‘Climategate’ was PR disaster that could bring healthy reform of peer review – Peer-review was meant to be a safeguard against the publication of bad science but the balance is shifting towards open access

We may regard the present state of the universe as the effect of its past and the cause of its future. An intellect which at a certain moment would know all forces that set nature in motion, and all positions of all items of which nature is composed, if this intellect were also vast enough to submit these data to analysis, it would embrace in a single formula the movements of the greatest bodies of the universe and those of the tiniest atom; for such an intellect nothing would be uncertain and the future just like the past would be present before its eyes.

Closely aligned with this faith in pure reason was the view that only that which can be demonstrated empirically is epistemically valid. Thus, positivism, the philosophical child of enlightenment hubris, holds that the only valid knowledge is that which is derived directly through sense experience. In other words, a positivist would say that if one cannot test a proposition through the scientific method, it is literally meaningless.

Reality is, of course, the wall you smack into when you are wrong, and even at the height of Enlightenment hubris great thinkers knew that reason has limits. “The heart has reasons that reason cannot know,” Pascal famously exclaimed, and positivism has long since been debunked. Popper perhaps gave it its most succinct epitaph when he wrote that, “positivists, in their anxiety to annihilate metaphysics, annihilate natural science along with it. For scientific laws, too, cannot be logically reduced to elementary statements of experience.”

So now we know better. Or do we? Pride must be dug out root and branch, and that is a very hard thing to do. Long after positivism has been utterly discredited as a philosophical enterprise, I look around me and see intelligent people brandishing their Enlightenment hubris like a sword: “If I cannot fit a concept into my rational categories I refuse to accept it.”

But surely this is a prideful, adolescent way of thinking. If the demise of positivism has taught us anything, it is that we must learn to live with some degree of uncertainty (even mystery) in our epistemology. We cannot know everything (some would say “anything”) with absolute apodictic certainty? Therefore, we must approach the whole business of “knowing” with humility. We must accept the fact that we see “through a glass darkly,” and this means that some very important concepts can only ever be grasped partially or by analogy.

Consider the question of the existence of God. Aquinas believed that God’s existence could be demonstrated with certainty through reason. He was wrong. Kant demolished every one of Aquinas’ five “proofs.” Therefore, God does not exist. No. This statement is a non sequitur. The fact that God cannot be proved to exist with certainty does not mean that he does not in fact exist. Aquinas’ proofs still retain considerable force; they are just not, as he thought, absolute. They cannot compel acceptance on pain of giving up on reason altogether in the manner of a geometric proof. But a reasonable man acting in good faith can ground his acceptance of God’s existence in Aquinas’ demonstrations. Indeed, the reader will not be surprised to learn that I believe Aquinas has the better of the argument – but I must always remind myself that it is just that – an argument – and not an infallible proof, that Aquinas has advanced. There is room for doubt. Why should a Christian be surprised that God has left room for doubt concerning his existence? Does not the scripture itself proclaim that without faith one cannot please God? And what is doubt except that which we have faith against? Therefore, if doubt is not possible, faith is not possible either, and it would be impossible to please God according to the writer of Hebrews.

This is not a strange or unfamiliar concept. Indeed, it is an everyday occurrence in our courts of law. When I argue a case before a jury I appeal to the evidence and to their reason in an effort to convince them that I have “proved” my case. But if the jury decides for my client does that mean there is no room for doubt that they were wrong? Of course not. It only means they have evaluated the evidence, applied their reasoning skills, and concluded that the evidence preponderates in favor of my client. In the same way I have evaluated the evidence, applied my reasoning skills, and decided that the evidence preponderates in favor of the existence of God. But I acknowledge that I might be wrong, and that is where faith comes in. The gap between the admittedly inconclusive evidence and my conclusion that God exists is bridged by faith. I am persuaded that the gap is not so wide, and the bridge of my faith grounded in reason need not be so long. Indeed, I am firmly persuaded that the opposite view would take a far, far longer bridge of faith between evidence and conclusion. As Johnson famously said, “I would love to be a materialist. I just can’t manage the faith commitments.”

I believe in an infinitely munificent and loving God. Yet I acknowledge that evil exists. How could a loving God create a universe in which evil is given room to exist? This, of course, is the problem of the theodicy, about which countless barrels of ink have been spilt. Over the centuries Christian apologists have made some very strong arguments about the reasons God might have allowed evil to exist. Perhaps the strongest is that if evil cannot exist, free will cannot exist, and love – which is in its essence an act of choosing the other – cannot exist. Therefore, because he desired love God allowed us to choose, knowing we would choose wrong. Nevertheless, evil exists, and it seems that God could have created a universe in which it does not exist, but he did not and therefore, in some sense, he is responsible for its existence.

