Tuesday, July 15, 2008

Were Eldridge & Gould right?

Reading the article below seems to suggest that the theory of Punctuated Equilibrium (Periods of rapid evolution - on a geological time scale of course! - followed by prolonged periods of stasis and no change) might possibly be correct.

Even though I am a physician and not an evolutionist, I think that the world is a very dynamic place with lots of processes of nature taking place concurrently. To think that Natural Selection alone is the prime mechanism, seems a little too over "reductionistic" and naive to me.

I am all for reductionism and breaking complex things in to simple things and I believe that is no doubt necessary to understand the ways of nature. Its just that there is probably more than what meets the eye when it comes to the mechanisms of evolution that need to be sought after.

So while I do think Natural Selection is an important mechanism in the evolution of life on earth, I do not think it is the only mechanism. I am open to entertain the possibility of PE as an equally fascinating physical mechanism in addition to Darwin's grand theory of Natural Selection.



http://www.sciencedaily.com/releases/2008/07/080711090057.htm

Disproving Conventional Wisdom On Diversity Of Marine Fossils And Extinction Rates

ScienceDaily (July 14, 2008) — It took a decade of painstaking study, the cooperation of hundreds of researchers, and a database of more than 200,000 fossil records, but John Alroy thinks he's disproved much of the conventional wisdom about the diversity of marine fossils and extinction rates.

Alroy, a researcher with the National Center for Ecological Analysis and Synthesis (NCEAS) at UC Santa Barbara, is the principal author of the new report published in Science. A team that included 34 other researchers, who began their work in 1998, coauthored the report.

Alroy's report shows a new curve in the diversity of ancient marine invertebrate species such as clams, sand dollars and lobsters, while also revealing that most of the early propagation of invertebrates took place before the Late Cretaceous period. In addition, the research contends that the increase of those invertebrates in the period since is relatively small when compared to the 100 million years that elapsed.

"There's been 36 years of people arguing about this," Alroy said. "And I feel we finally resolved this debate, which is certainly one of the most high profile debates in the study of diversity of the fossil record.

"This is a big community project," he added. "The only reason we're able to do any of this is we have a very, very, very detailed database (the Paleobiology Database) that is built by a community of people over the Web. We record exactly what hole in the ground each fossil comes from."

By counting fossil records from all over the world, Alroy and his fellow researchers were able to conclude that much of what experts have been saying for the last 40 years might not be accurate. Instead of counting just the first and last instances of fossils, as others had done before, Alroy and his team set out to count them all, examining 284,816 fossil occurrences.

"We only count it where we've actually got it," Alroy said. "Say you're doing biomedical research and you want to know about the prevalence of a disease, say some kind of cancer."

The difference between the old and the new research, he said, would be like "the difference between checking medical records willy-nilly, and computing percentages with a standardized sample."

While the research of other scientists showed eventual recoveries in the diversity of fossils after periods of extinction - especially the extinction 250 million years ago between the Permian and Triassic periods (also known as the "mother of all mass extinctions") - Alroy said this report shows that the number of species comes back up quickly - at least on a geological time scale - and then stays relatively flat.

The data are also interesting, Alroy said, because they document that there have been only three truly major mass extinctions in the fossil record.

"For many years, our community has been saying that there have been five major mass extinctions, and it's gotten into the public consciousness that there's been a 'Big Five,' " Alroy said. "This (the last major spike in fossil diversity records) is supposed to be the sixth major extinction. This is really conventional wisdom, but it's not supported by the new data at all."

Instead, the new results suggest it's only the fourth one over the last half-billion years.

Monday, June 02, 2008

Put a Little Science in Your Life

Reading this article took my breathe away and almost moved me to tears. It reminded me of my first encounter with Science and how it shaped my way of thinking - that Science is more than a mere subject but rather a perspective that we all ought to carry with us when dealing with the nature of reality and making sense of why it is that we and the universe exist.

(NY Times article post from www.richarddawkins.net)


Put a Little Science in Your Life
By BRIAN GREENE

A COUPLE of years ago I received a letter from an American soldier in Iraq. The letter began by saying that, as we've all become painfully aware, serving on the front lines is physically exhausting and emotionally debilitating. But the reason for his writing was to tell me that in that hostile and lonely environment, a book I'd written had become a kind of lifeline. As the book is about science — one that traces physicists' search for nature's deepest laws — the soldier's letter might strike you as, well, odd.

But it's not. Rather, it speaks to the powerful role science can play in giving life context and meaning. At the same time, the soldier's letter emphasized something I've increasingly come to believe: our educational system fails to teach science in a way that allows students to integrate it into their lives.

Allow me a moment to explain.

When we consider the ubiquity of cellphones, iPods, personal computers and the Internet, it's easy to see how science (and the technology to which it leads) is woven into the fabric of our day-to-day activities. When we benefit from CT scanners, M.R.I. devices, pacemakers and arterial stents, we can immediately appreciate how science affects the quality of our lives. When we assess the state of the world, and identify looming challenges like climate change, global pandemics, security threats and diminishing resources, we don't hesitate in turning to science to gauge the problems and find solutions.

And when we look at the wealth of opportunities hovering on the horizon — stem cells, genomic sequencing, personalized medicine, longevity research, nanoscience, brain-machine interface, quantum computers, space technology — we realize how crucial it is to cultivate a general public that can engage with scientific issues; there's simply no other way that as a society we will be prepared to make informed decisions on a range of issues that will shape the future.

