Dawkins vs. Ratzi

September 18, 2010 • 4:47 pm

UPDATE: I’ve put up a much better video of the speech; this just appeared on YouTube, and you can actually see Richard this time. I’m told that, despite the large turnout, the British press largely ignored this protest.

There was a big turnout at the Protest the Pope rally in London today: I recall that they predicted 2,000 people but more than 10,000 turned out. Here’s Dawkins addressing the rally; as you might expect, he goes after Ratzi’s attacks on atheists and his claim that we’re responsible for Hitler.

Dawkins has become quite the firebrand.  He did read his talk, but the cadence and substance were very good.

Giberson excuses child indoctrination

September 18, 2010 • 10:22 am

Okay, I’m not gonna deal with Karl Giberson’s multi-part attack on me soon to appear at BioLogos, but you have to grant him this: the man is all over the place attacking atheists and defending faith. (Would that he were so active in damning creationists!)  And, at the ever-reliable HuffPo, he wrote yesterday that there’s nothing wrong with cramming religion and its doctrines down the throats of your kids.  No, you see, because we atheists just completely misunderstand religious education in the home and church:

Most recently we saw a lament on Coyne’s blog about proselytizing down under, which he labeled “a particularly noxious specimen of religious tomfoolery” that makes him question whether “the U.S. is the worst in cramming religion down the throats of its kids.”

This language evokes the harshest of images. What is a secular reader, unfamiliar with how religious children are actually raised, to think? They have never seen a Christmas pageant where dozens of happy children sing cute choruses under the direction of dedicated volunteer staff; they have not seen teenagers gathered in prayerful support around one of their friends whose little brother was just killed in a terrible accident; they have not seen older teens holding bake sales so they can raise enough money to spend two weeks in Haiti helping people in need. Instead, they must picture stern-faced parents dragging kids against their will to indoctrination sessions where they sit on hard wooden chairs until they affirm a set of beliefs in settings reminiscent of A Clockwork Orange. After years of such training, the once-open-minded children mature into narrow-minded adults who carry out the narrow-minded agendas of their parents — oppose healthcare, gay marriage, stem-cell research, Muslims, and anything else they can think of — and begin the process of having their own kids, with a new generation of throats down which more toxic ideas will be crammed.

But that’s all bogus, because in Giberson’s personal experience, that’s not what he sees:

My students don’t look like this to me, however. As far as I can tell, they are all religious, to varying degrees, but their religion doesn’t look harsh and judgmental as though it were forced on them. None of them seems interested in mounting crusades, bashing sinners, or signing up for witch-hunts. Whatever they had crammed down their throats, like the bland vegetables in their baby food, doesn’t seem to have made them unhealthy.

In the end, he sees religion as just one more thing that parents pass on to their kids.

Parents put lots of things down the throats of their children — religion, language, vegetables, ice cream, bacon, tofu, ideas of race, politics, gender and economics. This complex mix is occasionally toxic. But in the complex mixture that produces good citizens, there is no reason to single out religion as problematic. I am quite content to turn the future over to my students.

Well, I could talk about the thousands of kids warped forever by Catholic guilt and the fear of hell, ranks of people living in closeted shame because they’ve been taught that their homosexuality is wrong, thousands of little Muslims-to-be rocking back and forth in the madrasas, imbibing jihad with their Qur’an, little girls taught to be subservient (and having acid thrown in their faces if they’re not), other little girls having their genitals mutilated (because, after all, that’s part of religious indoctrination), thousands of people turned sexually dysfunctional (or not enjoying the pleasure of sex), all those people getting AIDS and other STDs because they were taught that using condoms was a sin, other children mentally warped and sexually abused by priests designated to teach them morality, and umpteen numbers of kids taught to hate other kids because they’re of the wrong faith.

I could talk about these things, but I don’t need to, because the commenters on Giberson’s post are handing him his tuchus on a salver.  Some were personally injured by religious brainwashing, and describe their experience.  (If you want to feel heartened at all the unbelievers out there, read through a couple pages of comments!) Another person mentions Jesus Camp.  Have a look at that, too, if you haven’t already. It’s pretty damn close to Giberson’s nightmare scenario of “stern-faced parents dragging kids against their will to indoctrination sessions where they sit on hard wooden chairs until they affirm a set of beliefs in settings reminiscent of A Clockwork Orange.” Have you seen that, Karl?

Read and weep, oh clueless Giberson.  Your liberal and sophisticated students aren’t the only ones who have learned their faith.

