Thursday, January 27, 2011

Climate crook Jones is protected by the reluctance of academic institutions to admit error

Last time, I examined the issue of data availability in climate science in the context of Phil Jones’ paper on the urban heat island in Nature. The case of the Jones paper is simple — data supporting conclusions of this important paper are not available and there are serious doubts whether such data was present at the time the paper was written. As first author, Jones has however categorically stated he does not intend to correct the situation or address it in any fashion.

It is notable that Nature magazine’s editorial policy states:
After publication, readers who encounter refusal by the authors to comply with these policies should contact the chief editor of the journal (or the chief biology/chief physical sciences editors in the case of Nature). In cases where editors are unable to resolve a complaint, the journal may refer the matter to the authors’ funding institution and/or publish a formal statement of correction, attached online to the publication, stating that readers have been unable to obtain necessary materials to replicate the findings.

In the present situation, after many years and attempts by several parties, Nature has reported a direct admission from the paper’s author Phil Jones that making data available is ‘impossible’. In some ways, this is quite unprecedented. A request that Nature publish a formal statement of correction therefore seems logical.

It has to be pointed out, perhaps much to the chagrin of climate science activists, that reproducibility of published studies is an acute concern in science.

Cancer research and the case of Anil Potti and Duke University

The case of cancer researcher Anil Potti at Duke University is illustrative of the consequences of full data availability. In 2006 Anil Potti published results of using gene microarray data to identify ‘signatures’ of chemosensitivities to anti-cancer drugs. His group published their work in the prestigious journal, Nature Medicine. They claimed to have developed a method to identify patients who would respond better to certain drugs. The paper was hailed as a breakthrough in oncology research.

The story takes a familiar turn at this point. Biostatisticians at the MD Anderson Cancer Center Keith Baggerly and Kevin Coombes attempted replication of the findings. Incomplete data and software code availability made their efforts difficult – they had to ‘recreate what was done, rather than just retest the model’. Eventually, Baggerly and Coombes employed forensic bioinformatics, working backwards to reconstruct prediction models Potti used. By November 2007, in their letter to Nature Medicine Coombes, Wang and Baggerly pointed out errors in Potti’s software code and column-data which was made available. They concluded:
We do not believe that any of the errors we found were intentional. We believe that the paper demonstrates a breakdown that results from the complexity of many bioinformatics analyses. This complexity requires extensive double-checking and documentation to ensure both data validity and analysis reproducibility. We believe that this situation may be improved by an approach that allows a complete, auditable trail of data handling and statistical analysis.

This produced no visible effect. What was more – Potti and allied researchers published more papers with the same method. Baggerly found further errors in these papers as well, but the journals refused to publish the findings. Matters at Duke had meanwhile evolved to the next stage – clinical trials on patients, employing Potti’s cancer genomic signature tests got underway. The MD Anderson team now changed their approach; Baggerly had a standalone paper ready, summarizing his findings. A prominent biological journal reportedly rejected their paper because “it was too negative”. In November 2009, they eventually published this paper in a statistics journal, the Annals of Applied Statistics.

As Baggerly and Coombes published their findings, Duke University initiated an internal review of Potti’s methods and data, and stopped the clinical trials. Surprisingly, the university concluded that its review found Potti’s conclusions were “confirmed”, but chose to keep the report confidential. The trials were restarted. The hidden nature of the review caused an uproar.
Duke administrators accomplished something monumental: they triggered a public expression of outrage from biostatisticians. In a first such action in anyone’s memory, 33 top-level biostatisticians wrote a letter [to NCI Director Harold Varmus] urging a public inquiry into the Potti scandal.

Duke remained unmoved. About 4 months later (May 2010), a FOI request submitted to the National Cancer Institute, finally made the Duke report public. Strangely enough, in contrast to the university’s claims the redacted report seemed to state that it could not confirm Potti’s results.

