Science Musings Blog

A recent issue of Nature had a special section on "Building a Cell". Here is the editors' introduction. Just scan it, don't worry about comprehension, and then I'll have something to say:

The living cell is a self-organizing, self-replicating, environmentally responsive machine of staggering complexity. The instructions for this complexity are contained within the cell's genetic code, but how this information is accessed, read and interpreted is influenced by development and differentiation.

To divide, a cell needs to create a second set of its genetic material to donate to the daughter cell. The review by Bloom and Joglekar examines how duplicated chromosomes are divided accurately between mother and daughter cells and packaged by proteins, mainly histones, in the nucleus. This packaging regulates gene expression, and Ho and Crabtree discuss how this occurs during development and differentiation. In eukaryotes, protein-coding genes are transcribed into precursor messenger RNAs that contain non-coding regions. As described by Nilsen and Graveley, these non-coding regions must be removed before the RNA can be translated into protein, in a process known as alternative splicing.

The shape, movement and positioning of organelles within the cell depend on dynamic, polymeric cytoskeletal proteins. Fletcher and Mullins analyze the principles that allow these proteins to produce and respond to mechanical forces, as well as to establish order in the cytoplasm over long distances. In a process called endocytosis, portions of the cell membrane are internalized into the cytoplasm. This enables the cell to capture material from the extracellular environment and to respond to cues detected by externally oriented receptors. Scita and Di Fiore discuss the integral role of the endocytic system in the cell's signaling network.

The articles that follow this introduction describe our current understanding of what goes on in every one of the mostly invisibly small 10 trillion cells of our bodies.

Now I know I've written about this before, but I keep coming back to it: The unceasing hive of activity that is our body, every cell like a hugely complex petrochemical factory on full blast, none of which requires the slightest conscious attention from me. Breath. Heartbeat. Digestion. Scratching an itch. The healing of wounds. The maintenance of memories. Dreams. It all happens by autopilot. This huge colony of multiplying, replenishing, differentiated cells which is me. And in it and on it flickering that thing which is self-awareness, the thing I think of as the "real" me, which exists only by the grace of all this other unconscious biochemical activity.

Yes, it all happens without our thinking about it. But it's worth thinking about. It's easy enough to see why our ancestors imagined an immaterial "me" that came into the world full-blown at birth and goes on living after death. They had no clue of the frenetic machinery of life, the buzz of self-sustenance that goes on in every cell of our bodies, the tiny furnaces of the lungs, the throbbing pistons of the heart, the ever-ready mousetraps of the immune system, the recycling plant of the gut. And there, at the top of the spine -- the flame on the wick -- a scintillating ball of neurons, firing, recharging, firing, like the constantly regenerative pixels of a television screen that give the illusion of continuity.

And when it all stops, the self goes off like a light.

I spend a shameful amount of time each day watching the hummingbirds and bananaquits forage at our feeders. The bananaquits can't quite fit their beaks into the hummingbird feeder, with its sugar water, so we put granulated sugar out for them. Still, they feel proprietary about the sugar water and do their best to keep the hummingbirds away. Unsuccessfully, of course. The hummingbirds dart and snitch with a velocity the bananaquits can't match. Beating hearts with feathers.

Lovely thing, the feather! An oar for the air. Featherlight. The association with flight is irresistible. But flight may have been an afterthought. It is now generally agreed that birds descended directly from dinosaurs, and feathers appear to have been a dinosaur feature before birds ever left the ground.

If not for flight, then why did feathers evolve? For insulation, perhaps. Or maybe camouflage. Or -- it is Valentine week, after all -- maybe to attract a mate.

In a recent Nature Online, paleontologists from the University of Bristol in the UK and the Institute of Vertebrate Paleontology and Paleoanthropology in Beijing offer the first evidence for coloration in dinosaurs -- fossilized evidence of pigmented feathers in a dinosaur called Sinosauropteryx. And here they are, in an illustration borrowed from Science, two Sinosauropteryx, with white and chestnut striped tails, doing a mating dance.

Why not more striking colors? Why not a Valentine red, for instance? Natural selection works with what it's got, cobbling together new things from bits and pieces of the old. You like my chestnut striped tail, I'll see if I can make it flashier. You have a taste for sugar, I'll bring you candy.

