I don't care if climate scientists consider Mcintyre an adversary. Does everyone remember how the shuttle software is written? The testing team has an adversarial relationship with the developers. This is how quality work is forged. If these guys can't stand to have an adversary review their work, I submit that something is seriously awry.

Peer review isn't strong enough right now. If you read these docs, you find that they are asking that reviewers be hand-picked for "objectivity", and it's clear from the context that this means "not global warming skeptics". Peer review needs to be more adversarial. I don't think the scientific literature is much less important than the shuttle software.

If the scientific method is working, then the data and methods should be able to withstand ANYONE'S scrutiny. It should be completely open. Most people here are strong supporters of open source software. Don't tell me for one second that free and open scientific debate doesn't benefit exactly as much from being open.

Climate research funding is not paid so well as to give researchers time to deal with these specific issues. Maybe it should be. But it isn't.

McIntyre is the main target of the Hadley Centre scientists' ire, which I suspect has more to do with the fact that he's actually competent and knows how to interpret the data they release, something they oddly seem to fear.

Lest we forget, scientists like those at the Hadley Centre have their own incentives, as their funding is directly correlated to the prevailing fear of global warming. Moreover, the debate has become so poisoned that few scientists would be brave enough to go far down a route which might dispute even a small part of the conventional wisdom for fear of being labelled a 'denier' (a term you used elsewhere in this discussion).

But this is not what scientific debate is supposed to be about. This is supposed to be a profession ruled by the Scientific Method and dedicated to the primacy of experiments and data. What your personal incentives are or who pays your salary should be secondary to the results you produce. Science should have no place for flippant ad hominem dismissals, nor for the talk of 'enemies' that pervades this thread and the emails of the Hadley scientists.

We should be thankful for the role played by men like McIntyre, because they act as an important quality check on data which will be used to make massively important political decisions which may have huge impacts on each of our lifestyles and finances. We should have more adversarial data analysts, not fewer.

There is so little fact checking being performed and present day thermometer readings are all but useless as most are contained within urban heat traps. Global Warming isn't a question of whether CO2 or Methane contribute to higher absorption of infrared energy. It's a question of what its effects are, and what the environment's reaction will be (IE will heated oceans produce more clouds and produce a sharp reversal in the effect or will it produce no effect at all, etc.).

The other thing that concerns me is the political nature of 'climate science', not only are so many politicians embedded in being 'green', but the organisations themselves have a political agenda that makes them (at least appear as though they're) prone to bias. Most emphatically claim that our only alternative to fossil fuels is the mass development of alternative energy, which is flat out bullshit.

Firstly before we get into any discussion of carbon sequestration, these 'scientists' and the public in general (thankfully many politicians - never thought I'd have thankfully and politicians in the same sentence without 'they're all dead' inserted between the two - haven't ignored the green-glowing Elephant in the room) make no discussion of the one main, technologically available alternative we have: Nuclear.

A renewed Nuclear power project in virtually every western country, including widespread MOX usage would vastly reduce our need for fossil fuels, whilst barely effecting the amount of highly radioactive nuclear waste we produce.

It's likely just me, but when 'scientists' purposefully neglect to mention existing and well established technology as a solution to our energy crisis it makes me question their motives. Who are really paying for these studies if their only suggestion is alternative energy?

http://news.ycombinator.com/item?id=952651

Sure, and if researchers are being forced to draw the line higher than usual due to external pressure from highly funded deniers, whose fault is that?

EDIT: Besides, if we define the adversary to be somebody making legitimate critical analyses of your data and models and showing up flaws in them, isn't dealing with that meant to be part of a scientists job? How different is it in practice to defending your work against criticism from other, supposedly more respectable, scientists?

It's ridiculous to claim that a lack of resources is a valid reason for intentionally hiding data from people with the skill to perform an adversarial analysis on it. If a scientist can't defend his results against Steve McIntyre, it means his results are indefensible. The person doesn't matter; the data, and its integrity, do.

EDIT: referring to McIntyre:

The guy is a semi-retired mineral consultant. He's been paid his whole life by energy companies. He is not a scientist and the so-called "valuable contributions" he made were determined to be of "little significance":

http://www.sourcewatch.org/index.php?title=Stephen_McIntyre

In the specific article you provided, all of the relevant links were broken.

1) Archive a copy of all raw data series used in publications with a public database

2) Archive a copy of the final processed data series used in publications with the same database.

3) Archive a copy of the source code used to produce figures and tables with the same database.

The default stance for publicly-funded science should be openness, not secrecy.

