Monday, October 31, 2005

Boo! Who?

posted by Chet at 11:22 AM UTC

A Halloween treat for you from my sister Anne. I'm not quite sure what the 13th-century mystic Meister Eckhart meant by this aphroism (I haven't been able to track down the source), but he was onto something that resonates today. For all we know, the universe may be infinite, containing an infinity of galaxies. But it is apparently only 14 billion years old, and only those galaxies are visible to us from which light has had time to reach us. Which means, perhaps, that the greater part of existence is forever beyond our direct perception.

In the face of such a universe we might reasonably conclude with Eckhart that "the most beautiful thing a person can say about God is silence."

Sunday, October 30, 2005

Moments of being

posted by Chet at 12:39 PM UTC

"A good part of every day is not lived consciously." -- Virginia Woolf

See this week's Musing.

Saturday, October 29, 2005

Natural history

posted by Chet at 1:15 PM UTC

While I'm on the subject of Virginia Woolf, I am reminded of a passage from a biography of Woolf by her nephew Quentin Bell, describing the "bug hunting" adventures of young Virginia and her sibs.
As blood sports go, the killing of lepidoptera has a good deal to recommend it: it can offend only the most squeamish of humanitarians; it involves all the passion and skill of the naturalist, the charm of summer excursions and sudden exhilarating pursuits, the satisfaction of filling gaps in the collection, the careful study of text books, and, above all, the mysterious pleasure of staying up late, and walking softly through the night to where a rag, soaked in rum and treacle, has attracted dozens of slugs, crawly-bobs and, perhaps, some great lamp-eyed, tipsy, extravagantly gaudy moth.

If you know Woolf's work, you will know that moths, especially, reappear affectionately in her writing. The collecting of insects, plants and fossils were common activities among Victorians of a certain class. Children from an early age engaged in natural history activities, with all of the intellectual and sensual pleasures enumerated by Bell. We have become more squeamish than were Victorians about killing for collecting, although the digital camera makes a satisfying substitute. Still, I cannot imagine children today tearing themselves away from their video games long enough to be attracted to slugs and crawly-bobs (whatever they are) -- or even a lamp-eyed, tipsy, extravagantly gaudy moth.

Friday, October 28, 2005

The great bran pie

posted by Chet at 12:32 PM UTC

Sharing several hours every week with Bailey and Greg -- so young, so eager, so curious, so bright -- reminds me of a passage from Virginia Woolf's The Waves, a book I discovered when I was about their age:
"The complexity of things becomes more close," said Bernard, "here at college, where the stir and pressure of life are so extreme, where the excitement of mere living becomes daily more urgent. Every hour something new is unburied the the great bran pie. What am I? I ask. This? No, I am that. Especially now, when I have left a room, and people talking, and the stone flags ring out with my solitary footsteps, and I behold the moon rising, sublimely, indifferently, over the ancient chapel -- then it becomes clear that I am not one and simple, but complex and many."

College as a great bran pie -- one of those Victorian Christmas confections in which were buried gifts and treats! What lesson is more important than this -- that we are complex and many? Churches, corporations, and tyrants want us to believe that the world is one and simple: tithe, buy, die. But of course the world is not as simple as all that. Lewis Thomas, the admired essayist, once said that the greatest discovery of 20th-century science is how little we know and understand. The philosopher Karl Popper concurred: "The more we learn about the world, and the deeper our learning, the more conscious, specific, and articulate will be our knowledge of what we do not know, our knowledge of our ignorance. For this, indeed, is the main source of our ignorance -- the fact that our knowledge can be only finite, while our ignorance must necessarily be infinite."

And that is what I felt when I read The Waves as a student: We are immersed in mystery up to our eyeballs; it soaks creation as water soaks a sponge.

Later, in maturity, Bernard confesses:
How tired I am of stories, how tired I am of phrases that come down beautifully with all their feet on the ground! Also, how I distrust neat designs of life that are drawn up on half sheets of notepaper. I begin to long for some little language such as lovers use, broken words, inarticulate words, like the shuffling of feet on pavement. I begin to see some design more in accordance with those moments of humiliation and triumph that come now and then undeniably. Lying in a ditch on a stormy day, when it has been raining, then enormous clouds come marching over the sky, tattered clouds, wisps of cloud. What delights me then is the confusion, the height, the indifference and the fury. Great clouds always changing, and movement; something sulfurous and sinister, bowled up, helter-skelter; towering, trailing, broken off, lost, and I forgotten, minute, in a ditch. Of story, of design I do not see a trace then.

And then, and then -- we scratch about to make our own meaning, trying, as best we can, to patch together a content of sorts.

