Winner: cat scan contest!

September 9, 2011 • 4:33 am

We have a winner for the cat scan contest, whose object was to produce the most bizarre/funniest image obtained from putting your cat on a computer scanner.  There were thirty entries, so the prize of an autographed copy of WEIT is on offer.  Three of them were close to the top, but unfortunately we can offer only one prize.  I’ll put up the top three today, and the other entries will be displayed in the next week.

Each image was scored by me and the two celebrity judges of our previous kitteh contest: Brother Russell Blackford and Miranda Hale.  Scores were tabulated and the cat with the highest total score was deemed the winner.

That WINNER happened to be Tom D. from California.  He didn’t include the name of his cat (he should post it below), but the image impressed all three judges.  Tom, write my email address (easily found on the web) and claim your prize:

A close second was this image, contributed by Theo Bromine and Eamon Knight. They graciously disqualified themselves from the contest as they’d already won a book, but they did nab a prizeless but honored second place:

Finally, the third place winner was blogger Catilin Burke, who sent in this disturbing image with the note, “I got my cat on the scanner once. I doubt it will ever happen again, though!”

Thanks to judges Russell and Miranda, and all the entrants. Watch for the other scanned cats to appear soon.

Adam and Eve: theologians squirm and sputter

September 8, 2011 • 12:36 pm

Over at EvolutionBlog, Jason Rosenhouse analyzes a problem that I consider critical to theology and modern Christianity: the absolute refutation by science of the Adam and Eve story. In his post, “What does original sin mean in light of modern science?” Rosenhouse details some theological responses to science’s discovery that the human population never went through a bottleneck of fewer than about 10,000 people (much less two!).

I’ve written about this several times before (here, for example), for the story demonstrates not only the clash between science and religion (a clash that accommodationists say doesn’t exist), but also the victory of the former over the latter, as well as the ludicrous and tortuous tactics the faithful take to justify their preconceptions.  Because Christian doctrine depends absolutely on original sin, Christians can’t simply discard the idea when it becomes untenable.  As Jason shows, that shows the real difference between science and religion: science discards ideas when they fall to pieces; faith tries to cobble them together into something that still convinces gullible believers .  In the end, nearly all scientific ideas can be falsified, while most religions ones can’t—for their falsification simply leads to reformulation in a newer and less falsifiable incarnation.

At any rate, Jason presents two “sophisticated” reformulations of the Adam and Eve story, and then deftly takes them apart. I wanted to briefly add my own take on these theological explanations.

1. Original sin is inherent in evolution.  This is from Daryl Domning’s book, Original Selfishness (oy vey!):

What I have sought to show is that the overt selfish acts which, in humans, demonstrate the reality of original sin (by manifesting it in the form of actual sin) do indeed owe their universality among humans to natural descent from a common ancestor. This ancestor, however, far from being identifiable with the biblical Adam, must be placed in the very remote past, indeed at the very origin of life itself. It was the common ancestor not only of humans but of all other living things on Earth as well. However, it is not this ancestor itself that is of real interest, but the “natural descent” that proceeded from it: the very nature of physical life and the process of natural generation, which are governed by natural selection and the selfish behavior it requires.

What a load of rubbish we must plow through here!  How can original sin be the result of differential replication of genes? Where’s the “sin” in that?  It’s a purely passive phenomenon which involves no decisions, no actions on the part of individuals. Why does that merit punishment and salvation through Jesus? Further, doesn’t Domning realize that “selfish gene” is just a metaphor for differential replication of genes, which can be thought of as acting as if they were selfish, but are not in reality selfish themselves (shades of Mary Midgley)?  Maybe the faithful aren’t so good at recognizing metaphors after all.

But of course the big mistake here is that “selfish genes” don’t always produce selfish behavior: they can also produce cooperation if that behavior benefits the propagation of the alleles that produce it.  This, of course, has occurred in many species, from slime molds to ants to human beings.

The fact that Domning thinks this is a serious response to the Adam and Eve problem shows the complete intellectual vacuity of theology.  It’s even worse because Domning is a professor of paleontology at Howard University, and should know better!

2. Original sin was bestowed on only two of many humans, and it is their descendants who populate the globe today. This hypothesis, from Edward Feser and biochemist Denis Alexander, also resembles the “federal headship” solution proposed by BioLogos president Darrel Falk, which we’ve discussed before.  Here is the always amusing Feser:

Supposing, then, that the smallest human-like population of animals evolution could have initially produced numbered around 10,000, we have a scenario that is fully compatible with Catholic doctrine if we suppose that only two of these creatures had human souls infused into them by God at their conception, and that He infused further human souls only into those creatures who were descended from this initial pair. And there is no evidence against this supposition.

