Congrats to Dr. Matute!

March 11, 2011 • 7:40 am

UPDATE: He passed (natürlich), with a departmental record closed session of only 35 minutes.

Five years ago I returned from a sabbatical in France to find a graduate student from Colombia sitting on a stool in my lab, peering at flies through the microscope.  His name was Daniel Matute, and he had decided to do a temporary “rotation” in my lab—one of those “let’s-spend-ten-weeks-doing-research-in-a-lab-to-see-how-it-feels” experiences.  Fortunately, Daniel never left, and this morning he will take his formal exam for the Ph.D.  In our department, this consists of presenting a one-hour public talk followed by a closed session in which the candidate is examined by the five members of his committee.

I suspect, however, that the examination will be perfunctory given that this is what he’s accomplished so far:

Matute D. R., C. J. Novak, and J. A. Coyne. 2009. Temperature-based extrinsic reproductive isolation in two species of Drosophila. Evolution 63: 595-612

Matute, D.R., Butler, I.A. & Coyne, J.A. Little or no effect of the tan locus on pigmentation levels inviable female hybrids between Drosophila santomea and D. melanogaster. Cell; 139: 1180-118

Matute D.R., Coyne JA. 2010. Intrinsic reproductive isolation between two sisters species of Drosophila. Evolution; 64: 903 – 920

Matute D.R. 2010. Reinforcement of gametic isolation in Drosophila. PLoS Biol. Mar 23;8(3):e1000341.

Comment in: Mair W. Reinforcing reinforcement. PLoS Biol. 2010 23;8(3):e1000340.

Matute D.R., Butler I.A., Turissini D.A. and Coyne J.A. 2010. The rate of evolution of hybrid incompatibilities in Drosophila. Science, 329: 1518-1521

Comment in: Milton J. Nature News. 2010. Animal and plant genes hardwired for speciation. doi:10.1038/news.2010.476
Research Highlight: Nature Reviews Genetics 11, 748 (November 2010) | doi:10.1038/nrg2895
Dispatch: Presgraves, D. C. Speciation Genetics: Search for the Missing Snowball. Current Biology, 20, R1073-R1074.

Matute D.R. 2010. Reinforcement can overcome gene flow during speciation in Drosophila. Current Biology, 20: 2229-2233.

And there are at least three more papers in the offing.  Daniel, you’ve been a great student and a credit to the lab.

It’s heartening but also sad to see the students come and go over the years: they move on to their careers while I, like a microscope, remain a aging and permanent fixture in the lab.  But let me publicly congratulate the lad, here, in advance.  Best wishes for a stellar career!

Daniel Matute, Ph.D. in statu nascendi

Earthquake in Japan

March 11, 2011 • 6:28 am

I woke up to the dismaying news that a huge earthquake struck Japan at 2:46 Toyko time, with the epicenter 80 miles off the northeast coast.  With a magnitude of either 8.8 or 8.9. that makes it the fifth biggest earthquake recorded this century.   The good news—if you consider anything good about such an event—is that deaths will be considerably fewer than in previous quakes in Japan, perhaps numbering in the hundreds rather than hundreds of thousands (as in the Great Kanto earthquake of 1923).  Japan now has strict earthquake building codes and everyone knows what to do when the tremors hit.

Our thoughts are with the people of Japan, and with our readers who live there.  Our official Japanese correspondent, Yokohamamama, is visiting California without her husband and three kids, and has posted updates on her website.  She was up all night, frantic, waiting to find out if her family back home was all right: there was no internet or power in Yokohama, and cellphone service was out.  I was speaking with her, however, at the moment when her husband managed to get through on Skype and assure her they were all okay. What a great relief!  She still can’t return home, though, as all airline flights have been canceled. If you live in Japan and are reading this, let us know how things are there.

The New York Times already has posted a page of videos of the quake, which show the great power of such a thing and of its attendant tsunami, which at this moment is working its way across the Pacific at five hundred miles an hour.

As I said, according to the US Geological Survey (USGS), this is the fifth largest earthquake recorded in the past century. Here are the top six with their magnitudes on the Richter scale and links to their descriptions.

Here’s a USGS map of the fifteen strongest earthquakes of the last century, all but one on striking on the Pacific Ring of Fire, where 90% of the world’s earthquakes occur.

A side note:  as Yokohamamama was sitting in her hotel lobby, where she had spent the night (internet reception was better there), desperate with worry, she was approached by a group of young Christians.  They sat with her a while, trying to be helpful, and—when she still hadn’t learned the fate of her family—told her that “everything happens for a reason.”  The reason, though, was not what they thought: it was simply the slipping of tectonic plates.

