Showing posts with label Harry_Read_Me. Show all posts
Showing posts with label Harry_Read_Me. Show all posts

07 May 2010

What Integrity?

Gleick, P. H. et al.. 2010. Climate change and the integrity of science. Science. 328: 689 - 690. DOI: 10.1126/science.328.5979.689.

The May 7 issue of Science Magazine contains a letter deploring "the recent escalation of political assaults on scientists in general and on climate scientists in particular." [emphasis added] The two hundred and fifty-five signatories are members of the National Academy of Sciences, which is once again sticking an activist snout into the public's business. One would think that the folks at Science would want to maximize the letter's accessibility. Apparently not. You can't read it at their website unless you're a subscriber. Fortunately, The Guardian has published the full text, here reproduced with commentary: Original in bold; comments, in square [ ] brackets. A follow-up post will focus on the signatories.

"We are deeply disturbed by the recent escalation of political assaults on scientists in general and on climate scientists in particular. All citizens should understand some basic scientific facts. There is always some uncertainty associated with scientific conclusions; science never absolutely proves anything. When someone says that society should wait until scientists are absolutely certain before taking any action, it is the same as saying society should never take action. For a problem as potentially catastrophic as climate change, taking no action poses a dangerous risk for our planet."

["Assaults" presumably refers to the email scandal, commonly referred to as "Climategate," and to the furor that ensued. To dismiss the latter, which does include investigations — this site hopes there will more — of the principals, as "political" is misleading. What the emails reveal is a small group of scientists conniving to promote their own work and to silence their critics. Further revealed are conscious, coordinated efforts to mislead the readers of the journals in which they published, i.e. their fellow scientists, the agencies that funded their research and the general public. The emails further show the principals conspiring to resist Freedom of Information requests that were legitimate, not only in the legal sense, but also in the sense that the individuals making the requests had both a genuine interest in the scientific issues and the requisite skills necessary to re-analyze the data. In some instances, the requesters were arguably better equipped by virtue of temperament and training to analyze the data than the scientists themselves.

All of this was done at taxpayer expense and with the purpose of promoting policies that, whatever their merit (or lack thereof), carry an enormous price tag. It was not, in short, an edifying performance, being, to the contrary, despicable, counter to the general welfare and detrimental to science.

"But wait," as the man hawking housewares says in the commercial, "There's more!" One of the files, Harry_Read_Me.txt leaked by the Climategate "hacker" documents problems with the methods by which East Anglia scientists, more accurately, their graduate students, attempted to measure the earth's temperature. One does not, after all, simply grab hold of a large rectal thermometer and ask the old girl to bend over. They don't make them large enough; and if they did, she probably wouldn't. Nope. What one does is to piece together weather station records, thousands of them, from around the globe. Problem is the stations were never intended to function as part of a world-wide network capable of estimating the earth's average temperature to ±0.2° C. The stations move around; cities grow up around them; instrumentation changes and, LOL, their identity codes change. Writes "Harry," a programmer brought in to clean up the code,
"Now, I admit the lats and lons aren't spot on. But c'mon, what are the chances of them being different? The two year 2000s are almost identical.

0-15501245012KURI BAYAUSTRALIA20002006-999-999.00
9420800-15481245229KURI BAYAUSTRALIA19651992-999-999.00

"Or:

0-15501281011WYNDHAMAUSTRALIA20002006-999-999.00
0-15501282011WYNDHAM AEROAUSTRALIA20002006-999-999.00
9421400-15491281211WYNDHAM POST OFFICEAUSTRALIA19682000-999-999.00
9421401-15471281020WYNDHAM (WYNDHAM PORAUSTRALIA18981966-999-999.00

"Come On!! This is one station isn't it."
Over at The Strata-Sphere, A. J. Stata reproduced additional gems. Try this one:
"But what are all those monthly files? DON’T KNOW, UNDOCUMENTED. Wherever I look, there are data files, no info about what they are other than their names. And that’s useless ... ."
Most important, the stations don't always report. As a result, the scientists felt compelled, to adjust, to average and to interpolate. And did they ever! There was raw data, original data, adjusted data, gridded data — Lord knows what else. To compensate for the urban heat island (UHI)
effect, older temperatures were reduced, the consequence in some (many? most?) cases being to increase the apparent warming. Even worse, missing records were replaced with "synthetic" data. Get that? Numbers were invented; "-999" became the average of "nearby" stations, where "nearby" could mean hundreds of miles away.

As Richard Brook observed,
"The complexity of the calculations, and the considerable element of human judgment ... leave the process wide open to error and bias. Thus, the final results may actually reflect, to one degree or another, no more than the opinions of the scientists producing them."
Brooks' assessment is mild. Not only was the methodology ad hoc, but the computer programs implementing it, poorly documented and "buggy." At one point in the log that records his efforts to sort things out, Harry remarks,
"Had a hunt and found an identically-named temperature database file which did include normals lines at the start of every station. How handy - naming two different files with exactly the same name and relying on their location to differentiate! Aaarrgghh!!"
Often, sometimes on purpose, run-time errors, the bane of programing, were not trapped for, with the consequence that programs could continue merrily on their way, generating garbage with no one the wiser. "So with a somewhat cynical shrug," writes Harry,
"I added the nuclear option — to [allow the user to] match every WMO [World Meteorological Organization] possible, and turn the rest into new stations ... . In other words what CRU [Climate Research Unit at East Anglia] usually do[es]. It will allow bad databases to pass unnoticed, and good databases to become bad ..." [hat tip HJS]
In short, there is staggering contrast between the cocksure comportment of the Climategate principals and the mess on which they based their conclusions. Like the rooster cock-a-doodle-doing from the highest dung heap in the barnyard, these self-appointed lords of the manor — dare I say, "manure" — didn't look down.

