Thursday, November 18, 2010

The Wayforward Machine

The bunnies, being young, have the habit of believing that what they see is the way it always was. Bishop Hill has an amusing post (UPDATE: and an acknowledgment of this post) example of this fallacy where he goes after Nature and Phil Jones

Nature has an editorial on the Climategate anniversary to add to its recent profile of Phil Jones.

For critics of CRU and their, sometimes legitimate, complaints about data access to be taken seriously, they must be more specific about who should be more open with what, and address their concerns at the correct target. It remains the case that many of the data used by CRU scientists are covered by agreements that prevent their wider distribution. This is not ideal, but it is hardly the fault of the CRU researchers — even if they did seem reluctant to share.

This is an extraordinary thing to say. Jones et al 1990 was published in Nature. Nature requires authors to make data available on request. How can they argue that it was restricted by confidentiality agreements?
Eli, trying to be a nice Rabett, pointed out in a comment, that Nature's policy on materials and methods only was established in January 1997
As a condition of publication authors are required to make materials and methods used freely available to academic researchers for their own use.
Before that, the only condition was that authors were that
Nature requests authors to deposit sequence and x-ray crystallography data in the databases that exist for this purpose.
Now anyone interested could go a few rounds about what constitutes an academic researcher, or whether means means means (gottcha) or software, but what is clear is that there was no data sharing condition established in 1990 for articles published in Nature, and to demean (again) people for not obeying rules that did not exist is so very Bishop Hill

Oh yes, the good clergy appears to have deposited Eli's comment directly into the memory hole, but one may always hope for resurrection.

UPDATE: The current Nature policy is (and the observant may note the changes)
An inherent principle of publication is that others should be able to replicate and build upon the authors' published claims. Therefore, a condition of publication in a Nature journal is that authors are required to make materials, data and associated protocols promptly available to readers without undue qualifications in material transfer agreements. Any restrictions on the availability of materials or information must be disclosed to the editors at the time of submission. Any restrictions must also be disclosed in the submitted manuscript, including details of how readers can obtain materials and information. If materials are to be distributed by a for-profit company, this must be stated in the paper.

50 comments:

John Mashey said...

But really, this is no surprise, given that Montford (aka Bishop Hill) in The Hockey Stick Illusion (HSI):

a) Twice cites David Deming from my favorite dog astrology journal, i.e., JSE, discussed here in bunny-land a while back, a classic discussion. In my mind, dog astrology has overtaken sheep suffocation, although reasonable people can argue.

b) But then:
"HSI, p.28: has:
"Although Deming himself did not identify the email's author, Richard Lindzen [23] of MIT has confirmed that the email was written by Jonathan Overpeck..."

The first is true, as Deming did not name Overpeck. He might have had to prove it. But in Lindzen p.11, we find:
"According to Demming, 2005, Jonathan Overpeck, in an email, remarked that one had to get rid of the medieval warm period." (Demming (sic)).

Montford's own words correctly contradict Lindzen's "confirmation."

No email, credible or otherwise, has been presented. Maybe the dogs ate it."

c) In essence, the only evidence that Overpeck sent this is the Overpeck email cited ~400 pages later wherein Overpeck says he didn't...

Fortunately, Montford is not an academic, where falsification/fabrication is seriously.

d) You can read all about it here.


d1) A talk page typically running 20 edits/day ... suddenly went to 0 for a day or so.
d2) Then, frantic attempts to delete it occurred, fended off by The Stoat.
d3) Of course, no one ever actually *answered* it, as it was more important to argue about what some business writer in a local newspaper said about HSI.

Marco said...

Make materials available freely? They nuts? Buy your own damn sodium chloride and supercomputer!

Belette said...

Yer pic is broked, wabbit.

Belette said...

Just for fun, I added this. We'll see if it survives:

Well, you already know the answer, because Eli posted a comment and you deleted it (http://rabett.blogspot.com/2010/11/wayforward-machine.html), but at least part of the answer is:

Nature's policy on materials and methods only was established in January 1997: "As a condition of publication authors are required to make materials and methods used freely available to academic researchers for their own use." Before that, the only condition was that "Nature requests authors to deposit sequence and x-ray crystallography data in the databases that exist for this purpose."

Bishop Hill said...

I've posted a response.

