Monday, December 31, 2007

Jay Fitzgerald hits the nail right on the head with regards to what's wrong with conservative journalism today:
Here's a dirty little secret about modern conservativism, as gleaned by yours truly while devouring National Review, American Spectator etc. during my brief hard-core conservative stint in the '80s: Many conservative pundits and intellectuals have an inferiority complex when it comes to arguing with liberals. They know that liberals have an all-encompassing view of the world that provides them with ready-made put downs (accusations of fascism, McCarthyism etc.) -- and for years that argumentative style infuriated conservatives to the point where the former publisher of National Review, William Rusher, wrote a book called 'How to Win Arguments.' For years, the book was heavily advertised in National Review -- along with countless articles dwelling on conservative frustrations with getting around the arguments of liberals and their allied lackeys in the media. That debate-club compulsion to win arguments became part of the modern conservative mindset -- with the ultimate debate-club tactic being to turn the tables on liberals, or 'to fight fire with fire,' as one conservative friend once put it to me.
As readers of this blog are aware (all three of them), I've long been a critic of the poor quality of conservative journalism when it comes to science. So Jay's take comes as no surprise. (But he puts it better than I did....)

Sunday, December 30, 2007

Life on the Road
It can be tough spending the post holiday in Montreal.

Here's to a Happy 2008.

Wednesday, December 26, 2007

Book Notes
Norman Leavitt deconstructs Steve Fuller.
Teresa Nielsen Hayden reminds us, this Christmas, of how important language is and why it is so much fun to trace its evolution:

Luke 2:1-14, Anglo-Saxon (via):

Soþlice on þam dagum wæs geworden gebod fram þam casere Augusto, þæt eall ymbehwyrft wære tomearcod. Þeos tomearcodnes wæs æryst geworden fram þam deman Syrige Cirino. And ealle hig eodon, and syndrige ferdon on hyra ceastre. Ða ferde Iosep fram Galilea of þære ceastre Nazareth on Iudeisce ceastre Dauides, seo is genemned Beþleem, for þam þe he wæs of Dauides huse and hirede; þæt he ferde mid Marian þe him beweddod wæs, and wæs geeacnod. Soþlice wæs geworden þa hi þar wæron, hire dagas wæron gefyllede þæt heo cende. And heo cende hyre frumcennedan sunu, and hine mid cildclaþum bewand, and hine on binne alede, for þam þe hig næfdon rum on cumena huse. And hyrdas wæron on þam ylcan rice waciende, and nihtwæccan healdende ofer heora heorda. Þa stod Drihtnes engel wiþ hig, and Godes beorhtnes him ymbe scean; and hi him mycelum ege adredon. And se engel him to cwæð, Nelle ge eow adrædan; soþlice nu ic eow bodie mycelne gefean, se bið eallum folce; for þam to dæg eow ys Hælend acenned, se is Drihten Crist, on Dauides ceastre. And þis tacen eow byð: Ge gemetað an cild hræglum bewunden, and on binne aled. And þa wæs færinga geworden mid þam engle mycelnes heofenlices werydes, God heriendra and þus cweþendra, Gode sy wuldor on heahnesse, and on eorðan sybb mannum godes willan.

Luke 2:1-20, tr. John Wycliffe, 1382 (via)

And it was don in tho daies, a maundement wente out fro the emperour August, that al the world schulde be discryued. :: This firste discryuyng was maad of Cyryn, iustice of Sirie. :: And alle men wenten to make professioun, ech in to his owne citee. :: And Joseph wente vp fro Galilee, fro the citee Nazareth, in to Judee, in to a citee of Dauid, that is clepid Bethleem, for that he was of the hous and of the meyne of Dauid, :: that he schulde knouleche with Marie, his wijf, that was weddid to hym, and was greet with child. :: And it was don, while thei weren there, the daies weren fulfillid, that sche schulde bere child. :: And sche bare hir first borun sone, and wlappide hym in clothis, and leide hym in a cratche, for ther was no place to hym in no chaumbir. :: And scheepherdis weren in the same cuntre, wakynge and kepynge the watchis of the nyyt on her flok. :: And lo! the aungel of the Lord stood bisidis hem, and the cleernesse of God schinede aboute hem; and thei dredden with greet drede. :: And the aungel seide to hem, Nyle ye drede; for lo! Y preche to you a greet ioye, that schal be to al puple. :: For a sauyoure is borun to dai to you, that is Crist the Lord, in the citee of Dauid. :: And this is a tokene to you; ye schulen fynde a yong child wlappid in clothis, and leid in a cratche. :: And sudenli ther was maad with the aungel a multitude of heuenli knyythod, heriynge God, :: and seiynge, Glorie be in the hiyeste thingis to God, and in erthe pees be to men of good wille. :: And it was don, as the aungelis passiden awei fro hem in to heuene, the scheephirdis spaken togider, and seiden, Go we ouer to Bethleem, and se we this word that is maad, which the Lord hath maad, and schewide to vs. :: And thei hiyynge camen, and founden Marie and Joseph, and the yong child leid in a cratche. :: And thei seynge, knewen of the word that was seid to hem of this child. :: And alle men that herden wondriden, and of these thingis that weren seid to hem of the scheephirdis. :: But Marie kepte alle these wordis, berynge togider in hir herte. :: And the scheepherdis turneden ayen, glorifyinge and heriynge God in alle thingis that thei hadden herd and seyn, as it was seid to hem.

Luke 2:1-20, tr. William Tyndale, 1530

And it chaunced in thoose dayes: yt ther went oute a comaundment from Auguste the Emperour that all the woorlde shuld be taxed. :: And this taxynge was ye fyrst and executed when Syrenius was leftenaut in Syria. :: And every man went vnto his awne citie to be taxed. :: And Ioseph also ascended from Galile oute of a cite called Nazareth into Iurie: vnto ye cite of David which is called Bethleem because he was of the housse and linage of David :: to be taxed with Mary his spoused wyfe which was with chylde. :: And it fortuned whyll they were there her tyme was come that she shuld be delyvered. :: And she brought forth her fyrst begotten sonne and wrapped him in swadlynge cloothes and layed him in a manger because ther was no roume for them within in the ynne. :: And ther were in the same region shepherdes abydinge in the felde and watching their flocke by nyght. :: And loo: the angell of ye lorde stode harde by them and the brightnes of ye lorde shone rounde aboute them and they were soare afrayed. :: But the angell sayd vnto them: Be not afrayed. For beholde I bringe you tydinges of greate ioye yt shal come to all ye people: :: for vnto you is borne this daye in the cite of David a saveoure which is Christ ye lorde. :: And take this for a signe: ye hall fynde ye chylde swadled and layed in a mager. :: And streight waye ther was with the angell a multitude of hevenly sowdiers laudynge God and sayinge: :: Glory to God an hye and peace on the erth: and vnto men reioysynge. :: And it fortuned assone as the angels were gone awaye fro them in to heven the shepherdes sayd one to another: let vs goo eve vnto Bethleem and se this thynge that is hapened which the Lorde hath shewed vnto vs. :: And they cam with haste and founde Mary and Ioseph and the babe layde in a mager. :: And when they had sene it they publisshed a brode the sayinge which was tolde them of that chylde. :: And all that hearde it wondred at those thinges which were tolde the of the shepherdes. :: But Mary kept all thoose sayinges and pondered them in hyr hert. :: And the shepherdes retourned praysinge and laudinge God for all that they had herde and sene evyn as it was told vnto them.

Read the rest!

Tuesday, December 25, 2007

Best wishes to all this Christmas, 2007.

Monday, December 24, 2007

This Christmas, it seems, life is not so good at the Origin:
Israel cannot afford to lose the Palestinian Christians: They have long represented a moderating force. A century ago, they accounted for 25% or more of the Holy Land population. Today, they represent less than 1.5%. Since 2000, Bethlehem alone has lost 10% of its Christian population.

Palestinian Christians regard their ancestors as the first Christians, and no doubt some of them were. They call themselves the "living stones" of Biblical Christianity, preserving ancient communities and traditions in the midst of repeated armed conflicts. They deserve to keep their land and work for "peace on earth, goodwill toward men."

In this crisis they deserve the support of all Americans, not just Christians. And not just at Christmas.