John Tierny, writing in the New York Times ("all the news that fits, we print"), put it this way:
"While Harry’s log shows him worrying about the integrity of the database, the climate scientists are e-mailing one another with strategies for blocking outsiders’ legal requests to see their data.

"While Harry is puzzling over temperatures ... the scientists are confidently making proclamations to journalists ... and plotting revenge against those who question the dangers of global warming. When a journal publishes a skeptic’s paper, the scientists ... focus instead on retaliation against the journal and the editor ... ."
The thermometer record is one of the principal pillars on which rests the argument for anthropogenic warming (AGW), and the problem is, not that there is "some uncertainty," but that it is utterly unconvincing. What about the other pillars? Well, there's the models and there's paleoclimatology. Regarding the models, I will comment below. As to paleoclimatology, three considerations undercut using it to justify anything with real world consequences.
  1. Reconstructions of climates past rely on proxy variables: tree ring widths, isotope ratios, etc., all of which can be influenced by multiple factors. As such, the view they provide of temperatures past is "through a glass darkly."

  2. Trying to distinguish "signal" from "noise" led to the use of esoteric statistics — calculations of the 'lies, damned lies and statistics" kind. This, in turn, resulted in considerable wrangling regarding over the calculations' legitimacy, the brouhaha surrounding the hockey stick, being a noteworthy example. Based on his own experience, admittedly limited, the present author believes that such techniques should be used with caution. Better to put time and money into searching for proxies with higher signal to noise ratios.

  3. Paleoclimatologists have not been above resorting to deception when the results don't go their way. "Mike's Nature trick" to hide the infamous "decline" — see Marc Sheppard's explication — is one example; replacement of the hockey stick in IPCC3 by the "spaghetti graph" in IPCC4 is another.
It is worth emphasizing that these considerations interrelate in multiple ways — see The Hockey Stick Illusion by A. W. Mountford.

Bottom line: The precautionary principle cuts both ways. Failure to base policy on what the NAS signatories characterize as "compelling, comprehensive, and consistent objective evidence," far from posing a "dangerous risk to the planet," will, in the short term, avert catastrophic damage to the world's economy and its human population. As to the consequences fifty or a hundred years down the road, only the Fellow Upstairs, by virtue of expertise and experience
, is qualified to an opinion.]

Scientific conclusions derive from an understanding of basic laws supported by laboratory experiments, observations of nature, and mathematical and computer modelling. Like all human beings, scientists make mistakes, but the scientific process is designed to find and correct them. This process is inherently adversarial— scientists build reputations and gain recognition not only for supporting conventional wisdom, but even more so for demonstrating that the scientific consensus is wrong and that there is a better explanation. That's what Galileo, Pasteur, Darwin, and Einstein did. But when some conclusions have been thoroughly and deeply tested, questioned, and examined, they gain the status of "well-established theories" and are often spoken of as "facts."

[This is sophistry. To equate AGW with the discoveries of Galileo etc. betrays cynicism on a truly grand scale. Who, but the ideologically committed, blinded by faith — see Botkin on "Global Warming Delusions" — would believe it? And let's get this straight. There are no potentially falsifying experiments. The models are "tuned," their parameters adjusted to fit the data already in hand. By the time predictions begin to fail, the modelers have a new set of models, better ones, they tell us, better because they are bigger, because they incorporate more processes, each of which requires more parameters to be estimated, more fudge factors to be adjusted. Moreover, the complexity of the models is such that it is impossible to understand their behavior mathematically. What the climate modelers offer humanity are models that can't be understood as substitute for a system that isn't understood. And for this, mankind pays — today, in treasure; tomorrow, in blood.

Historians of science have debated whether or not Eddington fudged his data in the famous experiment that confirmed General Relativity. The current opinion is that he did not. But the important point is that the theory could have been falsified. Had things worked out that way; had the theory failed, had Einstein been obliged to concoct a new one consistent with discordant observations, what would would have been been gained? A new hypothesis, nothing more. And that is the critical point. The climate models are hypotheses. What comes out of them are predictions, not results.

Right now,
those predictions aren't doing very well. From 1970, to 1995, if you believe the folks at East Anglia, the forecasts seemed to be holding: Atmospheric carbon was on the rise, and so was temperature. Since then, [CO2]atm has continued to increase, while temperatures have stabilized. Natural variability? Apparently. Soon to be overwhelmed by continuing greenhouse gas accumulation, maybe yes, maybe no.]

