Instant divergence times!

April 10, 2011 • 9:02 am

A group of scientists at Arizona State University have developed a really nice tool for instantly calculating the divergence time between any two groups of organisms—or individual species.

As we all know—or should know, especially if you’ve read Richard Dawkins’s The Ancestor’s Tale—every species on earth is related to every other, for we all share common ancestors.  Closeness of relationship is in fact defined as how long in the past this common ancestor lived.  More closely related species share more recent common ancestors.  And haven’t you wondered, for example, how closely related you are to a mushroom?  I know I have.

So go over to Time Tree and write in any pair of species.  The application (also available for iPhones, though I can’t imagine why) will tell you not only how closely related are your species of choice, in terms of when their common ancestor lived, but will also give you all the species and references involved in the calculations, and the type of molecular data used to do the calculation.

Here’s one example. When I was an undergraduate, people were arguing about whether the giant panda (Ailuropoda melanoleuca) was more closely related to raccoons (procyonids) than to bears (ursids).  I can’t remember why they thought that—perhaps because the raccoon and other procyonids have eye masks like pandas.  Anyway, the issue was settled with molecular analysis, described in a Nature paper by Vince Sarich whose title is a model of scientific concision: “The giant panda is a bear.”

Now you can settle this argument simply by looking at divergence times. Here’s the start: comparing pandas and raccoons on TimeTree. This is how the results look:


In contrast, the divergence between giant pandas and grizzly bears occurred 28 million years ago.  Case closed.

TimeTree is great for settling those thorny pub arguments!  Go see when you had a common ancestor with squirrels or ferns.

h/t: Matthew Cobb

It Never Entered My Mind: a sax duet

April 10, 2011 • 5:14 am

I feel saxophone postings coming on, and I’m so happy that I found this favorite on YouTube.  It’s a lovely duet between two tenor sax giants of the 20th century, Ben Webster (1909-1973; nicknamed “Frog”) and Coleman Hawkins (1904-1969; alternately called “Hawk” or “Bean”).  Starting off with Duke Ellington, Webster (whose solo on Ellington’s “Cotton Tail” is epochal) later struck out on his own, finishing his career in Europe.  Hawkins took off with Fletcher Henderson’s Orchestra, and then produced some of the most famous sax solos in jazz history, including “Body and Soul” and “The Man that I Love”.  I hope to highlight these this week.  Like Webster, Hawkins spent much of his later life in Europe, where jazz was more highly respected and blacks less denigrated.

Of the two, I’d give the nod to Hawk for his creativity, but it’s a tough call. Fortunately, we don’t have to choose on this recording of the two collaborating on the Rodgers and Hart ballad, “It Never Entered My Mind.”

The recording was made in 1957 in Los Angeles, when both men were at the end of their careers. But you couldn’t tell that from their marvelous playing. Webster starts the song off, and Hawkins cuts in at about 2:22.  Then Webster comes back at 4:27 to take it to the end. Notice the different styles of the two men: Webster’s playing is mellower and throaty, Hawk’s more flamboyant and raucous.  Oscar Peterson accompanies on piano.

If this song doesn’t chill you out, you’re not human!

Click on the “Watch on YouTube” line.

Jesus in a lab coat: the last word on Templeton

April 10, 2011 • 4:46 am

I think my interest (and your patience) for discussion of the Templeton Prize has run its course—at least for this year.   But let’s call it a good end with three new pieces, all on the anti-Templeton side.

You may remember science writer John Horgan’s article on his experiences with Templeton, “The Templeton Foundation: a skeptic’s take,” where he describes his experiences with—and expresses regret for—his tenure as a Templeton journalism fellow:

One Templeton official made what I felt were inappropriate remarks about the foundation’s expectations of us fellows. She told us that the meeting cost more than $1-million, and in return the foundation wanted us to publish articles touching on science and religion. But when I told her one evening at dinner that — given all the problems caused by religion throughout human history — I didn’t want science and religion to be reconciled, and that I hoped humanity would eventually outgrow religion, she replied that she didn’t think someone with those opinions should have accepted a fellowship. So much for an open exchange of views.