Friday, December 21, 2007

Overlooked reviews that shouldn't be overlooked (er, by me, that is):
Hitchens claims that some of his best friends are believers. If so, he doesn't know much about his best friends. He writes about religious people the way northern racists used to talk about "Negroes" -- with feigned knowing and a sneer. God Is Not Great assumes a childish definition of religion and then criticizes religious people for believing such foolery. But it is Hitchens who is the naïf. To read this oddly innocent book as gospel is to believe that ordinary Catholics are proud of the Inquisition, that ordinary Hindus view masturbation as an offense against Krishna, and that ordinary Jews cheer when a renegade Orthodox rebbe sucks the blood off a freshly circumcised penis. It is to believe that faith is always blind and rituals always empty -- that there is no difference between taking communion and drinking the Kool-Aid (a beverage Hitchens feels compelled to mention no fewer than three times).
Former college classmate and now Our Man in Rome, Father John Wauck, says it's too soon to give up on "old" Europe.

He's right.
I hereby second Jay Fitzgerald on his endorsements.
Friday dose of Krauthammer:

It took Bush three years to find his general (as it did Lincoln) and turn a losing war into a winnable one. Baghdad and Washington are currently discussing a long-term basing agreement that could give the United States permanent military presence in the region and a close cooperative relationship with the most important country in the Middle East heartland -- a major strategic achievement.

Nonetheless, the pressure on this administration and the next to get out prematurely will remain. There are those for whom our only objective in Iraq is reducing troop levels rather than securing a potentially critical Arab ally in a region of supreme strategic significance.

On North Korea and Iran, with no real options at hand, the Bush administration heads to the finish line doing what Sen. George Aiken once suggested for Vietnam: Declare victory and go home. With no good options available, those decisions are entirely understandable. But if Bush or his successor does an Aiken on Iraq, where success is a real option, history will judge him severely.

Thursday, December 20, 2007

Nick Fraser, the editor at Storyville, is just one of the Brits sizing up the overrated and underrated for 2007:
Ian McEwan’s On Chesil Beach (and for that matter the overrated film based on another overrated book Atonement). McEwan’s work is in the image of contemporary British genteel culture; underpowered, negligible in impact and yet genteelly fêted at bookfests and on the BBC.

Wednesday, December 19, 2007

God's Mechanics

I just finished reading Brother Guy Consolmagno's new book, God's Mechanics. Brother Guy is a Vatican astronomer who specializes in the study of meteorites and dwarf planets. He's also a regular at various science fiction conventions (and I'm hoping to catch up with him at this coming February Boskone), and the thing I liked most about his book, aside from his techie sense of humor, is he gives a very interesting answer (or set of answers) to the question: how do scientists, who are trained to be skeptics, make sense of religion?

Here's a brief sample:
So if doing science is ultimately a religious act, why does the story of a split between science and religion exist in out culture today? Because too many religious people have been scared away from science by the very stories of this split. Because most scientists keep their religion private, as is their right. Because the religious people most likely to be heard in the news are those whose strong bent in engineering hides their very limited education in science: the creationists. Because the scientists who do speak publicly about these topics have been precisely those whose very limited education in religion (people like Richard Dawkins or Stephen Jay Gould) have made them "science fundamentalists"," every bit as narrow as the religious fundamentalists and probably not the best representatives of their fields--just the best known. (p. 169--emphasis mine)
[You can just hear all the caterwauling that will take place on the skeptic blogs once they get wind of this.]

Couldn't resist another bon mot:
"Atheism is a luxury of the well-to-do; it goes hand in hand with flush toilets." (p. 186)

Highly recommended.

It Never Snows on Summer Street

This is a little snippet of my father, the late David J. Farrell, from a new documentary I'm working on over the next several months, in cooperation with other Boston media and political figures, which I hope will give a nice sense of how the city and its media landscape have changed over the last 40 years. Any Boston area journalists or pols who are interested in being interviewed or contributing photos or video from the era, please let me know in the comments section--or email.

Hating Celine...

This is pretty funny:
Wilson’s real obsession here is not Céline but the thorny philosophical problem on which her reputation has been impaled: the nature of taste itself. What motivates aesthetic judgment? Is our love or hatred of “My Heart Will Go On” the result of a universal, disinterested instinct for beauty-assessment, as Kant would argue? Or is it something less exalted? Wilson tends to side with the French sociologist Pierre Bourdieu, who argues that taste is never disinterested: It’s a form of social currency, or “cultural capital,” that we use to stockpile prestige. Hating Céline is therefore not just an aesthetic choice, but an ethical one, a way to elevate yourself above her fans—who, according to market research, tend to be disproportionately poor adult women living in flyover states and shopping at big-box stores. (As Wilson puts it, “It’s hard to imagine an audience that could confer less cool on a musician.”)

Comments anyone? (Don't all holler at once.)

After some prodding by friendly readers, I'm enabling comments. I haven't in the past, mainly because I've found glitches...but it seems that hand-coding the feature on my old template has allowed the proper functioning with we'll see.

Monday, December 17, 2007

Online now: My recent feature article for the Oct/Nov issue of Streaming Media Magazine, Whatever Happened to QuickTime? Those who've been devotees of Apple's coolest software may like this.

Sunday, December 16, 2007

Barfield Reconsidered (by accident)
We're pleasantly snowed in today, and during my morning coffee and reading, a footnote led me off to my attic bookcases and Owen Barfield. I was thumbing through The Rediscovery of Meaning, Barfield's 1977 collection of essays, and landed on "The Coming Trauma of Materialism."

Barfield was an eloquent opponent of reductionism and its effects on society. I had not read him in years however, and about halfway through this essay I stopped short at this pothole:

But it is a long step from an eccentric professor's study with the doors shut to the popular cheap edition of the Origin of Species. Is the surface quite so solid as it looks through the media? According to the Los Angeles Times in October last, an Indiana professor of anthropology criticized his colleagues sharply for declaring "as a fact" that man descended from apelike creatures and suggested that they did so "for fear of not being declared serious scholars or of being rejected from serious academic circles." George MacBeth's Darwin Retried (1971), which is not the only radical critique in the English language published in the last two or three years, consists almost entirely of the quoted utterances of contemporary biologists ranging from Sir Julian Huxley (on television): "The first point to make about Darwin's theory is that it is no longer a theory but a fact" to Professor Ernst Mayr of Harvard: "The basic theory is in many instances hardly more than a postulate." Divergence of opinion on subsidiary details is not less striking; and the book leaves one with a startling impression of head-on conflicts of opinion and a state of general disarray in the citadel, which do not suggest that the garrison is particularly well-equipped to withstand a daylight assault from pure reason.
This paragraph could've been written last week by almost any one of the flaks at several conservative think tanks or journals. Rhetorical juice spectacularly innocent of any acquaintance with scientific facts.

I don't mind saying this has depressed me, for it's evident that Barfield as much as anyone else who was a conservative in the 1970s, was taken in by the romantic notion that Darwin's theory was really a house of cards about to collapse.

Note by the way that Darwin Retried was written by a lawyer (Norman MacBeth, not George), and if you look at the table of contents, it bears more than a passing resemblance to another lawyer's more recent vaunted tome, Darwin on Trial. Happily, the former is out of print.

Note what else has not changed in 30 years:
1. The assumption that scientific academia is a garrison of correct thought. (i.e. what's true in English departments must also therefore be true of science departments.) 2. That the suggestion of differing viewpoints in science is punishable by banishment. And that 3. Darwin's theory doesn't have a leg to stand on, based on selective quotes from aged specialists taken out of context.

One expects this kind of depressing swill from murmurantes like Bethell and Gilder. (I couldn't resist that one, I've also just rediscovered one of St. Thomas's gems: "There is no contradiction in affirming that a thing was created and also that it was never non-existent" from De aeternitate mundi contra murmurantes. You gotta love St. Thomas: "Hey you. Yeah, you, murmurante, what the hell are you talking about?") But still, it was disheartening to rediscover it in Barfield of all people. It makes me question now how seriously I should read him on the other subjects.

That now, 30 years later, amongst an increasingly aged and ossified 'thinking class' of conservatives in institutes and at journals, the same unexamined rhetoric is routinely regurgitated is not a matter for inspiration.