Martin Vermeer said...

FOI/EIR legislation didn't exist in 1990 either... here is a bit of history.

What also didn't exist was the paranoia behind this nonsense.

Anonymous said...

I'm assuming that the good Bishop will be providing the sequel to the HSI. Perhaps 'The Wegman Chimera' could be a working title, and it could be based on Deep Climate's and John Massey's work.

Sounds like a plan.

DangerMouse

Marco said...

Great, Montford added another lie to his response:

http://www.cru.uea.ac.uk/cru/data/availability/agreements.pdf

There, several agreements, with such choice words as
"The condition is that you do not use them commercially or give them to a third party."

"UKMO data / software so obtained may be used solely for the purpose for which they were supplied. They may not be used for any other projects unless specific prior permission has been obtained in writing from the UKMO by a NERC Data Centre. Note that this applies
even for other bona fide academic work."

"Please do not supply t h i s data to third parties, unless
authorized by us."

Ah well, I guess Montford will come up with yet another pathetic excuse, just like he did with the false claim that an article was kept out of the literature because it contradicted the IPCC. Montford's defense when someone pointed out that the paper WAS published, just not in Nature? Pointing to one positive comment from one reviewer (that one positive reviewer was David Deming).

Horatio Algeranon said...

I'm assuming that the good Bishop will be providing the sequel to the HSI. Perhaps 'The Wegman Chimera' could be a working title,

or maybe "The Hokey, Slick Delusion (aka Wegman Report)" by Lord Montford (with a Wayforward by Judith Curry?)

Jim Bouldin said...

Some of the comments to that editorial are "interesting". People believe what they want to.

John Mashey said...

Since the Bishop is here, perhaps he will address the issue that I raised, which appears to be base the key setup for the whole book on:

a)Quotes from an Oklahoma geophysicist Deming, doing a gushing review of Crichton's book, in the JSE, publisher of dog astrology.

b) Falsification/fabrication of a claim by Richard Lindzen.
Search: ffp falsification


c) That sure looks like defamation of Jonathan Overpeck.
Defamation is complicated of course, and UK laws are especially interesting, but:

1) We all know about the dangers of out-of-context emails ... but Deming never presented any proof it was Overpeck, and would not say so in his statement to Congress. Lindzen wrote an untruth when he cited Deming's article saying it was Overpeck. The Bishop then wrote a further untruth in saying that Lindzen confirmed it.

Now, it could be that the Bishop has problems reading simple English, or it could be that he didn't actually study the 2 articles, esp. Lindzen (i.e., he might have gotten this from some other blog) ... but it is certainly a clear *untruth* that is fairly integral to setting up the storyline of HSI. (At the very least, this is "reckless disregard of the truth").

2) People have to read the untruth and believe it. Fortunately, the blogosphere makes that easy to find, as people propagate things. Even better, the wonderful record of the intensity of belief shown in the HSI Wikipedia talk page discussions is a real help. Should there ever be a defamation lawsuit, there's some great material to mine there, especially given the attempts to eradicate the dog astrology discussion.

3) Finally, reputation must be damaged (in US, anyway, not in UK). Overpeck's scientific reputation is certainly undamaged, but he is certainly one of various people whose reputation with the general public has been hurt. One need only rummage the Web a bit to find tons of posts. But, again, that doesn't matter in UK. I'm not sure about Canada or Australia, but the Internet is everywhere.

===
HSI publisher is Stacey International.

I'm too busy with other things right now, but a nice polite letter to them might be in order (no deluges, please).

Polytroll said...

I think we need to go more in the direction of what crystallography has done. There was a long pattern of wrong structures, even by well-meaning workers. The imposition of a requirement to file data at the time of paper submission really cleaned up that field a lot (errors still occur but much less). It;s not just what the reviewers catch (or people looking at databases and resolving structures)...yes that happens more...but really that authors tend to be more careful. It's just human nature.

J Bowers said...

Marco -- "There, several agreements,.."

And referenced in the emails themselves. For instance;

"Data that we can't release is a tricky thing here at NCDC. Periodically, Tom Karl will twist my arm to release data that would violate agreements and therefore hurt us in the long run"

EliRabett said...

Polytroll, yeah, that and better software to solve structures. . .

Horatio Algeranon said...