The title of Horgan’s new post at Scientific American, “Prize in the sky: The Templeton Foundation rewards ‘spriritual progress’, but what the heck is that?“, tells it all.  It’s a hard-hitting piece, arguing that Templeton is just Jesus in a lab coat. Here are some excerpts; note that the present head of the Foundation, Jack Templeton, gives away the game in his letter soliciting nominations for this year’s Prize:

What bothers me most about the Templeton Foundation is that it promotes a view of science and religion—or “spirituality,” to use the term it favors—as roughly equivalent. Consider this e-mail that Jack Templeton sent me last summer soliciting nominations for the Templeton Prize. He wrote: “The Templeton Prize parallels growing attention to the idea that progress in spiritual information is just as feasible as progress in the sciences.” First of all, the Templeton Foundation has artificially created the “growing attention” to which Jack refers with enormous infusions of cash into science and other scholarly fields.

Moreover, the claim that “progress in spiritual information is just as feasible as progress in the sciences” is absurd, because there is no such thing as “spiritual information”. To answer the question I posed at the beginning of this post, the notion of a spiritual fact, finding or discovery is an oxymoron. Spiritual claims abound, of course—”God is love,” for example—but there isn’t a shred of empirical evidence for any of them, certainly nothing resembling the overwhelming evidence compiled for heliocentrism, evolution by natural selection, atomic theory and the genetic code. And if spiritual information doesn’t exist, how can there be “progress in spiritual information”?

Some Templeton-funded scholars have tried to drag science down to the level of religion by arguing that science can’t produce truth either. I heard this claim in 2005 when I spent three weeks at the University of Cambridge participating in a Templeton fellowship for journalists, which featured talks by scientists and other scholars. In one talk the Christian theologian Nancey Murphy asserted that scientific claims are just as tentative as religious ones, hence scientists such as Richard Dawkins—who was in the audience—have no right to be so condescending to people of faith.

This postmodern tactic is ludicrous, because millennia of theology, Murphy’s scholarly discipline, have not generated a single “discovery” (and historical or archaeological findings, such as the discovery of the Gnostic Gospels, don’t count).

In today’s Guardian, columnist Nick Cohen has an equally “strident” piece: “Science has vanquished religion, but not its evils.”  It’s well worth reading in its entirety, but here are some bits:

In his often brilliant work and teaching, Rees has never “affirmed life’s spiritual dimension”. He has always said that he is a Darwinist without religious dogma. All he shares with the religious is a “sense of wonder at the universe”.

The religious nevertheless showered him with money because he is a symptomatic figure of our tongue-biting age. Like millions who should know better, Rees is not religious himself but “respects” religion and wants it to live in “peaceful co-existence” with it. . .

. . . But the respect the secular give too freely involves darker concessions. It prevents an honest confrontation with radical Islam or any other variant of poor world religious extremism and a proper solidarity with extremism’s victims. “I don’t want to force Muslims to choose between God and Darwin,” Rees says, forgetting that scientists “force” no one to choose Darwin, while theocracies force whole populations to bow to their gods. So cloying is the deference that few notice how the demand for “respect” gives away the shallowness of contemporary religious thought. . .

. . . Today, you have to be a very ignorant believer to imagine that your religion or any religion can provide comprehensive explanations. When they study beyond a certain level, all believers learn that the most reliable theories of the origins of life have no need for the God of the holy books. The most brilliant scientists and the best thought have moved beyond religion. It is for this reason that religion, which once inspired man’s most sublime creations, no longer produces art, literature or philosophy of any worth; why it is impossible to imagine a new religious high culture. . .