And then they wonder why most college students majoring in science are liberal?

Friday, December 14, 2007

Probably the best assessment of Dawkins I've read yet:
The God Delusion cannot be understood as a work of scholarship or of effective engagement of a topic. It's frequently idiotic, and engages in rhetorical misconduct that disqualifies it as a work of intellectual value. Understood as folk scholarship (we might call it folk theology or folk philosophy), it makes perfect sense. The God Delusion isn't intellectually sound, and it's not meant to be. Its purpose is to make people feel better about their world-view. I have the impression that it's effective in that regard.

Thursday, December 13, 2007

Brendan Hodge takes a closer look at one of the Church's more interesting encyclicals from the last century on social teaching (is capitalism an unfettered good?).
In this sense, what I see as the correct conservative approach to social teaching does not have nearly the warm and comforting glow as the "progressive" approach. And yet, I think it more correctly accounts for the reality of our nature as moral and mortal beings, living out our time on earth in expectation of what is to come.

The phrase "you cannot legislate morality" has been very much overused, and yet in this instance there is a very real truth to it. We cannot achieve the twin aims of respecting people's natural right to property and leaving room for people to behave in a virtuous manner by helping their fellow men unless we simultaneously allow people the opportunity to sin against their fellow men by refusing to help anyone.

Perhaps it is not surprising that in a society in which many loudly blame God (or suggest that he does not exist) for having given us the freedom to sin, many also feel reluctant to leave individual citizens the liberty to sin, or be virtuous, in their use of their personal wealth.

Tuesday, December 11, 2007

Steve Matheson posts a lot less frequently than I would like--but when he does, he's always excellent. From today's post on gene duplication:
First, take note that this article is another example of a sophisticated, hypothesis-driven experimental analysis of a central evolutionary concept. Research like this is reported almost daily, though you'd never learn this by reading the work of Reasons To Believe or the fellows of the Discovery Institute. The mis-characterization of evolutionary biology by the creationists of those organizations is a scandal, and as you might already know, my blog's main purpose is to give evangelical Christians an opportunity to explore the science that is being so carefully avoided by those critics. You don't need to understand sign epistasis or the structure of transcription factors to get this take-home message: evolutionary biologists are hard at work solving the problems that some prominent Christian apologists can't or won't even acknowledge. How does gene duplication lead to the formation of genes with new functions? The folks at the Discovery Institute can't even admit that it happens. Over at Reasons To Believe, they don't mention gene duplication all, despite their fascination with "junk DNA." That's from a ministry that claims to have developed a "testable model" to explain scores of questions regarding origins.

This makes me mad. No matter what you think of the age of the earth or the need for creation miracles, you should be upset by Christians who mangle science to serve apologetic ends.

Monday, December 10, 2007

Larry Krauss is a good scientist who has written some fascinating articles and books. But as Bill Vallicella makes clear, that doesn't excuse him for saying something totally stupid.

Einstein wasn't kidding when he said the man of science is a poor philosopher.
The New York Post has a funny review of the Golden Compass. Best line:
The film is not as silly as it sounds; it's much sillier. Remember the worst line in "Star Wars"? "But I was gonna go to the Tashi station to pick up some power converters!" Imagine a whole movie like that.

Friday, December 07, 2007

Memo to Dinesh D'Souza: Hire a debating coach. D'Souza debated Daniel Dennett at Tufts on November 30th, on the question of whether God is a man-made invention. The QuickTime of the full debate is here. While Dennett was laid back, I didn't find his points particularly challenging, but in response D'Souza was shrill beyond belief. He makes Pat Buchanan look like Ian McKellan. It's painful to watch, and while he had some good points, the heavy-handed delivery undercut his entire performance. Doesn't exactly inspire me to run out and buy his books.
Intelligent Design as scientific career killer. John M. Lynch takes a closer look.

Wednesday, December 05, 2007

There's simply nothing else to say about this appreciation, except...beautiful.

Is it possible to be on the cutting edge of science...for (gasp) religious reasons? Siris looks back to the 17th century...when religion and science were cool with each other.

Monday, December 03, 2007

Steve Matheson has a nice post showing just how seriously biologists take one of the extremely rare examples of peer-reviewed papers published by 'senior' fellows at the Discovery Institute:
What was Wells' idea? Well, he thinks that centrioles look like turbines. So he thinks maybe they are turbines. And so maybe they rotate around each other, just at the right moment during cell division, and create an oscillation in all those microtubules, thereby generating a vortex that drives the polar ejection force. And maybe that rotation is regulated by calcium. That's the Rivista paper in a nutshell.

The ideas are testable, and plausible to the extent that they don't invoke functions or phenomena from way far out. But they aren't based on any data. There are no observations that even suggest that centrioles rotate (and Wells postulates rotation rates of up to 10,000/second), nor have microtubules been seen to exhibit the vortex-like oscillations that Wells' hypothesis predicts. And most importantly, the polar ejection force is not known to affect anything other than chromosomes. But Wells' hypothesis predicts a "wind" blowing into the center of the cell, a wind that would exert force on every particle between the two poles. In other words, even when the paper was published, its ideas came out of left field.

I doubt that the paper has ever been cited by another cell biologist. No one has published any observations to suggest that centrioles rotate or that a vortex is induced in a dividing animal cell. A proof-of-principle experiment would have been technically challenging but perfectly feasible, if a little expensive. (Here's one idea: use video microscopy to look for movement of inert particles, perhaps fluorescent beads, inside the postulated vortex of the mitotic spindle.) Whether Wells ever tested his hypothesis (or whether he meant to), I don't know.

But now, in 2007, there's no need. Two different lines of evidence make Wells' hypothesis unworthy of further consideration.
Either one of those results would have killed the idea.

Sunday, December 02, 2007

A Question of Boundaries
Well, it's been a year since the paperback came out and two years since the hardcover. The reception from most magazine reviewers has been very good. And I can't complain about sales given the modest print run.

Still, there has been a particular criticism raised by two journals which I think deserves response.

The First Things 'briefly noted' review is the more recent example (December 2007 issue, online for subscribers only). It basically hints at the same complaint that Touchstone made in the close of their review of November 2006.

Here's Briefly Noted from First Things:
"Lemaitre, in the author's telling, subscribed to a radical division between scientific and religious truth that many thinkers today would view as naive."

Here's Touchstone. The review, it's worth noting by the way, is by Dr. Guillermo Gonzalez, who is currently (whether he likes it or not I imagine) being held up by the Intelligent Design movement as a martyr because he was recently denied tenure.

"Anyone who has been accused of allowing his religion to cloud his scientific judgment will understand the pressure Lemaître was under. Nevertheless, he and Farrell seem overly zealous in denying any relationship between faith and science generally.

"Scripture is obviously not a twenty-first-century science textbook, but that simple point hardly answers every question at the boundary of faith and science. For instance, surely some scientific evidence could have theological implications. And what could be more theologically suggestive than evidence that the universe had a beginning? Even atheists like Fred Hoyle saw this point clearly. What is perplexing is why it eluded both Lemaître and his biographer."

I'm responding to both--not because I think their point isn't valid, but because I don't think it applies to Lemaître, that Lemaître was too guarded, too strict about a "radical" separation be supposedly built between his faith and his science.

And what could be more theologically suggestive than evidence that the universe had a beginning? Even atheists like Fred Hoyle saw this point clearly. What is perplexing is why it eluded both Lemaître and his biographer.

Well, it didn't if you read the book carefully. First off, recall that Fred Hoyle was dead wrong about the steady state theory, so it's hardly a mark in his favor or the reviewers to remind us that he had metaphysical reasons (his dislike of the Big Bang's implications) for his developing a failed theory in the first place. If anything, Hoyle proves my point: don't mix your science with faith (whether it's good faith or bad). By the way, this might be good advice for Michael Behe who has essentially done more to discredit natural theology with his theory of irreducible complexity than any poorly trained theologian who'd never seen a biology book in his life might have.

