Guest Post by Willis Eschenbach
From an interesting post entitled “Trust and Don’t Bother To Verify” on Judith Curry’s excellent blog , I’ve taken the following quote:
Journals’ growing insistence that at least some raw data be made available seems to count for little: a recent review by Dr Ioannidis which showed that only 143 of 351 randomly selected papers published in the world’s 50 leading journals and covered by some data-sharing policy actually complied.
I’ve written before about the data and code archiving policies of the journal Science, and how they are not enforced for certain favored papers. In this regard, consider the case of Pinsky et al. This was a study that said that fishes were moving in the direction of the “climate velocity”. As a fisherman, I’m always interested in such studies. Their results appeared too regular to me, and I wanted to check their work. However, I found that neither their data nor their code was available. So last month, I wrote to the good folk at Science to see if they would enforce their own policies.
From: Willis Eschenbach
Subject: TO: Dr. Marcia McNutt
Date: September 14, 2013 6:30:37 AM PDT
To: Science Editorial <science_editors@aaas.org>
Dear Dr. McNutt:
I have commented publicly in the past on Science magazine not following its own data archiving policy, but only for the favored few with whom the editors agree.
This issue has come up again with the recent publication of the Pinsky et al. study on the migration of fishes in response to climate velocity. Once again, it appears you have published a study without requiring archiving of the data, as is specifically required by your policies. I cannot find a public archive of their data anywhere.
Since that means that their study is not replicable or auditable, it also means their study is not science … so what is it doing in your magazine?
I assume that you will rectify this oversight as soon as possible.
Best regards,
w.
Mmmm. Upon re-reading it, in retrospect I see that I was not as polite as I might have liked … but then I’ve grown bone-weary of Science not following its own data and code archiving policies for certain climate articles. In response to my email, I got … nothing. Zero. Zip. Nada word from anyone at Science.
Undaunted, I persevered. After waiting for two weeks, I wrote again, and this time I copied it around the organization:
From: Willis Eschenbach
Subject: Fwd: TO: Dr. Marcia McNutt
Date: October 1, 2013 11:24:03 PM PDT
To: Science Editorial <science_editors@aaas.org>, science_letters <science_letters@aaas.org>, science_bookrevs@aaas.org, Science News <science_news@aaas.org>, gchin@aaas.org, hjsmith@aaas.org
Dear Friends:
I sent the following message two weeks ago to Dr. McNutt. However, it seems to have miscarried.
From: Willis Eschenbach
Subject: TO: Dr. Marcia McNutt
Date: September 14, 2013 6:30:37 AM PDT
To: Science Editorial <science_editors@aaas.org>
Dear Dr. McNutt:
I have commented publicly in the past on Science magazine not following its own data archiving policy, but only for the favored few with whom the editors agree.
This issue has come up again with the recent publication of the Pinsky et al. study on the migration of fishes in response to climate velocity. Once again, it appears you have published a study without requiring archiving of the data, as is specifically required by your policies. I cannot find a public archive of their data anywhere.
Since that means that their study is not replicable or auditable, it also means their study is not science … so what is it doing in your magazine?
I assume that you will rectify this oversight as soon as possible.
Best regards,
w.
I have not received a reply. Perhaps Dr. McNutt was not the proper person to address this to. So I am sending it to other addresses, in the hopes of getting some reply. I’m sorry to bother you, but if you could pass this to someone who could explain why you are not following your own written policies in this instance.
Many thanks,
w.
This time, I actually got a response, the very next day:
From: Andrew Sugden
Subject: Re: FW: TO: Dr. Marcia McNutt
Date: October 2, 2013 2:59:33 PM PDT
To: Willis Eschenbach
Dear Dr Eschenbach
Thank you for your message to Dr McNutt. I can assure you that we require all data supporting the conclusions of Science papers to be in the public domain; the location of the data is usually specified in the Acknowledgements of each paper, as it was in the case of the Pinsky paper. Please can you double-check the Supplementary Material to the Pinsky et al paper and then specify the data to which you have been unable to gain access? At that point we can ask the authors to provide further details if necessary.
Your sincerely
Andrew Sugden
And the following day, I replied:
From: Willis Eschenbach <willis@surfacetemps.org>
Subject: Re: TO: Dr. Marcia McNutt
Date: October 3, 2013 9:48:34 AM PDT
To: Andrew Sugden <asugden@science-int.co.uk>
Cc: Science Editorial <science_editors@aaas.org>, science_letters <science_letters@aaas.org>, science_bookrevs@aaas.org, Science News <science_news@aaas.org>, gchin@aaas.org, hjsmith@aaas.org
Dr. Sugden, thank you most kindly for your reply. However, I fear that I’ve double-checked the paper and the SI, and there is far, far too little information, either in the paper itself or in the Supplementary Information, to allow their results to be confirmed, replicated, or falsified.