Cobbling together whatever works, and look! The feathers on my forelimbs help me glide as I lope along the ground, escaping a predator. And look! I take to the air.

I have just finished reading Andrea Levy's Little Island, a novel that won or was shortlisted for many prizes in 2004 -- and which was dramatized on the BBC this past December. Levy was born in Britain to Jamaican parents in 1956. She lives and works in London today. Her novel explores racism in Jamaica, Britain and India during and just after the Second World War, through the lives of two women and two men, black and white, Jamaican and British.

My children, and especially my grandchildren, would scarcely recognize the world she describes. To me, it is intensely familiar. I came of age at the time of her novel, in a thoroughly segregated Chattanooga, Tennessee. Jim Crow ruled. Public toilets, water fountains, lunch counters, restaurants, movie theaters, parks and recreation facilities were separated by race, and woe betide the person who crossed the line.

All that is gone now. Gone in Chattanooga. Gone in Britain. Gone in these Caribbean islands. Which is not to say that latent racism doesn't still exist. But on the whole things have changed enough that we can read Levy's novel and wonder that we were once beholden to so much hate.

What was the nature of the transformation? Did human nature change? Did a fear of the other inbred by millions of years of evolution suddenly vanish? Or was fear of the other suppressed by a cultural upwelling of an innate altruism?

Maybe it wasn't biological at all? Maybe both the racism and its amelioration are driven by cultural imperatives? Maybe we truly discover our better angels as we evolve culturally?

Since I was raised in a racist culture (although not by racist parents) and now count myself without prejudice (I hope), it would seem that self-reflection might provide something of an answer.

I suspect that both fear of the other and solidarity within a group are deeply embedded in our cultural traditions and maybe our DNA. In which case, it is a broadening of "us" that has diminished the "other", probably driven by technology -- radio, television, movies, air travel, the internet.

Then too, I suspect the growing promise of empirical knowledge over faith-based knowledge -- seeing what is there to see, not what we want to see or have been taught to see -- has lessened our beholdenness to the past and to our genes.

Made an omelet last evening. Four eggs cracked into a bowl. Chopped crisp bacon. Tomatoes and chives from the porch. Grated cheese.

Those eggs! Jumbo. Perfect shells, eggshell white. Golden yolks. Twelve ovoids nestled in their styrofoam box. All the way from Gettysburg, Pennsylvania.

Forget for the moment the miracle of refrigerated transportation that connects those thousands of caged layers in Pennsylvania to our little island a thousand miles away. Try to put out of your mind the chickens that laid the eggs -- plop, plop, one a day, like clockwork, day in day out, chickens that spend their short lives turning chicken feed (containing, no doubt, spent chickens) into delicious globes of nutrients. Forget the factory in Gettysburg and focus on the internal production line, devised by nature and fine tuned by human ingenuity.

Begin with that pinhead-sized dot of white we see attached to the yolk, the germ cell that contains the hen's DNA, one of the several thousand germ cells she is born with in her single ovary. The germ starts growing the yolk, the ball of nutrients that would feed the embryonic chick if there were one. The rest of the egg comes along once the ovary releases the yolk into the oviduct. Down it goes, gathering layers along the way, a biological assembly line -- white, membranes, water, shell, cuticle and color. Plop!

Forget all that if you can -- the external and internal assembly lines. Think instead of Julia Child cracking an egg into a white enamel bowl. Meringue. Mayonnaise. Custard. Smooth sauces. Flavor, substance and nutrition to breads, soups, pastas and cakes. Omelets. Or, what the heck. A fried egg sandwich. A hard boiled egg in a lunch box.

No wonder so many ancient thinkers in so many cultures imagined the cosmos as an egg. A construction of concentric shells. That a clucking, flapping, dirt-pecking chicken could come out of a package that begins as an undifferentiated blob was a fertile metaphor for existence itself.

So bon appetit! You can't make an omelet without breaking a few eggs. And as you are wolfing it down, meditate on the mystery of why there is anything at all.

