Caturday felid: The making of “Jedi Kittens”

November 12, 2011 • 4:37 am

You might have seen the sixteen-second video “Jedi Kittens,” which went viral and now has more than 2 million views on YouTube. There’s also a sequel, “Jedi Kittens Strike Back.”

They feature two adorable kittehs in a furious light-saber battle and spaceship chase.  Here are the two original videos, and then two in which the directors explain how they made the original ones. It wasn’t easy!

Jedi Kittens (original video):

The making of Jedi Kittehs:

Jedi Kittens Strike Back:

The making of Jedi Kittens Strike Back:

h/t: Michael

Another paper on “symbiotic speciation” by Donald Williamson is retracted

November 11, 2011 • 9:09 am

About two years ago, I called attention to a bizarre paper in The Proceedings of the National Academy of Sciences (PNAS) by Donald Williamson, claiming that the life cycle of Lepidoptera, with a distinct caterpillar and adult stage, was produced by the hybridization between an ancestral butterfly (lacking a caterpillar stage) and an onycophoran (a velvet worm, the presumed ancestor of the caterpillar). This was palpably ridiculous since DNA sequencing would have revealed such a strange agglomeration immediately.

As I expected, that paper was thoroughly debunked by several people, including Michael Hart and Rick Grosberg, and now carries no weight. It also shook up things at the journal, because the paper’s editor, Lynn Margulis, appeared to have violated editorial procedure by submitting only the good reviews and ignoring the bad ones. 

A site called RetractionWatch, of which I was unaware, has reported that yet another paper by Donald Williamson—one on the same topic—has been formally retracted.

Retraction Watch has saved the original article, which you can find here. Williamson’s thesis is that complex life cycles of animals, involving larvae that are very different from adults, involved the acquisition of foreign genomes through either symbiogenesis (engulfing of one species by another, as in the formation of mitochondria from nommed bacteria) or hybridogenesis (two completely different species hybridize, as in Williamson’s previously retracted PNAS paper). Here’s the abstract of the retracted paper:

My larval transfer hypothesis asserts that mature adults became larvae in foreign animal lineages by genome acquisition. Larval genomes were acquired by hybridizationwhen sperm of one animal fertilized eggs of another animal, often remotely related. There were no larvae in any phylum until the classes (and, in some cases, the orders) of that phylum had evolved. Since larvae were acquired by hybrid transfer, they are not directly related to the adults that metamorphose from them. The widely accepted classification that associates echinoderms and chordates as deuterostomes, and annelids and molluscs as trochophorates or lophotrochozoans, is flawed. Symbiogenesis, the generation of new life forms by symbiosis, accounts for the discontinuous evolution of eukaryotic cells from prokaryotes. Hybridogenesis, the generation of new life forms and life histories by hybridization in sexually reproducing animals, occurred at all taxonomic levels from species to superphyla. Not only were larvae acquired by transfer from foreign adults from the late Palaeozoic to the present, but also complex animals were generated from simpler ones by this process in the Cambrian explosion, and organ systems were transferred between remotely related animals. There are several types of evolution. Symbiogenesis and hybridogenesis are saltatory genome transfer processes that dramatically supplement the gradual accumulation of random mutations within separate lineages described by Darwin.

The problem, of course, as Hart and Grosberg (and others) pointed out in their critique, is that Williamson’s original hypothesis has already been refuted by genetic analysis: butterfly genomes should show significant amounts of DNA more closely related to onycophorans than to other butterflies, and they don’t.  That’s also the case for the present paper at all: no phylogeny supports the idea of larvae arising by symbiosis or hybridogenesis.

Williamson’s new paper has been not only retracted, but completely effaced: here’s what you get when you go to the article’s pdf:

And the journal’s editor, David Richardson, issued only a terse remark:

I am not willing to discuss this matter except to say that it did not involve any matter of wrong-doing by the author, simply that  a significant amount of the information in the paper closely duplicated that published earlier without sufficiently addressing previous concerns  about the significance of particular findings.

Can you imagine a similar retraction issued when a claim of theology was falsified?  It’s as if Albert Mohler admitted that he now denies the factuality of Adam and Eve in light of new genetic findings.

At any rate, this shows once again that the truth will out in science. And it also refutes claims by Lynn Margulis and others that hybridization and symbiosis are more than just important events in the creation of evolutionary novelty—as they were indeed for things like chloroplasts and mitochondria—but are ubiquitous, with that ubiquity constituting a refutation of the tenets of modern evolutionary theory.


What’s the probability that you exist?

November 11, 2011 • 7:50 am

Ali Binazir went to a Tedx talk in San Francisco and heard some probabilities being bandied about that he considered dubious:

One of the talks was by Mel Robbins, a riotously funny self-help author and life coach with a syndicated radio show.  In it, she mentioned that scientists calculate the probability of your existing as you, today, at about one in 400 trillion (4×1014).

