Whence the beaver? They’re kangaroo rats, not squirrels!

March 9, 2017 • 1:00 pm

Of course the title is clickbait, but it does express a new finding: that, among Rodentia (yes, beavers are rodents), whose phylogeny was till now a bit unclear, we now learn that beavers are more closely related to kangaroo rats than to squirrels. For a long time, beavers had been thought to be closely related to squirrels (the “sciurid rodents”) because of the similar arrangement of their masseter muscles—the muscles that close the jaw. Recently, there was some slight but not completely convincing evidence, however, that beavers may be more closely related to kangaroo rats: those cute hopping mice in the family Heteromyidae. (Heteromyids also include pocket mice, kangaroo mice, and spiny pocket mice.) The molecular evidence was based on a similar piece of DNA in beavers and heteromyids: a single “retrotransposon,” a “jumping gene” that moves around the DNA by being transcribed from its RNA and then stuck in different places in the genome.

So we have a muscle similarity coming up against a single molecular similarity. Well, a new paper in Nature Scientific Reports by Liliya Doronina et al. (reference below; free download), using a lot more molecular data, shows that the kangaroo-rat affinity wins. This is based on a phylogeny constructed from both DNA sequences as well as the presence and position of retrotransposons.

It turns out that beavers, compared to other groups of rodents, share seven new retrotransposons with the kangaroo rat, and none with other groups of rodents. This shows that beavers and kangaroo rats are monophyletic: they have a common ancestor that is not a common ancestor with any other rodent. Below you can see what the new rodent phylogeny looks like, and you can also see, along the right, the similarity of the muscles between squirrels and beavers.

Note that they used the Eurasian beaver (Castor fiber), rather than its good old New World counterpart, the North American beaver (Castor canadensis). But that doesn’t matter, for the two species of beavers—there are only two and they diverged about 9 million years ago—are more closely related to each other than to kangaroo rats or any other rodent.

Before I give the reveal, here are the animals:

A Eurasian beaver:

A North American beaver (much cuter!):

A kangaroo rat (Dipodomys sp.):

It turns out that a similar arrangement of the masseter muscle evolved three times independently in rodents, so that’s not a good character to use for making evolutionary trees; it’s an “evolutionary convergence” that doesn’t tell us much about ancestry. DNA is much better, and here’s the final tree:

(From paper): 3,780 potential phylogenetically informative retroposons were extracted from the beaver reference assembly and projected onto sequence information of other rodent genomes and onto PCR-amplified orthologs from Anomaluromorpha. These newly revealed markers are shown as enlarged red balls. Previously identified phylogenetically diagnostic retroposon markers are indicated by black and two conflicting yellow balls. The two screening strategies and the resulting diagnostic presence/absence patterns are indicated for Castorimorpha and also the mouse-related clade. The myomorphous, sciurimorphous, and hystricomorphous zygomasseteric systems are illustrated to the right (blue and red lines show anterior parts of medial and lateral masseter, respectively; for details of zygomasseteric systems in rodents see Potapova27). The mandible types20 are noted: sciurognathous and hystricognathous. For the squirrel-related clade, only the zygomasseteric system of Sciuridae is presented. The rodent paintings were provided by Jón Baldur Hlíðberg.

At last we can rest easy, knowing that the beaver is not a close relative of the squirrel. The similarity of their muscle configuration undoubtedly comes from their similar habits of gnawing tough stuff, which led to a convergent arrangement of strong jaw muscles.

h/t: Matthew Cobb

________

Doronina, L., A. Matzke, G. Churakov, M. Stoll, A. Huge, and J. Schmitz. 2017. The beaver’s phylogenetic lineage illuminated by retroposon reads. Nature Scientific Reports 7, Article number: 43562 (2017) doi:10.1038/srep43562

When ideology trumps biology

March 9, 2017 • 11:00 am

If I was the late Andy Rooney, I’d say “You know what really bothers me? When science shows some facts about nature, and then someone rejects those facts because they’re inconvenient or uncomfortable for their ideology.”

