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.
The first Trump administration official has gone down, barely a year after the election. According to many sites, including CNBC, Special Counsel Robert Mueller has charged Michael Flynn, Trump’s ex national security advisor, with one count of lying to the FBI about his contacts with Russian officials. He’s pleading guilty, I suspect as part of some deal in which he’ll implicate others. The CNBC report:
Flynn is expected to plead guilty to a criminal information charging him with knowingly making materially false, fictitious and fraudulent statements to FBI agents.
Specifically, Flynn is accused of falsely claiming that he had not asked Russia’s ambassador to the United States last Dec. 29 “to refrain from escalating the situation in response to sanctions that the United States had imposed against Russia that same day.”
Flynn also allegedly lied by telling the FBI “he did not recall the Russian Ambassador subsequently telling him that Russia had chosen to moderate its response to those sanctions as a result of his request,” the information says.
That didn’t take long. Every time I travel, I have to emphasize that I despise Trump and his administration, for everywhere I go people are baffled that we elected such a moron. So far, the Republicans haven’t accomplished anything despite a year of controlling Congress and the Presidency (as well as the Supreme Court), and our governance is in shambles. This is why they’re so desperate to pass a misguided and harmful tax bill: simply to demonstrate that they can do something besides talk.
I guess I haven’t been paying much attention to the finer points of Republican perfidy, and so discovered three things only last night:
1.) The Republican tax bill in the House (if it passes, it still has to be reconciled with a Senate bill), has a provision that will allow parts of the Arctic National Wildlife Refuge to be opened for oil and gas drilling. The state of Alaska has been trying to get this done for years, but Congress has stood in its way. Now they’re caving. There is no amount of damage to wildlife or the environment that the Trump administration won’t tolerate in the name of capitalism. They’ve already proposed allowing imports of big-game hunting trophies, like elephant heads (though that’s on hold), and have passed a measure allowing hunters to shoot hibernating bears and their cubs, or wolves in their dens. These people have no respect for the lives or suffering of animals. And what does this have to do with taxes? It’s a sneaky add-on!
2.) The new bill will allow ministers to endorse political candidates from their pulpits, though churches still won’t be able to make contributions to political candidates. I agree with these humanists who claim that this now creates an entanglement between church and state (ministers are still allowed to express their private opinion in other places):
The Rev. Barry Lynn, the executive director of Americans United for the Separation of Church and State, said in an email, “The House GOP leadership and President Trump want to turn America’s houses of worship into centers of partisan politics. It’s a reckless scheme that may please Trump’s allies in the religious right, but could spark a blowback since the vast majority of Americans, faith leaders and houses of worship are firmly opposed to it. This is a bad idea that should be immediately dropped.”
Larry T. Decker, the executive director of the Secular Coalition for America, called the proposal in a statement “a brazen attack on the separation of church and state.” And the Baptist Joint Committee for Religious Liberty argued in a statement that inviting politics into the sanctuary is bad for churches, saying the House proposal “threatens to destroy our congregations from within over disagreements on partisan campaigns. … This change has been pushed by a tiny minority and is opposed by the vast majority of Americans and churchgoers, across party lines and faith traditions.”
If they’re gonna do that, then let’s eliminate the tax exemption for churches and pastors. This, too, is a sneaky add-on
The bill will, of course, drastically slash the corporate tax rate, almost halving it from 35% to 20%, while it’s likely that the tax bill for middle-class Americans will rise. Mortage interest deductions are being slashed, students will no longer be able to deduct the interest on their educational loans from their taxes, and graduate students will have to pay taxes on the tuition waiver they get. Since grad student tuition is often high, but waived for many students, this will hit them with a tax bill that they may not be able to afford. I had such a waiver at Harvard, and I’m not at all sure I could have afforded to pay taxes on that. In the net, this bill is going to hurt American undergraduate education in many ways.
It’s hard to avoid seeing this bill as one aimed at helping the rich at the expense of the poor. I wonder if those poor schlemiels who voted for Trump might start to dimly realize that they didn’t act in their own interest.
Karen Bartelt is back with some lovely bird photos; her text and IDs are indented:
In early November, my husband and I took a birding/”lepping” trip to the southern tip of Texas, travelling from S. Padre island through Brownsville, and along the border to just south of Laredo. It’s a surreal region, with many miles of border wall, and it would not be an exaggeration to say we saw 100 Border Patrol vehicles in the space of a week. And it was over 90 degrees every day. I’ve been trying to figure out how to organize these photos, and decided to start with the eastern end of the trip and go west. Here are some photos from the South Padre Island Birding Center.
