Why Evolution is True is a blog written by Jerry Coyne, centered on evolution and biology but also dealing with diverse topics like politics, culture, and cats.
Well, this is a new one, but what do you expect from such a muddleheaded administration—one intent on insulating itself from the truth and from accusations of malfeasance. As Mueller’s investigation gets closer and closer to Trump, with the possibility that the Prez obstructed justice by telling FBI director James Comey to stop investigating the now-guilty Michael Flynn (along with Trump’s claim that he knew that Flynn had lied when firing him), they’re pulling their desperation moves to stave off the possibility that Trump could even be charged. As CNN reports:
President Donald Trump’s personal attorney, John Dowd, claims the President cannot be guilty of obstructing justice, according to an interview with Axios.
“(The) President cannot obstruct justice because he is the chief law enforcement officer under (the Constitution’s Article II) and has every right to express his view of any case,” Dowd told Axios.
The new defense comes after a tweet from Trump’s account suggested the President knew former White House national security adviser Michael Flynn had lied to the FBI when he was fired in February, raising questions about whether Trump knew about Flynn’s lying before pressuring former FBI Director James Comey to let go of inquiries into Russian election meddling.
The position that Trump cannot obstruct justice — which evokes a similar claim once made by former President Richard Nixon, who resigned over the Watergate scandal — is sure to be debated as special counsel Robert Mueller’s investigation intensifies. Flynn is the first administration official to be charged as part of the probe.
That is, to put it mildly, lame. Well, it didn’t work for Nixon, who had to be pardoned in advance by Gerald Ford (look for the same from Pence!), and it won’t work for Trump. Things are looking as if President Donald himself may be caught up in all this, and wouldn’t it be Schadenfreude to see him go down, regardless of the conservatism of his successor.
Perhaps you didn’t realize, like reader Gregory (who sent me the Science paper), that scallops have eyes. But they do indeed—up to 200 tiny eyes lining the mantle, each a millimeter across: about the size of an “o” on a printed page.
Here’s what the array looks like in the scallop Pecten:
And a close up of the miniscule baby blue eyes:
A close-up view of a scallop’s eyes. Photo Dan-Eric Nilsson/Lund University, source: New York Times
Why do they need them? Because scallops aren’t sedentary molluscs: they swim actively by “jet propulsion,” flapping their shells to get away from predators or to find new resting sites. To wit:
It’s been known for a while that these eyes probably involve mirror reflection of incident light onto a retina, but how that reflection was achieved wasn’t clear, except that the mirror probably involved guanine crystals (guanine is one of the four nucleotide basis that make up the “code” of DNA). But a new paper in Science by Benjamin Palmer et al. (free access, reference below), elucidates how the eye works, and it’s amazing. The mirror, formed of overlying sheets of guanine crystals, reflects light back on retinal tissue that sits in front of the reflector, and there is not one but two retinas, each giving information about different parts of the scallop’s environment. And the mirror, besides functioning very efficiently, is a thing of beauty: a marvel of natural selection.
First, though, another picture (from the paper) of the eyes lining the mantle (captions of all figures come from the paper):
The scallop Pecten maximus with numerous eyes lining the mantle (the white arrow points to an individual eye)
So here’s how the eye works. Figure “A” below is an image produced by the technique that enabled this research to be done: cryogenic scanning electron microscopy (cryo-SEM), in which a frozen sample is scanned. (A Nobel Prize in Chemistry was awarded this year to the researchers who developed the method.) This enabled the researchers to visualize not only the entire structure of the eye, as in “A” below, but also sections of it, so they could look at the fine structure of the guanine “mirror” as well as make computer models of how light would travel after entering the eye.
Image “A” is analyzed in “B”, with different colors represent the parts of the eye and the directions of light. Incoming light (red lines) hits the mirror (green) after passing through the cornea (black), the iris (navy blue), the lens (light blue), and the transparent retinas (gray cloud). After hitting the mirror, light rays (now yellow) are reflected through the guanine layers, eventually striking the two retinas. One retina is proximal (closer to the scallop’s body) and the other distal (closer to the front of the eye):
A) Volume rendering of an x-ray micro-CT scan of a whole scallop eye, showing the eye anatomy. (B) Segmentation of the micro-CT in (A). Black, cornea; navy, “iris;” blue, lens; gray, gross retinal volume; green, mirror. Rays traced through the eye from a point source aligned with the axis of the lens (red) are reflected (yellow) and focused on the retina. The border of the best-focused region encompassing all reflected rays denotes a 3D circle of least confusion (COLC; black line). The inset is a side view of the mirror showing the optical axes of the lens (blue), central mirror (green), and center of the visual field (cyan). The lens and mirror axes are offset by 7.3°.
