Saxothon: John Coltrane

April 13, 2011 • 3:23 am

I guess this song is sort of a Coltrane cliche, but it never grows old.  Who else could take a sappy Rogers and Hammerstein song from The Sound of Music and turn it into a jazz classic?

Here’s the great John Coltrane playing “My Favorite Things” live (it appeared on the eponymous album in 1961).  Coltrane has a fantastic group here: McCoy Tyner on piano,  Elvin Jones on drums, and Steve Davis on bass.  And Trane plays a soprano rather than a tenor sax.  I don’t know who does the flute solo (I’m sure one of you knows), but I could have done without it.

The liner notes on the YouTube site say more about this remarkable performance.

The Passion of Joan of Arc

April 12, 2011 • 11:59 am

The movie named in the title, made in 1928, is by far the best silent movie I’ve ever seen.  In a four-minute video in today’s New York Times, critic A. O. Scott shows scenes from the movie and discusses its significance (be sure to enlarge the video to full screen).  Maria Falconetti’s performance is one of the most powerful of any I’ve seen on film, and she does it without saying a word.

If you have NetFlix, or can get it otherwise, don’t miss it!

Lynn Margulis disses evolution in Discover magazine, embarrasses both herself and the field

April 12, 2011 • 10:00 am

Around 1970, biologist Lynn Margulis achieved renown for suggesting, and then showing, that eukaryotic cells originated by a symbiotic union of early prokaryotes, with some engulfing others and then the engulfed bacteria evolving into at least two of the cell’s vital organelles:  mitochondria and (in plants) chloroplasts.  Although others had suggested this before, Margulis gets the credit for pushing the theory forward, supporting it with biochemical and microbiological data, and recognizing its implications.  Later work on DNA sequencing supported her completely.  She became famous and was elected to the National Academy of Sciences.

To reword the old political slogan for science: fame corrupts, and huge fame corrupts hugely.  This isn’t always true, but if a scientist achieves tremendous fame and adulation, there’s always the temptation to think that what you say on every topic bears special weight and consideration. Such solipsism is especially likely to develop in those who, like Margulis, have to push a correct theory against the entrenched doubt and scorn of their colleagues.

And Margulis has become corrupted in this way.  In the last couple decades she’s been going around casting doubt on modern evolutionary theory. She has said, for example, that modern evolutionary biology is “a minor twentieth-century religious sect within the sprawling religious persuasion of Anglo-Saxon biology” and that  “Neo-Darwinism, which insists on (the slow accrual of mutations), is in a complete funk.”  Since she’s famous, she’s invited many places, and often uses these occasions to dump on modern evolutionary biology.  In this respect she may be worse for science than creationists, since her scientific credibility remains high.  You may also remember that Margulis “handled” (i.e., allowing it to be published despite dissenting referees) the Williamson paper positing a hybrid origin of the lepidopteran life cycle (caterpillar then adult) through mating of an ancestral volant butterfly with a velvet worm.  (The paper was subsequently debunked.)  I suspect she forced it into publication because it fits her notion that symbiosis—and I suppose you can consider hybridization as something akin to symbiosis—is the overarching factor in evolution.

Margulis and her son, Dorion Sagan, even wrote a book on speciation, Acquiring Genomes, suggesting that the criticial factor in the origin of species was endosymbiosis.  I was asked to review it for The New York Times, but it was so dreadful, so completely ignorant of decades of work on speciation (including observations that reproductive barriers nearly always map to genes, not cytoplasmic organelles), that, although I enjoy writing for the Times, I refused on this occasion. I didn’t want to publicize such a misguided book.

But today I am giving publicity to Margulis’s new six-page interview in Discover magazine.  There is lots of dreadful stuff in the interview, including her notion that AIDS is really syphilis, not viral in origin at all. But let’s concentrate on the evolution-dissing, where she sounds awfully like a creationist:

This is the issue I have with neo-Darwinists: They teach that what is generating novelty is the accumulation of random mutations in DNA, in a direction set by natural selection.  If you want bigger eggs, you keep selecting the hens that are laying the biggest eggs, and you get bigger and bigger eggs. But you also get hens with defective feathers and wobbly legs.  Natural selection eliminates and maybe maintains, but it doesn’t create.

You don’t always get creatures that are so defective under artificial selection:  house cats are doing pretty well, so long as you don’t screw with their faces to create Persians.  True, many artificially selected species wouldn’t survive in nature, for humans often desire traits that would be maladaptive in the wild. Corn, for example, has been selected to keep its seeds on the cob rather than “shatter”, or scatter them about.  Not scattering your seeds is about the worst thing you can do as a plant in nature.