For instance, there is compelling scientific evidence that our planet is about 4.5bn years old (the theory of the origin of Earth), that our universe was born from a single event about 14bn years ago (the Big Bang theory), and that today's organisms evolved from ones living in the past (the theory of evolution). Even as these are overwhelmingly accepted by the scientific community, fame still awaits anyone who could show these theories to be wrong. Climate change now falls into this category: there is compelling, comprehensive, and consistent objective evidence that humans are changing the climate in ways that threaten our societies and the ecosystems on which we depend.

[More sophistry. In the first place, the theories with which AGW is compared are well established. AGW is a far weaker hypothesis. Gorian sturm und drang to the contrary, there is no convincing evidence that humans are causing climate change, nor, for that matter, that contemporary climates are in any way extraordinary. Second, note the spin. What is known and what remains problematic are blended together. Take the "fact of evolution," what Darwin called "descent with modification." For this, the evidence is overwhelming and continues to accumulate. But the pattern, common descent, should be distinguished from the mechanism that produces it, and about that matter, hypotheses continue to come and go.

Even if one accepts the reality of late twentieth century warming, and that's a big "if," one is left with question as to "Why?" And, if the mechanism turns out to be other than AGW, what then? What if today's stabilized temperatures are harbingers of tomorrow's cooling? What if we reduce our capacity to produce energy and wake up one morning to find the glaciers once more advancing? I'll tell you what: Should the future bring ice, not fire, today's proponents of carbon abatement will hang from lamp posts — from which vantage they can contemplate a freezing, starving and, yes, vengeful humanity, whose misery will have been exacerbated by science in the service of ideology.]

Many recent assaults on climate science and, more disturbingly, on climate scientists by climate change deniers, are typically driven by special interests or dogma, not by an honest effort to provide an alternative theory that credibly satisfies the evidence. The Intergovernmental Panel on Climate Change (IPCC) and other scientific assessments of climate change, which involve thousands of scientists producing massive and comprehensive reports, have, quite expectedly and normally, made some mistakes. When errors are pointed out, they are corrected.

[Ah yes! The fabled thousands! But, as those familiar with the IPCC process know full well, the folks who write the reviews and those who write the literature on which the reviews are based are far fewer in number. And guess what? Surprise! Surprise! The folks who do the reviewing and the folks who do the research are often the same. Let's be clear. I'm not speaking of camp followers. I'm speaking of the Mann's, the Briffa's, the Jones's, etc. For it is on their shoulders that all else rests. Of course, there are thousands of others — mainly environmental scientists of one stripe or another — who piggyback on the process. I call these people "what-iffers;" they do "what if" studies: what are the consequences to X if the climate warms, where X is a species, a renewable resource, an ecological process, etc. Like the birds that follow army ants, "what-iffers" rely on beaters to flush out the next meal. In the case of the birds, the beaters are the ants, whose passage through the forest is marked by an eruption of insects leaping out of the foliage to escape being being devoured by the advancing column. In the case of "what-iffers," the beaters are climatologist fear mongers, who stir up taxpayer dollars. An acquaintance tells the following story: A prospective graduate student walked into her office announcing that he intended to study the consequences of global warming to some ecological process. "And if the climate cools?" my friend inquired. The student, unnerved by such heresy, mumbled something incoherent and fled.]

But there is nothing remotely identified in the recent events that changes the fundamental conclusions about climate change:

[See above. See also recent studies supporting the reality of the Medieval Warm Period (hotter than now, but without concomitant elevations in [CO2]atm), and that of the Little Ice Age from which we are now recovering. See studies (below) suggesting that most of the late twentieth century warming may be artifactual (UHI). See studies suggesting the existence negative feedback (adaptive iris) omitted from most (all?) general circulation models (GCMs). See studies suggesting the importance of fluctuating solar output, etc.

With regard to UHI, Roy Spencer recently posted the graph shown at the right. Here, raw data are used to sort rates of twentieth century warming (° C / decade) by population density (persons / Km2. Unsurprisingly, the least densely populated regions manifest the least warming, less than half than the 0.2 ° C / decade estimated by Jones. If one extrapolates the curve back to zero density, the estimate of the "true" warming is 0.06 ° C, less than a third of Jones' estimate and well within the range of observational error. Of course, this was posted on a blog — no peer review. We'll see if Spencer gets it past the lions defending the gate.If he doesn't, I'd like to read the reviews.

And note the spin. Evidence contrary to AGW is not a recent phenomenon. It has been emerging at a steady pace, the efforts of the Climategate correspondents to suppress it notwithstanding.]

(i) The planet is warming due to increased concentrations of heat-trapping gases in our atmosphere. A snowy winter in Washington does not alter this fact.

[Studies of Pleistocene deglaciation suggest that increasing [CO2]atm follows, rather than precedes, increasing temperatures. To say that this is consistent with AGW is like arguing that lynx, by virtue of being predators, exert a negative effect on hare populations even were the latter to increase when there are more lynx. Were this the case — it's not, the example is hypothetical — one can imagine explanatory scenarios: maybe lynx eat other predators that prey on the hare; maybe lynx eat animals that compete with the hare for food. But they don't just eat "wabbits." Nor would assuming such allow you to predict the consequences of ordering a halt to the taking of lynx for their pelts.