Does it follow that God does not exist? No. Here is one of those mysteries that I was talking about. The existence of evil cannot be considered in an evidential vacuum. It must be weighed with other evidence, including versions of Aquinas’ proofs, my personal experience, Christ’s sacrifice, the empty tomb, scripture (including the powerful witness of prophesy), etc., etc., and when I do that I find that the evidence taken as a whole continues to weigh very strongly toward a conclusion that God exists. I cannot fit the existence of evil into neat and satisfactory epistemic categories along with that conclusion. But just like a juror weighing conflicting evidence, I evaluate the existence of evil as only one part of the body of evidence, and I find that there are plausible (though perhaps ultimately emotionally unsatisfying) arguments regarding why God would allow evil to exist, and when I consider those arguments in the mix of other evidence, the existence of evil comes far short of compelling a conclusion that God does not exist. In other words, the evidence, again admittedly inconclusive, still strongly preponderates in favor of God’s existence.

But the western mind, imbued as it has been with centuries of Enlightenment hubris, rebels against uncertainties. How can God be both immanent within his creation and at the same time transcend his creation? How can God by utterly sovereign over the universe and yet allow free will to exist? How can God be three yet one? These and other questions haunt the Enlightenment mind. We are tempted to say, “that which I cannot place in the categories of reason, I must reject.” But when we are dealing with God isn’t this an obvious mistake? Indeed, can we not define God as “that which transcends all categories”? And if we define God in this way, why should we be surprised that he does not fit neatly into our intellectual boxes?

Do not misunderstand. I am not advancing an anti-rational sophistry. I believe in the law of non-contradiction as firmly as the next guy. But it is also clear to me that “there are more things in heaven and earth . . . than are dreamt of in [our] philosophy,” and I will not be able to figure everything out. I am not always comfortable with that uncertainty, because my worldview too is heavily influenced by the lingering effects of Enlightenment hubris. But I know that I must deal with uncertainty one way or the other. There really is no alternative. Certainly not disbelief – it is more uncertain than belief. So with humility and with the grace I believe God has given me I proclaim with the apostles, “I believe . . .”

A LEADING British government scientist has warned the United Nations’ climate panel to tackle its blunders or lose all credibility. Robert Watson, chief scientist at Defra, the environment ministry, who chaired the Intergovernmental Panel on Climate Change (IPCC) from 1997 to 2002, was speaking after more potential inaccuracies emerged in the IPCC’s 2007 benchmark report on global warming. The most important is a claim that global warming could cut rain-fed north African crop production by up to 50% by 2020, a remarkably short time for such a dramatic change. The claim has been quoted in speeches by Rajendra Pachauri, the IPCC chairman, and by Ban Ki-moon, the UN secretary-general. This weekend Professor Chris Field, the new lead author of the IPCC’s climate impacts team, told The Sunday Times that he could find nothing in the report to support the claim.

Read the rest of the story here.

Andrew Sibley here discusses a thoughtful article by Fred Pearce in the Guardian (02 February 2010) on the climate change scandal, an article which had also been mentioned to me by a kind reader recently. The article takes a critical look at peer review, a well-justified critical look in my view.

I have written about the problem with peer review here, and would recommend Frank Tipler’s paper on the subject.

The basic problem is that the peer review process, intended to enforce quality, can end up enforcing mere orthodoxy or, worse, mediocrity. Or worst of all, as in the now-famous climategate e-mails, it can lead to a classic “bunker” mentality.

I would be inclined to treat all science-based dissent as legitimate. The mere fact that some scientists cannot replicate others’ work or support their conclusions is not evidence of incompetence or dishonesty. It may lead to useful corrections or valuable new information.

Of course, if someone claims that climate change is caused by space aliens, an evil plot by a minority group, or proof that Jesus is coming again soon, I would say, please, this is not science. Science is about evidence from nature.

I was trying to remember recently what peer review reminded me of, and then I suddenly remembered:

For some time, politicians in my country have tried to prevent interest groups from publishing the opinions of politicians about controversial issues during an election. All the parties voted for that. Of course they voted for it! They piously informed the public that their policy prevented wealthy special interests from hijacking the election.*

But that was nonsense. What the policy really did was guarantee that politicians could keep off the table issues that no party wanted to tackle, even though much of the electorate wanted the politicians to tackle them.

Peer review can function the same way. It can simply prevent the publication of problematic data that the current establishment in science does not want to tackle.

*This problem of wealthy special interests could be dealt with simply by requiring any participant to identify the funders within the ad itself. If it turned out to be Microsoft or Ford or McDonald’s, well, anyone smart enough to find their way to the polling station without falling down a hole somewhere would consider the possible motives.

1.

Moving the Goalpost: How Darwin’s Theory Survives

It’s easy to win the game when you can move the goalpost.

On this episode of ID the Future, biologist and Discovery Institute Senior Fellow Jonathan Wells explains how Darwinism, unlike football, has only one rule: survival of the fittest. The fittest are those who survive, and Darwinists are determined to survive at all costs—even if it means moving the goalpost.