But where on earth does Margulis get the idea that artificial selection shows that “natural selection doesn’t create”?  Artificial selection, of course, does create, in that, as Darwin famously noted, humans can mold animals or plants into pretty much anything they like. This shows that combining different mutations can make something new: it can turn an ancestral plant into either a cauliflower, a kohlrabi, a Brussels sprout, or a cabbage (all derived from the same species).  And if those changes increased fitness in nature, as for example the combination of traits that turned an ancestral artiodactyl into a whale, why wouldn’t natural selection create something new?  The fossil record for the evolution of major taxa attests to this completely—unless Margulis thinks that flippers, feathers, and the like all arose by symbiosis or hybridization.  I suspect that she does, which would be a ludicrous and unsupported point of view.  After all, that is how, in her speciation book with Dorion Sagan, she suggested that most new species arise.

Margulis goes on to tout punctuated equilibrium—the observation that some evolutionary change in the fossil record happens quickly, while most of the time species are static.  The jury is still out on how many lineages really show that pattern, but no exponent of punctuated equilibrum—not Gould, not Eldredge, not my own colleagues here in Chicago—would say that the observation of “jerky” evolution vitiates natural selection. Margulis simply doesn’t understand punctuated equilibrium.

Margulis agrees with the creationists about the inefficacy of selection and of the neo-Darwinist paradigm:

The critics, including the creationist critics, are right about their criticism. It’s just that they’ve got nothing to offer but intelligent design or “God did it.” They have no alternatives that are scientific.

Well, at least she’s not crazy enough to accept god as a scientific explanation.  But she is crazy enough to proffer her “alternative” theory, which of course is symbiosis.  But think about how we could explain either speciation or adaptation as results of symbiosis—either narrowly construed as engulfing and incorporating a different organism into your own body, or broadly construed as hybridization.  If that were the case, major evolutionary innovations would arise instantly, and by “instantly” I mean within a few generations.  Yes, that’s what happened when bacteria and mitochondria became organelles in cells, and we occasionally do see the rapid origin of species through hybridization (e.g., the phenomenon of “polyploidy” in plants and “diploid hybrid speciation” in plants and animals).

But these events are not the rule, as Margulis implies, but—with the exception of polyploidy in plants—very rare occurrences.  Why do we think so? Because we can see the origin of new adaptations and lineages in the fossil record, and they ain’t instantaneous!  Think of the evolutionary transition from fish to amphibians, from amphibians to reptiles, from reptiles to mammals, from theropod dinosaurs to birds, from landlubber artiodactyls to whales. Or the evolution of our own species from smaller ancestors with apelike skulls. Each of these transitions took millions of years, and we can see the changes gradually accumulating in the fossils.  If this all occurred by symbiosis—a ludicrous notion on the face of it—you’d see either one or a series of instantaneous jumps creating evolutionary novelty.  We don’t see that.

And genetic analysis, which can pinpoint genes responsible for both new traits and new species, invariably shows that these new phenomena are due not to the wholesale engulfing of other species, but to changes in an organism’s DNA. Examples abound: see my own book with Allen Orr, Speciation, for the data on traits distinguishing closely related species.

Finally, Margulis seems to have a special beef against population geneticists:

Darwin was saying that changes accumulate through time, but population geneticists are describing mixtures that are temporary.  Whatever is brought together by sex is broken up in the next generation by the same process. Evolutionary biology has been taken over by population geneticists. They are reductionists ad absurdum.

This is insane.  Genes become “fixed” (i.e., come to characterize entire species) because they positively affect survival and reproduction.  And you can have sets of genes that do the same thing.  A gene moving the nostrils of an ancestral whale atop its head, so that they become a blowhole enabling it to breathe while partly submerged, will become fixed.  And so will genes that, at the same time, transform the species’ front limbs into flippers.  There is no “breaking up” of these good genes by sex—they become fixed at the same time because they’re all good, as are other genes for hair loss, reduction of the hind limbs, losing external ears, and the like.  Attacking population genetics as unworkable reductionism really shows Margulis’s ignorance about the field, and exposes her as not a thinker but a demagogue.

Finally, Margulis said something about my Ph.D. advisor, Dick Lewontin, that really bothered me.  She characterized him as a money-grubbing scientist driven to take grant money for work that he knows is meaningless:

Population geneticist Richard Lewontin gave a talk here at UMass Amherst about six years ago, and he mathematized all of it—changes in the population, random mutation, sexual selection, cost and benefit. At the end of the talk he said, “You know, we’ve tried to test these ideas in the field and the lab, and there are really no measurements that match the quantities I’ve told you about.” This just appalled me. So I said, “Richard Lewontin, you are a great lecturer to have the courage to say it’s gotten you nowhere. But then why do you continue to do this work?”  And he looked around and said, “It’s the only thing I know how to do, and if I don’t do it I won’t get my grant money.”

