In Guatemala

October 8, 2009 • 12:46 pm

A brief post from Santa Cruz on Lake Atitlan, where I’m installed in a backpacker’s hotel on this most beautiful lake.  I have seen my quetzal (a juvenile male flying) and have been embraced (four limbs and a tail) by a spider monkey.  Despite the deforestation, Guatemala remains a gorgeous country and a traveller’s paradise.

I see that the blog kerfuffle about Dawkins continues, and that the Unholy Trio continue their furious backpedaling, even trying to make blog hay from their mistake.  Here, far from the madding crowd, it seems laughable and a bit pathetic.

Thanks to Matthew and Greg for their guest hosting. I’ll return to the fray about October 18.

Holy infrared cameras, Batman!

October 7, 2009 • 2:31 pm

by Matthew Cobb

Over at The Scientist, there’s a page devoted to “tools and techniques for tracking mammalian behavior”. The latest addition relates to the work of Nickolay Hristov, at Winston-Salem State University. Hristov was working as a postdoc with Thomas Kunz at Boston University, and they wanted to study what bats were doing in the Carlsbad Caverns National Park in New Mexico. Using military-grade thermal infrared imaging technology, they were able to observe the bats in the dark, and produced this amazing video (not sure about the Bach soundtrack, myself):

Hristov and his co-workers published an article (open access) in Integrated and Comparative Biology at the beginning of 2008 describing their technique, and its advantages for studying the aerosphere. They were able to estimate the size of the bat colony (it seems to fluctuate with time, by as much as 1 million bats), and also get greater insight into how individual bats navigate inside the cavern, and how they chase moths outside.

We know that in Venezuela bats have to deal with a giant centipede that snarfs them in mid-air. Maybe – like snakes – the centipede can detect passing bats using infrared? Or maybe there are just so many bats it’s easy to get one…

h/t: John Altrincham (Leeds, UK) and his EZNews

“Home” – What have we done to the Earth?

October 7, 2009 • 5:39 am

by Matthew Cobb

Yann Arthus-Bertrand is the French photographer who produced that fantastic book and travelling exhibition, The Earth from the Air. Earlier this year, he produced a feature film, called simply Home, which surveys the history and state of the planet in a poetic, striking and somewhat depressing way, focusing on what we are doing to it.

The commentary is a bit over the top (sounds better in French), but the film is unmissable. You can watch the whole thing, for free, on YouTube. It lasts 90 minutes, so settle back and get the popcorn and beer out…

Mind you, it’s not a cheery view, and recalls Jim Morrison’s cry on an old Doors track “When The Music’s Over” – “What have we done to the Earth? What have we done to our fair sister? Ravaged and plundered and ripped her and bit her, stuck her with knives in the side of the dawn, and tied her with fences and dragged her down.”

Warning: Contains scenes of unbearable beauty, and will probably turn you into a vegetarian and stop you driving a car ever again.

I’m afraid I can’t embed the Youtube link for some reason, so you’ll have to click here.

Richard Dawkins is not an accommodationist

October 4, 2009 • 11:06 am

Oh for God’s sake! An alert reader called my attention to two blog posts by Josh Rosenau and Chris Mooney/Sheril Kirshenbaum, both claiming that Richard Dawkins explicitly voiced accommodationist views in a Newsweek interview. “He’s changed!” they say.

Well, I know Richard Dawkins. I am at a meeting with Richard Dawkins. I just discussed these accusations of accommodationism with Richard Dawkins. And I can tell you, Chris, Sheril, and Josh, that Richard is not one of you.

Right now I feel like Woody Allen in Annie Hall. If you’ve seen the movie, you’ll remember that in one scene Allen standing in line with Diane Keaton, waiting to see a movie, and becomes annoyed by some pompous guy trying to impress his date by nattering on about the work of Marshall McLuhan. Allen goes behind a movie sign and pulls out McLuhan himself, taking him over to confront Mr. Pomposity. McLuhan coldly eyes him and says, “Excuse me, but I am Marshall McLuhan, and I couldn’t help overhearing what you said. I have to tell you that you know nothing of my work!” Allen turns to the camera and quips, “Don’t you wish life could be like this?”

