Monday, November 30, 2009

November paradise

A few lines from a poem, "Ode to Entropy", by John Updike:
Death exists nowhere in nature, not
in the minds of birds or the consciousness of flowers,
not even in the numb brain of the wildebeest calf
gone under to the grinning crocodile, nowhere
in the mesh of woods or the tons of the sea, only
in our forebodings...
As far as we know, no other creature, animal or plant, has an awareness of self-mortality. Only in human consciousness is death anticipated, as a dark foreboding, or promise of release. So much is carried along in the baggage of anticipation. Courage. Fear. Virtue. Sin.

In the R.C. theology of my youth only humans had immortal souls. In the Heaven of our imaginations there were no animals or plants. Or, for that matter, no Sun, Moon, stars or weather. No dawns or dusks. No seasons. As a kid, I pictured Heaven as a hospital sort of place, all stainless steel and pale green gowns and white paint and angels with push-carts and mops going around swabbing up all the invisible microbes that managed to slip in on our resurrected feet, and some little device going ping-ping-ping over the intercom counting off the seconds of eternity.

Not a terribly attractive prospect.

The funny thing is, nothing more attractive has come along to take its place; that is to say, as hard as I try I cannot conjure up any notion of immortality that meets the loosest criterion of plausibility.

But a morning last week came close. It had rained all night, stopping just before I set out for the college at sunrise. The leaves that carpeted the floor of the woods glistened wet. A summery golden light filtered through the mist -- this in late November -- transmuting every surface with a Midas touch. Soft. And silent, except for the tap-tap-tap of a downy woodpecker. And for about a microsecond I might have imagined...

No, never mind. Ray Kurzweil, age 61, wants to live long enough to live forever; that is, to hang in until science solves the riddle of aging and gives us immortality on Earth, assuming, of course, that we don't get knocked down in the street by a bus or blow ourselves up in some intrahuman squabble. Not me. I'll settle a few more of those microseconds when the here and now seems more desirable than the aseptic, creatureless hospital-in-the-sky or the long, drawn-out forebodings of a Kurzweilian future.

Sunday, November 29, 2009

What is religious naturalism?

My skeptical son-in-law was razzing me on Thanksgiving for my willingness to call myself religious, as in "religious naturalist." For him, the very word reeks of the supernatural. Religous naturalism, he suggested, is an oxymoron.

How to explain?

Let's start with an old metaphor I have used many times before: Knowledge as an island in a sea of mystery. Religion is whatever transpires as we stand at the shore looking out to sea -- from Aztec human sacrifice to Rachel Carson's sense of wonder, from Appalachian snake handlers to Mary Oliver's poetry, from Hindus to UUs.

Naturalists do not think of the island and the sea as different species of existence, natural and supernatural. Rather, it is all one existence, which for convenience we call natural, of which we have some small but ever-growing measure of reliable, communal knowledge (the island). Naturalists are committed to pushing back the tide of mystery, increasing the store of reliable knowledge, expanding the island, and coincidentally increasing the shoreline where we encounter mystery. Naturalists are aware of our ignorance, and try to avoid projecting the known onto the unknown, as, for example, ascribing to the mystery human qualities such as personhood, love, or justice.

"Religious" naturalists are creatures of the shoreline. We forgo the safe inner uplands of the island for the risk of confronting the unknown. Attentive and curious, we wait for the tingle in the spine. We relish knowing, but live in a state of gape-jawed astonishment. We know that science is a necessary but not sufficient basis for a life. The poetry of praise is never far from our lips.

Saturday, November 28, 2009

The inner savage

In The Creation, E. O. Wilson has a chapter called "How To Raise a Naturalist." It's full of good advice: buy the child a microscope; take the child to museums, zoos, aquaria; provide ample outdoor play time; and so on. All good advice, but I would guess pretty much irrelevant. Forty years ago when I did my one-mile walk to college through woods and meadows, along streams and pond, I never failed to encounter kids, mostly boys, building "forts," fishing, rafting, whacking each other with clubs made of goldenrod galls, and otherwise getting grass-stained and dirty. Today I meet no one along the Path except walking or jogging adults with ear buds. The kids, I would guess, are at home sitting in front of a computer. Nothing wrong with computers, but don't expect naturalists. "The child is a savage, "in the best meaning of that word," writes Wilson. "He needs to thrill to the excitement of personal discovery, to mess around a lot and learn as much as possible on his own."

I mentioned here once before the time I attended a gathering of nature writers on Martha's Vineyard, which included Ed Wilson, as always his soft-spoken, gentlemanly self. On the first morning, we took time to introduce ourselves and say a bit about how we came to be interested in the natural world. I was struck by how often the experience of a drainage ditch gave direction to our lives. I wrote later: "We were mostly children of the suburbs. More often than not it was while mucking about in a ditch that we discovered what would become the passion of our lives. Ditch water, in dribble or flood, is the stuff of creaturedom, the great animator that turns cracked suburban mud into Darwin's tangled bank. Loosestrifes soak their feet in it. Knotweeds slurp it up. Striders stride and whirligigs whirl on its slovenly surface. A seasonal zodiac of frogs, newts, salamanders, mudpuppies, crayfish, turtles and snakes. Even a trickle of ditch water is an invitation to play -- dams, canals, bridges, boats -- squishing barefoot in the mud among the cattails, shattering the gothic webs of argiope spiders. That was the story for so many of us: ankle-deep in ditches, struck unconsciously and unalterably with the prodigiousness of life, a burry, buggy, algae-slicked introduction to nature's inexhaustible capacity to surprise."

When we have paved over the woods and fields, when chemically-addicted suburban lawns stretch in unbroken continuity from sea to sea, when ATVs and snowmobiles have invaded the last vestiges of wildness, there will still be ditches. Down at the back of the subdivision, at the side of the road, behind the mall. Places where a curious, outdoorsy kid might discover her inner savage -- in the best messing-about, budding-naturalist sense of that word.

Friday, November 27, 2009

Galileo's finger -- Part 2

On Wednesday I reflected on the unresolved issues at work in the Galileo affair. I believe that Galileo himself, in a way prescient for his time, understood what was at stake.

Let's be clear. It's not just about whether religion and science are "non-overlapping magisteria" (to use Stephen Jay Gould's phrase). That depends on how one defines religion.

Overwhelmingly, however, throughout the world, religion invokes revelation and miracles, two things profoundly at odds with science. Not with the content of science; one can believe, say, in evolution by natural selection and accept on faith the interventions of a supernatural agency. Rather, we are talking about two ways of knowing that are not only mutually exclusive, but contradictory in spirit.

Why contradictory? The astonishing success of science came only with the exclusion of the supernatural and the miraculous as categories of knowing. After centuries of the exacting scrutiny of nature, scientists have not encountered a single reliably-attested event that requires a supernatural explanation. On the contrary, countless events that were previously thought to have supernatural explanations have been shown to have natural causes. As for "truths of revelation" -- well, the fact that there are as many revealed truths as there are religions suggests the fragility of that concept.

The essential tension is not between two sets of truths, but between two ways of knowing -- two worldviews, if you will. One can live with both at once, I suppose, since many do. But not, I would guess, without a considerable degree of cognitive dissonance.