Well, fortunately I have a good relationship with Dick, and, like Woody Allen with Marshall McLuhan, I have him here behind the sign.  And, like Marshall McLuhan, Lewontin affirms that Margulis knows nothing of his work. (Yes, life can be like that!)

I called up Dick this morning and read him Margulis’s quote.  He said that it completely mischaracterized his views and what he must have said at Amherst.  Lewontin said that he thinks that purely mathematical models of population genetics have largely failed to help us understand the distribution of gene frequencies in nature, because those models often make assumptions that are either incorrect or untestable.  So while mathematical theory in population genetics has had some successes, he said, it hasn’t been nearly as useful as we hoped. That’s why, Dick claimed, he stopped doing pure equations and started doing computer simulations, which he considers a more realistic way to see what can happen in nature. In simulations one can vary the parameters more easily and check the models’ sensitivity to varied conditions.  In fact, Dick said that ages ago he stopped submitting grants that proposed purely mathematical approaches. So Margulis’s characterization of Lewontin as a dishonest huckster trying to fund work that he knew was bogus is inaccurate and unfair.

Lewontin wanted me to add (for I have permission to quote him here), that his purpose in getting grant money was not simply to fund designated projects described in his research proposals, but to “run an institution”: to “fund a group of creative people to do what they want.”  And indeed, that’s what he did—and that’s what many grant-funded investigators do.  We can’t always predict how our proposed research will turn out; in fact, we know it will turn out differently from the projects we describe in our proposals.  And the granting agencies like the NIH also know this well.  In many ways, grants are not just given for proposed projects, but for demonstrated accomplishments of a group of investigators. For many years Lewontin ran one of the most productive groups in modern evolutionary genetics. I was proud to be a part of it.

When I read him Margulis’s statement, designed to denigrate population genetics, Lewontin didn’t recognize at all the caricature she had drawn.  Margulis simply distorted his views, which I’ve just described, as another way of dismissing modern evolutionary biology.

When discussing evolutionary biology, then, Margulis is dogmatic, willfully ignorant, and intellectually dishonest.  She does deserve plaudits for not only her early work on symbiosis, but for having the tenacity to push for her ideas in the face of considerable opposition. But that tenacity is being misapplied here.  She’s simply wrong—and wrong in the worst way a scientist can be wrong: ignoring all the data that go against her theories.  But what do you expect of someone who answers the interviewer’s last question like this?:

Dick Teresi (the inteviewer): Do you ever get tired of being called controversial?
Margulis:  I don’t consider my ideas controversial. I consider them right.

She’s almost religious in her fanaticism.

I’m not sure what I think about Discover publishing this.  The reviewer isn’t critical at all—Teresi doesn’t offer any counterarguments to her specious assertions about evolution, which a good interviewer should do.  You could argue that this isn’t 60 Minutes, but a scientific magazine.  Nevertheless, Margulis’s interview comes off as unsullied, uncontested, and ultimately unwarranted criticism of modern evolutionary biology (it has, of course, already been picked up by the creationist Discovery Institute). It would seem incumbent on Discover to offer a counteropinion.  Otherwise, they’ve acted like a boxing referee who lets a favored pugilist get away with punching below the belt.

Charlie Parker: Embraceable You

April 12, 2011 • 5:03 am

To me, one of the most amazing human activities is musical improvisation, especially in jazz. How can somebody come up with a new and appealing variation of a theme, and play it on the spot? It’s this instant translation of thought into music—good music—that so baffles me.

One of the best examples comprises two takes of the George and Ira Gershwin classic “Embraceable You,” by perhaps the greatest jazz saxophonist in history:  Charlie Parker (1920-1955).  Parker recorded both versions in New York City on October 28, 1947.  The differences between them, reflecting Parker’s tastes at the moment of playing, are profound.  I won’t go on about Parker, but would recommend a nice biography, not very scholarly but immensely readable:  Bird Lives!

The group is the Charlie Parker Quintet, including Duke Jordan on piano, Tommy Potter on bass, Max Roach on drums, and a young Miles Davis on trumpet.  I like the first take better, but both are great.  This is in fact my favorite Parker recording, for he was just as great on ballads like this as he was on hard-driving bebop.