The ontological argument (again)

March 10, 2011 • 9:23 am

Over at Cosmic Variance, Sean Carroll takes on the ontological argument (i.e., God is perfect, anything perfect must exist since existence is a essential criterion of perfection, therefore God exists), and dissects it with formal symbolic logic.  As you might expect, he finds it wanting.  Carroll sees the argument as logical but unconvincing because its premises are dubious.

Most of us have a vague feeling that one can’t demonstrate that something exists by logic alone, but Carroll hits on one of the critical flaws in this particular “demonstration”.

The basic problem is that our vague notion of “perfection” isn’t really coherent. Anselm assumes that perfection is possible, and that to exist necessarily is more perfect than to exist contingently. While superficially reasonable, these assumptions don’t really hold up to scrutiny. What exactly is this “perfection” whose existence and necessity we are debating? For example, is perfection blue? You might think not, since perfection doesn’t have any particular color. But aren’t colors good, and therefore the property of being colorless is an imperfection? Likewise, and somewhat more seriously, for questions about whether perfection is timeless, or unchanging, or symmetrical, and so on. Any good-sounding quality that we might be tempted to attribute to “perfection” requires the denial of some other good-sounding quality. At some point a Zen monk will come along and suggest that not existing is a higher perfection than existing.

We have an informal notion of one thing being “better” than another, and so we unthinkingly extrapolate to believe in something that is “the best,” or “perfect.” That’s about as logical as using the fact that there exist larger and larger real numbers to conclude that there must be some largest possible number. In fact the case of perfection is much worse, since there is not single ordering on the set of all possible qualities that might culminate in “perfection.” (Is perfection sweet, or savory?) The very first step in the ontological argument rests on a naive construal of ordinary language, and the chain is no stronger than its weakest link.

Another problem with the argument is that God may not be perfect.  Some people may find perfection an essential property of a deity, but lots of liberal religious people don’t necessarily buy it.  And of course earlier and now-discarded deities, like the Greek gods, weren’t perfect by modern standards.

I’m still amazed that anyone finds this a convincing argument for God’s existence.  For other problems, see the excellent discussion in the Stanford Encyclopedia of Philosophy.

Why I’m a cultural Jew

March 9, 2011 • 6:42 am

As a form of self-affirmation, I submit for your consideration the pastrami sandwich at Harold’s New York Deli in Edison, New Jersey:

And it’s great pastrami.  There’s also a pickle bar.  Go hungry.  Oh, and don’t forget the latkes.  The decision between sour cream and applesauce is one of the great Jewish dilemmas, which I always settle by having both.

Here’s an awesome video of Harold’s. Note the huge cakes, the gargantuan matzo balls, and the triple-decker ten pound sandwiches:

Moshe Averick: another creationist rabbi

March 9, 2011 • 5:43 am

Perhaps I was wrong to assume that rabbis have higher respect for science, and less tolerance for theological bullshit, than do Christian preachers or Muslim imams.  Yesterday we saw the sorry spectacle of two smart rabbis, David Wolpe and Bradley Shavit Artson, tie themselves into intellectual knots over the afterlife, trying desperately to argue that it both does and does not exist, and that religion both is and is not made by man.

The day before that we witnessed the even sorrier spectacle of Rabbi Adam Jacobs arguing, on PuffHo, that because scientists don’t have a full understanding of how life originated on Earth 3.6+ billion years ago, God must have done it.  This is the god of the gaps argument, Jewish style, but I saw it as an embarrassing deviation from a Jewish tradition of thoughtful argument. I also caught Rabbi Jacobs pulling the old creationist trick of taking a quote out of context to distort its original meaning: he truncated a quote by Francis Crick, making it seem that Crick accepted life’s origin as a “miracle.”  The full quote showed that Crick believed no such thing.

Now another rabbi has weighed in in the “comments” section of my piece about Rabbi Jacobs’s missteps.  This time it’s Rabbi Moshe Averick, also known on his website as “Rabbi Maverick“, who posted a defense of Jacobs.  The rebbe is Orthodox, and had an interesting career: he was a floor trader at the Mercantile Exchange here in Chicago, wrote an album of rock music and, two months ago, wrote an anti-atheist book called Nonsense of a High Order: The Confused and Illusory World of the Atheist (see his blurbs for the book here).  Now he apparently lives in Chicago.