"We all know about the dangers of out-of-context emails"

...especially when the "context" in this case might be that the claimed email never existed to begin with.

Anonymous said...

Lets all worry about a paper published pre 1997. No climate science since?

There is so much evidence over so many fields over such a long period, but one imagined fault in one paper disproves the whole lot. There is an imagined fault because it comes up with an answer they do not like.

You won't provide the data you have already given me, you must be hiding something.

Are they going to criticise Guy Callendar next?

Little Mouse

Anonymous said...

I had a fit of the giggles when I read the dog astrology article in JSE. It's so unintentionally funny, it's an absolute scream. Thank you, John Mashey!

Are the faithful readers of Rabett Run aware of the existence of ANOTHER kind of skepticism??? Some people think cholesterol is not bad for you. Seriously.

http://www.amazon.com/Cholesterol-Myths-Exposing-Fallacy-Saturated/dp/0967089700/ref=sr_1_1?ie=UTF8&s=books&qid=1290235696&sr=1-1

What's next? "Alternative geology" a. k. a. flat earthers?

And informed citizens know all about the "birthers", who obsessively think that Obama is actually from Kenya.

Gotta go. Getting the giggles again....

Jim Bouldin said...

"It's so unintentionally funny, it's an absolute scream."

When I first looked at that, there was no doubt in my mind that it had to be a parody.

It's not a parody. Full stop. Blank expression. Silence.

John Mashey said...

Well, reasonable people can have different opinions about dog astrology, and I did struggle to decide whether that or the sheep suffocation were more illustrative. but really, JSE is *not* JIR. If it is parody, it is subtle beyond my comprehension. It is just too earnest. I offer the issue (Search for 19:2)

19:2
1) Balls of Light: The Questionable Science of Crop Circles
pdf

2) Children of Myanmar Who Behave like Japanese Soldiers: A Possible Third Element in Personality
pdf

3) Challenging the Paradigm pdf

4) The PEAR Proposition
pdf

5) Global Warming, the Politicization of Science, and Michael Crichton’s State of Fear
pdf

So, let us examine the rich veins of data to be mined in just this one issue. Even without dog astrology or sheep suffocation we have:

1) This is a scholarly debunk of electromagnetic influences in crop circles by the Italian equivalent of CSI(COP). Decent article.

2) Some Myanmar children behave like Japanese soldiers who died there in WW II. It concludes:
"The word reincarnation is applicable here, although this term is difficult to define in behavioral terms. We wish to suggest that some
aspects of the deceased person's personality-not necessarily all of them-are transferred in a way which cannot readily be explained by the alternatives we have discussed."

3) 'Abstract-During the last 30 years I have made several attempts to publish UFO-related articles in conventional science journals. Most of my papers or letters have been rejected. However, quite by luck, in my opinion, I was able to publish two short articles concerning the New Zealand sightings of December 1978 in the journal Applied Optics. This paper presents the story behind the publications."

Sadly, he has spent his life since trying to replicate his great success, but paradigm-ridden editors at places like Nature just do not understand.

4) a 50-page article: "Abstract-For more than a quarter century, the Princeton Engineering Anomalies Research (PEAR) laboratory has engaged in a broad range of experiments on consciousness-related physical anomalies..." ends with:
"It is our hope that when this laboratory, like Brigadoon, dissolves back into the mist of the more conventional academic countryside, that sublime spirit, along with the more tangible accomplishments, will also survive to inspire, sustain, and delight those who believe enough in the power of love to seek its manifestation in the future."

One can read of PEAR.

After running from 1979 to 2007 to detect various psychic phenomena, it didn't, but did spend money and embarrassed Princeton. People who had dedicated their lives to it were sad when it closed, but declared victory and went home.

5) That's Deming's article, quoted by the Bishop twice for key elements of his basic proposition. With company like this, how could it not be a reliable source?

Parody? No way. I invite you to pick an issue at random, take a quick look at all the articles.

Sou said...

"The bunnies, being young, have the habit of believing that what they see is the way it always was."

Eli, I thought you had more sense than that. BH doesn't believe what he wrote above any more than he believes anything else he writes. He's just trying to shore up dwindling support, saying what he thinks the conspiracy theorising deniers want to hear.