These are the standard — and enormously important — reasons many would give in explaining why science matters.

But here's the thing. The reason science really matters runs deeper still. Science is a way of life. Science is a perspective. Science is the process that takes us from confusion to understanding in a manner that's precise, predictive and reliable — a transformation, for those lucky enough to experience it, that is empowering and emotional. To be able to think through and grasp explanations — for everything from why the sky is blue to how life formed on earth — not because they are declared dogma but rather because they reveal patterns confirmed by experiment and observation, is one of the most precious of human experiences.

As a practicing scientist, I know this from my own work and study. But I also know that you don't have to be a scientist for science to be transformative. I've seen children's eyes light up as I've told them about black holes and the Big Bang. I've spoken with high school dropouts who've stumbled on popular science books about the human genome project, and then returned to school with newfound purpose. And in that letter from Iraq, the soldier told me how learning about relativity and quantum physics in the dusty and dangerous environs of greater Baghdad kept him going because it revealed a deeper reality of which we're all a part.

It's striking that science is still widely viewed as merely a subject one studies in the classroom or an isolated body of largely esoteric knowledge that sometimes shows up in the "real" world in the form of technological or medical advances. In reality, science is a language of hope and inspiration, providing discoveries that fire the imagination and instill a sense of connection to our lives and our world.

If science isn't your strong suit — and for many it's not — this side of science is something you may have rarely if ever experienced. I've spoken with so many people over the years whose encounters with science in school left them thinking of it as cold, distant and intimidating. They happily use the innovations that science makes possible, but feel that the science itself is just not relevant to their lives. What a shame.

Like a life without music, art or literature, a life without science is bereft of something that gives experience a rich and otherwise inaccessible dimension.

It's one thing to go outside on a crisp, clear night and marvel at a sky full of stars. It's another to marvel not only at the spectacle but to recognize that those stars are the result of exceedingly ordered conditions 13.7 billion years ago at the moment of the Big Bang. It's another still to understand how those stars act as nuclear furnaces that supply the universe with carbon, oxygen and nitrogen, the raw material of life as we know it.

And it's yet another level of experience to realize that those stars account for less than 4 percent of what's out there — the rest being of an unknown composition, so-called dark matter and energy, which researchers are now vigorously trying to divine.

As every parent knows, children begin life as uninhibited, unabashed explorers of the unknown. From the time we can walk and talk, we want to know what things are and how they work — we begin life as little scientists. But most of us quickly lose our intrinsic scientific passion. And it's a profound loss.

A great many studies have focused on this problem, identifying important opportunities for improving science education. Recommendations have ranged from increasing the level of training for science teachers to curriculum reforms.

But most of these studies (and their suggestions) avoid an overarching systemic issue: in teaching our students, we continually fail to activate rich opportunities for revealing the breathtaking vistas opened up by science, and instead focus on the need to gain competency with science's underlying technical details.

In fact, many students I've spoken to have little sense of the big questions those technical details collectively try to answer: Where did the universe come from? How did life originate? How does the brain give rise to consciousness? Like a music curriculum that requires its students to practice scales while rarely if ever inspiring them by playing the great masterpieces, this way of teaching science squanders the chance to make students sit up in their chairs and say, "Wow, that's science?"

In physics, just to give a sense of the raw material that's available to be leveraged, the most revolutionary of advances have happened in the last 100 years — special relativity, general relativity, quantum mechanics — a symphony of discoveries that changed our conception of reality. More recently, the last 10 years have witnessed an upheaval in our understanding of the universe's composition, yielding a wholly new prediction for what the cosmos will be like in the far future.

These are paradigm-shaking developments. But rare is the high school class, and rarer still is the middle school class, in which these breakthroughs are introduced. It's much the same story in classes for biology, chemistry and mathematics.

At the root of this pedagogical approach is a firm belief in the vertical nature of science: you must master A before moving on to B. When A happened a few hundred years ago, it's a long climb to the modern era. Certainly, when it comes to teaching the technicalities — solving this equation, balancing that reaction, grasping the discrete parts of the cell — the verticality of science is unassailable.

But science is so much more than its technical details. And with careful attention to presentation, cutting-edge insights and discoveries can be clearly and faithfully communicated to students independent of those details; in fact, those insights and discoveries are precisely the ones that can drive a young student to want to learn the details. We rob science education of life when we focus solely on results and seek to train students to solve problems and recite facts without a commensurate emphasis on transporting them out beyond the stars.

Science is the greatest of all adventure stories, one that's been unfolding for thousands of years as we have sought to understand ourselves and our surroundings. Science needs to be taught to the young and communicated to the mature in a manner that captures this drama. We must embark on a cultural shift that places science in its rightful place alongside music, art and literature as an indispensable part of what makes life worth living.

It's the birthright of every child, it's a necessity for every adult, to look out on the world, as the soldier in Iraq did, and see that the wonder of the cosmos transcends everything that divides us.

Saturday, May 31, 2008

KARMA COMEDIANS

by The Guardian

http://www.c.co.uk/commentisfree/2008/may/31/chinaearthquake.china


KARMA COMEDIANS

Stone's claptrap about China is of a piece with a thriving industry dealing in unscientific nonsense

By: Ariane Sherine

So Sharon Stone thinks the Sichuan earthquake was caused not by friction between tectonic plates on the Longmenshan fault, but by Beijing being "not nice" to the Dalai Lama. Given that Tibet has been under Chinese rule since 1951, karmic retribution must have a 57-year time lag, but that didn't stop Stone musing on the seismic catastrophe: "I thought, 'Is that karma?' When you are not nice, bad things happen to you."