In the end, revelations that Potti had falsely stated or implied that he was a Rhodes scholar in grant applications resulted in a final suspension of the clinical trials. Writing in Oncology Times magazine, Rubiya Tuma said that the oncology community was “shocked” at the falsification regarding a well-known scholarship as the Rhodes. In November last year, Anil Potti resigned from Duke University. His papers in Nature Medicine and the Journal of Clinical Oncology have been retracted. Some termed the whole episode ‘Pottigate‘.

Keith Baggerly estimated their team spent 15,000 hours trying to recreate Potti’s methods from published descriptions. What is interesting is that Baggerly and colleagues stumbled upon a recurring problem in science – inadequate description of methods and reluctance to share code. In their paper in Annals of Applied Statistics, Baggerly and Coombes noted:
High-throughput biological assays such as microarrays let us ask very detailed questions about how diseases operate, and promise to let us personalize therapy. Data processing, however, is often not described well enough to allow for exact reproduction of the results, … Unfortunately, poor documentation can shift from an inconvenience to an active danger when it obscures not just methods but errors.

They were more pointed in their conclusions.
In the case of reproducibility in general, journals and funding agencies already require that raw data (e.g., CEL files) be made available. We see it as unavoidable that complete scripts will also eventually be required.

Speaking about descriptions of methods, David F Ransohoff, professor of cancer epidemiology at University of North Carolina said,
“If you look at the really big picture— and this is the key point—the entire purpose of methods sections in science articles is to let someone else reproduce what you did,” “That is really why it is there. So I can see what you’ve done, build on that, or, if I want, see if it is right or wrong. And what has happened as studies have gotten more complex, is that is harder to do. But we, as a scientific field, may have to decide if the solution to that is to say that we are not going to try anymore, or to try to figure out how we can preserve that goal, which is a very important goal in science.”

From cancer to climate science

Involved statistical errors can have real consequences. Joyce Shoffner, a cancer patient who was enrolled in the Potti Duke University trial felt “betrayed”, reported the Raleigh News Observer. Shoffner had received a drug based on tests that suggested it would work very well against her tumor, but this was not borne out in her clinical course. Shoffner volunteered: — “There needs to be some kind of auditor of the data”.

For anyone following the climate debate, the parallels between examination of Potti’s results by biostatisticians Kieth Baggerly et al and examination of Michael Mann’s work by Steve McIntyre and Ross McKitrick are glaring. There are startling parallels between how the University of Albany investigated Doug Keenan’s fraud charge against Jones’ co-author Wei-Chyung Wang and Duke University’s internal investigations of Potti as well. The blog Duke.Fact.Checker recalled the story thus:
For four years, some entrenched people at Duke tried to discredit these challenges in any way they could, including disparaging remarks that biostatisticians were not scientists are all, and that the MD degree yields more expertise in the emerging genome field than a Ph.D. At one point a Dean asked aloud who would believe a bunch of internet fools.

Recounting their conclusions, Baggerly and a joint team of 43 biostatisticians wrote in a joint letter to Nature recently:
The independent reanalysis of these signatures took so long because the information accompanying the associated publications was incomplete. Unfortunately, this is common: for example, a survey of 18 published microarray gene-expression analyses found that the results of only two were exactly reproducible (J. P. Ioannidis et al. Nature Genet. 41, 149–155; 2009). Inadequate information meant that 10 could not be reproduced.

To counter this problem, journals should demand that authors submit sufficient detail for the independent assessment of their paper’s conclusions. We recommend that all primary data are backed up with adequate documentation and sample annotation; all primary data sources, such as database accessions or URL links, are presented; and all scripts and software source codes are supplied, with instructions. Analytical (non-scriptable) protocols should be described step by step, and the research protocol, including any plans for research and analysis, should be provided. Files containing such information could be stored as supplements by the journal.


Warmists peeved that Obama did not mention warming in his SOTU address

See below. Not a sigle scientific fact is mentioned, of course, just the mythical "consensus"

In his 2009 State of the Union-esque speech, Obama spoke of "saving our planet from the ravages of climate change." In his 2010 SOTU, he affirmed the "overwhelming scientific evidence on climate change." In 2011, fresh off the hottest year on record, Obama said ... nothing about climate change. It didn't come up.