“That’s a pretty big number,” I thought to myself.  If I had 400 trillion pennies to my name, I could probably retire.

Previously, I had heard the Buddhist version of the probability of ‘this precious incarnation’.  Imagine there was one life preserver thrown somewhere in some ocean and there is exactly one turtle in all of these oceans, swimming underwater somewhere.  The probability that you came about and exist today is the same as that turtle sticking its head out of the water — into the middle of that life preserver.  On one try.

Like a good skeptic, Binazir first calculated the turtle-head-into-life-preserver probability, making due allowances for the area of the world’s oceans and the area of the hole in a life preserver. That turns out to be 1 in 6.82×1014, or about 1 in 700 trillion. Pretty close to the probability-that-you-exist-figure.

But when Binazir calculated the second figure, he found out that Robbins was off. Way off. But Binazir made that calculation, too, which of course involves some ancillary assumptions and calculations. The probability that you’d exist on Earth today includes the probability that your parents would meet 20 years ago, that they’d have a relationship that would result in pregnancy, and of course that the right egg would meet the right sperm.

But it also includes the probability that your parents would also have existed with the genes they have, which means calculating that every one of your ancestors would have reproduced successfully, and that for each pair of them the right egg would have met the right sperm as well.

He comes up with this probability that you’d exist (by “you”, of course, he means those individuals resulting from the concatenation of a sperm and egg genetically to those who formed your zygote:

Probability of your existing at all: 1 in 102,685,000

As a comparison, the number of atoms in the body of an average male (80kg, 175 lb) is 1027.  The number of atoms making up the earth is about 1050.  The number of atoms in the known universe is estimated at 1080.

So what’s the probability of your existing?  It’s the probability of 2 million people getting together – about the population of San Diego – each to play a game of dice with trillion-sided dice. They each roll the dice, and they all come up the exact same number – say, 550,343,279,001.

A miracle is an event so unlikely as to be almost impossible.  By that definition, I’ve just shown that you are a miracle.

Now go forth and feel and act like the miracle that you are.

Well, somebody’s going to point out to me that although the specific genetic “you” who exists is improbable, the probability that some you, that is, some offspring of your lineage that could be reading this piece, is much higher. Others will pick nits and question Binazir’s calculations. (Given that the number of chromosomes is limited, the probability of getting an individual nearly identical to you is higher.)

But the principle is still the same: it shows the fallacy of the anthropic principle—or of Douglas Adams’s self-reflecting puddle.  But it’s still a cool calculation nonetheless. The read probablity that you exist, of course, is 1.

Ali Binazir’s website, Smart ideas for smart living, is here.

h/t: Matthew Cobb

Hitchens fêted in London

November 11, 2011 • 5:10 am

On Wednesday Christopher Hitchens (ill with pneumonia in Washington, D.C.) was fêted in an event at Royal Festival Hall.  Richard Dawkins and Stephen Fry were the hosts, but a gaggle of luminaries weighed in by video. As The New Statesman reports,

Richard Dawkins, Hitchens’s fellow anti-theist, appeared on stage with Fry in London, and Martin Amis, his dearest friend, appeared via video link from New York, as did James Fenton and Salman Rushdie. The line-up also included actor Sean Penn (who Hitchens enjoys pool games with), former Harper’seditor Lewis Lapham and novelist Christopher Buckley, son of the late conservative intellectual (whether there can be such a thing is a subject for another occasion) William F. Buckley, whom Hitchens often debated on US TV show Firing Line. It felt like a hyper-intelligent version of Question Time. . .

. . . But the most significant and poignant intervention came from Ian McEwan, who was watching the event live with Hitchens in Texas. “I talked until late last night with Hitch, we were discussing the non-communist left of the early 50s,” he wrote in an email read out by Fry. “He can’t run a mile just now but be reassured his Rolls Royce mind is purring smoothly.”

Sadly, the Rolls Royce is running out of gas.  The Statesman describes the evening, which appears as an elegy/eulogy.  I fear it won’t be long now, and when Hitch is gone we have absolutely nobody to replace him. They say that no one is indispensable, but “they” are wrong.

Miranda Hale paid the $7 fee to watch this via computer livestream, and I expect she’ll report on what she saw. I also understand that at least one of our readers was at the event, and if you were there, or saw it, do weigh in below.

Andrew Brown fails again

November 11, 2011 • 4:32 am

It continues to amaze me how this guy (and I have to bite my fingers to keep from calling him a moron) continues to get space at the Guardian to broadcast his inanities.  In his latest public embarrassment, Brown defends the odious William Lane Craig in “Richard Dawkins is wrong to call William Lane Craig morally repulsive.”