I needn’t go over all the problems that Jason finds with this, including the absence of a population of unsouled zombies in the Bible; but I wanted to mention one obvious flaw that Jason overlooked.  If souls and sin are transmitted vertically, from parents to offspring—as suggested by the hypothesis above—then we should still see a two-person genetic bottleneck some time in the past, tracing back to those two lucky individuals who won the soul lottery. We don’t see that.

Moreover, all the genes of every living human should “coalesce” back to the same time and the same two people. But we don’t see that either: each gene segment had its ancestor at a different time (and often at a different place) in the past: the Y chromosome, for instance, coalesces back to an ancestor who lived about 60,000 years more recently than the female ancestor who bequeathed us the genes in our mitochondria.  So this solution is also untenable.

The fact that rational and intelligent people can’t see through the ruse here—that religion isn’t a process of finding truth, but of rationalizing, post facto, hopes and ideas that one pulls out of thin air—is perhaps the saddest aspect of faith in America.  It is just so bloody obvious.  And the guilty ones here are not so much the credulous believers who are fed this kind of pablum, but the theologians who get good salaries for making this stuff up, and who have the temerity to label themselves “sophisticated.”


The Hermitage 1: the building

September 8, 2011 • 5:45 am

I took so many pictures in the Hermitage of St. Petersburg that I’ll divide them among two posts: the buildings and the paintings.  First the building itself, which was a palace of the Russian tsars until Nicholas II was deposed in 1917, with Catherine the Great installing the original art collection in 1764.

The museum itself comprises several connected buildings, and I’d recommend buying tickets online in advance; they’re cheaper, you avoid the long lines of tourists, and you get the right to photograph thrown in for free.

Considering both the paintings, which range from the medieval through post-Impressionists, and the setting, which is incomparable, I consider the Hermitage the finest art museum I’ve been to. It also has the largest art collection of any museum in the world: almost 3 million objects.

The building (click this and all photos to enlarge):

The sign at the entrance kiosk.  I found it cool because of all the various kinds of heroes, veterans, and “gentlemen” who got free or reduced entry:

The Jordan Staircase is the main entry to the Winter Palace. Designed by architect Bartolomeo Rastrelli, it is flanked by Italian sculptures acquired by Peter the Great, and was used by dignitaries visiting the tsar.  Every January 6, the imperial family would walk down these stairs to celebrate Christ’s baptism at the adjoining Neva River (the tsar would drink a cup of water from the river presented by the Metropolitan of the city):

One of the imperial rooms off the throne room, showing the building’s opulence:

Since the building was a palace, it’s very elaborate, although much of it was restored after the German siege during World War II.  Here is a parquet floor in one part of the building:

The throne room, with the double-headed eagle of the Romanov dynasty:

Throughout the building the settings are opulent, and the paintings are often illuminated by natural light since they’re hung in outside corridors. Here’s a display of ceramics:

and a lavish display of paintings:

Leonardo is one of my favorite painters, and the Hermitage has two of his dozen or so paintings.  They’re displayed in this room, which is always full of tourists:

The paintings are behind glass, and surrounded by tourists, so it’s hard to get a good look.  Here are photos of the two Leonardos. The first is the Madonna Litta (1490; note that there is some doubt about whether these really are by Leonardo, but most art scholars think they are):

This is the “Benois Madonna” (1478), once considered lost but found in 1909 to be part of a private collection:

Finally, a huge and beautiful malachite vase (malachite is my favorite mineral):

Susan Jacoby on the misuses of 9/11

September 8, 2011 • 5:00 am

In three days it will be the tenth anniversary of the attack on the World Trade Center, and we can expect the press and television to be flooded with pieces about “what it all meant.”

In her column The Spirited Atheist at the Washington Post’s “Faith” section, “The sacrilized myth of 9/11“, Susan Jacoby objects to the “sacralization” of this event:

By sacralization, I do not mean the phantasms of those who see a crucifix in a surviving piece of metal among the ruins but an ongoing attempt, usually in religious but also in secular rhetoric, to elevate this event from one more chapter in the history of human evil to “the day that changed everything.”