This is a failure on Obama's part. A moral failure, a failure of leadership, but also, I would argue, a political failure.

Andy Revkin and Bryan Walsh both note the obvious reason for the omission: climate change has become a "partisan issue." It's "divisive." As Revkin says, Obama is trying to "build a new American energy conversation on points of agreement rather than clear ideological flash points like global warming." I understand that. But I think capitulating to that logic is myopic and counterproductive.

First of all, consider the larger analogy at the heart of Obama's speech: America is at a "Sputnik moment." Well, why was Sputnik a Sputnik moment? Not because Americans said, "Wow, the USSR is getting really good at technology! We're getting outcompeted!" No, what the public said was, "Holy sh*t! Our mortal enemy is putting stuff in space! They're going to rain rockets down on us and we're all going to die!" In other words, Sputnik was not some friendly challenge to see who can win the race to the future (or whatever). It was a threat. That's what lit a fire under America's ass and that's why America rose to the challenge.

Obama wants to launch a clean energy race. And good for him. But what are the stakes? What is the threat? Where is the urgency? If it's just about international competition, why not focus on good macroeconomic policy -- why go to such lengths to build up this economic sector, these technologies? Why not just leave it to the market?

Here's why: The U.S. needs to get at or close to zero carbon emissions by the middle of this century or there will be severe and possibly irreversible changes in the climate, leading to massive, widespread human suffering. That's why we don't have time to wait for the invisible hand of the market. That's why we need massive investments, tighter regulations, and a price on climate pollution. That's the threat. Without it, a push for clean energy is a nice slogan that can easily be shunted aside when, oh, gas prices are rising, or there's a recession, or Joe Manchin need to get reelected.

The threat of climate change is what justifies and animates the clean energy race. That's the substantive need.

But telling the truth about climate change is also good politics. Avoiding the issue because it's an "ideological flash point" is just to allow Republicans to succeed in making it an ideological flash point! It is to affirm that it's partisan and divisive, which is exactly what conservatives have been trying to make it for years. If they can do it to climate, why won't they go right on to do it to clean energy, or innovation, or investment? (Hint: They already are.) It gives them control over public dialogue.

In fact, the best American scientists, along with scientists all over the world, say climate change is a pressing threat to our nation's health and security. One does not tiptoe around such threats because a core group of ideologues in the other party doesn't like hearing about them. That's not leadership.


Did you think global warming alarmism was about saving polar bears?

From across the pond, AFP reports from Paris: “From being a marginal and even mocked issue, climate-change litigation is fast emerging as a new frontier of law where some believe hundreds of billions of dollars are at stake. Compensation for losses inflicted by man-made global warming would be jaw-dropping, a payout that would make tobacco and asbestos damages look like pocket money.”

We’re shocked, shocked to find people are going to sue you because of your carbon footprint. Shocked.

AFP continues: “In the past three years, the number of climate-related lawsuits has ballooned, filling the void of political efforts in tackling greenhouse-gas emissions. . . Seminars on climate law are often thickly attended by corporations that could be in the firing line — and by the companies that insure them.”
Profiteering? Who would have guessed? Well, OK. It was transparently obvious from Day 1.

But there is a glimmer of hope, says AFP’s report: “… legal experts sound a note of caution, warning that this is a new and mist-shrouded area of justice. Many obstacles lie ahead before a Western court awards a cent in climate damages and even more before the award is upheld on appeal.

“There’s a large number of entrepreneurial lawyers and NGOs who are hunting around for a way to gain leverage on the climate problem,” said David Victor, director of the Laboratory on International Law and Regulation at the University of California at San Diego.

The bottom line (so far)? “The number of suits filed has increased radically. But the number of suits claiming damages from climate change that have been successful remains zero.”