This green jay (Cyanocorax yncas) was at our B&B. They were common throughout this part of Texas:
White ibis (Eudocimus albus) at the Briding center boardwalk:
Mottled duck (Anas fulvigula). Mottled ducks have a black spot at the base of the beak, but they also interbreed with mallards, so this may possibly be a “muddled duck”, a hybrid.
It’s December now! December 1, 2017, Friday, and the day of our department’s Christmas party, where I will stuff myself with Middle Eastern food and get somewhat buzzed on wines I picked out for the occasion. It’s also National Fried Pie Day, something that might well be unique to the U.S. A small fried peach pie is a good finish to a BBQ dinner. It’s also World AIDS Day, in existence since 1988. Finally, Cook County’s ill-advised and much hated soda tax expires today, allowing me to purchase my diet sodas without the stupid 2¢-per-ounce tax that was touted as a health-improving measure but was really intended to raise revenue. (The tell was that diet sodas were also taxed.)
People have been sniping at each other on the posts lately, and I urge new readers to have a look at the Da Roolz, or posting rools, to the left of this post, or here. Please be civil, and no name-calling or suggestions that another commenter is ignorant or brainwashed.
On this day in 1824, and for the only time in American history, the U.S. Congress had to decide the winner of the Presidential election, as none of the four candidates (William Crawford, Andrew Jackson, Henry Clay, and John Quincy Adams) received a majority of the electoral vote. This was according to the Constitution’s Twelfth Amendment, and Adams became the winner. On this day in 1913, the Ford Motor Company introduced the assembly line: a moving belt on which cars were assembled, with each worker specializing in a single task. On December 1, 1919, Lady Astor became the first woman member of Parliament in the House of Commons (she was elected on November 28). It was on this day in 1955 that Rosa Parks, riding a bus in Montgomery, Alabama, refused to give up her seat to a white man, was arrested for violating the city’s segregation laws, and the rest is history. It was a pivotal moment in the U.S. Civil Right movement. Finally, on this day in 1990, the two ends of the Channel Tunnel, dug from England on one side and France on the other, met—40 m below the seabed.
Notables born on this day include Marie Tussaud of the wax museum (1761), the “poet” Julia A. Moore of Michigan, perhaps the worst poet who ever lived (1847), Lou Rawls (1933), Woody Allen (1935), Richard Pryor (1940), Bette Midler (1945), and Pablo Escobar (1949).
Here’s one of my favorite Julia A. Moore poems (her sarcastic nickname was “The Sweet Singer of Michigan”), honoring a little girl who choked to death. The third verse from the end is sheer genius.
LITTLE LIBBIE
One more little spirit to Heaven has flown,
To dwell in that mansion above,
Where dear little angels, together roam,
In God’s everlasting love.
One little flower has withered and died,
A bud near ready to bloom,
Its life on earth is marked with pride;
Oh, sad it should die so soon.
Sweet little Libbie, that precious flower
Was a pride in her parents’ home,
They miss their little girl every hour,
Those friends that are left to mourn.
Her sweet silvery voice no more is heard
In the home where she once roamed;
Her place is vacant around the hearth,
Where her friends are mourning lone.
They are mourning the loss of a little girl,
With black eyes and auburn hair,
She was a treasure to them in this world,
This beautiful child so fair.
One morning in April, a short time ago,
Libbie was active and gay;
Her Saviour called her, she had to go,
E’re the close of that pleasant day.
While eating dinner, this dear little child
Was choked on a piece of beef.
Doctors came, tried their skill awhile,
But none could give relief.
She was ten years of age, I am told,
And in school stood very high.
Her little form now the earth enfolds,
In her embrace it must ever lie.
Her friends and schoolmates will not forget
Little Libbie that is no more;
She is waiting on the shining step,
To welcome home friends once more.
Those who bought the farm on this day include George Everest (1866), Aleister Crowley and G. H. Hardy (1947), J. B. S. Haldane (1964), David Ben-Gurion (1973), James Baldwin (1987), Alvin Ailey (1989), and Stéphane Grappelli (1997). Grappelli, of course was most famous for his jazz violin played with guitarist Django Reinhardt. Who would have thought that a fiddle player and a gypsy guitarist missing two fingers on his fretting hand could make musical history? Here’a rare video of them playing; the hot stuff starts at 1:30:
Meanwhile in Dobrzyn: Hili is housebound and grumpy:
Hili: It’s snowing.
