Monday: Hili dialogue

July 31, 2017 • 6:30 am

Good morning on the last day of July, 2017. As August begins tomorrow, the long sobs of the violins of autumn will begin to wound my heart with a monotonous languor. It’s National Cotton Candy Day (I believe it’s called “candy floss” in Britain), a pretty useless confection containing only sugar and a bit of dye. And it’s also Ka Hae Hawaii Day, celebrating the state flag of Hawaii, which looks like this:

It’s the only U.S. state flag that also contains the flag of a foreign nation. Can you guess why?

On this day in 1492, the same year that Columbus sailed the ocean blue, his patrons King Ferdinand and Queen Isabella expelled all the Jews from Spain via the Alhambra Decree. This was to prevent the remaining Jews from influencing those Jews who had already converted to Catholicism. July 31, 1970 was also Black Tot Day, the last day that sailors in the Royal Navy were given their official rum ration. Curiously, the bibulous Aussies had abolished the rum ration in 1921. After Britain abolished the obligatory tot, the Royal Canadian Navy followed suit on March 31, 1972, followed by the very last Commonwealth navy to abolish the ration, the Royal New Zealand Navy, which deep-sixed the tot on February 27, 1990. I’ve read, however, that the British Royal Navy tried to compensate by allowing sailors to buy three daily cans of beer in the ship’s canteen rather than two. That’s not much solace compared to free rum.

You can buy a bottle of the unused “last consignment” rum for about $1200.

Here’s a short video about the End of the Tot (note the black armbands on the mourning sailors):

On this day in 2006, Fidel Castro ceded power to his brother Raúl, and, on July 31, 2012, Michael Phelps broke the Olympic record of Russian gymnast Larisa Latynina by winning yet another gold medal in swimming. Phelps is now by far the most decorated Olympian of modern times, with a total of 28 medals—23 of them gold. Now he’s racing virtual sharks.

Notables born on this day include Milton Friedman (1912), Primo Levi (1919), Geraldine Chaplin (1944), and J. K. Rowling (1965). Those who died on this day include Ignatius of Loyola (1556), Franz Liszt (1886), Bud Powell (1966), and Gore Vidal (2012). Meanwhile in Dobrzyn, the princess is seeking solitude in the empty upstairs apartment:

Hili: I told you not to come here.
A: You didn’t tell me why.
Hili: Everybody needs some privacy.

In Polish:

Hili: Mówiłam, żebyś tu nie przychodził.
Ja: Nie powiedziałaś dlaczego.
Hili: Każdy potrzebuje trochę prywatności.

Here’s a tw**t found by Heather Hastie:

https://twitter.com/planetepics/status/891813928262664192

And here’s a nice cartoon produced by reader Pliny the in Between with a double-entendre title: “Nero my God to thee”:

And here’s a black dog for Black Dog Day:

When evolution goes wrong. . .

July 30, 2017 • 2:30 pm

Here’s a cartoon sent by reader Thomas; it’s from “Wrong Hands“, drawn by John Atkinson:

I don’t mind the birds evolving from dinosaurs, or the evolutionary stasis of the platypus (if indeed there was any stasis, for the earliest monotremes, which did exist about 110 million years ago, looked nothing like a platypus). But oy, those Crocs!

The complex evolution of the big cats

July 30, 2017 • 1:30 pm

A new paper in Science Advances by Henrique V. Figueiró et al. (reference below, free download with legal UnPaywall app) resolves the contested phylogeny (family tree) of five big cat species: lion, leopard, jaguar, snow leopard, and tiger. In so doing, the researchers uncovered some interesting evolutionary history.

Previously, the family tree of this group had been a bit confusing, as different genes gave different phylogenies. That’s normal for recently evolved species (the speciation in this group occurred within the last 4.5 million years), for the genes that were variable in the common ancestors could remain variable in the descendants, and depending on which gene you looked at, you could find evolutionary phylogenies that were really the histories of the genes themselves rather than the history of the species that contained them. But there was another reason for the confusing phylogenies as well, and we’ll get to that shortly.