This tension was present in an incipient way in the Galileo affair and remains unresolved in the Church today -- and perhaps to some degree in all of us.

Thursday, November 26, 2009

Giving thanks


From fragments of the molecules of life, Anne has contrived a Thanksgiving blessing (click to enlarge, and again if you wish). Thanks to all of the hundreds of people who visit here each day, and especially to those of you who have made yourselves comfortable on the porch. Thanks for your wisdom, your mutual respect, and for indulging my foibles with such kindly forbearance.

Wednesday, November 25, 2009

Yet it moves...

So they found Galileo's other fingers. The thumb and index finger of his right hand, which have been missing for a century. Now they rejoin the middle finger, which has resided at the Istituto e Museo di Storia della Scienza in Florence. I saw it there in 1969, a shriveled stick of bone and mummified skin. Pointing to the heavens. Or was it flipping a bird to his enemies?

On June 22nd, 1633, Galileo Galilei was condemned by a tribunal of the Roman Catholic Church for teaching that the Earth revolves about the sun, rather than the other way round. On his knees before the assembled cardinals, the seventy-year-old man recanted his belief in the Earth's motion and renounced his life work. So doing, he escaped torture or death by burning at the stake, and won instead the lighter sentence of house arrest in Florence. Legend has it that after reciting the official recantation he whispered under his breath, "Eppur si muove", "Yet it moves."

Whether Galileo actually whispered the legendary words hardy matters; he surely thought them. He returned to Florence, frail and blind, and continued his experiments in physics.

And the Earth went on revolving about the sun.

Here is a painting of the trial, Joseph-Nicolas Robert-Fleury's Galileo before the Holy Office,, 1847. Click to enlarge.


On October 31, 1992, Pope John Paul II formally proclaimed that the Church erred in condemning Galileo. The condemnation resulted from a "tragic mutual incomprehension," said the Pope, and became a symbol of the Church's "supposed rejection of scientific progress."

Certainly, the condemnation of Galileo involved misunderstandings on both sides, but the phrase "mutual incomprehension" is not quite accurate. Galileo, at least, had a clear comprehension of the issue: In turning its back on the new science the Church risked undermining its moral and intellectual authority.

The Church's rejection of scientific progress was more than "supposed"; it was, and remains, very real. In particular, official Roman Catholic theology remains wedded to a dualistic and miracle-ridden philosophy that has long since been demonstrated to be superfluous.

The photograph that accompanied media stories about the church's admission of error in the condemnation of Galileo showed John Paul II dressed in Renaissance garb sitting on a Renaissance throne in a Renaissance palace, surrounded by other men (no women) also dressed in Renaissance clothes -- very reminiscent of the painting above. All that was missing was the seventy-year-old man on his knees on the marble floor. The photograph was symbolic: In spite of the Pope's cautious and carefully-worded proclamation to the contrary, orthodox theology and science remain essentially at odds.

I have scoured the internet for that symbolic 1992 photograph, including the Vatican's own photo archive, unsuccessfully. Can anyone help?

Tuesday, November 24, 2009

Musing in retirement


I'm often asked if I miss teaching, which after more than forty years in the classroom is a reasonable question. The answer, generally, is no. Now that the pension checks appear in the bank each month, I'm happy to spend my time learning rather than teaching. The next question, I suppose, is why learning? Why bother stuffing more stuff into the head when...when it's all going to evaporate soon? Well, because I can't think of anything I'd rather be doing.

But back to teaching: Do I miss it? Only occasionally. Like yesterday morning when the image above was the APOD (Astronomy Picture of the Day): a view of Earth from the third flyby of the European Rosetta spacecraft on its ten-year journey to a rendezvous with Comet Churyumov-Gerasimenko in 2014.

A breathtaking picture. And, as they say, a teachable moment.

I'd love to project this image onto a huge screen in a darkened classroom, and then spend an hour talking about it. Not lecturing. Just asking questions.

For example, the APOD text says we are looking at "a bright crescent phase [of the Earth] featuring the South Pole to the passing rocket ship." Presumably they mean the white mass at the bottom center of the crescent is Antarctica. Can that be right?

Time to get out the 16-inch globe. Where is the Sun? A spotlight will serve. Now let's reproduce the crescent. The flyby was in mid-November; what was the orientation of the Earth relative to the Sun? Can we find the image's time of day on the ESA (European Space Agency) website? Let's sort out exactly what we are looking at.


Here's a closer look at the crescent (click to enlarge the pics). Notice the illuminated cloud tops in the shadow at bottom right. How high are they? Can we work it out? Sure. All we need to know is the diameter of the Earth. A few measurements off the screen and a big sketch on the blackboard will do the trick. This is how Galileo estimated the height of mountains on the Moon.

Etc. Etc.

Some years ago, Eric Hirsch published a A First Dictionary of Cultural Literacy: What Our Children Need to Know, a compendium of core knowledge that he believes kids should acquire by the time they enter junior high school. The chapters on science list 442 terms, from acid to x-ray. It's a good list, but, as Hirsch would surely be the first to acknowledge, a vocabulary is not a sufficient basis for scientific literacy. What is required is a gut feeling for how the world works and our place in it. And a sense of wonder.

That's what I miss about teaching. Give me an image of the crescent Earth looming -- breathtakingly -- in a darkened classroom and I'll do my very best to send a student's imagination hurtling through space into a universe that is deep and vast beyond our present knowing. Once you've caught the virus of wanting to know, the 442 vocabulary terms will come along in their own good time.

Monday, November 23, 2009

The plot thickens

President Obama seems to be the focus of a disproportionate number of conspiracy theories: he was born in Africa, he was involved in domestic terrorist bombings during his university years at Columbia, Bill Ayers wrote Dreams of My Father, and so on. Why? Why do people believe this nonsense, or the hundreds of other "urban myths" that make their way through the Internet?

As Francis Bacon put it four centuries ago: "What a man would like to be true, he preferentially believes."

Several years ago, Michael Shermer, who writes the Skeptic column for Scientific American magazine, published a book called Why People Believe Weird Things. He lists fallacies common to most conspiracy theories, belief in the paranormal, and assorted superstitions, including: 1) anecdotes are accepted as evidence; 2) coincidence is mistaken for causality; 3) heresy is assumed to imply correctness ("They laughed at Copernicus, too."); and 4) the unexplained is assumed to be conventionally unexplainable.

Science, too, is not immune to these fallacies, which is why organized doubt is built into the process. Scientific method is a highly evolved b-s detector that relies on double-blind experiments, quantitative observations, reproducibility, and rigorous citation of all other relevant work, pro or con. In science, it is as important to show something is wrong -- even a favored theory -- as to show it is right.

Is the scientific b-s detector perfect? Of course not. But it's the best tool the human race has yet evolved for choosing between various weird theories. What could be more weird than the big bang, say, or the four-letter DNA code of all life?

Of course, none of the above is relevant to conspiracy theorists. They tailor evidence to belief, rather than the other way around.

Sunday, November 22, 2009

OK, let's put two and two together...

