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By Carlin Romano Standing up for science excites some intellectuals the way beautiful actresses arouse Warren Beatty, or career liberals boil the blood of Glenn Beck and Rush Limbaugh. It's visceral.

A brave champion of beleaguered science in the modern age of pseudoscience, this Ayn Rand protagonist sarcastically derides the benighted irrationalists and glows with a self-anointed superiority. Who wouldn't want to feel that sense of power and rightness?

You hear the voice regularly—along with far more sensible stuff—in the latest of a now common genre of science patriotism, Nonsense on Stilts: How to Tell Science From Bunk (University of Chicago Press), by Massimo Pigliucci, a philosophy professor at the City University of New York.

Science stories usually fall into three families: wacky stories, scare stories and "breakthrough" stories.

these stories are invariably written by the science correspondents, and hotly followed, to universal jubilation, with comment pieces, by humanities graduates, on how bonkers and irrelevant scientists are.

A close relative of the wacky story is the paradoxical health story. Every Christmas and Easter, regular as clockwork, you can read that chocolate is good for you (www.badscience.net/?p=67), just like red wine is, and with the same monotonous regularity

The first group are those with an overly simplistic or naive sense of how science functions. This is a view of science similar to those films created in the 1950s and meant to be watched by students, with the jaunty music playing in the background. This view generally respects science, but has a significant underappreciation for the flaws and complexity of science as a human endeavor. Those with this view are easily scandalized by revelations of the messiness of science.

The second cluster is what I would call scientific skepticism – which combines a respect for science and empiricism as a method (really “the” method) for understanding the natural world, with a deep appreciation for all the myriad ways in which the endeavor of science can go wrong. Scientific skeptics, in fact, seek to formally understand the process of science as a human endeavor with all its flaws. It is therefore often skeptics pointing out phenomena such as publication bias, the placebo effect, the need for rigorous controls and blinding, and the many vagaries of statistical analysis. But at the end of the day, as complex and messy the process of science is, a reliable picture of reality is slowly ground out.

The third group, often frustrating to scientific skeptics, are the science-deniers (for lack of a better term). They may take a postmodernist approach to science – science is just one narrative with no special relationship to the truth. Whatever you call it, what the science-deniers in essence do is describe all of the features of science that the skeptics do (sometimes annoyingly pretending that they are pointing these features out to skeptics) but then come to a different conclusion at the end – that science (essentially) does not work.

The problem of replicability in science from xkcdby Massimo Pigliucci

In recent months much has been written about the apparent fact that a surprising, indeed disturbing, number of scientific findings cannot be replicated, or when replicated the effect size turns out to be much smaller than previously thought.

Arguably, the recent streak of articles on this topic began with one penned by David Freedman in The Atlantic, and provocatively entitled “Lies, Damned Lies, and Medical Science.” In it, the major character was John Ioannidis, the author of some influential meta-studies about the low degree of replicability and high number of technical flaws in a significant portion of published papers in the biomedical literature.

being both a working scientist and a science writer gives me a unique perspective on science, scientific publications, and the significance of scientific work. The final disclosure should be that I have never published in any of the top rank physics journals or in Science, Nature, or PNAS. I don't believe I have an axe to grind about that, but I am also sure that you can ascribe some of my opinions to PNAS envy.

If you asked most scientists what their goals were, the answer would boil down to the generation of new knowledge. But, at some point, science and scientists have to interact with money and administrators, which has significant consequences for science. For instance, when trying to employ someone to do a job, you try to objectively decide if the skills set of the prospective employee matches that required to do the job. In science, the same question has to be asked—instead of being asked once per job interview, however, this question gets asked all the time.

Because science requires funding, and no one gets a lifetime dollop-o-cash to explore their favorite corner of the universe. So, the question gets broken down to "how competent is the scientist?" "Is the question they want to answer interesting?" "Do they have the resources to do what they say they will?" We will ignore the last question and focus on the first two.

Scientists these days tend to keep up a polite fiction that all science is equal. Except for the work of the misguided opponent whose arguments we happen to be refuting at the time, we speak as though every scientist's field and methods of study are as good as every other scientist's and perhaps a little better. This keeps us all cordial when it comes to recommending each other for government grants.

