Damned Heretics

Condemned by the established, but very often right

I am Nicolaus Copernicus, and I approve of this blog

I am Richard Feynman and I approve of this blog

Qualified outsiders and maverick insiders are often right about the need to replace received wisdom in science and society, as the history of the Nobel prize shows. This blog exists to back the best of them in their uphill assault on the massively entrenched edifice of resistance to and prejudice against reviewing, let alone revising, ruling ideas. In support of such qualified dissenters and courageous heretics we search for scientific paradigms and other established beliefs which may be maintained only by the power and politics of the status quo, comparing them with academic research and the published experimental and investigative record.

We especially defend and support the funding of honest, accomplished, independent minded and often heroic scientists, inventors and other original thinkers and their right to free speech and publication against the censorship, mudslinging, false arguments, ad hominem propaganda, overwhelming crowd prejudice and internal science politics of the paradigm wars of cancer, AIDS, evolution, global warming, cosmology, particle physics, macroeconomics, health and medicine, diet and nutrition.

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Henry Bauer, Peter Breggin , Harvey Bialy, Giordano Bruno, Erwin Chargaff, Nicolaus Copernicus, Francis Crick, Paul Crutzen, Marie Curie, Rebecca Culshaw, Freeman Dyson, Peter Duesberg, Albert Einstein, Richard Feynman, John Fewster, Galileo Galilei, Alec Gordon, James Hansen, Edward Jenner, Benjamin Jesty, Michio Kaku, Adrian Kent, Ernst Krebs, Thomas Kuhn, Serge Lang, John Lauritsen, Mark Leggett, Richard Lindzen, Lynn Margulis, Barbara McClintock, George Miklos, Marco Mamone Capria, Peter Medawar, Kary Mullis, Linus Pauling, Eric Penrose, Max Planck, Rainer Plaga, David Rasnick, Sherwood Rowland, Carl Sagan, Otto Rossler, Fred Singer, Thomas Szasz, Alfred Wegener, Edward O. Wilson, James Watson.
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Many people would die rather than think – in fact, they do so. – Bertrand Russell.

Skepticism is dangerous. That’s exactly its function, in my view. It is the business of skepticism to be dangerous. And that’s why there is a great reluctance to teach it in schools. That’s why you don’t find a general fluency in skepticism in the media. On the other hand, how will we negotiate a very perilous future if we don’t have the elementary intellectual tools to ask searching questions of those nominally in charge, especially in a democracy? – Carl Sagan (The Burden of Skepticism, keynote address to CSICOP Annual Conference, Pasadena, April 3/4, 1982).

It is really important to underscore that everything we’re talking about tonight could be utter nonsense. – Brian Greene (NYU panel on Hidden Dimensions June 5 2010, World Science Festival)

I am Albert Einstein, and I heartily approve of this blog, insofar as it seems to believe both in science and the importance of intellectual imagination, uncompromised by out of date emotions such as the impulse toward conventional religious beliefs, national aggression as a part of patriotism, and so on.   As I once remarked, the further the spiritual evolution of mankind advances, the more certain it seems to me that the path to genuine religiosity does not lie through the fear of life, and the fear of death, and blind faith, but through striving after rational knowledge.   Certainly the application of the impulse toward blind faith in science whereby authority is treated as some kind of church is to be deplored.  As I have also said, the only thing ever interfered with my learning was my education. My name as you already perceive without a doubt is George Bernard Shaw, and I certainly approve of this blog, in that its guiding spirit appears to be blasphemous in regard to the High Church doctrines of science, and it flouts the censorship of the powers that be, and as I have famously remarked, all great truths begin as blasphemy, and the first duty of the truthteller is to fight censorship, and while I notice that its seriousness of purpose is often alleviated by a satirical irony which sometimes borders on the facetious, this is all to the good, for as I have also famously remarked, if you wish to be a dissenter, make certain that you frame your ideas in jest, otherwise they will seek to kill you.  My own method was always to take the utmost trouble to find the right thing to say, and then to say it with the utmost levity. (Photo by Alfred Eisenstaedt for Life magazine) One should as a rule respect public opinion in so far as is necessary to avoid starvation and to keep out of prison, but anything that goes beyond this is voluntary submission to an unnecessary tyranny, and is likely to interfere with happiness in all kinds of ways. – Bertrand Russell, Conquest of Happiness (1930) ch. 9

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The Times surveys the ID vs Darwin scene with equanimity

Perhaps inspired by George W’s suggestion for schools, the New York Times yesterday had on the front page for Hampton’s beach reading a nicely balanced, typically non-combative survey of the science, politics and funding of Intelligent Design and its bid to elbow aside evolution to share the center of the stage in the schools and in the media.