The Mayan calendar predicts the end of the world on December 21, 2012. I mean, it must be true; there are hundreds of web sites asserting imminent apocalypse. And just wait till you see the forthcoming movie. If you are not getting ready for doomsday, you are missing the boat -- er, ark. At the very least, don't bother doing your Christmas shopping in 2012.

And then there's the Large Hadron Collider, warming up -- or I should say, "cooling down" -- near Geneva. Once it gets up to speed, which could conceivably take another three years, it's going to create microscopic black holes that will suck the Earth into oblivion. I mean, it must be true; I read it on the internet.

Put two and two together. On December 21, 2012, we all go down the cosmic tube.

But wait, maybe not all!

Doomsday is deeply ingrained in human psychology. Stories of apocalypse have been stock in trade for religious prophets since time immemorial, and, lately, for writers of science fiction. I wrote a novel about the end-of-the-world that was expected in the year 1000 A.D. In virtually all doomsday stories a chosen few survive to become the germ for a new creation.

When the biblical deluge subsided, Noah's sons and their wives repopulated an emptied world. In Norse mythology, Yggdrasil, the world-tree, survived apocalypse to bear Lif and Lifthrasir, the parents of a new human race. Christians look forward to a New Jerusalem that will rise from the ashes of the present world's destruction. In the film 2012, apparently a few plucky souls ride out the tsunamis that engulf the planet. As for my novel -- well, you'll have to read it to find out.

The stories are endless, the theme universal. So who will escape the LHC's world-gobbling black hole? And how can we ensure that the survivors include we happy few on the porch?

Meanwhile, as we ponder Armageddon, the world goes on, the planets whirl in their ancient tracks, the galaxies spin, and the Sun rises each day in a blaze of goodness and life -- this life, so delicate and precarious and fine.

The internet notwithstanding.

Saturday, November 21, 2009

Many dreams have been brought to your doorstep...


Yesterday we followed Leonardo da Vinci to his final abode at Amboise in France, in the shadow of the king's palace. Before we leave him there, let's ponder for a moment the thing he was perhaps most famous for: the Mona Lisa's smile.

No kidding. A zillion words have been written about Leonardo, and I would guess that the smile tops the chart for volume of interest. Even at age fourteen, I laid abed in a dreamy reverie listening to Nat King Cole croon her praises:
Mona Lisa Mona Lisa, men have named you
You're so like the lady with the mystic smile
Is it only 'cause you're lonely, they have blamed you
For that Mona Lisa strangeness in your smile?
That was before I ever saw a reproduction of the painting, and long before I stood in the Louvre with the original.
Do you smile to tempt a lover, Mona Lisa?
Or is this your way to hide a broken heart?
Many dreams have been brought to your doorstep
They just lie there and they die there
Lyrics like that would be considered silly by kids today, but to a hopelessly romantic teenager in 1950 Nat's sexy voice churned up the promise of bliss in the presence of the eternal feminine. Of course, at that age, I wouldn't have known a "mystic smile" from a come-hither or a sneer.

The person who turned on the spigot of words about the enigmatic expression was Sigmund Freud, in his Leonardo da Vinci and a Memory of His Childhood, in which he provided a psychoanalysis of the artist, focusing, as you might expect, on the child's oral fixation on his mother. Freud guessed that Leonardo rediscovered his mother's smile in the person of Mona Lisa del Giocondo, a Florentine noblewoman whose portrait he was commissioned to paint, and employed the same feature on every figure, female and male, that he subsequently painted.

Since Freud, the Mona Lisa's smile has inspired a cascade of psychological and even physiological interpretation (look at Mona Lisa with your left-hand peripheral vision).

Contradiction seems to be the key. The smile has been described (by various scholars, all male) as "tenderness and coquetry, modesty and secret sensuous joy," "the charm of deceit, the kindness that conceals a cruel purpose," and "good and wicked, cruel and compassionate, graceful and feline." Freud himself professes to find in the beautiful Florentine's expression "the most perfect profile of women; the contrast between reserve and seduction, and between the most devoted tenderness and a sensuality that is ruthlessly demanding -- consuming men as if they were alien beings." Yipe!

None of this was apparent to me at age fourteen. Women were then deeply mysterious, but my image of them was altogether a product of my own fervid adolescent imagination. It wasn't until mid-life -- the early fifties, say -- that my fantasies had been finally peeled away to be replaced by utter bafflement. Perhaps significantly, this was the same age at which Leonardo painted the lady Giocondo, and the same age at which Freud wrote his Leonardo essay. That cryptic smile expresses the realization that comes to men at a certain age that they haven't a clue what makes women tick. For Leonardo, who was perhaps bisexual, the smile swung both ways, from female madonnas to beautiful male youths.

No doubt the women here on the Science Musings porch will have their own interpretation of the Giocondo smile, and they will certainly be wiser than me. After a lifetime of preoccupation with women, I prefer to look at the Florentine lady out of the left-hand corner of my eye, which for various reasons presumably involving "different cells in the retina transmit[ing] different categories of information or 'channels' to the brain" simplifies the "mystic" expression to one of benign condescension. Condescension I can live with; the inscrutable contradiction of the feminine is another thing altogether.
Are you warm, are you real, Mona Lisa?
Or just a cold and lonely, lovely work of art?

Friday, November 20, 2009

To look and to know

Screws, rivets, ball bearings, pins, axles, couplings, belts, chains, gears, flywheels, levers, rods, ratchets, brakes, pipes, pistons, valves, springs, cranks, cams, pulleys.

I have just spent an afternoon perusing again Leonardo da Vinci's Notebooks, or facsimiles thereof. Anyone with an interest in engineering cannot turn these pages without pleasure. What an explosion of ingenuity! A mind racing pell-mell through an encyclopedia of mechanical contrivance, moving at such frenetic speed that application gets left in the lurch. Everything is conceived; nothing is built.

Anatomy. Hydraulics. Optics. Architecture. Aeronautics.

Paralyzed by genius. An unquiet mind. A mind so teeming with possibilities that nothing becomes possible. At the end of his life the catalog of his accomplished works is slim indeed.

A mind bewildered by contradictions. For every delicate wildflower among his drawings there are sketches of violent storms, explosions, and turbulence. For every beatific madonna and child there are men and animals locked in mortal combat. He bought birds from cages in the market so that he might free them, and then went home and drew horrible weapons of war -- spinning scythes surrounded by dismembered bodies, bombards raining fire, and shells exploding in star-bursts of shrapnel.

Freud's psychological essay on Leonardo is one of the most interesting things the Viennese psychiatrist ever wrote, but I never thought it explained very much. Leonardo's head was bursting with so many roiling, endlessly-fragmenting, colliding ideas that I doubt if the quintessential "Renaissance man" understood himself.

In 1516, at age 64, he was invited (as a trophy of war?) to France by the French king Francis I, who had recaptured Milan, and who liked and admired Leonardo. He was given the use of a grand house, the Chateau du Clos-Luce, a short walk away from the king's own palace at Amboise in the valley of the Loire (I have labeled the chateaux on the Google Earth image below). Here Leonardo lived out the final three years of his life in the company of his young student and friend, Count Francesco Melzi.