Why should there be such rapid advances in some fields and not in others? I think the usual explanations that we tend to think of - such as the tractability of the subject, or the quality or education of the men drawn into it, or the size of research contracts - are important but inadequate. I have begun to believe that the primary factor in scientific advance is an intellectual one. These rapidly moving fields are fields where a particular method of doing scientific research is systematically used and taught, an accumulative method of inductive inference that is so effective that I think it should be given the name of "strong inference." I believe it is important to examine this method, its use and history and rationale, and to see whether other groups and individuals might learn to adopt it profitably in their own scientific and intellectual work. In its separate elements, strong inference is just the simple and old-fashioned method of inductive inference that goes back to Francis Bacon. The steps are familiar to every college student and are practiced, off and on, by every scientist. The difference comes in their systematic application. Strong inference consists of applying the following steps to every problem in science, formally and explicitly and regularly: Devising alternative hypotheses; Devising a crucial experiment (or several of them), with alternative possible outcomes, each of which will, as nearly is possible, exclude one or more of the hypotheses; Carrying out the experiment so as to get a clean result; Recycling the procedure, making subhypotheses or sequential hypotheses to refine the possibilities that remain, and so on.

On any new problem, of course, inductive inference is not as simple and certain as deduction, because it involves reaching out into the unknown. Steps 1 and 2 require intellectual inventions, which must be cleverly chosen so that hypothesis, experiment, outcome, and exclusion will be related in a rigorous syllogism; and the question of how to generate such inventions is one which has been extensively discussed elsewhere (2, 3). What the formal schema reminds us to do is to try to make these inventions, to take the next step, to proceed to the next fork, without dawdling or getting tied up in irrelevancies.

a very natural way for atheists to react to religious claims: to ask for evidence, and reject these claims in the absence of it. Many of the several hundred comments that followed two earlier Stone posts “Philosophy and Faith” and “On Dawkins’s Atheism: A Response,” both by Gary Gutting, took this stance. Certainly this is the way that today’s “new atheists”  tend to approach religion. According to their view, religions — by this they mean basically Christianity, Judaism and Islam and I will follow them in this — are largely in the business of making claims about the universe that are a bit like scientific hypotheses. In other words, they are claims — like the claim that God created the world — that are supported by evidence, that are proved by arguments and tested against our experience of the world. And against the evidence, these hypotheses do not seem to fare well.

But is this the right way to think about religion? Here I want to suggest that it is not, and to try and locate what seem to me some significant differences between science and religion

To begin with, scientific explanation is a very specific and technical kind of knowledge. It requires patience, pedantry, a narrowing of focus and (in the case of the most profound scientific theories) considerable mathematical knowledge and ability. No-one can understand quantum theory — by any account, the most successful physical theory there has ever been — unless they grasp the underlying mathematics. Anyone who says otherwise is fooling themselves.

The Templeton Foundation claims to be a friend of science. So why does it make so many researchers uneasy?

With a current endowment estimated at US$2.1 billion, the organization continues to pursue Templeton's goal of building bridges between science and religion. Each year, it doles out some $70 million in grants, more than $40 million of which goes to research in fields such as cosmology, evolutionary biology and psychology.

however, many scientists find it troubling — and some see it as a threat. Jerry Coyne, an evolutionary biologist at the University of Chicago, Illinois, calls the foundation "sneakier than the creationists". Through its grants to researchers, Coyne alleges, the foundation is trying to insinuate religious values into science. "It claims to be on the side of science, but wants to make faith a virtue," he says.

It is far from accurate to refer to “science” as a single entity (as I just have). Many arguments that dispute the consensus about climate change being the result of man made activity talk about “scientists” as though they are “all in it together” and “supporting each other”. This implies some grand conspiracy. But science is a competition, not a collusion. If anything they are all against each other. No given person or research team has the whole picture of climate science. The range of scientific disciplines that work in this area is vast. Indeed there are few areas of science which do not potentially have something to contribute to the area. But put a geologist and a geneticist in a room together and they can barely speak the same language. Far from some great conspiracy, the fact that the Intergovernmental Panel on Climate Change has come to a consensus about climate change is truly extraordinary.

So the report is recommending that journalists do what they should always have done – investigate and verify. By all means ask another expert’s point of view, determine whether the latest finding is in fact good science or what its implications are. But we need to move away from the idea of “balance” between those who believe it is all a big conspiracy and those who have done some work and looked at the actual evidence. The report concludes that in particular the BBC must take special care to continue efforts to ensure viewers are able to distinguish well-established fact from opinion on scientific issues, and to communicate this distinction clearly to the audience. In other words, to remember that the plural of anecdote is not data.

One part of Matthew Nisbet's recent report that has received very little attention is its comparative analysis of ideological and partisan perspectives of members of the American Association for the Advancement of Science. Nisbet shows that AAAS members are extremely partisan and ideological.  The word "extremely" is mine, and what do I mean by it?  Look at the figure above:  AAAS members are more partisan than MSNBC viewers and even Tea Party members.  AAAS members are more ideological than evangelical churchgoers but less so than Fox News viewers.  In both cases AAAS members are very different than the public as a whole.