Once again, note the spin: No significant warming for the past 10+ years — Jones now says since 1995 — and unpredicted in simulo, becomes "a snowy winter in Washington."]

(ii) Most of the increase in the concentration of these gases over the last century is due to human activities, especially the burning of fossil fuels and deforestation.

[If one accepts the reality of past temperatures in excess of those currently observed, the correct conclusion is that increasing [CO2]atm isn't the principal driver of temperature.]

(iii) Natural causes always play a role in changing Earth's climate, but are now being overwhelmed by human-induced changes.

[This is a postulate, more accurately, the cardinal precept of AGW canon. For the past 10-15 years, temperatures have been stable, whereas [CO2]atm has continued to increase.]

(iv) Warming the planet will cause many other climatic patterns to change at speeds unprecedented in modern times, including increasing rates of sea-level rise and alterations in the hydrologic cycle. Rising concentrations of carbon dioxide are making the oceans more acidic.

[These and related claims are all subjects of dispute. Most recently, tropical upper ocean heat content appears to have declined precipitously. Regarding this observation, Roger Pielke Sr. writes as follows:
"An interesting question is to where this heat has gone. It could have moved north and south in the upper ocean, however, to the extent the sea surface temperature anomalies map to the upper ocean heat content, there is no evidence of large heat transfers except, perhaps, in the tropical Atlantic see [here].

The heat could have been transferred deeper into the ocean. However, if this is true, this heat would have been seen moving to lower levels, but, so far, there is no evidence of such a large vertical heat transfer.

The heat could, of course, be lost to space. This appears to be the most likely explanation." [Emphasis added.]

So we are back to my friend's question: "And if the climate cools?"]

(v) The combination of these complex climate changes threatens coastal communities and cities, our food and water supplies, marine and freshwater ecosystems, forests, high mountain environments, and far more.

[More what-iffing.]

Much more can be, and has been, said by the world's scientific societies, national academies, and individuals, but these conclusions should be enough to indicate why scientists are concerned about what future generations will face from business- as-usual practices. We urge our policymakers and the public to move forward immediately to address the causes of climate change, including the unrestrained burning of fossil fuels.

[Two points: First. The world's scientific societies, etc. need to get out of the business of promoting policy and back to the business of doing science, which is figuring out how Nature works, as opposed to predicting the unpredictable. The climate system is the mother of all nonlinear dynamical systems. It is undoubtedly chaotic — where else could all those cycles: AO, PDO, etc., come from? And predicting the time evolution of chaotic systems is effectively impossible. Failure to get back to doing science will result in the scientific community's being perceived as what it has already become — another interest group sucking the public teat, concerned principally with the promotion of its own agenda: power, money, influence; power, money, influence; ... .

Second. The burning of fossil fuels is what makes civilization as we know it possible. Shut down the coal mines; stop the flow of oil and calamity is certain and immediate, not probable and not prospective.]

We also call for an end to McCarthy-like threats of criminal prosecution against our colleagues based on innuendo and guilt by association, the harassment of scientists by politicians seeking distractions to avoid taking action, and the outright lies being spread about them. Society has two choices: we can ignore the science and hide our heads in the sand and hope we are lucky, or we can act in the public interest to reduce the threat of global climate change quickly and substantively. The good news is that smart and effective actions are possible. But delay must not be an option.

[Pulease! Whether or not the behavior of the Climagegate principals was illegal, it stinks to high Heaven. What they did, they did with taxpayer money. When you feast at the public trough, your business becomes public business. Neither the climatologists, nor the "what-iffers," etc., were forced to become scientist-activists. They did this on their own, worked hard at it and, having done so, became public figures subject to public scrutiny. As to the "good news," sober economic analysis suggests that if one accepts AGW premises, carbon abatement will achieve little beyond wrecking the world economy. The NAS signatories, being men and women of intelligence, one can only wonder if that isn't what they really want: consigning H. sapiens to his proper place, the diminution of his works and especially his numbers — go search on "Optimum Population" if you think that's a stretch.]