Secondly, Lemaître never denied that science can have theological implications--and neither do I. But when he took issue with the Pope in the passage Touchstone's review cited, it's worth recalling what the Pope actually said at the Papal Audience in 1951:

"What was the nature and condition of the first matter of the universe? The answers given differ considerably from one another according to the theories on which they are based. Yet there is a certain amount of agreement. It is agreed that the density, pressure and temperature of primitive matter must each have touched prodigious values.

"Clearly and critically, as when it [the enlightened mind] examines facts and passes judgment on them, it perceives the work of creative omnipotence and recognizes that its power, set in motion by the mighty Fiat of the Creating Spirit billions of years ago, called into existence with gesture of generous love and spread over the universe matter bursting with energy. Indeed, it would seem that present-day science, with one sweep back across the centuries, has succeeded in bearing witness to the august instant of the Fiat Lux, when, along with matter, there burst forth from nothing a sea of light and radiation, and the elements split and churned and formed into millions of galaxies." [emphasis mine]

I think this comes across pretty obviously as more than simply presenting the theological implications of what was at the time a very tentative theory (this was over ten years before the cosmic background radiation was discovered and Hoyle's theory was getting more support from scientists in the UK). The Pope was straightforwardly identifying the Big bang with the "instant of the Fiat Lux". I don't think Lemaître was out of line to point out this was going too far.

It's one thing to keep a wall of separation between your science and faith. I don't think Lemaître did that. He was simply and always careful to distinguish the boundaries between the two, and he thought the Pope was assuming too much in his enthusiasm for the Big Bang. (I might recommend that more enthusiasts of Intelligent Design rethink the theological implications of their own support for it. See, for example, the excellent Edward T. Oakes deconstructing the usual suspects from the Discovery Institute on this point. And Scott Carson.)

Pius XII by the way, was no wallflower. I think he certainly would have stood up for himself if he thought he was right; but he seems to have agreed with Lemaître, as he did not rebuke him on the score when Lemaître later discussed the situation, or continue insisting the Big Bang was "the instant of the Fiat Lux", since he was well aware, as any theologian could have reminded him, God's word preceded all in ontological, not just temporal terms, and therefore could not be subject to or defined by a temporal instant (or any other scientifically measurable quantity) at all.

Lemaître was a better Thomist, I think, than Pius in this case.

Recall that in the great dispute about the eternity of the world in St. Thomas' time, he was careful to point out that 1. philosophically it could not be demonstrated that the world had a temporal beginning, and further, that even if it could be shown the universe was temporally eternal, it in no way changed its radical existential dependence on God. "Hence that the world began to exist is an object of faith, but not of demonstration or science."˜St. Thomas Aquinas, Summa Theologiae, Question 46, Article 2

Lemaître was simply making the same point when he said this:
"As far as I can see, such a theory [Big bang] remains entirely outside any metaphysical or religious question. It leaves the materialist free to deny any transcendental Being. He may keep, for the bottom of space-time, the same attitude of mind he has been able to adopt for events occurring in non-singular places in space-time. For the believer, it removes any attempt at familiarity with God, as were Laplace's chiquenaude or Jean's finger. It is consonant with the wording of Isaias speaking of the "Hidden God", hidden even in the beginning of creation....Science has not to surrender in face of the Universe and when Pascal tries to infer the existence of God from the supposed infinitude of Nature, we may think that he is looking in the wrong direction."

This last sentence bears thinking on.

According to Paul Dirac, he and Lemaître had a conversation once about God and the universe. Dirac was an atheist: "When I was talking with Lemaître about this subject and feeling stimulated by the grandeur of the picture that he has given us, I told him that I thought cosmology was the branch of science that lies closest to religion. However Lemaître did not agree with me. After thinking it over he suggested psychology as lying closest to religion."

It may seem strange that one of the 20th century's greatest physicists saw God more in the actions of his fellow men...and yet that's probably what most ordinary Christians do in our daily lives when we see examples of holiness, heroic courage, kindness, mercy, and self-sacrifice.

If it seems pedantic to point this out, profuse apologies. But I stand my ground in disagreeing with the reviewers at First Things and Touchstone that Lemaître was being too careful about the distinctions all Christians should keep in their minds between science and faith.

Wednesday, November 28, 2007

I've been tagged by DarwinCatholic for my additions to the AFI's less than comprehensive list of the 100 Best Movies of the last century.

Here goes:

1) Your favorite five movies that are on the list.
All About Eve
It Happened One Night
Silence of the Lambs
French Connection
The Wild Bunch

2) Five movies on the list you didn't like at all.
West Side Story
The Sound of Music
The Apartment

3) Five movies on the list you haven't seen but want to.
Yankee Doodle Dandy
Bringing Up Baby
From Here to Eternity

4) Five movies on the list you haven't seen and have no interest in seeing.
Singing in the Rain
The Grapes of Wrath
Mr. Smith Goes to Washington
Birth of a Nation
Rebel Without a Cause

5) Your favoritve five movies that aren't on the list.
Monty Python and the Holy Grail
The Adventures of Baron Munchausen
A New Leaf
The Horror of Dracula
The Cowboys

Tuesday, November 27, 2007

Should we be surprised that the New York Times 2007 100 Notable Books list contains NOT ONE science book? Not really. Patrick Nielsen Hayden sums it up nicely:
You can probably write your own viewing-with-alarm essay about this, complete with obligatory reference to C. P. Snow. All I can say is, what an impoverished mental landscape the people who drew up this list must live in.
Impoverished is the word.
The continuing implosion of William Dembski. This is beyond the kind of thing that makes you wince or shake your head. Seriously, what is wrong with this guy?

Monday, November 26, 2007

Thanksgiving. It's been a good news/bad news holiday. Bad news is a prominent publisher that was seriously interested in my latest book proposal decided ...after several months to pass. Good news is that I'm having my best month in terms of sales for my movies at CustomFlix (now CreateSpace).

Tuesday, November 20, 2007

Did the Church evolve? You might be surprised to find the answer is yes, as explicated by Mike Liccione.
Christopher Hitchens takes a muched need break from ranting about God to pass on the increasingly good news about Iraq:
The surge is only a part of this story. Quite obviously, if the Sunnis of Anbar Province had not of their own volition turned on the hideous forces of al-Qaida, then no amount of extra troops could have made the difference. But some combination of the two things appears to have altered the chemistry, and not just in that province, and all the reporters and soldiers I can get hold of (who include some direly skeptical people in both categories) seem agreed on one thing: The forces of Abu Musab al-Zarqawi stink in the nostrils of the Arab world, and have been—here I borrow some words of Thomas Paine—"in point of generalship … outwitted, and in point of fortitude outdone." Bin Ladenism in Iraq has been dealt a stinging defeat. Surely this is something to celebrate.

Monday, November 19, 2007

I was saddened to hear from Sean Carroll that Harvard physicist Sydney Coleman passed away. He was kind enough some years back to let me interview him for a piece on quantum physics for the American Spectator (Chris Caldwell was an editor there at the time) that, alas, was never published.

Coleman was a realist in the best sense of the word, and he had a great sense of humor. One of my favorite quotes from him occurred during the 1989 World Science Fiction convention in Boston. On a panel about quantum physics, he said,
"If you mentioned quantum physics at a cocktail party ten years ago, everyone would leave the room. More recently a woman approached me and said, 'Isn't quantum physics just what Eastern mystics have been saying for the last two thousand years?' I had to summon every ounce of dignity and told her, 'No.!'

"Reality is still blue, and clouds fly through it."
God rest his soul.
Lowell is staying.
Free-agent third baseman Mike Lowell has agreed in principle to the framework of a three-year deal to return to the Red Sox, major league baseball sources close to the negotiations have confirmed.
("...and there was much rejoicing...")

Sunday, November 18, 2007

Congratulations are in order. Author Gene Wolfe, of whom I wrote in the April issue of First Things, has won the World Fantasy Award for 2007 for Soldier of Sidon. The last time he won was in 1981 for Shadow of the Torturer, the first volume in his Book of the New Sun. Sidon is a masterpiece, in my opinion, in a cycle that I believe is destined to become his defining work.