Being Green Is Not a Sign of Health

There are two new reports in the Wall Street Journal about flops in the green energy movement — further illustrations of how much hype there is in it.

The first (Jan. 19) reveals that the vaunted new “amazingly energy efficient,” compact fluorescent light bulbs aren’t so energy efficient after all.

Pushing the hapless consumer to replace incandescent bulbs with CFLs (compact fluorescent lamps) has been the received wisdom among lawmakers for years, and no more so than in California, the ever-green state. California’s utilities alone spent $548 million over the past seven years in CFL subsidies. In fact, California utilities have subsidized over 100 million CFLs since 2006. And on the first of this year, the state started phasing out incandescent bulb sales.

Of course, when I say that the California utilities have been subsidizing the CFLs, I really should say that the aforementioned hapless consumers have been doing so, because all the subsidy money — about $2.70 out of the actual $4.00 cost of the CFL, i.e., more than two thirds of the actual cost — is paid by the consumer in the form of higher utility rates.

Naturally, the rest of the country — and, for that matter, the world — is set to follow California’s lead on CFLs. A federal law effective January 1 of next year will require a 28% step-up in efficiency for incandescent bulbs, and bans them outright by 2014. One consequence of this federal policy — unintended, perhaps, but none the less foreseeable — is that the last US plant making incandescent bulbs has been shut down, and China (which now makes all the CFLs) has seen even more of a jobs expansion, and is able to buy even more of our debt.

The UN is also pushing CFLs to help solve global warming, estimating that about 8% of all greenhouse gas emissions worldwide are caused by lighting. The World Bank has been funding the distribution of CFLs in poorer nations. Last year, for example, Bangladesh gave away five million World Bank funded CFLs in one day.

But now — surprise! — California has discovered that the actual energy savings of switching to CFLs were nowhere near what was originally estimated. Pacific Gas and Electric, which in 2006 set up the biggest subsidy fund for CFLs, found that its actual savings from the CFL program were collectively about 450 million kilowatt hours, which is only about one-fourth of the original estimate.

There are several reasons for the fact the switch to CFLs hasn’t lived up to expectations. First, not as many of the heavily subsidized CFLs were sold as originally estimated. PG & E doesn’t say why, but I will hazard a guess, based on personal experience. Many consumers dislike the light produced by CFLs, which they find dimmer or more artificial in its effect. Also, many complain that lights create static in AM radio reception. In a free market (i.e., one that, among other things, contains no subsidies), it is likely that few consumers would want to switch.

Second, the useful life of the CFLs is less than 70% of original estimates. Amazingly, the estimates were based on tests that didn’t factor in the actual frequency with which consumers turn them on and off. CFLs burn out more quickly the more often they are turned on and off than do the old incandescent bulbs.

Not mentioned in the story is the fact that CFLs contain mercury, and so are supposed to be specially disposed of (which presents an added cost to the consumer in time, money, and energy). The alternative is for the consumer to throw them out in the regular trash, making toxic waste sites out of ordinary trash dumps, with future clean-up costs of God only knows what.

The second Journal story (Jan. 18) reports that Evergreen Solar has closed its Massachusetts plant and laid off all the workers there.

This is deliciously ironic. Evergreen Solar was the darling of Massachusetts. Governor Deval Patrick, devout green and all-around Obama Mini-Me, gave Evergreen a package of $58 million in tax incentives, grants, and other handouts to open a solar panel plant there. In doing so, he simply ignored Evergreen’s lousy track record — a record of losing nearly $700 million bucks in its short life (its IPO was in 2000), despite lavish subsidies from federal and state governments.

Now Evergreen is outsourcing its operations, blaming competition with China, and whining like a bitchslapped baby about China’s subsidies of its solar energy and its lower labor costs. But Evergreen has itself sucked up ludicrously lavish subsidies, and it knew all along about China’s labor rates compared to Massachusetts’.

So Patrick winds up looking like a complete ass, and the taxpayers of Massachusetts wind up eating a massive loss.