I’ve put Rabbi Averick’s argument against evolution, and defense of Rabbi Jacobs, in its proper place on the Jacobs thread, but also want highlight it here, above the fold, for readers’ attention. Averick posted it under his real name, so I’m not breaking confidence.

Frankly, I’m weary of arguments like this one, and deeply saddened that they come from Jews, so I’ll throw his comment open for readers to dissect.  Rabbi Averick apparently reads this site, and I’ll alert him to this thread via email, so address your remarks to him. And PLEASE, no invective, name-calling, etc.  You can certainly argue strongly against his views, but if we want him to reply, it would behoove us to be polite.

Have at it:

I don’t know who wrote the “response” to Rabbi Jacob’s article above, but if that is the best he can do then I am truly ashamed of “cultural Jews.”
I’ll limit myself to one point that the writer makes. Rabbi Jacobs did not take Francis Crick’s statement out of context. Crick was being totally candid when he said that it looks like life is a miracle. His caveat afterward is only a reflection on his own illogical and unreasonable committment to atheism. Just because Crick did not have the intellectual integrity to follow his very true assessment of the evidence to its logical conclusion is his problem, not mine.

If someone was thrown out of a Las Vegas Casino for winning 100 hands of black jack in a row and then pleaded, “I know it seems miraculous that I won so many times by luck, but it’s not IMPOSSIBLE”  we would laugh as such a ridiculous argument. This is exactly what Crick does. He admits that a naturalistic emergence of life is “miraculous”, but then quickly adds, “but it’s not impossible.”

The writer admits that we do not know how life started on Earth but he is confident that in 50 years or so Science will figure it all out. Whoever you are: You are entitled to your faith in science, it is protected by the Constitution. The notion that something that contains the amount of digitally encoded specified information and is as functionally complex as a bacterium could emerge through an undirected process without intelligent intervention is such an absurd notion that it can be rejected out of hand. If you want me to believe such a ridiculous idea then prove it. And don’t be a crybaby and ask for special consideration because we are unable to recover the evidence because of time factors. That is your problem, not mine.  The extraordinarily heavy burden of proof is on you.

My only comment is this:  I remain a cultural Jew, but now my pastrami sandwich (see post above) is salted with my tears.

Smackdown! Hitch and Sam take apart two rabbis

March 8, 2011 • 8:36 am

What do you get when you pit Christopher Hitchens and Sam Harris in debate against two smart and liberal rabbis?  A debacle—for the rabbis, of course.  In a comment on yesterday’s post about Hitchens, Heber Gurrola revealed that the “afterlife debate” between Harris, Hitchens, and rabbis David Wolpe and Bradley Shavit Artson is now online at Purim, the Jewish Television Network.

The debate was held on February 15th at the Witzin Center at American Jewish University in Los Angeles, and was moderated by Rob Eshman.  The topic, “Is there an afterlife?,” was particularly poignant given that three of the participants—all but Harris—had had cancer, with two of them (Hitchens and Wolpe) in remission.

You can watch the debate here, and I recommend your doing so. It’s an hour and 37 minutes long, but you won’t be wasting your time. It is, at times, hilarious, and the clash of intellects immensely stimulating.  Pour yourself a drink and think of it as an erudite but entertaining movie.  SPOILER ALERT: the afterlife gets pwned.

Don’t expect to find good arguments for an afterlife—these are “modern” rabbis, and their capacity for waffling and turning religious “truths” into insubstantial metaphors was astounding. Trying to pin them down about what they think the afterlife really is was a futile endeavor.  When asked whether the afterlife is a place, Wolpe responded with a deepity: “The sages are not in Paradise, but Paradise is in the sages”.  One rabbi even asserted that when he says he’ll meet his grandmother after death, he really means that as a metaphor.

Silly Rabbi–don’t you know that tricks are for kids?

On the rabbinical side, Wolpe was particularly eloquent and learned, but he and Artson were trounced by Harris and Hitchens (of course, I’m hardly unbiased here, even though I’m a cultural Jew).  As always, Hitchens gave a sterling performance despite his illness, putting the rabbis in their place time after time and refusing to let them get away with assertions like, “Oh, religion doesn’t believe that stuff any longer,” or “The hope for an afterlife gives us solace and direction.” The man is a tiger on the platform. Sam showed his characteristic dry wit, and was the good cop to Hitchens’s bad one.  Do watch it.

Oh, and Landon Ross, who went to the debate, gives a pretty accurate summary at The Rational Ape.