A: But you are inside.
Hili: I feel aggrieved anyhow.
In Poliah:
Hili: Śnieg pada.
Ja: Ale ty jesteś pod dachem.
Hili: I tak mam pretensje.
From reader Taskin in Winnipeg, who constitutes half of Gus’s staff:
A couple of Gus pics for you. Gus spent the morning on the Katzenbaum and the afternoon in the sunny front window. It’s been a good day.
From Matthew Cobb—the world’s bravest (or craziest) goose:
I am of course deeply smitten with Jacinda Ardern, the new Prime Minister of New Zealand, as she is smart, funny, has a good sense of humor, and is Labour! Here, according to the Guardian, she’s recorded an answer to Ed Sheeran, an English singer, songwrite, and producer, who, anticipating his tour in New Zealand, broached the idea of becoming a citizen. Ardern recorded an answer, which is great. The Guardian:
This week Sheeran recorded a video message for New Zealanders before his much-anticipated March concerts there. “Hey New Zealand I can’t wait to see you very soon, I’m not yet a citizen of New Zealand but I’m working on it – hook me up prime minister, please,” said Sheeran, in the video for local radio station ZM.
New Zealand’s leader, 37-year-old Jacinda Ardern – a well-known music fan and occasional DJ – responded to the singer’s request with a 35-second video of her own, recorded in her parliamentary office in Wellington.
Her citizenship test actually included two questions that I couldn’t answer, which surprised me as I’d absorbed as much as I could of Kiwi culture when I was there (I’ve now been dubbed an Honorary Kiwi™ and a little bird told me I’m getting a genuine replica of an All Blacks jersey for my birthday). At any rate, looking up the answers to the first two questions, I found photos to go with the Guardian‘s answers:
“Hello Ed, my name is Jacinda Ardern, I’m the prime minister of New Zealand and I understand you’ve put through a very informal request for citizenship,” says Ardern, mock-serious.
“Before we’re able to think about that a little bit more I’ve got some very important questions for you; the first, do you like pineapple lumps? Do you even know what they are?”
Pineapple lumps are a distinctly nostalgic New Zealand treat, a chewy chocolate-covered sweet with a sweet pineapple-flavoured soft centre, which New Zealanders often keep in the freezer.
[JAC: I didn’t have these or see these in NZ!]
Ardern continues: “Two, are you willing to wear jandals in semi-inappropriate situations, and also, do you know what jandals are?”
Jandals – also known as flip-flops or thongs – are often worn by New Zealanders throughout the year, including winter, and sometimes with suits or dresses to formal events (for comfort’s sake). It is thought to be a derivation of “Japanese sandals”.
[JAC: I would have no problem with this as I wear flip-flops during the summer.]
I think I know where Ardern got the “semi-inappropriate situations” thing, for this is on her Facebook page. They aren’t jandals, I think, but come close. . .
Here’s an editorial from a Texas State University student newspaper that’s all over right-wing media (ignored by the Left, of course); it’s about why white DNA is “an abomination” and why white people shouldn’t exist. I don’t want to dissect it, because it’s a racist abomination in itself, and I don’t have the spoons to enact the emotional labor, I’ll just give a bit of the background from (yep) Fox News:
The column was written by Texas State University senior Rudy Martinez, a philosophy major who said in a past article he was one of the more than 200 people who was arrested on Jan. 20 protesting “the inauguration of proto-fascist Donald Trump.”
The University Star’s Editor-in-Chief, Denise Cervantes, said in a statement issued late Tuesday the column received “widespread criticism from readers.”
“The University Star’s opinion pages are a forum for students to express and debate ideas,” she said. “While our publication does not endorse every opinion put forth by student columnists or guest contributors, as the editor I take responsibility for what is printed on our pages.”
Cervantes said the original intent of the column was to provide a commentary on the idea of race and racial identities.
“We acknowledge that the column could have been clearer in its message and that it has caused hurt within our campus community,” she said. “We apologize and hope that we can move forward to a place of productive dialogue on ways to bring our community together.”
The article has apparently been removed from the online paper. I don’t think that’s so great; after all, it’s an instantiation of free speech and while I don’t agree with it, I do think that if the editor thought it was okay, she had every right to publish it. Once published, it should stay up.
