Joe Wilson and race

September 13, 2009 • 7:32 am

Say what you will about Maureen Dowd, she hits the mark often enough to reamain interesting.  Her column in today’s New York Times, “Boy, Oh, Boy,”  about Joe “You Lie” Wilson and race, says what everyone else was afraid to.

The normally nonchalant Barack Obama looked nonplussed, as Nancy Pelosi glowered behind.

Surrounded by middle-aged white guys — a sepia snapshot of the days when such pols ran Washington like their own men’s club — Joe Wilson yelled “You lie!” at a president who didn’t.

But, fair or not, what I heard was an unspoken word in the air: You lie, boy!

Dawkins 17, Armstrong 0

September 12, 2009 • 7:36 am

Oh Lord, can there be a match more uneven than this?  In one corner: Karen Armstrong, embracer of apophatic theology, a wooly-headed apologist who insists that we can say nothing about God but who somehow keeps cranking out book after book on the subject.  In the other: Richard Dawkins, the Oxford Mauler, who will have none of that nonsense.  The venue: the conservative Wall Street Journal.  The topic: “Man vs. God.” According to Richard, both he and Armstrong were commissioned to write on the topic “Where does evolution leave God?” Each knew that the other was writing, but neither saw the other’s essay.

The outcome: Armstrong handily k.o.’ed  But that’s nothing new.  If you want a good take (and a good laugh) on “sophisticated” modern theology — and on its contrast with clear, empirically-based thinking — have a look.  You’ll be emboldened in your rationalism, but also curious about why Armstrong keeps finding places that will publish her repetitive nonsense. If this is the best that accommodationism can produce, WE WIN!

Excerpts:

Armstrong:

Religion was not supposed to provide explanations that lay within the competence of reason but to help us live creatively with realities for which there are no easy solutions and find an interior haven of peace; today, however, many have opted for unsustainable certainty instead. But can we respond religiously to evolutionary theory? Can we use it to recover a more authentic notion of God?

Darwin made it clear once again that—as Maimonides, Avicenna, Aquinas and Eckhart had already pointed out—we cannot regard God simply as a divine personality, who single-handedly created the world. This could direct our attention away from the idols of certainty and back to the “God beyond God.” The best theology is a spiritual exercise, akin to poetry. Religion is not an exact science but a kind of art form that, like music or painting, introduces us to a mode of knowledge that is different from the purely rational and which cannot easily be put into words. At its best, it holds us in an attitude of wonder, which is, perhaps, not unlike the awe that Mr. Dawkins experiences—and has helped me to appreciate —when he contemplates the marvels of natural selection.

But what of the pain and waste that Darwin unveiled? All the major traditions insist that the faithful meditate on the ubiquitous suffering that is an inescapable part of life; because, if we do not acknowledge this uncomfortable fact, the compassion that lies at the heart of faith is impossible. The almost unbearable spectacle of the myriad species passing painfully into oblivion is not unlike some classic Buddhist meditations on the First Noble Truth (“Existence is suffering”), the indispensable prerequisite for the transcendent enlightenment that some call Nirvana—and others call God.

Dawkins:

Darwinian evolution is the only process we know that is ultimately capable of generating anything as complicated as creative intelligences. Once it has done so, of course, those intelligences can create other complex things: works of art and music, advanced technology, computers, the Internet and who knows what in the future? Darwinian evolution may not be the only such generative process in the universe. There may be other “cranes” (Daniel Dennett’s term, which he opposes to “skyhooks”) that we have not yet discovered or imagined. But, however wonderful and however different from Darwinian evolution those putative cranes may be, they cannot be magic. They will share with Darwinian evolution the facility to raise up complexity, as an emergent property, out of simplicity, while never violating natural law.

Where does that leave God? The kindest thing to say is that it leaves him with nothing to do, and no achievements that might attract our praise, our worship or our fear. Evolution is God’s redundancy notice, his pink slip. But we have to go further. A complex creative intelligence with nothing to do is not just redundant. A divine designer is all but ruled out by the consideration that he must at least as complex as the entities he was wheeled out to explain. God is not dead. He was never alive in the first place.

Now, there is a certain class of sophisticated modern theologian who will say something like this: “Good heavens, of course we are not so naive or simplistic as to care whether God exists. Existence is such a 19th-century preoccupation! It doesn’t matter whether God exists in a scientific sense. What matters is whether he exists for you or for me. If God is real for you, who cares whether science has made him redundant? Such arrogance! Such elitism.”

