fewer academic freedoms.

published (1)

cheezemonkhai (638797) | more than 9 years ago | (#12010756)

Surely by publishing the data they have to publish how they came to the conclusion that the data leads to and why that data should be trusted as accurate.

If they have published, then nobody else can patent the idea, and i would hope that somewhere in the paper would be an explanation of the methods used to calculate the data.

Otherwise it would be like saying AMD/Intel is crap because I say so, here is a link to some data that compares a 486 to a n modern CPU.

(Actually as an aside that does kinda sound like th press release for the Turion Mobile thing or what ever it's called :S)

Where? (1)

Megasphaera Elsdenii (54465) | more than 9 years ago | (#12010775)

McKitrick & McIntyre (M&M), the critics, have published their complete source code


Uhrm ... where? I haven't been able to find any code on any on of the pages mentioned. I agree it's essential to disclose all data and source code ...


and it's written using the well-known R statistics package
... especially since R can be such a pain (sorry, struggling right now)

Arguments for & against open-source (5, Interesting)

G4from128k (686170) | more than 9 years ago | (#12010784)

Arguments for open-source science:
  1. Replication: Science thrives on replicable results. If researchers don't publish everything, others cannot replicate the results and the original findings become suspect.
  2. Knowledge Sharing: If the point of publicly funded academic research is to advance human understand of the world, then open access to methods (code) is a key part of that.
  3. Reduce/Eliminate Stealth Patents: Releasing knowledge into the public domain will help nip patents in the bud.
  4. Preserve Fair Use: University's trends toward turning research into money is threatening the basis of fair use for researchers. How long will it take intellectual property owners to get regulations on "fair use" because academic research has turned into another big, for-profit, corporate enterprise.

Arguments against open-source science:
  1. Replication: Science thrives on replicable results. But the key is independent verification. If one scientist simply reuses another scientist's code, there is a chance (high, some would argue) that faults in that original code would corrupt both scientists' results. Closed-source forces independent verification.
  2. Commercialization: If the point of publicly funded academic research is to create widely-used products and services, then the system needs some scheme for protecting the value of intellectual assets. Where the cost of bringing the product to market is very high (e.g., pharma), the company/investors needs some assurance that another company can't just copy the results when the product comes out.

I'm sure there are arguments on both sides.

Re:Arguments for & against open-source (1)

orin (113079) | more than 9 years ago | (#12010876)

Few experiments are directly replicated unless the original experiment found something really unusual. The reason for this is that it is difficult enough to get funding for novel research, trying to get funding to replicate what someone else has already done is even more difficult. Sure, there are some experiments that you can throw a grad student at - but for the most part, faculties and sponsors want you to find out something new with their dollars. A lot of scientists as well aren't willing to spend years/months following exactly in someone else's footsteps.

Re:Arguments for & against open-source (1)

KiloByte (825081) | more than 9 years ago | (#12010909)

Well, we're talking about publically funded research. Commercialization is a valid concern only if the research was done using private funds.

The "value of intellectual assets" is paid by the government, and thus, is a property of the government (and thus goes into Public Domain).

If you want a monopoly on the fruits of your research, sure, go ahead! Just use your own funds for it. We deserve the results of the research we paid for with our taxes.

Re:Arguments for & against open-source (1)

kenthorvath (225950) | more than 9 years ago | (#12010927)

Where the cost of bringing the product to market is very high (e.g., pharma), the company/investors needs some assurance that another company can't just copy the results when the product comes out.

You mean a patent? Anyone care to comment on a related note about why publicly funded research (like at a university) should be able to secure patents for the researchers? I have seen many an experiment hampered by a patent/NDA/legal nightmare when collaborating with other universities. The university pushes for their researchers to secure patents. Why shouldn't the taxpayers benefit immediately? Why have to wait 17 years?

I have been asked several times to try to secure a patent for the university on some piece of code or algorithm that I needed to devise for doing data analysis. I have always refused. But I am just a student. It's not clear to me that a professor or paid researcher has that right.

Voodoo, not science (5, Insightful)

climb_no_fear (572210) | more than 9 years ago | (#12010786)

I'm of the opinion that anything that gets published should be published in its entirety, at least at some point. For example, people who publish protein structures can put the coordinates "on hold" for up to 18 months.

And to say because the research is done with "taxpayer's money" is missing the point: If you can't reproduce every step, it's voodoo, not science. And we make policy decisions based on science, not voodoo (I hope).