Thursday, October 27, 2005

Faith-based reality -- Mousetrap!

posted by Tom at 5:58 PM UTC

To explain the concept of "irreducible complexity" to the layman, Michael Behe offered the example of the common spring mousetrap. Remove any one part of the mousetrap and it fails to catch mice. Therefore, like complex life processes Behe reasoned, it could not have developed gradually from component parts, but conceived and created as a working whole. It seemed impossible to him that the mousetrap could work with fewer parts, therefore it must be impossible. Personal Incredulity = Irreducible Complexity.

It didn't seem impossible, however, to University of Delaware Professor John MacDonald. On his personal website, he presents a clever and illuminating demonstration of how the complexity of a mousetrap can be reduced and still function to catch mice.

Faith-based reality

posted by Chet at 11:21 AM UTC

I've said here before that intelligent design is not just bad science, it is the end of science. Michael Behe, that indefatigable advocate of ID, offers the cilia of cells -- the propellerlike appendages that, among other things, give cells mobility -- as an example of a biological system that is "irreducibly complex," i.e. beyond any natural explanation and therefore prima facie evidence of design. Or, more simply: "I don't know how cilia evolved, therefore God did it." This is what Richard Dawkins calls "the argument from personal incredulity."

Here is the abstract of a paper on celia biology in the October 13th issue of Nature:

The unanticipated involvement of several intraflagellar transport proteins in the mammalian Hedgehog (Hh) pathway has hinted at a functional connection between cilia and Hh signal transduction. Here we show that mammalian Smoothened (Smo), a seven-transmembrane protein essential for Hh signalling, is expressed on the primary cilium. This ciliary expression is regulated by Hh pathway activity; Sonic hedgehog or activating mutations in Smo promote ciliary localization, whereas the Smo antagonist cyclopamine inhibits ciliary localization. The translocation of Smo to primary cilia depends upon a conserved hydrophobic and basic residue sequence homologous to a domain previously shown to be required for the ciliary localization of seven-transmembrane proteins in Caenorhabditis elegans. Mutation of this domain not only prevents ciliary localization but also eliminates Smo activity both in cultured cells and in zebrafish embryos. Thus, Hh-dependent translocation to cilia is essential for Smo activity, suggesting that Smo acts at the primary cilium.


I don't know what most of this means, but I recognize science when I see it, and appreciate that knowledgeable researchers are not simply throwing up their hands in the face of complexity, but are chipping away at the mystery.

Meanwhile, Mr. Bush's current nomination to the Supreme Court, Harriet Miers, belongs to a church in Texas that holds to the inerrant truth of Scriptures. Their website links to a creationist museum that promotes the coexistence of humans and dinosaurs. The possibility that we might have a judge sitting on the nation's highest bench who believes such nonsense beggars belief.

The current issue (November-December) of Skeptical Inquirer is largely devoted to the creationism/ID assault on science. An assembly of SI articles on the subject can be found here.

Late breaking addition: Ms. Miers has withdrawn.

Wednesday, October 26, 2005

Attention to the mystery -- Part 2

posted by Chet at 5:51 PM UTC

In response to the Chuck Kramer video, Steve asks if there are any more like it. As a matter of fact, another filmmaker, Stu Siegal from the Hallmark Channel, is taking a walk with me tomorrow along The Path. He was here a year or so ago, and you can see the result here (mpg) or here (realplayer).

Ottewell's calendar

posted by Chet at 11:25 AM UTC


This is the time each year when I submit my order for Guy Ottewell's Astronomical Calendar. Anyone who watches the sky with care must have this extraordinary annual guide to all things astronomical. Scroll down his web page and you'll see in more detail what I think about the calendar. Guy has been putting out this large-format wonder for as long as I can remember. He has a genius for graphics.

Guy is an artist too, and his covers are always original paintings. This year's (2006) is a little different. He has rendered in color a traditional and mysterious Navajo star map drawn in 1908, and invites us, the readers, to puzzle out what constellations are represented by Monster-Slayer, Black God, Horned Rattler, Whirling Female, and all the rest.

Tuesday, October 25, 2005

Attention to the mystery

posted by Chet at 12:24 PM UTC

The writer Barry Lopez visited the college yesterday, worked with students (including my two young colleagues Bailey and Greg), and talked to an all college audience. He was received with warmth and appreciation.

This final passage from his essay The Naturalist, originally published in Orion, could stand as a manifesto for how I have tried to live my own life:

What being a naturalist has come to mean to me, sitting my mornings and evenings by the river, hearing the clack of herons through the creak of swallows over the screams of osprey under the purl of fox sparrows, so far removed from [Gilbert] White and [Charles} Darwin and [Aldo] Leopold and even [Rachel] Carson, is this: Pay attention to the mystery. Apprentice yourself to the best apprentices. Rediscover in nature your own biology. Write and speak with appreciation for all you have been gifted.