It is interesting to note the Harvard student roots of this phenomenon, and the fact that some of the original boosters have fallen by the way side, put off by the streaks of archconservatism and religious fundamentalism they found under the surface layer of open minded reason and speculation.

From our scientific perspective we can only ask both sides again why the gaps in evolutionary explanation need to be denied, and why God is needed to fill them.

See Politicized Scholars Put Evolution on the Defensive, by Jodi Wilgoren

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The New York Times

August 21, 2005

Politicized Scholars Put Evolution on the Defensive

By JODI WILGOREN

SEATTLE – When President Bush plunged into the debate over the teaching of evolution this month, saying, “both sides ought to be properly taught,” he seemed to be reading from the playbook of the Discovery Institute, the conservative think tank here that is at the helm of this newly volatile frontier in the nation’s culture wars.

After toiling in obscurity for nearly a decade, the institute’s Center for Science and Culture has emerged in recent months as the ideological and strategic backbone behind the eruption of skirmishes over science in school districts and state capitals across the country. Pushing a “teach the controversy” approach to evolution, the institute has in many ways transformed the debate into an issue of academic freedom rather than a confrontation between biology and religion.

Mainstream scientists reject the notion that any controversy over evolution even exists. But Mr. Bush embraced the institute’s talking points by suggesting that alternative theories and criticism should be included in biology curriculums “so people can understand what the debate is about.”

Financed by some of the same Christian conservatives who helped Mr. Bush win the White House, the organization’s intellectual core is a scattered group of scholars who for nearly a decade have explored the unorthodox explanation of life’s origins known as intelligent design.

Together, they have mounted a politically savvy challenge to evolution as the bedrock of modern biology, propelling a fringe academic movement onto the front pages and putting Darwin’s defenders firmly on the defensive.

Like a well-tooled electoral campaign, the Discovery Institute has a carefully crafted, poll-tested message, lively Web logs – and millions of dollars from foundations run by prominent conservatives like Howard and Roberta Ahmanson, Philip F. Anschutz and Richard Mellon Scaife. The institute opened an office in Washington last fall and in January hired the same Beltway public relations firm that promoted the Contract With America in 1994.

“We are in the very initial stages of a scientific revolution,” said the center’s director, Stephen C. Meyer, 47, a historian and philosopher of science recruited by Discovery after he protested a professor’s being punished for criticizing Darwin in class. “We want to have an effect on the dominant view of our culture.”

For the institute’s president, Bruce K. Chapman, a Rockefeller Republican turned Reagan conservative, intelligent design appealed to his contrarian, futuristic sensibilities – and attracted wealthy, religious philanthropists like the Ahmansons at a time when his organization was surviving on a shoestring. More student of politics than science geek, Mr. Chapman embraced the evolution controversy as the institute’s signature issue precisely because of its unpopularity in the establishment.

“When someone says there’s one thing you can’t talk about, that’s what I want to talk about,” said Mr. Chapman, 64.

As much philosophical worldview as scientific hypothesis, intelligent design challenges Darwin’s theory of natural selection by arguing that some organisms are too complex to be explained by evolution alone, pointing to the possibility of supernatural influences. While mutual acceptance of evolution and the existence of God appeals instinctively to a faithful public, intelligent design is shunned as heresy in mainstream universities and science societies as untestable in laboratories.

Entering the Public Policy Sphere

From its nondescript office suites here, the institute has provided an institutional home for the dissident thinkers, pumping $3.6 million in fellowships of $5,000 to $60,000 per year to 50 researchers since the science center’s founding in 1996. Among the fruits are 50 books on intelligent design, many published by religious presses like InterVarsity or Crossway, and two documentaries that were broadcast briefly on public television. But even as the institute spearheads the intellectual development of intelligent design, it has staked out safer turf in the public policy sphere, urging states and school boards simply to include criticism in evolution lessons rather than actually teach intelligent design.

Since the presidential election last fall, the movement has made inroads and evolution has emerged as one of the country’s fiercest cultural battlefronts, with the National Center for Science Education tracking 78 clashes in 31 states, more than twice the typical number of incidents. Discovery leaders have been at the heart of the highest-profile developments: helping a Roman Catholic cardinal place an opinion article in The New York Times in which he sought to distance the church from evolution; showing its film promoting design and purpose in the universe at the Smithsonian; and lobbying the Kansas Board of Education in May to require criticism of evolution.

These successes follow a path laid in a 1999 Discovery manifesto known as the Wedge Document, which sought “nothing less than the overthrow of materialism and its cultural legacies” in favor of a “broadly theistic understanding of nature.”

