L’Affaire Mukherjee: the last word

May 7, 2016 • 10:30 am

Barring unforseen circumstances, this will be the last post I put up about Siddhartha Mukherjee’s misleading article about epigenetics and The New Yorker (see my posts on it here and here).

First, on the website of the Scripps Translational Science Institute, Mukherjee has written a rebuttal, which is not really directed at the posts on this site but to a bunch of emails sent to the New Yorker that criticized his piece.  As far as I know, those critical emails were sent directly to the magazine rather than the author, and then the NYer passed them on to Mukherjee. He then wrote a big email response and sent it to the critics (I was not among them, though I eventually saw his response). That email  is what Scripps published, so you should consider his rebuttal as a response to the criticisms sent to the New Yorker and not to what I posted.

One example of this difference: in point 8 of his rebuttal, Mukherjee asserts that he did indeed criticize the “epigenetic-Lamarckian” process as being unlikely to cause adaptive evolution. Yes, that’s true—and I said in my original post that I agreed with him, but thought he could have made this point a bit more strongly in the New Yorker piece. Perhaps some other critics faulted him in the emails sent to the New Yorker. So, for the record, let me say this: all of us, including Mukherjee, agree on the gist of what follows (though I don’t know if he’d sign off on this wording):

There is absolutely no evidence for any Lamarckian form of evolution based on “epigenetic” markers on the DNA produced by the environment. Further speculations about this—and claims that it shows that the modern theory of evolution is wrong—are misguided and should be ignored pending some real evidence. 

Although I don’t think Mukherjee’s response on the Scripps site is very convincing, nor rebuts the faults of the New Yorker piece enumerated by the various scientists on my site  (see especially Ptashne and Greally’s criticisms, and the letters by Madespacher and Henikoff), I’m not going to deal with this further. I will let readers and other scientists judge the entire exchange. The only future posts I will put up about this matter will be notices and comments on any press coverage (see below).

But I do fault the New Yorker for failing to print any criticisms of Mukherjee’s piece, for that piece will then stand unsullied, forever, in its pages. Only those who have read my posts or the press coverage to come (see below) will know of the problem.  The New Yorker really needs to look seriously at how it vets its science pieces, and, as I noted before, its entire attitude towards science. But their arrogance suggests that they won’t do this.

Finally, there will be several press pieces about the controversy, as I (and several others, surely including Mukherjee) have talked to reporters. The first press piece, “Right but wrong” (subtitle: “The field of epigenetics is poorly understood by non-scientists. Did a recent New Yorker magazine article help matters?”), was published yesterday by Aleszu Bajak in Undark, an online organ of MIT’s Knight Science Journalism Program. There you can read Mukherjee’s “explanation” of why his New Yorker piece wasn’t a thorough (and I’d add “accurate”) summary of the field. (Hint: not enough space!)

One plaint about the Undark piece (and about the Vox piece that I just saw and will dissect tomorrow): you cannot excuse inaccuracies or misleading information on the grounds that you didn’t have enough space to tell the truth. From Bajak’s conclusions:

At the same time, it’s worth asking if such a thing [providing “an honest explanation of the nuances of gene regulation”] can be done at all, by anyone, in a popular magazine — the goal of which, in any case, is not to mimic a scientific journal, but to communicate to the general public the alluring frontiers of science — in this case, epigenetics (however that might be defined). It’s possible that Mukherjee fell short, but his critics would do well to consider the exceedingly difficult challenge he and his editors sought to undertake.

Sorry, but I’m not sympathatic to the problems of journalists who decide to tell a distorted story because they are either too lazy or don’t have enough space to tell the right story.

In fact, Mukherjee could have told the true story of gene regulation, rather than the cute but incorrect story, in the same amount of space that he had. But of course if he described the real state of the field, he wouldn’t have a novel story to tell.