Well, I have a Woody moment now. Nobody who has followed Dawkins’s work and writing could possibly think he’s an accommodationist. Since I’m here with Richard at at the Conclave of the Godless, I simply emailed him the links to Rosenau and Mooney-and-Kirshenbaum’s websites. Here is Richard’s email response to the claims that he’s an accommodationist; it’s posted here with his permission, and was verified in person:

How utterly ridiculous. All I was saying is that it is possible for a human mind to accommodate both evolution and religion because F. Collins’s mind seems to manage the feat (along with lots of vicars and bishops and rabbis). I also needed to make the point that TGSOE [The Greatest Show on Earth] is not the same book as TGD [The God Delusion] because many interviewers who are supposed to be interviewing me about TGSOE have simply ignored it and gone right back to assuming that it is the same book as TGD.

I sympathize with politicians who have to watch every syllable they utter for fear it will be misused by somebody with an agenda.

So there”s your answer, Josh, Sheril, and Chris. I wish you weren’t so keen to validate your own ideas that you need to distort the views of others in a desperate ploy to show that they agree with your accommodationism. Really, you’ve read The God Delusion and, presumably, Dawkins’s other writings. Anybody with two neurons to rub together should know that the man is not an accommodationist.

Now that Dawkins has verified this, it would be nice to see Rosenau, Mooney, and Kirshenbaum correct their postings. And they need to stop pretending that the existence of religious scientists and religious people who accept evolution proves that science and faith are compatible. We settled that issue long ago. The issue is philosophical compatibility. Is that really so hard for anyone to understand?

From the atheist meetings

October 4, 2009 • 10:30 am

Time is short, as I’m off to Guatemala this evening, but I wanted to post a brief report on the AAI meetings. I’ve had a look at Pharyngula, and of course P.Z. has been doing a good job reporting on the salient events.

It’s the first time I’ve been in a group of fellow atheists (and I haven’t detected one sign of stridency or militancy), and it gives one a warm supportive feeling. One of the functions of speaking at these meetings, even if one is preaching to the choir, is to give solidarity to the atheist community, many of whom feel isolated and alone.

Pharyngula reported on Robert Richert’s talk on his experiences in Vietnam, but what P.Z. didn’t mention is that Richert broke down in sobs at the end, while he was describing how one of his fellow soldiers bragged that he had been protected by God, while a Vietnamese woman wailed helplessly as the last blood pumped out of her infant son’s body (he had been hit by a grenade fragment). “Where was his miracle?” asked Richert, with tears streaming down his face. It was an enormously moving moment.

P.Z.’s talk was also good (it’s the first time I’ve heard him speak). Although he’s low key on the dais, his message is hard-hitting, and it was about how “design” can result from purely naturalistic processes. Lots of jabs at Dembski et al. P.Z. really shone in the long question session, where he handled the many questions with perspicacity and humor.

It was great to finally meet Russell Blackford, a nice guy who gave a great talk on anti-religion “blasphemy” laws that are passing in various places, including one under consideration by the UN.

I attended a talk (and had breakfast with) William Dav is, better known as “The Cigarette Smoking Man” of X-Files fame. Davis’s nominal topic was a response to Dawkins, who has criticized The X-Files for being inimical to reason (the supernatural explanation always won). Davis’s response basically boiled down to “Well, we all knew it was fiction,” which I think is inadequate. Davis also gave a bit of biography (I learned this morning that his X-Files cigarettes were herbal, and he had somebody else light them), and threw out a few bizarre statements, to wit: it might have been better not to fight against Hitler in WWII, and that perhaps democracy isn’t the best political system for the US (he feels that it’s inefficient at confronting our enormous global challenges).