We grew up with Chinua Achebe, the Nigerian writer. His 1958 book Things Fall Apart was the perceived epitome of African literature, and a promise of a bright cultural future for that continent. Since that time, some bright things have happened -- notably, the end of apartheid in South Africa. But we have also witnessed chaos and atrocity in Rwanda, Congo, Sudan and elsewhere.

Now Achebe has published a collection of essays called (whimsically and ironically) the Education of a British Protected Child, reviewed in last Sunday's NYT Book Review. Apparently, the overarching theme is the colonial legacy in Africa.

According to the reviewer, Achebe's voice, as always, is moderate, eschewing extremes of radicalism or reaction. He occupies what he calls "the middle ground," what he defines as "the home of doubt and indecision, of make-believe, of playfulness, of the unpredictable, of irony."

I suppose there are those who would chastise Achebe for his moderation, who would call him wishy-washy, and urge him to thunderous wrath in the face of manifest injustice. Yet, there he sits, with his sweet, ironic smile, his critical faculties intact and held on a gentle rein.

In a world so fraught with sloganeering from left and right, with anger, self-righteousness and true belief, I am happy to resort to Achebe's place of measured doubt and playfulness, of humor and irony. There is truth in the middle ground, but it comes wrapped in hesitation, humility, tolerance, and (let us hope) grace.

There is a line of dialogue in another novel I read back in 1958. The narrator asks the eponymous Mr. Blue: "Isn't the golden mean the secret of something or other?" "Yes," replies Blue, "mediocrity." At the time, I was ready to agree with Blue, to opt for a muscular religion and politics, to avoid the namby-pamby gray. No more. I'll leave the doctrines of infallibility and placard-wielding indignations to those who have the stomach for them -- and play with Achebe in the artful middle.

Whenever anyone asks me to recommend a good book on biology, I always suggest Ursula Goodenough's The Sacred Depths of Nature. In a little over 100 pages, Ursula presents the most lucid and concise survey of the subject I have ever read. Biology, pure and simple.

Of course, there is another part of the book, the "Reflections" at the end of each chapter, where she puts what she has said into the context of religious naturalism. If you are just interested in biology, you can skip that. But I wouldn't. It's the icing on the cake.

Ursula is a first-rate microbiologist. We've had a sometime e-mail relationship (and one lovely breakfast in Harvard Square). The Sacred Depths of Nature is a demonstration that one can be religious without believing in miracles or the existence of a personal God.

Ursula worships with a traditional Presbyterian congregation, singing in the choir, reciting the liturgy and the prayers. I would find it difficult to do that. On those celebratory occasions when I attend a Catholic Mass, I remain silent and sit out Communion. It seems to me that if one recites the Creed, the words should mean what the universal church assumes them to mean. Anything else strikes me as disingenuous.

But I respect Ursula's ability to revel in all forms of traditional religion.

I love traditional religions. Whenever I wander into distinctive churches or mosques or temples, or visit museums of religious art, or hear performances of sacred music, I am enthralled by the beauty and solemnity and power they offer. Once we have our feelings about Nature in place, then I believe hat we can also find important ways to call ourselves Jews, or Muslims, or Taoists, or Hopi, or Hindus, or Christians, or Buddhists. Or some of each. The words in the traditional texts may sound different to us than they did to their authors, but they continue to resonate with our religious selves. We know what they are intended to mean.

Goodenough knows that awe and gratitude in the face of mystery are part of human nature. "Hosannah!" she exclaims; "Not in the highest, but right here, right now, this." Her little book is a splendid manifesto for religious naturalism, and a useful antidote to the stridency of a Dawkins or Hitchens. She exemplifies what William James said about religion: "There must be something solemn, serious and tender about any attitude that we denote religious. If glad, it must not grin or snicker; if sad, it must not scream or curse."

In the American news this morning you will read about Punxsutawney Phil, the famous Pennsylvania groundhog that will or will not see his shadow when he emerges from his burrow today. If he does, we are in for six more weeks of winter. If it doesn't, we can put away the parkas and welcome spring.

The fat woodchuck is part of a web of solar lore with roots in prehistory. Phil presides at the year's first "cross quarter" day. The fuss that attends his emergence from his burrow is connected to the Sun by more than a shadow.