Are we still evolving? Part 2

September 18, 2010 • 6:35 am

The perennial question I’m asked in public lectures is this:  Are we still evolving? (“We,” of course, means “humans.”)  A while back I highlighted a paper by Byars et al. that measured selection on various traits in a human population, showing that features like weight, blood pressure, and age of menopause were indeed under selection.  This shows that we’re undergoing selection, but not necessarily whether we’re evolving—for whether selection causes evolution depends on other factors like the amount of genetic variation that’s available to respond to selection, and whether there are correlated traits that may be selected in other directions.

But if you want a more comprehensive answer to the question of selection, check out the penultimate issue of Nature Reviews Genetics, where you’ll find a review paper by the same group of researchers summarizing all available studies in Homo sapiens. It’s a very good analysis, discussing the problems encountered in human studies, the methods used to estimate selection, and, of course, the data.

Those data come mostly from long-term studies in which individuals were followed over long spans of time.  Various traits of interest were measured (height, age at menopause,  blood pressure and so on) and were correlated with “fitness”, which the authors took as completed family size.  Differential fitness, which incorporates both survival and reproductive output, is the index of natural selection. For obvious reasons, this is more accurately measured in women than in men, so most measures of selection come from females.

The authors find three consistent results among the studies:

  • Both women and men are under selection for earlier age at first birth in all populations.  The authors see this as a result of lowered juvenile mortality resulting from improvements in medical care, nutrition, and sanitation.  If it costs you to reproduce early, but the benefits are increased because your kids no longer die so often, then selection will favor your reproducing at an earlier age.
  • “Women are under selection for later age at last birth in a pre-industrial population [Finland, 17th-19th century] and later age at menopause in two post-industrial populations [USA and Australia, 20th century]. The authors don’t explain the basis of this finding, but I suppose it’s because women now live longer, giving a selective advantage to females who can produce more offspring at ages that they wouldn’t have attained earlier.  Combined, these first two observations show the “temporal window of reproductive opportunity” is broadening in humans:  we reproduce both earlier and later than populations a few centuries ago.
  • “Women are under selection for increased height in one pre-industrial population [Gambia, 20th century] and for decreased height in three post-industrial populations [Great Britain and USA, 20th century].” The authors suggest that, for the same reasons that it’s adaptive to reproduce earlier in industrial populations, it’s also adaptive to mature at a smaller size and divert your effort to reproduction.  To explain the Gambian data, they suggest that this trade-off doesn’t exist in populations where infant mortality of shorter and younger mothers is higher.  This is, of course, special pleading, but that’s just speculation. The data are what is important here.

I don’t have the expertise to judge the authors’ evolutionary speculations, but these three conclusions represent the best answer to the question of “are we under selection?”.  Again, whether that selection produces evolutionary change depends on other factors that weren’t measured.  It will take a few centuries (if ever!) to determine if this selection really has caused evolutionary change.

Finally, the authors estimate selection on some behavioral traits, but take these estimates less seriously.  That’s because there are likely to be substantial cultural components to inheritance here, but also—though the authors don’t say this—because traits like IQ, income, and education are political minefields.  For what it’s worth, the authors conclude that “contemporary humans are under directional selection for less education, less income in women, and more income and wealth and higher rank in men, and decreased intelligence in both sexes.”  Reality shows and Tea Party members instantiate the last process.

Why is this important?  Given that these indices of selection, if real, aren’t all that strong, and will take centuries to produce any substantial evolutionary change, why does this matter?  I’m not sure, actually.  It does provide a solid answer to the question I’m asked most frequently, but remember that cultural changes can produce much more rapid and pronounced changes in human populations than can genetic evolution itself.

Since 1900, for example, the average height of Japanese has increased by more than 11 cm.—about 4.3 inches!  That’s only a couple of generations, and these changes are certainly due not to genetic change but to improved nutrition and medical care.  (Note that they’re also in the opposite direction to selection acting in other “post-industrial” populations.)  Even if selection is acting on us, the evolutionary change it causes is likely to be overwhelmed by changes due not to genes but to culture. And that’s something I always add when asked about whether we’re evolving now.

_________

Stearns, S. C., S. G. Byars, D. R. Govindaraju and D. Ewbank. 2010.  Measuring selection in contemporary human populations.  Nature Reviews Genetics 11:611-622.

Caturday felids: interspecific love

September 18, 2010 • 5:27 am

Behavior genes can be shared even beyond the species boundary.  When I was a graduate student, and sociobiology was all the rage, I conceived of a new field: sociotaxonomy.  The goal of this discipline was to understand evolutionary relationships through behavior, by having the animals themselves reveal their relatedness.