President Bush’s signature education law, known as No Child Left Behind, also helped, as mandatory testing prompted states to rewrite curriculum standards. Ohio, New Mexico and Minnesota have embraced the institute’s “teach the controversy” approach; Kansas is expected to follow suit in the fall.

Detractors dismiss Discovery as a fundamentalist front and intelligent design as a clever rhetorical detour around the 1987 Supreme Court ruling banning creationism from curriculums. But the institute’s approach is more nuanced, scholarly and politically adept than its Bible-based predecessors in the century-long battle over biology.

A closer look shows a multidimensional organization, financed by missionary and mainstream groups – the Bill and Melinda Gates Foundation provides $1 million a year, including $50,000 of Mr. Chapman’s $141,000 annual salary – and asserting itself on questions on issues as varied as local transportation and foreign affairs.

Many of the research fellows, employees and board members are, indeed, devout and determinedly conservative; pictures of William J. Bennett, the moral crusader and former drug czar, are fixtures on office walls, and some leaders have ties to movement mainstays like Focus on the Family. All but a few in the organization are Republicans, though these include moderates drawn by the institute’s pragmatic, iconoclastic approach on nonideological topics like technology.

But even as intelligent design has helped raise Discovery’s profile, the institute is starting to suffer from its success. Lately, it has tried to distance itself from lawsuits and legislation that seek to force schools to add intelligent design to curriculums, placing it in the awkward spot of trying to promote intelligent design as a robust frontier for scientists but not yet ripe for students.

The group is also fending off attacks from the left, as critics liken it to Holocaust deniers or the Taliban. Concerned about the criticism, Discovery’s Cascadia project, which focuses on regional transportation and is the recipient of the large grant from the Gates Foundation, created its own Web site to ensure an individual identity.

“All ideas go through three stages – first they’re ignored, then they’re attacked, then they’re accepted,” said Jay W. Richards, a philosopher and the institute’s vice president. “We’re kind of beyond the ignored stage. We’re somewhere in the attack.”

Origins of an Institute

Founded in 1990 as a branch of the Hudson Institute, based in Indianapolis, the institute was named for the H.M.S. Discovery, which explored Puget Sound in 1792. Mr. Chapman, a co-author of a 1966 critique of Barry M. Goldwater’s anti-civil-rights campaign, “The Party That Lost Its Head,” had been a liberal Republican on the Seattle City Council and candidate for governor, but moved to the right in the Reagan administration, where he served as director of the Census Bureau and worked for Edwin Meese III.

In late 1993, Mr. Chapman clipped an essay in The Wall Street Journal by Dr. Meyer, who was teaching at a Christian college in Spokane, Wash., concerning a biologist yanked from a lecture hall for discussing intelligent design. About a year later, over dinner at the Sorrento Hotel here, Dr. Meyer and George Gilder, Mr. Chapman’s long-ago Harvard roommate and his writing partner, discovered parallel theories of mind over materialism in their separate studies of biology and economics.

“Bruce kind of perked up and said, ‘This is what makes a think tank,’ ” Dr. Meyer recalled. “There was kind of an ‘Aha!’ moment in the conversation, there was a common metaphysic in these two ideas.”

That summer of 1995, Mr. Chapman and Dr. Meyer had dinner with a representative of the Ahmansons, the banking billionaires from Orange County, Calif., who had previously given a small grant to the institute and underwritten an early conclave of intelligent design scholars. Dr. Meyer, who had grown friendly enough with the Ahmansons to tutor their young son in science, recalled being asked, “What could you do if you had some financial backing?”

So in 1996, with the promise of $750,000 over three years from the Ahmansons and a smaller grant from the MacLellan Foundation, which supports organizations “committed to furthering the Kingdom of Christ,” according to its Web site, the institute’s Center for Science and Culture was born.

“Bruce is a contrarian, and this was a contrarian idea,” said Edward J. Larson, the historian and author of a Pulitzer Prize-winning book on the Scopes Monkey Trial, who was an early fellow at the institute, but left in part because of its drift to the right. “The institute was living hand-to-mouth. Here was an academic, credible activity that involved funders. It interested conservatives. It brought in money.”

Support From Religious Groups

The institute would not provide details about its backers “because they get harassed,” Mr. Chapman said. But a review of tax documents on www.guidestar.org, a Web site that collects data on foundations, showed its grants and gifts jumped to $4.1 million in 2003 from $1.4 million in 1997, the most recent and oldest years available. The records show financial support from 22 foundations, at least two-thirds of them with explicitly religious missions.