Re:Voodoo, not science (1)

hununu (585852) | more than 9 years ago | (#12010988)

I'm of the opinion that anything that gets published should be published in its entirety, at least at some point. For example, people who publish protein structures can put the coordinates "on hold" for up to 18 months.

This is not true. If they publish the structure in any high-profile scientific journal [rutgers.edu] (which usually means that the protein structure is of extreme relevance) they are forced to **immediatly** disclosure it. Normally, no one holds structure information after the paper is published.

BA

Re:Voodoo, not science (1)

climb_no_fear (572210) | more than 9 years ago | (#12011070)

Pharma companies do it all the time.

real government research goals (5, Informative)

MyRuger (443241) | more than 9 years ago | (#12010787)

Obviously you have never written an SBIR or BAA. You when you do research "At the tax payers expense", you need to show your plans to commercialize the results of the research. The government wants you to create a IP twoards a commerial project which will spur the economy, not to contribute to the scientific community as a whole. Take it as you will, but I think that most research would not get funded if your commertilization plan was to release it on sourceforge.

Re:real government research goals (0)

Anonymous Coward | more than 9 years ago | (#12010971)

The taxpayer contributes to the economy. Otherwise he wouldn't have any income to pay taxes on.

Patents afford one the opportunity to protect ones IP whether it's published or not.

Going a bit further consider that publicly funded research made available for ANY member of the public to commercialize could well result in greater economic growth than protecting the results for company 'A'. What proof is there that this is not the way things would work out?

Not in all cases. (3, Insightful)

Shivetya (243324) | more than 9 years ago | (#12010795)

While I would like all works performed for the government that are not of National Security importance to be more open I don't think it is necessary.

A lot of work peformed for government agencies is contractual with businesses. These same businesses employ tricks of the trade and such to deliver what is required. To have them detail how the work is just suicidal. The same goes for software they develop for use by the government. Unless specifically addressed in the contract I do not believe there is a right to disclose the code, let alone make it available to the public.

That last part is key. Even if they disclose the source to the government there is no obligation on either party to make it public.

This argument that they have something to hide is childish. It is designed to provide no leeway. Simply put, once labeled as such what other option other than disclosure exist? You might as well say "You have to release it, its for the children" and then proceed to use whole "hates kids, wants kids to die" guilt trip that is far to common in politics today.

Summary. Release it if only its an upfront requirement of the project and agreed upon by both parties. In the future a requirement by law that all government projects must be fully disclosed to include the source of any software may be nice but I bet it would have so many exceptions written into it that it would result only in a "feel-good" law.

Re:Not in all cases. (1, Insightful)

Scareduck (177470) | more than 9 years ago | (#12010989)

There's a difference between "work for the government" and fundamental research. If I'm building a missile guidance system, or a database application to manage government carpools, or a light rail control system, there's no reason to let the code out. On the other hand, if these guys are telling us their model is the whole of the argument, that the model says the ice caps are melting and it's CO2 doing the damage, we damn well better have that code.

Re:Not in all cases. (1)

Vo0k (760020) | more than 9 years ago | (#12011024)

Actually, THIS code is not only of National Security importance. It's of Global Security importance and NOT disclosing it may endanger whole planet. Sure disclosing it CAN endanger several of US businesses, therefore impacting the US economy -> National Security, but PLEASE set your priorities straight!

taxpayers vs boffins (5, Informative)

dos_dude (521098) | more than 9 years ago | (#12010810)

This is an extremely difficult issue, although it sounds pretty trivial.

For one thing, the taxpayer is rarely participating in discussions like this one. Moreover, the success of scientific institutions is often measured in terms of number of patents, successfully launched businesses by former students/researchers, etc. So not only is there little or no opposition to closed-source software (or scientific articles!), there are also good reasons for researchers to go the closed-source road.

Some researchers have a tendency towards secrecy. Some even seem a little paranoid when it comes to their data and methods. You could compare this to the tendency of the OSS zealot to suspect bugs, glitches, and omissions in any piece of closed-source software.

And as a German side-note: There are laws over here that require you to have the patentability of any piece of software you develop checked by university lawyers. GPLing something is technically illegal for a researcher. I have no idea how this is regulated in other countries.