Hell, these would be good steps for any serious journal to take, on any subject, regardless of federal funding.

edit: Example of the pathology we need to fight:

>>"We should be able to conduct our scientific research without constant fear of an "audit" by Steven McIntyre; without having to weigh every word we write in every email we send to our scientific colleagues. In my opinion, Steven McIntyre is the self-appointed Joe McCarthy of climate science. I am unwilling to submit to this McCarthy-style investigation of my scientific research. As you know, I have refused to send McIntyre the "derived" model data he requests, since all of the primary model data necessary to replicate our results are freely available to him. I will continue to refuse such data requests in the future. Nor will I provide McIntyre with computer programs, email correspondence, etc. I feel very strongly about these issues. We should not be coerced by the scientific equivalent of a playground bully. I will be consulting LLNL's Legal Affairs Office in order to determine how the DOE and LLNL should respond to any FOI requests that we receive from McIntyre."

I fear that by the time the political debate ends, a lot of good research is going to become collateral damage, which would be an awful result.

If i may extract quote from the message you replied to: As you know, I have refused to send McIntyre the "derived" model data he requests, since all of the primary model data necessary to replicate our results are freely available to him. I will continue to refuse such data requests in the future. Nor will I provide McIntyre with computer programs, email correspondence, etc. I feel very strongly about these issues. We should not be coerced by the scientific equivalent of a playground bully. I will be consulting LLNL's Legal Affairs Office in order to determine how the DOE and LLNL should respond to any FOI requests that we receive from McIntyre." (emphasis added by me)

I do agree with you that transparency is the litmus test of good science. At the same time, catering to that can lay you open to abuses from, well, trolls.

As an analogy, suppose I had a bee in my bonnet about Linux security and I kept demanding that Linus send me copies of his binaries every time he did a new commit. He would rightly tell me to get the sources and build it myself and leave him alone. and in turn I could post lonely rants along the lines of 'why won't Linus Torvalds come clean about Linux security'. It would be quite meaningless, but it would sucker in some people. If I was sufficiently clever I could probably get quoted by someone at Microsoft or in the BSD camp.

The parallel I am drawing here is to the public datasets and methods laid out in published, peer-reviewed papers. If McIntyre is so sure that either the methods or the datasets are flawed, why not follow the established practice of writing to the journal and challenging the paper, or even submitting his own analysis of the public data and explaining how it improves on existing analyses? Instead he posts in some minor journal which is not part of the scientific corpus, not a hard science journal, and has been widely accused of lax publication criteria.

One of the things that really bothers me about the skeptical crowd (as opposed to individual skeptics) is that they employ a lot of same kind of arguments as the proponents of 'intelligent design' do, claiming there's an ivory-tower conspiracy that silences all dissenting views and shuts them out of publication. Any time you have a bunch of people going 'OMG teh conspiracy', it's time to whip out the old bullshit detector...and all too often, comparing their claims with the published literature sends the BS detector way into the red.

Sad fact: most journal articles do not include all the details necessary to reproduce their results. There are usually all sorts of heuristics and tricks used which are not interesting enough to include in the paper. Typically, the experts in the field all know each other and share source code/tricks in private conversation.

As for the "ivory-tower conspiracy", it apparently isn't bullshit. As these emails reveal, there is a conspiracy to make it difficult for Steve McIntyre to examine published scientific results. There is also a conspiracy (revealed in other emails) to oust climate skeptics from scientific societies. It isn't paranoia if they are really out to get you.

It looks like, from the emails, (and I hate to prejudge) that "submitting his own analysis" is not going to be an option for him.

Which leads me to the discriminating factor -- if publicly available data and publicly available processes allow an independent to process the data and reach different conclusions and be published that's fine. But that's not what is happening here.

There is no mystery about what happens between Linus' source code and the compiled executable. It's imminently transparent and reproducible. Science should be exactly the same way.

I also agree with having alarm bells ring whenever you hear "OMG the conspiracy!". I would humbly add, however, that groupthink is a real and prevalent problem -- not just among academics but everybody. If your groupthink reaches a point where you view that it's "us against them" and that your job in academia is to defend a pre-established position? I'm thinking you should be fired and never work in that field again. It's critical among scientists more than anybody else to have an open mind and a large dose of humility. The entire idea of science is that what you're working on will be replaced or fine-tuned later on down the road. Everybody is going to be wrong to some degree. It's part of the job. Big egos are not such a great thing.

I don't have a lot of tolerance for taking public money and playing politics with it, even if you are proven correct in the long run. One man's troll is another man's skeptic, and it's your job as an honest scientist to deal with them. Good scientists should first and foremost always be open about data and methods. Good grief, it's 2009, publishing all of this on a wiki somewhere is trivial.

This is the meat of the matter. Scientists write letters to journals all the time saying that they think an author overstretched. Those letters, in and of themselves, do not negate the previous research. Scientists also write original papers showing that a previous hypothesis is invalid. Those papers, if they are well written, are easy to publish, especially if they make the journal more interesting.

This is useful not just for the purposes of auditing, but also for the purpose of scientific progress. I would be able to build on other people's work much faster if I could download and modify their code rather than just rebuilding it myself.

In all seriousness, though, a lot of labs view their in-house codes as a competitive advantage. You may not like it, but science has become commercialized, the labs/unis are all competing about the same grants, which creates a competitive enviroment.