Indeed, when people ignore such inconvenient truths, it not only makes their cause look bad, but can produce palpable harm. Case in point: the damage that the Russian charlatan-agronomist Lysenko did to Soviet agriculture under Stalin. Rejecting both natural selection and modern genetics, Lysenko made all sorts of wild promises about improving Soviet agriculture based on bogus treatment of plants that would supposedly change their genetics. It not only didn’t work, failing to relieve Russia of its chronic famines, but Lyesnko’s Stalin-supported resistance to modern (“Western”) genetics led to the imprisonment and even the execution of really good geneticists and agronomists like Niklolia Vavilov. The ideological embrace of an unevidenced but politically amenable view of science set back Russian genetics for decades.

Other cases in point: the denial of evolution by creationists, and of anthropogenic global warming by conservatives. I needn’t belabor these.

We see this in other areas, too—especially with issues like differences between the sexes, ethnic groups, and evolutionary psychology. The assumption here is that any research on these areas could only serve to reinforce sexism and bigotry, so not only is that research denigrated, but there is an a priori ideological assumption that all groups are genetically equal for areas like behavior, mentation, and so on.  The error of this viewpoint is that whatever the truth is, it shouldn’t—and largely doesn’t—matter in the modern world. Society has advanced to the point where we recognize that equality of treatment and opportunity is the proper way to treat men, women, those of different ethnicities, the transgendered, and so on. There’s no need to assume that a biological “is” translates into a societal “ought”. As Steve Pinker has emphasized many times, we’re well past that view.

But the opposition to research on group and sex differences continues. One of its big exponents is the author Cordelia Fine, who has written two books with the explicit aim of showing that there are no reliably accepted evolved and biological differences in behavior between men and women. I read her first book, Delusions of Gender, and found it a mixed bag: some of her targets did indeed do bad science, and she properly called them out; but the book was also tendentious, and wasn’t objective about other studies. I’m now about to read her second book, Testosterone Rex: Myths of Sex, Science, and Society.  Judging from the reviews, which have been positive, it’s just as much a polemic as the first book, and has an ideological aim.

Because I haven’t finished it, I won’t judge it as a whole, but I do want to concentrate on one argument Fine makes that reviewers have found congenial.  That is her supposed debunking of the claim that men have often evolved to be promiscuous, and women to be more choosy, because of the potentially greater reproductive payoff for multiply-mating males compared to multiply-mating females. Lots of psychological studies have supported this difference in human sexual behavior, and of course it holds widely across the animal kingdom as well (there are exceptions exactly where we expect: when the reproductive payoff for multiple matings is greater for females than for males, as in seahorses). This difference between the sexes is in fact the evolutionary basis for sexual selection, and for the consequent observation of males courting females with behavior, ornaments, calls, and the like, with females choosing among displaying males. This is so common in animals as to constitute almost a biological “law”, with the exceptions proving the rule.

Fine denies this evolutionary basis, leaving her unable, of course, to explain sexual dimorphism in humans or any species. Her denial appears to be based on an early flawed experiment of Angus Bateman in fruit flies, which indeed turned out upon reanalysis to be inconclusive.  I’ve discussed this whole issue before, and you can read about it here, and how Sarah Ditum, the Guardian’s reviewer of Fine’s new book, was taken in by Fine’s bogus arguments. (Ditum is not a scientist.)

In my earlier post I pointed out the pervasive biological evidence that in both humans and other species,  the conditions for sexual selection  hold—a greater variance in male than in female reproductive output—probably explaining why men are bigger and stronger than women, and have beards and other secondary sexual differences. It also explains why male peacocks have showy tails, why male sage grouse do “jumping displays” to attract females, why male insects have weapons and ornaments, and so on. (See my bullet-point list of biological facts in that post.) Further, though Bateman’s experiments were flawed, they have been repeated properly in other species and have shown that, yes, males in general have the potential to have many more offspring than females: a higher variance in offspring number).

On February 23 the New York Times also reviewed Testosterone Rex, and the reviewer, the journalist Annie Murphy Paul, also fell for the bogus no-difference-in-reproductive-variance argument (she’s not a scientist). As she said:

Well, then, what about the even more entrenched idea that evolution has primed men to desire many and varied sex partners? Here Fine quotes the Bradley University psychologist David Schmitt: “Consider that one man can produce as many as 100 offspring by indiscriminately mating with 100 women in a given year, whereas a man who is monogamous will tend to have only one child with his partner during that same time period.” Fine expertly fillets this familiar premise, noting, among other inconvenient facts, that “the probability of a woman becoming pregnant from a single randomly timed act of intercourse is about 3 percent,” and that in historical and traditional societies, as many as 80 to 90 percent of women of reproductive age at any one time might already be pregnant, or infertile while they were breast-feeding. “The theoretical possibility that a male could produce dozens of offspring if he mated with dozens of females is of little consequence if, in reality, there are few females available to fertilize,” Fine comments. Think about it: For every man on the prowl, there simply aren’t a hundred women available to bear his child. For all men not named Genghis Khan, monogamy must have started to look like a pretty smart bet.