Bill Maher’s award and talk on Friday were, as P. Z. noted, absolutely hilarious: Maher read from Rick Warren’s “Purpose Driven Life,” making spontaneous sarcastic comments throughout. The guy is a hoot, despite his views on medicine (to which Richard did draw attention during his speech). I sat next to Maher at the ceremony; he has a very young partner with an Archaeopteryx fossil tattooed on her forearm

Yesterday was “science day,” organized by the Dawkins Foundation. Larry Krauss talked on cosmology. Richard called him “The Woody Allen of Cosmology,” and that’s absolutely accurate. The talk was fantastic; one of the best popular talks on physics I’ve ever heard. Krauss is a riveting and hilarious speaker, who leavens his physics with plenty of bon mots (and, in this case, attacks on creationism). I was a bit disappointed in Carolyn Porco’s talk, as I expected her to discuss her work on planet imaging. Instead, she talked about the compatibility of science and faith (she appears to be a bit of an accommodationist), and left the images and science to the very end. But do look at the website for some stunning pictures of Saturn.

Dan Dennett talked about interviews with active priests and ministers who are atheists, and also mounted a hilarious attack on theologians like Karen Armstrong, who mouth pious nonsense like, “God is the God behind God.” Dennett calls this kind of language a “deepity”: a statement that has two meanings, one of which is true but superficial, the other which sounds profound but is meaningless. His exemplar of a deepity is the statement “Love is just a word.” True, it’s a word like “cheeseburger,” but the supposed deeper sense is wrong: love is an emotion, a feeling, a condition, and not just a word in the dictionary. He gave several examples of other deepities from academic theologians; when you see these things laid out — ripped from their texts — in a Powerpoint slide, they make you realize how truly fatuous are the lucubrations of people like Armstrong, Eagleton, and Haught. Sarcasm will be the best weapon against this stuff.

I think my talk on the evidence for evolution went well, but I’ll let others be the judge of that. Annoyingly, I was slated for a book-signing, and somebody forgot to order my book!! Anybody who wants an autographed copy should feel free to order the book on Amazon, send it to me (with return postage please!), and I’ll sign it and send it back.

Finally, Richard read from the last chapter of The Greatest Show on Earth, which is an exegesis of the famous last paragraph of The Origin.

Eugenie Scott, director of The National Center for Science Education, is speaking in an hour, and I’ll go to her talk (I may report on it later this evening) and take off for LAX.

This is written in haste, in a hotel lobby, so I apologize for any infelicities of grammar, misspellings, and the like.

The discovery of heredity

October 4, 2009 • 7:45 am

by Matthew Cobb

In a previous post on the genetics of dog coat variation, I stated that ‘dog “breeds” are an incredibly recent invention – less than 200 years’. In the discussion that followed, David Burbidge commented that this wasn’t quite right. Citing  two 17th century examples (Shakespeare’s Macbeth and the King Charles spaniels) as proof, he wrote: “Major breeds like greyhounds, wolfhounds, mastiffs, and spaniels all go back much further than 200 years, though of course the modern pedigree breeds are not identical to their ancestors.”

There are two points here. First, he’s right, of course. There was indeed artificial selection for general dog shape/behaviour, presumably going back even before the 17th century. However, the point being made in the article (and in my post) is that contained in the final part of David’s comment. Pedigree breeds, with strict control of breeding, and the development of so many more kinds of dog breed, beyond the key hunting types, with a few pets thrown in (like the King Charles Spaniel), is indeed extremely recent. Most of the examples of coat variation described in the article have accumulated in less than 200 years.

The second, and more intriguing point, relates to what on earth all those dog breeders thought they were doing prior to the 19th century. For evolution by natural selection to occur, you need three conditions: characters need to be variable between individuals, some element of that variability needs to be inherited, and the variability must affect fitness (ultimately expressed in terms of the number of copies of the genes underlying the character that are present in the next generation).

With those three conditions, any set-up, be it organic life-forms or a computer model, will lead to evolution by natural selection.