Scientism

April 11, 2011 • 7:29 am

After reading a dire piece at the National Public Radio (NPR) website about novelist Marilynne Robinson and her continuing beef about “scientism”, I think I’ve finally figured out why atheists are constantly accused of this behavior.  When we’re said to be guilty of “scientism”, it’s not intended to mean that atheists or scientists are cold, unfeeling rationalists, blind to the beauty and wonder of this world. Nor does it mean that we employ science in every interaction we have with the world, including viewing art, being in love, and so on.  Nobody with eyes to see could support such an accusation.  Scientists are a well read group (I still maintain that we read far more novels than English professors read science books), have families and fulfilling relationships, and many of us, like Sagan and Dawkins, are outspoken about the beauty we find in our work and our world.

No, when used as a derogatory adjective, “scientism” means this:

the practice of applying rationality and standards of evidence to faith.

For religious people and accommodationists, that practice is a no-no.  That’s why the adjective is pejorative.

“Scientism”, then, is a religious code word in the same sense that “spirituality” is code for “feelings of transcendence that should be considered religious.”  Perhaps I’m belaboring the obvious.

Robinson, a superb novelist (I much enjoyed Housekeeping and Gilead, which nabbed a Pulitzer), is also religious—a Congregationalist who sometimes preaches at her church.  And she’s been on a crusade against atheism, writing and speaking about it often—and always connecting it with scientism.  Her new book, Absence of Mind (I haven’t read it) continues this critique; the Yale University Press describes it as “challeng[ing] postmodern atheists who crusade against religion under the banner of science.”  Yep, that’s nasty us, asking for evidence. But what is a “postmodern” atheist?

Marcelo Gleiser’s NPR piece, engagingly titled “Can scientists overreach?” (the answer of course is “yes”), is merely regurgitation and adulation of Robinson’s views.  (Gleiser is a physics professor at Dartmouth.)

Robinson is particularly critical of fundamentalist scientism as preached by Richard Dawkins, Daniel Dennett and Steven Pinker, among others. The reading is tough, but well worth it.

“Fundamental scientism”? Is that what characterizes “postmodern atheism”?

This, in a nutshell, is the crux of her argument: Science paints a wonderful picture of the world, but a necessarily incomplete one. To reduce everything to science and its methods impoverishes humanity. We need cultural diversity and that includes the culture of religion.

Of course I agree that we need cultural diversity, but I’m not on board with an aspect of cultural diversity that endorses lies, enables superstition, or propagandizes children.  Gleiser goes on:

What makes some scientists so sure of their science? The practice of science, after all, relies precisely on uncertainties; a theory only works until its limits are exposed. In fact, this is a good thing, since new theories sprout from the cracks of old ones.

For science to advance it needs to fail. The truths of today will not be the truths of tomorrow. So, asks Robinson, whence comes this certainty? She goes on to examine several cases, pointing out their weaknesses. Essentially, scientists shouldn’t be making sweeping generalizations based on their science alone.

Religionists’ claim that scientists are arrogant always amuses me.  Really, who are the arrogant ones?  Scientists are nearly always tentative in their conclusions. Lately I’ve been reading a bunch of papers on evolution, and was struck by how often conclusions are qualified by words like “this suggests that” or “this conclusion should be regarded as provisional”.  Many papers suggest additional lines of research that could support or falsify their conclusions. In the end, it is religious people who are the certain ones, the overbearing ones.  How often do you hear, in religious discourse, that “my conclusion that there is god should, of course, be seen as provisional, subject to refutation by findings of unjustifiable evil,” or “maybe there’s a heaven, but maybe not; I don’t have much evidence.”  If they relied at all on evidence, the faithful wouldn’t be able to say anything.

And it’s bogus to suggest that all scientific truth is ephemeral, for some truths of today will remain truths of tomorrow.  A water molecule will still have two hydrogen atoms and one oxygen atom; AIDS will still be caused by a virus; the Earth will still go around the Sun.  Although the concept of absolute and unchangeable truth is alien to science, we’ve found out a lot of things that are likely to remain “true” in that they’re unlikely to be overturned.   In her postmodern claim that scientific “evidence” is weak and changeable, Robinson clearly intends to denigrate science by showing that, after all, it’s not so different from religion. (Perhaps she doesn’t remember that she is religious?)  Robinson sees other similarities as well: science, like religion, can be used for bad ends:

In 2006, Robinson wrote a scathing review of Dawkins’s The God Delusion for Harper’s Magazine, “Hysterical Scientism: The Ecstasy of Richard Dawkins.”

“So bad science is still science in more or less the same sense that bad religion is still religion. That both of them can do damage on a huge scale is clear. The prestige of both is a great part of the problem, and in the modern period the credibility of anything called science is enormous. As the history of eugenics proves, science at the highest levels is no reliable corrective to the influence of cultural prejudice but is in fact profoundly vulnerable to it.” . . .