Well, if that’s what floats your canoe, you’ll be paddling it up a very lonely creek. The mainstream belief of the world’s peoples is very clear. They believe in God, and that means they believe he exists in objective reality, just as surely as the Rock of Gibraltar exists. If sophisticated theologians or postmodern relativists think they are rescuing God from the redundancy scrap-heap by downplaying the importance of existence, they should think again. Tell the congregation of a church or mosque that existence is too vulgar an attribute to fasten onto their God, and they will brand you an atheist. They’ll be right.

Oh, the juicy takedown of Armstrong in Dawkins’s last two paragraphs!  No matter how sophisticated modern theologians like Armstrong, Eagleton, and Haught consider themselves, they are always too removed from the world to understand what “religion” means to most people. Hint: it’s not apophatic.

Caturday felids: trifecta!

September 12, 2009 • 6:54 am

Three cat items up today, all contributed by readers.

The Cat of the Week, Mr. Darcy, belongs to one of our posters, Matthew.

Mr. Darcy was a stray who lived in our back yard. We left food out for him and he eventually took to staring patiently in at us from the back door. After a very cold winter we arranged to have him snipped so that we could take him to a rehoming shelter. One of the landlords didn’t want a third cat in the house, but after a week indoors recovering from his operation, much to my delight, he became a full member of the household. I think he was very appreciative of his improved living arrangements (as you can see, we fed him well). Unfortunately, as a stray he must have got into some fights and, after two years with us, he became ill and succumbed to FIV. He was a very gentle cat and extremely loyal. He is much missed, but I’m very glad we got the chance to give him a good life for those two years and a much more peaceful end than he would have found outdoors. He certainly left his mark on those of us who loved him. I think this should serve as encouragement to those lookng for a cat to check their local shelters first. A genuine cat lover should find the thought of a homeless cat heart-breaking and knowing a cat is a rescue can add something special to the bond between owner and human.

As for his name, well, it’s not from D’Arcy Thompson.  Think Pride and Prejudice:

He was called Mr. Darcy for two reasons. He used to stare at Peanut, a chocolate Burmese and one of the female cats in the house, but held off on courting her aggressively. There was a veneer of disdain on her part, but we suspected she was interested. Secondly, we always thought he looked very gentlemanly, especially with his impressive jowls and chest.

Mr. Darcy0Fig. 1.  The late Mr. Darcy.  Un matou formidable!

Darcy and Perrin25

Fig. 2.  Darcy and his friend Perrin, “a troublesome
Tonkinese who Mr. Darcy helped calm down somewhat.”

Up second is an unknown marbled tabby who visited reader Aaron this week.  It has one of the prettiest coats I’ve seen.  Aaron notes, “I don’t know much about it except that it was friendly and well taken care of.  (If it had been a stray we probably would have adopted it, which might not have gone over well with our current cat.)”

tabby

Fig. 3.  Unknown but elegant.

Finally, from substitute-blogger Greg Mayer, an article from yesterday’s New York Times, “Meow Spoken Here,” about New Yorker Tammy Cross and her kitten-rescuing operation, which she runs out of her apartment on the West Side. Cross is decidedly not a crazy cat lady, and it’s a nice read.  If you’re an ailurophile, you’ll want to watch the audio slide show.

Dead genes for tooth enamel

September 10, 2009 • 5:52 pm

Vestigial organs are commonly cited as evidence for evolution; indeed, I wrote most of a chapter about them in WEIT. And although some of these organs may have a function (the appendix, for example, is now thought to play a small role in the immune system), the fact of functionality doesn’t detract from their vestigiality — or their usefulness as evidence for common ancestry. The fact that the penguin’s “wings” now serve as flippers doesn’t mean that they say nothing about penguins’ ancestry from birds that could fly. (My own definition of a vestigial trait is loosely “a trait that now serves a function completely different from what impelled its initial evolution, and for which traces of its original structure still remain.”)

And, anyway, some vestigial organs appear to have no function at all. You’d be hard pressed to claim that there was a function for the tiny nub-like wings of the kiwi bird, buried deep within the feathers on its flanks.

But you’d be even harder pressed to argue that dead genes have a function.