So listen up, journalists: it’s better to tell the truth than mislead readers with fine words and a false story. Not all scientific explanations are equal, and the first job of a science journalist is to get the facts right. After that you can dress it up with fine words.

Caturday felids: Chill cat meets 50 d*gs, woman and her cat sail around the world, gluttonous cat uses up one life

May 7, 2016 • 8:45 am

As usual, we have three cat-related items today. First, here’s a video of Boomer, a Bengal who’s the recently-acquired companion of Didga, the famous Australian skateboarding cat. For some reason the staff of Didga and Boomer has a remarkable ability to get his moggies to behave in unusual ways: in this case Boomer insouciantly encounters a bunch of dogs.

You can see more videos of Didga and Boomer at the “Katmantoo” YouTube site.

As the staff says, do NOT try this at home, or without cat-training experience:

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From the Torygraph we have the story of Liz Clark, a woman who’s sailing around the world with her cat Amelia. It’s a lovely thought, but I’m quite worried that the unleashed moggie will fall overboard.

Apparently they’ve been on the road (or sea) for ten years.

Parts taken from the Torygraph story are indented:

Clark told BuzzFeed she adopted Amelia when she was only six months old and is now giving her the adventure of her nine lives.

She said: “She has adapted to living surrounded by water. She’s learned to trust that she will be safe with me.”

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Liz Clark, originally from San Diego, and now from The Ocean, told the website she had been dreaming of sailing around the world since she was a child.

Setting sail in 2006 from California, Amelia has now traveled along the western coast of Mexico and Central America, as well as to the South Pacific.

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Captain Clark has now logged an impressive 18,000 nautical miles.

 Clark said Amelia especially enjoys fishing from the boat.“On calm nights, she fishes off of a soft top surfboard attached to the side of Swell with a small light that attracts fish,” the captain explained.
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Liz and Amelia (photo by Liz):

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The title of this cat’s story came from reader Diane G., who found the link to the ASPCA story. Diane notes, “A scary event but with a happy ending and some cute comments about the relationship of a man and his cat.  (Plus the moggie is adorable.)”

It’s about Tommy, a cat in Queens, New York, who swallowed a wishbone. Things looked bad, but now he’s all right:

One Sunday evening, Tommy’s pet parent David D. enjoyed a take-out meal of rotisserie chicken in his Queens, New York, apartment. The next morning, David found Tommy crouched in the kitchen corner, bleeding from the neck.

“At first I thought he had fallen,” says David. He then realized that his 10-lb. tomcat had likely torn open the trash and swallowed the leftover chicken—wishbone and all.

The X-ray; arrow shows the ingested wishbone:

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David and his mother, Darlene, rushed Tommy to the ASPCA Animal Hospital, where Veterinarian Dr. Yvonne Kline conducted an oral exam and noticed a bone deep inside Tommy’s throat.  After sedating Tommy, Dr. Kline plucked out the bone, then cleaned and sutured his wound with 12 stitches. Tommy was also neutered, and the next day, he went home with antibiotics.

Tommy: post surgery. Poor moggie!

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“I was glad to have my soul mate back,” says David, who first found Tommy when he was working as shop supervisor for an auto mechanic. “A driver came in complaining that cat noises were coming from the car’s motor bay,” he recalls. “Tommy was behind the gas and brake pedals.”

David adopted Tommy on the spot. “I never even thought of giving him to someone else,” he says. “We relate to each other, and he trusts me. He even has a sense of humor, like me.”

David’s brother Daniel, along with Darlene, brought Tommy back to the ASPCA two weeks later to have his sutures removed. After the re-check exam, veterinarians gave Tommy a clean bill of health.

At home, David reports Tommy is better than ever. “He means so much to me. We were destined to be together.”

Tommy and his staff:

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h/t: dd, Barry, Ginger K.

