President Obama talks with Marilynne Robinson

October 26, 2015 • 1:30 pm

As I’ve mentioned recently, novelist Marilynne Robinson has taken to bashing scientism, atheism, and science itself in her latest nonfiction works, for she believes in an immaterial soul and just can’t forgive science for neglecting it. She’s a devout Congregationalist and sometimes preaches at her church in Iowa City.

On September 14, Robinson and President Obama had a long conversation at the Iowa State Library in Des Moines, a discussion that’s now  published in two parts in the New York Review of Books (free; links below).

It’s really more of an interview of Robinson by Obama, but the President gives a lot of his own views on writing, the economy, democracy, and the difficulties of governing. I didn’t find much that was new, but the discussion of religion was mercifully brief and tepid, and perhaps some of you will find some meat.

What I found bracing was the rediscovery of Obama’s intelligence and respect for literature: he’s actually read Robinson’s novels, and the discussion couldn’t have been scripted by Obama’s staff. Have at least a cursory look at the two parts of the interview, and see if you can imagine such a conversation between Robinson and either Donald Trump or Ben Carson. NO WAY.

Part 1

Part 2

WordPress wants information

October 26, 2015 • 12:45 pm

As I’ve mentioned twice, I am getting quite a few comments that post as “Anonymous” because people aren’t filling in (or their device isn’t auto-filling-in) their names and email addresses. If you’re one of these, could you answer the WordPress person’s questions below? (Just put the info in a comment.)

Thanks.

If you’re still having this issue, could you let me know if you’ve noticed any common threads from people who have emailed you to let you know that their names have appeared as anonymous?
For instance, are they using a particular browser, or are they using an autocomplete feature rather than typing their names?

More Republican madness in Iowa

October 26, 2015 • 11:30 am

If you really need more evidence that Republican politics in this country is becoming like the religion of so many of its adherents, driving them to madness and irrationality, read this article from Rachel Maddow’s blog giving the reasons why Iowa Republicans like Ben Carson, who’s now leading Donald Trump by 9 percentage points in a new state poll.

First, a summary of why the Republicans from that state like him. THIS IS NOT FROM THE ONION!:

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Had a good laugh (or facepalm) yet? Here are all the data:

If we combine “very attractive” and “mostly attractive” responses, these are Iowa Republicans’ positive feelings about Ben Carson:
1. “He is not a career politician”: 85%
2. “He has no experience in foreign policy”: 42%
3. “He was highly successful as a neurosurgeon”: 88%
4. “He has said the Affordable Care Act, also known as Obamacare, is the worst thing since slavery”: 81%
5.  ”He has an inspirational personal story”: 85%
6. “He has raised questions about whether a Muslim should ever be president of the United States”: 73%
7. “He has said he would be guided by his faith in God”: 89%
8. “He has said that Hitler might not have been as successful if the people had been armed”: 77%
9. “He approaches issues with common sense”: 96%
10. “He has conducted research on tissue from aborted fetuses”: 31%
The blog notes that we should pay attention to items 4, 6, and 8.
It’s clear that it’s nearly impossible for either Carson or Trump to say something so manifestly stupid or offensive that it would hurt their standings among Republicans. That party is so desperate for a candidate that many adherents have become completely irrational. I wonder what the more liberal Republicans think of this madness.
h/t: Grania

“Concealed carry” of guns doesn’t make us safer

October 26, 2015 • 10:15 am

My loathing of private gun ownership, of the laxity of American gun regulations, and of the NRA is no secret, but when I call for the virtual abolition of private gun ownership in the US (hunting for necessity and target shooting are possible exceptions), I get pushback. “We need to defend ourselves against the bad guys,” say the dissenters. “Given the prevalence of weapons in the U.S.,” they add, “we’re safer if we’re allowed to have our guns.”

Well, we can see how often this kind of justifiable self-defense really occurs, for it’s one of the main justifications for “concealed carry” permits in the US—including a new law allowing concealed carry on Texas college campuses. But, according to several reports, justifiable self defense is extremely rare, whether or not the weapon is concealed. A New York Times op-ed today, “The concealed-carry fantasy,” gives statistics from a new report. The Times summarizes the data:

The more that sensational gun violence afflicts the nation, the more that the myth of the vigilant citizen packing a legally permitted concealed weapon, fully prepared to stop the next mass shooter in his tracks, is promoted.