I like to imagine him there, bundled up in a thick robe by a roaring fire, locked in reverie. His body is weakened by the illness he had contracted in Rome, but his mind is still alert. The flames dance, his eyes roam the flickering shadows. He is overwhelmed by melancholy, wondering at how little he has to show for so long a life. Only three of his paintings accompanied him to France, including the Mona Lisa (of which more tomorrow). Of course, there is the vast trove of drawings, the record of a lifetime of insatiable curiosity, which will devolve upon Melzi at Leonardo's death, the majority of which will subsequently disappear.

But enough remain to confirm his genius. What was his contribution? A few simple but important truths. Looking is the basis for knowing. Behind nature's apparent turbulence there are fixed mechanical laws. The anticipation of nature is a fraud.

Thursday, November 19, 2009

The mysterious corridors of the mind

I said I would not write about Paul Dirac until my review of his new biography appeared in the Globe and Mail. The review has now long since appeared. So let me touch on a subject not mentioned there: age and theoretical physics.

Dirac made most of his epoch-making contributions to physics while still in his twenties. At thirty-one, he was the youngest theoretician ever to win the Nobel Prize for physics. At thirty-three, he wondered if his career was over.

It has long been an axiom of theoretical physics and mathematics that if you haven't made your mark by thirty, you might as well fold your tent and go away. There are exceptions, of course, but in general the exceptions seem to prove the rule. Abstract thought is a young person's game.

In physics and mathematics, there is a necessary period of coming up to speed, absorbing what is already known and mastering the current theoretical tools. This is often accomplished by the early twenties. The mark of a truly great scientist is the ability to identify a fundamental research problem that is waiting to be cracked. Then comes a burst of creative activity that might exhaust itself sooner than the theoretician might like.

Dirac lived on into his eighties, revered like Einstein but frustrated by his inability to repeat his youthful triumphs. When, in the last months of his life, he was invited to give a talk at the University of Florida, he responded: "No! I have nothing to talk about. My life has been a failure." This from a man who was universally recognized as one of the great geniuses of the century -- but prone by his nature to disillusion.

Wednesday, November 18, 2009

Climbing out of darkness

Earlier this year (July 16-19) I posted a series of comments on Karen Armstrong's newest book, The Case for God: The Real Meaning of Religion. I had many good things to say about the book, and a few quibbles. In particular, I took issue with her thesis that prior to the Scientific Revolution and Enlightenment people understood God mythically and metaphorically, and only subsequently has God been understood as an objective being. It is this falsely objectified modern God who is the target of New Atheists like Richard Dawkins, says Armstrong.

I think it far more likely that the great majority of people at all times and in all places understood their divinities objectively. In fact, I made the case that by calling the supernatural into question the Scientific Revolution laid the groundwork for exactly the sort of apophatic religion Armstrong espouses: mythos vs. logos, feeling vs. belief, practice vs. discourse, love vs. doctrine.

I wrote:
[S]cience cannot tell us what sort of life to build. Logos alone cannot give meaning to a life. For that, as Armstrong suggests, we need a mythos, a program of action, a way of acting out our relationship to what we do not understand. Humans by nature seem compelled to ask questions that science cannot answer: Who am I? Why am I here? What is the source of the Mystery I intuitively feel in interaction with the world? This, in Armstrong's account, is the "real meaning" of religion.

It is no accident that religious feeling has given us some of the greatest art -- literature, architecture, painting, sculpture, music, dance -- that the world has known. Art is to mythos what science is to logos. The two are not opposed, as Armstrong sometimes seems to suggest, but complementary. In science we built a solid platform to approach the Mystery, ever higher, ever closer; in art we leap into the unknown.
This past weekend I read Armstrong's 2004 memoir The Spiral Staircase: My Climb Out of Darkness, an account of her life from the time she left the convent at age 24 to the flowering of her career as a writer on religious subjects. The book is an honest and moving account of her struggles with what she and her psychiatrists assumed to be debilitating neuroses. It was only when she was correctly diagnosed as an epileptic and given proper pharmaceutical treatment that she began to function fully and successfully in the world. That is to say, it is only because she lives in the post-Enlightenment world of scientific medicine that she was able to find the stability and clarity in her life that enabled her to become such a forceful and valued advocate for apophatic religion.

One wonders if in some earlier time she might have been subjected to exorcisms to rid her of the devils that -- according to her -- no one took literally.

**********************

On another note, let me enthusiastically recommend the award-winning 2007 documentary Manufactured Landscapes, based on the work of the renowned photographer Edward Burtynsky, shot mostly in China. I guarantee it will change forever the way you think about your "stuff," where it came from and where it's going. Mind-blowing, depressing -- and breathtakingly artful.

And then, the next evening, to restore your balance, watch again the documentary I recommended once before, Philip Groning's Into Great Silence, recording life in the Grand Chartreuse, a thousand-year-old Carthusian monastery in the French Alps -- mostly silent and exquisitely beautiful.

Tuesday, November 17, 2009

The wind in the willows


The image here is from a news story in the 30 October issue of Science": "DOE Gives $151 Million to 'Out-of-Box' Research." The U. S. Department of Energy has awarded grants to 37 companies, universities and national labs that are pursuing cutting-edge energy technologies, including funding for the novel wind turbine design illustrated here. This is an artist's reconstruction of what the turbines might look like on an unidentified coastline, presumably chosen from a stock photo archive.

As it turns out, I recognize this bit of coast. It is at the western end of the Dingle Peninsula in Ireland, just over the hill from my summer cottage -- one of the most unspoiled land-and-seascapes in Ireland, and the setting for the films "Ryan's Daughter" and "Far and Away."

Over the years I have been involved in two efforts to preserve the visual integrity of this stretch of shoreline, once to prevent the Irish telephone company from stringing wires on poles along the coast road, and once to stop the building of an interpretive center celebrating the Irish-language culture of the Great Blasket Island (just off the coast to the left of the photograph).

The telephone wires were buried. The interpretative center got built, in an environmentally sensitive way, and a fine thing it is too. I was deeply moved by the human story on my first visit.

Ireland is aggressively pursuing wind power. I have written here before of my ambiguous feelings about the sleekly beautiful turbines, turning majestically in formerly wild landscapes -- torn between my enthusiasm for alternate energy sources and my dismay at the loss of wildness.

I think it fair to say that the particular scene presented in the above illustration would never be allowed to happen, not in this iconic place. But not so far away new turbines sprout up every day. In New England, the battle rages about building a massive wind farm in the waters off Cape Cod, between the Cape and the islands of Martha's Vineyard and Nantucket. Alternate energy sources are inevitably small scale and widely distributed. Sooner or later each of us will have to decide how we feel about having the sources of our power in our own backyards.

Monday, November 16, 2009

Seeing

I was browsing my Collected Poems of Wallace Stevens, looking for a line I sorta remembered, when I came upon this: "Description is revelation."

It is a line I used in Honey From Stone. "Description is revelation," I wrote, quoting (I thought) the Irish poet Michael McLaverty (as quoted by Seamus Heaney).

Actually, I wrote "Description is revelation. Seeing is praise."

