Open v. Closed Source-Climate Change Research 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?"
real government research goals (Score:5, Informative)
Re:The debate (Score:4, Informative)
CRAN is your friend (Score:1, Informative)
However, the name still sucks.
taxpayers vs boffins (Score:4, Informative)
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.
Re:Just because it's code it should be open? (Score:2, Informative)
Re:The debate (Score:4, Informative)
Re:But the Hockey Stick is True! (Score:3, Informative)
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].
If you were wondering what real scientists think (Score:3, Informative)
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)
Read the rest [realclimate.org] for more explanation.Re:The debate (Score:2, Informative)
Replication (Score:3, Informative)
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... (Score:3, Informative)
with open source, everyone can see you're dumb (Score:5, Informative)
Re:But the Hockey Stick is True! (Score:3, Informative)
http://www.geocraft.com/WVFossils/Carboniferous
Re:How much is enough? (Score:1, Informative)
if anyone wants to pad their resume they
are looking for a new editor.
Re:Taxpayer funded whitewashes (Score:4, Informative)
Mr. Tobin. Well, probably the most prominent--actually, there were two main areas negating the missile theory. One, of course, again, is the absence of impulsive loading, or very high-speed fracture and failure mechanisms.
But second was there were serious issues with every theory, or almost every theory, as to access of an external missile to the fuel, to the fuel tank. Even with, as I indicated earlier, if one would focus on an area where we did not recover all of the fuel tank, there were components nearby that would have blocked or at least recorded passage of any externally penetrating object. And if that were not the case, there were many layers, including the external underbelly of the aircraft, and that was recovered almost--a huge portion of that was recovered.
So that, basically, the only plausible theory for some of the missiles to have occurred would have been if there were missiles such that could maybe get through a 1- or 2-inch opening, make an immediate left, go 90 degrees through a seam, and then maybe take another 90-degree right, and then maybe reverse itself and come back over. But those were some of the considerations.
Re:But the Hockey Stick is True! (Score:3, Informative)
Yes, but that is why the Kyoto protocol is flawed. The authors of the cooking fire study estimated the warming effect of the soot was 30 times worse than that of the same mass of CO2.
Re:But the Hockey Stick is True! (Score:3, Informative)
http://abob.libs.uga.edu/bobk/whiteb03.html
The "doctrine of the antipodes" asserted that even if the Earth was spherical, no humans lived on "the other side" because they'd have their feet in the air, wouldn't be able to observe the descent of Christ at the 2nd coming, etc.
Variants of this doctrine persisted long after the nominal sphericity debate had been settled, and I'd argue that until something like the modern view of a spherical Earth, antipodes and all, was generally accepted, it is not quite correct to claim that it was "generally accepted that the earth is round".
Ancient ideas are alien to our own, and it is easy to impose our modern understanding on the words the ancients used, creating great distortion. So I get to disagree with everyone: in the first millenium C.E. people neither believed that the Earth was flat, nor that the Earth was round in the modern sense. They believed the Earth had a special place in the universe, and their understanding of the shape and geography of the Earth grew out of Church doctrine as much as emprical observation.
--Tom
Re:If you were wondering what real scientists thin (Score:4, Informative)
Second of all, there was a flaw in the original algorithm that was pointed out by McIntyre and McKitrick before they even got to the bad data being put into the equation.
And, to top it off, Mann's equation always produces hockey-stick graphs [newsweekly.com.au], even with randomly distributed data.
Don't point at Mann's own site as a defense of Mann.
Replication (Score:3, Informative)
1) Science functions only on open review. If you can't duplicate someone's results, they are useless (c.f. Ponds and Fleischman [sp?]). A scientific result is only of value if it describes a consistent replicatable process. This is why I consider the closed source work to be completely meaningless. It may be perfect, it may be bug-ridden garbage, we'll never know!
2) Every tax paying American has paid for my code and work. While I regularly feel they're not getting their money's worth, I definitely don't feel they're paying me to enrich me. They are, in a very real sense, my bosses, and I AM obligated to report to them, if they care. Think of it as a company requiring rights to your work.
3) As an academic working on a fairly limited budget, open source and free software have been a godsend for me and everyone else I know. We run linux because it's more efficient, secure and FREE; we use free or open-source compilers; and we cobble together high-perormance computers and beowulf clusters out of miscellaneous bare metal and lots of googling. The only piece of software I routinely have to pay for is MATLAB.
how about yes and no instead (Score:2, Informative)
Basically the government might give with one clenched fist, and take back with a team of mules pulling. The National Security Archives [gwu.edu] are one group of folks constantly struggling with the layers of governmental coverups. It's ongoing and pretty telling. They are having mixed results, some good finds, then a lot of what they are calling "over classification and pseudo classification" still existing. And then the problem becomes getting the information out to joey and janey citizen and voter, the "news" only mostly covers current, people have just been conditioned to accept todays fairy tales as "data and fact", over and over again. Then years later the real story comes out, by then it's too late to influence elections, etc. Look at the finally revealed data on the "Tonkin Gulf attack" that was the primary "lawful" reason for the Viet Nam war. They have (relatively historically recently)finally and quietly admitted it was an invention, but years too late to make it matter for most purposes.
So, in part I agree, some of what the government does needs to be kept secret, but it appears quite a bit is still overzealously kept hidden, primarily to protect the guilty-of-corruption-and-malfeasance aspects of government.
Re:Voodoo, not science (Score:2, Informative)
http://www.rcsb.org/pdb/cgi/explore.cgi?pid=40021
You can use the status search link at PDB
http://www.rcsb.org/pdb/status.html [rcsb.org]
to find lots of things on hold (I found 211 when searching for Status "release on a certain date" AND "Release date" > 1 April 2005.
Also, I work at a pharma company, do publish and have seen lots of competitors do the sort of thing above.
The Bayh-Dole Act changed all that (Score:3, Informative)
It's worth noting that, while it makes sense that taxpayer-funded research should generate 'open-source' solutions, federal law dictates otherwise.
The Bayh-Dole Act [uc.edu] was passed 25 years ago, which dictates:
So in other words the government has dictated since 1980 that government-funded research should not produce open-source solutions, necessarily, as the results of research are to be considered private-sector profit-generating centers for the host universities. (The implications for the 'next BSD4.3 TCP/IP stack', or similar advanced research, are obvious.)
Anyway, regarding the 'hockey stick' controversy, Tim Lambert's weblog [unsw.edu.au] is worth a read.
Re:Where? (Score:3, Informative)
Unless I'm mistaken...
Source [climate2003.com] Data [climate2003.com]
Re:If you were wondering what real scientists thin (Score:3, Informative)