If you'd like to go on a walk with me along The Path, you can do so here, thanks to Chuck Kramer, lately of WGBH, who was kind enough several years ago to invite himself and his camera along.

Monday, October 24, 2005

Yuk, yipe, yow

posted by Chet at 11:49 AM UTC

Here's a verse by J. D. Whitney from the October issue of Poetry, one of eight little poems called collectively All My Relations:

COUSIN WHIRLIGIG:

You're already
there
      where
you all seem
to be going.


We all know the whirligigs, those pond skitterers, those little motor boats going in circles. Ready morsels for fish, you would think, silhouetted as they are against the sky. How do they survive?

Just one of the little mysteries illuminated by Thomas Eisner's new book (with Maria Eisner and Melody Siegler) Secret Weapons: Defenses of Insects, Spiders, Scorpions, and Other Many-Legged Creatures. Sixty-nine delectable short chapters on sixty-nine potentially delectable creatures by the author of that marvelous book, For Love Of Insects -- which I sincerely hope I have recommended here before.

When attacked, the whirligig beetle coats itself in a foul-tasing fluid. Any fish that takes a whirligig into its mouth will soon spit it out. Bass have a way of flushing their food by opening and closing mouth and gills to pump water through the mouth. The maximum time a bass will flush before giving up and expelling an unpalatable bug is one minute. Meanwhile, the ever-resourceful whirligig can keep excreting a steady stream of yuk for a minute-and-a-half -- and live to see another day. Intelligent design for the whirligig; bad news for the bass.

Sunday, October 23, 2005

Apocalypse now?

posted by Chet at 1:43 PM UTC


See this week's Musing.

Saturday, October 22, 2005

On Golden Pond

posted by Chet at 11:12 AM UTC

I suppose my generation of American youth was the last to be told that masturbation could make us blind. Now, having reached our golden years with more or less normal vision, we are told that Viagra can make us blind. They get you coming and going.

And speaking of golden years, I find myself increasingly helpless in the face of cybertechology. This website wouldn't exist without Tom's computer savvy. At the college, I avail myself of the IT staff for problems that ten years ago I could have figured out in a snap. These guys are smart, helpful, and unfailingly courteous, but their slightly raised eyebrows suggest impatience.

Ah, fellows, there was a time before you were born when I introduced the first academic computer programing to the college campus. We used punch cards and ran our programs on an off-campus IBM 1620. I toggled in programs on DEC PDP-8s. Then came teletype tape and borrowed time with a Boston bank. I taught the first computer course on campus, called "How Computers Work," later "Computer Logic and Design."

But, alas, my brain is no longer as nimble as all that. So what is that Help Desk number again? Be patient, lads -- and remember, too much time playing computer games can make you blind.

Friday, October 21, 2005

Talking bacteria

posted by Chet at 11:54 AM UTC


Consider the meadow of grazing organisms in the photograph above. These are bacteria, Pseudomonas aeruginosa, a human pathogen that is a particular problem in the lungs of cystic fibrosis patients. How big? Well, a thousand of the "meadows" shown in the photo would fit on the period at the end of this sentence.

Certainly, bacteria are not as sophisticated as cows or sheep, but don't sell them short. Not least among their talents is their ability to communicate with friends. Their "speech" is molecular. For example, when the density of emitted "quorum sensing" molecules reaches a certain density, whole sets of genes are activated within a bacterial population, including genes for infecting plants, animals and humans.

But many "speech" molecules are poorly water soluble, which limits the ability of bacteria to talk to one another in aqueous environments. "Speech" molecules can also be broken down and made unintelligible by rival bacteria. To keep their chat intact, P. aeruginosa wrap their messages in protective, water-transportable membranes.

Imagine, then, if you will, the bacteria in the photograph with little cartoon bubbles of speech over their "heads." "Are you here?" "Friend or enemy?" "Time for attack!" "Let's go."

This is why I read Science and Nature every week; there is no end of wonderful stuff to be learned about the world. The deciphering of P. aeruginosa speech is described in the September 15th issue of Nature, by Lauren Mashburn and Marvin Whiteley of the University of Oklahoma. Learning how bacteria talk among themselves -- coordinating their attacks, for example -- is an advantage if we want to beat them at their own game.

And while I'm at it, here is a stanza from a poem on one-celled creatures by the inimitable Pattiann Rogers in the September issue of POETRY:

Far too ancient for scripture, each
one bears in its one cell one text --
the first whit of alpha, the first
jot of bearing, beneath the riling
sun the first nourishing of self.