Bad things did happen: within 24 hours of her statement, the Xinhua news agency had dubbed Sharon the "public enemy of all mankind", perhaps an epithet more suited to US televangelist John Hagee, who in 2005 announced that God unleashed Hurricane Katrina because He was cross after a "homosexual parade". And, to prove that retribution-based stupidity hasn't bypassed the UK, Glenn Hoddle also asserted in 1999 that "some people have not been born [with two hands and two legs and half-decent brains] for a reason ... the karma is working from another lifetime. It is not only people with disabilities. What you sow, you have to reap."

Worryingly, though all this lunacy generated the ridicule it deserved, the last few years have seen a spate of new age "self-help" books blaring out an identical, if less targeted, message: that everything in an individual's life is created by them. From infamous bestseller The Secret (DVD excerpt: "everything that's coming into your life, you're attracting into your life") to weirdo-manual Ask And It Is Given, which channels "the teachings of the non-physical entity Abraham" (sample chapter title: "Unwanted things cannot jump into your experience uninvited"), the philosophy is the same: whatever is happening to you, it's your fault.

It's religion for the non-religious, with all the shame, guilt and illogical pronouncements but none of the community. Instead of acts of God, we are told there are no accidents; instead of God's will, all happenings are manifestations of our own consciousness. And many people accept either the religious or new age explanations because, given the devastation caused by disasters and traumatic events, it's less scary to think they are a response to wayward human behaviour. That way, if we just change our actions, we won't have to fear pain and suffering in the future.

In truth, we can only make sense of the world by rejecting these ideas and the more pervasive "everything happens for a reason" mentality, and by accepting that life is random and unjust. Bad things happen to kind people every day, for no reason at all. Our chances in life are largely predetermined by our place of birth, and religious people are as likely to die in tragedies as atheists. Earthquakes, tsunamis and hurricanes hit for scientific reasons alone; to attribute them to the wrath of God or "the universe" is to deny the victims of these catastrophes their innocence.

Paradoxically, though Stone apologised for her errant statement - which seemed more an ill thought-out comment on China's treatment of the Dalai Lama than an intentional slur on the victims of the disaster - she has been pulled from the country's billboards, and her films are now banned in its cinemas. The authors of books like The Secret have profited from pushing sinister anti-scientific nonsense on to the disadvantaged, sick and desperate, but have never been forced to deliver an acknowledgement or apology, let alone been penalised. And homophobe John Hagee has become a millionaire by driving the fear of God into the weak and gullible while also endorsing John McCain, who might just become the next US president.

"Is that karma?" No, Sharon. It's anything but.

· Ariane Sherine is a television comedy writer

Friday, May 16, 2008

Is Science Killing the Soul?

The entire discussion between Richard Dawkins and Steven Pinker can be found at www.richarddawkins.net

I just thought Richard's segment was brilliant and I thought of posting it below. Enjoy!

Murtaza Hameer, MD


RICHARD DAWKINS: Thank you very much, Tim. But the word debate does appear up on the notice there. It may turn into more of a dialogue than a debate. I suspect that Steve Pinker and I are perhaps largely of the same mind here, so there's a risk that anybody who's come here expecting a confrontation will go away disappointed by too much agreement. I don't know if this will happen, but if it does, I don't think there's any need to apologize. The adversarial approach to truth isn't necessarily always the best one. On the contrary, when two people disagree strongly, a great deal of time may be wasted. It's been well said that when two opposite points of view are advocated with equal vigor, the truth does not necessarily lie mid-way between them. And in the same way, when two people agree about something, it's just possible that the reason they agree is that they're both right. There's also I suppose the hope that in a dialogue of this sort each speaker may manage to achieve a joint understanding with the other one, better than he would have done on his own.

Is science killing the soul? This is a cunning title, because it cunningly mixes two different meanings of soul. The first and oldest meaning of soul, which I'm going to call Soul One, takes off from one set of definitions. I'm going to quote several related definitions from the Oxford dictionary:

"The principle of life in man or animals -- animate existence."

"The principle of thought and action in man commonly regarded as an entity distinct from the body, the spiritual part of man in contrast to the purely physical."

"The spiritual part of man regarded as surviving after death, and as susceptible of happiness or misery in a future state."

"The disembodied spirit of a deceased person regarded as a separate entity and as invested with some amount of form and personality."

So Soul One refers to a particular theory of life. It's the theory that there is something non-material about life, some non-physical vital principle. It's the theory according to which a body has to be animated by some anima. Vitalized by a vital force. Energized by some mysterious energy. Spiritualized by some mysterious spirit. Made conscious by some mysterious thing or substance called consciousness. You'll notice that all those definitions of Soul One are circular and non-productive. It's no accident. Julian Huxley once satirically likened vitalism to the theory that a railway engine works by "force-locomotif." I don't always agree with Julian Huxley, but here he hit the nail beautifully. In the sense of Soul One, science has either killed the soul or is in the process of doing so.

But there is a second sense of soul, Soul Two, which takes off from another one of the Oxford dictionary's definitions:

"Intellectual or spiritual power. High development of the mental faculties. Also, in somewhat weakened sense, deep feeling, sensitivity."