This mass murder did not change everything; it changed only some things. And what it did change, it generally changed for the worse. . . . Memorialization rightly recalls the names and lives of the individuals who died so senselessly on that day, not because they were all heroes but because they were all human beings worthy of remembrance. Sacralization and mythicization, by contrast, look for some sort of sense and transcendent meaning where there is none.

Her objections range from George Bush’s odious pronouncement that “God’s purposes are not our own,” to President Obama’s speeh from the National Cathedral in Washington this Sunday.

They [Presidents] ought not to be addressing the nation from the altar of any church or assuring us that God is still here. That is the job of the clergy, for those who cling to belief in a benevolent deity.

It stinks that Obama has to give his speech from an Episcopal church rather than from the White House or another secular venue.  There should be no privileging of religion in this issue, especially since Obama, in his inaugural address, gave a shout-out to atheists: “We are a nation of Christians and Muslims, Jews and Hindus, and non-believers.”

While she also decries the use of 9/11 to restrict immigration, she also mentions that it restricts dissent:

Sacralization mistakes honest discourse for sacrilege. On the one hand (let us call it the hand of left-wing political correctness), it is now considered at worst hateful, at best bad taste, to refer to radical Islam as one important actor in this event. We all know, don’t we, that “true” religion is always good.

Well said!  It’s one of the salient characteristics of theologians, like those that infest BioLogos, that all faiths other than theirs are “improper” or “untrue.”

She goes on to channel Wendy Kaminer’s plaint, in I’m Dysfunctional, You’re Dysfunctional, that Americans are almost revelling in their status as traumatized “victims:”

Another element in the process of mythicization is a bloviated exaggeration of the traumatic effects of 9/11 on those who experienced the event only vicariously. The farther you get from New York, which bore the brunt of the attacks and where most lives were lost, the more Americans seem to insist on their ownership of the insult to the national psyche. It is as if I were to claim that I suffered from post-traumatic stress disorder because, like millions in November 1963, I saw Jack Ruby shoot Lee Harvey Oswald on television.

Finally, what change really occurred on “the day that changed everything”?  Only this:

“. . . we are an angrier, more politically polarized people than we were the day before 9/11? Our economic crisis is certainly a big part of the country’s sullen mood, but the two costly wars that can be directly traced to the emotions generated by 9/11 have exacerbated our financial problems. . .

. . . I do know that before we Americans do any more lying to ourselves about external attacks having changed everything, we need to ask ourselves honest questions about why the initial sense of unity after 9/l1 disappeared so quickly. That is not the terrorists’ fault and cannot be remedied by sanctimonious meditations about American suffering that was, for most Americans, second-hand suffering. But then, perhaps the psychobabblers are right, and stress from watching television has become as bad as being killed or breathing in poison yourself. That is certainly a subject for a sermon.

Let us by all means mourn the nearly 3,000 lives lost on that day, each a human being embedded in a network of love and caring, but let us also remember that it was faith—blind, obedient faith in Allah—that was behind it all. If you have any doubts about this, and share the fashionable view that the tragedy reflected only the  dispossession of the oppressed, or the presence of U.S. troops in the Middle East, read Lawrence Wright’s absorbing but distressing book, The Looming Tower.  That work, which won a Pulitzer, shows with palpable clarity that what happened on 9/11 had its roots embedded deep in radical Islam and its idea of jihad.

____

We watched the second plane hit, and the towers collapse, on a television in our lab.

_____

h/t: Diane G

I’m a BILL!

September 7, 2011 • 11:00 am

I had the honor today of being chosen by The Panda’s Thumb website as the deliverer of the fourth designated BILL (“Brilliant and Illuminating Lecture”). My lecture was actually delivered at the Atheist Alliance International meeting at Burbank, California, in October of 2009.  While Panda describes this as “a tour de force of scientific explanation, presented by a well-known scholar described by a colleague (who introduces him in the video) as “the principal guru to go to on evolutionary genetics in the world,” I have to admit I’ve never watched the whole thing. Like many speakers, I can’t bear to watch myself on video.  I may, however, have posted this before, in which case my apologies.

Anyway, if you haven’t seen it, here it is.  I was introduced by Richard Dawkins, whose remarks were very kind:

The Thumb suggests you watch for the following highlights:

Richard Dawkins being coy.“Maybe you don’t realize how multifarious this evidence really is.”

What we mean by a “scientific fact.”

A good outline of the facets of evolutionary theory.

On preaching to the choir: “Why am I doing this? I like it. What can I say.”

A nice emphasis on predictions of Darwin’s original proposal.