Thursday, October 20, 2005

What is science?

posted by Chet at 10:47 AM UTC

Meanwhile, down in Harrisburg, PA, they are still debating in court the definition of science, as if that will make the slightest difference as to how scientists ply their trade. The always entertaining intelligent design enthusiast Michael Behe admits to being comfortable with a definition of science so broad as to make astrology also a candidate for our public school science classrooms.

Here is my litmus test for science.

In the October 7 issue of Science, the weekly journal of the American Association for the Advancement of Science, Robin Allshire, of the prestigious Wellcome Trust Centre for Cell Biology at the University of Edinburgh, offers a retraction for a paper previously published in the journal, titled "Hairpin RNAs and retrotransponson LTRs effect RNAi and chromatin-based gene silencing." He admits that his laboratory and others have been unable to reproduce the results reported in the paper.

When we see the first peer-reviewed experimental data supporting intelligent design or astrology that is reproducible in other laboratories by skeptics and believers alike, then these hypotheses can make a legitimate claim to being sciences.

When we see the first published retraction, we will know that intelligent design or astrology has reached maturity as a science.

It's as simple as that.

Wednesday, October 19, 2005

The courage to be

posted by Chet at 5:46 PM UTC

In the current issue of The New York Review of Books, the ever-engaging biologist Richard Lewontin takes on the question: What drives the Christian Right's obsession with evolution?

It cannot be fidelity to scriptures, says Lewontin. Physics, astronomy and geology are no less in conflict with a literal interpretation of Genesis, yet there is no equivalent attempt to introduce creationism into the teaching of these subjects. Nor is right wing politics the driving force; Christian fundamentalists have been inconstant in their politics.

Lewontin writes: "What is at issue here is whether the experience of one's family, social, and working life, with its share of angst, pain, fatigue, and failure, can provide meaning in the absence of a belief in an ordained higher purpose. The continued appeal of a story of a divine [special] creation of human life is that it provides, for those for whom the ordinary experience of living does not, a seductive relief from what Eric Fromm called the Anxiety of Meaninglessness."

If memory serves me right, it was Paul Tillich, not Fromm, who coined the phrase "anxiety of meaninglessness," but I think Lewontin is right in his analysis. Tillich wrote: "The anxiety of meaninglessness is anxiety about the loss of ultimate concern, of a meaning which gives meaning to all meanings. This anxiety is aroused by the loss of a spiritual center, of an answer, however symbolic and indirect, to the question of the meaning of existence."

As an antidote to the anxiety of meaninglessness Tillich offered "the courage to be."

He wrote: "Everyone who lives creatively in meanings affirms himself as a participant in these meanings...The scientist loves both the truth he discovers and himself insofar as he discovers it...This is what one can call 'spiritual self-affirmation.' And if he has not discovered but only participates in the discovery, it is equally spiritual self-affirmation. Such an experience presupposes that the spiritual life is taken seriously."

Those of us who embrace the empirically real as the basis for our ultimate concern may in fact be more anxious than those who place their hopes and fears into the hands of a Supreme Being. But we relish the creative transformation of "the ordinary experience of living" into something fulfilling and hopeful. And we cherish in ourselves and in others, to the extent that we can find it, the "courage to be."

Healing words

posted by Chet at 11:28 AM UTC

When I retired from teaching after 40 years, Stonehill College was kind enough to honor me by establishing a series of annual literary lectures in my name. So far the college has welcomed national poet laureate Robert Pinsky, novelist Anne Michaels, and Nobel prize-winning poet Seamus Heaney.

This year the college's guest will be Barry Lopez, esteemed writer, conservationist, and champion of wild places. Among his many works of fiction and nonfiction he is perhaps best known for his bestselling Arctic Dreams, which won a National Book Award. He has said this of writing: "Writing is not something to fool around with; the course of history is changed by language...language has a power to heal and to elevate and to instill hope in the bleakest of circumstances" -- a reminder of particular importance to those of us who ply words in the raucus, anything goes, top-of-the-voice blogosphere.

His program is at 7 P.M. on Monday, October 24, in Alumni Hall on the Stonehill College campus in North Easton, MA. The public is welcome.

Tuesday, October 18, 2005

Ringside

posted by Tom at 6:14 PM UTC


Lonely Dione espied by Cassini.

Lord of the flies

posted by Chet at 11:21 AM UTC


I blogged this patch of mushrooms last year, Aminita muscaria, the Fly Agarics, growing under white pines. They reappear at this spot every October, as reliably as treat-or-treaters.

Mushrooms are the short-lived fruiting bodies of a fungus, as apples are the fruiting bodies of an apple tree. The organism that persists from year to year is called the mycelium, a web of branching fibers hidden in the earth, threads so fine as to be individually almost invisible, but cobwebby white when seen en masse.

The mycelium secretes digestive enzymes, which break down organic matter, then absorbs the products. Because the digestive reaction takes place outside the fungal cells, living plants also benefit from the released nutrients. The reaction generates carbon dioxide, also of use to plants.