So McLaverty, apparently, was quoting Stevens. Or was he?

A note on the internet suggested that McLaverty was quoting Gerard Manley Hopkins. I checked a concordance of Hopkins' poetry yesterday, and found no incidence of "description" or "revelation." Nor was either word in the index of his correspondence.

So, for the moment, Wallace Stevens gets the credit.

Except now I am surprised that I used the line at all. If I were writing Honey From Stone today, I would reverse the terms: "Seeing is revelation. Description is praise." In this, I would be echoing the 19th-century critic John Ruskin: "The greatest thing a human soul ever does in this world is to see something, and tell what it saw in a plain way."

I know what Stevens and McLaverty meant by "Description is revelation": The power of art to illuminate the deeper, hidden meaning of things, to go to the place where mind and things intersect. And that was probably what I meant too, all those years ago when I wrote Honey From Stone. But the older I get, the less interested I am in hidden meanings, in revelation, in the supposed transcendent. More and more I value close observation and plain description. Art, yes, but not art that obfuscates, that smothers the thing itself with imposed "meaning." I don't want interpretation. Give me art or science that separates the thing itself from the matrix of confused existence and lets us see it as it is.

The photographer Edward Weston was much concerned with exact seeing and description. His most controversial photograph was titled "Shell and Rock -- Arrangement," for which he carefully placed a shell in a hollow of rock before photographing it. A friend called it "a stunt," a theatrical ploy. "The greatness of your work, Edward, is that you allow nature to talk her own language," said the friend, disapprovingly. Weston defended the photograph, but one can tell from his Daybooks that he had niggling doubts. It is, I believe, one of his least successful photographs. Shell or rock alone, allowed to speak for themselves, would have been more typical of his work. By arranging them together he let mind intrude in a way that diluted the power of the thing itself.

Am I being pedantic? Perhaps. Or perhaps it's the hankering of someone growing older for the pure, unadorned selfness of existence.

Sunday, November 15, 2009

A pic from Anne...


...click, and again, to enlarge, and a commercial from me. Two love stories, one set in the late-3rd-century Roman Empire, and the other in France and the remote Irish isle of Skellig Michael on the eve of the year 1000. Julia and Valentine. Melisande and Aileran. And the eternal tension between skepticism and true belief. Valentine. In the Falcon's Claw.

Saturday, November 14, 2009

A drum roll, please...

The great advantage of belonging to a literate civilization is not having to rely entirely on one's self to make one's way through the world.

Each of us, on our own, will most likely follow the path of least resistance, the one laid down for us by our parents, neighbors and teachers. And nothing wrong with that; respect for the wisdom of elders is surely a beneficial attribute.

It can also be parochial. In matters of religion, for example, the vast majority of people believe the religion of their parents or culture to be "the true faith." In politics, too, we are influenced by our early experience, although perhaps not to the same extent as in religion. It's conceivable that a tendency toward liberalism or conservatism might be genetic, but that too links us in an "accidental" way to our immediate predecessors.

I don't doubt for a minute that if I were born of other parents in another culture I would be writing a very different sort of blog.

But here I sit in an excellent collegiate library, surrounded by many thousands of books offering the best (and some of the worst) of civilization. Not just Western civilization, but a substantial component of other civilizations from around the globe. And from this wealth of learning I piece together a world view, shaped, inevitably, from the clay of my origins. Liberal, Roman Catholic, agnostic, rational, romantic, naturalistic -- and informed by the only tradition I have recognized that is based on voluntary consensus-building and systematically applied doubt. Science.

I voluntarily surrender some measure of my intellectual autonomy to a tradition that seems to have served humankind well. Galen. Lucretius. Galileo. Boyle. Faraday. Maxwell. Pasteur. Curie. Einstein. Salk. McClintock. Watson and Crick. Their story is cumulative, it builds like a drum roll, it is measured constantly against empirical experience, its "proof" is the stunning successes of science, medicine and technology.

Yes, I recognize and freely confess that who I am is in some measure who I was, and I know too that science is not a sufficient guide to life. But I am careful to hew to both the letter and the spirit of the scientific way of knowing. Not because I concede to dogma, or because I scorn my origins, or because I lack confidence in myself, but because I am gifted by a literate civilization with the greatest minds of a grand tradition.

Friday, November 13, 2009

Pied beauty

Q: What distinguishes religious naturalism from plain old naturalism.

A: An abiding sense of Mystery...

...which evokes in response awe, wonder, thanksgiving, praise.

Mystery. A word that has often appeared on this site, frequently capitalized, as a substitute -- you might say -- for the discarded word "God".

What do I mean by "Mystery"?

Not mystery as in "mystery story," a case to be solved if only Miss Marple or Inspector Poirot is clever enough.

Not mystery as in "the Mystery of the Incarnation" or "the Mystery of the Holy Trinity", which provides a sort of respectable cover for beliefs that are on the face of it absurd.

Not mystery in the paranormal X-Files sense of the word.

No. By Mystery I mean the intuition that there is more to the world than meets the eye, even the eye of science.

I am not suggesting anything supernatural. Rather, I refer to the simple recognition, amply affirmed by science, that the finite part will never comprehend the (possibly) infinite whole.

By what right should we expect that a softball-sized glob of meat at the top of the human spine can contain the universe?

Religious naturalism whole-heartedly embraces naturalism -- and adds an adjective.

Ludwig Wittgenstein famously said: "The limits of my language mean the limits of my world?" That's naturalism.

Gerard Manley Hopkins intuited an "inscape" of things -- a deficit in our knowledge -- and struggled to make language bend to his intuition. That's religious naturalism.

The zoologist seeks to understand the speckled skin of the trout in categories of genetics and biochemistry. That's naturalism.

Hopkins considers "rose-moles all in stipple upon trout that swim" and is moved by "all things counter, original, spare, strange." That's religious naturalism.

Why not then use Hopkins' word "God" for his intuited inscape of things? Why substitute "Mystery"? Because "God" comes burdened with too much supernatural baggage, too much "outscape," too much anthropomorphic personhood. Too much that is conventional, unoriginal, convoluted, and familiar. Too much that suggests an illusion of understanding, as if a mere three-letter word could comprehend that which -- for reasons we do not fully understand -- stirs us to the core of our being.

Thursday, November 12, 2009

Light and smoke

Some of you may know of medieval heresies in the south of France from Emmanuel Le Roy Ladurie's Montaillou, a widely-read, groundbreaking reconstruction of village life in 14th-century Europe. Ladurie based his book on exhaustive records kept by Jacques Fournier, bishop/inquisitor, during his efforts to cleanse the village of Montaillou of the Cathar heresy. Fournier later became Pope Benedict XII and moved the records to the Vatican Library.

The Cathars, I suppose, were heretics in the true sense of the word, holding theological doctrines firmly in conflict with Roman orthodoxy. No doubt Fournier sincerely believed he was doing God's work in sending Cathar villagers to the stake or to prison.

The Beguins of southern France were a somewhat different kettle of fish. They espoused the radical poverty of Saint Francis of Assisi, believing they should possess nothing individually or in common except what was utterly essential to life. In this they thought to emulate more exactly the life of Christ. They were avid followers of Peter Olivi, a charismatic 13th-century Franciscan, who they identified with the Angel of the Sixth Seal in Revelations. And, as you might expect, they believed the Final Days were at hand.