But that’s not all. Near the end of last year, the Journal (Dec. 20) revealed still another case of American crony capitalism, of the green sort. It turns out that the wind industry — aptly dubbed “Big Wind” — copped a one-year, $3 billion extension of government support for wind power. It was part of the end-of-2010 tax deal.

Originally, this government subsidy was a feature of the infamous 2008 stimulus bill, under which taxpayers were forced to cover 30% of the costs of wind power projects. The American Wind Energy Association (AWEA) begged for the subsequent bailout, because without it 20,000 wind power jobs would be lost (one-fourth of all such jobs in America). But despite the billions in subsidies, Big Wind is sucking wind; its allure is dropping like a stone. The AWEA’s own figures show a 72% decline in wind turbine installations from 2009, down to the lowest since 2006.

Besides trying to make the 30% subsidy(!) permanent, the AWEA is pushing for a national “renewable energy” mandate that will force utilities to buy a large chunk of the power they sell from renewable sources (mainly solar and wind), irrespective of the fact that the price of renewable energy is sky high. The association has gotten more than half the states to enact such mandates, with higher energy bills for consumers as the result. Not surprisingly, Big Wind is also pushing the EPA to make energy from fossil fuels vastly more costly.

According to the federal government’s own figures, wind and solar take 20 times the subsidy to produce electricity than do coal and natural gas. So you can see why Big Wind keeps blowing smoke up the public’s rear about the fabulous future of renewable energy. You can also see why Big Wind is such a big contributor to the campaign coffers of Democratic politicians. They are the only ones who keep this outrageous boondoggle awash in money.

Meanwhile, the promises of green energy look more and more hollow, every day.


Earth's climate crisis ain't necessarily so

Viscount Monckton writes for an Australian audience below

WHILE the Gillard government's climate-change parliamentary committee plots to wreck Australia's economy with a rigged market to make motoring and electricity unaffordable as soon as the new Greens-infected Senate starts work in July, thoughtful pollies are at last - privately, quietly - beginning to ask the Gershwin question.

What if it ain't necessarily so? Suppose there's no climate crisis?

The Romans used to farm out tax collection to "tax farmers" such as St Matthew. The cap-and-tax boondoggle is a tax-farming scam to impoverish the working man and enrich the new tax farmers: bankers, traders, ministers, officials and media moguls. None of them saints.

Cap-and-tax in Europe has been a wickedly costly fiasco. The rigged market has collapsed twice. Member states cheated by allowing themselves more rights to emit than their actual emissions, so the price of emission rights plummeted. Then the tax farmers simply invented 90 per cent of their carbon trades.

Result: electricity prices have doubled. In the name of preventing global warming, many Britons are dying because they cannot afford to heat their homes.

Cap and tax is as pointless as it is cruel. Australia accounts for 1.5 per cent of global carbon emissions. So if it cut its emissions, the warming forestalled would be infinitesimal.

It's worth explaining exactly why. Suppose the Australian committee's aim is to cut emissions by 20 per cent by 2050. Anything more ambitious would shut Australia down, especially while the Greens insist on not letting the country use its own zero-carbon-emitting uranium as fuel.

A 20 per cent cut by 2050 is an average 10 per cent cut from now until then. Carbon dioxide concentration by 2050 probably won't exceed 506 parts per million by volume, from which we deduct today's concentration of 390 ppmv. So humankind might add 116 ppmv from now until then.

The CO2 concentration increase forestalled by 40 years of cap-and-tax in Australia would be 10 per cent of 1.5 per cent of that 116 ppmv, or just 0.174 ppmv. So in 2050 CO2 concentration would be - tell it not in Gath and Ashkelon - 505.826 ppmv, not 506.

Thus what we maths wonks call the proportionate change in CO2 concentration if the committee got its way would be 505.826 divided by 506, or 0.9997. The UN says warming or cooling, in Celsius degrees, is 3.7 to 5.7 times the logarithm of the proportionate change.