And here they are again, on schedule, the apples of death, costumed for Halloween in pumpkin garb. We don't trust mushrooms. Something deep in our folk consciousness shudders at the sight. Is it that some of them are poisonous? One of my mushroom handbooks mentions a 13th-century wall-painting in an old chapel at Plaincourault, France, depicting the Tree of Life as a Fly Agaric, with Eve beside it clutching her tummy, plainly put out by her bite of forbidden fruit.

Or is it something deeper? Do they remind us of the fairy spirits of our forest-living European ancestors? Is this what Shakespeare's Prospero had in mind when he addressed the elves "whose pastime is to make midnight mushrooms"?

Monday, October 17, 2005

Faith-based reality vs. reality-based faith

posted by Chet at 12:59 PM UTC

As noted by Thomas Friedman in a recent New York Times column (October 14), a bipartisan committee of the National Academy of Sciences, the National Academy of Engineering, and the Institute of Medicine have released a report detailing America's poor showing worldwide in science and mathematics, and proposing ways to reverse our race to the bottom of the heap. The report was requested by Republican senator Lamar Alexander (TN) and Democratic senator Jeff Bingaman (NM).

Fewer American undergraduates study science and mathematics than in almost any other developed nation (about half as many as in China). American 12th-graders perform below 21 other countries in math and science testing. In 1999 only 41 percent of U.S. 8th-graders had a math teacher who had majored in mathematics at the undergraduate or graduate level or studied the subject for teacher certification -- a figure that was considerably lower than the international average of 71 percent. And so on. If the trend is not reversed, by mid-century this nation could be an economic backwater of Europe and Asia.

The National Academies make sensible and practical proposals on how to buttress teaching in math and science, and senators Alexander and Bingaman will introduce legislation based on the proposals. What the report does not address directly is the fact that America is being driven into the science education hole by a growing fundamentalist Christian political constituency with a profound antipathy to empirical science.

Sunday, October 16, 2005

Einstein's big idea

posted by Chet at 10:31 AM UTC

Yesterday I gave a talk at the Hingham, MA, Public Library sponsored by the WGBH Community Outreach Program, in association with last week's Nova program on Einstein's Big Idea. This week's Musing is a riff on that talk, the theme of which was the mysterious consonance between the universe and the human mind.

Saturday, October 15, 2005

In this unceasing rain...

posted by Chet at 5:27 PM UTC

...I rememember the season's last cardinal flower.

My field guide calls the cardinal flower "bright red." Those simple words are hardly adequate to describe the plant's brazen presence in the ditch.

Shall we call in the people who invent the names on paint chips? Stoplight red? Chili pepper red? Red Ridinghood red? No, none of these quite work.

Thoreau once referred to the cardinal flower's "red artillery." A nice image, but not what we are looking for. On another occasion he was reminded of the scarlet of sin. Ah, now we are getting close. Hester Prynne's scarlet letter.

Green is the color of making a living, harvesting energy from the sun. Green, for plants, is nine-to-five, nose-to-the-grindstone, earning one's keep.

Red is the color of reproduction -- something to attract the hummingbirds and moths, those necessary partners in cardinal flower sex. Cardinal flower red is the red of rouged cheeks, ruby lips, flashy cummerbunds, long-stemmed roses and valentines. And from the come-hither look of it, that last red-blossomed plant in the ditch is ready for some frisky fun.

Friday, October 14, 2005

On heresy and heretics

posted by Chet at 11:19 AM UTC

I used the adjective "Pelagian" in yesterday's post. Pelagius was a monk from the British Isles, perhaps an Irish Celt, who tangled with Augustine in the 5th century, and was condemned by the Church as a heretic. He taught that the world was not corrupted by Adam's sin, and that humans can live good lives by the ordinary powers given them by nature. "Concupiscence" loomed large in Augustine's theology, and subsequently in Christian doctrine. Pelagius -- bless him -- had a more positive view of human nature, and of nature itself -- sufficient grounds for condemnation by an institution that claimed to alone possess the keys to salvation.

I was educated at a time when heresies loomed large in Catholic apologetics. I recall a little Handbook of Heresies by M. L. Cozens, published, of course, by Sheed & Ward, and which I have just found a battered copy of in the college library. Here they are, all the ways of being wrong, starting with the Judaic heresy and moving on through Gnosticism, Montanism, Sabellianism, Arianism, Semi-Arianism, Apollinarianism, Nestorianism, Eutychianism, Monothelitism, Pelagianism, and so forth, to Protestantism and Modernism. Some of these heresies turned on fine points of theological debate; thus the need of the Church's infallible magisterium to keep one on the straight and narrow

Some folks claim that science is a secular religion. Well, in all of my years of science-watching, I don't recall hearing the word "heresy" applied to an unorthodox scientific theory. If science is a religion, then there is only one established doctrine: that nature's laws can be known ever more reliably by the application of human reason and reproducible empirical observation. We treasure our rebels -- Galileo, Darwin, Einstein, Wegener -- but don't warmly welcome to the fold those who arrive forearmed with handbooks of heresies. Science seeks a balance between dogmatic certitude and intellectual anarchy. My way of putting it is this: Science must be radically open to marginal change and marginally open to radical change. Sometimes dissent can be a healthy step forward.

