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

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.

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.