For example, at that time it wasn’t clear whether we were more closely related to chimps or gorillas. My solution: put a man, a gorilla, and a chimp in a small boat with a hole in it, and set it afloat.  Whomever the human saved as the boat sank would be H. sapiens‘ closest relative, since they’d clearly share more genes.

For some reason this field never got off the ground, but examples of interspecific altruism still abound:

Cat gets baff from deer:

Cat adopts baby squirrels.  The fun stops when the teeth erupt.

Finally, human gives tonsorial aid to hairless cat:

[vodpod id=ExternalVideo.963252&w=425&h=350&fv=]

News: Maru’s on Twitter.

Final Friday felid: a miracle cat!

September 17, 2010 • 11:38 am

I know we’ve had a surfeit of felids this week, but I couldn’t resist posting this one because it’s so weird.  Could it be a sign from God?  Polly, a ten-week-old tabby from Staffordshire in England, clearly has the word “cat” spelled out in her fur. (Click to enlarge.)

As The Daily Mail reports:

All the clues are there: the whiskers, the purring, the miaowing and even the toy mouse under her front paws.

But just in case you were in any doubt as to what sort of animal Polly is, the ten-week-old tabby is happy to help out, thanks to her unusual markings, which spell out the word ‘cat’ on her left flank.

Garry Marsh and wife Joan, both 57, adopted Polly from a local cat rescue centre last weekend.

But it was only as they admired their new pet’s colouring three days later that they noticed the marks.

Mr Marsh, a teacher, said: ‘We were commenting on how symmetrical her tabby patterns seemed when Joan suddenly noticed the letters.

‘Once somebody points it out, it is obvious – the word stands out a mile.’

The couple, who live with their sons Simon, 28, and Alex, 23, in Newcastle-under-Lyme, Staffordshire, also have a seven-year-old cat called Katina.

The article helpfully suggests other signs of divine intervention in tabby coats:

Tabbies have an ‘M’ marking on their forehead, between the eyes, with various legends suggesting why this is the case.

One suggests that the Virgin Mary made the mark of her own initial out of gratitude after a tabby snuggled up to the baby Jesus in the manger to stop him from shivering.

And an Islamic legend says that the Prophet Mohammed had a tabby called Muezza that saved his life by killing a snake which had crawled up his sleeve.

When the cat later fell asleep on his arm, he cut his sleeve off so as not to disturb the cat.

From that day on, all tabbies were born with the ‘M’ marking to signify that Mohammed held the animals in high esteem.

I doubt that there’s an “M” in the Arabic word for Mohammed.

Catholics demand that atheists apologize for Hitler

September 17, 2010 • 8:44 am

I wouldn’t have believed that even somebody as wacko as Catholic League president Bill Donohue would do this if I hadn’t seen it myself.  The Catholic League has just posted a demand that atheists apologize for Hitler. And not just for Hitler:

The pope cited Hitler today, asking everyone to “reflect on the sobering lessons of atheist extremism of the 20th century.” Immediately, the British Humanist Association got its back up, accusing the pope of “a terrible libel against those who do not believe in God.”

The pope did not go far enough. Radical atheists like the British Humanist Association should apologize for Hitler. But they should not stop there. They also need to issue an apology for the 67 million innocent men, women and children murdered under Stalin, and the 77 million innocent Chinese killed by Mao. Hitler, Stalin and Mao were all driven by a radical atheism, a militant and fundamentally dogmatic brand of secular extremism. It was this anti-religious impulse that allowed them to become mass murderers. By contrast, a grand total of 1,394 were killed during the 250 years of the Inquisition, most all of whom were murdered by secular authorities.

Why should atheists today apologize for the crimes of others? At one level, it makes no sense: apologies should only be given by the guilty. But on the other hand, since the fanatically anti-Catholic secularists in Britain, and elsewhere, demand that the pope—who is entirely innocent of any misconduct—apologize for the sins of others, let the atheists take some of their own medicine and start apologizing for all the crimes committed in their name. It might prove alembic.

(Alembic? That’s a still used by alchemists, not, as far as I know, an adjective.)  I’m not going to explain how the murderous agenda of people like Hitler wasn’t driven by atheism; that’s been noted by many others (see the list of Hitler’s religious statements that P.Z. Myers put up today). Nor will I discuss how Nazi oppression was largely directed at a religious minority.  I just want to note that this kind of demonization of atheists and gross stupidity is promulgated by a mainstream religious organization.  Ratzi, Donohue and all their minions are slowly starting to realize that Catholicism is just not on in the modern world, and, like a cornered cat, they lash out with Hitler analogies.

h/t: Miranda Hale

Our new Science paper

September 17, 2010 • 7:31 am

Publishing in the journals I call “magazines”—Science and Nature—has become the goal of every graduate student.  A paper in those places is seen as the key to professional success, and I suppose it does help.  But for some reason publishing in magazines doesn’t excite me nearly as much as it does the kids.  I was brought up in an era when there was not so much competition to publish, and when one’s reputation was made by producing a whole corpus of good work.  Where that work appeared was not so important.