As you probably know, Craig believes in the “divine command theory” of ethics: that is, whatever God decrees is moral simply because God decrees it.  So when God commanded that the Israelites massacre the Canaanites, and destroy women and children occupying the Promised Land, that was totally okay by Craig.  God said it; Craig believes it; that makes it right.

That’s a monstrous view, and who would want to afford somebody like that the privilege of a debate? Dawkins has refused to share the platform with Craig, but Brown takes Richard to task for that refusal. Craig’s view, as Brown sees it, is perfectly reasonable for a religious person:

The attack on Lane Craig does not just maintain that he is wrong to believe in heaven, but that his belief renders him so morally repulsive that no decent person should share a platform or shake hands with him. And I don’t see why.

In all the fuss about Craig there are two things mixed up. The first is whether God commands genocide. The second is whether he is able to take innocents to heaven. It is possible, and perhaps necessary, to get morally outraged about the first question. That’s the Euthyphro problem. But I think there is a transference of outrage to the second question, too.

Of course there’s a transfer of outrage, because the two views are of a piece.  For Craig, it is okay to kill innocents precisely because their sorrow will be redeemed in heaven! As Craig says:

Moreover, if we believe, as I do, that God’s grace is extended to those who die in infancy or as small children, the death of these children was actually their salvation.  We are so wedded to an earthly, naturalistic perspective that we forget that those who die are happy to quit this earth for heaven’s incomparable joy.  Therefore, God does these children no wrong in taking their lives.

Back to Brown:

The first thing to say is that there is genocide in our world. More generally, innocents suffer, and injustice is rewarded. If God does not exist, he is not to blame for this. If he does exist, he is in some sense responsible, and there is some mechanism, clearly not of this world, by which he can be forgiven. I don’t accept that our present state of comfort somehow justifies the sufferings of people who were sacrificed for it. We can’t, I think, forgive God or the universe for the horrors of the world that other people suffer. That would be precisely the sin of the Pharisees, or, as Swift put it, “When we are lashed, they kiss the rod, obedient to the will of God.”

There are two possibilities. Either the suffering of the innocent is meaningless, and goes unredeemed. Or it is eventually understood – and accepted – by them as meaningful, and so redeemed. It seems obvious that the second of these two possibilities would be better. That, on its own, is not grounds for believing it is true. But it is clearly more desirable.

Remember, Brown is an atheist.  Why is he justifying, then, this ridiculous argument?  Just because a possibility is more “desirable” doesn’t give it a shred of extra credibility, though of course “the assurance of things hoped for” is what faith is all about.

In fact, Brown goes on to equate atheists with Craig and other theistic apologists, since in both cases the problem of evil is insoluble:

There are people who claim to take this view, and claim that the problem of evil is a delusion of theism which vanishes if you put theism aside. But I don’t think they are sincere. Evil and injustice are insoluble problems whether or not God exists, if we look at them straight. A world without hope for the hopeless is quite as terrible as one which contains a hope.

If you believe there is no God, neither is there any possibility of redemption or setting such things right. All you can say to the victims is “tough luck”. That may be the world that we live in.

But I can’t see any reason for supposing that it’s morally preferable to one where justice is finally done, however incomprehensibly and invisibly to us right now. Such a world may not exist. But to believe in it can’t in itself be morally repulsive.

Well, evil is an insoluble problem under theism, but not under naturalism.  We are probably genetically hard-wired to be, at times, aggressive and selfish (as well as altruistic!), and social conditions also impel people to do evil acts.  (That, by the way, is no admission that it must always be that way: we’re genetically hard-wired to reproduce, too, but we have birth control.)  Yes, “tough luck” it is, but t least we can do something about it—something real and helpful rather than just sitting around making stuff up—as does Craig—about why God allows evil.

Brown’s view that Craig’s scenario isn’t morally repulsive is repulsive in itself.  Suffering is suffering, even if the suffering of children be redeemed in heaven (and note again that Brown does not believe in this stuff!).  So what if the children find salvation in heaven? They’re still suffering on Earth, and the parents of suffering children are also tormented.

God could not only give everyone heaven, but he could prevent such suffering on our own planet.  His failure to do so, when he has the power to fix things, is morally repulsive.  The naturalistic/humanistic view, in contrast, is not morally repulsive: it just sees things as they are, doesn’t blame a nonexistent deity, and then goes about trying to fix things.

Dear Guardian,

Contrarian views do deserve an airing in the press, but why Brown’s?  They don’t even make any sense. What’s more, he continually argues for positions that he claims not to believe. If you’re going to publish religious apologetics, could you at least find someone to do it who is religious?  And Brown is not only a hypocrite, but he can’t write, either.  If you publish him simply to inspire controversy without substance, then you might as well be The Sun.  Your lad Brown is the intellectual equivalent of a Page 3 Girl.