Here’s an example. It just happens to be the first area on their list, their study of the Eastern Bering Sea. The source of the data is given as being the RACE survey … but other than that we know nothing.
For example. The RACE survey covers 112 species … which of these species did they actually look at, and which ones did they leave out of their survey? Then they say they didn’t look at all tows … so which individual tows did they look at, and which did they leave out of their survey? Their only information on the subject is as follows:
While surveys were conducted in a variety of seasons (Table S1), we analyze each survey separately and use season-specific temperature data to account for these differences. We restricted our analysis to tows without gear and duration problems, to taxa that were resolved at least to genus, and to taxa that were sampled at least once per year to reduce effects from changes in taxonomic recording or resolution.
Unfortunately, that is far from enough information to be able to tell if their results are real or not.
Look, Dr. Sugden, this is not rocket science. To verify if what they have reported is a real effect, what we readers of Science need is very, very simple. It is a list in plain text that looks like this:
Year Month Day Tow# Species Catch Lat Start Long Start Lat End Long End Depth Temperature Result 1998 3 12 116 capelin 17.6 kg 56.712N 176.55E 56.914N 177.25E 72-75m 11.6-11.9°C Utilized1998 3 12 116 sculpin 1.6 kg 56.712N 176.55E 56.914N 177.25E 72-75m 11.6-11.9°C Excluded, uncertain identification…
Without that list showing exactly which data was used, and which data was excluded, and why, their results cannot be falsified … and unfalsifiable claims are not science, and not worth reporting in Science magazine
What they have done is just waved their hands and pointed at a huge pile of data, and said, We got our data from that pile … I’m sorry, but in 2013 that doesn’t cut it. To check their work, we need to know, not where they got their data, but exactly what data was used and what data was excluded. For all we know, there were transcription errors, or bugs in their computer code, or incorrectly categorized results, could be anything … but there’s no way to tell.
Nor is this an onerous requirement. The block of data representing the entire analysis would be a few megabytes. And presumably, in order to analyze the data, it’s all on the computer. So outputting a list of the data that was actually used or excluded is a few minutes work for a junior analyst.
I fear Science magazine and your Reviewers have dropped the ball on this one, Dr. Sugden. You have not done your due diligence and required the archiving of the data actually used in the study. Without that, you’re just publishing an anecdote, a charming fairy tale told by Dr. Pinsky.
It’s an interesting anecdote, to be sure … but it’s not science.
Please let me know what your magazine intends to do in this case. As it stands, you’ve published something which is totally unfalsifiable, in direct contravention of your own policies. Here are your relevant policies:
Data and materials availability
All data necessary to understand, assess, and extend the conclusions of the manuscript must be available to any reader of Science. All computer codes involved in the creation or analysis of data must also be available to any reader of Science. …
Science supports the efforts of databases that aggregate published data for the use of the scientific community. Therefore, appropriate data sets (including microarray data, protein or DNA sequences, atomic coordinates or electron microscopy maps for macromolecular structures, and climate data) must be deposited in an approved database, and an accession number or a specific access address must be included in the published paper. We encourage compliance with MIBBI guidelines (Minimum Information for Biological and Biomedical Investigations).
Details include but are not limited to:
- …
- Climate data. Data should be archived in the NOAA climate repository or other public databases.
- Ecological data. We recommend deposition of data in Dryad.
Clearly, the information that they provided falls woefully short of that required by your policies. No archive of their data. And pointing at a huge pile of data is not sufficient to let me “understand, assess, and extend the conclusions” as your policies require. I don’t have a clue what in the huge pile of data they used and what they excluded, so the information they gave about the location of the huge pile of data is useless.
The requirements, your own requirement, are bozo-simple, and easy to comply with. All they need to do is archive the collection of data that they actually used or rejected, and archive the computer code that they used to analyze that data.
They have done neither one …
Please let me know your plan of action on this, both for this paper and in general. As it stands, your magazine is passing off the unverifiable, unfalsifiable anecdotes recounted by Pinsky et al. as if they were real science. This is not the first time that your magazine has done that … and I don’t think that’s good for you personally as a scientist, for the reputation of Science magazine, or for science itself. People are trusting science less and less these days … and the publication of unverified anecdotes as if they were real studies is one of the reasons.