There is the Henry P. and Susan C. Crowell Trust of Colorado Springs, whose Web site describes its mission as “the teaching and active extension of the doctrines of evangelical Christianity.” There is also the AMDG Foundation in Virginia, run by Mark Ryland, a Microsoft executive turned Discovery vice president: the initials stand for Ad Majorem Dei Glorium, Latin for “To the greater glory of God,” which Pope John Paul II etched in the corner of all his papers.

And the Stewardship Foundation, based in Tacoma, Wash., whose Web site says it was created “to contribute to the propagation of the Christian Gospel by evangelical and missionary work,” gave the group more than $1 million between 1999 and 2003.

By far the biggest backers of the intelligent design efforts are the Ahmansons, who have provided 35 percent of the science center’s $9.3 million since its inception and now underwrite a quarter of its $1.3 million annual operations. Mr. Ahmanson also sits on Discovery’s board.

The Ahmansons’ founding gift was joined by $450,000 from the MacLellan Foundation, based in Chattanooga, Tenn.

“We give for religious purposes,” said Thomas H. McCallie III, its executive director. “This is not about science, and Darwin wasn’t about science. Darwin was about a metaphysical view of the world.”

The institute also has support from secular groups like the Verizon Foundation and the Gates Foundation, which gave $1 million in 2000 and pledged $9.35 million over 10 years in 2003. Greg Shaw, a grant maker at the Gates Foundation, said the money was “exclusive to the Cascadia project” on regional transportation.

But the evolution controversy has cost it the support of the Bullitt Foundation, based here, which gave $10,000 in 2001 for transportation, as well as the John Templeton Foundation in Pennsylvania, whose Web site defines it as devoted to pursuing “new insights between theology and science.”

Denis Hayes, director of the Bullitt Foundation, described Discovery in an e-mail message as “the institutional love child of Ayn Rand and Jerry Falwell,” saying, “I can think of no circumstances in which the Bullitt Foundation would fund anything at Discovery today.”

Charles L. Harper Jr., the senior vice president of the Templeton Foundation, said he had rejected the institute’s entreaties since providing $75,000 in 1999 for a conference in which intelligent design proponents confronted critics. “They’re political – that for us is problematic,” Mr. Harper said. While Discovery has “always claimed to be focused on the science,” he added, “what I see is much more focused on public policy, on public persuasion, on educational advocacy and so forth.”

For three years after completing graduate school in 1996, William A. Dembski could not find a university job, but he nonetheless received what he called “a standard academic salary” of $40,000 a year.

“I was one of the early beneficiaries of Discovery largess,” said Dr. Dembski, whose degrees include a doctorate in mathematics from the University of Chicago, one in philosophy from the University of Illinois and a master’s of divinity from Princeton Theological Seminary.

Money for Teachers and Students

Since its founding in 1996, the science center has spent 39 percent of its $9.3 million on research, Dr. Meyer said, underwriting books or papers, or often just paying universities to release professors from some teaching responsibilities so that they can ponder intelligent design. Over those nine years, $792,585 financed laboratory or field research in biology, paleontology or biophysics, while $93,828 helped graduate students in paleontology, linguistics, history and philosophy.

The 40 fellows affiliated with the science center are an eclectic group, including David Berlinski, an expatriate mathematician living in Paris who described his only religion to be “having a good time all the time,” and Jonathan Wells, a member of the Unification Church, led by the Rev. Sun Myung Moon, who once wrote in an essay, “My prayers convinced me that I should devote my life to destroying Darwinism.”

Their credentials – advanced degrees from Stanford, Columbia, Yale, the University of Texas, the University of California – are impressive, but their ideas are often ridiculed in the academic world.

“They’re interested in the same things I’m interested in – no one else is,” Guillermo Gonzalez, 41, an astronomer at the University of Iowa, said of his colleagues at Discovery. “What I’m doing, frankly, is frowned upon by most of my colleagues. It’s not something a ‘scientist’ is supposed to do.” Other than Dr. Berlinski, most fellows, like their financiers, are fundamentalist Christians, though they insist their work is serious science, not closet creationism.

“I believe that God created the universe,” Dr. Gonzalez said. “What I don’t know is whether that evidence can be tested objectively. I ask myself the tough questions.”

Discovery sees the focus on its fellows and financial backers as a diversionary tactic by its opponents. “We’re talking about evidence, and they want to talk about us,” Dr. Meyer said.

But Philip Gold, a former fellow who left in 2002, said the institute had grown increasingly religious. “It evolved from a policy institute that had a religious focus to an organization whose primary mission is Christian conservatism,” he said.