Here’s a cross section of the tiny eye with the elements labeled. You can see the two retinas (iii and iv), with the bowl-shaped mirror (v) right below the retinas. As I said, the retinas are transparent so they don’t block incoming light. Yellow arrows show the direction of light entering the eye:
Fluorescence microscopy image of an eye cross section, showing the cell nuclei stained with DAPI (4′,6-diamidino-2-phenylindole). The (i) cornea, (ii) lens, (iii) distal retina, (iv) proximal retina, and (v) concave mirror are indicated.
Here’s a colored cross section that makes identification of the parts easier (see the caption). The two retinas are olive-green and orange, and the mirror is bright green:
Low-resolution cryo-SEM micrograph of an eye cross section after high-pressure freezing and freeze-fracturing. The lens (blue), distal retina (yellow), proximal retina (orange), and concave mirror (green) are shown in pseudo-colors. The cilia and microvilli of the photoreceptors were used to identify the locations of the distal and proximal retinas.
What’s truly remarkable about the eye is the “mirror”, composed of a tiled “floor” of guanine crystals in the shape of squares (not their natural crystalline configuration—how does the scallop do this?). Each “floor” is a sheet, and there are 20-30 of them set one above the other, interspersed with cytoplasm. Here’s a cryo-SEM image (see caption), and isn’t it remarkable?
The ultrastructure of the multilayer mirror. (A to C) Cryo-SEM micrographs of high-pressure–frozen, freeze-fractured cross sections through the eye of P. maximus. (A) The mirror viewed perpendicular to the eye axis. White arrow, direction of on-axis incident light. (B) The tiled mirror viewed from above. (C) Crystals in adjacent layers, stacked directly on top of one another, viewed in a fracture through the mirror. (D) TEM micrograph of a single, regular square crystal extracted from the eye. The crystals are 1.23 × 1.23 ± 0.08 μm (N = 20) with internal corner angles of 90.16 ± 2.78° (N = 28) (means ± SD).
Why the multiple layers? As this site from Duke University explains:
. . . .by carefully choosing the thickness of each layer, one can arrange for light that reflects at each interface to interfere constructively such that all incoming light (within a certain range of wavelengths) is reflected back toward its source, that is the layers act as a high quality mirror. It is fairly easy for biological creatures to secrete such alternating clear layers with slightly different properties, rather harder for humans to do so using chemical and mechanical engineering.
That is a remarkable feat of natural selection.
Equally remarkable is the calculation (from the authors’ simulation) that the light best reflected is in the blue-green spectrum, with a wave length of about 500 nanometers: just the wavelength of light that reaches the sea-floor environment of the scallop.
But wait! There’s more! As suggested by another of the authors’ models, light from different parts of the eye reaches the two retinas differentially. Light entering the center of the eye is preferentially directed toward the distal, or outer retina, while light coming in from the sides of the eye goes to the proximal or inner retina. Thus the two retinas give information about different parts of the habitat. Why would this be useful? As the authors suggest, the peripheral vision could help the scallop guide its movement while swimming and help it to find a new settling site, while the central vision could give information about a predator approaching them.
Finally, the data coming from the different eyes is integrated and sent to a scallop “brain”, or, as the authors describe it, “the lateral lobes of the parieto-visceral ganglion (PVG), the site of visual processing in scallops.” Thus there’s no independent data from each eye, which isn’t really needed here given that the retinas single out different parts of the scallop’s environment.
The mirror reflecting light onto an image-detector is precisely the way reflecting telescopes work, though human-constructed mirrors are very different from those of the scallop. In fact, I don’t think humans are capable of making mirrors like this bivalve does. As Leslie Orgel once said, evolution is cleverer than you are.
Reader Andree Sanborn (flickr site here, FB page here) sent a series of photos taken by her daughter. It shows nature red in tooth and mouth, so be warned. Andree’s notes:
My 2nd daughter, Amelia Michaud, is the manager of the Frontier Animal Society in Orleans, VT. She is crazy busy and never posts her nature sightings but has given me permission to do so. While out walking dogs on August 17, 2017, she captured this drama of a Garter snake (Thamnophis sirtalis) eating an American toad (Anaxyrus americanus). I’m so glad she had her phone with her. These may be gruesome sights for some — just be warned. It is something most of us will never see again. And I swear that in one video you can hear the toad vocalizing (it seems amazingly calm, if one can use that word to describe its state of mind).