Dan Sarewitz has discussed the problems with the ideological and partisan likemindedness of our scientific community, which has been exploited and reenforced in political debates: During the Bush administration, Democrats discovered that they could score political points by accusing Bush of being anti-science. In the process, they seem to have convinced themselves that they are the keepers of the Enlightenment spirit, and that those who disagree with them on issues like climate change are fundamentally irrational. Meanwhile, many Republicans have come to believe that mainstream science is corrupted by ideology and amounts to no more than politics by another name. Attracted to fringe scientists like the small and vocal group of climate skeptics, Republicans appear to be alienated from a mainstream scientific community that by and large doesn't share their political beliefs. The climate debacle is only the most conspicuous example of these debilitating tendencies, which play out in issues as diverse as nuclear waste disposal, protection of endangered species, and regulation of pharmaceuticals. How would a more politically diverse scientific community improve this situation? First, it could foster greater confidence among Republican politicians about the legitimacy of mainstream science. Second, it would cultivate more informed, creative, and challenging debates about the policy implications of scientific knowledge. This could help keep difficult problems like climate change from getting prematurely straitjacketed by ideology. A more politically diverse scientific community would, overall, support a healthier relationship between science and politics.

It should come as no surprise that the increasing politicization of science has come to make science more political rather than politics more scientific.  At the same time, the more partisan and/or and ideological that you are, the more welcome and comfortable that you will find the politicization of science, as it reenforces your preconceptions.

John Beddington, the Chief Scientific Advisor to the UK government, has identified a need to be "grossly intolerant" of certain views that get in the way of dealing with important policy problems: We are grossly intolerant, and properly so, of racism. We are grossly intolerant, and properly so, of people who [are] anti-homosexuality... We are not—and I genuinely think we should think about how we do this—grossly intolerant of pseudo-science, the building up of what purports to be science by the cherry-picking of the facts and the failure to use scientific evidence and the failure to use scientific method. One way is to be completely intolerant of this nonsense. That we don't kind of shrug it off. We don't say: ‘oh, it's the media’ or ‘oh they would say that wouldn’t they?’ I think we really need, as a scientific community—and this is a very important scientific community—to think about how we do it.

Fortunately, Andrew Stirling, research director of the Science Policy Research Unit (which these days I think just goes by SPRU) at the University of Sussex, provides a much healthier perspective: What is this 'pseudoscience'? For Beddington, this seems to include any kind of criticism from non-scientists of new technologies like genetically modified organisms, much advocacy of the 'precautionary principle' in environmental protection, or suggestions that science itself might also legitimately be subjected to moral considerations. Who does Beddington hold to blame for this "politically or morally or religiously motivated nonsense"? For anyone who really values the central principles of science itself, the answer is quite shocking. He is targeting effectively anyone expressing "scepticism" over what he holds to be 'scientific' pronouncements—whether on GM, climate change or any other issue. Note, it is not irrational "denial" on which Beddington is calling for 'gross intolerance', but the eminently reasonable quality of "scepticism"! The alarming contradiction here is that organised, reasoned, scepticism—accepting rational argument from any quarter without favour for social status, cultural affiliations  or institutional prestige—is arguably the most precious and fundamental quality that science itself has (imperfectly) to offer. Without this enlightening aspiration, history shows how society is otherwise all-too-easily shackled by the doctrinal intolerance, intellectual blinkers and authoritarian suppression of criticism so familiar in religious, political, cultural and media institutions.

tirling concludes: [T]he basic aspirational principles of science offer the best means to challenge the ubiquitously human distorting pressures of self-serving privilege, hubris, prejudice and power. Among these principles are exactly the scepticism and tolerance against which Beddington is railing (ironically) so emotionally! Of course, scientific practices like peer review, open publication and acknowledgement of uncertainty all help reinforce the positive impacts of these underlying qualities. But, in the real world, any rational observer has to note that these practices are themselves imperfect. Although rarely achieved, it is inspirational ideals of universal, communitarian scepticism—guided by progressive principles of reasoned argument, integrity, pluralism, openness and, of course, empirical experiment—that best embody the great civilising potential of science itself. As the motto of none other than the Royal Society loosely enjoins (also sometimes somewhat ironically) "take nothing on authority". In this colourful instance of straight talking then, John Beddington is himself coming uncomfortably close to a particularly unsettling form of unscientific—even (in a deep sense) anti-scientific—'double speak'.