That was certainly how many people read the Wedge Document, a five-page outline of a five-year plan for the science center that originated as a fund-raising pitch but was soon posted on the Internet by critics.

“Design theory promises to reverse the stifling dominance of the materialist worldview, and to replace it with a science consonant with Christian and theistic convictions,” the document says. Among its promises are seminars “to encourage and equip believers with new scientific evidence that support the faith, as well as to ‘popularize’ our ideas in the broader culture.”

One sign of any political movement’s advancement is when adherents begin to act on their own, often without the awareness of the leadership. That, according to institute officials, is what happened in 1999, when a new conservative majority on the Kansas Board of Education shocked the nation – and their potential allies here at the institute – by dropping all references to evolution from the state’s science standards.

“When there are all these legitimate scientific controversies, this was silly, outlandish, counterproductive,” said John G. West, associate director of the science center, who said he and his colleagues learned of that 1999 move in Kansas from newspaper accounts. “We began to think, ‘Look, we’re going to be stigmatized with what everyone does if we don’t make our position clear.’ “

Out of this developed Discovery’s “teach the controversy” approach, which endorses evolution as a staple of any biology curriculum – so long as criticism of Darwin is also in the lesson plan. This satisfied Christian conservatives but also appealed to Republican moderates and, under the First Amendment banner, much of the public (71 percent in a Discovery-commissioned Zogby poll in 2001 whose results were mirrored in newspaper polls).

“They have packaged their message much more cleverly than the creation science people have,” said Eugenie C. Scott, director of the National Center for Science Education, the leading defender of evolution. “They present themselves as being more mainstream. I prefer to think of that as creationism light.”

A watershed moment came with the adoption in 2001 of the No Child Left Behind Act, whose legislative history includes a passage that comes straight from the institute’s talking points. “Where biological evolution is taught, the curriculum should help students to understand why this subject generates so much continuing controversy,” was language that Senator Rick Santorum, Republican of Pennsylvania, tried to include.

Pointing to that principle, institute fellows in 2002 played important roles in pushing the Ohio Board of Education to adopt a “teach the controversy” approach and helped devise a curriculum to support it. The following year, they successfully urged changes to textbooks in Texas to weaken the argument for evolution, and they have been consulted in numerous other cases as school districts or states consider changing their approach to biology.

But this spring, at the hearings in Kansas, Mr. Chapman grew visibly frustrated as his supposed allies began talking more and more about intelligent design.

John Calvert, the managing director of the Intelligent Design Network, based in Kansas, said the institute had the intellectual and financial resources to “lead the movement” but was “more cautious” than he would like. “They want to avoid the discussion of religion because that detracts from the focus on the science,” he said.

Dr. West, who leads the science center’s public policy efforts, said it did not support mandating the teaching of intelligent design because the theory was not yet developed enough and there was no appropriate curriculum. So the institute has opposed legislation in Pennsylvania and Utah that pushes intelligent design, instead urging lawmakers to follow Ohio’s lead.

“A lot of people are trying to hijack the issue on both the left and the right,” Dr. West said.

Dr. Chapman, for his part, sees even these rough spots as signs of success.

“All ideas that achieve a sort of uniform acceptance ultimately fall apart whether it’s in the sciences or philosophy or politics after a few people keep knocking away at it,” he said. “It’s wise for society not to punish those people.”

Jack Begg, David Bernstein and Alain Delaquérière contributed reporting for this article.

Now this morning we have another informative Times piece by Kenneth Chang, a science reporter with a wide perspective and a mathematical objecticity, on exactly what evidence in evolution the ID promoters are saying has to be explained by divine intervention. In Explaining Life’s Complexity, Darwinists and Doubters Clash, by Kenneth Chang

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The New York Times

August 22, 2005

In Explaining Life’s Complexity, Darwinists and Doubters Clash

By KENNETH CHANG

At the heart of the debate over intelligent design is this question: Can a scientific explanation of the history of life include the actions of an unseen higher being?

The proponents of intelligent design, a school of thought that some have argued should be taught alongside evolution in the nation’s schools, say that the complexity and diversity of life go beyond what evolution can explain.

Biological marvels like the optical precision of an eye, the little spinning motors that propel bacteria and the cascade of proteins that cause blood to clot, they say, point to the hand of a higher being at work in the world.

In one often-cited argument, Michael J. Behe, a professor of biochemistry at Lehigh University and a leading design theorist, compares complex biological phenomena like blood clotting to a mousetrap: Take away any one piece – the spring, the baseboard, the metal piece that snags the mouse – and the mousetrap stops being able to catch mice.

Similarly, Dr. Behe argues, if any one of the more than 20 proteins involved in blood clotting is missing or deficient, as happens in hemophilia, for instance, clots will not form properly.