This foolhardy notion of quick-draw resistance, however, is dramatically contradicted by a research projectshowing that, since 2007, at least 763 people have been killed in 579 shootings that did not involve self-defense. Tellingly, the vast majority of these concealed-carry, licensed shooters killed themselves or others rather than taking down a perpetrator.

The death toll includes 29 masskillings of three or more people by concealed carry shooters who took 139 lives; 17 police officers shot to death, and — in the ultimate contradiction of concealed carry as a personal safety factor — 223 suicides. Compared with the 579 non-self-defense, concealed-carry shootings, there were only 21 cases in which self-defense was determined to be a factor.

And yet:

. . . A Gallup poll this month found 56 percent of Americans said the nation would be safer if more people carried concealed weapons.

In other words, American’s assertion of concealed-carry as an assurance of safety is a fantasy: it’s security theater. The proportion of killings via concealed carry that involve justifiable self-defense is just 3.6%. The other 96.4% of killings were either murders, suicides, or mistakes. That means that over 96% of the time, concealed carry leads not to the aims used to justify it, but to tragedies. And remember, these are not illegal guns, but guns properly licensed for concealed carry. Overall, the policy leads to far more deaths of innocent people than of criminals.

The study cited by the Times is from The Violence Policy Center (free pdf), which includes not just concealed-carry deaths, but all deaths from handguns. Here’s part of its summary:

Guns are rarely used to kill criminals or stop crimes.

In 2012, across the nation there were only 259 justifiable homicides involving a private citizen using a firearm reported to the Federal Bureau of Investigation’s Uniform Crime Reporting (UCR) Program as detailed in its Supplementary Homicide Report (SHR). That same year, there were 8,342 criminal gun homicides tallied in the SHR. In 2012, for every justifiable homicide in the United States involving a gun, guns were used in 32 criminal homicides. 3 And this ratio, of course, does not take into account the tens of thousands of lives ended in gun suicides or unintentional shootings that year.4 This report analyzes, on both the national and state levels, the use of firearms in justifiable homicides. It also details, using the best data available on the national level, the total number of times guns are used for self-defense by the victims of both attempted and completed violent crimes and property crimes whether or not the use of the gun by the victim resulted in a fatality.

. . . The reality of self-defense gun use bears no resemblance to the exaggerated claims of the gun lobby and gun industry. The number of justifiable homicides that occur in our nation each year pale in comparison to criminal homicides, let alone gun suicides and fatal unintentional shootings. And contrary to the common stereotype promulgated by the gun lobby, those killed in justifiable homicide incidents don’t always fit the expected profile of an attack by a stranger: in 35.5 percent of the justifiable homicides that occurred in 2012 the persons shot were known to the shooter.

Now of course gun advocates will argue that guns used in homicides that are not “legally concealed” are stolen or obtained by other illegal means, but many of those guns were stolen from those who acquired them legally. No legal guns, no theft of legal guns for illegal acts. What I argue is that banning all guns will drastically stem the tide of criminal homicides in the U.S., both directly and indirectly. Here are the overall data on criminal homicides versus justifiable homicides between 2008 and 2012. Note the last row that gives their ratio, which is about forty to one:

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Finally, I refer you to this site about concealed carry homicides: Concealed Carry Killers, which tracks deaths due to that policy. You can investigate for yourself; I’ll just present their conclusions:

Concealed Carry Killers is a resource maintained by the Violence Policy Center that includes hundreds of examples of non-self defense killings by private citizens with permits to carry concealed, loaded handguns in public. These incidents include homicides, suicides, mass shootings, murder-suicides, lethal attacks on law enforcement, and unintentional deaths. Only a tiny fraction of these cases are ever ruled to be in self-defense. Any homicide that is legally determined to be in self-defense is documented and removed from the Concealed Carry Killers database and the ongoing tallies.

It saddens and maddens me that we could eliminate so many killings of innocent people, prevent so many suicides, and largely halt mass murders if we’d only get rid of guns in the U.S.  And yet, because we already have so many guns, people tells us that there’s no way to go back, even if we didn’t have a Second Amendment used to justify mass ownership of handguns—an amendment designed to allow states to have militias. I will never own a gun, and I feel safer without one. We’re a civilized society, or so we like to think. There must be a way to stop the madness.

