CNN science completely botches natural selection in the headline, and is confusing in the text

March 24, 2017 • 10:00 am

I have little time to post this morning, but I call your attention to a really dreadful piece of science journalism at CNN.

It refers to a new paper in PLoS Genetics by Arslan Zaidi et al. (reference below, free access) describing how natural selection based on climate (temperature and humidity) may have molded the nose shape of populations of humans in different parts of the world (I’d call these groups “races” but I’d get my tuchas chewed for that). Here’s the paper’s abstract:

Abstract

The evolutionary reasons for variation in nose shape across human populations have been subject to continuing debate. An import function of the nose and nasal cavity is to condition inspired air before it reaches the lower respiratory tract. For this reason, it is thought the observed differences in nose shape among populations are not simply the result of genetic drift, but may be adaptations to climate. To address the question of whether local adaptation to climate is responsible for nose shape divergence across populations, we use Qst–Fst comparisons to show that nares width and alar base width are more differentiated across populations than expected under genetic drift alone. To test whether this differentiation is due to climate adaptation, we compared the spatial distribution of these variables with the global distribution of temperature, absolute humidity, and relative humidity. We find that width of the nares is correlated with temperature and absolute humidity, but not with relative humidity. We conclude that some aspects of nose shape may indeed have been driven by local adaptation to climate. However, we think that this is a simplified explanation of a very complex evolutionary history, which possibly also involved other non-neutral forces such as sexual selection.

We know of course that selection has been responsible for many local adaptations in humans (see here for a summary), so this is nothing new, though it’s an interesting piece of work. Sexual selection may also be responsible, as the authors say, though it’s not the kind of sexual selection that leads to sexual dimorphism (in this case, to any different nose shape between males and females).

Now look at the CNN headline reporting this result (clicl on screenshot to go to article):

The headline (which probably wasn’t written by author Susan Scutti) gets natural selection completely wrong, implying that it’s something that involves genetics and the selective pressure itself as different and separable entities. Of course we know that if climate-based natural selection caused evolutionary changes in nose shape, those changes would have to be genetic! Climate, after all, is not some Lamarckian force that molds an nose shape that gets passed on without the intervention of genes. Climate cannot evolutionarily mold nose shape, at least in a heritable way, without genes!

The authors of the PLoS paper discuss the differential replication of gene forms (alleles) based on their contribution to well being mediated through nose shape. That process involves both climate and genes interacting in a nonrandom way. The headline is grossly misleading, though Scutti herself seems to get it pretty much right in the article (but see below).

I was sent this headline by Richard Dawkins, who was just as appalled as I was. Here’s what he wrote (quoted with permission):

But if you read the CNN story it turns out, as you would expect, that the study shows natural selection, in different climates, has shaped the nose. In what possible sense is that NOT genetics?

Well, as I said, the story itself is okay, but the headline is horrible.

But there’s still a bizarre bit of Scutti’s story. Here’s what she reports further:

So it’s easy to understand why many people, past and present, “have this sense that human populations are very distinct and have been separated for a long time,” said Mark D. Shriver, lead author of the study and a professor of anthropology at Penn State University. Still, he noted, “human populations have always split and come back together, split and come back together, so there’s no separate origin.”

In fact, genetic differences between various population groups is not that great. Using noses as just one example, said Shriver, “the surface, the appearance of people in different populations is much greater than what the genetic differences show on average.”

There are three things wrong here. Yes, human populations have exchanged migrants for a while—ever since forms of transportation came about. And this process is accelerating. But the statement that “populations have always split and come back together” and that “there’s no separate origin” is flatly wrong. Populations don’t meld completely and then split again: they simply send individuals back and forth, and historically have maintained many of their genetic and phenotypic differences.

Further, there is a separate origin for many populations. Native Americans, including those in North and South America, came over the Bering Strait about 15,000-20,000 years ago. They did not repeatedly fuse back to their Eurasian ancestors and separate again. Ditto with Polynesians, the indigenous people of Australia, and so on. I have no idea what Shriver is talking about.

In the second paragraph, I am simply confused by Shriver’s statement that “the surface, the appearance of people in different populations is much greater than what the genetic differences show on average.” What genetic differences is he talking about? For surely there are substantial genetic differences involved in the nose shape differences, be they small differences in the frequency of alleles at many loci, big differences in the frequency of alleles at a few loci, or a mixture.

Perhaps he is saying that the allele frequency differences in nose shape (and other distinguishable traits among populations) are greater than those of the “average” gene, including “neutral” sites where different gene forms make no difference in appearance, phyisology, or so on. That would be a nod to the fact that wholesale genetic differentiation of our genome hasn’t had time to evolve over the 60,000-100,000 years since we spread out over the globe from Africa. But if Shriver meant that, why didn’t he say it more clearly, and why didn’t Scutti ask him to clarify it? After all, there’s no good way to compare the differences in the configuration of a character like the nose with the frequency differences of genes in the genome. They are apples and oranges.