Such all-or-none systems, Dr. Behe and other design proponents say, could not have arisen through the incremental changes that evolution says allowed life to progress to the big brains and the sophisticated abilities of humans from primitive bacteria.

These complex systems are “always associated with design,” Dr. Behe, the author of the 1996 book “Darwin’s Black Box,” said in an interview. “We find such systems in biology, and since we know of no other way that these things can be produced, Darwinian claims notwithstanding, then we are rational to conclude they were indeed designed.”

It is an argument that appeals to many Americans of faith.

But mainstream scientists say that the claims of intelligent design run counter to a century of research supporting the explanatory and predictive power of Darwinian evolution, and that the design approach suffers from fundamental problems that place it outside the realm of science. For one thing, these scientists say, invoking a higher being as an explanation is unscientific.

“One of the rules of science is, no miracles allowed,” said Douglas H. Erwin, a paleobiologist at the Smithsonian Institution. “That’s a fundamental presumption of what we do.”

That does not mean that scientists do not believe in God. Many do. But they see science as an effort to find out how the material world works, with nothing to say about why we are here or how we should live.

And in that quest, they say, there is no need to resort to otherworldly explanations. So much evidence has been provided by evolutionary studies that biologists are able to explain even the most complex natural phenomena and to fill in whatever blanks remain with solid theories.

This is possible, in large part, because evolution leaves tracks like the fossil remains of early animals or the chemical footprints in DNA that have been revealed by genetic research.

For example, while Dr. Behe and other leading design proponents see the blood clotting system as a product of design, mainstream scientists see it as a result of a coherent sequence of evolutionary events.

Early vertebrates like jawless fish had a simple clotting system, scientists believe, involving a few proteins that made blood stick together, said Russell F. Doolittle, a professor of molecular biology at the University of California, San Diego.

Scientists hypothesize that at some point, a mistake during the copying of DNA resulted in the duplication of a gene, increasing the amount of protein produced by cells.

Most often, such a change would be useless. But in this case the extra protein helped blood clot, and animals with the extra protein were more likely to survive and reproduce. Over time, as higher-order species evolved, other proteins joined the clotting system. For instance, several proteins involved in the clotting of blood appear to have started as digestive enzymes.

By studying the evolutionary tree and the genetics and biochemistry of living organisms, Dr. Doolittle said, scientists have largely been able to determine the order in which different proteins became involved in helping blood clot, eventually producing the sophisticated clotting mechanisms of humans and other higher animals. The sequencing of animal genomes has provided evidence to support this view.

For example, scientists had predicted that more primitive animals such as fish would be missing certain blood-clotting proteins. In fact, the recent sequencing of the fish genome has shown just this.

“The evidence is rock solid,” Dr. Doolittle said.

Intelligent design proponents have advanced their views in books for popular audiences and in a few scientific articles. Some have developed mathematical formulas intended to tell whether something was designed or formed by natural processes.

Mainstream scientists say that intelligent design represents a more sophisticated – and thus more seductive – attack on evolution. Unlike creationists, design proponents accept many of the conclusions of modern science. They agree with cosmologists that the age of the universe is 13.6 billion years, not fewer than 10,000 years, as a literal reading of the Bible would suggest. They accept that mutation and natural selection, the central mechanisms of evolution, have acted on the natural world in small ways, for example, leading to the decay of eyes in certain salamanders that live underground.

Some intelligent design advocates even accept common descent, the notion that all species came from a common ancestor, a central tenet of evolution.

Although a vast majority of scientists accept evolution, the Discovery Institute, a research group in Seattle that has emerged as a clearinghouse for the intelligent design movement, says that 404 scientists, including 70 biologists, have signed a petition saying they are skeptical of Darwinism.

Nonetheless, many scientists regard intelligent design as little more than creationism dressed up in pseudoscientific clothing. Despite its use of scientific language and the fact that some design advocates are scientists, they say, the design approach has so far offered only philosophical objections to evolution, not any positive evidence for the intervention of a designer.

‘Truncated View of Reality’

If Dr. Behe’s mousetrap is one of the most familiar arguments for design, another is the idea that intelligence is obvious in what it creates. Read a novel by Hemingway, gaze at the pyramids, and a designer’s hand is manifest, design proponents say.

But mainstream scientists, design proponents say, are unwilling to look beyond the material world when it comes to explaining things like the construction of an eye or the spinning motors that propel bacteria. What is wrong, they ask, with entertaining the idea that what looks like it was designed was actually designed?