This is someone who doesn’t know what she’s talking about. Humans in Western society are now socially monogamous, but in effect many are polygamous, committing adultery. Men have been shown, time after time, to be less discriminating and more promiscuous than females. And many of those women who were pregnant were not pregnant by their social mate—if indeed our early ancestors had social mates—but by “alpha” males who got more than their share of offspring, or by those who mate with other males’ mates on the sly—what John Maynard Smith called “sneaky fuckers”. Most species of birds that look socially monogamous, for instance, pairing up in the nest and cooperating in brood care, have been found by DNA analysis to actually be committing adultery all over the place, so that the appearance of pairing gives a false idea of who’s really producing the chicks.

Such is the invidious result of having a non-scientist judge a scientific argument; and yes, the Times screwed up big time.  But someone who should know better is the evolutionary biologist and blogger P. Z. Myers, who bought into Fine’s bogus argument and fallacious mathematics in a post called “Cordelia Fine is doing the math.” Myers accepts Fine’s contention that promiscuous males don’t really have more offspring than do choosy human females—females who are prevented from getting fertilized when they’re pregnant.  Her arguments are wrong—for one thing, she sets unrealistic error limits for promiscuous males to outdo monogamous ones—but Myers has always rejected biology that is ideologically unpalatable to him.

In a rare occurrence at his site, the commenters, usually a choir of osculatory praise, gave him pushback. In fact one,  “Charly”, did the math correctly and showed that males in relationships with multiple females (bigamous or polygamous) have the potential to have more offspring than do monogamous males, supporting the ideas that men are selected to compete for women. (Duh!) Charly ended his calculations with this statement: “But maybe my reasoning and math is wrong, I am sure someone will point flaws out.”

In the next comment, Myers admitted that Charly’s math was actually right—math that invalidates Fine’s argument—but then he said this:

And there we have it, ladies and gentlemen, brothers and sisters: an admission that the biology is right, at least in theory, but the person who did the calculations is immoral.  What better example can we find of someone who opposes the truth because it’s ideologically repugnant? Even Myers’s regular commenters couldn’t live with that pronouncement, with one even asking if he was all right. I won’t speculate on his state of mind, but I will say that he’s on the wrong side in this argument.

Well, be that as it may, we have two lessons from this kerfuffle.

a). Magazines and newspapers should get scientists, or at least journalists who are scientifically educated, to review books about science. Science journalists without training in math and evolution are unqualified to review Fine’s book.

b). It’s always better to accept a scientific fact than to reject it on ideological grounds. For people will know the truth, and when they see it rejected because of confirmation bias, they can see what’s going on.

It always hurts your cause to behave that way. If science finds that men and women behave differently for evolutionary and genetic reasons, or that humans have behaviors that are holdovers from selection in our ancestors, we can deal with that. Such findings do not inexorably lead to racism, sexism, or bigotry, and there’s no reason why they should. Sure, there may be a few misguided individuals who mistake an “is” for an “ought,” but society no longer works that way.  Rejecting the facts because you don’t like them, or because they go counter to your political leanings, is a sure recipe for sinking your cause. First apprehend the facts, and then just deal with them.


Readers’ wildlife photos

March 9, 2017 • 8:15 am

Reader John Conoboy sent. . . CATS!  His notes are indented:

Here are some photos from my recent trip to Tanzania. I will start with cats. Lions, leopards and cheetahs are the big draws, and the guides all communicate by radio whenever there is a sighting and swarms of vehicles converge at the site and jockey for position so their clients can get a good picture.