 

Readers’ wildlife photos

May 7, 2016 • 7:30 am

First we’ll put up the last moiety of reader John Phelps’s submission: photos he took in and around Kruger National Park in South Africa. His captions are indented:

White backed vulture (Gyps africanus) – just left a carcass to roost in a nearby tree:

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Vervet Monkey (Chlorocebus pygerythrus)– quite a common sighting and the young are amusing. This youngster was putting on a show of Jacko’s Thriller dance moves. . . :

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Giraffe Calf (Giraffa camelopardalis) – this was part of a large family group:

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God’s Window (two photos)– spectacular views looking eastwards over the Kruger NP towards Mozambique:

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Three Rodavals – a feature that looks like 3 traditional African huts standing high above the Blyde River Canon near Graskop:

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Dragonfly – taken at Spion Kop Lodge in the Drakensberg region of Natal. Spion Kop was the location of a significant battle in the Angle/Boer War of 1899-1901. The battle is also famous because 3 of the participants were Churchill, Gandhi and Jan Smuts. ‘SpionKop’ also became the name of the famous ‘Kop’ at Liverpool football ground…

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Impala (Aepyceros melampus) – very common sighting and the fauns are staple for the medium sized predators:

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Saturday: Hili dialogue

May 7, 2016 • 6:30 am

It’s Saturday, May 7, and today I must get the Ceiling CatMobile emissions tested. This is always a traumatic time, which resembles my exams in college. Will the car pass? It always has but it’s now 16 years old. . . .

But enough First World problems. On this day in 1824, Beethoven’s Ninth Symphony was premiered—in Vienna. In 1915, the Germans sunk the Lusitania, and, in 1945, General Jodl signed an unconditional surrender on behalf of Germany, ending the war in Europe. Notable births on this day include David Hume (1711), Johannes Brahms (1833), and, exactly 7 years later, Pyotr Ilyich Tchaikovsky. Gary Cooper was born on May 7, 1901, and Jimmy Ruffin on the same day in 1936. Those who died on this day include Douglas Fairbanks, Jr. (2000).

Meanwhile in Dobrzyn, Hili is relentless in her pursuit of birds, and has all kinds of schemes to catch them:

A: Hili, what are you plotting?
Hili: I’m pretending that I’m practicing yoga. Maybe the bird will be fooled.

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In Polish:
Ja: Hili, co ty knujesz?
Hili: Udaję, że uprawiam jogę, może ten ptaszek się nie zorientuje.

Lagniappe: Cat? Or elephant? (h/t: Taskin):

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Amy: Back to Black

May 6, 2016 • 4:00 pm

I’ve already posted one of Amy’s versions of this song, but this lively rendition, from the Isle of Wight concert, is better; in fact, that gig is one of her best live performances (I haven’t seen the one at Dingle yet). She appears bright eyed and bushy-haired, not drugged out at all—although she’s swilling something that may be Guinness, or Coke with booze in it. I doubt she ever drank any non-alcoholic beverages on stage. My earlier post explains the song.

By the way, I don’t know who her two backup singers/dancers are (they remind me of the Blues Brothers with the suits and fedora), but they’re superb.

So, to rev you up for the weekend:

Jeff Tayler on the vilification of Muslim and ex-Muslim progressives

May 6, 2016 • 2:00 pm

Jeff Tayler seems to have moved his “blog” articles on religion and politics from Salon to Quillette. I approve. In late April, Jeff wrote a widely-read piece on Quillette whose title tells it all: “In defense of Sam Harris.” Now he’s written a new piece that might well be called “In defense of Maajid Nawaz,” except that it’s a defense of all progressive Muslims and ex-Muslims, so its real title is “Free speech and Islam—the Left betrays the most vulnerable.”