I suppose that my Ph.D. advisor, Dick Lewontin, published three or four hundred papers in his career, but I can’t recall one in Science or Nature.  Ditto for his advisor Theodosius Dobzhansky, although I seem to remember one Science paper of his.  In those days you’d succeed if you published good work in Genetics or Evolution.

Do I sound like an old fogey? I guess I am.  All this is a preliminary disclaimer to introducing our Science paper that came out yesterday (see also the news report in Nature).  I can blame the venue on the first author, my terrific graduate student Daniel Matute.  Daniel likes to have fun, but he’s never far from work:

What is the paper about?  It deals with the genetics of hybrid inviability in Drosophila flies.  I’ll describe what we found, and will be as brief as I can given the technical nature of the work.

The problem of how evolution can produce sterile (or inviable) hybrids is an old one.  It occupied Darwin, for instance, in The Origin.  The question that puzzled early evolutionists is how natural selection can “select for” the sterility of hybrids between species. Sterility and inviability, of course, are maladaptive traits, so how can they be produced by natural selection?

With the wisdom of hindsight, we can see that the answer is obvious: sterility/inviability is not selected for directly, but is simply a byproduct of evolutionary changes—adaptive or otherwise—in isolated lineages.  When two evolutionarily isolated lineages have undergone separate and sufficient evolutionary divergence, their genes no longer work well when they’re put together in a hybrid.  And this malfunction can make those hybrids sterile or dead.  That seems simple enough, but it eluded workers for many years after Darwin.

During the Modern Synthesis, both Theodosius Dobzhansky and H. J. Muller made explicit genetic models of how natural selection, for instance, could produce sterile or inviable hybrids.  Although the model was also suggested much earlier, in 1909, by William Bateson, it’s become known as the “Dobzhansky-Muller”, or “DM”, model of hybrid dysfunction.  For those interested in the historical background, see the Genetics paper by my first student, Allen Orr.

The underlying genetic model is simple.  Suppose you start with a single ancestral species, assuming evolution at two genes, gene “A” and gene “B”.  Each gene is fixed for one allele, so the ancestral genotype is aabb.

In one lineage evolution occurs at the “A gene,” with allele A replacing allele a:

Lineage 1:  aabb —> AAbb

In the other lineage evolution occurs at the “B” gene, with allele B replacing allele b.

Lineage 2: aabb —>aaBB

Then all you need to suppose is that in the hybrid between these two lineages, the A and B alleles interact to cause problems, either sterility or inviability:

Hybrid:  AaBb.  Combination of A and B alleles causes dysfunction.

Note that although I use capital letters for the new alleles, there is no assumption about dominance or recessivity.  Note also that the evolutionary change need not have been caused by selection; it could just as easily have been produced by genetic drift or other “nonadaptive” forms of genetic change.

The key insight here is that sterility or inviability of hybrids results from a genetic interaction between alleles at different loci (we call such interactions “epistasis”).  The problems in hybrids stem from combinations of genes that have never “seen” each other in evolution until they co-occur in a hybrid.

That’s pretty simple, but it took an explicit model to ram it home.  Remember, though, that this was still a hypothesis.  There wasn’t much direct evidence for it, and there are other processes, not involving epistasis, that can cause hybrid dysfunction (chromosomal rearrangements are one).

Later work by Allen Orr and his colleagues showed that if the “epistasis” model of hybrid dysfunction is correct, it makes an explicit prediction: the number of genes involved in these deleterious interactions should “snowball” as time passes, increasing exponentially rather than linearly with divergence time.  For dysfunction caused by two-gene interactions, the number of genes involved should go up as the square of the time (t) since the species diverged: t2.  That is, if species have been diverged for two million years, there should be four times more genes causing hybrid problems than when they had diverged for only one million years. (If the bad interactions involve three genes, the number goes up as the cube of time, and so on.)  This more-than-linear increase simply reflects the fact that the process involves interactions between new alleles, and as those alleles accumulate the number of interactions between them goes up exponentially.

So you can test the DM model if you have a way of estimating how many genes cause problems in hybrids, and know the relative divergence times of the species you’re testing.  This is the subject of the Matute et al. paper.