The story begins 4 1/2 billion years ago in the chaos of the pre-solar nebula from which the solar system was born.

In a corner of the Milky Way Galaxy, a vast cloud of dust and gas began to contract under the influence of gravity. As the cloud got smaller, it spun faster, as an ice skater spins faster as he draws his arms close to his body. As the cloud spun faster, it flattened out, like a mass of spinning pizza dough.

This whirling pancake of dust and gas became our solar system. Most of the material was pulled to the center to form the Sun. Other whirling eddies within the cloud were collected by gravity to become planets. There was considerable chaos within the cloud. When the third planet from the sun settled into place, its spin axis had a tilt of 23 1/2 degrees to the plane of the pancake.

It was the luck of the draw. It might have been 30 degrees. It might have been zero.

If it were zero, no Punxsutawney Phil.

As the Earth revolves in its annual orbit, sometimes the northern hemisphere is tipped towards the Sun, sometimes away. In the first instance, the Sun's rays fall more directly upon the surface and heat it efficiently: our northern summer. In the latter case, the sun's rays shine obliquely and spread their energy more diffusely: winter.

If there had been no tilt, there would be no seasons. Climate, yes -- poles cold, equator hot -- but no seasonal variation. But there was a tilt, and the waxing and waning of the Sun's warmth and light was the central fact of life for our ancestors.

The bonfires of St. John's Eve, June 23rd, which are still lit in some parts of Europe, celebrate the Sun's ascension to its highest point in northern skies. Likewise, the winter solstice, when the Sun stood lowest, was marked with feasts of light to ensure the Sun's return. These ancient rites linger in the Christian feast of Christmas and the Jewish Hanukkah.

The equinoxes, when the Sun is halfway between its extremes of strength and weakness, were celebrated too. The spring equinox retains a place in our calendar through its connection with the Christian feast of Easter, or alternately, as the Ides of March or St. Patrick's Day. Celebrations of the fall equinox have slipped from prominence.

The cross-quarter days, midway between the solstices and equinoxes, are less familiar, but they too figured in ancient rites, and also lurk in our traditions.

The first cross-quarter day should mathematically fall about Feb. 4th or 5th. This became Candlemas Day, Feb. 2nd, in the Christian calendar. An old European rhyme asserts:

If Candlemas be fair and bright,
Come winter, have another flight.
If Candlemas brings clouds and rain,
Go, winter, and come not again.

Some Europeans looked for the shadow of the hedgehog on Candlemas. German immigrants brought the tradition to Pennsylvania and substituted the American woodchuck.

Punxsutawney Phil bears a weight of tradition on his fat, furry shoulders. His contrived appearance may seem inconsequential, a bit of local fun for the folks of Punxsutawney, but it is good that the old traditions live on in secular form to remind us of our common humanity on the tilted third planet from the sun.

(By the way, we celebrate the second cross-quarter day as May Day. The third cross-quarter day, which falls on or about August 7th, was perhaps remembered in the Christian calendar as Lammas, or "loaf-mass," a harvest feast, but it has vanished from our attention. The fourth cross-quarter day remains prominently with us as Halloween.)

It has become something of a habit here to comment on the Astronomy Picture of the Day (APOD), usually to call attention to something not mentioned in the caption. A few days ago it was Kemble's Cascade, an unusual (and accidental) alignment of about twenty stars in the constellation Camelopardalis (the Giraffe), now high in the northern sky in the evening. (Click to enlarge.)

First, note that none of the stars in this view are likely to be seen with the naked eye. There are no stars in the constellation brighter than the 4th magnitude, which means from a typical light-polluted location Camelopardalis is a big blank part of the sky.

But look what a telescope can see in this view which covers about 4 degrees of the sky -- about 8 times the width of the full Moon. What a delicious serving of stars!

The size of the dots on the photograph have nothing to do with the relative size of the stars; at the distance of the stars they are all effectively points of light. Rather, the size of the dots indicates the relative apparent brightness of the stars; how much light soaked into the film while the shutter was open (think of water dripping onto a paper towel). And keep in mind that the apparent brightness of a star is not necessarily an indication of its distance; the intrinsic brightness of stars varies greatly.