Marine microfossils showing the “instant” of speciation

Horse evolution… one toe left…[audience laughs and applauds] [JAC note: this was an unplanned, spontaneous, somewhat rude gesture. What can I say–I was angry at creationists!]

A nice breakdown of a feathered dinosaur and a very clear discussion of whale evolution.

Retrodictions and embryology: a mutant dolphin with hind limbs.

Linking vestigial features with vestigial genes that used to control those features: yolk!

Very concise and clear discussion of oceanic islands and biogeography.

Bad design and the prostate: “a miracle of bad engineering.”

A list of observations that could falsify evolution.

There are six other lectures online from the AAI, including Larry Krause’s animated performance and the lecture in which Dan Dennett coined the term “deepity.” Others BILLs are #1 (Richard Dawkins), #2 (Sean Carroll), and #3 (V. S. Ramachandran).

h/t: Michael

Science’s publication frenzy—and a solution

September 7, 2011 • 8:06 am

One of the onerous parts of being a research scientist is the pressure to publish lots of papers, which ranks second only to getting grants as a prime inducer of stress.  To obtain tenure or promotion, young scientists now must publish prolifically.  I remember that Mel Green, one of my mentors as a postdoc at The University of California at Davis, told me that in his day (he’s now in his early nineties, and still pushing flies at the bench), a mere one or two quality publications per year was considered a good output.

No longer.  Today almost nobody stands a chance of getting tenure at a major research institution without at least four or five papers per year, good or not.  Numbers are important.  When we were discussing how the administration at the University of Chicago regarded publications at tenure time, my friend Russ Lande told me, “They may count ’em, and they may weigh ’em, but they won’t read ‘em!”  Young students are pushed to submit their papers to Science or Nature, a sure recipe for disappointment since those journals are so selective.  The pressure also leads to what I see as a destructive level of competition and ambition in young scientists.

My own output has been modest: I have 119 peer-reviewed papers since I started graduate school, which works out to about 3.1 per year.  On the other hand, I do have two books, and pride myself on not gratuitously slapping my name on my students’ papers—one reason why some scientists with big labs can have more than 600 publications in their lifetime!

In Monday’s Guardian, David Colquhoun, a well known pharmacology professor at University College London, a fellow of the Royal Society, science critic, and author of the website Improbable Science, decries the publication frenzy that characterizes modern science.  His essay, “Publish-or-perish: peer review and the corruption of science,” points out how the the publication culture has spawned a number of low-quality “peer reviewed” journals, some of such absymal standards that they’ll publish anything.

Peer review is the process that decides whether your work gets published in an academic journal. It doesn’t work very well any more, mainly as a result of the enormous number of papers that are being published (an estimated 1.3 million papers in 23,750 journals in 2006). There simply aren’t enough competent people to do the job. The overwhelming effect of the huge (and unpaid) effort that is put into reviewing papers is to maintain a status hierarchy of journals. Any paper, however bad, can now get published in a journal that claims to be peer-reviewed.

Colquhoun gives one example of an infamous paper by a group at Exeter University that studied the medical efficacy of acupuncture.  Despite the finding of at best a tiny effect of the procedure (barely a placebo effect!), the authors—and the journal (The British Journal of General Practice)—trumpeted that acupuncture “resulted in improved health status and wellbeing.”  Have a look at the figures Colquhoun presents to see how “improved” the status really was!  (note that Colquhoun’s column is followed by a response from the study’s authors as well as the journal’s editor, standing by the paper).  But clearly, there are substantial problems with the research, and the results are so unimpressive that they’re hardly an endorsement of acupuncture.

Colquhoun’s solution is self publication:

So what can be done about scientific publishing? The only service the publishers provide is to arrange for reviews and to print the journals. And for this they charge an exorbitant fee, a racket George Monbiot rightly calls “pure rentier capitalism”.

There is an alternative: publish your paper yourself on the web and open the comments. This sort of post-publication review would reduce costs enormously, and the results would be open for anyone to read without paying. It would also destroy the hegemony of half a dozen high-status journals. Everyone wants to publish in Nature, because it’s seen as a passport to promotion and funding. The Nature Publishing Group has cashed in by starting dozens of other journals with Nature in the title.

Interestingly, Colquhoun suggests Mel Green’s formula of “an average of two original papers per year” (and adds that scientists should hold only one research grant at a time, a presciption that I agree with).