It might also have been called “The perfidy of Nathan Lean,” that unctuous defender of all things Islam and ample employer of the term “Islamophobia.” For it was Lean who wrote a New Republic piece on Maajid Nawaz that was one of the most odious and unscrupulous pieces of “journalism” I’ve ever seen. (It may not be irrelevant that Lean is employed at the Saudi Arabian-funded Prince Alaweed bin Talal Center for Muslim-Christian Understanding. ) Lean’s was a hit piece, concentrating not on Nawaz’s ideas but on his dress, and on innuendo about his motives—popularity and money. (That’s an odd stand to take for someone who takes money from a Saudi-funded institution.) Anyway, if you haven’t read the Lean piece, do so, but then read Tayler’s piece on Quillette. Two excepts:

The misguided progressives who denounce “Islamophobia” and turn a blind eye to the mistreatment of, say, women, gays, and adherents of other religions in Muslim communities or in Islamic countries constitute what Maajid Nawaz has dubbed the “regressive left.”  Regressive leftists are not genuine progressives at all, of course, but deeply confused de facto apologists for the most illiberal notion conceivable: namely, that one group of humans has, on account of its religion, an inalienable right to dominate and abuse other humans — and to do so unmolested by criticism.

No better evidence of this strain of illogical, muddled intolerance of free expression exists than the suspicion and ire regressive leftists reserve for former Muslims and Muslim reformers working to modernize their religion.  In her moving, 2015 must-watch address, Sarah Haider, who is of Pakistani origin, recounts being called everything from Jim Crow to House Arab to native informant by American liberals for having abandoned Islam — by, that is, the very folk who should support women, regardless of their skin color, in their struggle for equality and freedom from sexist violence and chauvinism.

The brave, Somali-born ex-Muslim (and advocate of reforming Islam) Ayaan Hirsi Ali has received even harsher treatment, and to this day, for her outspokenness about her former faith and for making a film in 2004 portraying misogyny in Islamic societies, has to live under armed protection.  (The director, Theo van Gogh, was assassinated that year by an Islamist on the streets of Amsterdam.)  There are many other examples, but the point is this: those who criticize or abandon Islam may well be taking their life into their hands.  Quisling regressive leftists add insult to the injury (or worse) suffered by these people, who, by any progressive standards, should be celebrated.

Why are moderate Muslims (or ex-Muslims) so vilified by the Left? I still don’t understand it completely, for they are the people whom liberals say they want to empower—the people know the faith and, in the case of liberal believers, are our one hope to “reform” it.  Perhaps its true that, as someone said, the only credible Muslim for these folks has a Qur’an in one hand and a Kalashnikov in the other. But that’s precisely what all enlightened people oppose! I am still mystified.

One more quote (but read the whole piece, which is longish):

The larger issue is not only that reform-minded Muslims and ex-Muslims face danger from repressive Islamic regimes (in, for instance, Saudi Arabia, where atheism is legally equated with terrorism, or in Bangladesh, where secular bloggers are routinely hacked to death by Islamists), they suffer slings and arrows of disdain from those witless progressives who decry “Islamophobes,” “porch monkeys,” “House Arabs,” and so on.  Their much-suppressed voices of reason are, though, beginning to find an audience.  Check out this fine essay by Zubin Madon, which contains the following quote from the Pakistani-Canadian blogger Eiynah about the plight of former Muslims:

“We are cast out of conversations about our own communities and lives, we are refused platforms in mainstream media to avoid offending Muslim sentiments, and more recently we are viciously targeted on social media.”

This is disgraceful treatment from progressives, who should be standing shoulder to shoulder with these courageous souls endeavoring, often at great risk, to live free and dignified lives without religion.  They, and all Muslims working to end Islamist violence (including, of course, Maajid Nawaz), deserve our full-throated support.

And, as Jeff argues, we should deep-six the term “Islamophobia,” and correct those who misuse it. What they mean is “MUSLIMophobia” fear of Muslims as a group and bigotry against them. Our argument is about the pernicious ideology behind Muslim malfeasance, and THAT is the real “Islamophobia.” Since so many people confuse these two issues, it’s best to avoid the “Islamophobia” canard.