But -- it's the colors of the stars that strike me here. Reddish-orange. Yellow. White. Blue. Like a cascade of jewels, or the rainbow of colors in a waterfall's mist.

The celebrated 19th-century British observer William Henry Smyth professed to see stars the color of sardonyx, damson and smalt, which suggests either especially perceptive vision or a vivid imagination. He listed a dozen shades of white, including pearly, lucid, creamy, silvery, and just plain whitely white. Smyth could have had a career as one of those folks who make up names on paint chips.

Smyth's almost exact contemporary, the Russian-German astronomer Wilhelm Struve, used Latin labels to classify star colors: egregie albae, albaesubflavae, aureae, rubrae, caeruleae, virides, purpureae, and even olivaceasubrubicunda, which translates as something like pinkish-olive. I'm not sure I've ever seen a pinkish-olive star, but maybe you can pick one out in the photograph. By the way, the brightest (double) star in the little cluster at left is named for Struve.

The color of stars tells us how hot they are -- red is cool, blue-white is hot. Match up the color of the star to the color of a filament in a clear light bulb and they'll be the same temperature.

Usually we think of stars as uniformly white, but that's because the human eye is not sensitive to color in dim light -- and maybe because we just don't look closely enough. Anyway, as I look at this photograph, I think of lines from Yeats poem "He Wishes for the Cloths of Heaven":

Had I the heavens' embroidered cloths,
Enwrought with golden and silver light,
The blue and the dim and the dark cloths
Of night and light and the half-light,
I would spread the cloths under your feet.

As now I do.

Anne returns to grace our blog with a Sunday illumination. Please click to enlarge, and then again if you wish.

Today at 1600 GMT a company called Steron will demonstrate in Dublin, Ireland, a device called Orbo that produces -- so they claim -- more energy than it uses. That is, the energy-out/energy-in ratio is greater than unity.

Spunky little Orbo is proclaimed to be the long-sought perpetual motion machine, the answer to all of humankind's energy needs.

I know about the demo because I have a friend in Ireland who keeps me posted. He's a big fan of free energy, and we have a long-standing bet about Orbo. If Steron's claim turns out to be true, I owe him a beer. Heck, I'll buy him all the beer in the pub.

I know nothing about Orbo except that it works with magnets. Certainly, I could find out a lot more by going on the web, starting, I suppose, with Wikipedia. But I can't be bothered. The bet stands, sight unseen and word unheard.

Does that make me close-minded, as my friend claims?

Well, let's put it this way. The search for perpetual motion machines is as old as machines themselves, so far unsuccessful. The idea violates the laws of physics as we know them. If Orbo is greater than unity it will be the greatest breakthrough in science since science, not what you'd expect to come out of a virtually unknown outfit in Dublin with nothing to show for past success except a website making extravagant claims. All the other bells ring too. This is just not the way science works.

So I think my bet is safe.

Could I be wrong? Of course I could be wrong. Who would have thought, for example, that a 747 could get off the ground, much less fly across the ocean in hours, or that a softball-sized lump of "dirt" could blow up a city?

But some things just don't bear wasting time thinking about. Perpetual motion machines. Antigravity shields. Teleportation. The Fountain of Youth. Better to get on with the joys of living. Like knocking back a cold pint in a pub with my Orbo-fixated friend. And, what the hell, I'll pay for the beers no matter what the outcome of today's demonstration.

I stood on the terrace, newly tiled and damp with dew, and held my breath, sucked in a deep draught of air and held it, knowing that any second the fiery Sun would lift over the horizon. And there! On schedule. To the second. As if someone opened the circular door of a furnace.

And the wind whispered hosannahs. The clouds paused processing in their gorgeous vestments. Geckos ceased their skitterings and genuflected. I let out my breath in a long slow prayer: Introibo ad altare Dei.

Teilhard de Chardin called one of his essays "The Mass on the World." Sunrise is my daily Mass.

I think of an image of Mary Oliver, in a poem called Morning in a New Land:

I stood like Adam in his lonely garden
On that first morning, shaken out of sleep,
Rubbing hs eyes, listening, parting the leaves,
Like tissue on some vast, incredible gift.