Apparently, Beguin poverty was not looked upon kindly by those prelates and abbots who lived the high life on the backs of the poor. Louisa Burnham recounts the persecution of the sect in her scholarly book, So Great a Light, So Great a Smoke. The smoke in her title refers to the inquisitional flames that consumed so many Beguins.

The Beguins, in their turn, believed the pope was the Antichrist of Revelations, and that their immolated brethren were holy martyrs to a pure and uncorrupted faith. As Burnham reminds us, "Heresy is in the eye of the beholder."

The Church no longer burns heretics, but, as the current brouhaha regarding American nuns confirms, it still nurtures an inquisitional streak. But lest we think tolerance of diversity is slow in coming, remember that my most recent book, which would surely have earned me "so great a smoke" in the 14th century, was published in the 21st century by one of America's finest Catholic presses.

Wednesday, November 11, 2009

Egg and nest

Every now and then a book comes along that combines natural history and fine photography in such a brilliant synthesis that I feel compelled to mention it here. This has been the case with books on pollen and creatures of the deep sea, among other subjects. So let me add one more: Egg & Nest, with photographs by Rosamond Purcell and text by Linnea Hall and Rene Corado (Harvard University Press, 2008) -- a visual hymn to the eggs and nests of birds.

The eggs are beautiful, in their colors, glosses, surface markings, and shapes, often exquisitely adapted for camouflage, or even to keep them from rolling off a nesting ledge. Lovely, yes, but no more so than we would expect from the refining nudge of natural selection.

Every egg is a "miracle" of development -- as is the development of any embryonic organism -- but somehow we become immune to the wonder of it. After all, the making of an egg takes place out of sight, the chemical machinery of the body doing what it is supposed to do, as automated as a clockwork. We no more marvel at the making of an egg as -- to use a crude analogy -- the making of a turd. But oh, what a difference!

The nests are something else.

And here, in these photographs, they are marvels of animal architecture, constructed of various materials, in various designs, sometimes elaborately woven, lined with fluff and fuzz. Beak and claw guided by eye and brain. In plain sight. Behavior, we call it, to distinguish it from the making of an egg on autopilot. Those clever birds, we say.

Of course, the nests are no less genetically determined than the eggs. A bird doesn't have to be taught to make the nest characteristic of its species. It is somehow encoded in the DNA, in the same "four-letter" code that makes the egg, but how is a matter of such deep mystery that, for the time being, we turn the mystery over to the artist -- in this case to Rosamond Purcell -- to rub our noses in the sheer mind-blowing beauty of nature's bounty.

Tuesday, November 10, 2009

Science and technology

How are they related? Does science drive technological innovation? Or is it the other way around?

I grew up in the Jacques Elluh generation. Oswald Spengler's 1931 Man and Technics was already old hat, with it's pessimistic view of technology and industrialization. Lewis Mumford's 1934 Technics and Civilization sought to place technology in a more comprehensive organic notion of human development, but seemed oddly-dated by the time I got to it. Siegfried Giedion's 1948 Mechanization Takes Command was a teeming idiosyncratic take on the technological accouterments of modern life, but I don't think I ever understood what he was getting at.

Elluh's 1964 The Technological Society emphasized the inevitable progress of technology, but warned of the moral consequences. Technology does not make us happy, he asserted. Too many tradeoffs.

Since my early academic immersion in this stuff, I more or less lost track of the ongoing debate between the technological utopians and the neo-Luddite handwringers. Technology may or may not make us happy, but that has not slowed technological development or curbed our appetite for the latest innovations. Even the most avid of contemporary Luddites have their laptops and cell phones and travel to anti-technology conferences on the latest jet aircraft.

My own relationship with technology has been one of trying to find a balance between the technological and the organic. I suspect technological and organic evolution is symbiotic, and follow something of the same Darwinian logic. Science does not lead technology, nor vice verse; their evolution goes hand in hand. The future -- to the dismay of my nature-writer friends -- will inevitably be a human artifact, synthetic from the get go. But because biological evolution does not proceed at the same pace as technological evolution, and because the human factor cannot be removed from technique, our bodies provide a modest brake on the mechanization of culture.

I passed a young couple on the campus yesterday. They were each listening to their own iPod through their own earbuds. And they were holding hands. Somehow it seemed an apt image of our techno-organic future.

Monday, November 09, 2009

Everything is holy

Last week, I alluded to the beehive of continuous activity that goes on in every cell of our bodies as protein "motors" identify and repair DNA, even as the DNA spins off proteins. Today, a few more words.

Each of the 10 trillion cells of your body receives tens of thousands of DNA lesions per day; that's tens of thousands of incidents of damage to your genome. The damage might be caused by mismatches during DNA replication, chemical interference, radiation, or ultraviolet light. Such damage, if not detected and repaired, can lead to mutations or other genomic aberrations that threaten cell viability, or even the health and well-being of the organism -- you.

Tens of thousands of incidents of DNA damage in every cell every day! Our genomic integrity is under constant attack -- the integrity that makes you you and me me, and keeps our bodies on track to a normal healthy life.

To combat these threats, cells have evolved mechanisms -- collectively called the DNA-damage response (DDR) -- to detect damage and facilitate repair.

Imagine, if you will, little quality-control inspectors patrolling up and down the DNA strands, checking for mismatches or breaks, then calling on their cell phones for repair crews to speed up in their vans and put things back in order. It is proteins -- yes, proteins, strings of amino acids folded into elaborate shapes -- that do the job of inspecting, signaling and repair!

In the 22 October issue of Nature, biochemists Stephen Jackson and Jeri Bartek take eight pages to sketch what we know about the DDR. They conclude:
Great progress has been made towards understanding the DDR but much remains to be learned. One major future challenge is to understand in more detail how the activities of DDR proteins are controlled. Other challenges are to determine precisely how and why the DDR impacts on myriad cellular functions and how such complex programmes are orchestrated. Additional important issues to be addressed are how the DDR can be shaped and fine-tuned by other pathways and events, and how the same DDR stimulus can yield markedly different responses in different cells and tissues, including cancer cells and stem cells. Such knowledge will not only enhance our appreciation of DDR functions but will undoubtedly present exciting opportunities for better understanding and managing human health and disease.
So what does all this incredibly sophisticated biochemistry have to do with you and me, aside, that is, from the fact that it keeps you you and me me? It happens without the slightest necessity of consciousness on our part. It was evolving for 4 billion years before any conscious organism even knew it existed. Why think about it now?

Because knowing is better than not knowing. Because knowing is what makes us human. Because even a superficial awareness of what is happening in every one of the 10 trillion cells of our bodies is a source of wonder, and ground for a -- yes -- religious response to the world -- a response that affirms a Mystery made more manifest by every advance in knowledge, and doesn't cheapen that Mystery by invoking the shabby agency of an anthropomorphic God.

Sunday, November 08, 2009

A fourth Jesus

I was browsing Deepak Chopra's latest offering on the new book shelf of the college library -- The Third Jesus: The Christ We Cannot Ignore.