In this sense, our question tonight means, Is science killing soulfulness? Is it killing esthetic sensitivity, artistic sensibility, creativity? The answer to this question, Is science killing Soul Two?, is a resounding No. The very opposite is the case. But it is a question worth pursuing, because there have been many people, from genuinely great poets all the way down to Brian Appleyard and Fay Weldon, who've given a strong Yes answer to the question, Is science killing the soul? It's Soul Two that Keats and Lamb meant when they thought that Newton had destroyed all the poetry of the rainbow when he unwove it.

"Do not all charms fly
At the mere touch of cold philosophy?
There was an awful rainbow once in heaven;
We know her texture; she is given
In the dull catalogue of common things,
Philosophy will clip an Angel's wings,
Conquer all mysteries by rule and line,
Empty the haunted air, and gnomed mine‹
Unweave a rainbow . . ."

Well, I've written a book which is one long reply to that particular kind of anti-scientific attitude. In the sense of Soul Two, science doesn't kill the soul, it gives the soul constant and exhilarating re-birth.

Turning back to Soul One -- in the first chapter of Steve Pinker's book How the Mind Works he says, "I want to convince you that our minds are not animated by some godly vapor or single wonder-principle. The mind, like the Apollo spacecraft, is designed to solve many engineering problems, and thus is packed with high-tech systems, each contrived to overcome its own obstacles." In the same paragraph, he moves on to Soul Two when he says, " . . . I believe that the discovery by cognitive science and artificial intelligence of the technical challenges overcome by our mundane mental activity is one of the great revelations of science, an awakening of the imagination comparable to learning that the universe is made up of billions of galaxies or that a drop of pond water teems with microscopic life." Well, awakening of the imagination is a pretty good definition of Soul Two. And in that sense, far from killing the soul, science may prove to be its greatest awakener.

Carl Sagan wrote, shortly before he died,

"How is it that hardly any major religion has looked at science and concluded, 'This is better than we thought! The Universe is much bigger than our prophets said, grander, more subtle, more elegant'? Instead they say, 'No, no, no! My god is a little god, and I want him to stay that way.' A religion, old or new, that stressed the magnificence of the Universe as revealed by modern science might be able to draw forth reserves of reverence and awe hardly tapped by the conventional faiths."

Well it's common enough for people to agree that religions have got the facts all wrong, but "Nevertheless," they go on to say, "you have to admit that religions do provide something that people need. We crave a deeper meaning to life, a deeper, more imaginative understanding of the mystery of existence." Well, in the passage I've just quoted, Sagan seems to be criticizing religions not just for getting it wrong, which many people would accept, but for their deficiencies precisely in the sphere in which they are supposed to retain some residual virtue. Religions are not imaginative, not poetic, not soulful. On the contrary, they are parochial, small-minded, niggardly with the human imagination, precisely where science is generous.

Now, there are, of course many unsolved problems, and scientists are the first to admit this. There are aspects of human subjective consciousness that are deeply mysterious. Neither Steve Pinker nor I can explain human subjective consciousness -- what philosophers call qualia. In How the Mind Works Steve elegantly sets out the problem of subjective consciousness, and asks where it comes from and what's the explanation. Then he's honest enough to say, "Beats the heck out of me." That is an honest thing to say, and I echo it. We don't know. We don't understand it.

There's a cheap debating trick which implies that if, say, science can't explain something, this must mean that some other discipline can. If scientists suspect that all aspects of the mind have a scientific explanation but they can't actually say what that explanation is yet, then of course it's open to you to doubt whether the explanation ever will be forthcoming. That's a perfectly reasonable doubt. But it's not legitimately open to you to substitute a word like soul, or spirit, as if that constituted an explanation. It is not an explanation, it's an evasion. It's just a name for that which we don't understand. The scientist may agree to use the word soul for that which we don't understand, but the scientist adds, "But we're working on it, and one day we hope we shall explain it." The dishonest trick is to use a word like soul or spirit as if it constituted an explanation.

Consciousness is still mysterious. And scientists, I think, all admit it. But we ought to remember that it's not that long ago that life itself was thought to be equally mysterious. I'm going to quote from a book, A Short History of Biology by Charles Singer, a reputable historian of science, published in 1931, where he says, about the gene,

". . . despite interpretations to the contrary, the theory of the gene is not a 'mechanist' theory. The gene is no more comprehensible as a chemical or physical entity than is the cell or, for that matter, the organism itself. . . . If I ask for a living chromosome, that is, for the only effective kind of chromosome, no one can give it to me except in its living surroundings any more than he can give me a living arm or leg. The doctrine of the relativity of functions is as true for the gene as it is for any of the organs of the body. They exist and function only in relation to other organs. Thus the last of the biological theories leaves us where the first started, in the presence of a power called life or psyche which is not only of its own kind but unique in each and all of its exhibitions."

That was 1931. In 1953, Watson and Crick drove a coach and horses through it, blew it out of the water. Genes are isolatable, they can be taken out of bodies, they can be sequenced, they can be put in bottles, they can be written out in a book and stored away in a library, and then at any time in the future they can be simply typed back into a machine and the original gene reconstituted. It could be put back into a living creature where it will work exactly the way it originally did. In the context of the gene, the understanding, the explanation is more or less total. And it was completely unexpected only a few decades ago.

My suspicion, my hunch, my hope, is that the same thing is going to be done for the conscious mind. Probably within the next century. Soul One will finally be killed, and good riddance. But in the process, Soul Two, far from being destroyed, will still be finding new worlds to conquer.

