[Paleopsych] NYT: In Explaining Life's Complexity, Darwinists and Doubters Clash

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In Explaining Life's Complexity, Darwinists and Doubters Clash
http://www.nytimes.com/2005/08/22/national/22design.html

    By [3]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."