You are not entitled (1, Interesting)

Anonymous Coward | more than 9 years ago | (#12010822)

Are you entitled to all of the NSA's or CIA's secrets just because your tax dollars paid for it? No. In science, when you publish results, you publish it in such a way that others could reproduce it. If they can't, they publish their results and discredit yours. There is no need for everyone to make their source code available for everything they do. Also, it may give your competitors an advantage if you are forced to publish code for which you are going to do more with. Science is fairly open but it is competitive for grants and people are entitled to keep source closed that they intend to do further cutting edge work with. Having said that, I and others often make their code available. It is rare to find cases where people selfishly hoard useful code in my field anyways.

Re:You are not entitled (2, Insightful)

linuxdoctor (126962) | more than 9 years ago | (#12010881)

In science you don't simply show the results of your research, you also describe you arrived at them. Science has always been like that. With more and more science becoming dependent on computers, it naturally means that one must describe the algorithms used to arrive at those results.

The easiest way to do that is to show the source code.

These "closed source" scientists need to remember their high school math teacher's admonitions to show their work.

Re:You are not entitled (1)

Ignignot (782335) | more than 9 years ago | (#12011054)

Except we are entitled to all of the NSA and CIA's and postal service and FDA and TSA and DoJ secrets. Sometimes they can be witheld for reasons of national security, but eventually they are supposed to be released to the public. And while the pentagon does think that global warming is a threat to national security, I doubt we can deal with it by keeping facts about it secret.

Taxpayer funded projects should be free. (1, Insightful)

Anonymous Coward | more than 9 years ago | (#12010835)

Most projects the ideas are free, but the results are not. Seems strange...

Everything funded by the taxpayers should be free, regardless; ideas, results, and any tools built to obtain those results.

too good to be true (1, Funny)

Anonymous Coward | more than 9 years ago | (#12010841)

This article has the potential for 2 flamewars. For or against global warming and for or against open source. Oh joy!

Taxpayer's expense? (0, Offtopic)

flajann (658201) | more than 9 years ago | (#12010867)

Rather than worrying about whether taxpayers should be paying for closed-sourced solutions, ask the question of why taxpayers are paying taxes at all, given that the ROI is mighty poor.

Eliminate compulsory taxes, which are unconstitutional anyway, and let people choose where their money goes, if it goes anywhere at all.

That way, silly projects like this would never see any funding.

If you were wondering what real scientists think (3, Informative)

Uksi (68751) | more than 9 years ago | (#12010904)

The blurb author attempts to paint one side as having something to hide, since they only released a part of their source code. Nevermind that both papers' data can be independently validated--no no, one side is bad for only describing the algorithm and not its source code!

So a team of real scientists (that is, by folks who work in climate science, not reporters or pundits) wrote a Dummies Guide [realclimate.org] to the latest controversy. Click on the link for a nice question-by-question breakdown, but I'll spoil the conclusion for you:

(MBH98 is the old paper with "closed" source, MM05 is the new "open source") paper)

7) Basically then the MM05 criticism is simply about whether selected N. American tree rings should have been included, not that there was a mathematical flaw?

Yes. Their argument since the beginning has essentially not been about methodological issues at all, but about 'source data' issues. Particular concerns with the "bristlecone pine" data were addressed in the followup paper MBH99 but the fact remains that including these data improves the statistical validation over the 19th Century period and they therefore should be included.

8) So does this all matter?

No. If you use the MM05 convention and include all the significant PCs, you get the same answer. If you don't use any PCA at all, you get the same answer. If you use a completely different methodology (i.e. Rutherford et al, 2005), you get basically the same answer. Only if you remove significant portions of the data do you get a different (and worse) answer.

9) Was MBH98 the final word on the climate of last millennium?

Not at all. There has been significant progress on many aspects of climate reconstructions since MBH98. Firstly, there are more and better quality proxy data available. There are new methodologies such as described in Rutherford et al (2005) [realclimate.org] or Moberg et al (2005) [realclimate.org] that address recognised problems with incomplete data series and the challenge of incorporating lower resolution data into the mix. Progress is likely to continue on all these fronts. As of now, all of the 'Hockey Team' reconstructions (shown left) agree that the late 20th century is anomalous in the context of last millennium, and possibly the last two millennia.

Read the rest [realclimate.org] for more explanation.

Re:If you were wondering what real scientists thin (1)

Uksi (68751) | more than 9 years ago | (#12010951)

I think the important conlusion of this guide is that if you take all of the original Mann, Bradley and Hughes data and run it using the same fully open-source algorithms of McKitrick & McIntyre [uoguelph.ca] , you get the same results.