. . . I also quote her last words:

“It is diversity that makes any natural system robust, and diversity that stabilizes culture against the eccentricity and arrogance that have so often called themselves reason and science.”

According to this theory, Scandinavia should be far less “robust” than America or, indeed, Saudi Arabia.  But the opposite is true.  As Greg Paul has shown, there’s actually a negative correlation between the religiosity of a society and sociological indices of its well being.  That doesn’t prove that religion destabilizes society, but it does suggest that unstable and dysfunctional societies become religious in a defensive way—either to find succor in a celestial sky-father or as a circling of the wagons, an ingroup-outgroup stance that one assumes when feeling beleaguered.

It’s really sad that a brilliant novelist like Robinson uses her brainpower to denigrate science in a public attempt to buttress her faith. At the end, Gleiser parrot’s Robinson’s accommodationism:

Frontal attacks on religion and its practices will only produce more animosity. Fundamentalism leads to further entrenchment, not to conciliation. Perhaps a better approach is to teach science as it truly functions, constantly engaged in a two-way exchange with the culture of its time.

Perhaps a better approach is to teach religion as it truly functions, constantly engaged in lying to children and retooling its dogma as science and secular morality advance.  Why do we need conciliation?

Hitch extols the Bible, revises Ten Commandments

April 11, 2011 • 3:48 am

The story of the King James Bible, and how it was written by committee, is fascinating.  I highly recommend Adam Nichol’s volume on the topic, God’s Secretaries, one of the most engrossing books about religion I’ve ever read.  Over at Vanity Fair, Christopher Hitchens writes about the King James and Tyndale Bibles in “When the King saved God,”  If you’re a Hitchens aficionado, a lot of this is familiar, but there are some nice tidbits:

It’s [the attempt to get the Bible printed in English] a long and stirring story, and its crux is the head-to-head battle between Sir Thomas More and William Tyndale (whose name in early life, I am proud to say, was William Hychyns). . .

Upon hearing the words “Hoc” and “corpus” (in the “For this is my body” passage), newly literate and impatient artisans in the pews would mockingly whisper, “Hocus-pocus,” finding a tough slang term for the religious obfuscation at which they were beginning to chafe.

Hitchens compares the King James version (1611) to William Tyndale’s 1525 translation (Tyndale, of course, was ultimately strangled for his efforts); the later version doesn’t always come off better:

Tyndale, incidentally, was generally good on the love question. Take that same Epistle of Paul to the Corinthians, a few chapters later. For years, I would listen to it in chapel and wonder how an insipid, neuter word like “charity” could have gained such moral prestige. The King James version enjoins us that “now abideth faith, hope and charity, these three; but the greatest of these is charity.” Tyndale had put “love” throughout, and even if your Greek is as poor as mine you will have to admit that it is a greatly superior capture of the meaning of that all-important original word agape. It was actually the frigid clerical bureaucrat Thomas More who had made this into one of the many disputations between himself and Tyndale, and in opting to accept his ruling it seems as if King James’s committee also hoped to damp down the risky, ardent spontaneity of unconditional love and replace it with an idea of stern duty. Does not the notion of compulsory love, in any form, have something grotesque and fanatical about it?

Hitchens argues that to be considered educated, even in our era, you simply must know the Bible, preferably the Tyndale or King James versions. Few of us would disagree.  One example:

Though I am sometimes reluctant to admit it, there really is something “timeless” in the Tyndale/King James synthesis. For generations, it provided a common stock of references and allusions, rivaled only by Shakespeare in this respect. It resounded in the minds and memories of literate people, as well as of those who acquired it only by listening. From the stricken beach of Dunkirk in 1940, faced with a devil’s choice between annihilation and surrender, a British officer sent a cable back home. It contained the three words “but if not … ” All of those who received it were at once aware of what it signified. In the Book of Daniel, the Babylonian tyrant Nebuchadnezzar tells the three Jewish heretics Shadrach, Meshach, and Abednego that if they refuse to bow to his sacred idol they will be flung into a “burning fiery furnace.” They made him an answer: “If it be so, our god whom we serve is able to deliver us from the burning fiery furnace, and he will deliver us out of thy hand, o King. / But if not, be it known unto thee, o king, that we will not serve thy gods, nor worship the golden image which thou hast set up.”

Finally, Hitchens excoriates, as only he can, the attempts to modernize the Bible and make it user friendly.

Here, from last year, is Hitchens on the Ten Commandments.  He handles the spoken word like a jazzman handles notes.  At the end, he creates his own Ten Commandments; my favorite is Number Eight.

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