Your requirements for data and code archiving are simple and transparent. Now … you just have to enforce them.
Thanks for your assistance in all of this,
w.
Perhaps overly verbose but I wanted them to understand the issue. I waited almost two weeks, and when I’d gotten nothing, I wrote back:
From: Willis Eschenbach
Subject: Re: TO: Dr. Marcia McNutt
Date: October 14, 2013 11:00:05 AM PDT
To: Andrew Sugden
Cc: Science Editorial <science_editors@aaas.org>, science_letters <science_letters@aaas.org>, science_bookrevs@aaas.org, Science News <science_news@aaas.org>, gchin@aaas.org, hjsmith@aaas.org
Dear Dr. Sugden;
As I detailed in my attached letter, neither the data nor the computer code for the Pinsky et al. study on the migration of fishes in response to climate velocity is available in a usable form.
While the data is publicly available, there is no detailed list or other means to identify the data actually used in the Pinsky study. Without that, in fact their data is not available—it is a needle in a haystack of needles. And without that, the study cannot be replicated, and thus it should not be published.
In addition, the computer code is nowhere to be found.
Both of these violate your express policies, as detailed below.
It’s been almost two weeks now since my attached letter was sent … I’m sorry to bother you again, but is there any progress in this matter? Or should I just submit this to the Journal of Irreproducible Results? Hey, just kidding … but it is very frustrating to try to see if there are flaws in published science, only to find out that Science itself is not following its own published policies.
My apologies for copying this around, but it may be that I’m not talking to the person in authority regarding this question. Do you have plans to rectify your omission in the Pinsky study, and require that they archive the actual data and code used? And if so, what are the plans?
Or are you going to do the Pontius Pilate?
In any case, any information that you have would be most welcome.
Many thanks for your assistance in this matter.
w.
PS—Please, do not tell me to contact the scientists directly. This is 2013. The exact data and code that the scientists used should be available at 2AM their time to a teenaged researcher in Ghana who doesn’t even speak the scientists’ language. That’s the reason you have a policy requiring the authors to archive or specifically identify their data, and to post their code. Pinsky et al. have done neither one.
That was sent on the 14th. Today’s the 21st. So I figured, at this point it’s been almost three weeks without an answer … might as well post up the story.
Now, would I have caught more flies with honey than with vinegar? Perhaps … perhaps not.
But the issue is not the quality or politeness of my asking for them to follow their own policies. Look, I know I can be abrasive at times, and that Dr. McNutt has no reason to like me, but that’s not the issue.
The issue is whether the journal Science follows their own policies regarding the archiving of data and code, or not. If you don’t like the way I’m asking them to do it, well, perhaps you might ask them yourself. I may be overly passionate, I might be going about it wrong, but at least I’m working in my own poor way to push both Science and science in the direction of more transparency through the archiving of data and code.
Sadly,
w.
Andrew Harding hits it right on the head. As the individual who posted this comment – “Why should they let you see their data when all you want to do is find something wrong with it?” is apparently happy to accept anything that is claimed to be correct, rather then wasting it’s time checking the results. That appeal to authority just does not work anymore and rightly so. We have already witnessed what damage that practice has generated. So it’s either put up the data and the required information or throw the lot into the garbage bin where it belongs. Finished.
Let’s face it, the editors at “Science” sold their souls for warmism long ago. Science has nothing to do with it. You are the enemy.
Two words: [snip . . site rules . . mod] magazine
It’s high time for database of “scientific” journals rated on an ABCDF scale. A link to said database should be top, front and center..
— Why aren’t we doing this?
I disagree.
They have made the raw data available that is all you should need. An important part of science is reproducibility of results. However, in order to make the reproductions useful they shouldn’t just be a rework of the original methodology. It is the result that is important. If they were to give you a step by step walkthrough. It would very likely bias the person trying to reproduce the result to apply the same methodology and that isn’t as useful as someone who thinks for themselves about how they’d analysis the data.
Also if you are just looking in detail at what someone else has done. The likely result is “I wouldn’t have done it that way I think you are wrong”. This is not useful. The most useful thing Willis could do is take the raw data do his own analysis and present the result. If it’s different then this prompts the debate about why and which way is better. If Willis does indeed have the better solution then we end up with a new piece of science that is an improvement on the previous version and this is what we want in the end.
James may disagree but he is wrong.
You have to have the plans for the machine before you can figure out if it is doing what it is supposed to do in the way that it is claimed.
A paper should be like a patent and contain all knowledge required to replicate the invention. What you have instead is the equivalent of a patent disclosure which is just a bunch of claims.