Chopra, of course, is the fabulously successful New Age/Eastern guru who offers in books and motivational seminars "physical wellness", "emotional wellbeing" and "spiritual awakening", along with massage oils and ayurvedic sinus support. Not to mention quantum healing, "Love Poems from God," and a CD called "Drum Sex", whatever that is.

Not to be too snarky. Chopra is a positive force for mutual tolerance and global peace, and lord knows we need more of that. His new book is filled with lots of good sense, so more power to him. But needless to say, his brand of mystico-transcendentalism is not for me.

Who is this "Third Jesus"?

Chopra's first Jesus is the historical person who lived in Galilee two thousand years ago, about whom we know almost nothing that can be called historically reliable. We know nothing that meets the standard of scientific evidence.

The second Jesus is the divinity of the institutional churches, constructed over the centuries by theologians, reformers and self-appointed prophets. This is the Jesus who was born of a virgin, rose from the dead, sits at the right hand of the Father, and who will come again, etc. "He became the foundation of a religion that has proliferated into some twenty thousand sects," says Chopra. "[Sects that] argue endlessly over every thread in the garments of a ghost."

The third Jesus, now on offer, is the mystical guru who taught his followers God-consciousness, and who "spent his brief adult life describing it, teaching it, and passing it on to future generations." That is to say, Chopra's third Jesus looks a lot like Deepak Chopra. Which again is fair enough; presumably, the founder of every one of those twenty thousand sects proffered a Jesus who looked pretty much like himself/herself.

So I will too. Here is my Jesus, the boy in the painting below, Georges de la Tour's Saint Joseph, the Carpenter, c. 1640s (click to enlarge). The Jesus of the painting is a creature of the artist's imagination, and he exists only in our imaginations too. A lad helping his father in the workshop. What the boy understands of his future life work, we have no idea. Maybe he has no idea either.


What do we see? Not Truth. Not God-consciousness. Not a Vatican staffed with men in Renaissance garb waited on by nuns. Not Lourdes holy water or ayurvedic sinus support. What we see is a child's simplicity, love, work, family, craft. And if that auger in Joseph's hands anticipates the cross, well, death comes to us all.

"I am the light" Jesus is supposed to have said: A candle flame hidden by a child's translucent fingers.

Saturday, November 07, 2009

Thorns


Tell me, if you know,
the name of this sprawling woodland plant
with small paddle-shaped leaves,
November-red, and bright red berries.

And thorns.

Thorns seemingly too thin
and soft to be of much use
deterring browsers. What deer
would hesitate to nibble here?

And yet, this lovely plant --
whose name I do not know --
bristles menacingly, pretending
a keenly-whetted defense.

How often has natural selection
gone down this path, nature-red-
in-tooth-and-claw adopting spikes,
spines, prickles, thorns.

Thorny devil lizard.
Puffer fish.
Spiky sea urchin.
Hedgehog.
Spiny king crab.
Crown-of-thorns starfish.

Cactus.
Rose.
Honey locust.
Green briar.
Tear-thumb.
Thistle.

You and I with our
soft and silky skin
facilitating love, caresses,
the apparently un-Darwinian invitations
to intimacy. Left vulnerable by
nature's oversight we provide
our own swords, daggers, lances, spears.

Friday, November 06, 2009

Match.com

As a service to lovers everywhere, Science Musings has previously considered the perennial question, "What does the other half want?"

But before I return to that muddlesome topic, take a minute or so to watch this video of the courtship display of the spatuletail hummingbird of Peru.

********

I don't know if what you have just watched is an argument for natural selection or for intelligent design. If the latter, the Designer has a quirky sense of humor. If the former, the male spatuletail hummingbird has been dealt an unfortunate hand by female sexual preference.

Hummingbirds live on the metabolic edge, burning up calories as fast as they can stoke themselves with nectar, and this poor fellow has to carry around those two absurdly long tail feathers that serve no other purpose than pleasing a potential mate. And think of the energy required to wave them so seductively.

Did he score? Or did she sit there waiting for another fellow with slightly longer flags, all that exhausting foreplay for nothing. If the male spatuletail hummingbird is able to formulate an inarticulate thought, it is surely the same one men have always asked: "What do women want?"

Thursday, November 05, 2009

Euclid alone has looked on...


Ponder for a moment this exquisite glass sculpture by the glassblower/artist Luke Jerram. About the size of a melon. A shell of sorts made up of glistening clustered spheres. Inside, a twisting snake of translucent glass.

Guess what? It's a sculptural representation of the swine flu virus. A protein shell. Inside, eight segments of single-strand RNA. Here, at the smallest dimension of life -- if you can call a virus living -- at a scale too small to be observed even with the best optical microscope, nature has contrived structures of stunning elegance.

The beauty of a virus is a matter of necessity. A virus has only enough genes to encode for a few proteins -- eleven for H1N1. To build its shell, the virus uses the same proteins over and over, like the repetitive pattern of patches on a soccer ball. They can only reproduce and build their protein shells by hijacking the chemical machinery of a living host cell. Your cells and my cells. And what they leave behind is a mess.

A virus is a shoestring operation, a paragon of frugality. Making do with the bare minimum, it comes up with beauty bare.

Wednesday, November 04, 2009

Tears of joy


I have known about the quiltmakers of Gee's Bend, Alabama, for some time. My friend Candace in the Art Department ordered books on the subject for the college library, which I have perused. Astonishing that a group of older black women from one of the poorest communities in America took the art world by storm with their quilts of inspired and idiosyncratic design.

But I was not prepared for my reaction when I watched last evening an hour-long documentary, The Quiltmakers of Gee's Bend (produced by Alabama Public Television, directed by Celia Carey). It recounted the history of the quiltmakers, spoke of the uniqueness of their work, and ended with a bus trip of the women to a major show of their quilts at Milwaukee's futuristic Art Museum (designed by Santiago Calatrava).

I don't cry easily, but the film brought me to tears.

Why, exactly? Why did I weep? I have no immediate connection to the women or their work. There was something of the Cinderella story, of course -- a few dozen desperately poor descendants of slaves become the toast of major museums, their quilts suddenly selling for thousands. There was the beauty of the quilts, and of the women who made them. There was the haunting loveliness of the Negro gospel songs that figure so prominently in the film and make up so much of the soundtrack. And the goodness.

William Blake wrote: "Excess of sorrow laughs. Excess of joy weeps."

The tears -- nature or nurture? Are we born with empathy, or do we learn it? There has been some discussion here on the possibly innate origins of male aggression. A genetic predisposition to empathy might be even more problematic. There are reasons why natural selection would favor empathy between mothers and infants, and between close kin, but that hardly accounts for my weeping with the women of Gee's Bend.

Tears are physiological, and can be triggered by cold, onions, irritants, and other purely physical stimuli. But what is the connection between emotion and tear ducts? Studies have shown that women and girls are more empathetic -- and prone to tears -- than men and boys, but that doesn't overwhelmingly suggest nature or nurture, since boys and girls tend to be raised differently. Tom Lutz has written a book on the subject of weeping -- Crying: The Natural and Cultural History of Tears -- which I read some time ago, and, although interesting, I don't recall that it threw much light on the nature vs. nurture question.