This is the kind of dire science reporting, with the journalist not asking the right questions (not atypical for science journalists who haven’t had extensive training in science), and therefore the body of the article (and the headline!) remaining confusing. It was confusing for me, and I’m an evolutionary biologist.

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Zaidi A. A. et al. 2017. Investigating the case of human nose shape and climate adaptation. PLoS Genetics  http://dx.doi.org/10.1371/journal.pgen.1006616.

The Great Kea Hunt meets with success

March 24, 2017 • 8:30 am

On Wednesday I booked bus tickets up to Arthur’s pass and back, giving me over eight hours in the area. Surely I’d see a kea, then, and that was my goal.

This bird (Nestor notabilis) is the world’s only alpine parrot, and has been largely extirpated by human activity, including clearing land and shooting the birds, who sometimes rip open the backs of sheep to eat the fat. They also have a fondness for lead, which they chew on car wheels and old houses. That has poisoned many.  The ranger told me that 3 birds were taken to hospital for lead poisoning last year, and released after recovery. But they’ll just poison themselves again, for, smart as these birds are, I doubt they can make the connection between chewing lead and getting ill later.

The ranger also told me that farmers and ranchers had shot 150,000 keas over the years, and the conservation folks seem helpless to prevent loss of the present population, estimated at between 1,000 and 5,000 birds. I could hear the frustration in his voice as he described the situation. He added that next week the conservation folks are having a big meeting to figure out how to save this bird. I hope they don’t have to take them into captivity!

Anyway, in my discussion with the ranger, I asked him where the greatest chance was to see kea. He recommended a 2-hour (total) hike up one trail to the south, where there were keas not accustomed to humans, and which I might be able to spy in the trees. But the best spot, he said, was in the village by the cafe, where these cheeky birds come around to cadge treats. So I did both. More below.

Here is the tiny tourist village of Arthur’s Pass from a trail on the north side. Beeches abound.

Lovely beech forests cloak the slopes.

It’s another Lord of the Rings backdrop. Does anyone know what the plant is sticking up in the middle of the photo?

Beech forest.

My guess is that this is red beech.

Old miner’s huts, from the turn of the 20th century (about 1908, I was told) still remain; some are used as vacation cottages, but this one looks abandoned:

Everywhere there are signs about the keas and warnings not to feed them. The ranger also told me that avocado will kill them quickly (he said avocados are toxic to many parrots), and bread and chocolate are also bad for them. I of course was determined not to feed them.  They lay eggs on the ground (apparently two eggs per clutch), and that’s bad, for introduced predators like the common brushtail possum from Australia (Trichosurus vulpecula), as well as stoats and rats, eat the eggs. Before Europeans came, there were no land mammals on New Zealand save two species of bats, so egg predation was low, and many birds evolved flightlessness.

Again from the ranger: at least 15 keas disappeared during the last year around the pass.

Possum trapping and killing is encouraged, as they are huge predators of native birds. Much as I hate the idea of killing anything, this seems reasonable if we want to keep the marvelous products of evolution that fly around New Zealand. A few decades of predation can destroy millions of years of evolution.

Possum skins are on sale in many places, including the ranger station, and they encourage people to buy them so that a “possum skin trade” will develop, encouraging further reduction of these invasive animals.

So. . . . how I found my kea.

After my hike, i sat in front of the village store and cafe for what must have been four hours, waiting for kea to come. It was tedious, though I had the galley proofs of Richard Dawkins’s latest book (out in August) to distract me. I finished the book and waited on.

Nothing.

I asked the cafe workers if there were often kea there, and they said that yes, nearly every day they came. That was bad: I felt that I was going to have another non-experience, like that I had at Milford Sound. The weather was warm and sunny, which may have driven the birds up the mountain.

At 4:30 it was time to meet the bus going back to Greymouth. It was the same shuttle driven by the same guy, who let me ride up front with him. When I told him of my futile quest for kea, he regaled me with stories of his encounters with them (they sit in the middle of the road and won’t move when cars come by, they destroyed the top of his van once, and so on). But then he told me that, on the way back, he would stop in places where he’d seen kea before and give me a Last Chance to See. And so we stopped at several overlooks and pullouts on the way back to the coast.

And, at the very last one, there was a plump bird waddling around the parking lot. It was a kea, scrounging what food it could from the ground. I was so excited that I hopped from the van with my camera almost before it stopped.