A good friend tells me via e-mail that she is reading Leo Tolstoy's Anna Karenina. I read the book for a second time two years ago, in the new translation by Richard Pevear and Larissa Volokhonsky. It's one of those novels I had to read twice -- once in middle age (I would not have had the patience in youth) and once in settled maturity. In middle age, it was all about Anna, and passion, and doubt. In old age -- for me at least -- it's about Levin, settled, happily married, enjoying as much intellectual peace as might be possible in this big, sprawling epic of a world.

The book ends with Levin on the terrace of his house under a starry sky. Away on the horizon a storm has gathered and lightning flashes. He meditates on his Christian faith and its ethical imperatives, and on the vast and seemingly indifferent universe of nebulas and distances spread out before his eyes. He thinks about how it is that the stars appear to move, when in fact it is the Earth that turns under the sky. And he thinks too about how a moral imperative is apparently part of the human condition, as much so for the Jew, the Muslim, the Confucian, the Buddhist -- and, one must suppose, the secular agnostic -- as for the Christian. The accident of Christian faith make as little difference to the moral trajectory of his life as does the question of whether it is the stars or the Earth that turns.

In the last words of the novel, Levin muses: "There will be still the same wall between the holy of holies of my soul and other people, even my wife; I shall still go on scolding her for my own terror, and being remorseful for it; I shall still be as unable to understand the mystery of existence, and I shall still go on attending to the mystery; but my life now, my whole life apart from anything that can happen to me, every minute of it is no more intrinsically meaningful or meaningless than it was before, but it still has the positive meaning of goodness which I have the power to put into it."

"Mysteries are not necessarily miracles," said Johann Wolfgang von Goethe. That was two hundred years ago and it is still a lesson we have a hard time learning.

Mysteries surround us on every side, the inevitable consequence of being a finite creature in a possibly infinite universe. For a long time, mystery was subsumed as the province of the gods. Every mysterious event had a miraculous cause. The ways of the gods might be inscrutable, but they had some purpose in the divine mind.

Slowly, mysterious events were shown to have a recurrent causes -- comets followed calculable paths, specific diseases were associated with specific germs, earthquakes occurred along geologic faults. We call this the history of science. And eventually, something rather remarkable dawned in the human mind: a recognition of our own ignorance.

Ignorance may be the most important discovery in the intellectual history of our species. As Goethe suggested, mysteries are not miracles; they are riddles to be solved. We chip away at our ignorance. Mysteries are illumined by the light of reason. And with every "miracle" made commonplace, more mysteries are revealed.

There is a U. S. Christian missionary society that for years has flown its members back and forth to Haiti in a DC3 that stops here in Exuma to refuel. Once, a dozen years or so ago, the plane crashed in a driving rain storm into a hillside near our house. We arrived at the scene just as the passengers, all of whom survived, made their out of the bush to the road. "God was with us," they exclaimed.

I don't want to disparage good people who take themselves to a poor country to help those less fortunate than themselves. The missionaries are certainly less selfish than me. But I couldn't help wonder: If God let them all survive the crash, why did he let the plane crash in the first place? I would be inclined to give the credit for survival not to an interposing divinity, but to that sturdy little DC3 that banged into the hillside and held together.

This incident comes back to mind because the society's replacement DC3 has been making more frequent trips to Haiti in the aftermath of the devastating earthquake, part of a generous outpouring of support -- religious and secular -- for the Haitians. And everyone it seems, is talking about God. Pat Robertson's infamous attribution of God's wrath to a Haitian "pact to the devil." President Obama's "but for the grace of God, there go we." Haitian bishop Eric Toussaint's "What happened is the will of God." And any number of Haitian locals and visitors interviewed by the media who thanked God for their survival.

We are faced here with the problem of theodicy: If God is good, just, and all-powerful, why does he (he!) let bad things happen to good people? Why does he scourge some and favor others?

After millennia of struggling with this question, theologians are no closer to an answer than ever. The best they can do is ascribe inscrutable motives to the divinity; only God knows what he has in mind but it's surely all for the best. Writing in the New York Times, James Woods draws the logical conclusion: If God's actions are as capricious as nature, then he is effectively nonexistent.