Scientists engage in civil disobedience, share copyrighted papers

October 26, 2015 • 8:30 am

I can’t say that I’m encouraging this activity as that would be encouraging scientists to break the law, but I will call your attention to a piece in The Atlantic describing a new development. Scientists, or anyone, can now request paywalled academic papers on Twi**er, and authors or others who have the paper (you surely have to use Twi**er to see the request) can respond by sending the pdf file to the requestor.  Added bonus: the hashtag is cat-related. An excerpt:

Most academic journals charge expensive subscriptions and, for those without a login, fees of $30 or more per article. Now academics are using the hashtag #icanhazpdf to freely share copyrighted papers.

Scientists are tweeting a link of the paywalled article along with their email address in the hashtag—a riff on the infamous meme of a fluffy cat’s “I Can Has Cheezburger?” line. Someone else who does have access to the article downloads a pdf of the paper and emails the file to the person requesting it. The initial tweet is then deleted as soon as the requester receives the file.

Andrea Kuszewski, a San Francisco-based cognitive scientist who started the hashtag, tells Quartz that “the biggest rule is that you don’t thank people.” Those who willingly share papers are, in most cases, breaking copyright laws. But Kuszewski says it’s an important act of “civil disobedience,” adding “it’s not an aggressive act but it’s just a way of saying things need to change.”

Yes, indeed: things need to change. It’s simply absurd for academic papers to charge $30 or more per paper. Access to papers is the lifeblood of many scientists, and to grossly inflate the prices of single papers in this way is as invidious—though not as deadly—as the practices of those entrepeneurs who have raised the prices of pills manyfold after getting rights to the drug. There is no justification for companies like Elsevier to charge so much money to get a single pdf and, in fact, I’ve always maintained that the American public, who funds most research through government agencies like the NSF and NIH, have a right to see that research without paying for it. Open access journals are the way to go.

3½ years ago I urged scientist/readers to boycott the publisher Elsevier, notorious for price-gouging libraries and restricting access to scientific information. My own boycott still stands: I refused to review a paper for an Elsevier journal this weekend, and told them why. I’m heartened to see that the petition urging the boycott, “The cost of knowledge,” now has 15,261 signers. And you can still sign it. But Elsevier isn’t the only culprit.

h/t: Cindy

Readers’ wildlife photos

October 26, 2015 • 7:30 am

It’s Cormorant Monday! Three—count them, three—species! Reader and biologist Bruce Lyon sent a bunch of photos from California, and some useful information.

 I would have sent these earlier but I am swamped because I am teaching Ornithology (including a lab) while trying to run a full on field season on the winter social behavior of migrant golden-crowned sparrows. I will send some sparrow photos at some point as well.

A head shot of a Pelagic Cormorant (Phalacrocorax pelagicus). The dark red facial coloration is diagnostic among the three local species, as are the prominent crest feathers on the top and back of the head. Note the iridescent plumage. All of the cormorants have beautiful jewel-like eyes too.

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Below: Several nesting pairs of Pelagic Cormorants just beginning nests on a cliff face, their typical nesting habitat.  They often nest on ridiculously skimpy ledges.

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A Double-crested Cormorant (Phalacrocorax auritus) with a fish. The facial coloration is much more orange than that of the Pelagic, and is more extensive on the throat (gular pouch). Don’t waste time looking for the “crests”—the crests are nuptial plumes donned only during the breeding season. Cormorants are “foot propelled divers” that hunt for fish under water using their feet for propulsion. Double-crested Cormorants are less coastal that the other two species and often frequent lakes. Unlike the other two species, they also nest in trees.

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Below: A Double-crested Cormorant dries its wings. Cormorants apparently have wettable plumage, presumably to make them less buoyant during their foraging dives. A brief check of the literature suggests there has been a debate over whether this wing-spreading behavior functions to dry wings or is used in thermoregulation. One paper I found suggest that the main function is to dry the wings.

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During the breeding season Brandt’s Cormorants (Phalacrocorax penicillatus) have gorgeous blue throat coloration, with striking blue eyes to match. The blue gular pouch coloration largely disappears at the end of the breeding season, and based on photos on the web, it seems that the eyes may become less colorful as well. The white hairlike facial plumes are also grown for the breeding season. This might make a great (nerdy) Halloween costume?

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A Brandt’s cormorant nesting colony at Año Nuevo State Park just north of Santa Cruz (with California Sea Lions in the background).