It expects only 57 per cent of manmade warming to occur by 2100: the rest would happen slowly and harmlessly across 1000-3000 years.

To be charitable to the committee, let us take the UN's high-end estimate. The warming forestalled by cutting Australia's emissions would be very unlikely to exceed 57 per cent of 5.7 times the logarithm of 0.9997: that is - wait for it - a dizzying one-thousandth of a degree by 2050.

I have set out this calculation to show how certainly it is known that all attempts to cut CO2 emissions will expensively fail. Focused adaptation to any adverse consequences of such warming as may occur would be orders of magnitude more cost-effective. But do we need to cut CO2 at all? Some cold facts:

Satellite datasets show last year was not the warmest on record. It was not the least snow-covered year but the most snow-covered: a largely unreported gain in Antarctic sea ice since 1979 almost matches the widely reported loss of Arctic sea ice.

It was not the worst year for hurricanes, but the best year: the accumulated-cyclone-energy index shows less tropical-cyclone activity worldwide than for 30 years.

The forest fires in Russia and southern Australia, and the floods in Pakistan and eastern Australia, were far from the worst ever. Nor can they be attributed to human influence: the UN's climate panel has warned us against that.

They were caused by naturally occurring weather patterns called blocking highs. And global warming can scarcely be blamed after a decade without any.

Nor did 2010 see the second-highest level of natural catastrophes. Yes, 90 per cent of them were weather-related, but in most years that is true, and was true long before we could have influenced climate.

Nor is sea level rising fast. It has risen at the rate of just 0.3m a century since satellites measured it reliably in 1993, under a quarter of the average rate during the past 11,400 years. The Greens don't believe their own whining about sea level: their Hobart office is just metres from the "dangerously" rising ocean.

Nor do most scientists believe man-made global warming will be catastrophic. Most are not climate scientists and take no view, and only a few climatologists have published on the central question how much warming there will be.

Of these, the researchers using measurement and observation rather than modelling have shown that much of the radiation the models say should be warming the surface is escaping to space as before.

The upper air in the tropics that the models predict should warm at thrice the surface rate is warming only at the same rate; model-predicted surface evaporation in response to warming is a third of the observed rate.

The missing heat energy imagined by the models but not present as warming in the past decade is not lurking in the oceans; and the entire warming of the late 20th century can easily be explained without blaming man.

Just one of these fatal discrepancies between prediction and reality - and each points to very little future warming - would normally be enough to dismiss climate catastrophism.

As the Gershwins rightly concluded, "It ain't nessa, ain't nessa, ain't nessa, ain't nessa, ain't necessarily so."


Study: Biofuels of no benefit to military

A new analysis presented to Congress yesterday paints a stark picture for the Defense Department's current efforts to secure renewable fuels. Fuels made from plant waste or algae will not be achievable in large or cheap enough quantities to make sense for military applications in the next decade, concluded the report penned by the RAND Corporation.

"The use of alternative fuels offers the armed services no direct military benefit," it added, urging the military and Congress to rethink dedicating defense appropriations to alternative fuels research.

Though the Defense Department has said using more renewable energy will reduce the need for fuel convoys in the battle zone, RAND questions biofuel's role in that effort, saying that any alternative fuels -- either with biofuel blends or coal-to-liquid technology -- would still require those fuel convoys or compound logistical challenges on the front lines.

"In short, the military is best served by efforts directed at using energy more efficiently in weapon systems and at military installations," it said.

The work assessed the current status of the alternative fuels market and concluded that the only fossil fuel substitutes that could be attainable in the foreseeable future would be those produced through the Fischer-Tropsch process, a method with a hefty carbon footprint that produces synthetic diesel from coal, natural gas or coal-biomass blends.

"Considering economics, technical readiness, greenhouse gas emissions and general environmental concerns, [Fischer-Tropsch] fuels derived from a mixture of coal and biomass represent the most promising approach to producing amounts of alternative fuels that can meet military, as well as appreciable levels of civilian, needs by 2030," the report said.

More here


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