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And there’s a video playlist of this event (7 short clips), which you can see here. Start with this one and they’ll play sequentially (not in the order of swallowing, though!):
We’ve lived through another week, making it to Monday, December 4, 2017, or National Cookie Day. Only 27 days remain until the end of the year; 21 until the beginning of Coynezaa. (I just discovered that my birthday is also National Bicarbonate of Soda Day.)
There’s a Google Doodle today, a game you can play, but it’s intended for children to learn coding. As Time Magazine notes:
Google celebrated the 50th anniversary of Logo, the world’s first programming language designed for kids, on Monday with a Doodle that celebrates kids coding languages and is aimed at teaching children to code.
In an interactive Doodle, called “Coding for Carrots,” users help an animated rabbit navigate a block maze. The rabbit hops from block to block in response to increasingly complex code sequences the game directs its players to input.
MIT’s Champika Fernando, who worked on Coding for Carrots with Google, said she was nine-years-old when she first coded through Papert’s program.
“It makes me happy to think of all of the nine-year-olds who will get their first coding experience playing with today’s Doodle,” Fernando said. “My hope is that people will find this first experience appealing and engaging, and they’ll be encouraged to go further.
Click on screenshot to go there. I must be dumber than a kid, because I can’t even start the damn game! Can any readers give a tip?
It’s one of those days when not much happened in history. On December 4, 1674, Father Jacques Marquette founded a mission on Lake Michigan to convert the Native Americans; this was the first settlement of what would become CHICAGO. On this day in 1954, the first Burger King opened in Miami. And it was exactly two years later when the Million Dollar Quartet (Elvis Presley, Jerry Lee Lewis, Carl Perkins, and Johnny Cash) assembled by accident at the Sun Studios in Memphis, Tennessee, and a one-off jam session ensued. A few recordings survive. Read the Wikipedia link in the last sentence to find out how it happened (i.e., by chance); here’s a snippet:
Whatever Elvis’ feelings may or may not have been in regard to “following” Lewis, Presley was clearly the “star” of the impromptu jam session, which consisted largely of snippets of gospel songs that the four artists had all grown up singing. The recordings show Elvis, the most nationally and internationally famous of the four at the time, to be the focal point of what was a casual, spur-of-the-moment gathering of four artists who would each go on to contribute greatly to the seismic shift in popular music in the late 1950s.
And eleven minutes of recording from the session. Some of it’s quite good!
More fun music facts: on this day in 1965, the Grateful Dead first played in concert under that name. Finally, on this day in 1991, Pan American World Airways (“Pan Am”) ended its operations. I used to fly it internationally all the time, and was saddened.
Notables born on December 4 include Thomas Carlyle (1795), Samuel Butler (1895), Edith Cavell (1865), Wassily Kandinsky (1866, the first true abstract artist), Rainer Maria Rilke (1875), Alfred Hershey (1908), Chris Hillman and Dennis Wilson (both 1944), and Marisa Tomei (1964). Those who ceased to be on this day include Omar Khayyám (1131), Cardinal Richelieu (1642), Thomas Hobbes (1679), John Tyndall (1893), Thomas Hunt Morgan (my academic great-grandfather; 1945), Frank Zappa (1993), and Liam Clancy (2009). Kandinsky is one of my favorite artists, but before he went abstract he made this print, called “Katze”:
Meanwhile in Dobrzyn, Hili is loath to get her cute paws in the snow:
Hili: Here we go again.
A: How’s that?
Hili: My paws are going to be freezing again.
In Polish:
Hili: Znowu.
Ja: Co znowu?
Hili: Znowu będzie mi zimno w łapki.
And some tweets from Matthew Cobb. The first pair came with this message: “Here are two from Jill Pruetz, who is Director of the Fongoli Savanna Chimpanzee Project, Senegal.”
He was, according to the popular website Feministing—indeed, he was made into a “martyr” by the press.
Now it seems to me that Lauer is guilty: multiple women have given consilient stories of his predatory behavior, though I think too much has been made on the button on his desk that locked his door. That’s common among executives to allow them privacy when they get phone calls or have a visitor. I’m not aware that he used it to trap women in his office (such locks would have to be easily open-able from the inside to adhere to fire codes). Regardless, for him to be fired almost instantly by NBC suggests that the evidence against him was strong and credible. And if he broke the law, he should be tried.