And here are the results. Notice that the bird is gorgeous, with green feathers that turn violet on the edges and turquoise on the tail. Its wings are orange-red underneath, but I didn’t see that. Note, too, the wicked beak, with which these birds strip chrome and rubber from cars. Also, it’s banded, as nearly every kea is around Arthur’s Pass (they know them all).

LOOK AT THAT BIRD!

This kea found apple peelings in the carpark. He held down some with his ungainly feet while eating them bit by bit.

Nomming crumbs from the pavement:

The photo below is a tad out of focus, but it shows the lovely colors of the bird, as well as its small eyes and wicked beak.

I am SO happy I got to see kea, even if I saw only one. One was enough, and it was worth the eight-hour wait.

Many thanks to Mike of West Coast Shuttle for giving me the chance to see this bird.

I also met up with another South Island Robin (Petroica australis), which, as one did on the Routeburn Track, followed me down the trail and, when I stopped, jumped onto my feet to tug at my shoelaces. It also made a dive at my jeans, trying to pluck at them. They are splendid little birds with gray coloration, glossy black eyes and beaks, whitish to yellowish breasts, and little stick legs. They are very curious and fearless:

On my shoe:

And today (this will be published in the US on Friday), I head to Nelson, delighted that I’ve bagged a kea with my camera.

Friday: Hili dialogue

March 24, 2017 • 6:30 am

by Grania

Well done, you have reached the end of the week!

Today is World Tuberculosis Day, so chosen because it is the day in 1882 that Robert Koch announced the discovery of the bacterium responsible for the disease: Mycobacterium tuberculosis. The discovery was a vital breakthrough in the fight against a disease that was responsible for 25% of all deaths in the 1800s. Koch is also famous for his work with anthrax which provided evidence supporting the germ theory of disease as opposed to the theory of spontaneous generation.

It is the birthday of Dorothy Height (1912-2010), American civil rights and women’s rights activist. Amongst the many campaigns she worked for during her life were the desegregation of schools (during Eisenhower’s term) and the appointment of African American women to government (Lyndon B. Johnson’s term). She was also appointed to the Commision that published the Belmont Report that investigated the ethical behavior in research prompted by the appalling breaches of ethics and violation of human rights of the Tuskegee syphilis experiment.

It’s also the birthday of Harry Houdini (1874 – 1926), magician, escape artist and investigator of charlatans and claims of the paranormal.

Some of his escape stunts still make my hair stand on end (what sort of nutter signs up for the Water Torture Cell stunt?) but I always found the debunking part of his career fascinating. Even his own death was not without drama and controversy, firstly because the true cause of a ruptured appendix was possibly exacerbated or completely overlooked because of blows to his abdomen from visitors to his dressing-room. Then his widow held a number of séances for the next decade trying to test whether there was life after death – they had previously agreed to a code should communication be possible. Needless to say, Houdini did not turn up, although one pastor Arthur Ford claimed to have made contact. Bess Houdini discontinued her search after ten years, saying that it was “long enough to wait for any man”.

Speaking of daring stunt masters, this morning Hili is performing some stunts of her own.

Hili: Do you see me?
A: Of course.
Hili: Do I look like a cat on the roof?
A: One hundred percent so.

In Polish:

Hili: Widzisz mnie?
Ja: Oczywiście.
Hili: Czy wyglądam jak kot na dachu?
Ja: W stu procentach.

As as a lagniappe, here’s Business Cat, that furry little psychopath, doing cat stuff.

 

 

Hat-tip: Blue

Gorsuch nomination in danger, and other news

March 23, 2017 • 1:36 pm

As my CNN news bulletins tell me, Trump’s nomination of Neil Gorsuch as Supreme Court justice is in serious danger. Gorsuch needs 60 “yes” votes in the Senate for confirmation, and there are only 52 Republicans. Further, several key Democrats, including Chuck Schumer, have already said they’ll vote no on Gorsuch. So did Bernie Sanders.

My view? Given that the Republicans unconscionably and reprehensibly held up the nomination of Merrick Garland until after the election, this is not only payback, but payback that’s warranted since Gorsuch himself will tilt the court to the right for many years to come.  Although I don’t like stalling the legislative process, like holding up budgets, in this case I think it’s justified. The Democrats should stick together and vote “no” on every one of Trump’s choices until he nominates a centrist to the court. Until then, the Court can proceed with eight members, which is fine by me.

And I note with approval that the “TrumpCare” bill, which will render millions more Americans unable to afford healthcare, appears deeply mired in Congress, with Republicans unable to agree on it. The conservative Republican Freedom Caucus in the House of Representatives wants an extreme version of the bill that doesn’t appeal to mainstream Republicans (if that’s not an oxymoron), but won’t approve a bill that the mainstream GOP wants. No Democrat will vote for the bill. The passage of the bill, then, is stalled by an internecine war between “mainstream” and conservative Republicans.