We'll know eventually, as the genome is decoded. I suspect it is a bit of both -- genes and nurturing. Still, what a thing it is that the story of quiltmakers from a one-horse town in rural Alabama can have me reaching for the tissues.

(The quilt above by Minnie Sue Coleman, born 1926.)

Tuesday, November 03, 2009

Believing six impossible things before breakfast

Here is a little digression for your breakfast edification.

A typical animal cell is about 16 micrometers (16 millionths of a meter) in diameter. Thinner than a sheet of tissue paper. Tinier than the period at the end of this sentence. There are ten trillion or so cells in your body.

Lot's of stuff packed into each cell, including an arm's length of DNA, the code of life. Yes, really! I know it sounds impossible that an arm's length of anything would fit in such a small space, with room left over for other stuff, but it does. And it's not just sitting there. Tiny protein-based "motors" crawl along the strands of DNA, transcribing the code into single-strand RNA molecules, which in turn provide the templates for fabricating the proteins that build and maintain our bodies. Other proteins help pack DNA neatly into the nuclei of cells and maintain the tidy chromosome structures. Still other protein-based "motors" are busily at work untying knots that form in DNA as it is unpacked in the nucleus and copied during cell division. Others are in charge of quality control, checking for accuracy and repairing errors. Working, spinning, ceaselessly weaving, winding, unwinding, patching, repairing -- each cell like a bustling factory of a thousand workers. Ten trillion cells humming with the business of life.

All this in a cell smaller than this period.

And now I see an article in a recent issue of Nature (8 October): "Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes." Here is the abstract. Don't worry about understanding it; I don't. Just scan it.
The slicer activity of the RNA-induced silencing complex resides within its Argonaute (Ago) component, in which the PIWI domain provides the catalytic residues governing guide-strand mediated site-specific cleavage of target RNA. Here we report on structures of ternary complexes of Thermus thermophilus Ago catalytic mutants with 5'-phosphorylated 21-nucleotide guide DNA and complementary target RNAs of 12, 15 and 19 nucleotides in length, which define the molecular basis for Mg2+-facilitated site-specific cleavage of the target. We observe pivot-like domain movements within the Ago scaffold on proceeding from nucleation to propagation steps of guide-target duplex formation, with duplex zippering beyond one turn of the helix requiring the release of the 3'-end of the guide from the PAZ pocket. Cleavage assays on targets of various lengths supported this model, and sugar-phosphate-backbone-modified target strands showed the importance of structural and catalytic divalent metal ions observed in the crystal structures.
And just to give all those words a bit of substance, here is one of the diagrams that accompany the article (click to enlarge).


It seems impossible that anyone could know in such detail what's going on at such a tiny scale. For the first time in human history we are learning about the basic machinery of life in action, machinery that not so long ago we had no idea existed, machinery that is in one sense stunningly simple (that 4-letter code of DNA for all of life, that elegant double helix), and in another sense is so staggeringly complex that we wonder that it works at all, so reliably, for such a long time. The unceasing chemical dance that makes you you and keeps you you. And we sit here sipping our coffee, ten trillion cells, a seething miracle -- all unawares.

Monday, November 02, 2009

Burning books


We all heard about the looting of the Baghdad Archeological Museum in the immediate aftermath of the the US invasion of Iraq. We heard less about the libraries.

A million books in the National Library were burned. The National Archive, with millions of records from the republican and Ottoman periods, went up in smoke. The same took place at the University of Baghdad library, the Awqaf Library, and dozens of university libraries across the country. In Basra, the Museum of Natural History was burned, along with the Central Public Library, the university library, and the Islamic Library. Libraries and archives in Mosul and Tikrit witnessed major destruction. I glean this sad accounting from A Universal History of the Destruction of Books: From Ancient Sumer to Modern Iraq, by Fernando Baez, director of Venezuela's National Library and scholar of the history of libraries. Baez visited Iraq soon after the invasion as part of the U.N. committee investigating the destruction of that country's cultural treasures.

It's a sad, heartbreaking book, tracing the wanton burning of books from ancient times to the present, in cultures east and west. Often the motive is to erase the traces of an overthrown regime, or to eradicate political or religious ideas considered heretical. Sometimes the motive is sheer anti-intellectualism. Whatever the reason, the result is the same, as described to Baez by a university professor in Baghdad: "Our memory no longer exists."

The book had a special poignance for me as I read it sitting in my usual chair in the stacks of my college library.

It is a convention in science, strictly adhered to, that any paper or book purporting to advance the state of knowledge cites the relevant preceding literature. The idea is that knowledge grows like a tree, each new twig attached to an ever-branching trunk. Burn the trunk or branches and the twig dies. In science, memory is sustenance.

I like to imagine a personal library containing every book I've ever read, in the order that I read them, starting with the Hardy Boys and ending -- for the moment -- with Fernando Baez Such a collection would be a pretty fair picture of who I am. I wonder if anyone has ever done that?

Cultures and civilizations, too, are fairly represented by libraries. It is inconceivable to me that anyone could be so afraid of alien ideas as to send them up in smoke. The painting above, by Pedro Berruguete (15th c.), shows Saint Dominic presiding over the burning of books by Albigensians.

Sunday, November 01, 2009

Evolution or stasis?

As I have noted on this site before, it has been my honor over recent years to meet and learn from several groups of American Roman Catholic nuns of different congregations. Mostly these have been older women who entered their convents pre-Vatican II and have subsequently reinvented themselves to serve the Church and society in ways that would have been unthinkable in earlier times. Wimples have been discarded in favor of modest modern dress. Rote liturgical practice and adherence to antique doctrine has been replaced by a creative, socially liberal, and ecumenical engagement with modernity. I have been deeply moved by the sisters' joyous identification with the gentle Galilean, and by their willingness to redefine spirituality in ways that recognize the goodness of nature and the exhilarating vision of scientific cosmology. I have detected nothing but loyalty to the Church -- albeit a Church that bears little resemblance to the misogynistic, homophobic patriarchy in Rome.

For this, they are currently being investigated by two Vatican commissions, one focussed on the sisterly "quality of life," the other on doctrinal orthodoxy. Apparently, Rome is worried that American nuns have "failed to 'promote' the church's teachings on three issues: the male-only priesthood, homosexuality and the primacy of the Roman Catholic Church as the means to salvation."

In the current issue of Commonweal (October 9), a longtime sister provides a moving and quietly angry response to the investigations. She chooses to remain anonymous for reasons she describes, and which are relevant to the subject in question. "In the Catholic Church," she writes, "it is men who tell women how they should understand themselves as women. Rome wants women religious to accept such understandings not merely without dissent, but without comment." To put it bluntly, she says, American women religious are being "bullied." You can read the article in its entirety here.

On Thursday, I discussed a book that prescribes the empowerment of women as a way to ameliorate the (presumed) biological predisposition of our species to male intergroup violence and the social disorders that accompany rampant population growth. One would think the Church would prefer to be on the peaceable side of these issues -- even if the simple justice of female equality were not enough.