Friday, November 16, 2007

Could this be the start of a new trend (please, God!)? Another Christian biologist breaks his silence on Intelligent Design.
So in light of the issue’s new prominence and with a desire to improve the mental hygiene of others, I would just like to say that Intelligent Design is a really, really bad idea --scientifically, politically, and theologically. I say this as a dedicated conservative, who has on many occasions defended and espoused religion and religious conservatism. I also say it as a professional molecular biologist, who has worked daily (or at least week-daily) for years with biological problems to which the theory of evolution has contributed significant understanding -- and to which Intelligent Design is incapable of contributing any understanding at all.
More of this, please.

(Hat tip: Ed Brayton.)
Martin Scorcese has a beautiful tribute to Christopher Lee right here, on the occasion of a concert Lee performed recently at Estepona.

Thursday, November 15, 2007

George Vecsey on A-Rod:

This is a good sign. It shows that even baseball owners can learn. Back in the mid-1980s, the owners openly committed collusion by not pursuing free agents, a mistake that eventually cost them money and embarrassment. This time, most of the richer clubs just shrugged — but separately — when Boras peddled his newly liberated client.

“We know there are other opportunities for us,” Rodriguez said yesterday. “But Cynthia and I have a foundation with the club that has brought us comfort, stability and happiness.”

In other words, Boras tossed and lost — with A-Rod’s image. Rodriguez has never justified himself to Yankees fans, having driven in nine runs in 24 postseason games since joining the Yankees with that huge contract in 2004. Even in the highly individualistic sport of baseball, there is a foxhole mentality. The players know Rodriguez works hard, but they also know he has not come through in the postseason.

Alex Rodriguez let his agent opt out for him, right during the World Series. Now the Yankees should opt out on him.

The fallout of the clergy abuse crisis continues to spread. Patricia Snow has a sobering piece today:

Everyone has a story. A priest friend of mine was assigned to a parish in New York City only to discover that his predecessor, in a panic, had eliminated every program involving children. There were no altar servers; there was no religious education. Everything was gone. A woman in another Connecticut parish was forbidden by her pastor to drive her students to a soup kitchen. Another woman, in another parish, couldn’t take a group of teenagers to see The Passion.

In parish after parish, programs have been curtailed or eliminated. When the bishops in Dallas went too far, essentially stripping priests of due process with their policy of zero tolerance, Rome eventually stepped in, restoring balance and justice. Who will step in on behalf of the laity, whose innocence in so many cases is being impugned? Who, in effect, will speak for our girls? “You can’t have community without trust,” I murmured at the workshop, but by that point the momentum was all the other way.

Wednesday, November 14, 2007

I can confirm from personal experience, that Curt Schilling is exactly right:

On coming into next season in good shape ...
"It's not a diet, it's a lifestyle change," said Schilling, who said he woke up around 4:30 a.m. for a short run yesterday, and ran again this morning. "You can't diet. There's just no chance of that happening."

Schilling, who turns 41 years old today, will receive a bonus of up to $2 million if he meets goals at six different weigh-ins. He said he wasn't sure when the first Red Sox weigh-in was, but he said the goals were doable
Diets are for suckers. You're whole lifestyle has to change. My own favorite guide in this area is Walter Willett's Eat, Drink and Be Healthy.
I watched Nova's Judgment Day documentary on the Dover case last night. Larry Arnhart is surely correct that the Discovery Institute and Michael Behe made a disastrous mistake in refusing to be interviewed for the production. I really think this is the end for Behe as a credible scientist.

The PBS documentary accurately conveyed the drama, which is clear in the transcripts of the case, of three turning points: the humiliation of Michael Behe through cross-examination, the evidence from the early drafts of the book OF PANDAS AND PEOPLE, and the perjury of the Dover school board members.

Behe was not able to respond effectively when confronted with a stack of articles and books on the evolution of the immune system. He claimed that there were no evolutionary explanations of the immune system. But he could not explain why this research was not worth studying. Behe should have agreed to be interviewed for this documentary to refute this conclusion.

Tuesday, November 13, 2007

Via Glenn Reynolds (via Rob Long)...

Bill Vallicella has more fun poking easy holes in just about anything tossed off by the tiresome A.C. Grayling.

Monday, November 12, 2007

Is the Church Indifferent to Science?

UPDATE: 7.15.08: This post has been removed. A revised version is now available online in the July '08 issue of Faith.

Saturday, November 10, 2007

It's a working Saturday night for me. Just finished the book trailer for Doctor Janeway's Plague. And it was fun.

Wow. I'm humbled. Thanks to Steve Matheson via Larry Moran for spreading this one. Apparently my blog is at the post-graduate level!

cash advance

Friday, November 09, 2007

Want to see the first HD video of the moon? Check it out.

Thursday, November 08, 2007

My bloglines subscriptions are getting so stacked I have a hard time keeping up with all the good (and often great) material that appears, even over the course of a few days.

For example, here are two excellent posts by Bill Vallicella. Does the Atheist Deny What the Theist Affirms? and A. C. Grayling and a Stock Move of Militant Atheists. The comments at Bill's blog are always excellent.

Monday, November 05, 2007

Jason Rosenhouse, PZ Myers, et al, meet Scott Carson:
It doesn't help that many modern day Christians have abandoned their Neoplatonic roots and think that physical suffering is a Bad Thing that trumps just about everything else, including the fact that our souls are supposedly immortal. If you really have an immortal soul, and if you really believe that everyone else has one too, then you will not worry as much about physical suffering as a person who thinks that the present material existence is the only one there is. But of course, we are called by the Gospel to care for others and to alleviate suffering where we find it, but the call here is not so much to prevent suffering as to cherish life. Although these two things are functionally very similar (indeed, in many cases they are the same), they are not by any means identical, and the failure to see this is often behind the inability to see that the "problem of evil" is not really a problem at all.

As long as we are the byproducts of evolutionary forces--and of course we are--we will have the capacity to feel pain. It is a mistake of a rather elementary kind to try to equate a natural property of a material entity with a moral category like "evil". Sure, we don't like pain and suffering, but it is a mechanism, nothing more. Only a moral relativist of the most distasteful variety would associate moral goodness and badness with what we like and don't like. We feel pain in the way that certain kinds of plants wilt when they don't get enough water--it is just an artifact of the way we are put together, it is not something that an omnibenevolent God "ought" to have prevented if he had cared enough about us to have put us together in a different way. Again, you'd have to be some sort of bizarre fundamentalist committed to intelligent design and young-earth creationism to fall for the kind of crap that equates mere physical suffering with evil in the world.

People sometimes act as though God's justice is at stake in all this. Young babies dying of starvation in Ethiopia are supposed to show us that God is himself somehow evil (or, more benignly, simply non-existent), just as we would accuse a human parent of "depraved indifference" if he calmly watched as his young child wandered out into a busy highway and did nothing to prevent the inevitable. It really does take a village, doesn't it? Why anyone would be attracted to a theology in which God is just one more citizen in the universe, who can be expected to throw himself in front of oncoming traffic or pull careless swimmers out of riptides, is beyond me, but there you have it: if God is just one of us, then we can criticize the rationality of his decisions regarding particular human fates out there in the world. If my theology was as banal as that I would lose my faith, too, because that really is a stupid way to look at things.

Friday, November 02, 2007

Excellent post today by Massimo Pigliucci over at Rationally Speaking:
So we observe the pathetic attempts to undermine science by practitioners of so-called “science studies,” who usually know very little about the science they criticize; on the other hand, high-caliber scientists of the like of physicist Steven Weinberg and biologist E.O. Wilson dismiss philosophy as “armchair speculation,” when they know little about either how philosophy is done or what its goals are (e.g., Weinberg complains that philosophy hasn't solved any scientific problem, apparently without understanding the elementary fact that philosophy is not about solving scientific problems – that's what science is for!).
Weinberg can be surprisingly vacuous, considering he has a Nobel Laureate in physics. His vaunted statement at the close of The First Three Minutes, 'the more the universe seems comprehensible, the more it also seems pointless', gives you an idea of what just one semester introductory course on Philosophy might have spared him back when he was a freshman in college. (And spared his readers.)

For all I know, he did take a course, and slept through it.