“If we’ve defined science such that it cannot get to the true answer, we’ve got a pretty lame definition of science,” said Douglas D. Axe, a molecular biologist and the director of research at the Biologic Institute, a new research center in Seattle that looks at the organization of biological systems, including intelligent design issues. Dr. Axe said he had received “significant” financing from the Discovery Institute, but he declined to give any other details about the institute or its financing.

Stephen C. Meyer, director of the Center for Science and Culture at the Discovery Institute, compares the design approach to the work of archaeologists investigating an ancient civilization.

“Imagine you’re an archaeologist and you’re looking at an inscription, and you say, ‘Well, sorry, that looks like it’s intelligent but we can’t invoke an intelligent cause because, as a matter of method, we have to limit ourselves to materialistic processes,’ ” Dr. Meyer said. “That would be nuts.”

He added, “Call it miracle, call it some other pejorative term, but the fact remains that the materialistic view is a truncated view of reality.”

William Paley, an Anglican priest, made a similar argument in the early 19th century. Someone who finds a rock can easily imagine how wind and rain shaped it, he reasoned. But someone who finds a pocket watch lying on the ground instantly knows that it was not formed by natural processes.

With living organisms so much more complicated than watches, he wrote, “The marks of design are too strong to be got over.”

Mainstream scientists say that the scientific method is indeed restricted to the material world, because it is trying to find out how it works. Simply saying, “it must have been designed,” they say, is simply a way of not tackling the hardest problems.

They say they have no disagreement with studying phenomena for which there are, as yet, no explanations.

It is the presumption of a designer that mainstream scientists dispute, because there are no artifacts or biological signs – no scientific evidence, in other words – to suggest a designer’s presence.

Darwin’s theory, in contrast, has over the last century yielded so many solid findings that no mainstream biologist today doubts its basic tenets, though they may argue about particulars.

The theory has unlocked many of the mysteries of the natural world. For example, by studying the skeletons of whales, evolutionary scientists have been able to trace the history of their descent from small-hoofed land mammals. They made predictions about what the earliest water-dwelling whales might look like. And, in 1994, paleontologists reported discovering two such species, with many of the anatomical features that scientists had predicted.

Darwin’s Finches

Nowhere has evolution been more powerful than in its prediction that there must be a means to pass on information from one generation to another. Darwin did not know the biological mechanism of inheritance, but the theory of evolution required one.

The discovery of DNA, the sequencing of the human genome, the pinpointing of genetic diseases and the discovery that a continuum of life from a single cell to a human brain can be detected in DNA are all a result of evolutionary theory.

Darwin may have been the classic scientific observer. He observed that individuals in a given species varied considerably, variations now known to be caused by mutations in their genetic code. He also realized that constraints of food and habitat sharply limited population growth; not every individual could survive and reproduce.

This competition, he hypothesized, meant that those individuals with helpful traits multiplied, passing on those traits to their numerous offspring. Negative or useless traits did not help individuals reproduce, and those traits faded away, a process that Darwin called natural selection.

The finches that Darwin observed in the Galápagos Islands provide the most famous example of this process. The species of finch that originally found its way to the Galápagos from South America had a beak shaped in a way that was ideal for eating seeds. But once arrived on the islands, that finch eventually diversified into 13 species. The various Galápagos finches have differently shaped beaks, each fine-tuned to take advantage of a particular food, like fruit, grubs, buds or seeds.

Such small adaptations can arise within a few generations. Darwin surmised that over millions of years, these small changes would accumulate, giving rise to the myriad of species seen today.

The number of organisms that, in those long periods, ended up being preserved as fossils is infinitesimal. As a result, the evolutionary record – the fossils of long-extinct organisms found preserved in rock – is necessarily incomplete, and some species appear to burst out of nowhere.

Some supporters of intelligent design have argued that such gaps undermine the evidence for evolution.

For instance, during the Cambrian explosion a half a billion years ago, life diversified to shapes with limbs and shells from jellyfish-like blobs, over a geologically brief span of 30 million years.

Dr. Meyer sees design at work in these large leaps, which signified the appearance of most modern forms of life. He argues that genetic mutations do not have the power to create new shapes of animals.

But molecular biologists have found genes that control the function of other genes, switching them on and off. Small mutations in these controller genes could produce new species. In addition, new fossils are being found and scientists now know that many changes occurred in the era before the Cambrian – a period that may have lasted 100 million years – providing more time for change.

The Cambrian explosion, said David J. Bottjer, a professor of earth sciences at the University of Southern California and president of the Paleontological Society, is “a wonderful mystery in that we don’t know everything yet.”

“I think it will be just a matter of time before smart people will be able to figure a lot more of this out,” Dr. Bottjer said. “Like any good scientific problem.”