The first three are of a lion (Pathera leo nubica) we managed to spot in Tarangire National Park when there were no other vehicles around, which is extremely lucky.  Our guide said that she probably had cubs hidden somewhere while she was hunting as she is obviously nursing. We watched her stop to take a drink and then she walked directly toward our vehicle. She stopped just under the window where I was sitting. Except for my fondness for having my arm and hand attached at the shoulder, I could have reached out the window and touched her. She paused and then went around the back of the vehicle and started moving towards some zebras. Before she could do anything, the zebras moved off. We were able to follow her as she stalked some other zebras and wildebeest. She waited patiently crouched low in the grass waiting for stragglers when another safari vehicle drove through the herd and spooked the wildebeest, which all ran off.  A while later, we, and a dozen or so other vehicles, saw her with two cubs, but I was unable to get any pictures of her and the cubs due to so many vehicles crowding around and blocking the view. As she had the cubs with her, it is likely that she had made a kill.

Next are two photos of two cheetahs (Acinonyx jubatus raineyi) in Serengeti National Park. Our guide identified them as brothers. We first saw them just lying on a rock, but then they got up and started moving towards some wildebeest. They stopped and watched as a young wildebeast, possibly an orphan, tried unsuccessfully to join a group of adults. They watched as the youngster started to move away from the group and as it moved off alone, they started to close in.  We saw one of the cheetahs put on an amazing burst of speed and take the wildebeast down, but it was too far away to photograph. The second cheetah joined in to finish the kill and then they took turns eating.

We saw lots of lions, mostly sleeping and a few leopards (Panthera pardus). I include a few shots of both. In one photo of two lions eating a carcass it is clear that one has a radio collar.

A real treat, however, was getting to see an African Wildcat (Felis sylvestris lybica). It is rare to see this small cat during the daytime, and this one was quite close to the road. [JAC: this is thought to be the ancestor of the housecat.]

Finally is  picture of our first cat sighting in Africa at the Arusha Hotel, where the local moggie joined us for our initial briefing by our guide.


Fleetwood Mac: “Landslide”

March 9, 2017 • 7:15 am

I’ve saved my favorite song for the last day of Fleetwood Mac week: “Landslide“. First appearing on the 1975 album named for the group, it was of course written by Stevie Nicks. This song, and Rhiannon, were Nicks’s first original songs for the band when she and Lindsey Buckingham joined—and what a pair of songs!

I’ll never forget the first time I heard this song: someone was playing the “Fleetwood Mac” album for me (the LP of course), and when this song ended I asked that the needle be moved back to the start of the track. It’s a gorgeous and mesmerizing song, but one that reached only #51 in the US top 100. Wikipedia gives a bit about its genesis comes from Wikipedia:

Nicks has said that she wrote this song while she was contemplating going back to school or continuing on professionally with guitarist Lindsey Buckingham. Their album Buckingham Nicks had been dropped by Polydor Records and she and Buckingham were not getting along. She wrote the song while visiting Aspen, Colorado, sitting in someone’s living room “looking out at the Rocky Mountains pondering the avalanche of everything that had come crashing down on us … at that moment, my life truly felt like a landslide in many ways”.

You can read Nicks’s full account of the song’s genesis here.

It always amazes me that someone can just come out with a song like this, even when inspired by the Rockies. It’s been covered many times, with the most famous covers by the Dixie Chicks and The Smashing Pumpkins, but nothing comes close to Fleetwood Mac’s version. I can’t find a video featuring the original 1975 recording (it’s been blocked), but I love Nicks’s live duets with Buckingham on the acoustic guitar, and there are several on YouTube. I have no idea when or where this was filmed, but I’d guess some time around 2005.

Buckingham’s solo at is especially poignant as Nicks, his former lover, walks behind him and embraces him, making him close his eyes. They’d broken up years before, but the chemistry is still palpable. I can only imagine how intense their relationship had been.

Thursday: Hili dialogue

March 9, 2017 • 6:30 am

Good morning this fine (well, chilly) Thursday, March 9, 2017. It’s National Crab Day, so go be mean to someone! And it’s one of those Catholic holidays celebrating a fictional event: the Forty Martyrs of Sebaste.