. . . But the notion Lord Rees so casually endorses – that you must respect the privacy of ideologies that mandate violence, the subjugation of women and the persecution of homosexuals and treat them as if they were beyond criticism and scientific refutation – is the most cowardly evasion of intellectual duty of our day.

Finally, at his website Choice in Dying, Eric MacDonald (I’d call him “Uncle Eric”, but that adjective has unfortunately been bestowed on someone else) has two back-to-back posts on the topic, “Big bucks, big splash, small puddle,” and “The betrayal of reason.”  From the latter:

In a parody of argument some are claiming that the fact that Newton was also religious shows that religion and science are compatible. So why should the Master of Trinity not have accepted the Templeton Prize? Well, quite aside from exposing Newton — as it does – to some well justified ridicule for his absurd alchemical fantasies and beliefs about the Jerusalem temple, this proves nothing more than that Newton, like most of his contemporaries, was, in some sense of that compendious word, religious, there being at the time little alternative, and all of them dangerous. Even Spinoza, rightly regarded as an atheist by his contemporaries, was a deeply “religious” man, and who, as a pantheist to Newton’s deist, illustrated clearly the deeply conflicted nature of thought about religion in the opening years of the scientific revolution. That Templeton is endeavouring to return human thought to that deeply conflicted state is a testimony at once to the persistence of the illusions of religion, as well as to the unceasing desire of the religious to restore theology as the Queen of the Sciences. That a scientist of Martin Rees’ stature should have aided and abetted this reactionary tendency towards irrationalism that continues to dog the heels of human thought is, in my opinion, a serious betrayal of reason. That he should have done so in evident ignorance of the Templeton Foundation’s continuing attempt to subvert reason in favour of its own Christian ideology is simply an act of treason against the science of which he has become a master.

QED.

Stenger on evolutionary convergence

April 9, 2011 • 10:25 am

Victor Stenger is PuffHo‘s skunk in the religious woodpile, a bracing antidote to the nausea-inducing posts of Michael Ruse.  Stenger’s latest post in the Religion section, “Contingency or convergence?“, takes on paleontologist Simon Conway Morris’s claims that the history of life proves Jebus.

Conway Morris’s claims rest on evolutionary convergence, the observation that evolutionarily distinct lineages can sometimes converge on similar “solutions” to similar environmental problems.  Ichthyosaurs, dolphins, and tuna are from independent lineages, but all have the fusiform shape necessary for swimming in the sea. We all know the remarkable similarity (with a few telling differences) between the “camera eyes” of octopi and vertebrates—eyes that evolved completely independently.  Conway Morris has a whole book on these, Life’s Solution: Inevitable Humans in a Lonely Universe, and he now runs a big project, the “Map of Life,” that collects lots of examples of evolutionary convergence.

Stenger dissects Conway Morris’s connection between convergence and Jebus and, as would anyone with a lick of sense, finds it wanting.  What amazes me about Conway Morris’s argument, something I banged on about in a New Republic piece, is that not only are there good biological and physical reasons for convergence (Stenger concentrates on the physics), but the phenomenon is completely irrelevant to Conway Morris’s claim that the evolution of humans was inevitable. (He uses this “inevitability”, of course, as evidence for God.) Humans are not an example of evolutionary convergence, for our big, reasoning brain—the brain that Conway Morris sees as enabling us to apprehend and worship The Big Man in the Sky—is an evolutionary one off.  That is, it evolved exactly once.  If convergence is used to show evolutionary inevitability, by showing that natural selection channels organisms into similar phenotypic pathways, why on earth would he apply that notion to an evolutionary singleton? A singleton like Homo sapiens is the worst way to show evolutionary inevitability.

This is a terrible flaw in Conway Morris’s logic. I can understand it only in light of the desire of a Catholic scientist to find the needle of Jebus in the haystack of evolution.