Purposeful Patterns

Intelligent design proponents have been stung by claims that, in contrast to mainstream scientists, they do not form their own theories or conduct original research. They say they are doing the mathematical work and biological experiments needed to put their ideas on firm scientific ground.

For example, William A. Dembski, a mathematician who drew attention when he headed a short-lived intelligent design institute at Baylor University, has worked on mathematical algorithms that purport to tell the difference between objects that were designed and those that occurred naturally.

Dr. Dembski says designed objects, like Mount Rushmore, show complex, purposeful patterns that evince the existence of intelligence. Mathematical calculations like those he has developed, he argues, could detect those patterns, for example, distinguishing Mount Rushmore from Mount St. Helens.

But other mathematicians have said that Dr. Dembski’s calculations do not work and cannot be applied in the real world.

Other studies that intelligent design theorists cite in support of their views have been done by Dr. Axe of the Biologic Institute.

In one such study, Dr. Axe looked at a protein, called penicillinase, that gives bacteria the ability to survive treatment with the antibiotic penicillin. Dr. Meyer, of the Discovery Institute, has referred to Dr. Axe’s work in arguing that working proteins are so rare that evolution cannot by chance discover them.

What was the probability, Dr. Axe asked in his study, of a protein with this ability existing in the universe of all possible proteins?

Penicillinase is made up of a strand of chemicals called amino acids folded into a shape that binds to penicillin and thus disables it. Whether the protein folds up in the right way determines whether it works or not.

Dr. Axe calculated that of the plausible amino acid sequences, only one in 100,000 trillion trillion trillion trillion trillion trillion – a number written as 1 followed by 77 zeroes – would provide resistance to penicillin.

In other words, the probability was essentially zero.

Dr. Axe’s research appeared last year in The Journal of Molecular Biology, a peer-reviewed scientific publication.

Dr. Kenneth R. Miller, a professor of biology at Brown University and a frequent sparring partner of design proponents, said that in his study, Dr. Axe did not look at penicillinase “the way evolution looks at the protein.”

Natural selection, he said, is not random. A small number of mutations, sometimes just one, can change the function of a protein, allowing it to diverge along new evolutionary paths and eventually form a new shape or fold.

One Shot or a Continual Act

Intelligent design proponents are careful to say that they cannot identify the designer at work in the world, although most readily concede that God is the most likely possibility. And they offer varied opinions on when and how often a designer intervened.

Dr. Behe, for example, said he could imagine that, like an elaborate billiards shot, the design was set up when the Big Bang occurred 13.6 billion years ago. “It could have all been programmed into the universe as far as I’m concerned,” he said.

But it was also possible, Dr. Behe added, that a designer acted continually throughout the history of life.

Mainstream scientists say this fuzziness about when and how design supposedly occurred makes the claims impossible to disprove. It is unreasonable, they say, for design advocates to demand that every detail of evolution be filled in.

Dr. Behe, however, said he might find it compelling if scientists were to observe evolutionary leaps in the laboratory. He pointed to an experiment by Richard E. Lenski, a professor of microbial ecology at Michigan State University, who has been observing the evolution of E. coli bacteria for more than 15 years. “If anything cool came out of that,” Dr. Behe said, “that would be one way to convince me.”

Dr. Behe said that if he was correct, then the E. coli in Dr. Lenski’s lab would evolve in small ways but never change in such a way that the bacteria would develop entirely new abilities.

In fact, such an ability seems to have developed. Dr. Lenski said his experiment was not intended to explore this aspect of evolution, but nonetheless, “We have recently discovered a pretty dramatic exception, one where a new and surprising function has evolved,” he said.

Dr. Lenski declined to give any details until the research is published. But, he said, “If anyone is resting his or her faith in God on the outcome that our experiment will not produce some major biological innovation, then I humbly suggest they should rethink the distinction between science and religion.”

Dr. Behe said, “I’ll wait and see.”

While there are certainly baffling mysteries in the all-or-none leaps that evolution seems to have achieved in a number of instances, why is it that “God” is a better explanation than “we don’t know”?

If anything it seems to us that there is a paradox here, in that such seekers of truth lack the humility that all religions teach, and in saying that human understanding having not yet found an explanation of the mechanics of such leaps, therefore the explanation is supernatural, are close to the kind of hubris which has always made humanity ridiculous, especially in the early days of Darwinism when many were outraged at the idea that man could share the same ancestors as apes.

Now we have the likes of William Dembski arguing that what is not explained is therefore a sign of an unseen guiding hand. Well, maybe it is, but we would bet it isn’t a supernatural one.

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