Wednesday, October 31, 2007

Publisher's Weekly weighs in on Gene Wolfe's latest novel.
Fantasist extraordinaire Wolfe (The Wizard) dabbles in time travel paradoxes for this charming tale of a monastic novice in postcommunist Cuba. As the years pass, Christopher, the son of an American crime lord, gradually loses touch with his family and decides against taking holy orders. He leaves the monastery and finds himself in the 18th century. This unexplained time slip, along with Chris's equally mysterious jump to the late 20th century, are the only fantastic elements in what's otherwise a fairly straightforward tale of derring-do on the high seas. Wolfe describes his plucky young hero's rise from much abused common seaman to successful pirate captain, filling his story with duels, treachery, ship-to-ship combat and an abundance of accurate period detail, avoiding both the larger than life romanticism and the fantastical elements often associated with such pirate tales. Captain Chris is a laconic and rather unemotional narrator, which may put off some readers, but Wolfe's elegant prose still makes this relatively minor effort (my emphasis) worth reading.

"This unexplained time slip, along with Chris's equally mysterious jump to the late 20th century, are the only fantastic elements in what's otherwise a fairly straightforward tale of derring-do on the high seas." I haven't read it yet myself, so I can't say, but one then wonders why Wolfe bothered to incorporate them into the novel at all.

As with some of his other works, Free Live Free comes to mind, every so often I think Wolfe writes a great novel and, upon revising it, finds it necessary to 'tack on' some SF or fantasy elements to plots that otherwise stand on their own. Or perhaps he begins with the fantasy elements and then the story becomes so good on its own that it outgrows the need for them.

All of which confirms my admittedly snobby opinion that Wolfe has outgrown the genre, and maybe he should just drop the trappings altogether.

(I say this as an inveterate SF reader. )
I've been infected! But in a good way by Steve Matheson's meme which originated with PZ Myers.

The Pharyngula mutating genre meme

There are a set of questions below that are all of the form, "The best [subgenre] [medium] in [genre] is…". Copy the questions, and before answering them, you may modify them in a limited way, carrying out no more than two of these operations:

  • You can leave them exactly as is.

  • You can delete any one question.

  • You can mutate either the genre, medium, or subgenre of any one question. For instance, you could change "The best time travel novel in SF/Fantasy is…" to "The best time travel novel in Westerns is…", or "The best time travel movie in SF/Fantasy is…", or "The best romance novel in SF/Fantasy is…".

  • You can add a completely new question of your choice to the end of the list, as long as it is still in the form "The best [subgenre] [medium] in [genre] is…".

You must have at least one question in your set, or you've gone extinct, and you must be able to answer it yourself, or you're not viable.

Then answer your possibly mutant set of questions. Please do include a link back to the blog you got them from, to simplify tracing the ancestry, and include these instructions.

Finally, pass it along to any number of your fellow bloggers. Remember, though, your success as a Darwinian replicator is going to be measured by the propagation of your variants, which is going to be a function of both the interest your well-honed questions generate and the number of successful attempts at reproducing them.

Okay, here I go:

First, my phylogeny:

My great-great-great-great-grandparent is Metamagician and the Hellfire Club.
My great-great-great-grandparent is Flying Trilobite
My great-great-grandparent is A Blog Around the Clock
My great-grandparent is The Anterior Commissure
My grandparent is Laelaps
My parent is Quintessence of Dust

And my contributions to the meme pool:

The best scary movie in futuristic dystopias is: The Matrix

The best sexy song in pop rock is: Jewel: Near You Always

The best scary story in gothic short stories is: 'Berenice' by Edgar Allan Poe.

The best b-movie style film in 1980's horror films is: Big Trouble in Little China

The best sports moment in the 1980s: Roger Clemens striking out 20 Seattle Mariners in April, 1986.

I hereby tag Scott Carson.
These are not your father's Red Sox.
Tom Verducci of Sports Illustrated sums up the year nicely.

Tuesday, October 30, 2007

Just minutes ago at 500 Boylston Street. Enjoy....

The Sox parade is just getting underway, and I hope to post video from my perch here at Boylston Street later.

Meanwhile, for your viewing pleasure:

Monday, October 29, 2007

One of the greatest heroes of last night's game wasn't even on the roster. But he's someone every dad and mom ought to hold up as a model for their kids.

Curses are just so...last century.

Friday, October 26, 2007

What does it tell you when the American Spectator looks at Mike Huckabee and says...."I don't think so."
Rod Dreher is on a roll:
Another dad, surveying with his wife the options for a Halloween costume for their young daughter, found the following choices:
Witch slut. Witch whore. Baby witch cheerleader slut. From hell. Who dresses their kids in this crap? I'm not some Puritan -- if you're an adult or my prom date and you feel like Witch Crack Whore looks good on you, fine, here's a pipe and $5 for a blow job -- but the thought of dressing up young girls in midriff-baring costumes, slinky skirts and laced-up baby heels had me spinning. It got worse as the girl costumes got older, as if every year in a girl's life means another inch of skirt above the knee. And it had me wondering. "Would anyone ever sell a Chippendale outfit for young boys? Would a parent ever buy one?" Of course not.

Thursday, October 25, 2007

Ten years ago today...when I had basically given up on the idea I was ever going to meet 'the right girl' and was becoming resigned to the reality that I was going to be an Irish bachelor (and a pretty pathetic one) for the rest of my life, I met my wife in a movie theater.

It was this theatre. They were showing this movie, which was okay, as far as the Edwardian style movies go. I spent most of it thinking about the blonde sitting next to me. My sister introduced us. They had met as bridesmaids at the wedding of a mutual friend of theirs a couple of months before...and my sister kept saying 'we should all go out' and I kept saying, 'yeah, whatever,' because, as I mentioned, I was turning into a pathetic Irish bachelor.

In fact, just before we went to the theatre where my future wife was waiting to meet me and my sister, I was hanging out here, and thinking I really didn't want to go to the movies. I just wanted to hang out at the bar with some friends who were there. That's always the way, it seems, just before your life changes forever, you're really thinking you'd rather being doing the same old shi.... um, thing. (See above, and Irish Bacheloritis.)

After the movie the three of us had dinner at the Blue Room. I'm happy to say both institutions--the theatre and the restaurant--are still in existence. Too many other old Boston and Cambridge haunts are long gone.

A week or so later, I called the blonde for a date.

Haven't been back to the Hill since. Now I'm thinking the two of us should maybe make a little pilgrimage.
Edward T. Oakes, S.J. on Cardinal Schönborn's latest book:
...Schönborn can be quite witty. He recounts the story of one of his brother Dominicans harping at table every day about a book he planned to write that was going to prove that man is not essentially different from the other animals. Finally, another Dominican grew weary of these tiresome annunciations and asked, “Father, will this be an autobiography?” The rest of the brethren all laughed—except for the putative author, who kept silent.
Steve Matheson, writing up more good science:
1. Does the evolution of new features require new, rare, mutations in major genes?

Perhaps this seems like a stupid question to you. Anti-evolution propagandists are eager to create the impression that evolutionary change only occurs when small numbers of wildly improbable mutations somehow manage to help and not hurt a species. And in fact, experimental biology has produced good examples of just such phenomena. But there is at least one other genetic model that has been put forth to explain the evolution of new forms. This view postulates that many major features exhibited by organisms are "threshold" traits, meaning that they are determined by many converging influences which add together and -- once the level of influence exceeds a threshold -- generate the trait. The model predicts that certain invariant (i.e., never-changing) traits would nevertheless exhibit significant genetic variation, since evolutionary selection is acting on the overall trait and not on the individual genetic influences that are added together. Hence the implication that...
...populations contain substantial cryptic genetic variation, which, if reconfigured, could produce a discrete shift in morphology and thereby a novel phenotype. Thus, evolution would not be dependent on rare mutations, but on standing, albeit cryptic, genetic variation.
--from Nick Lauter and John Doebley, "Genetic Variation for Phenotypically Invariant Traits Detected in Teosinte: Implications for the Evolution of Novel Forms," Genetics 160:333-342, 2002.

He ends with a note that frankly should be faxed by every thoughtful theist to the ex-Reagan Administration hack who currently runs the Discovery Institute:
So in summary, we can do the experiment. And we've done the experiment. ('We' being John Doebley and his many able colleagues.) And we've learned a lot about evolution and development. Now if we can just get people to read it. Then they'll know more about evolution, and about God's world, and about the trustworthiness of the anti-evolution propaganda machines that are exploiting the credulity of evangelical Christians.
Well said.