Thursday, October 13, 2005

The beautiful externals

posted by Chet at 11:48 AM UTC

I wonder: Do students read Augustine's Confessions anymore? The book was assigned reading for me as a sophomore at the University of Notre Dame in 1956. Not an easy read, as I recall, but something of a revelation. Here was one of the great fathers of the Church, sainted no less, spilling the beans about his youth. Sex, drugs, and rock-and-roll, so to speak. A guy just like the rest of us, horny and ambitious. Then, the dramatic conversion. Lifted out of the world of concupiscence and dross matter into an eager anticipation of the Beatific Vision. Saved from what he called the "beautiful externals."

The book -- in my case, at least -- had the desired effect: a binge of inward-turning, otherworldly renunciation. To the curse of sexual lust Augustine added "a cupidity which takes delight in perceptions acquired through the senses...a vain inquisitiveness called knowledge and science." Beware, he cautioned, of "what is agreeable to look at, to hear, to smell, to taste, to touch." Even the beauty of the stars became for Augustine a distraction from the Divine.

I started down that road, but not so far that my steps were irreversible. I suppose the stars are what saved me, restored my good Pelagian regard for nature, brought me back to that down-to-earth thing which now seems most to be cherished: human curiosity, the desire to know. Not sacred knowledge, not the cabala, not the rites and mysteries of initiates, but the kind of reliable public knowledge that comes through -- yes -- sight, sound, smell, taste, touch. That "vain inquisitiveness" called science.

Wednesday, October 12, 2005

Beating malaria

posted by Chet at 11:39 AM UTC

Malaria kills more than a million people a year, most of them children under the age of 5 in sub-Saharan Africa. Hundreds of millions of people have the disease, in varying degrees of severity.

The agent of infection is a nasty little parasite named Plasmodium falciparum that requires two other species to complete its life cycle: the Anopheles mosquito, and the primate Homo sapiens.

That's us.

Plasmodium doesn't bear us any grudge. From the parasite's point of view, we are a necessary blob of meat in which to breed.

Here's how it works.

An infected female Anopheles mosquito bites a human and injects parasites into the victim's bloodstream. The parasites make their way to the liver and multiply. The teeming parasites explode from the liver cells back into the bloodstream, where they invade red blood cells and multiply again. They fill the cells to bursting, then invade more red blood cells. Again. And again. The malaria victim sustain bouts of fever with each cycle of cell infection.

If an uninfected female Anopheles mosquito bites an infected human, she sucks up parasites with her blood meal. These multiply in her stomach wall, then make their way to her salivary glands, ready for transfer to another human.

And so it goes, around and around -- human liver, human blood, mosquito stomach, mosquito salivary gland. Each stage of Plasmodium's life cycle involves a specialized form of the parasite. No other hosts will do but Homo sapiens and Anopheles. All of this can be given a plausible evolutionary explanation. If it's to be explained by "intelligent design," the designer must really have had it in for humans.

A team of scientists at Imperial College London now think they can break the cycle. They have added a jellyfish gene to the mosquito's genome that makes the testicles of male larvae glow fluorescent, allowing them to be mechanically separated from otherwise identical female larvae, sterilized, then released into the wild as adults. Release enough infertile males to mate with females and a natural population will collapse.

Now the story becomes political. Any attempt to release genetically-modified organisms into the wild is controversial. The promises and perils of genetic engineering test the wisdom of nature's only moral species, and the decisions are too important to be left to scientists alone. The best insurance that this new power will be used wisely is a citizenry solidly educated in science. Real science. The science of cause and effect.

Tuesday, October 11, 2005

A killer back from the dead

posted by Chet at 1:18 PM UTC

Only a week or so ago I was lamenting that few Americans were aware of the threat of avian flu. Now suddenly, the story is everywhere. No need to rehash here the potential catastrophe that has in recent days been splashed all over the media.