What the Republicans are doing is madness. Their only goal is to undo Obama’s Affordable Healthcare bill—simply because it was enacted by Obama. They have no credible replacement, and the government’s own nonpartisan Congressional Budget Office has estimated that under the Republican bill, 24 million fewer Americans will have healthcare than under Obama’s present plan. That is a lot of sickness, death, and disease—all to get back at Obama. In other words, Republicans, to make a political point, are willing to let many Americans die.

Thursday: Hili dialogue

March 23, 2017 • 6:30 am

Good morning (and good night to those of you in countries with their noses on the International Date Line).

Today is the birthday of the man who invented the safety elevator, Elisha Otis (1811). The invention was born out of necessity – he wanted to use hoisting platforms at his bedstead factory, but they were unreliable as the lifting cable often broke. Initially he didn’t seem to think much of his invention, he’d created other things before: a safety brake for trains and an automatic bread baking oven. However he showed it at the New York World’s Fair in 1854, and the rest, as they say, is history.

German physicist and mathematician Emmy (Amalie) Noether was born today in 1882. She is the discoverer of Noether’s theorem which Wikipedia states as:

“…every differentiable symmetry of the action of a physical system has a corresponding conservation law.”

German aerospace engineer Wernher von Braun was also born today in 1912. He moved to the US after World War II, recruited through the secretive Operation Paperclip, where he worked on the Saturn V program.

Franz Schreker (1878) is a little-known Austrian composer born to a Jewish father and Catholic mother. His promising career was cut short by the Weimar Republic; rising anti-Semitism and National Socialist demonstrations irreparably damaged his reputation. He died in 1934 in relative obscurity. Since 2004 however, there has been a revival of interest his works, and they have been performed in Germany and Austria.

And so, onto Dobrzyń where Hili the cat is being obscure. Maybe she is showing off to Cyrus, or perhaps she is an astute observer of trends and weaknesses in philosophy.

A: What are you thinking about?
Hili: I’m thinking that philosophers didn’t arrive at post-existentialism yet.

In Polish:

Ja: Nad czym myślisz?
Hili: Nad tym, że filozofowie nie dotarli jeszcze do postegzystencjalizmu.

Iran sentences art gallery owners to death

March 22, 2017 • 3:43 pm

By Grania

Although it has been not been reported very widely in the Western press, on March 12th Iran sentenced Iranian-American Karam Vafadari and Afarin Nayssari to death.

They were originally arrested on charges of serving alcohol in their home and hosting mixed-gender parties. Vafadari is Zoroastrian and thus is technically not bound to these Islamic laws. Minority religions in Iran are protected in their Constitution.

Kateh Vafadari, the sister who lives in the USA claims that the case is really about “extortion, property seizure and national security threats“. Former Italian ambassador to Iran, Roberto Toscano, agrees:

“The reason must be a different one…political blackmail toward the US (of which they are also citizens), envy for their success, intimidation toward the Zoroastrian community, desire to grab their properties, [and] repression of contemporary art (the reported destruction of works of art at their home would point in this direction).”

Earlier this month these charges appear to have been changed to now include attempting to overthrow the Islamic Republic of Iran and recruiting spies. The Center for Human Rights in Iran says these charges are completely without evidence, and notes:

The imprisonment of Vafadari and Nayssari also appears motivated by greed: the Islamic Republic has a long and documented history of unlawfully confiscating private property, especially that belonging to those with whom the authorities do not favor. The family of Vafadari reported continuous calls right after the couple’s arrest demanding money, and noted that the charges brought would allow the seizure of the couple’s extensive properties.

 

FDD’s Senior Iran Analyst Tzvi Kahn agrees:

 

The prognosis is not good. The New York Times notes:

The continued inclusion of Iran among the six predominantly Muslim nations in Mr. Trump’s revised visa ban has only aggravated matters, according to Iranian-American advocates. Iran, which has described the ban as insulting, has retaliated by prohibiting most American visitors.

“The problem is that no one has a clue about Trump administration policy,” said Hadi Ghaemi, the executive director of the Center for Human Rights in Iran. With the American prisoners in Iran, he said, “there is limbo, really.”

 

Hat-tip: Malgorzata

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Further reading:

Former Italian Ambassador to Iran Denounces Detention of Iranian-American Dual National and Wife

Grave and Baseless New Charges Against Imprisoned Iranian-American and Wife

http://www.defenddemocracy.org/media-hit/khan-tzvi-tehran-sentences-iranian-american-to-death/

http://freekaranandafarin.blogspot.ie/2017/03/new-charges-against-karan-vafadari-and.html

http://blog.camera.org/archives/2017/03/_wheres_the_coverage_iran_sent.html

New York Times

The New Yorker