I'm going to end my prepared remarks by saying a little bit about Darwinism, because Darwinism is something which obviously Steve Pinker and I have in common in our approach to science. This, I think, may be the one place where possibly some slight disagreement may emerge. For me, Darwinism is not actually, surprisingly enough, the theory of the selfish gene. It's the theory of the selfish replicator. Darwinism is a much more general idea than the particular version of Darwinism which happens to explain life on this planet. Darwinism in this more general universal sense refers to the differential survival of any kind of self-replicating coded information which has some sort of power or influence over its probability of being replicated. DNA is the main kind of replicating entity that we know on this planet that has that property. When we look at living things on this planet, overwhelmingly the kind of explanation we should be seeking, if we ask what the functional significance is an explanation in terms of the good of the genes. Any adaptation is for the good of the genes which made that adaptation.

Friday, April 18, 2008

Evolution as Fact and Theory

by Stephen Jay Gould

(article obtained from www.stephenjaygould.org)


Kirtley Mather, who died last year at age ninety, was a pillar of both science and Christian religion in America and one of my dearest friends. The difference of a half-century in our ages evaporated before our common interests. The most curious thing we shared was a battle we each fought at the same age. For Kirtley had gone to Tennessee with Clarence Darrow to testify for evolution at the Scopes trial of 1925. When I think that we are enmeshed again in the same struggle for one of the best documented, most compelling and exciting concepts in all of science, I don't know whether to laugh or cry.

According to idealized principles of scientific discourse, the arousal of dormant issues should reflect fresh data that give renewed life to abandoned notions. Those outside the current debate may therefore be excused for suspecting that creationists have come up with something new, or that evolutionists have generated some serious internal trouble. But nothing has changed; the creationists have presented not a single new fact or argument. Darrow and Bryan were at least more entertaining than we lesser antagonists today. The rise of creationism is politics, pure and simple; it represents one issue (and by no means the major concern) of the resurgent evangelical right. Arguments that seemed kooky just a decade ago have reentered the mainstream.

The basic attack of modern creationists falls apart on two general counts before we even reach the supposed factual details of their assault against evolution. First, they play upon a vernacular misunderstanding of the word "theory" to convey the false impression that we evolutionists are covering up the rotten core of our edifice. Second, they misuse a popular philosophy of science to argue that they are behaving scientifically in attacking evolution. Yet the same philosophy demonstrates that their own belief is not science, and that "scientific creationism" is a meaningless and self-contradictory phrase, an example of what Orwell called "newspeak."

In the American vernacular, "theory" often means "imperfect fact"—part of a hierarchy of confidence running downhill from fact to theory to hypothesis to guess. Thus creationists can (and do) argue: evolution is "only" a theory, and intense debate now rages about many aspects of the theory. If evolution is less than a fact, and scientists can't even make up their minds about the theory, then what confidence can we have in it? Indeed, President Reagan echoed this argument before an evangelical group in Dallas when he said (in what I devoutly hope was campaign rhetoric): "Well, it is a theory. It is a scientific theory only, and it has in recent years been challenged in the world of science—that is, not believed in the scientific community to be as infallible as it once was."

Well, evolution is a theory. It is also a fact. And facts and theories are different things, not rungs in a hierarchy of increasing certainty. Facts are the world's data. Theories are structures of ideas that explain and interpret facts. Facts do not go away when scientists debate rival theories to explain them. Einstein's theory of gravitation replaced Newton's, but apples did not suspend themselves in mid-air, pending the outcome. And humans evolved from apelike ancestors whether they did so by Darwin's proposed mechanism or by some other, yet to be discovered.

Moreover, "fact" does not mean "absolute certainty." The final proofs of logic and mathematics flow deductively from stated premises and achieve certainty only because they are not about the empirical world. Evolutionists make no claim for perpetual truth, though creationists often do (and then attack us for a style of argument that they themselves favor). In science, "fact" can only mean "confirmed to such a degree that it would be perverse to withhold provisional assent." I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms.

Evolutionists have been clear about this distinction between fact and theory from the very beginning, if only because we have always acknowledged how far we are from completely understanding the mechanisms (theory) by which evolution (fact) occurred. Darwin continually emphasized the difference between his two great and separate accomplishments: establishing the fact of evolution, and proposing a theory—natural selection—to explain the mechanism of evolution. He wrote in The Descent of Man: "I had two distinct objects in view; firstly, to show that species had not been separately created, and secondly, that natural selection had been the chief agent of change. . . . Hence if I have erred in . . . having exaggerated its [natural selection's] power . . . I have at least, as I hope, done good service in aiding to overthrow the dogma of separate creations."

Thus Darwin acknowledged the provisional nature of natural selection while affirming the fact of evolution. The fruitful theoretical debate that Darwin initiated has never ceased. From the 1940s through the 1960s, Darwin's own theory of natural selection did achieve a temporary hegemony that it never enjoyed in his lifetime. But renewed debate characterizes our decade, and, while no biologist questions the importance of natural selection, many doubt its ubiquity. In particular, many evolutionists argue that substantial amounts of genetic change may not be subject to natural selection and may spread through the populations at random. Others are challenging Darwin's linking of natural selection with gradual, imperceptible change through all intermediary degrees; they are arguing that most evolutionary events may occur far more rapidly than Darwin envisioned.