(On the other hand, maybe he is as stupid as he pretends to be.)

Anonymous said...

Dear bunnies and mices,

I bring you this:

http://curryquotes.wordpress.com/

I hope it will be an endless source of amusement.

Anonymous said...

"Since the Bishop is here,"

That was probably a drive by comment. The Bishop doesn't like being out of his back slapping comfort zone, like most denialists.

Anonymous said...

An @5:04,

Should that not be "Since the climate science paparazzi are here"?

Montford is a desperate, desperate man.


and Anon @5:01,

'Curry quotes' sounds interesting.....

Former Skeptic said...

I hope it will be an endless source of amusement.

No kidding. Her colleagues at GTech's SEAS should be reading this during faculty meetings just to see how their Chair's musings are viewed elsewhere...

Martin Vermeer said...

Anonymous 19/11/10 10:53 PM, I wasn't giggling when an article espousing this cholesterol denial made it to Finnish television...

John Mashey said...

JSE IS NO PARODY
HWQDAJ (He Who Quotes from a Dog Astrology Journal (well, He Who Must Not Be Named is on the screens again) would never quote a parody for crucial support for his book, would he?

JSE is absolutely serious, containing much work with carefully-done charts, formulae, statistics.

Here are the past research articles from JSE. All issues are freely available, except the last 4, which you can see if you join. Otherwise, you need to wait a year until you can read Ishida’s analysis of Hollander’s sheep death weight gains, “An automated test for telepathy in connection with emails” or “A brief history of abduction research.”

To be fair, one must of course sample, as I do occasionally whenever I need a break. Since this started with HWQDAJ’s use of Deming as a reliable source, I thought I would search for “Deming” and use that issue a fair sample. Deming was a moderately-frequent contributor in 2004-2005, with a burst of 3 articles.

Look for issue 19:2. When you see the PEAR article, it is worth knowing that PEAR members were long involved with JSE, which they assure us elsewhere is peer-reviewed. SO THERE. No parody, this.

clearscience said...

Curryquotes really is an interesting site. I think the more and more I learn about Dr. Curry, the more I wonder about her real intentions. Her recent post on Michaels' testimony practically agreeing with most of his supposed "findings" is all the proof I need.

Polytroll said...

Better software has allowed many more structures to be solved, but I don't think it has changed the habit of poor solutions. If anything, I see more people slagging away without having to understand what they are doing.

Ever solved a structure, Eli? The problems often have to do with a lack of knowledge of symmettry and thermal ellipses. If anything having done simpler structures by hand, gives you a better physical insight into what is actually going on. Also having seen a lot of problems, you can see the places where a grad student is likely to go wrong.

In any case, both better software AND more transparency can have an effect.


I maintain that it is human nature to be more careful when you know it is easier for people to check you.

John Mashey said...

Since "He-Who-Must-Not-Be-Named" has just returned to the movie screens, I'm inspired to create a new acronym:

HWQDAJ = He Who Quotes Dog Astrology Journal

but of course he must not actually be named.

EliRabett said...

Eli is more in the line of a Gaussian abuser, which suffers many of the same problems.

Polytroll said...

Popple died in 2004. Didn't realize he was gone...

http://en.wikipedia.org/wiki/John_Pople

Anonymous said...

Eli:

So let me get this right. You're saying that "team" member Jones never distributed data to other people because of this rule? Bullshit.

And Jones hasn't at this stage detailed the list of those entities that his group had an agreement with.

Stop supporting 3 week old road kill.

Martin Vermeer said...

John, finding this on cursory inspection of the HSI suggests that a thorough job, like you did on the WG, would hit paydirt big time.

Unfortunately His Eminence is not academically employed. Academic misconduct is so much more obviously, unambiguously and relevantly bad than libel, especially on Airstrip One.

Anonymous said...

We all will one day, John.

EliRabett said...

Dear Bullshit,

Jones was not OBLIGATED to distribute HIS data from that 1990 paper to anyone. His choice. He was under ethical restrictions with regard to proprietary data that was shared with him for that paper.

This is a point that McIntyre appears oblivious to also esp. wrt Yamal, MBH 98 and 99 and other such.

Anonymous said...

"An inherent principle of publication is that others should be able to replicate and build upon the authors' published claims."

EliRabett said...