Go here to listen.

(Note: This one is quite interesting because Wells talks about how his observation that a specific type of speciation needed by Darwinism has not been observed was recently distorted in a science mag to say that speciation – as such – has never been observed. This tells me that the commitment of many scientists to Darwinism is not to the idea of speciation as such, but to a broader philosophical commitment to a method by which it must happen, a method that supports broader philosophical ideas. Remember that 78% of evolutionary biologists are pure naturalists – no God and no free will.)

2.

Is the Cell Like a Computer?

On this episode of ID the Future, Casey Luskin interviews Dr. Donald Johnson, author of Probability’s Nature and Nature’s Probability: A Call to Scientific Integrity. As both a chemist and a computer scientist, Dr. Johnson explains how the cell uses programming code, much like a computer, and he elucidates how the information is processed and converted from proteins into DNA. Listen in as Dr. Johnson shares the science of how the cell is like a computer.

Donald E. Johnson holds PhDs in Computer & Information Sciences from the University of Minnesota and in Chemistry from Michigan State University. He can be reached at his website,ScienceIntegrity.net.

Go here to listen.

(Note: In two important ways, cells are not like computers.

When my machine is bust, it is just bust, and my local nerd must visit. If I need a new one, it must be bought and unpacked, and inevitably, I will need him back again as something is sure to go wrong. Millions of cells die every day and are replaced, with no loss of function. Fancy that, computer!)

3.

Alfred Russel Wallace: Champion of Natural Selection or Intelligent Design?

On this episode of ID the Future, CSC’s Robert Crowther takes a look at Alfred Russel Wallace, who, along with Darwin, co-presented the theory of natural selection in letters to the Linnean Society of London over 150 years ago. Contrary to Darwin, Wallace actually believed that it was possible to detect design in nature. What would modern Darwin defenders make of Wallace today? Listen in and find out.

Go here to listen.

(Note: Actually, they have been doing a number on Wallace for centuries, as Mike Flannery points out. Go here or here for an example. Wallace, with thought design played a role in evolution, was just not as useful for propaganda purposes and was of a much lower social class than Darwin. Here is somewhat from my review of Flannery’s book.)

4.

Deepening Darwin’s Dilemma With Jonathan Wells

This episode of ID the Future features biologist and Discovery Institute Senior Fellow Jonathan Wells, who explains why Darwin saw the Cambrian explosion as a serious argument against his theory. Darwin countered it by supposing that fossils of the ancestors of Cambrian animals once existed, but were destroyed.

Listen in and learn how the discovery of microscopic and soft-bodied Precambrian fossils makes Darwin’s excuse sound hollow.

Go here to listen.

(Note: It gets better. The Smithsonian sat on the Cambrian fossils for decades because they did not support Darwin’s theory. Yes, yes, that Smithsonian, currently alleged to have pressured California Science Center into cancelling a Cambrian film that – I gather – raises the Cambrian problem. [Almost all modern phyla of life forms appeared rather suddenly about 550 million years ago. This is just not the story Darwin was telling and he knew it and so did his supporters, and now so do more and more people.])

Any chance all those dusty drawers in the Smithsonian’s cellar will be seized as evidence? Maybe we could learn something, and not about the current functionaries’ e-mails.

Free advice to the public in general, not to anyone in particular: Do NOT feed bones to the shredder. Nor paper clips. Never feed anything but paper to the shredder, and feed paper with staples only if the firm warrants that the shredder will accept staples.]

5.

“A Matter of Dismal Wet Plops”: Stephen Meyer Interviews David Berlinski on Darwinism

This episode of ID the Future features a clip from the recent “Signature in the Cell” event in Tampa, FL, featuring Stephen Meyer, Michael Medved, David Berlinski and Tom Woodward. Listen in as Dr. Meyer interviews Dr. Berlinski about the questions that led him to criticize Darwinism.

Go here to listen.

(Note: Besides being brilliant, Berlinski, a mathematician, is as funny as heck – not always a common combination. We are all familiar, I suppose, with the genius who doesn’t get a joke. Well, that’s not him, as the title of this pod suggests. I had a lot of fun reading his Devil’s Delusion, a shot at publicly funded nonsense in science, of which many people are getting royally tired. Science advisor to Marie Antoinette, check your e-mail.

Never forget: Most people fund science because they think it will help find cures for cancer or get one’s country a Nobel Prize in physics [and ain't we proud!] or offer one’s kid a stable, respectable job wearing a lab coat. So take that away – make science mean folly about Stone Age Man, exposed e-mail plots, court cases about broken contracts, reasonable doubts subjected to inquisition and persecution – and what happens?

One thing that might very well happen is that people who used to just sigh and pay the bill might start thinking differently. As in … we’ve got the headache already, Now, where is the payload?)