That’s not at issue. But was the press guilty of making him into a hero?
First read these three leads for three stories, and you tell me if they valorized the man:
The fast-moving national reckoning over sexual harassment in the workplace toppled another television news star on Wednesday . . .
The downfall of Mr. Lauer, a presence in American living rooms for more than 20 years, adds to a head-spinning string of prominent firings over sexual harassment and abuse allegations.
The wave of sexual harassment allegations roiling American society broke over a familiar figure, “Today” host Matt Lauer . . . . Lauer, 59, may be the best-known, and perhaps best-liked, of the men whose highflying careers have crashed in the wake of accusations besetting the news media, the government and the entertainment industry over the past two months.
America woke up without another one of the most recognizable faces in morning television Wednesday, as the rapid-fire sexual harassment allegations that have been rocking Hollywood and Washington brought down one of the most prominent figures to date.
I’ve unbolded the words that the Feministing author, Dana Bolger, were used by the press to turn Lauer into a “martyr”. See if you can find them. Look hard. You can click here to see them.
Here’s the interpretation from Feministing:
Now Lauer was very popular, but among viewers, not necessarily by the people who knew him or worked with him. Nevertheless, here’s the article’s take on the words above.
Matt Lauer was “toppled” like a tree unlucky enough to be caught in the path of a “fast-moving” tornado. Matt Lauer was “broken over” by a “wave”, like a surfer in the ocean. Matt Lauer (the best-liked of men!) got stuck on the bad end of a “rapid-fire” firing squad intent on bringing him down.
To state the obvious: Matt Lauer isn’t a victim of circumstance, a puppy caught in the eye of the storm. Like all the other Harveys, he made choices. He decided to exploit his subordinates. He opted to harass people with less power than him. He used a button under his desk to lock women in his office.
The language we use to tell these stories matters. It’s not only that whole swaths of people in this country, including actual victims of violence, don’t get to be humanized by the press in this way, but also this: lazy, sexist writing that paints aggressors as victims and victims as aggressors fuels the idea — already gaining steam across the right and left alike — that two months of accountability is a “witch hunt”, a “sex panic”, and “anti-male sexual McCarthyism”.
We can grapple with the complexity of violence in our lives — perpetrated by people we may love — without turning these “fallen” men into tragic victim-heroes.
This is the way you analyze words when your conclusions are preordained. I never watched Lauer, have no feelings of admiration for him, and think he’s guilty. Nevertheless, I can’t see what the author sees. “Best-liked” is certainly true of viewers, who kept him on the air for decades. And he was, like everyone, a victim of circumstances, in that he couldn’t freely choose what he did. But, as I repeat endlessly, that doesn’t mean he shouldn’t be punished. That includes firing and shaming to stop the tsunami (whoops, sorry—too close to “wave”) of sexual harassment in the workplace and deter others from such behavior, legal sanctions if Lauer broke the law. And although sexual predators are hard to reform, it’s not impossible.
As I mentioned in yesterday’s Hili Dialogue, Sunday was the 75th anniversary of the first controlled nuclear fission reaction, which it took place here at the University of Chicago. On December 2, 1942, in an old racketball court beneath the stands of the Stagg Field football stadium, Chicago Pile-1 was activated by Enrico Fermi and his team, producing gazillions of neutrons from cans of uranium oxide that were allowed to reach critical mass. Wikipedia describes the moment, which lasted less than five minutes:
[On] 2 December 1942, everybody assembled for the experiment. There were 49 scientists present. Although most of the S-1 Executive Committee was in Chicago, only Crawford Greenewalt was present, at Compton’s invitation. Other dignitaries present included Szilard, Wigner and Spedding. Fermi, Compton, Anderson and Zinn gathered around the controls on the balcony, which was originally intended as a viewing platform. Samuel Allison stood ready with a bucket of concentrated cadmium nitride, which he was to throw over the pile in the event of an emergency. The startup began at 09:54. Walter Zinn removed the zip, the emergency control rod, and secured it. Norman Hilberry stood ready with an axe to cut the scram line, which would allow the zip to fall under the influence of gravity.[95][96] While Leona Woods called out the count from the boron trifluoride detector in a loud voice, George Weil, the only one on the floor, withdrew all but one of the control rods. At 10:37 Fermi ordered Weil to remove all but 13 feet (4.0 m) of the last control rod. Weil withdrew it 6 inches (15 cm) at a time, with measurements being taken at each step.