But here is another story, and an important one: Biologists have recreated the virus responsible for the 1918 flu pandemic that killed as many as 50 million people worldwide. Fragments of viral RNA were retrieved from a flu victim buried in Alaskan permafrost in 1918. The RNA was converted into DNA and sequenced. Overlapping sequences were pieced together to get the entire genome, and the viral DNA was synthesized in the lab. The synthesized DNA was injected into human kidney cells, which produced tens of viruses. These were isolated and used to infect mice. The mice all died within days of a virus that was indeed many times more virulent than the pathogens responsible for the pandemics of 1957 and 1968.

A century old flu virus has been recreated. Good or bad? Some say good. The team that synthesized the virus got permission from the Centers for Disease Control and the National Institute of Allergy and infectious Diseases, the relevant national overseers. Apparently, they consider the benefits outweigh the risks. As it turns out, the 1918 virus was derived wholly from a bird virus, and thus may help understand the current threat and perhaps hasten the development of effective vaccines. Others say bad. What has in fact been recreated is a virulent killer that might escape the laboratory by accident or malfeasance. The DNA sequence of the 1918 virus has been published, available to any terrorist organization that might muster the technical requirements to recreate the virus. Not quite the Jurassic Park scenario, but not far from it.

On being good

posted by Chet at 12:33 AM UTC

In the newspaper over the weekend, I read another powerful evangelical politician state that only a literal reading of the Bible -- God's revealed word -- stands between us and moral chaos, not unlike the creationist posters I quoted here last week.

I am reminded of the response of the 19th-century newspaper The Times of London when Darwin's theory was vigorously defended by Thomas Huxley against Bishop Wilberforce at the Oxford debate. The editors wrote: "If our humanity be merely the natural product of the modified faculties of the brutes, most earnest-minded men will be compelled to give up those motives by which they have attempted to live noble and virtuous lives, as founded on a mistake."

The Times, of course, was dead wrong to believe that only Bible-reading Christians might choose to lead noble and virtuous lives. It was Bible-reading Christians, after all, who initiated and sustained the African slave trade, the greatest moral abomination of the century. Darwin and Huxley were agnostic, yet both men found ample reasons to live virtuous lives, and both were firmly on the side of progressive social and political change.

It was progressive social and political change that the Times of London feared most. The mid-19th century was a time of social upheaval throughout the European continent. Old class structures were being dismantled, inherited privilege wrested away, the power of monarchies and churches challenged. In England, the established powers felt under siege. The new working class, crowded into factory towns, seethed with unrest. The Anglican Church, that great prop of crown and privilege, understood well enough that once the divine origin of the existing order was questioned the whole house of cards would come tumbling down.

Our new Biblical moralists are not the old guard establishment, but the increasingly numerous and powerful architects of an American theocracy, once again playing the moral-chaos card to further their political agenda.

Sunday, October 09, 2005

Hey, Ray

posted by Chet at 11:42 AM UTC

Are humans the endpoint of evolution? See this week's Musing.

Saturday, October 08, 2005

Animal minds

posted by Chet at 2:26 PM UTC

My hobbit-hole chipmunk has decided that it is easier to harvest pine cone seeds by dragging cones to the door than by carrying seeds home one by one. A glimpse into an animal mind.

I have a friend who is the son of a well-known primate researcher. He grew up with a bonobo, "like a brother." Don't tell S. that animals don't have minds.

His mother once said that "there is a huge capacity on the part of apes and probably all kinds of other animals that's being ignored. By ignoring it, humans are separating ourselves from the natural world we've evolved from."

Friday, October 07, 2005

One Nation, under God

posted by Chet at 11:41 AM UTC

In his book Tower of Babel: The Evidence against the New Creationism, the scholar Robert Pennock describes his visit to the Institute for Creation Research's Museum of Creation and Earth History. The exhibit attacks "Evolutionism," and concludes with two panels that depicts the fruits of two world views.

The fruits of creationism:

True Christology, True Evangelism, True Missions, True Fellowship, True Gospel, True Faith, True Morality, True Hope, True Americanism, True Government, True Family Life, True Education, True History, True Science.


Buy into evolutionism and you get:

Communism, Nazism, Imperialism, Monopolism, Humanism, Atheism, Scientism, Slavery, Racism, Pantheism, Behaviorism, Materialism, Promiscuity, Pornography, Genocide, Drug Culture, Abortion, Euthanasia, Chauvinism, Infanticide, Homosexuality, Child Abuse, Bestiality.


Oh dear. Take your pick.

Thursday, October 06, 2005

Having fun

posted by Chet at 11:12 AM UTC

It is widely held by biologists that the first self-replicating molecules, RNA perhaps, appeared on Earth about 4 billion years ago. How did this happen? Scientists don't know, but they are working on it. This is one of the unsolved problems that IDers adduce as evidence for intelligent design.