Yours sincerely, A concerned reader.

Oh, and over at Choice in Dying, Eric takes apart not only this piece by Andrew Brown, but another in which Brown seemed enormously chuffed to find a few “mistakes” in Steve Pinker’s new book.  What’s curious is not only that the “mistakes” aren’t mistakes, but matters of empasis or interpretation, and, more important, Brown reviewed the book without having read it.  What a Kw*k-like behavior, and how unconscionable for a professional journalist.

h/t: “J”

Robert L. Park on Templeton

November 10, 2011 • 11:46 am

by Greg Mayer

Robert L. Park is a physicist, fellow of CSICOP, and former head of the American Physical Society‘s Washington office who has long been active in the skeptical community. His first book, Voodoo Science (Oxford, 2000), is one that I have used in preparing my undergraduate non-majors course on “Science & Pseudoscience”. Until yesterday, I had overlooked his second book, Superstition (Princeton, 2008). I’ve only had a chance to skim through it, but, apropos of Jerry’s post about Massimo Pigliucci’s take on the Templeton Foundation, Park takes a rather dim view of the  foundation and its goals as well. A sample of what he has to say:

Not everyone was happy about the American Association for the Advancement of Science (AAAS) selling its soul to Templeton. Why had the most important scientific organization in America, perhaps in the world, allowed the voice of antiscience to assume the guise of a dialog between science and religion?

Park also mentions Francis Collins and other religious scientists. As I said, I’ve only skimmed it, but the book seems worth a read.

Dover ID movie, “Judgment Day,” now in one video

November 10, 2011 • 11:35 am

The excellent NOVA movie “Judgment Day” was previously available on YouTube only in snippets.

Now, though, one of our ambitious readers, Brian, has combined the parts and posted them as a single two-hour movie. I’ve embedded it below.

The movie details the shenanigans in Dover, Pennsylvania, when creationists tried to sneak the “theory” of intelligent design into high-school science classes.  After an illuminating trial, during which IDers like Michael Behe were thoroughly trounced, Judge Jones pronounced intelligent design as “not science.”

The defeat marked, I think, the beginning of the end for the intelligent design movement.  The Discovery Institute hasn’t been the same since:  they’re now reduced to carping and whining about evolution, and criticizing the theological sophistication of people like me.  A while back they promised that they’d produce “real science” and that this was right around the corner.  So far, despite mighty hacks, they’ve coughed up nothing.

If you haven’t seen the film (and you should), here it is.  Thanks to Brian for combining the bits and posting them.

The Last Waltz

November 10, 2011 • 7:01 am

I’m ashamed to admit this, but it wasn’t until yesterday that I finally got to see The Last Waltz, the famous movie (directed by Martin Scorsese) documenting the last concert of The Band, one of the most innovative groups in rock history. I’ve always loved their music and felt that, although they were quite popular at the time, they didn’t get near the attention they deserved.

The film was made on Thanksgiving Day in 1976 and was released two years later. It’s a magnificent achievement—in my opinion one of the three best films about rock in history, including Stop Making Sense and Woodstock.  The musicianship is superb, and there are many guest stars, including Bob Dylan, Neil Young, Joni Mitchell, Muddy Waters, Emmylou Harris, Van Morrison, Dr. John, and Eric Clapton.

Here are a couple clips from the movie, but they don’t come close in quality or sound to the Blu-Ray DVD version I saw.

“The Night They Drove Old Dixie Down” (one of my two favorite Band songs, the other being “The Weight”):

What impressed me most about this movie was Rick Danko’s work on bass, which was fantastic. Robbie Robertson, of course, is also a world-class lead guitarist. Everyone in the band, including Garth Hudson, Levon Helm, and Richard Manuel, was a superb musician, even if they were often drugged out. Sadly, both Manuel and Danko are now dead, the former by suicide the latter from drugs.

Here’s Clapton and Robertson with duelling guitars on “Further on up the road”:

And “Helpless”,  with Neil Young. Wikipedia says that this number was edited to remove a blob of cocaine that was hanging from Young’s nose (apparently there was a white room backstage, adorned with plastic noses, where the performers would go for a snort). Joni chimes in from offstage; the audience couldn’t see her.

And don’t miss Joni Mitchell’s performance of “Coyote” (I can’t embed it, but you can see it here), one of the best performances of the concert and a wonderful live rendition of a difficult song. Sadly, the sound quality is poor and a bit muted.  Check out Danko’s lively work on the bass.

I suppose that, taking into account both production quality and the musicianship, I’d consider this the best rock concert movie ever made. Woodstock was great but had some forgettable performances as well as the great ones (Santana, Hendrix, Richie Havens).

Do weigh in below with your opinions and choices of other concert movies.