Stenger highlights an article in the Guardian that Conway Morris wrote in 2009, which I criticized at the time.  After arguing that Darwinism is completely inadequate to explain evolutionary convergence (it’s not), Conway Morris goes on to tout religion and bash atheists:

To reiterate: when physicists speak of not only a strange universe, but one even stranger than we can possibly imagine, they articulate a sense of unfinished business that most neo-Darwinians don’t even want to think about. Of course our brains are a product of evolution, but does anybody seriously believe consciousness itself is material? Well, yes, some argue just as much, but their explanations seem to have made no headway. We are indeed dealing with unfinished business. God’s funeral? I don’t think so. Please join me beside the coffin marked Atheism. I fear, however, there will be very few mourners.

(Jerry raises his hand here, “I do!, Dr. Conway Morris.  I really, seriously believe that consciousness is material.”  Some proof: when I had my sinus operation, they gave me gas that instantly removed my consciousness. When they turned the gas off, my consciousness returned.)

Who funds Conway Morris’s work on convergence and his Map of Life project?  Templeton, of course!  For those misguided souls who insist that Templeton has no intention of using its money to pollute science with woo, just have a look at the connection between the well-funded work of Conway Morris on convergence and what he says it shows about God.  It’s a blatant attempt to hijack the respectability of evolutionary biology in the service of faith.

h/t: Jon

Our visit with Dr. Sam

April 9, 2011 • 5:11 am

Sam Harris talked here yesterday on the topic of his new book, The Moral Landscape.   He spoke for about a half an hour—what he said was similar to his opening statement in his debate with William Lane Craig at Notre Dame the evening before—followed by an hour of questions.  Debate was very lively, and we had to bring the session to an end since the lecture hall was needed for another function. (I’m told, by the way, that the Harris/Craig debate will eventually be online; the livestream was dreadful because the audio was weak.)

There were questions that, I suspect, Sam has gotten quite used to.  What is the reason for choosing “well being” as the overarching criterion for morality?  When we make personal moral decisions (in his book Sam talks about giving his daughter a birthday present versus donating that money to starving African children), how do we weigh off our interests towards kin, friends, and lovers against the well-being of the rest of the world?

I asked Sam whether he shouldn’t simply dispense with the word and concept of “morality”—as it’s this freighted word that seems to motivate much of the opposition to his ideas—and simply talk about “well being”.  His response, which I think is right, is that the notion and feeling of morality is too deeply ingrained in human society to jettison, and that his own mission was to co-opt the word to denote well-being.  Above all, he argued, we must prevent religion from being the adjudicator of morality, since faith lays moral opprobrium on acts that either are morally irrelevant or that increase people’s well being, like the desire to have sex with those of the same gender, or in any position you want.

I also asked Sam if his theory wasn’t really tautological, since if one found a palpably moral act that unquestionably decreased well being, he could simply assert that it actually did increase well being since such calculations are often hard and sometimes impossible.  That would make his claim unfalsifiable and therefore unscientific.  In response he could claim that in such cases our moral judgments are simply wrong.  That’s clearly true for some judgments, since we’re starting to realize that, for instance, branding homosexual acts as “immoral” is simply a false morality.

I am quite interested in whether any acts indisputably considered moral can be shown to conflict with Sam’s criterion by decreasing well being.  That, I think, would be the real way one would have to go about falsifying Sam’s neo-utilitarianism. I haven’t been able to think of any such acts, but perhaps readers can.  If you think the criterion of well being is not a good one for morality, give me an example of an act that we’d all consider moral that unquestionably decreases well being.   I’m not talking about religiously-based morality here, since that’s rife with such examples.  Judgments about sex acts, homosexuality, and persecution of infidels come to mind.

After the talk we took Sam to an archetypal species of Chicago restaurant: the steakhouse.  In this case we repaired to David Burke’s Primehouse, known for dry-aging its meat in rooms lined with Himalayan salt.  We started with the tableside Caesar salad for four, which was absolutely terrific.