The existence of the second of these three conditions for evolution – heredity – seems completely obvious to us today. But less than 200 years ago, the concept of “heredity” in biological terms simply did not exist. In the 17th century, the great physician William Harvey tried to work out why some characters seemed to reappear in different generations, others seemed to “skip” a generation, some (like skin colour) appeared to be a mixture of  the parents, while others again (like sex) were either one or the other but never (or very rarely) a mixture.

As he put it: “why should the offspring at one time bear a stronger resemblance to the father, at another to the mother, and, at a third, to progenitors both maternal and paternal, farther removed?” In the end, Harvey simply gave up – it was too complicated for him.

In a way, this isn’t surprising. Genetics is complicated – there is not, at first sight, a common explanation for skin colour (blending inheritance), eye colour (dominance in most cases) and sex (chromosomal determination – in humans at least). Harvey couldn’t see a pattern because, on the surface, there isn’t one.

You might think that although “scientists” like Harvey didn’t get it, there must have been some general folk knowledge that “like breeds like”. Yes and no, is the answer. For example, in the second half of the first century CE, Lucius Junius Moderatus Columella summarized Roman agricultural knowledge in De Re Rustica (‘On Rural Matters’). Problems associated with animal breeding take up only a few sentences, but Columella did note that, althought most coat colours were a mixture of the parental kinds, the grandsire’s coat colour could reappear in the second generation. What that meant, of course, was completely opaque. In other words, like does not always breed like.

Furthermore, until the experiments of Francesco Redi and Jan Swammerdam in the mid-1660s, it was thought that insects and all other “bloodless animals” appeared from decay, rather than from mating between male and female. It took Redi’s careful experimentation, and Swammerdam’s observations, for them to come to the radical conclusion that “all animals come from an egg laid by a female of the same species”.

The question of the role of the male and the female in producing the offspring remained hugely contentious right up until the 1840s. Aristotle had argued that the male produced a “seed” (= “semen”), which the female nourished. Swammerdam, Steno and others turned this argument on its head and argued that the egg was the origin of all life – including in humans. Within a few years, matters became even more complicated when Antoni Leeuwenhoek observed spermatozoa in human semen. Leeuwenhoek thought that these sperm were the origin of life, and that the egg was simply food. Most people, however, argued they were parasitic worms (hence the name we still use today – “spermatoZOA”, or animal found in semen).

While the mechanics of what eventually became known as reproduction were finally worked out in the 1840s, in the middle of the 18th century people had begun to suspect that something else was going on. Two parallel sources of information helped gel the idea of heredity. Both involved large data sets – which is when the patterns of heredity start to become really clear.

The transmission of polydactyly – having five or more fingers – in human families was separately studied by two French thinkers, Réaumur and Maupertuis, and they began to suspect that something was passing across the generations. Then, in the middle of the 18th century, Robert Bakwell, an entreprising English sheepfarmer, decided to make a better breed of sheep that would grow quicker and make him more money. By carefully selecting sheep in a very large flock, he soon produced his desired changes.

These ideas were soon applied to the centre of the European wool industry, in Moravia, where local thinkers started to predict what plant hybrids would look like. In 1837, one of the leading intellectuals of the area, Abbot Napp of the Brno monastery, asked “what is inherited and how?” Six years later, he welcomed a new recruit to the monastery – Gregor Mendel.

The final certainty that there was such a thing as “heredity” came with French thinkers looking at patterns of disease. People knew that some diseases reappeared across the generations. For example, in the seventeenth-century, the philosopher Sir Francis Bacon wrote that: “Long Life, is like some Diseases,a Thing Hereditarie”. By the end of the 18th century, French physicians had become convinced that many human characteristics were “hereditary”.

However, at this stage “heredity” did not exist, either as a concept or as a word. You won’t find the word in the first Edition of The Origin of Species, either, although the idea is fundamental for Darwin’s view of evolution. The English word was first used in print by Spencer in 1863, and Darwin used it in his notes at about the same time.

It is well known that although Darwin knew there was a “force” of heredity, he did not understand how it worked (any more than Harvey did). Many of his ideas were wrong, and he recognised this was a major weakness in his theory.