One of the predictions of evolution is that if vestigial organs exist, then surely vestigial genes must exist, for traits that shrink or disappear must surely be based, at least sometimes, on genes that disappear. But genes aren’t just snipped out of the DNA when they’re no longer needed: natural selection will inactivate them, usually by favoring a mutation that removes one or a few DNA bases (a deletion), putting in a “stop codon” (a change in the DNA that prematurely terminates the protein being read from that DNA’s code, making a “frameshift” mutation (changing the triplet code so that the entire coding frame of a DNA sequence is thrown off), or changing the regulatory region of a gene so its protein is no longer made. But the remnants of the gene will remain in the DNA, testifying to its ancestry from a gene that was active in an ancestor. These dead genes are called pseudogenes.

Now that genome sequencing is routine, evolutionists can do large-scale searches for dead genes. And, as predicted, they’re all over the place — in nearly every species that has been examined. Some of the “dead” genes I discuss in WEIT include human genes that used to make vitamin C or egg yolk in our ancestors, but have now been rendered mute. It would be hard to argue that these genes still have a “function,” for they produce no protein at all. Their existence is a powerful argument in favor of evolution and against creationism.

A new paper in PLoS Genetics continues the search for predicted dead genes — this time for genes that once made tooth enamel — and finds a lot of these wrecks. They’re exactly where you expect to find them — in toothless animals long thought to have descended from animals with teeth. So the “theory” of evolution is once again confirmed, although we hardly need further confirmation. But this paper goes beyond a mere redudant proof of common ancestry. The authors also make models of how the “enamel” genes degenerated, and, by calculating when this degeneration happened, predict what the teeth of common ancestors should look like. This prediction is in principle testable by finding the relevant fossils and looking at their teeth.,

There are two kinds of mammals that lack tooth enamel: those that are completely toothless (e.g., armadillos, pangolins, aardvarks, baleen whales), and those that have teeth that lack enamel (e.g., dwarf sperm whales, two-toed sloth). From other evidence, including fossils and comparative morphology, scientists have confidently predicted that every one of these species descended from ancestors that had enameled teeth. The researchers sequenced, in many mammals species, the critical gene enamelin (ENAM), which helps deposit hydroxyapetite into the tooth. If ENAM is knocked out in mice, enamel doesn’t form.

Sure enough, in every species lacking teeth or enameled teeth, ENAM was rendered nonfunctional, either by the accumulation of frameshift mutations or stop codons. The authors give a very nice graph of how the genes have degenerated in each lineage, which I show below (the caption is at the bottom of this post if you’re a geneticist).

Mammal teeth

Figure 1. Enamelin gene phylogeny for mammal species with no teeth, un-enameled teeth, or fully enameled teeth (tooth type illustrated at right, before species name). Caption for this figure, showing the various genetic changes that have inactivated ENAM, is at the bottom of this post.

Well, that’s evidence for evolution and common ancestry, and it’s neat. But we hardly need more evidence of this type to support Darwinism, because there are many such reports of pseudobenes. What makes the paper unique is the authors’ model of how and when ENAM was inactivated in several lineages.

The details are complicated, but in essence the authors modeled a two-step process of gene evolution: before the mutation inactivating ENAM (whose occurrence can be estimated from the gene tree), and thereafter. Before inactivation the gene was assumed to evolve slowly since gene changes were largely deleterious. After inactivation, the gene evolved faster — since it was no longer making a useful product, changes were assumed to accumulate “neutrally” (that is, all changes carried neither selective penalty nor advantage). This analysis made several predictions. One of them is that ancestral xenarthans (armadillos, sloths, and anteaters), had teeth with enamel, even though living representatives don’t. This is a testable prediction: find early ‘basal” xenarthans, and look at their teeth.

You may have noticed that after the gene was inactivated, it was assumed to degenerate through the accumulation of random, neutal mutations. This is a valid assumption for gene inactivation, but not necessarily for the disappearance or shrinkage of entire traits. If a trait is no longer useful, there are actually three ways it can degnerate:

1. As posited for genes, the accumulation of inactivating mutations, which carry no penalty since they affect a trait that makes no contribution to reproduction.

2. Traits can degenerate through positive natural selection. One way is simply that an animal (or plant) can be seen as an economic compromise among biological materials, and if you don’t need a feature, selection can favor rerouting its building blocks to other features. The material used to build the wing of a flightless bird, for example, could be diverted to making or strengthening bones in other parts of the body.

3. Likewise, traits that are no longer useful might be easily injured. Selection would then favor degeneration of that trait as a way of preventing injury. This may, for example, explain the reduced eyes of cave fauna or burrowing animals like moles.