Adams, Robert McCormick, University of California, San Diego

Amasino, Richard M, University of Wisconsin

Anders, Edward, University of Chicago

Anderson, David J, California Institute of Technology

Anderson, Wyatt W, University of Georgia

Anselin, Luc E, Arizona State University

Arroyo, Mary Kalin, University of Chile

Asfaw, Berhane, Rift Valley Research Service

Ayala, Francisco J, University of California, Irvine

Bax, Adriaan, National Institutes of Health

Bebbington, Anthony J, University of Manchester

Bell, Gordon, Microsoft Research

Bennett, Michael V L, Albert Einstein College of Medicine

Bennetzen, Jeffrey L, University of Georgia

Berenbaum, May R, University of Illinois

Berlin, Overton Brent, University of Georgia

Bjorkman, Pamela J, California Institute of Technology

Blackburn, Elizabeth, University of California, San Francisco

Blamont, Jacques E, Centre National d' Etudes Spatiales

Botchan, Michael R, University of California, Berkeley

Boyer, John S, University of Delaware

Boyle, Ed A, Massachusetts Institute of Technology

Branton, Daniel, Harvard University

Briggs, Steven P, University of California, San Diego

Briggs, Winslow R, Carnegie Institution of Washington

Brill, Winston J, Winston J. Brill and Associates

Britten, Roy J, California Institute of Technology

Broecker, Wallace S, Lamont-Doherty Earth Observatory and Columbia University

Brown, James H, University of New Mexico

Brown, Patrick O, Stanford University School of Medicine

Brunger, Axel T, Stanford University

Cairns, Jr John, Virginia Polytechnic Institute and State University

Canfield, Donald E, University of Southern Denmark

Carpenter, Stephen R, University of Wisconsin

Carrington, James C, Oregon State University

Cashmore, Anthony R, University of Pennsylvania

Castilla, Juan Carlos, Pontificia Universidad Católica de Chile

Cazenave, Anny, Centre National d' Etudes Spatiales

Chapin, III F, Stuart, University of Alaska

Ciechanover, Aaron J, Technion-Israel Institute of Technology

Clapham, David E, Harvard Medical School

Clark, William C, Harvard University

Clayton, Robert N, University of Chicago

Coe, Michael D, Yale University

Conwell, Esther M, University of Rochester

Cowling, Ellis B, North Carolina State University

Cowling, Richard M, Nelson Mandela Metropolitan University

Cox, Charles S, University of California, San Diego

Croteau, Rodney B, Washington State University

Crothers, Donald M, Yale University

Crutzen, Paul J, Max Planck Institute for Chemistry

Daily, Gretchen C, Stanford University

Dalrymple, Brent G, Oregon State University

Dangl, Jeffrey L, University of North Carolina

Darst, Seth A, Rockefeller University

Davies, David R, National Institutes of Health

Davis, Margaret B, University of Minnesota, Minneapolis

De Camilli, Pietro V, Yale University School of Medicine

Dean, Caroline, John Innes Centre

DeFries, Ruth S, Columbia University

Deisenhofer, Johann, University of Texas Southwestern Medical Center at Dallas

Delmer, Deborah P, University of California, Davis

DeLong, Edward F, Massachusetts Institute of Technology

DeRosier, David J, Brandeis University

Diener, Theodor O, University of Maryland

Dirzo, Rodolfo, Stanford University

Dixon, Jack E, Howard Hughes Medical Center

Donoghue, Michael J, Yale University

Doolittle, Russell F, University of California, San Diego

Dunne, Thomas, University of California, Santa Barbara

Ehrlich, Paul R, Stanford University

Eisenstadt, Shmuel N, Hebrew University of Jerusalem

Eisner, Thomas, Cornell University

Emanuel, Kerry A, Massachusetts Institute of Technology

Englander, Walter S, University of Pennsylvania School of Medicine

Ernst, W, G, Stanford University

Falkowski, Paul G, Rutgers, State University of New Jersey

Feher, George, University of California, San Diego

Ferejohn, John A, Stanford University

Fersht, Sir Alan, University of Cambridge

Fischer, Edmond H, University of Washington

Fischer, Robert, University of California, Berkeley

Flannery, Kent V, University of Michigan

Frank, Joachim, Columbia University

Frey, Perry A, University of Wisconsin

Fridovich, Irwin, Duke University Medical Center

Frieden, Carl, Washington University School of Medicine

Futuyma, Douglas J, Stony Brook University

Gardner, Wilford R, University of California, Berkeley

Garrett, Christopher J R, University of Victoria

Gilbert, Walter, Harvard University

Gleick, Peter H, Pacific Institute, Oakland [corresponding author]