What we did was use two pairs of Drosophila species of known divergence times.  One pair diverged roughly 5.4 million years ago, the other about 12.8 million years ago (we estimated these ages using DNA divergence and the assumption of a molecular clock).  The divergence times between these species then differed by a factor of 2.4 (12.8/5.4).  If the DM model was correct, then the number of genes involved in hybrid problems (we measured the inviability of hybrids) should differ by a factor of at least 5.8 (2.42).

We then estimated the number of genes causing inviability of hybrids in both pairs of crosses using a method I developed years ago, a method based on “deficiency mapping” pioneered by early fly geneticists.  This was laborious, and I’ll omit the messy details, which are given in the paper.

The upshot was that in the younger pair of species, about 10 genes were responsible for hybrid inviability.  In the older pair, about 65 genes were responsible.  Since the pairs differed in age by a factor of 2.4, the number of genes involved went up much faster than the divergence time. In fact, the relative number of genes involved, 6.5, was pretty close to the estimate of at least 5.8.  In other words, the number of genes causing hybrid problems “snowballed” over time, as predicted if those hybrid problems were due to deleterious epistatic interactions between diverged genes.

A paper by by Leonie Moyle and Taluya Nakazato in the same issue (these were published back to back because, fortuitously, another group was working on the same test, but in the plant genus Solanum) showed similar results.  The number of genes  involved in seed sterility “snowballed” over time, but this effect wasn’t seen for pollen sterility.

Together, the two papers provided a nice confirmation of a prediction from the first explicitly genetic model of speciation.  The results do suggest that hybrid problems are the accidental byproducts of evolutionary divergence in separate lineages.

As always, more work is needed.  In flies, for example, we tested only two species pairs, and it would be nice to have a whole array of different species pairs, all differing in divergence times, so you could plot how the genes involved in dysfunction increase over a wide span of time.  That will be very difficult, at least in flies, because the method we used to estimate gene number requires genetic tools available in only one species. But other methods are possible: Moyle and Nakazato used a different one.

The nice thing about this result, from the standpoint of an old fogey, is that my newest student tested and confirmed a population-genetic model of speciation devised by my first student.  The circle is unbroken!

_________

Matute, D. R. I. A. Butler, D. A. Turissini, and J. A. Coyne.  2010.  A test of the snowball theory for the rate of evolution of hybrid incompatibilities.  Science 329:1518-1521.

Moyle, L. C. and T. Nakazato.  2010.  Hybrid incompatibility “snowballs” between Solanum species.  Science 329:1521-1523.

Cat travel week: home again (lab cats)

September 17, 2010 • 6:03 am

There’s something ineffably comforting about sitting at the microscope and pushing flies while a furry felid sits nearby watching.  Although it’s illegal to keep cats in a lab, from time to time we’ve had visiting felids—for both short and long stays.  The longest resident, and my all-time favorite lab cat, was Dusty.

Dusty was part of a litter of kittens rescued from an alley by my technician.  Since she already had cats, and I had a territorial male cat, we had to keep him in the lab until we found an owner.  This lasted a few weeks, and by then we’d grown very attached to him.  We named him Dusty not only because of his color, but because he liked to explore all the crannies in the lab, thereby acquiring a coating of dust.  He would greet me every day as I opened up the lab and gave him his breakfast.  He also sat on my lap as I worked in my office.

Dusty liked to sleep in a large potted plant in my office.

One of his “tricks” was to claw his way up my legs to get a treat.  Although his tiny claws were painful, I tolerated it because it was cute.

We eventually found a good home for Dusty.  His new owners renamed him Odin, after the Norse god.  I disliked that name and thought “Dusty” was much better.  But he’s now grown into a lovely, sleek adult.

Perhaps the most beautiful cat we’ve ever housed was Maya, a longhair who belonged to a research student.  We had her during hot summer days.

Maya lived in a non-airconditioned apartment over the summer.  Being a longhair, she suffered terribly from the heat, so her owner decided to bring her, every day, to our airconditioned lab.  She arrived and left in a soft cat carrier.

Like Maru, Maya liked to rest in enclosed spaces.  She particularly favored the Plexiglas Drosophila cages where we ran mating experiments with flies.

When you have a cat around the lab for a while, you start wondering what you can do with it.  All of us were into infinite felid regressions, so we did this:

Finally, we have Gordon, who belonged to my technician.  Gordon would visit from time to time when it was too hot, or when there were too many visitors at home.  We made him part of the Infinite Cat Project, an online site where you post a picture of your cat looking at a screenshot of the previous cat, who is looking at a screenshot of the previous cat, and so on ad infinitum.  Such is the way one wastes time in the age of the internet.