The process was abruptly halted by the automatic control rod reinserting itself, due to its trip level being set too low. At 11:25, Fermi ordered the control rods reinserted. He then announced that it was lunch time.
The experiment resumed at 14:00. Weil worked the final control rod while Fermi carefully monitored the neutron activity. Fermi announced that the pile had gone critical (reached a self-sustaining reaction) at 15:25. Fermi switched the scale on the recorder to accommodate the rapidly increasing electrical current from the boron trifluoride detector. He wanted to test the control circuits, but after 28 minutes, the alarm bells went off to notify everyone that the neutron flux had passed the preset safety level, and he ordered Zinn to release the zip. The reaction rapidly halted. The pile had run for about 4.5 minutes at about 0.5 watts. Wigner opened a bottle of Chianti, which they drank from paper cups.
Compton notified Conant by telephone. The conversation was in an impromptu code:
Compton: The Italian navigator has landed in the New World.
Conant: How were the natives?
Chianti! There might as well have been fava beans. This of course led to the atomic bomb (I’m not going to argue whether or not our dropping it twice on Japan was the right thing to do), and the nuclear powderkeg that is today’s world. One could make a case that nuclear fission also has benefits, like the generation of nuclear power. But we’ll never know whether fission was a good or bad thing until humanity is gone, with or without a nuclear annihilation.
But somehow the celebration of nuclear fission by calling attention to atomic bombs seems, well, a bit weird. Yes, we must be mindful of the mixed legacy of nuclear fission, but showing a bomb?
For instance, Henry Moore’s famous sculpture just a block from where I sit, called “Nuclear Energy” certainly represents a mushroom cloud. It sits atop the exact spot where Fermi’s group created the fission reaction.
Henry Moore: “Nuclear Energy,” 1967, placed near the site of the first self-sustaining chain reaction, Dec. 2, 1942, University of Chicago campus, on Ellis.
What is even weirder is that often Japanese tourists descend on that sculpture in packs, with tour buses disgorging people who can’t wait to pose for selfies in front of the bomb statue. Are they mindful of the irony? It always gives me a shiver to see it, and I see it often.
Yesterday and the day before, the University celebrated the Fermi team’s work with a series of lectures, symposia, and, to cap the “celebration”, a daytime fireworks display by Cai Gu-Quian, a 59 year old Chinese artist who lives in New York and stages ephemeral art based on fireworks and gunpowder. For yesterday’s grand finale, right across the street from me, he created a colorful mushroom cloud firework that went off over Regenstein Library. Here’s a video of Gu-Quian describing the event, which begins with 75 peals of a tower bell at Rockefeller chapel. If you want to skip the preliminaries and the bells, start at 7:21.
The show is over in about 30 seconds, but I suspect someone paid the artist a lot of dosh to create and stage this “performance art.” Note the clapping afterwards. Cai as well as other University people explain it further in the University announcement of the events:
Cai Guo-Qiang said: “In the 1990s, I used black gunpowder to create mushroom clouds, humankind’s most iconic visual symbol for the 20th century. These mushroom clouds formed part of my Projects for Extraterrestrials. Today, the color mushroom cloud symbolizes the paradoxical nature of employing nuclear energy: Who is it for?”
“The work dramatizes the creative and destructive forces of nuclear fission,” said Steward [Laura Steward, curator at the Smart Museum of Art on campus]. “It takes the iconic shape of nuclear energy’s most destructive form and animates it with color as a profound symbol of creativity and peace.”
“Cai’s artwork reflects the yin-yang nature of the December 2, 1942 experiment’s impact. Its dualism places medicine and energy on one side, and weapons and massive destruction on the other side,” said Young-Kee Kim, the Louis Block Distinguished Service Professor of Physics and the College and chair of the Department of Physics at the University of Chicago.
There’s that dualism again. Where’s the medicine and energy bit? Is that the fireworks themselves, which have nothing to do with nuclear energy?
Now maybe I’m curmudgeonly about this, but do we really need to celebrate nuclear fission by showing mushroom clouds? Yes, it’s a complex legacy, but it’s like celebrating chemistry by displaying cans of Zyklon-B. I found this “highlight” of the events here bizarre and tasteless.
Here’s Robert Oppenheimer describing the reaction of himself and others who witnessed the successful Trinity bomb test on July 16, 1945 in New Mexico. Oppenheimer was the head of the Los Alamos lab that created the first atomic bomb—the one dropped on Hiroshima and Nagasaki. There wasn’t much celebration then. (Oppenheimer’s quote of course has become quite famous.)