Scientists regard debates on fundamental issues of theory as a sign of intellectual health and a source of excitement. Science is—and how else can I say it?—most fun when it plays with interesting ideas, examines their implications, and recognizes that old information might be explained in surprisingly new ways. Evolutionary theory is now enjoying this uncommon vigor. Yet amidst all this turmoil no biologist has been lead to doubt the fact that evolution occurred; we are debating how it happened. We are all trying to explain the same thing: the tree of evolutionary descent linking all organisms by ties of genealogy. Creationists pervert and caricature this debate by conveniently neglecting the common conviction that underlies it, and by falsely suggesting that evolutionists now doubt the very phenomenon we are struggling to understand.

Secondly, creationists claim that "the dogma of separate creations," as Darwin characterized it a century ago, is a scientific theory meriting equal time with evolution in high school biology curricula. But a popular viewpoint among philosophers of science belies this creationist argument. Philosopher Karl Popper has argued for decades that the primary criterion of science is the falsifiability of its theories. We can never prove absolutely, but we can falsify. A set of ideas that cannot, in principle, be falsified is not science.

The entire creationist program includes little more than a rhetorical attempt to falsify evolution by presenting supposed contradictions among its supporters. Their brand of creationism, they claim, is "scientific" because it follows the Popperian model in trying to demolish evolution. Yet Popper's argument must apply in both directions. One does not become a scientist by the simple act of trying to falsify a rival and truly scientific system; one has to present an alternative system that also meets Popper's criterion — it too must be falsifiable in principle.

"Scientific creationism" is a self-contradictory, nonsense phrase precisely because it cannot be falsified. I can envision observations and experiments that would disprove any evolutionary theory I know, but I cannot imagine what potential data could lead creationists to abandon their beliefs. Unbeatable systems are dogma, not science. Lest I seem harsh or rhetorical, I quote creationism's leading intellectual, Duane Gish, Ph.D. from his recent (1978) book, Evolution? The Fossils Say No! "By creation we mean the bringing into being by a supernatural Creator of the basic kinds of plants and animals by the process of sudden, or fiat, creation. We do not know how the Creator created, what process He used, for He used processes which are not now operating anywhere in the natural universe [Gish's italics]. This is why we refer to creation as special creation. We cannot discover by scientific investigations anything about the creative processes used by the Creator." Pray tell, Dr. Gish, in the light of your last sentence, what then is scientific creationism?

Our confidence that evolution occurred centers upon three general arguments. First, we have abundant, direct, observational evidence of evolution in action, from both the field and laboratory. This evidence ranges from countless experiments on change in nearly everything about fruit flies subjected to artificial selection in the laboratory to the famous populations of British moths that became black when industrial soot darkened the trees upon which the moths rest. (Moths gain protection from sharp-sighted bird predators by blending into the background.) Creationists do not deny these observations; how could they? Creationists have tightened their act. They now argue that God only created "basic kinds," and allowed for limited evolutionary meandering within them. Thus toy poodles and Great Danes come from the dog kind and moths can change color, but nature cannot convert a dog to a cat or a monkey to a man.

The second and third arguments for evolution—the case for major changes—do not involve direct observation of evolution in action. They rest upon inference, but are no less secure for that reason. Major evolutionary change requires too much time for direct observation on the scale of recorded human history. All historical sciences rest upon inference, and evolution is no different from geology, cosmology, or human history in this respect. In principle, we cannot observe processes that operated in the past. We must infer them from results that still surround us: living and fossil organisms for evolution, documents and artifacts for human history, strata and topography for geology.

The second argument—that the imperfection of nature reveals evolution—strikes many people as ironic, for they feel that evolution should be most elegantly displayed in the nearly perfect adaptation expressed by some organisms—the camber of a gull's wing, or butterflies that cannot be seen in ground litter because they mimic leaves so precisely. But perfection could be imposed by a wise creator or evolved by natural selection. Perfection covers the tracks of past history. And past history—the evidence of descent—is the mark of evolution.

Evolution lies exposed in the imperfections that record a history of descent. Why should a rat run, a bat fly, a porpoise swim, and I type this essay with structures built of the same bones unless we all inherited them from a common ancestor? An engineer, starting from scratch, could design better limbs in each case. Why should all the large native mammals of Australia be marsupials, unless they descended from a common ancestor isolated on this island continent? Marsupials are not "better," or ideally suited for Australia; many have been wiped out by placental mammals imported by man from other continents. This principle of imperfection extends to all historical sciences. When we recognize the etymology of September, October, November, and December (seventh, eighth, ninth, and tenth), we know that the year once started in March, or that two additional months must have been added to an original calendar of ten months.

The third argument is more direct: transitions are often found in the fossil record. Preserved transitions are not common—and should not be, according to our understanding of evolution (see next section) but they are not entirely wanting, as creationists often claim. The lower jaw of reptiles contains several bones, that of mammals only one. The non-mammalian jawbones are reduced, step by step, in mammalian ancestors until they become tiny nubbins located at the back of the jaw. The "hammer" and "anvil" bones of the mammalian ear are descendants of these nubbins. How could such a transition be accomplished? the creationists ask. Surely a bone is either entirely in the jaw or in the ear. Yet paleontologists have discovered two transitional lineages of therapsids (the so-called mammal-like reptiles) with a double jaw joint—one composed of the old quadrate and articular bones (soon to become the hammer and anvil), the other of the squamosal and dentary bones (as in modern mammals). For that matter, what better transitional form could we expect to find than the oldest human, Australopithecus afarensis, with its apelike palate, its human upright stance, and a cranial capacity larger than any ape’s of the same body size but a full 1,000 cubic centimeters below ours? If God made each of the half-dozen human species discovered in ancient rocks, why did he create in an unbroken temporal sequence of progressively more modern features—increasing cranial capacity, reduced face and teeth, larger body size? Did he create to mimic evolution and test our faith thereby?