There are three ways to approach the problem without invoking miracles. One way is to synthesize RNA in the laboratory under conditions that might have existed on the early Earth. So far, this hasn't happened. Another way is to simulate with computers the molecular chemistry that might have given rise to RNA. A third way is to invent mechanical or electromechanical "organisms" that self-replicate -- and that might conceivably have got themselves together on their own from components with sufficient potential.

In the September 29 issue of Nature, scientists from the Center for Bits and Atoms at the MIT Media Laboratory describe a 5-unit-long electromechanical "molecule" that can assemble copies of itself from randomly distributed parts floating on an air table. Self-correction is built into the system.

You can watch a seed "molecule" reproduce itself here (and in the last frames get a sense of scale).

What does this prove? Nothing really, except that curiosity, inventiveness and perseverance can be both instructive and fun.

Wednesday, October 05, 2005

On language

posted by Chet at 10:56 AM UTC

In my meeting yesterday with Bailey and Greg, we shared their readings of poems and prose of Charles Goodrich. The language of the poet relies on the way words are steeped in cultural associations. Each word comes tripping with habiliments and garlands of metaphor. Which is precisely why scientists sometimes find it best to start from scratch, even to the point of inventing fresh vocabularies. Little x, y and z marching naked through the world.

In the Introduction to his Wildflower Guide, Roger Tory Peterson lists sixty ways that a botanist can say that a plant is not smooth: aculeate, aculeolate, asperous, bristly, bullate, canescent, chaffy, ciliate, ciliolate, coriaceous, corrugated, downy, echinate, floccose, flocculent, glandular, glanduliferous, glumaceous, glutinous, hairy, hispid, hispidulous, and so on. The dictionary defines both "aculeate" and "echinate" as prickly, and one might reasonably ask why a good English word like prickly won't serve the purpose. The botanist, I am sure, has an answer, involving subtle shades of meaning. The poet, though, knows prickly works in ways aculeate would never work in a poem -- puncturing, piercing, impelling, impregnating, standing erect, pointing heavenward.

Tuesday, October 04, 2005

Paradisio

posted by Chet at 12:21 PM UTC


In the final book of The Divine Comedy, Dante looks down on the Empyrean Sphere, the sphere of stars that encloses the Earth:

I saw light in the shape of a river
Flashing golden between two banks
Tinted in colors of marvelous spring.
Out of the stream came living sparks
Which settled on the flowers on every side
Like rubies ringed with gold. . .


Click your way to Paradise. Be sure to click on the pics to enlarge and view the animation.

Monday, October 03, 2005

Is the bird flu virus intelligently designed?

posted by Chet at 10:13 AM UTC

Anyone who keeps up with the scientific literature (or gets news from a source like the BBC) knows that a health threat is brewing in Asia that is potentially far more dangerous than the Indonesian tsunami or Hurricane Katrina. Conditions are ripe for a global pandemic of influenza, originating with the bird flu virus H5N1. Deaths could be in the tens of millions.

The Centers for Disease Control (CDC), the World Health Organization (WHO), and Asian scientists and health agencies are on the front line, monitoring the spread of the virus and its potential for human infection and transmission.

Meanwhile, in America, according to polls, more than half of our citizens believe creationism should be taught in our science classrooms as an alternative to evolution (82 percent of Republicans, 52 percent of Democrats).

But I wonder how Americans would respond if the question were posed this way: Who would you rather have attending to bird flu in Asia, the scientists of the CDC, WHO and other agencies who are universally trained in and exclusively embrace evolutionary biology, or creation scientists and intelligent design advocates?

Sunday, October 02, 2005

Intelligent design

posted by Chet at 3:41 PM UTC

These are the two front epigraphs for my book Skeptics and True Believers:

To invoke God as a blanket explanation of the unexplained is to make God the friend of ignorance. If God is to be found, it must surely be through what we discover about the world, not what we fail to discover.

     -- Paul Davies, physicist

When it's over, I want to say: all my life
I was a bride married to amazement.
I was the bridegroom, taking the world into my arms.


     -- Mary Oliver, poet

See this week's Musing.

Saturday, October 01, 2005

Prie-dieu

posted by Chet at 11:01 AM UTC

You do not have to walk on your knees
for a hundred miles through the desert, repenting.
You only have to let the soft animal of your body
          love what it loves.

A few lines from Mary Oliver's poem Wild Geese. I thought about them this morning as I knelt with my camera waiting for a chipmunk to reveal his soft nose at the hobbity door of its den in the roots of a white pine -- its front yard littered with husks, a kitchen midden of nibbled acorns and cones. But of course I was unsuccessful. My five-year-old digital camera has the habit of taking a deep breath before allowing a picture. By the time the shutter snapped and the flash flashed, the chipmunk had retreated. Still, it was a worthwhile wait, like those interminable Latin prayers we knelt through as children before the tinkle of bells announced the moment of miracle.