Goldberg, Robert B, University of California, Los Angeles

Goodenough, Ward H, University of Pennsylvania

Goodman, Corey S, venBio, LLC

Goodman, Morris, Wayne State University School of Medicine

Greengard, Paul, Rockefeller University

Hake, Sarah, Agricultural Research Service

Hammel, Gene, University of California, Berkeley

Hanson, Susan, Clark University

Harrison, Stephen C, Harvard Medical School

Hart, Stanley R, Woods Hole Oceanographic Institution

Hartl, Daniel L, Harvard University

Haselkorn, Robert, University of Chicago

Hawkes, Kristen, University of Utah

Hayes, John M, Woods Hole Oceanographic Institution

Hille, Bertil, University of Washington

Hökfelt, Tomas, Karolinska Institutet

House, James S, University of Michigan

Hout, Michael, University of California, Berkeley

Hunten, Donald M, University of Arizona

Izquierdo, Ivan A, Pontifical Catholic University of Rio Grande do Sul

Jagendorf, André T, Cornell University

Janzen, Daniel H, University of Pennsylvania

Jeanloz, Raymond, University of California, Berkeley

Jencks, Christopher S, Harvard University

Jury, William A, University of California, Riverside

Kaback, H Ronald, University of California, Los Angeles

Kailath, Thomas, Stanford University

Kay, Paul, International Computer Science Institute

Kay, Steve A, University of California, San Diego

Kennedy, Donald, Stanford University

Kerr, Allen, University of Adelaide

Kessler, Ronald C, Harvard Medical School

Khush, Gurdev S, University of California, Davis

Kieffer, Susan W, University of Illinois

Kirch, Patrick V, University of California, Berkeley

Kirk, Kent C, University of Wisconsin

Kivelson, Margaret G, University of California, Los Angeles

Klinman, Judith P, University of California, Berkeley

Klug, Sir Aaron, Medical Research Council

Knopoff, Leon, University of California, Los Angeles

Kornberg, Sir Hans, Boston University

Kutzbach, John E, University of Wisconsin

Lagarias, J Clark, University of California, Davis

Lambeck, Kurt, Australian National University

Landy, Arthur, Brown University

Langmuir, Charles H, Harvard University

Larkins, Brian A, University of Arizona

Le Pichon, Xavier T, College de France

Lenski, Richard E, Michigan State University

Leopold, Estella B, University of Washington

Levin, Simon A, Princeton University

Levitt, Michael, Stanford University School of Medicine

Likens, Gene E, Cary Institute of Ecosystem Studies

Lippincott-Schwartz, Jennifer, National Institutes of Health

Lorand, Laszlo, Northwestern University

Lovejoy, Owen C, Kent State University

Lynch, Michael, Indiana University

Mabogunje, Akin L, Foundation for Development and Environmental Initiatives

Malone, Thomas F, North Carolina State University

Manabe, Syukuro, Princeton University

Marcus, Joyce, University of Michigan

Massey, Douglas S, Princeton University

McWilliams, Jim C, University of California, Los Angeles

Medina, Ernesto, Venezuelan Institute for Scientific Research

Melosh, Jay H, Purdue University

Meltzer, David J, Southern Methodist University

Michener, Charles D, University of Kansas

Miles, Edward L, University of Washington

Mooney, Harold A, Stanford University

Moore, Peter B, Yale University

Morel, Francois M M, Princeton University

Mosley-Thompson, Ellen, Ohio State University

Moss, Bernard, National Institutes of Health

Munk, Walter H, University of California, San Diego

Myers, Norman, University of Oxford

Nair, Balakrish G, National Institute of Cholera and Enteric Diseases

Nathans, Jeremy, Johns Hopkins University School of Medicine

Nester, Eugene W, University of Washington

Nicoll, Roger A, University of California, San Francisco

Novick, Richard P, New York University School of Medicine

O'Connell, James F, University of Utah

Olsen, Paul E, Lamont-Doherty Earth Observatory of Columbia University

Opdyke, Neil D, University of Florida

Oster, George F, University of California, Berkeley

Ostrom, Elinor, Indiana University

Pace, Norman R, University of Colorado

Paine, Robert T, University of Washington

Palmiter, Richard D, University of Washington School of Medicine

Pedlosky, Joseph, Woods Hole Oceanographic Institution

Petsko, Gregory A, Brandeis University

Pettengill, Gordon H, Massachusetts Institute of Technology

Philander, George S, Princeton University

Piperno, Dolores R, Smithsonian Tropical Research Institute

Pollard, Thomas D, Yale University

Price Jr. Buford P, University of California, Berkeley

Reichard, Peter A, Karolinska Institutet

Reskin, Barbara F, University of Washington

Ricklefs, Robert E, University of Missouri

Rivest, Ronald L, Massachusetts Institute of Technology

Roberts, John D, California Institute of Technology

Romney, Kimball A, University of California, Irvine

Rossmann, Michael G, Purdue University

Russell, David W, University of Texas Southwestern Medical Center of Dallas

Rutter, William J, Synergenics, LLC

Sabloff, Jeremy A, University of Pennsylvania Museum of Archeology and Anthropology