An obvious problem is that junior people would be afraid, in the comments section, to criticize more established ones.  Colquhoun suggests that comments can be anonymous: after all, reviewers’ comments in regular journals are not attached to names.  As for worries of fraud because of the lack of peer review, Colquhoun responds:

Deer [Brian Deer, a journalist who exposed Andrew Wakefield’s vaccine/autism fraut] has recently backed a proposal from the House of Commons Science and Technology select committee that an official regulator should be appointed to police science. I don’t think this could work. Is the regulator going to repeat experiments, or even check original data, to make sure all is well? In all probability, a regulator would soon degenerate into yet another box-ticking quango, and end up, like the Quality Assurance Agency, doing more harm than good. The way to improve honesty is to remove official incentives to dishonesty.

By and large, the problem does not arise from outright fraud, which is rare. It arises from official pressure to publish when you have nothing to say.

The last sentence is absolutely on the mark.

Colquhoun’s proposal has substantial merit. What I see as the biggest problem is that it forces tenure and promotion committees, as well as granting agencies. to actually read and evaluate a candidate’s papers, rather than relying on secondary indicators of “quality” like journal “impact factors,” grant dollars, or numbers of publications.   The main impediment to this system is the laziness of university administrations.

h/t: Dom

The last of its kind

September 7, 2011 • 5:04 am

One of the saddest parts of studying biology is to see the complete disappearance of a species—especially to witness the death of the very last individual.  Science knows of no way to bring back an extinct species, and so its passing represents an irretrievable loss.

Today is the 75th anniversary of the death of the last thylacine (Thylacinus cynocephalus, also known as the “Tasmanian wolf”), a marsupial that once inhabited New Guinea, Australia, and Tasmania.  “Benjamin,” a captive individual on display in the zoo at Hobart, Tasmania, died on September 7, 1936.  Below I’ve put a 42-second video clip of Benjamin in his cage (despite his name, this individual may have been female).

Thylacines were top predators, and a superb example of evolutionary convergence, resembling, in both behavior and appearance, the wild placental dogs to which it’s only distantly related. As a marsupial, it did of course have a pouch in which it sequestered its young.

Note how doglike Benjamin looks.  The stripes on the species’ hindparts also gave it the name “Tasmanian tiger.”  Thylacines died off on the Australian mainland about 2,000 years ago (see the cave painting below), probably from hunting and competititon with introduced dingos, but survived in Tasmania until the 1930s. There its extinction was promoted by its reputation as a killer of chickens and sheep, and there were bounties on its hide.

The website The Thylacine Museum will tell you everything you want to know about this animal.

There are only seven movie clips of living thylacines (from London and Hobart zoos), and you can find them all at this link.  The longest is only 54 seconds, so you can watch them all. Note that  at the beginning of this clip, the beast shows the species’ wide mouth gape: it could open its maw about 120 degrees!

Wikipedia gives a good account of not only the species, but of the death of Benjamin:

The last captive thylacine, later referred to as “Benjamin” (although its sex has never been confirmed) was captured in 1933 by Elias Churchill and sent to the Hobart Zoo where it lived for three years. Frank Darby, who claimed to have been a keeper at Hobart Zoo, suggested “Benjamin” as having been the animal’s pet name in a newspaper article of May 1968. However, no documentation exists to suggest that it ever had a pet name, and Alison Reid (de facto curator at the zoo) and Michael Sharland (publicist for the zoo) denied that Frank Darby had ever worked at the zoo or that the name Benjamin was ever used for the animal. Darby also appears to be the source for the claim that the last thylacine was a male; photographic evidence suggests it was female  This thylacine died on 7 September 1936. It is believed to have died as the result of neglect—locked out of its sheltered sleeping quarters, it was exposed to a rare occurrence of extreme Tasmanian weather: extreme heat during the day and freezing temperatures at night.[This thylacine features in the last known motion picture footage of a living specimen: 62 seconds of black-and-white footage showing it pacing backwards and forwards in its enclosure in a clip taken in 1933 by naturalist David Fleay. National Threatened Species Day has been held annually since 1996 on 7 September in Australia, to commemorate the death of the last officially recorded thylacine.

It’s sad to think that Benjamin didn’t know she was the last of her kind, even if she was lonely.

There is almost an “Elvis cult” around the thylacine, with many believing that it still remain alive.  There have been sporadic reports, and photos, and even one movie of thylacines on mainland Australia; for a summary and pictures go here.   I’m not convinced that they’re genuine (how could they survive at such low density?), but it’s pretty to think that they may still be with us.

A cave painting of a thylacine from the Pilbara in Australia.  See more paintings here.