I’ve found a screenshot and enlarged it. To me it sounds remarkably similar to ISIS’s piece in its own magazine Dabiq: “Why we hate you and why we fight you“.
First, the overview, which you won’t be able to read:
And the piece itself in readable form:
I’ll leave comments to the readers as this saddens me.
When an animal population changes over time for some trait, there are several possible causes. For instance, the animal could be responding nongenetically to environmental changes, just as a cat grows a longer coat in winter (this is within a single generation, but could also apply if cats move to colder climes). This is called “phenotypic plasticity”. Such changes aren’t considered evolutionary change because there are no changes in the frequencies of different gene forms, just in the expression of genes caused by the environment. Evolution, after all, is usually construed as genetic change over time.
Alternatively, the changes over time could reflect genetic change and thus instantiate genuine evolution. This has been seen many times—even during a human lifetime. The most famous of these studies was Peter and Rosemary Grant’s work on the increase in beak size in a Galápagos finch when there was a drought in the late 1970s, but there are other studies as well (e.g., industrial melanism in the peppered moth and many other insects), the changes in mouthpart size in the soapberry bug (coincident with new, invasive plant species) described on pp. 134-135 of my book Why Evolution is True, and, of course, the many cases of response to human changes in the environment: DDT and organophosphate resistance in insects, antibiotic resistance in bacteria, herbicide resistance in crops, and so on.
Finally, there could be an interaction between or a combination of environmental plasticity and genetic response, so that both factors could cause a population to change over time.
The point is this: if we see a population at time A, and then it’s changed in some feature at a later time B, with the difference between A and B being at least one generation, we can’t automatically assume that the population has evolved. It could be simply a change in the trait due to effects of the environment on development. This mistake is not uncommon: a paper was once published in Science showing that lizards transplanted to tiny islands on which they had to climb trees had a big increase in limb length over a couple of generations. The paper was published in Science because this was taken to be a case of evolution in real time, like the Grants’ work (their work is not in question). When I read it, though, I saw they hadn’t done any tests to show the change was genetic. And, sure enough, it wasn’t: the authors later showed you could effect the same changes just by letting the lizards crawl around on artificial trees. Another example is the well known difference in height between North and South Koreans (3-8 cm., or 1.2-3.1 inches)—surely due to differences in nutrition and not evolutionary change since the 1950s! For previous posts by Greg and me on this issue, see here and here.
A new paper in Nature Ecology & Evolution by Christopher Catteau et al. (reference and free access below, free pdf here) reports changes in beak, body, and tarsus size in the snail kite (Rostrhamus socialbilis subspecies plumbeus) in Florida, a change that occurred after the area was invaded by a larger prey item: snail. Bigger birds can eat the larger invasive snails, so there could be natural selection favoring bigger birds with bigger beaks, for they would get more nutrition and possibly produce more offspring. But it’s also possible that the change (observed over 1-1.4 generations) was nongenetic: the new source of food could cause the birds to simply grow bigger, making their bodies larger, and that includes the tarsus and beak. Finally, the changes in size could be due to both factors.
The authors conclude that the main effect here is not evolution but phenotypic plasticity; as they say:
The increase in sizes of morphological traits was probably due to phenotypic plasticity based on three lines of evidence.
You can read that evidence itself; it’s a bit genetic-y and arcane for the general reader, but they’re right.
However, you wouldn’t know that conclusion from the paper’s blurb article (from the “Trilobites” column) in the New York Times (click on screenshot below):
First of all, the title is wrong: we are not at all sure that the birds evolved bigger beaks. In fact, the genetic evolution was tiny at best, and the authors of the paper admit that the bulk of the bird’s response in beak size was due to phenotypic plasticity. The author, Douglas Quenqua, alludes obliquely to a nongenetic cause in the passage below, but he still says that the body size change is an “evolutionary trick,” which clearly implies “evolutionary change” rather than a plastic response. After all, when your cat grows longer fur in a colder year than in a warmer year, it’s not pulling off an “evolutionary trick”. From Quenqua’s piece:
Dr. Fletcher and his colleagues analyzed 11 years of morphological data they had collected on the birds. Because snail kites can live to the relatively old age of 8, that time period represented fewer than two generations for the birds. Nonetheless, the researchers found that beak and body sizes had grown substantially (about 8 percent on average, and up to 12 percent) in the years since the invasion.