Returning to reality, it was on March 9, 1566, when David Rizzio, secretary of Mary Queen of Scots and most likely her lover, was murdered in her presence by henchmen of her jealous husband. On this day in 1796, Napoleon married his great love Joséphine; he later divorced her to produce an heir with another wife. In 1831, the French Foreign Legion was established (it’s still around), and in 1954 CBS television broadcast the famous See It Now episode on Senator Joseph McCathy which, thanks to producer Fred Friendly and reporter Edward R. Murrow, brought down the witch-hunting charlatan.  This is a highlight of American political reporting, and here it is:

On this day in 1959, the Barbie Doll made its first appearance at a Toy Festival in New York, giving little girls ever since a distorted idea of the female frame. Finally, on March 9, 2011, the Space Shuttle Discovery made its 39th and final landing, setting a record.

Notables born on this day include Vita Sackville-West (1892), Samuel Barber (1910), Mickey Spillane (1918), Yuri Gagarin (1934; he was the first man to orbit the Earth, and died in a training flight at age 34), Bobby Fischer (1943), Bobby Sands (1954), and Juliette Binoche (1964). Those who died on this day include, besides David Rizzio, Mary Anning (1847), Menachem Begin (1992), Charles Bukowski, (1994), George Burns (1996), and Notorious B.I.G. (1997, shot to death, with the murderer never found).  Meanwhile in Dobrzyn, the Princess is already contemplating her upcoming spring activities:

Hili: Nature is coming to life.
A: The grass is not growing yet.
Hili: But the birds are already making a racket.

(Photo: Sarah Lawson)

In Polish:
Hili: Przyroda budzi się do życia.
Ja: Trawa jeszcze nie rośnie.
Hili: Ale ptaki już się wydzierają.
(Foto: Sarah Lawson)

And out in Winnipeg, where there are signs of Spring, Gus is getting in a nap, preventing his staff from making the bed:

 

Jonathan Pie on language policing

March 8, 2017 • 1:00 pm

From today until I get back from New Zealand (April 17), posting will be light, as I’m preparing to leave and have tons of stuff to do. Bear with me, and after March 15 I’ll ask readers to ratchet back on emailing me when I’m on the road.

Meanwhile, here’s a 3½-minute video by “Jonathan Pie” that’s relevant to the last post.

As I’ve mentioned before, “Jonathan Pie” is the pseudonym for the comedic alter ego of Tom Walker, who, acting as a newsman, suddenly goes off on unhinged rants—rants that contain a kernel of truth. At 1:30, Pie begins to rant about the offense culture of the British Left, which, he says, comes from students.

TRIGGER WARNING: Bad language!

Highly recommended reading: “On Political Correctness”

March 8, 2017 • 12:00 pm

The American Scholar is the house magazine of the Phi Beta Kappa honorary society, with the journal’s name taken from a speech given to that society by Ralph Waldo Emerson in 1837.  It’s published a number of distinguished articles, but a new one stands out: “On political correctness: Power, class, and the new campus religion“. It’s by William Deresiewicz, a widely published author and literary critic; and I wish I’d written the piece.

It’s long, and covers a lot of territory, but I highly recommend it. Its thesis is that “political correctness”, which Deresiewicz defines as “the persistent attempt to suppress the expression of unwelcome beliefs and ideas”, is proliferating in American private universities (not so much in public ones), and has many pernicious effects, including these

  • Homogenizing the student body, so that anyone with dissident views (read: conservatives, religious people, moderate feminists, pro-Israelis) is afraid to express them for fear of being demonized
  • Turning liberals into a group unable to defend its own arguments
  • Masking “deeply legitimate concerns” about racism and sexism by diverting them into trivial channels about microaggression, trigger warnings, language policing, and so on
  • Completely ignoring class differences, which aren’t the subject of the campus liberal agenda
  • The perpetuation of class differences by “laundering privilege”: preferentially accepting students who are largely well off, and from the upper classes
  • Turning private colleges into “socialization machines for the upper-middle class, ideological enforcers of progressive dogma.”
  • Suppressing free speech, coming with the presumption that liberals know what speech can and should be suppressed. This leads to the inability to make progress (see below):

Now many of these ideas aren’t new, but Deresiewicz has a new take on them. He himself is a liberal, but decries the authoritarian mentality of today’s students—and their professors. You may disagree with some of Deresiewicz’s arguments, but I found this a fascinating and compelling read. There are so many good ideas and quotable sentences in it that I can’t even give a flavor of the piece by quoting excerpts. I’ll give just two:

What does it mean to say that these institutions are religious schools? First, that they possess a dogma, unwritten but understood by all: a set of “correct” opinions and beliefs, or at best, a narrow range within which disagreement is permitted. There is a right way to think and a right way to talk, and also a right set of things to think and talk about. Secularism is taken for granted. Environmentalism is a sacred cause. Issues of identity—principally the holy trinity of race, gender, and sexuality—occupy the center of concern. The presiding presence is Michel Foucault, with his theories of power, discourse, and the social construction of the self, who plays the same role on the left as Marx once did. The fundamental questions that a college education ought to raise—questions of individual and collective virtue, of what it means to be a good person and a good community—are understood to have been settled. The assumption, on elite college campuses, is that we are already in full possession of the moral truth. This is a religious attitude. It is certainly not a scholarly or intellectual attitude.

Dogma, and the enforcement of dogma, makes for ideological consensus. Students seldom disagree with one another anymore in class, I’ve been told about school after school. The reason, at least at Whitman, said one of the students I talked to there, is mainly that they really don’t have any disagreements. Another added that when they take up an issue in class, it isn’t, let’s talk about issue X, but rather, let’s talk about why such-and-such position is the correct one to have on issue X. When my student wrote about her churchgoing friend, she said that she couldn’t understand why anyone would feel uncomfortable being out as a religious person at a place as diverse as Scripps. But of course, Scripps and its ilk are only diverse in terms of identity. In terms of ideology, they are all but homogeneous. You don’t have “different voices” on campus, as these institutions like to boast; you have different bodies, speaking with the same voice.

That, by the way, is why liberal students (and liberals in general) are so bad at defending their own positions. They never have to, so they never learn to. That is also why it tends to be so easy for conservatives to goad them into incoherent anger. Nothing makes you more enraged than an argument you cannot answer. But the reason to listen to people who disagree with you is not so you can learn to refute them. The reason is that you may be wrong. In fact, you are wrong: about some things and probably about a lot of things. There is zero percent chance that any one of us is 100 percent correct. That, in turn, is why freedom of expression includes the right to hear as well as speak, and why disinviting campus speakers abridges the speech rights of students as well as of the speakers themselves.

If you want to see an example of a well-schooled conservative shredding the views of unthinking Leftists, simply look at some of conservative writer and speaker Ben Shapiro’s videos on YouTube. It’s cringe-inducing, but is a perfect example of what Deresiewicz says in the last paragraph. Shapiro has done his homework (not that I agree with most of what he says), while his questioning opponents are simply mouthing pieties of the Left that they haven’t examined.

And the piece’s end:

Selective private colleges are the training grounds of the liberal elite, and the training in question involves not only formal education for professional success, but also initiation into the folkways of the tribe.

Which means that fancy private colleges have a mission public institutions don’t. People arrive at public schools from a wide range of social locations, and they return to a range that is nearly as wide. The institutional mission is to get them through and into the job market, not to turn them into any particular kind of person. But selective private colleges (which also tend to be a lot smaller than public schools) are in the business of creating a community and, beyond that, a class. “However much diversity Yale’s freshman classes may have,” as one of my students once put it, “its senior classes have far less.”

And this, I believe, is one of the sources of the new revolt among students of color at elite private colleges and universities. The expectation at those institutions has always been that the newcomers whom they deign to admit to the ranks of the blessed, be they Jews in the 1950s or African Americans today, will assimilate to the ways of the blessed. That they will become, as people say, “more white.” That bargain, as uncomfortable as it has always been, was more readily accepted in the past. For various reasons, it seems that it no longer is. Students of color are telling the whites who surround them, No, we aren’t like you, and what’s more, we don’t want to be like you. As very different as their outlook is from that of the white working class, their rejection of the liberal elite is not entirely dissimilar.

Selective private colleges need to decide what kind of places they want to be. Do they want to be socialization machines for the upper-middle class, ideological enforcers of progressive dogma? Or do they want to be educational institutions in the only sense that really matters: places of free, frank, and fearless inquiry? When we talk about political correctness and its many florid manifestations, so much in the news of late, we are talking not only about racial injustice and other forms of systemic oppression, or about the coddling of privileged youth, though both are certainly at play. We are also talking, or rather not talking, about the pathologies of the American class system. And those are also what we need to deal with.

h/t: John T.