Which is reasonable since MM's argument is about source data and not methodology (as per this guide [realclimate.org] ).

Isn't it already? (0)

Anonymous Coward | more than 9 years ago | (#12010933)

I was under they impression that, with current laws, they have to disclose the entire source code. Any research that goes on at a university, without being directly classified (such as military funded research may be), should ("should" as in "by law") be obtainable for the general public some way or other.

I am not a lawyer, would anyone who is care to correct me if I am wrong?

Should they be _allowed_? (1)

Tom7 (102298) | more than 9 years ago | (#12010968)

should they be allowed to generate 'closed-source' solutions at the taxpayers' expense?

I think it's not fair for a public-funded project to do something like create a product and sell it without source code, or patent their work. But that doesn't mean that every artifact of the research project needs to be made public, necessarily. In this case, the end product that the grants paid for is the scholarly paper, not a computer program. Just as we don't demand their notebooks, time cards, e-mails, and meeting transcripts, it seems okay to not require them to publish the source code of a tool they wrote in the course of doing research. So I don't believe this is a behavior we should be legislating against.

But this only addresses the question of "should we require them to release the source?" Another undertone of the article is, "should they release the source?" I think it's clear that their work is at the center of a controversy, and that other researchers want to try to reproduce their results. It seems clear that making their specific methodology public (source code) would help answer the controversy, so as researchers interested in the truth, they should release it.

Re:Should they be _allowed_? (1)

nagora (177841) | more than 9 years ago | (#12011059)

In this case, the end product that the grants paid for is the scholarly paper, not a computer program.

But the program is part of the authority of the paper. Put it like this: if the program was revealed to be a random number generator, do you think it would reflect badly on the value for money the taxpayers got? In which case, don't researchers have a duty to publish the program in order to help show the validity of their research, in all cases, not just this one?

TWW

Replication (2, Informative)

mwvdlee (775178) | more than 9 years ago | (#12010985)

Significant research data is generally replicated independantly of the original researchers for verification of the results. Without a description of the method of research used (in this case; the computer model), how can the data be replicated and thus verified? Indeed the very methods itself are commonly scrutinized in the scientific world and, IMHO, any scientist that does not approve of this is not looking for truth but for something else (personal agendas, fame, etc.).

Not detailing the methods used (in this case; giving the entire algorithms, either as source or as a 100% comlete and unambiguous description) basically limits the usefullnes of the resultant data as mere speculation, not proof nor even theory.

If I remember correctly, the computermodel in this case is known to include a rather lacking model of rainfall, which seems like a pretty big omision in a climate model to me.

in biology it happens too... (3, Informative)

operon (688118) | more than 9 years ago | (#12011003)

Today biology heavily depends on specific software to analyse lab generated data. However, even academic, public funded software are not open-source. It's a sad situation, but there are efforts like Bioinformatics.Org [bioinformatics.org] trying to change the situation.

Climate models (0)

Anonymous Coward | more than 9 years ago | (#12011035)

The UK Meteorological Office model was published under a fairly liberal licence I hesitate to call it "Open Source" or "Free Software", but certainly inspectable and runnable if you had the need.

Whilst in theory you could inspect this to find issues with the model. For most organisations without extensive assistance from the UKMO, wide scientific expertise, would not be able to gain much utility from it I suspect. In practice the main groups who used the model were supercomputer vendors, and computer scientists interested in how to optimise numerical computing solutions.

In some ways I'm not sure it helps the climate debate. I know the UKMO model had bugs, I found some. But by the time software gets this complex you are interested in validating the global behaviour, as much as validating the minutae of the code. If the model can match past climate change accurately you assume that the bugs don't matter that much until proved otherwise.

But ultimately you take evidence for the climate debate from a number of sources. If glaciers many 10's of thousands of year old are disappearing, it is a reasonable bet in my mind this is the hottest it has been for 10's of thousands of years.

Then again you can stare at the evidence, and still miss it, witness the first person who skippered a ship through the North West passage without encountering ice, who thought that the idea humans could melt the arctic ice cap was ridiculous.

I think the important reasons to make government software "free software", have little to do with good science, and more to do with good governance.

Although I can't see how publishing the code would make the science less good, and I can see how it might help.

How can you repeat results? (1)

geoffrobinson (109879) | more than 9 years ago | (#12011052)

Besides paying for the research, how can another check on the accuracy/repeat the results without the original code?
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