Sagdeev, Roald Z, University of Maryland

Sahlins, Marshall D, University of Chicago

Salmond, Anne, University of Auckland

Sanes, Joshua R, Harvard University

Schekman, Randy, University of California, Berkeley

Schellnhuber, John, Potsdam Institute for Climate Impact Research

Schindler, David W, University of Alberta

Schmitt, Johanna, Brown University

Schneider, Stephen H, Woods Institute for the Environment

Schramm, Vern L, Albert Einstein College of Medicine

Sederoff Ronald R, North Carolina State University

Shatz, Carla J, Stanford University

Sherman, Fred, University of Rochester Medical Center

Sidman, Richard L, Harvard Medical School

Sieh, Kerry, Nanyang Technological University

Simons, Elwyn L, Duke University Lemur Center

Singer, Burton H, Princeton University

Singer, Maxine F, Carnegie Institution of Washington

Skyrms, Brian, University of California, Irvine

Sleep, Norman H, Stanford University

Smith, Bruce D, Smithsonian Institution

Snyder, Solomon H, Johns Hopkins University School of Medicine

Sokal, Robert R, Stony Brook University

Spencer, Charles S, American Museum of Natural History

Steitz, Thomas A, Yale University

Strier, Karen B, University of Wisconsin

Südhof, Thomas C, Stanford University School of Medicine

Taylor, Susan S, University of California, San Diego

Terborgh, John, Duke University

Thomas, David Hurst, American Museum of Natural History

Thompson, Lonnie G, Ohio State University

Tjian, Robert T, Howard Hughes Medical Institute

Turner, Monica G, University of Wisconsin

Uyeda, Seiya, Tokai University

Valentine, James W, University of California, Berkeley

Valentine, Joan Selverstone, University of California, Los Angeles

Van Etten, James L, University of Nebraska

Van Holde, Kensal E, Oregon State University

Vaughan, Martha, National Institutes of Health

Verba Sidney, Harvard University

Von Hippel, Peter H, University of Oregon

Wake, David B, University of California, Berkeley

Walker, Alan, Pennsylvania State University

Walker John E, Medical Research Council

Watson, Bruce E, Rensselaer Polytechnic Institute

Watson, Patty Jo, Washington University, St. Louis

Weigel, Detlef, Max Planck Institute for Developmental Biology

Wessler, Susan R, University of Georgia

West-Eberhard, Mary Jane, Smithsonian Tropical Research Institute

White, Tim D, University of California, Berkeley

Wilson, William Julius, Harvard University

Wolfenden, Richard V, University of North Carolina

Wood, John A, Harvard-Smithsonian Center for Astrophysics

Woodwell, George M, Woods Hole Research Center

Wright, Jr Herbert E, University of Minnesota

Wu, Carl, National Institutes of Health

Wunsch, Carl, Massachusetts Institute of Technology

Zoback, Mary Lou, Risk Management Solutions, Inc



Note.

1. The signatories are all members of the U.S. National Academy of Sciences but are not speaking on its behalf. [Signatory affiliations, originally available as a supporting document, added by The Guardian, along with links to signatory web pages — hat tip.]
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27 November 2009

It's the Code, Stupid!

Bad code offsets are rumored to have been purchased in bulk by the University of East Anglia's Climate Research Unit.
Previously, it was suggested that the CRU programmers are "in over their heads." As people dig further into the "hacked" files, the truth of this assessment becomes increasingly evident. Take, for example, the file in which "Harry" records his (possibly FOIA motivated) efforts in 2006-2009 to resurrect / repair his predecessors' handiwork.

The programs in question process data from thousand of weather stations world-wide. Now consider the following: Each station has an ID, of course. But, Station IDs don't conform to a standard format. Neither do the data they report. From time to time, the IDs change; likewise the format in which the data is reported. Not all stations report all of the data all of the time. Sometimes they report some of it; sometimes, none at all. For better or worse, the folks at CRU substitute "synthetic" data for the missing numbers which they create from data reported by nearby sites. To determine which sites to use, they locate each station on a map and draw circles around its position. If another station lies within the circle, its data goes into the mix. But coastal stations make for a problem because land temperatures and sea temperatures are handled differently. So a station's position (latitude and longitude) can be critical. And sometimes the stations move. In short, assembling the numbers from which CRU computes global temperature "anomalies" is a book-keeping nightmare. Add to this the fact that the programming was done by graduate students, who left thousands of poorly (if at all) documented files for their successors to puzzle over, and you get a witches' brew that cries out for external review and / or independent replication.>

Here are some gems culled from the Harry_Read_Me file by TickerForum.org poster Asimov — my comments in square brackets. They've been referenced elsewhere, but some things in this life merit repetition. Also, as of 1041 h (EST), 29 November, the site is unreachable:
  • "Well, dtr2cld is not the world's most complicated program. Wheras [sic] cloudreg is, and I immediately found a mistake! Scanning forward to 1951 was done with a loop that, for completely unfathomable reasons, didn't include months! So we read 50 grids instead of 600!!"
  • "... have just located a 'cld' directory in Mark New's disk [Mark New was one of the student programmers], containing over 2000 files. Most however are binary [and therefore unreadable] and undocumented."
  • "The conclusion of a lot of investigation is that the synthetic cloud grids for 1901-1995 have now been discarded. This means that the cloud data prior to 1996 are static. ... For 1901 to 1995 - stay with published data. No clear way to replicate process as undocumented. For 1996 to 2002: ... This should approximate the correction needed." [Emphasis added]
  • "I am seriously worried that our flagship gridded data product is produced by Delaunay triangulation [new to this author] - apparently linear [as opposed to great circles on a sphere?] as well. As far as I can see, this renders the station counts totally meaningless. [Not sure why, but for now, I'll take Harry's word for it] It also means that we cannot say exactly how the gridded data is arrived at from a statistical perspective - since we're using an off-the-shelf product that isn't documented sufficiently to say that. Why this wasn't coded up in Fortran I don't know - time pressures perhaps? Was too much effort expended on homogenisation, that there wasn't enough time to write a gridding procedure? Of course, it's too late for me to fix it too." [Emphasis added]
  • "On we go.. firstly, examined the spc database.. seems to be in % x10. Looked at published data.. cloud is in % x10, too. First problem: there is no program to convert sun percentage to cloud percentage. I can do sun percentage to cloud oktas or sun hours to cloud percentage! So what the hell did Tim [Mitchell, the other student-programmer] do?!! As I keep asking." [Emphasis added]
  • "Then - comparing the two candidate spc databases: spc.0312221624.dtb [and] spc.94-00.0312221624.dtb[,] I find that they are broadly similar, except the normals lines (which both start with '6190') are very different. I was expecting that maybe the latter contained 94-00 normals [not sure what these are, but apparently they're important; maybe 1994-2000 averages], what I wasn't expecting was that thet [sic] are in % x10 not %! Unbelievable - even here the conventions have not been followed. It's botch after botch after botch. Modified the conversion program to process either kind of normals line." [Emphasis added]
  • "Decided to go with the 'spc.94-00.0312221624.dtb' database, as it hopefully has some of the 94-00 normals in. I just wish I knew more." [Emphasis added]
  • "These [results of a trial run] are very promising. The vast majority in both cases are within 0.5 degrees of the published data. However, there are still plenty of values more than a degree out." [As Asimov notes, "He [Harry]'s trying to fit the results of his programs and data to PREVIOUS results." N.B. While discrepancies of 0.5 to 1.0 degrees C may not seem especially troubling, it should be recalled that a century's worth of CO2-induced warming (according to the models) is on the order of 3-5 degrees C.] [Emphasis added]
Runtime Errors. Additional discussion of the coding issues can be found at L'Ombre de l'Olivier — two posts, "The HADCRU Code as From the CRU Leak" and "More CRU Code Thoughts". Their author, a retired programmer, categorizes the various infelicities. Arguably the one with the greatest adverse potential is the
"use of program libra[r]y subroutines that ... fail at undefined times and ... when the function fails[,] the program silently continues without reporting the error" [Emphasis in the original].
Sigh! Runtime errors are the bane of programming. If they do something dramatic, like crash the program or produce obviously nonsensical output, it's OK. Eventually, you find the bug and squash it. But if the effects are subtle, your first notice that something's wrong may be a query from a colleague / competitor wondering why he couldn't replicate your results.