Faced with these facts of evolution and the philosophical bankruptcy of their own position, creationists rely upon distortion and innuendo to buttress their rhetorical claim. If I sound sharp or bitter, indeed I am—for I have become a major target of these practices.

I count myself among the evolutionists who argue for a jerky, or episodic, rather than a smoothly gradual, pace of change. In 1972 my colleague Niles Eldredge and I developed the theory of punctuated equilibrium. We argued that two outstanding facts of the fossil record—geologically "sudden" origin of new species and failure to change thereafter (stasis)—reflect the predictions of evolutionary theory, not the imperfections of the fossil record. In most theories, small isolated populations are the source of new species, and the process of speciation takes thousands or tens of thousands of years. This amount of time, so long when measured against our lives, is a geological microsecond. It represents much less than 1 per cent of the average life-span for a fossil invertebrate species—more than ten million years. Large, widespread, and well established species, on the other hand, are not expected to change very much. We believe that the inertia of large populations explains the stasis of most fossil species over millions of years.

We proposed the theory of punctuated equilibrium largely to provide a different explanation for pervasive trends in the fossil record. Trends, we argued, cannot be attributed to gradual transformation within lineages, but must arise from the different success of certain kinds of species. A trend, we argued, is more like climbing a flight of stairs (punctuated and stasis) than rolling up an inclined plane.

Since we proposed punctuated equilibria to explain trends, it is infuriating to be quoted again and again by creationists—whether through design or stupidity, I do not know—as admitting that the fossil record includes no transitional forms. Transitional forms are generally lacking at the species level, but they are abundant between larger groups. Yet a pamphlet entitled "Harvard Scientists Agree Evolution Is a Hoax" states: "The facts of punctuated equilibrium which Gould and Eldredge…are forcing Darwinists to swallow fit the picture that Bryan insisted on, and which God has revealed to us in the Bible."

Continuing the distortion, several creationists have equated the theory of punctuated equilibrium with a caricature of the beliefs of Richard Goldschmidt, a great early geneticist. Goldschmidt argued, in a famous book published in 1940, that new groups can arise all at once through major mutations. He referred to these suddenly transformed creatures as "hopeful monsters." (I am attracted to some aspects of the non-caricatured version, but Goldschmidt's theory still has nothing to do with punctuated equilibrium—see essays in section 3 and my explicit essay on Goldschmidt in The Pandas Thumb.) Creationist Luther Sunderland talks of the "punctuated equilibrium hopeful monster theory" and tells his hopeful readers that "it amounts to tacit admission that anti-evolutionists are correct in asserting there is no fossil evidence supporting the theory that all life is connected to a common ancestor." Duane Gish writes, "According to Goldschmidt, and now apparently according to Gould, a reptile laid an egg from which the first bird, feathers and all, was produced." Any evolutionists who believed such nonsense would rightly be laughed off the intellectual stage; yet the only theory that could ever envision such a scenario for the origin of birds is creationism—with God acting in the egg.

I am both angry at and amused by the creationists; but mostly I am deeply sad. Sad for many reasons. Sad because so many people who respond to creationist appeals are troubled for the right reason, but venting their anger at the wrong target. It is true that scientists have often been dogmatic and elitist. It is true that we have often allowed the white-coated, advertising image to represent us—"Scientists say that Brand X cures bunions ten times faster than…" We have not fought it adequately because we derive benefits from appearing as a new priesthood. It is also true that faceless and bureaucratic state power intrudes more and more into our lives and removes choices that should belong to individuals and communities. I can understand that school curricula, imposed from above and without local input, might be seen as one more insult on all these grounds. But the culprit is not, and cannot be, evolution or any other fact of the natural world. Identify and fight our legitimate enemies by all means, but we are not among them.

I am sad because the practical result of this brouhaha will not be expanded coverage to include creationism (that would also make me sad), but the reduction or excision of evolution from high school curricula. Evolution is one of the half dozen "great ideas" developed by science. It speaks to the profound issues of genealogy that fascinate all of us—the "roots" phenomenon writ large. Where did we come from? Where did life arise? How did it develop? How are organisms related? It forces us to think, ponder, and wonder. Shall we deprive millions of this knowledge and once again teach biology as a set of dull and unconnected facts, without the thread that weaves diverse material into a supple unity?

But most of all I am saddened by a trend I am just beginning to discern among my colleagues. I sense that some now wish to mute the healthy debate about theory that has brought new life to evolutionary biology. It provides grist for creationist mills, they say, even if only by distortion. Perhaps we should lie low and rally around the flag of strict Darwinism, at least for the moment—a kind of old-time religion on our part.

But we should borrow another metaphor and recognize that we too have to tread a straight and narrow path, surrounded by roads to perdition. For if we ever begin to suppress our search to understand nature, to quench our own intellectual excitement in a misguided effort to present a united front where it does not and should not exist, then we are truly lost.

Thursday, January 31, 2008

One Common Ancestor Behind Blue Eyes

By Jeanna Bryner, www.livescience.com

People with blue eyes have a single, common ancestor, according to new research.

A team of scientists has tracked down a genetic mutation that leads to blue eyes. The mutation occurred between 6,000 and 10,000 years ago. Before then, there were no blue eyes.