Wednesday, October 24, 2007

A great summary of the '07 ALCS by The Sports guy:
Baseball is the only sport where a single person can shut up 55,000 people for an extended period of time and eventually break their will. This was one of those times. Just a virtuoso performance.
Yep. It gets better with the emails he received:
Dan G. from Baltimore: Everyone is watching the Sox in their dorm rooms right now, and after J.D. Drew just hit that home run, 40 half-drunk college kids opened their doors and wandered into the hallway wondering if the world was going to end or they were more drunk that they thought. It was unbelievable.

Tuesday, October 23, 2007

The Coming of H.264:
H.264 is already supported in virtually every corner of the digital video universe. Now, with big internet players like Adobe, Google, and Apple behind it, H.264 is poised to become the format of convergence where all devices have access to an expanding universe of content available via physical media or high-speed networks. This will be a market-expanding transition leading to many exciting products and services in the near future.
Good article, and I have to say, having just now moved into the use of H.264-based videos for our DVD products, the quality blows the socks off of Flash video and Sorenson QuickTime (which has been old but reliable for some time now).

The file size of H.264 compression is impressive as well. One of our latest clips, at full screen 864 x 486, 29.97 frames per second, and 02:12 running time, was a mere 82MB in size--with better than DVD quality.

I'm more than whelmed.

Monday, October 22, 2007

Huge. Stayed up for the whole game....which was a lot closer than the final tally suggests.

Friday, October 19, 2007

You just knew that the anti-relativity crackpots weren't going to take a back seat to the Intelligent Design crowd for long....
One of the classic Monty Python sketches of all time....

Mark Shea makes a quite reasonable observation about the modern Israeli predictably misunderstood...and takes on all comers.
Joe Torre is a class act, and the Yankees are going to miss him.

After the Red Sox shocked the Yankees by rallying from a 3-0 series deficit to snare the 2004 A.L.C.S., Torre called Wakefield in Boston’s clubhouse. Since Wakefield had given up Aaron Boone’s game-winning homer in Game 7 of the 2003 A.L.C.S., Torre wanted Wakefield to know he was happy for him. Wakefield said Torre’s call was classy.

“I have so much respect for him as a manager that I hoped to be able to play for him at some point in my career,” Wakefield said. “I’ve talked to guys who have played for him, guys like Johnny Damon. They say he’s the best.”

From today's New York Times. Nice to see the Yankee's front office can be as clueless as Boston's.

Wednesday, October 17, 2007

It was nice to see my book back on the shelves at Border's this week. With the take-over of Avalon Publishing by Perseus Books, and the shut down of both Thunder's Mouth (under which imprint my book was published) and Carroll & Graf, the warehouses were merged and a new distributor took over for both imprints. During this 'reinvention' process, pretty much from June through this past September, my book disappeared from the shelves at Borders and Barnes and Noble.

I'm just relieved to see it back. These publishing mergers can sometimes cause a small book like mine to just vanish without a trace.

Happily that hasn't happened.
("Pass me a bottle, Mr. Jones...")
Can you win the Nobel Prize for science...and still be a moron?

Sadly, yes.

Tuesday, October 16, 2007

Steve Matheson has a great post today on How to Evolve a New Protein in (about) 8 easy steps, worth quoting in detail:
How, exactly, does a protein acquire a new function during evolution? This is one of those "big questions" in evolutionary biology. Broad concepts such as gene duplication are quite helpful in formulating explanations, but the specific question raised is focused on the details -- the actual steps -- that must occur during the step-by-step modification of a protein such that it performs a different job than the proteins from which it has descended. The constraints on the process of change are significant, and the issues are similar to those I discussed when describing the concept of fitness landscapes in morphospace. The problem, basically, is this: how can you change a protein without wrecking it in the process? In other words, can you get from function A to function B, step by step, without passing through an intermediate form, call it protein C, which is worthless (or even harmful)?

These are precisely the questions addressed in an elegant set of experiments reported in two reports over the last year or so. The second article, by Ortlund et al., was reported in the 14 September issue of Science, and built on work reported in Science in April 2006. Their studies focused on two closely-related proteins that are receptors for steroid hormones. In this case, the steroids of interest are corticosteroids (the kind often used to treat inflammation; think cortisone) and a mineralocorticoid (a less well-known hormone, aldosterone, that regulates fluid and salt intake). The hormones are structurally similar (being steroids).

Joseph Thornton, at the University of Oregon, has been studying the origins of these receptors for about 10 years, and has assembled an interesting (and detailed) account of their history. The basic outline is as follows: the original steroid receptor was an estrogen receptor, and is extremely ancient, apparently arising "before the origin of bilaterally symmetric animals" (Thornton et al., Science 2003). (That's seriously ancient, sometime in the Cambrian or earlier.) The progesterone receptor seems to have arisen next, followed by the androgen (i.e., testosterone) receptor. (Now that's intriguing.) Fairly late in this game, the two receptors of interest to us here, the corticosteroid receptor and the mineralocorticoid receptor, were added to the vertebrate repertoire. The two modern receptors are thought to descend from an ancestral corticosteroid receptor, which underwent a gene duplication. Hereafter, I'll refer to the receptors as the corticosteroid receptor and the aldosterone receptor, hoping that all the jargon won't obscure the message.

In a widely-discussed paper published in Science a year ago (Bridgham et al., Science 2006), Thornton's group determined the most likely DNA sequence of this ancestral gene, then "resurrected" it, meaning simply that they created that very DNA sequence in the lab. (Determining the ancestral sequence was a nifty piece of work; actually making the DNA is quite straightforward, especially if you have a little dough.)

Their experiments showed that the ancestral receptor could bind to a hormone that didn't exist yet (aldosterone) while it was functioning as a receptor for corticosteroids. In other words, the receptor was available for activation by aldosterone long before aldosterone was around. (All jawed vertebrates make corticosteroids, but only tetrapods make and use aldosterone, an innovation that occurred at least 50 million years later.) The modern corticosteroid receptor has since lost its ability to interact with aldosterone, and Bridgham et al. chart the most likely evolutionary path, at the molecular level, by which we and other tetrapods came to have a corticosteroid receptor that won't bind to aldosterone. The surprising result, however, is the fact that the ancient receptor was able to bind aldosterone, millions of years before aldosterone is thought to have been present.
It gets even more interesting.
The most recent paper adds significantly to the picture, and introduces some genetic concepts that Behe's fans should pray he understands. The authors (Ortlund et al.) took their analysis to a far more detailed level, by extending their previous observations in two ways. First, they assembled a detailed family tree for the receptors, by looking at DNA sequences from living species known to represent various branches on the tree of life. In other words, they chose organisms such as lampreys, bony fish, amphibians and mammals, and examined their DNA codes (for the receptors) to find the changes that occurred in each branch of the lineage. Now, please stop and think about this, because it's really cool. What the authors did was mine existing databases of DNA sequence data, pulling out the sequences of the two types of receptors from 30 different vertebrate species. You could repeat this part of the experiment right now, by referring to their list of organisms in Supplemental Table S5, which provides the ID codes needed to locate the DNA sequences in the Entrez Gene database. Then they charted the changes in the DNA sequence in the context of the tree of life as sketched out in the fossil record. The tree they assembled includes all the steroid receptors, and I've annotated it a little if you want to have a look. They used this tree to guide their further experiments, as I'll explain below. The second thing they added to their previous analysis was an analysis of the 3-D structure of the various postulated intermediates in the evolutionary pathway. And they accomplished this by making proteins from the "resurrected" genes, then crystallizing them and using X-ray diffraction techniques to determine their precise structures.