If top scientists such as John Polkinghorne and Bernard d'Espagnat believe in God, that challenges the simplistic claim that science and religion are completely incompatible. It doesn't hurt that this message is being pushed with the help of the enormous wealth of the Templeton Foundation, which funds innumerable research programmes, conferences, seminars and prizes as a kind of marriage guidance service to religion and science.

why on earth should physicists hold this exalted place in the theological firmament?

it can almost be reduced to a linguistic mistake: thinking that because both physicists and theologians study fundamental forces of some kind, they must study fundamental forces of the same kind.

science has long been married to mathematics. Generally it has been for the better. Especially since the days of Galileo and Newton, math has nurtured science. Rigorous mathematical methods have secured science’s fidelity to fact and conferred a timeless reliability to its findings.

a mutant form of math has deflected science’s heart from the modes of calculation that had long served so faithfully. Science was seduced by statistics, the math rooted in the same principles that guarantee profits for Las Vegas casinos. Supposedly, the proper use of statistics makes relying on scientific results a safe bet. But in practice, widespread misuse of statistical methods makes science more like a crapshoot.

science’s dirtiest secret: The “scientific method” of testing hypotheses by statistical analysis stands on a flimsy foundation. Statistical tests are supposed to guide scientists in judging whether an experimental result reflects some real effect or is merely a random fluke, but the standard methods mix mutually inconsistent philosophies and offer no meaningful basis for making such decisions. Even when performed correctly, statistical tests are widely misunderstood and frequently misinterpreted. As a result, countless conclusions in the scientific literature are erroneous, and tests of medical dangers or treatments are often contradictory and confusing.

Mendick, H. and Moreau, M. (2010). Monitoring the presence and representation of  women in SET occupations in UK based online media. Bradford: The UKRC.

Mendick and Moreau considered the representation of women on eight ‘SET’ (science, engineering and technology) websites: New Scientist, Bad Science, the Science Museum, the Natural History Museum, Neuroskeptic, Science: So What, Watt’s Up With That and RichardDawkins.net. They also monitored SET content across eight more general sites: the BBC, Channel 4, Sky, the Guardian, the Daily Mail, Wikipedia, YouTube and Twitter.

Their results suggest online science informational content is male dominated in that far more men than women are present. On some websites, they found no SET women. All of the 14 people in SET identified on the sampled pages of the RichardDawkins.net website were men, and so were all 29 of those mentioned on the sampled pages of the Channel 4 website (Mendick & Moreau, 2010: 11).

one day he took one of these – finding a mathematical proof about the properties of multidimensional objects – and put his thoughts on his blog. How would other people go about solving this conundrum? Would somebody else have any useful insights? Would mathematicians, notoriously competitive, be prepared to collaborate? "It was an experiment," he admits. "I thought it would be interesting to try."He called it the Polymath Project and it rapidly took on a life of its own. Within days, readers, including high-ranking academics, had chipped in vital pieces of information or new ideas. In just a few weeks, the number of contributors had reached more than 40 and a result was on the horizon. Since then, the joint effort has led to several papers published in journals under the collective pseudonym DHJ Polymath. It was an astonishing and unexpected result.

"If you set out to solve a problem, there's no guarantee you will succeed," says Gowers. "But different people have different aptitudes and they know different tricks… it turned out their combined efforts can be much quicker."

There are many interpretations of what open science means, with different motivations across different disciplines. Some are driven by the backlash against corporate-funded science, with its profit-driven research agenda. Others are internet radicals who take the "information wants to be free" slogan literally. Others want to make important discoveries more likely to happen. But for all their differences, the ambition remains roughly the same: to try and revolutionise the way research is performed by unlocking it and making it more public.

A recent editorial in the New York Times by Nicholas Wade raises some interesting points about the nature of basic science research – primarily that its’ risky.

As I have pointed out about the medical literature, researcher John Ioaniddis has explained why most published studies turn out in retrospect to be wrong. The same is true of most basic science research – and the underlying reason is the same. The world is complex, and most of our guesses about how it might work turn out to be either flat-out wrong, incomplete, or superficial. And so most of our probing and prodding of the natural world, looking for the path to the actual answer, turn out to miss the target.

research costs considerable resources of time, space, money, opportunity, and people-hours. There may also be some risk involved (such as to subjects in the clinical trial). Further, negative studies are actually valuable (more so than terrible pictures). They still teach us something about the world – they teach us what is not true. At the very least this narrows the field of possibilities. But the analogy holds in so far as the goal of scientific research is to improve our understanding of the world and to provide practical applications that make our lives better. Wade writes mostly about how we fund research, and this relates to our objectives. Most of the corporate research money is interested in the latter – practical (and profitable) applications. If this is your goal, than basic science research is a bad bet. Most investments will be losers, and for most companies this will not be offset by the big payoffs of the rare winners. So many companies will allow others to do the basic science (government, universities, start up companies) then raid the winners by using their resources to buy them out, and then bring them the final steps to a marketable application. There is nothing wrong or unethical about this. It’s a good business model.