"Originally, we all had brown eyes," said Hans Eiberg from the Department of Cellular and Molecular Medicine at the University of Copenhagen.

The mutation affected the so-called OCA2 gene, which is involved in the production of melanin, the pigment that gives color to our hair, eyes and skin.

"A genetic mutation affecting the OCA2 gene in our chromosomes resulted in the creation of a 'switch,' which literally 'turned off' the ability to produce brown eyes," Eiberg said.

The genetic switch is located in the gene adjacent to OCA2 and rather than completely turning off the gene, the switch limits its action, which reduces the production of melanin in the iris. In effect, the turned-down switch diluted brown eyes to blue.

If the OCA2 gene had been completely shut down, our hair, eyes and skin would be melanin-less, a condition known as albinism.

"It's exactly what I sort of expected to see from what we know about selection around this area," said John Hawks of the University of Wisconsin-Madison, referring to the study results regarding the OCA2 gene. Hawks was not involved in the current study.


Baby blues

Eiberg and his team examined DNA from mitochondria, the cells' energy-making structures, of blue-eyed individuals in countries including Jordan, Denmark and Turkey. This genetic material comes from females, so it can trace maternal lineages.

They specifically looked at sequences of DNA on the OCA2 gene and the genetic mutation associated with turning down melanin production.

Over the course of several generations, segments of ancestral DNA get shuffled so that individuals have varying sequences. Some of these segments, however, that haven't been reshuffled are called haplotypes. If a group of individuals shares long haplotypes, that means the sequence arose relatively recently in our human ancestors. The DNA sequence didn't have enough time to get mixed up.

"What they were able to show is that the people who have blue eyes in Denmark, as far as Jordan, these people all have this same haplotype, they all have exactly the same gene changes that are all linked to this one mutation that makes eyes blue," Hawks said in a telephone interview.


Melanin switch

The mutation is what regulates the OCA2 switch for melanin production. And depending on the amount of melanin in the iris, a person can end up with eye color ranging from brown to green. Brown-eyed individuals have considerable individual variation in the area of their DNA that controls melanin production. But they found that blue-eyed individuals only have a small degree of variation in the amount of melanin in their eyes.

"Out of 800 persons we have only found one person which didn't fit — but his eye color was blue with a single brown spot," Eiberg told LiveScience, referring to the finding that blue-eyed individuals all had the same sequence of DNA linked with melanin production.

"From this we can conclude that all blue-eyed individuals are linked to the same ancestor," Eiberg said. "They have all inherited the same switch at exactly the same spot in their DNA." Eiberg and his colleagues detailed their study in the Jan. 3 online edition of the journal Human Genetics.

That genetic switch somehow spread throughout Europe and now other parts of the world.

"The question really is, 'Why did we go from having nobody on Earth with blue eyes 10,000 years ago to having 20 or 40 percent of Europeans having blue eyes now?" Hawks said. "This gene does something good for people. It makes them have more kids."

Thursday, August 23, 2007

Researchers find fossils of 10-million-year old ape

by Michael Kahn, Reuters

http://uk.news.yahoo.com/rtrs/20070822/thl-uk-apes-fossil-b2e59e8_1.html

LONDON (Reuters) - Researchers working in Ethiopia have unearthed the fossils of a 10-million-year-old ape, a discovery they say suggests that humans and African great apes may have split much earlier than thought.

The Ethiopian and Japanese team named the species Chororapithecus abyssinicus and said it represents the earliest recognised primate directly related to modern-day gorillas, chimpanzees and bonobos.

"The human fossil record goes back six to seven million years, but we know nothing about how the human line actually emerged from apes," the researchers said in a statement on Wednesday that accompanied publication of their study in Nature magazine.

"Chororapithecus gives us the first glimpse of the ape side background to the human origins story."

The researchers found the fossils in steep, rough terrain about 170 km (105 miles) east of Addis Ababa.

The team, which dug up one canine tooth and eight molars, determined the molars were from a great ape because they shared special characteristics with modern gorillas for eating fibrous food such as stems and leaves.

They concluded Chororapithecus was either a primitive form of gorilla or an independent branch showing a similar adaptation at about the time when the gorilla line was emerging elsewhere.

"If it's not a gorilla relative, then it's something very similar to what an early gorilla must have looked like", Gen Suwa of the University of Tokyo, one of the researchers, said.

Peter Andrews, a palaeontologist at the British Natural History Museum and expert on human origins, called the discovery exciting because the fossil evidence from great apes, the closest living relatives to humans, is almost non-existent.

But he said he was not certain enough about some of the characteristics of the new fossil ape's teeth to name a new species ancestral to gorillas-- as the researchers have done -- that pushes back the timeline of the ape-human split.

"It is stretching the evidence to base a timescale for the evolution of the great apes on this new fossil," Andrews said in a telephone interview.

Some scientists have also speculated that the direct line of ancestral ape that spawned gorillas, chimpanzees and humans came to Africa from Eurasia.

But the researchers said their findings added to evidence that Africa was the place of origin of both humans and modern African apes and indicated that gorillas split off from a common ancestor with humans and chimpanzees long before the generally accepted time of 7 to 8 million years ago.

"Chororapithecus indicates that a reconsideration of this assumption is needed," the researchers said. "In fact, if the orang line was present in Africa prior (to the) first migration of Miocene (some 23-25 million years ago) apes from Africa to Eurasia, then the human-orang split could have easily have been as old as 20 million years ago."