Dear Bullshit

If they do the work. Something that Mann and Jones detractors do not appear willing to do.

Anonymous said...

Do you think this inherent principle did not apply to Jones in 1990?

pough said...

I think Anonymous Bullshit has gotten a bit confused by the Internet Age. Replication of work is not like downloading an app. It is like writing your own. Or maybe it's like getting the source code to an app that is made for a different OS and having to port it and find the data yourself. Although that last analogy might be a bit beyond most peoples' experience.

Anonymous said...

So, pough,
you think data of station histories is not like an 'app'. I think we would agree.

Former Skeptic said...

@Anonymous Bullshit:

Yawn. Do you have a point?

Anonymous said...

@ Martin Vermeer,
Isaiah 47:4
.)

Horatio Algeranon said...

RE "Curryquotes" site

That's all great and probably very enlightening, but just a bit balloonimous.

Horatio has a rather short atention span (being a mouse and wannabe poet and all) and what he really needs is "Curry Cliff Quotes" (as a "reference" for his goofy poems)

Horatio Algeranon said...

Horatio has discovered that (lo and behold) a "Curry Cliff Quotes" site already exists (ThinkExist.com) though Horatio must admit that the Judith Curry who is quoted there may be (sure seems like) a different one than the one who has been doing the blog shows recently (quoted at CurryQuotes)

Here's an example of the kind of thing "ThinkExist Judith Curry" (aka "Thinking Judith Curry") says:

“Even with imperfect data and some uncertainty, it's hard to imagine what kind of errors might be in the data set to give you a long-term trend.”
Judith Curry quote


By the way, in his search for Curry Quotes, Horatio also discovered another "Curry Quotes" site with some very important things to say:

Like this, for example: "I'm just a sweet transvestite, from Transsexual Transylvania."

The latter Curry (also a Thinking Curry) played the part of Dr. Frank-N-Furter in The Rocky Horror Picture Show, and had some very important things to say (and sing) --albeit about a different sort of climate change.

Antiquated Tory said...

Anyone have any idea why Anonymous at 21.11.10 16:39 quoted Isiah 47:4 at Martin? "Our Savior is named the Lord All-Powerful;
he is the Holy One of Israel." What has that got to do with anything?
Reading down, some of the other bits of Isiah 47 seem more relevant.
"Babylon, sit in darkness and say nothing.
You will no longer be called the queen of kingdoms...
13 You are tired of the advice you have received.So let those who study the sky—those who tell the future by looking at the stars and the new moons—let them save you from what is about to happen to you.14 But they are like straw;fire will quickly burn them up.They cannot save themselves from the power of the fire.They are not like coals that give warmth nor like a fire that you may sit beside.
I don't understand the Fundie Christian Denialist Bible thing. Because lots of the Bible seems to not really approve of *wealthy societies* that *love their luxuries too much to heed warnings* and think they are *too powerful to suffer the consequences of their actions.*

Anonymous said...

Eli:

You're racing after straw rabbits and getting awfully confused as usual in an attempt to cover up Teamster Jones.

Did Teamster Jones share the information he didn't pass on to some people with others of his choosing? Yes he did.

So I'm calling bullshit on your straw bunny.

I understand you're from Crooklyn where things are never up front, however your taking this too far.

Teamster Jones is a dishonest rodent.

EliRabett said...

Oh, you mean those Emails that Ed Wegman forwarded to his own computer and then wiped. Thanks for the thought.

Anonymous said...

If the 1990 paper data was Jones' personal property and proprietary, why did he end up releasing it under FOI?

Anonymous said...

Give it up, Eli. You're far more classy than the teamsters. Why on earth do you want to get tarred with the same brush as those deadend losers?

a_ray_in_dilbert_space said...

You know, the comments by "anonymous" above are classic denialist memes. They can't touch the science, so they disparage the scientists. They don't get it. Science is about the evidence and what it allows us to say with confidence. It has nothing to do with the behavior of scientists.

Now personally, I have not seen anything come out of the UEA emails that rises to the level of misconduct--even when the emails are taken out of context. However, even if it did, it doesn't touch the science. So at worst, some scientists are guilty of poor judgment in some situations where they were under pressure. In contrast, it's hard to find even best of the denialists who do not qualify amply as lying scum.