Quality Control. The mess that is CRU bears on quality control standards, on peer review and on the changing nature of scientific research. With regard to quality control, our L'Ombre de l'Olivier correspondent observes:
"When I was a developer, in addition to the concepts of version control and frequent archiving, one thing my evil commercially oriented supervisors insisted on were 'code reviews'. This is the hated point where your manager and/or some other experienced developer goes through your code and critiques it in terms of clarity and quality."
Obviously, nothing of the sort transpired at CRU, most likely because there were no "experienced developers" to go through the codes. This raises the question: "Should it have transpired?" Poster Patrick, at L'Ombre observes that "It is probably better to have scientists writing bad code than programmers doing bad science." Other posters note that confidence in science results, not by someone's approving the "how" of what was done, but by independent replication — if an experiment, then on someone else's lab bench; if a theoretical calculation, then with someone else's algorithm and if data analysis, then with someone else's ad hoc assumptions and the code that implements them. These are valid observations, but there are two important caveats. The first is that replication really has to be independent. A bot mot (at the expense of the computational physics crowd) that has stayed with me over the years involves the passing of code from one lab to another, gremlins intact. That's true for things as run of the mill as differential equation solvers, matrix inverters, etc. The important point is that as soon as things get too complicated to prove , i.e., proposition, lemma, theorem, Q.E.D, what's going on, one is doing experiments. So, if it's differential equations being studied, the sensible investigator convinces himself that his results are not solver-dependent. Likewise, in the case of data analysis, one wants to be sure that the results are robust with regard to the programs that crunch the numbers and, when data are manipulated prior to analysis, and, boy, are climatological time series ever, that trends, "statistical significance," etc. aren't artifactual.

Finally, there's the source of the data. AGW proponents like to point out that similar results have been reported by different groups. But as McIntyre, McKitrick and others have pointed out, the same data sets are used over and over, and the analyses therefore not independent. This appears to be the case in both paleoclimatological and historical studies that rely on a limited number.

Peer Review. In my honors and upper division classes, I insist that students reference the peer reviewed literature. If it's not peer reviewed, I tell them, they have no way of judging the truth of the conclusions. I also tell them that every scientific paper that's ever been published is wrong, the only questions being how wrong and how long it takes the scientific community to discover the errors. So how much protection does peer review actually provide? Not a whole lot if the article in question fails to provide enough information to allow the reader to replicate the results. Many (most? all?) of the climate change papers that I have seen fail this test resoundingly. Indeed, most reviewers restrict themselves to assessing a paper's overall plausibility, the appropriateness of the methods, the extent to which the results are consistent with previously published studies, etc. Only occasionally does a reviewer attempt to reproduce the results, and, in such cases, the editorial response is unpredictable. Sometimes, the reviewer receives a letter thanking him for going the extra mile; on other occasions, one accusing him of attempting a hit job. And, of course, reviewers sometimes have an ax to grind. If the paper in question goes against their own work, they may do what they can to see that it is rejected. Correspondingly, if the paper supports a reviewer's work, he may be inclined offer a favorable response, even if there are problems. Finally, peer review, to say nothing of the funding process, discriminates against ideas and approaches that are outside the box. Let me be clear. My object is not to deny the utility of peer review, but to suggest that it is something less than a guarantee of accuracy.

The Changing Nature of Science. More and more, scientific research is being carried out by teams who tackle projects that, because of their sheer magnitude, do not lend themselves to checking. This is true across disciplines, and it is certainly true of climatology. To verify the results of an outfit like CRU, one needs another group of roughly comparable size. Now it is true that CRU is not the only entity engaged in large-scale climate studies. But it is also true that there are only a couple of others, and they all cooperate. The result is what amounts to monopolistic practices and the need, for the scientific equivalent of anti-trust legislation.
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