To the modern reader, what appears so surprising at first sight is that it took so long for something to be discovered that now appears so obvious. What this history in fact shows is that the facts of heredity are in fact remarkably complicated, and it required  a lot of work by some very smart people over a long period of time to finally work out what was going on.

To learn more about this, you can download this article I published in 2006 (PDF format), or, even better, read my book, entitled Generation in the US, or The Egg & Sperm Race in the UK. You can also visit the website associated with the book.

Caturday Felid: Ollie the nose-scratcher

October 3, 2009 • 7:34 am

by Matthew Cobb

Ollie

Today’s Caturday Felid is one of my cats, Ollie. Last year, Jerry came over to the UK to go to a conference and give talks. I invited him up to Manchester, where he gave a special lecture to our First Year students on “Evolution and the New Creationism”, which went down very well. What also went down well were the pints of beer we drank at the Marble Arch Inn in Manchester. Before we went out, Jerry came round to my house to see our two cats, Ollie and Pepper. I held Ollie (who’s a bit skittish), and as Jerry peered at him, Ollie lashed out and scratched The Great Man’s Nose.

It wasn’t quite like Jack Nicholson in Chinatown, but it was still pretty uncomfortable for Jerry.

Anyway, the point of all this is: why do cats like to sit in boxes? (Or in this case, a laundry basket.)

Variation in dog coats

October 2, 2009 • 7:55 am

by Matthew Cobb

This blog normally (and rightly) gives pride of place to cats, but this post will be about dogs. I trust Jerry will forgive me when he returns.

Hidden away in the same issue of Science that deals with Ardi, there’s an article by a host of researchers from the US and France (you’ll need a subscription to get past the abstract), looking at the genetics of dog coat variation. Amazingly, it turns out that most of the massive range in coat phenotypes we can see between “pure breeds” and mongrels can be accounted for by mutations in just three genes. (If I were one of the authors, I’d be pretty peeved – all the media attention will be focused on Ardi; in a “normal” week, they could be sure of making the TV, press and radio…)

The authors studied three characteristics of the canine coat: (i) the presence or absence of “furnishings” (growth pattern marked by a moustache and eyebrows seenin wire-haired dogs); (ii) hair length; and (iii) the presence or absence of curl. To find the genetic bases of these characters, they created three genome-wide single-nucleotide polymorphism (SNP) data sets, based on a) 96 dachshunds showing three coat varieties (wire-haired with furnishings, smooth, and long-haired without furnishings); b) 76 Portuguese water dogs showing the curl phenotype and c)  903 dogs from 80 breeds representing a wide variety of phenotypes.

They found that variability in three genes, coding for R-spondin–2, fibroblast growth factor–5, and keratin-71, accounts for most of the different kind of coats that can be observed (“these three mutations in various combinations explain the observed pelage phenotype of 95% of dogs sampled”) . They summarise their findings in the following figure:

326_150_F3

Interestingly, they conclude “None of the mutations we observed were found in three gray wolves or the short-haired dogs, indicating that short-haired dogs carry the ancestral alleles (table S1). Our finding of identical haplotypes surrounding the variants in all dogs displaying the same coat type suggests that a single mutation occurred for each trait and was transferred multiple times to different breeds through hybridization.”

However, although they open their article by pointing out that dogs and humans have lived together for around 15,000 years, they point out in their conclusion that dog “breeds” are an incredibly recent invention – less than 200 years. Inother words, in a couple of hundred year, artificial selection on just three genes has produced an incredibly variety of phenotypes. Furthermore, that selection may have focused on different characters, such as aggressivity or size, the genes for which may be linked to the coat genes. They conclude, “Consequently, in domesticated species, the appearance of phenotypic complexity can be created through combinations of genes of major effect, providing a pathway for rapid evolution that is unparalleled in natural systems.”

This, of course, was also Darwin’s insight (although he did not put it in these terms). Artificial selection by 19th century breeders provided him with the key to understanding natural selection as the force that could generate apparently directed evolutionary change. And that is a much more powerful explanation than anything the creationists can come up with.