It isn’t easy to distinguish between these hypotheses. One way is to find a bunch of genes involved in the trait’s degeneration and, by sequencing them, see if the DNA has changed by natural selection since the trait was no longer useful. (There are statistical tests for this, though they have some problems.)
_________________

Meredith RW, Gatesy J, Murphy WJ, Ryder OA, Springer MS (2009). Molecular decay of the tooth gene enamelin (ENAM) mirrors the loss of enamel in the fossil record of placental mammals. PLoS Genet 5(9): e1000634. doi:10.1371/journal.pgen.1000634

Caption for Fig. 1 (above), from Meredith et al.: Figure 1. Species tree with frameshift mutations and dN/dS branch coding. Symbols next to taxon names denote taxa having teeth with enamel, taxa having teeth without enamel, and edentulous taxa. Branches are functional (black), pre-mutation (blue), mixed (purple), and pseudogenic (red). Vertical bars on branches represent frameshift mutations (see Table S1). Frameshifts that map unambiguously onto branches are shown in black. Frameshifts shown in white are unique, but occur in regions where sequences are missing for one or more taxa (Figure S7) and were arbitrarily mapped onto the youngest possible branch. Homoplastic frameshifts (deltran optimization) are marked by numbers. Numbers after taxon names indicate the minimum number of stop codons in the sequence (before slashes) and the length of the sequence (after slashes).

Got blood? Great tits hunt bats

September 9, 2009 • 6:41 am

It’s not enough that blue tits once learned to open milk bottles left on British doorsteps, sipping the cream from the top. Now their relatives, great tits, have acquired a taste for blood (see here as well) hunting and killing bats in Hungary.

As the BBC reports (the link contains a video as well as a grisly photo of a half-eaten bat):

During two field seasons in the Bukk Mountains of northeastern Hungary, the researchers documented 16 cases of great tits (Parus major) hunting, killing and eating a hibernating bat in the one cave.

Pipistrelle bats (Pipistrellus pipistrellus) are about one-quarter of a great tit’s size.

The birds would fly close to the cave walls, landing frequently and often disappearing into crevices. They would either eat the bats there and then or carry them away for feeding.

When their hibernation is disturbed, the bats squeak in the audible range for humans and great tits.

The researchers speculated that the birds may have learned to listen for these squeaks – and when they recorded some and played them back, the birds responded with interest about 80% of the time.

I’m on the road today, and can’t get the original paper in Biology Letters describing the behavior, but I suspect that, like cream-stealing in blue tits, it comes from observational learning. During the lean winter months, hungry birds presumably watch — and follow — other birds committing chiropticide. But it could be genetically based and evolved. The decisive experiment would be difficult, involving hand-rearing tits in the lab and releasing them in bat caves where they could not observe other tits hunting.

At any rate, there’s something unseemly about a songbird eating a mammal. But, as Darwin pointed out with reference to ichneumon wasps, nature doesn’t care a fig about our squeamishness.

h/t: Matthew Cobb and reader Raymond, who has a thread about this over at Secular Cafe.

How many “ways of knowing” are there?

September 8, 2009 • 6:56 am

I’ve become rather ambivalent about Eugenie Scott — and, indeed, about some of the policies of the organization she heads, the National Center for Science Education.  On the one hand, Scott is a really nice person (I used to count her as a friend, though I’m not sure she feels that way about me now!), and, more important, she and the NCSE have done absolutely terrific — and award-winning — work battling creeping creationism in America.  The NCSE’s intercession in the Dover intelligent-design trial, for example, was critical in the victory.

But Scott also travels around giving strongly accommodationist talks, reflecting the NCSE’s policy that science and religion, when properly conceived, are harmonious.  This is, of course, the NOMA stance.  The NCSE has made a tactical decision that selling evolution is most efficacious if you proclaim — never mind what you really think — that religion and science are compatible, occupying their own magisteria.

Over at Metamagician and the Hellfire Club, Russell Blackford reports on a talk Scott gave yesterday at Dragon*Con.  To be fair, Blackford didn’t take notes, and I haven’t heard the talk.  But if his memory is accurate, Scott told the audience that there are many valid “ways of knowing” beyond science.  As Russell reports:

. . . In any event, it was the first part of the speech that worried me. This emphasised the claim that science (Scott said “science”, not “reason”) is only one way of knowing. The others that she mentioned were personal insight and authority (I don’t think she was saying that these three are the only “ways of knowing”). She appeared to be happy to count all sorts of ideas gained from personal insight, perhaps assisted by rituals or drugs, as “knowledge”, which is rather odd, since knowledge is, at the least, justified belief. She counted revelation, including the words of holy books, as a sub-set of authority, and explained that the problem is when empirical claims are based on revelation.