Then onto the meat.  I had the 40-day aged ribeye, while Sam opted for the 55-day specimen, which he pronounced excellent. On the right of this photo is Dr. Alex Lickerman, an awesome GP at the University of Chicago Hospitals and now head of student health; he interfaced with the U of C Office of Spiritual Life to provide support, funds, and the lecture hall, which was in the hospital.  Alex, like Sam, is a secular practitioner of Buddhism, and has his own website, “Happiness in This World.

You can see two of our side dishes:  truffle fries (yum!) and bacon gnocchi.  We washed down the steaks with a good bottle of Cotes du Rhone from my own collection.

Having already polluted our circulatory systems with lipids, we all opted for dessert.  Here you can see mine: Burke’s famous “cheesecake lollipop tree with raspberry cream”.  Each branch of the tree is a sphere of cheesecake encased in either chocolate or some other coating. You dip the pops into a saucer of whipped cream infused with raspberries.  Fantastic!

To the left is Dr. Bob Richards, who also helped with Sam’s visit.  Bob is a historian and philosopher of science who has appointments in three departments. He’s written a definitive book on Haeckel and is now working on one about Darwin’s Origin.

Thanks to Bob and Alex for helping with the visit and, of course, to Sam for stopping by to talk to us on his way to the UK.  In England, Sam will be having events with both Dawkins and Ian McEwan, as well as giving two other talks.

Caturday felids: encounter at the air/water interface, and bonus vaccination

April 9, 2011 • 4:22 am

Alert readers Gayle and Jon both sent me this video of a tabby meeting a dolphin.  The cat seems bemused, as if it can’t decide whether the dolphin is food or a big toy.

Bonus: Like humans, lions need their flu shots.  Here’s a nice video of two lion cubs who just got their flu shots at Orana Wildlife Park in Christchurch, New Zealand.  These are tough little customers, though they don’t seem to notice the jab.  This was also sent by Gayle, who lives in NZ.

[vodpod id=ExternalVideo.992966&w=425&h=350&fv=movie%3Dhttp%253A%252F%252Fstatic2.stuff.co.nz%252F1301543547%252Fstatic%252Fflash%252Fmediaplayer%26mediaXML%3Dhttp%253A%252F%252Fwww.stuff.co.nz%252Fxml%252Fvideo%252F4860471%26siteSTEM%3Donl.stuff.lifestyle%252Fcutestuff%26allowscriptaccess%3D]

Read more at stuff.co.nz.

British creationism

April 8, 2011 • 9:51 am

In yesterday’s Independent, barrister Andrew Zak Williams discusses the latest obstacles Brits face in getting evolution taught in the classroom.  These include not only the rise of faith-based schools but the government’s seeming reluctance to allow evolution to be taught at the primary level.

There are also some LOLzy and defensive quotes from intelligent-design creationist Michael Behe:

Dr Michael Behe is the biologist whose theory of Irreducible Complexity forms the supposed scientific basis of ID. I asked him about the consensus in many quarters that it is not scientific. While genially admitting that I had “hit a nerve”, he defended its credentials as a science. “Science is just using physical evidence and reasoning to come to a conclusion about nature,” he says. “The definition of science is supposed to help us investigate nature and if it of itself becomes a barrier, it won’t serve a useful purpose.”

Not many of us reject ID simply because the “definition of science” says that we can’t investigate the supernatural.  We reject ID because it’s a superfluous hypothesis with not a shred of evidence in its favor.

Dr Behe believes that although the scientific community is presently allergic to ID, this will change after a generation or two. “As scientists retire,” he says, “the ones who are very antagonistic to ID will be replaced by those other scientists who have grown up hearing and wondering about it. And so I think that the atmosphere will change.”

If there were a heaven, and we could collect on postmortem bets there, I’d bet Behe a substantial sum that the atmosphere won’t change. (This presumes, of course, that Behe and I would wind up in the same place. He might go to Hell for lying . . .)