Exactly how the birds are pulling off this evolutionary trick is not clear, but natural selection does appear to play a part. Young snail kites with larger bills were more likely to survive their first year than snail kites with smaller bills, presumably because the large-billed birds were better able to eat the invasive snails.
. . . Young birds eating the invasive snails, which are two to five times larger than the native ones, were also growing faster than birds weaned on the smaller ones, which may account for the increase in overall body size.
But the researchers found suggestions of a genetic component to the changes, as well. By tracking the birds’ pedigrees, they found that large-beaked parents gave birth to large-beaked offspring, setting the stage for large-scale evolutionary change.
Here the NYT is simply guilty of not only overhyping its conclusions, but misleading readers. Quenqua absolutely fails to make a clear distinction between the two interacting causes of change in a trait over time.
Now a bit about the paper, but I’ll be brief. Here are the highlights:
In 2004 the large apple snail Pomacea maculata invaded a Florida lake and spread rapidly through the range of the snail kite (which eats almost exclusively snails and feeds them to their young). The big snail replaced the smaller native snail, P. paludosa. Here’s the difference in size:
From paper: The exotic apple snail (P. maculata; right) is a novel prey for snail kites, because it is much larger than the native congener (P. paludosa; left), leading to implications for foraging and demography.
The invasion of the larger snail led to a rapid increase in the population of the snail kite (from 700 to 2,000, still about half of its high point), almost certainly because there was a lot more food around. So in this case an invasion—usually considered undesirable by biologists–may have saved an endangered species.
Young with bigger beaks were more likely to survive their first year (this was basically a one-generation study), so there was a form of natural selection for large beaks. But for that selection (differential survival) to cause evolution of beak size there has to be genetic variation among individuals in beak size.
The problem was that the study showed very little genetic variation for beak size. Estimates of “heritability” (the proportion of variation in beak size among individuals that had a selectable genetic component) was rather small, and in some cases indistinguishable from zero.
Moreover, these heritability measurements appear to be based on the correlation between parents and offspring in beak size. Now that could be a valid estimate of heritability if there is no environmental factor causing a correlation, so that we can assume that the correlation reflects only genes passed to offspring from parents. But is that a good assumption? Not in many species: for example, the traits that have the highest “heritabilities” in our species include wealth and religion, but these don’t have major genetic components—the correlation is an environmental one because parents give their religion and their dosh to their kids. What about the snails? As far as I can see, there’s a possibility for such an environmental correlation here, too. If adult kites with bigger beaks manage to get more of the big invasive snail, and thus feed more of them to their young, their young could grow bigger because of food, not because (or just because) of their genes. That would lead to a spurious genetic correlation between parents and offspring, overestimating the genetic component of the trait’s variation—and thus its liability to respond to selection.
The offspring did get bigger in body size, beak, and tarsus, and beak size got bigger even taking into account its correlation with body size. So there clearly was change between generations.
The authors, as I noted, emphasize the environmental component as making the kites bigger within a generation, downplaying the genetics because of their heritability data. I gave one quote before, and here’s another from the paper (my emphasis):
The breeder’s equation and breeding values are often used to detect evolutionary change. By contrasting these methods to observed phenotypic change, we found that phenotypic plasticity, not evolution, is probably responsible for most of the morphological changes in the snail kite at this point in time.
We can’t rule out that some of the change in bill, tarsus, and body size was genetic, and thus true evolutionary change within a generation, but at best that change is trivial compared to the change due to plasticity. The authors are much more careful in their paper than is Douglas Quenqua in his column. I’m not sure whether Quenqua has any training in biology (his LinkedIn profile shows a bachelor’s degree from Adelphi University), but it doesn’t matter. What he needed to do in his piece was understand evolutionary biology, and you can do that without a Ph.D. in the field. And he failed in his attempt to communicate the main findings of the paper: the hegemony in this case of plasticity over genetic change in an important trait change. In fact, he not only failed to communicate it—he got it backwards.
The New York Times really needs to do better in its science reporting. The author of this piece should absorb the lesson I emphasized in caps in 2011:
I leave you with my admonition to ecologists: DO NOT ASSUME THAT DIFFERENCES IN A TRAIT BETWEEN CURRENT POPULATIONS, OR BETWEEN POPULATIONS OVER TIME, REFLECT EVOLUTIONARY CHANGE UNLESS YOU GIVE SOME EVIDENCE THAT THOSE DIFFERENCES ARE BASED ON DIFFERENCES IN GENES.