The most comprehensive inquiry was the Independent Climate Change Email Review led by Sir Muir Russell, commissioned by UEA to examine the behaviour of the CRU scientists (but not the scientific validity of their work). It published its final report in July 2010

It focused on what the CRU scientists did, not what they said, investigating the evidence for and against each allegation. It interviewed CRU and UEA staff, and took 111 submissions including one from CRU itself. And it also did something the media completely failed to do: it attempted to put the actions of CRU scientists into context.

The Review went back to primary sources to see if CRU really was hiding or falsifying their data. It considered how much CRU’s actions influenced the IPCC’s conclusions about temperatures during the past millennium. It commissioned a paper by Dr Richard Horton, editor of The Lancet, on the context of scientific peer review. And it asked IPCC Review Editors how much influence individuals could wield on writing groups.

Vegetarianism: is it a good idea? Vegetarianism is a complex set of beliefs and practices, spanning from the extreme “fruitarianism,” where people only eat fruits and other plant parts that can be gathered without “harming” the plant (though I’m sure the plant would rather keep its fruits and use them for the evolutionary purpose of dispersing its own offspring) to various forms of “flexitaranism,” like pollotarianism (poultry is okay to eat) and pescetarianism (fisk okay).

Is it true that a vegetarian diet increases one’s health? Yes, but only in certain respects, partially because vegetarians also tend to be health conscious in general (they exercise, don’t smoke, drink less, etc.), and it is not the case for the more extreme versions (including veganism), where one needs to be extremely careful to achieve a balanced diet which may need to be supplemented artificially, especially for growing children.

What is the ethical case for vegetarianism? Again, the answer is complex. It seems hard to logically defend fruitarianism, and borderline to make a moral argument for veganism, but broader forms of vegetarianism certainly get at important issues of suffering and mistreatment of both animals and industry workers, not to mention that the environmental impact of meat eating is much more damaging than that of vegetarianism. And so the debate rages on.

There is a growing anti-science streak on the American right that could have tangible societal and political impacts on many fronts — including regulation of environmental and other issues and stem-cell research.

The right-wing populism that is flourishing in the current climate of economic insecurity echoes many traditional conservative themes, such as opposition to taxes, regulation and immigration. But the Tea Party and its cheerleaders, who include Limbaugh, Fox News television host Glenn Beck and Sarah Palin (who famously decried fruitfly research as a waste of public money), are also tapping an age-old US political impulse — a suspicion of elites and expertise.

Denialism over global warming has become a scientific cause célèbre within the movement. Limbaugh, for instance, who has told his listeners that “science has become a home for displaced socialists and communists”, has called climate-change science “the biggest scam in the history of the world”. The Tea Party's leanings encompass religious opposition to Darwinian evolution and to stem-cell and embryo research — which Beck has equated with eugenics. The movement is also averse to science-based regulation, which it sees as an excuse for intrusive government. Under the administration of George W. Bush, science in policy had already taken knocks from both neglect and ideology. Yet President Barack Obama's promise to “restore science to its rightful place” seems to have linked science to liberal politics, making it even more of a target of the right.

Muller calls his latest obsession the Berkeley Earth project. The aim is so simple that the complexity and magnitude of the undertaking is easy to miss. Starting from scratch, with new computer tools and more data than has ever been used, they will arrive at an independent assessment of global warming. The team will also make every piece of data it uses – 1.6bn data points – freely available on a website. It will post its workings alongside, including full information on how more than 100 years of data from thousands of instruments around the world are stitched together to give a historic record of the planet's temperature.

Muller is fed up with the politicised row that all too often engulfs climate science. By laying all its data and workings out in the open, where they can be checked and challenged by anyone, the Berkeley team hopes to achieve something remarkable: a broader consensus on global warming. In no other field would Muller's dream seem so ambitious, or perhaps, so naive.

"We are bringing the spirit of science back to a subject that has become too argumentative and too contentious," Muller says, over a cup of tea. "We are an independent, non-political, non-partisan group. We will gather the data, do the analysis, present the results and make all of it available. There will be no spin, whatever we find." Why does Muller feel compelled to shake up the world of climate change? "We are doing this because it is the most important project in the world today. Nothing else comes close," he says.