Once you have access to a patent you can build it to see if it actually works and does what is claimed for it.
Note well that in order for a patent to be granted it is not required that the invention actually work – just Google “fuel saving patent”.
I read this Economist article on the plane and guessed that it would attract blog attention – rightly so. It is good that Willis has focused the issue on a specific Science paper.
Willis
I couldn’t agree more.
Without that, you’re just publishing an anecdote, a charming fairy tale told by Dr. Pinsky.
Excellent! And you’re 100% right of course. Problem is that one may need to vet their data against the raw source.
Like it says on the logo:
SCIENCE
my
AAAS !
I think they want you to go to the same pile of data, do your own study, and write your own paper that contradicts the results of Pinsky etal.
The first thing you need to do is realize that there has been some warming in the last 40 or so years (following cooling, which followed warming, etc.). Each warming or cooling cycle would likely cause a small shift in average location of fish. So what? There is no supporting evidence for the cause of warming (or cooling), so blaming it on human activity (other than overfishing) is without basis. This is a useless paper whether it is a valid study or not.
jorgekafkazar on October 22, 2013 at 1:14 am said;
“Why should they let you see their data when all you want to do is find something wrong with it?”
I think a couple of commenters missed the humour in what jorgekafkazar has posted. It’s a parody of a comment made by that arch-warmunist Phil Jones of UEA CRU.
James says:
October 22, 2013 at 4:06 am
I disagree.
They have made the raw data available that is all you should need. An important part of science is reproducibility of results. However, in order to make the reproductions useful they shouldn’t just be a rework of the original methodology.
===
Well that is one argument but it’s not the written policy of Science, which requires code.
SOOOO right to challenge them, Willis – that article was ‘BBC Science’ (i.e. ‘Headline it on the BBC News – but don’t whatever you do, verify it’….)
You tell ’em!
“… would I have caught more flies with honey than with vinegar?”
Perhaps, but do you really want the flies?
“James says:
October 22, 2013 at 4:06 am
I disagree.
They have made the raw data available that is all you should need.”
They being who? Raw data, since when? If we “take” the UEA CRU “data”, we know the RAW data was lost in the mid 1990’s in office moves. CET data disproves AGW.
Excellent approach Willis.
If one can be said to have met the “data requirement” by certifying, “the data I used is somewhere in pile A”, then the requirement can also logically be met by certifying, “I used data from somewhere”. All this reminds me of the famously evasive testimony by one of our politicians that, “It all depends on what the definition of ‘is’ is.” In both the politician’s and the SCIENCE journal’s responses, one can only conclude that, “Someone is hiding the pea!”
Police Arrest Procedure, make an omission or an error and criminal walks free
Thread winner!
For those suggesting that Willis just needs the pile of unanalyzed raw data to perform his own study, I would guess that he wants to find out if the authors cherry-picked the data to arrive at a foregone conclusion. So he needs to know their selection process and what analytic tools they used. As Willis points out, replication is the heart of science, and falsification is its brain.
If the study were federally-funded, maybe it’s time for a FOIA demand?
/Mr Lynn
Willis, what you could do is annoy them to death. Ask AAAS again for the data. Tell them you went public with their lack of response, and provide a link to this article. And then also tell them that you will be emailing them every day until you finally provide an answer. And make sure you email every day. If, after a long period of time, they still do not respond, go public again on as many venues as you can. You need to go public because there is a chance they put your emails on auto-delete. Shame and annoy them to follow their own requirements.
Where is the AAAS office? Someone who lives nearby could volunteer to try and talk to the people who work there and ask them why they are not following their own requirements. The key is volunteering, so the person cannot be accused of being paid to do this. Just annoy them until AAAS complies.
I’m with you Willis. After years of dealing with frivolous ‘science’ claims, and adversarial attitudes when trying to get to a reasonable bottom of things, it is hard to just play nice.
Jimmi_the_dalek says:
“Most authors are only too willing to help (and yes I know there have been exceptions)…”
The exceptions are fraudulent scientists. The editors of ‘Science’ and other scientific journals are not supposed to be enablers of fraud, they are supposed to be guardians of good science. Yet they routinely publish studies linking human activity to detrimental climate change, while actively stifling legitimate scientific debate. Thank you Willis for exposing yet another poisonous practice that permeates our current science culture. Irreproducible research is bullshit! The cure is to constantly point out the bullshit and hypocrisy and rub the miscreants’ noses in it.
Great stuff Willis, keep it up mate.
As to criticism of your approach, I consider that considering the gravity of the issue and the offhand fashion with which the representatives attempted to brush you off, you were most restrained.