Examination of their receptor family tree revealed something interesting. Most vertebrates have highly specific receptors: the corticosteroid receptor isn't strongly stimulated by aldosterone, and vice versa. But some living vertebrates (skates, in particular) show a different pattern: the corticosteroid receptor isn't all that specific for cortisone. Because the ancestral receptor also lacked specificity (as shown in the 2006 paper), the authors concluded that the receptor acquired its discriminating taste at some point between the branching-off of skates (and their kin) and the separation of fish from tetrapods. Their Figure 1 is a little crowded, but it illustrates this nicely:

To follow the evolutionary narrative in this graph, start at the blue circle, which represents the ancestral receptor that was "resurrected" in the 2006 paper and that happily binds to both corticosteroids and aldosterone. (The graphs on the right side of the figure demonstrate the specificity, or lack thereof, of the receptors at different times in history.) There's a branch leading up and to the left, to the various GRs (corticosteroid receptors), and one leading up and to the right, to the MRs (aldosterone receptors). At the green circle, another branching event occurred, 440 million years ago, at which point certain groups of fishes (skates among them) branched off, up and to the right. The receptor at that point is an ancestral corticosteroid receptor, and it still isn't specific for corticosteroids. But the receptor at the yellow circle, in the common ancestor of tetrapods and bony fishes, is specific. The authors conclude that specificity arose between those two points, between 420 and 440 million years ago. With some (deliberate?) irony, they indicate that process with a black box.
This will definitely be worth watching over the next few years.

Saturday, October 13, 2007

Sam Harris gets a clue that monomaniacal monotony is not the best way to win converts. Needless to say, the older geezers of 'New' Atheism...don't.
If you haven't come across Mike Liccione (and I hadn't until Scott Carson tipped me off), you don't know what you're missing:
Classical theism is committed to the claim that God's omnipotence and perfection are compatible with the evil in his world; but the same tradition precludes saying precisely how evil squares with God's omnipotence and perfection. If any Christian doubts that, they should remind themselves what religion they profess. Christianity teaches that the only-begotten Son of God, the King of the Universe, gave us a chance to escape the thralldom of evil first by becoming a perfectly good man and then, at his Father's behest, getting himself tortured and executed as a serious public nuisance.
Provocative is an understatement. There's more:
People sometimes talk as though the presence of any evil at all in the world poses an objection to believing the Creator to be all-powerful and perfectly good. St. Thomas Aquinas considers and rebuts such an objection in the article from the Summa Theologiae where he purports to prove that God exists. Surely he is right to maintain that the omnipotence and goodness of God are manifest partly in the fact that out of evil he can bring a greater good. To a much lesser extent, we do that sort of thing all the time: we learn from mistakes; we cure diseases; we find that some pleasures are all the greater for the pain that must precede them; and most important, people sometimes become better through suffering. We are, if you like, more powerful for all that: whatever doesn't kill you makes you stronger. That is how God has arranged things.
Scott Carson was the first blogger I heard make that statement, that the 'problem' of evil really isn't a problem at all, but I never quite understood it until reading Mike's post.

Friday, October 12, 2007

Via Tara Smith, a nice post for a Friday by one Greta Christina, on the Galileo Fallacy and its Gadfly Corrollary.

Thursday, October 11, 2007

Sean Carroll on the cutting edge of evolution in action?
A gene divided reveals the details of natural selection

MADISON -- In a molecular tour de force, researchers at the University of Wisconsin-Madison have provided an exquisitely detailed picture of natural selection as it occurs at the genetic level.

Writing today (Oct. 11, 2007) in the journal Nature, Howard Hughes Medical Institute investigator Sean B. Carroll and former UW-Madison graduate student Chris Todd Hittinger document how, over many generations, a single yeast gene divides in two and parses its responsibilities to be a more efficient denizen of its environment. The work illustrates, at the most basic level, the driving force of evolution.

Excellent bio tutorial site.

Wednesday, October 10, 2007

Hurrah for National Review
A conservative magazine finally published an article on evolution that wasn't nonsense!
Seriously, this is a nice piece by Jim Manzi (available online here), who runs his own software company and has a working appreciation for just how randomness works in Darwin's theory.

Look for the usual nitwits to show up in the next issue's letters section to dispute him.

One quibble, the free library web monkeys failed to format Jim's exponents properly...but hopefully they will fix.
Ah...the age old question: Mirror, Mirror on the Wall, Who's the Best Encoder of them All?
Providing Ammunition

Mark Shea is understandably dismayed by than rigorous IQ of some African bishops. He writes, "Is the pool of candidates really so shallow that these weird guys are the best they can get? How can Africa produce so many great priests (I've never met a bad one) and yet wind up with such strange bishops?"

PZ Myers is not only not dismayed, he thinks they're typical...and this guy, too.

Seriously. All I can think of is that line from Woody Allen's Hannah and Her Sisters, as delivered by Max von Sydow: "If Jesus ever came back and saw what was going on in his name...he wouldn't stop throwing up."


Tuesday, October 09, 2007

Holbert pretty much says it all.

(Hat tip: Hub Blog)

Friday, October 05, 2007

Larry Arnhart has a good post today, providing another example of why I think Aquinas and Darwin would have gotten along quite well:
Under the influence of Aristotle's biology, Thomas concluded that, although only human beings act from "free" judgment, other animals act from "estimative" judgment about what will satisfy their desires. Thus all animals have a natural capacity for practical judgment that shows a certain "participation in prudence and reason" and a certain "likeness of moral good" (ST, I, q. 83, a. 1; q. 96, a. 1; I-II, q. 11, a. 2; q. 24, a. 4; q. 40, a. 3). The influence of this biological psychology on the Thomistic understanding of natural law is evident in the account of marriage in the Supplement to the Summa Theologica (q. 41, a. 1; q. 54, a. 3; q. 65, a. 1-3; q. 67, a. 1).
Friday dose of Krauthammer:
We had no idea how lucky we were with Sputnik. The subsequent panic turned out to be an enormous boon. The fear of falling behind the Communists induced the federal government to pour a river of money into science and math education. The result was a vast cohort of scientists who gave us not only Apollo and the moon, but the sinews of the information age -- for example, ARPA (established just months after Sputnik) created ARPANET, which became the Internet -- that have ensured American technological dominance to this day.

Thursday, October 04, 2007

Michael Behe vs. Sean Carroll?

No contest.

Tuesday, October 02, 2007

Reconsidering Teilhard

I've been reading John F. Haught's God After Darwin, and he has an interesting section on the life and work of Teilhard de Chardin, the Jesuit paleontologist. I must confess I've never looked deeply into his career. I knew that he envisaged a sort of progressive direction to evolution which, while understandable at the time he wrote, is no longer taken seriously.

What I did not know, however, is how shabbily he's been treated by scientists like Stephen Jay Gould and Daniel C. Dennett. Dennett's attitude doesn't surprise me (most militant atheists are reflexively anti-clerical). But Gould's attitude is surprising.

Haught writes:
The late paleontologist Stephen Jay Gould, for example, was so certain that evolution is devoid of the directionality Teilhard discerned in it that he attempted to destroy completely the famous Jesuit's scientific reputation by making him appear to be an accomplice to the notorious Piltdown hoax. Gould's scurrilous attack, incidentally, has been thoroughly debunked; but, to my knowledge, he never publicly retracted his claims, in spite of clear evidence that Teilhard could not have been involved. (p.88)
Certainly takes my regard for Gould down a notch.

Friday, September 28, 2007

Even the New York Times is waking up to the bad faith behind the new 'Expelled' movie. I think Ben Stein is going to eventually regret his involvement in it. As usual, intelligent design proponents talk about the conspiracy of silence against new 'thinking' about evolution.
Krauthammer on France:

Sarkozy is no American lapdog. Like every Fifth Republic president, he begins with the notion of French exceptionalism. But whereas traditional Gaullism tended to define French grandeur as establishing a counterweight to American power, Sarkozy is not adverse to seeing French assertiveness exercised in conjunction with the United States. As Kouchner put it, "permanent anti-Americanism" is "a tradition we are working to overcome."

This French about-face creates a crucial shift in the balance of forces within Europe. The East Europeans are naturally pro-American for reasons of history (fresh memories of America's role in defeating their Soviet occupiers) and geography (physical proximity to a newly revived and aggressive Russia). Western Europe is intrinsically wary of American power and culturally anti-American by reflex. France's change from Chirac to Sarkozy, from Foreign Minister Dominique de Villepin (who actively lobbied Third World countries to oppose America on Iraq) to Kouchner (who supported the U.S. invasion on humanitarian grounds) represents an enormous shift in Old Europe's relationship to the U.S.