Scott also said that science is a limited way of knowing because it can only investigate natural phenomena and can only offer natural explanations for them, and so cannot deal with supernatural claims. She offered no argument for this claim. Indeed, she gave an example of scientific study of truth claims that appeared to refute it. This was a description of a controlled experiment to see whether people really can perform better than chance at dowsing for water. Clearly, if the claim “I can perform better than chance at dowsing for water” is refuted by scientific investigation, it follows, a fortiori, that the claim “I can perform better than chance at dowsing for water by using supernatural means” is also refuted.

Oh dear dear dear.  Russell, I, and others have addressed the idea of science and the supernatural many times before (see here, here, and here, for example), dispelling the soothing idea that “science has nothing to say about the supernatural.”  That is, of course, hogwash.  Science has plenty to say about the Shroud of Turin, whether faith healing works, whether prayer works, whether God seems to be both beneficent and omnipotent, world without end.  Science can, as we’ve repeated endlessly, address specific claims about the supernatural, though it’s impotent before the idea that behind it all is a hands-off, deistic Transcendent Force.

Scott admits that there is a problem when empirical claims are based on revelation, but seems completely unaware that empirical claims derived from revelation form the basis of nearly every faith.

I am absolutely sure that Scott is aware of these arguments. But she ignores them, and goes around spreading the same old accommodationism.  In this sense she’s like the Twins: she’s heard the counterarguments, but not only has she failed to answer them, she ignores them. What is even more distressing is that Scott is an atheist, so for her, at least, there are no supernatural ways of knowing.  Does she think she’s missing out on a kind of knowledge that only the faithful have? I doubt it.

As for “ways of knowing,” my response is always, “What do you find out? What do you “know”?  And how would you know if you were wrong? Was Jesus the son of God?  Christians’ “way of knowing” tells them, “Yes, of course!” But Islamic “ways of knowing” say, “No, of course not, and you’ll burn in hell if you believe that.”  Revelation, dogma, and scripture are not in fact ways of knowing; they are ways of believing.  There are no “truths” that religion can produce which are independent of truths derived from secular reason.

With his usual acumen, Russell dissects the problem in detail.  Read his post.  And I agree completely with his conclusion:

I am not suggesting that the NCSE enlarge its remit to attack religion more generally. That is not its raison d’etre at all. But it can be neutral about such questions as whether science undermines a large amount of religious thinking, far beyond the claims of creationism and Intelligent Design. It can stop relying on an unnecessarily narrow (and very dubious) view of scientific epistemology, designed to leave as much authority with religion as possible. It can stop selling Gould’s intellectually bankrupt principle of Non-Overlapping Magisteria on its website.

It’s perfectly clear by now that neither Scott nor the NCSE will ever deal with the ideas that 1) the other “ways of knowing” don’t produce truth, 2) science can indeed address the supernatural, at least some aspects of it, and 3) a lot of people DO NOT find science and faith compatible. By enabling superstition, and giving credibility to irrationality, Scott and the NCSE’s NOMA-ism will, I think, hamper the evolution of a rational America.  Yes, we’re on their side vis-a-vis creationism, and yes, I’ll be more than glad to join hands with them in fighting that scourge of rationality.   But so long as our allies keep spouting half-truths and untruths about the relationship between science and religion, we’ll keep calling them to task.

Where's the beef?

Fig. 1. Other ways of knowing: I can’t has cheezburger.

Jerry to speak at the University of Wisconsin-Parkside

September 7, 2009 • 9:12 pm

by Greg Mayer

As part of its Darwin 1809-1859-2009 commemoration of the bicentennial of Darwin’s birth and the sesquicentennial of the pJerry Coyneublication of the Origin, the University of Wisconsin–Parkside‘s Science Night series presents Prof. Jerry Coyne of the University of Chicago speaking on “Why Evolution Is True” at 7 PM on Wednesday, Sept. 9, in Greenquist Hall 103.  The event is free and open to the public, and sponsored by the University’s Committee on Lectures and Fine Arts, the College of Arts and Sciences, and the Department of Biological Sciences.  Parking is free after 6:30 PM. If you’re in southeastern Wisconsin or northern Illinois, we’re in Kenosha, and not hard to find or get to. (For one of our previous Darwin 1809-1859-2009 events, see here.)Diplomystus dentatus, Green River Formation, Eocene, WyomingA fossil fish, Diplomystus dentatus, with no particular relation to Jerry’s talk, but a nice picture.