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A male Brandt’s Cormorant giving a ‘flutter display’—this is a courtship display males use to attract females to check out their nest site. If courtship goes to the next step and the female is serious about pairing with the male, both sexes engage in mutual displays, some of which include displaying the blue gular pouch, which females also have.
Mutual sexual selection is one hypotheses for why both sexes are ornamented in a given species. Darwin proposed this idea but then instantly rejected it as unlikely: “…., this view is hardly probable, for the male is generally eager to pair with any female. It is more probable that the ornaments common to both sexes were acquired by one sex, generally the male, and then transmitted to the offspring of both sexes.”  Darwin missed the boat on this one, and mutual sexual selection has been confirmed in several animals. Notably, the first demonstration was in a socially monogamous seabird, the Crested Auklet (Aethia cristatella). Brandt’s Cormorants are also monogamous and both sexes help raise the kids.

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A male (center) apparently being visited by a few females who are checking him (and his nest site) out.

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A bird returns to the colony with nesting material, most of which comes from the sea.

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More nesting material:

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In Moss Landing Harbor, half way between Santa Cruz and Monterey, Brandt’s Cormorants use wooden pilings and a decrepit wooden pier as the site for their nesting colony. Baby Cormorants are born naked and helpless (‘altricial’ in the official ornithological terminology).

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Monday: Hili dialogue (and lagniappe)

October 26, 2015 • 4:43 am

The work week has begun again, although it’s a bank holiday in the Republic of Ireland, and what does a “work week” mean anyway to a retired professor? But somehow everything for me is the same as before.  And so it is for Hili, who’s using an old proverb to try to cajole food from Andrzej. (Her back paws are on the jar on which she used to sit as a kitten, and still sits occasionally.)

Hili: Eat your breakfast alone, share your dinner with a friend and give your supper to your enemy.
A: What do you mean?
Hili: What’s this you’re eating now, dinner or supper?

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In Polish:
Hili: Śniadanie zjedz sam, obiadem podziel się z przyjacielem, kolację oddaj wrogowi.
Ja: Co masz na myśli?
Hili: A to co jesz, to obiad, czy kolacja?
UPDATE: Here’s a photo of Baby Hili right after she was taken in. You can’t see this photo too often:
Baby Hili

Art with microbes (and enzymes)

October 25, 2015 • 2:00 pm

Reader Su called my attention to this really clever contest that garnered some amazing entries. I love it because it represents the fusion of art and science. What you’ll see below are the winners (and some other entries) in the American Society for Microbiology’s “Agar Art” contest, as shown by Stumbleupon (see also here).

If you look at the entries, the rules were clear: create a piece of art using only a Petri dish, nutrient agar, and various species of microbes. Those microbes differ in texture and color, and so, depending on how you inoculate the culture, you can get some nice designs. First the winners:

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FIRST PLACE: NEURONS Submitted by Mehmet Berkmen of New England Biolabs, with artist Maria Penil
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Second place: NYC Biome MAP, submitted by Christine Marizzi, an educator at a community lab. This art piece was created as a collaboration between citizen scientists and artists at Genspace: New York City’s Community Biolab.
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THIRD PLACE: HARVEST SEASON Created by Maria Eugenia Inda, a postdoctoral researcher from Argentina working at Cold Spring Harbor Labs
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PEOPLE’S CHOICE: CELL TO CELL With almost 3,500 likes on Facebook. This image was created by the group who won first place, Mehmet Berkmen with artist Maria Penil

The titles and artist/scientist creators of the next plates weren’t given, but they’re really nice plates:

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A special Halloween entry:

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And this surely must be a tribute to the Original Microbiologist: Louis Pasteur:
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I’ll add here my own attempt at this kind of stuff. My Ph.D. work involved revealing how much genetic variation there was at some enzyme loci by performing “gel electrophoresis”: separating variant enzymes by putting them on a gel subjected to an electric field, letting the variants of different size and charge separate over several hours, and then using specific stains to visualize the enzymes. This isn’t done much any more (DNA sequencing is easier), but in in the old days you’d get gels like this (not my gel):

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You can see several variants here, as well as heterozygotes, which have two forms of an enzyme and thus produce two bands.

After diligently doing this with a highly variable gene (esterase-5), I decided to produce a gel with legible words on it for my job talks. After some careful experimentation and calculation, and injecting gel lanes with several variants mixed together, I was able to spell “THE END” on a gel, and it was very clear. I used that as the last slide of my electrophoresis talks, and I still think it’s the only time that anybody’s used gel electrophoresis of any sort to spell out a phrase. (I’m sure a reader will correct me here!).

I have it only on a 35 mm Kodachrome slide, which is how we gave talks back in the Eocene, and I wasn’t going to show it, but I just went ahead and used my iPhone to take a photo of the gel slide held up against the sky. Nice, eh?:

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