From Publishers Weekly
The authors of this scattershot treatise believe in evolution, but think that the Darwinian model of adaptationism—that random genetic mutations, filtered by natural selection, produce traits that enhance fitness for a particular biological niche—is fatally flawed. Philosopher Fodor and molecular-biologist-turned-cognitive-scientist Piattelli-Palmarini, at the University of Arizona, launch a three-pronged attack (which drew fire when Fodor presented their ideas in the London Review of Books in 2007). For one thing, according to the authors, natural selection contains a logical fallacy by linking two irreconcilable claims: first, that creatures with adaptive traits are selected, and second, that creatures are selected for their adaptive traits. The authors present an ill-digested assortment of scientific studies suggesting there are forces other than adaptation (some even Lamarckian) that drive changes in genes and organisms. Then they advance a densely technical argument that natural selection can’t coherently distinguish between adaptive traits and irrelevant ones. Their most persuasive, and engaging, criticism is that evolutionary theory is just tautological truisms and historical narratives of how creatures came to be. Overall, the scientific evidence and philosophical analyses the authors proffer are murky and underwhelming. Worse, their highly technical treatment renders their argument virtually incomprehensible to lay readers. (Feb.)

Review
Praise for What Darwin Got Wrong
“Philosopher Fodor and cognitive scientist Piattelli-Palmarini challenge Darwinism more effectively than the entire creationist/intelligent-design movement has . . . Many may find this the hardest, absolutely essential reading they’ve ever done.” —Ray Olson, Booklist

“A challenging, intriguing argument that poses important scientific and philosophical questions about evolution . . . Fodor and Piattelli-Palmarini take a brave stance that will likely draw reaction . . . from across the scientific and theological spectrum. A dense, scholarly, engaging testament to modern scientific thinking and its ability to adapt and evolve.” —Kirkus Reviews

“From the shocking title onward, Fodor and Piattelli-Palmarini have set the cat among Darwin’s pigeons. In arguing why the operation of natural selection says nothing about the causal mechanisms underlying the evolution of coextensive traits in an organism, they take us to the conceptual fault line at the heart of Darwin’s theory. My prediction is that Fodor and Piattelli-Palmarini’s book will raise hackles galore wherever the theory of natural selection is all too glibly misused, not only in studies of the ontogeny and phylogeny of biology, but also in those great overlapping disciplines of philosophy, psychology, linguistics, and behavior—in short, human nature. This book will set the agenda for years to come. It cannot be ignored if the study of evolution is to be honest with itself.” —Gabriel Dover, Professor of Evolutionary Genetics, Universities of Leicester and Cambridge, and author of Dear Mr. Darwin: Letters on the Evolution of Life and Human Nature

“Evolution needs a persuasive theory if the struggle for public acceptance is to be won. Jerry Fodor and Massimo Piattelli-Palmarini’s bold treatise, What Darwin Got Wrong, convincingly shows that natural selection is not that theory. Drawing on scientific literature spanning the molecular, behavioral, and cognitive scales, with sophisticated excursions into evolutionary-developmental biology and the physics of complex systems, the authors perform a philosophical dismantling of the standard model of evolutionary change that is likely irreversible. Their unambiguous grounding in the factuality of evolution renders this work a service to science and a setback for its opponents.” —Stuart Newman, Professor of Cell Biology and Anatomy, New York Medical College

“In this provocative, enlightening, and very entertaining book, Fodor and Piattelli-Palmarini argue that natural selection (NS) cannot explain how evolution occurs. The argument is largely conceptual and proceeds in two steps: (1) that theories of NS are conceptually parallel to Skinnerian theories of learning and so share most of the same debilitating problems, and (2) that NS is actually in worse conceptual shape when its central explanatory notion, ‘selecting for,’ is properly unpacked. This argument will annoy a lot of important people, both for its conclusion and for the evident delight the authors display in getting to it. The ensuing fireworks should be delightful, and (possibly) enlightening.” —Norbert Hornstein, Professor of Linguistics, University of Maryland

“This highly informative and carefully argued study develops two central theses. First, there are alternatives to classical neo-Darwinian adaptationist theories that are plausible, and very possibly capture principles that are the rule rather than the exception even if the basic adaptationist account is accepted. Second, that account cannot be accepted. The two theses are sufficiently independent so that they can be evaluated separately. Whatever the outcome of intellectual engagement with this stimulating work, it is sure to be a most rewarding experience.” —Noam Chomsky

For 80 years it has been accepted that early life began in a ‘primordial soup’ of organic molecules before evolving out of the oceans millions of years later. Today the ’soup’ theory has been over turned in a pioneering paper in BioEssays which claims it was the Earth’s chemical energy, from hydrothermal vents on the ocean floor, which kick-started early life.

Rest of the story here.