I’ll try to be brief so we don’t have too many long posts today. Figueiró et al. did whole-genome sequencing of these species, which is not so hard these days, and based on the consensus relationships of all the genes, they came up with this phylogeny. The numbers above the lines of splitting give the estimated times at which those splits occurred:

The African cats are the most closely related, with the jaguar (a south American cat) splitting off from the ancestor of the leopard and lion about 3.6 million years ago. But how can that be, since Africa and South America themselves split over 150 million years ago? Yes, you guessed it: the jaguar evolved in Eurasia, and moved down to South America after crossing to North America. Jaguars once lived in what is now England!

The Asian cats—the tiger and snow leopard—are also “sister species”—each other’s closest relatives—having split about 3.5 million years ago. (The tree was “rooted” by using a species that wasn’t in the group of large cats: somebody’s moggie from Missouri.)

By looking at how fast DNA sequences evolved compared to the rest of the genome, each branch of the Big Cat Tree shows which class of genes show members subject to “positive selection”—genes favored by especially strong natural selection. Jaguars and tigers show evolution, for instance, of genes known to be involved in protein metabolism and smell; and jaguars, which have big thick heads compared to the other cats, have positive selection on genes involved in “craniofacial development.”

By looking at gene sequences and comparing them with population-genetic models, you can also get an idea of the number of individuals in the species at various times in its history (well, an underestimate of the size). Here’s that history for the big cats, and it shows two episodes of population reduction: one about 100,000-300,000 years ago, and a second round between 10,000 and 20,000 years ago, possibly connected with glaciation. Historically, jaguars, despite their large former range, seem to have had the lowest population size averaged over time.

One of the study’s striking findings was the degree of genetic interchange between branches of the tree that had already split; that is, between species. Like humans and Neanderthals, big cat species occasionally exchanged genes after the species had gone their separate evolutionary ways. This plot shows which branches exchanged genes as the ancestors gave rise to their descendants:

It is in fact this exchange of genes between ancient branches (not necessarily, for instance between living lions and jaguars but between the ancestors of each) that probably made the phylogenies confusing. If you looked just at the genes exchanged not that long ago between the ancestors of modern lions and jaguars, you’d come to a wrong conclusion: that lions are more closely related to jaguars than to leopards. That’s why it’s important to look at many genes instead of just a couple when making these trees.

Finally, there’s a striking association between the genes exchanged between species and the genes that have evolved quickly by natural selection. Genes that were exchanged between lineages and then evolved rapidly after those exchanges include genes affecting brain function and development, genes involved in the growth and guidance of axons (nerve connections), and genes affecting the optic nerves. The authors suggest that this means that “introgression” (genes coming via hybridization with another species) is a useful source of adaptive variation: a reservoir of variation that natural selection can use. (It’s analogous to mutation, which also introduces new variation into the genome.)

But I have another interpretation: a gene that gets in from another species one way or the other could be subject to rapid selection because it’s suddenly found itself in a foreign genome to which it’s not adapted, and has to change rapidly to “fit in” with the new genome rather than adapting to environmental circumstances. Now the first interpretation has clearly happened, as we see in introgressed butterfly color and pattern genes that are used, after hybridization, to make new mimetic patterns; but I don’t see that my interpretation can never apply.

Regardless, we now know the evolutionary history of this group of large cats (they’re more closely related to each other than to any other species of felid), and we’ve learned that genetic interchange between separated branches of the evolutionary tree is more extensive, in this and other groups, than we ever expected.

h/t: Matthew Cobb

_______________

Figueiró, H. V., et al. (2017).  Genome-wide signatures of complex introgression and adaptive evolution in the big cats. Science Advances 3(7). e1700299 DOI: 10.1126/sciadv.1700299

More outrage from the Right and the religious about infant euthanasia

July 30, 2017 • 10:00 am

UPDATE: Reader Pyers called my attention to a thoughtful piece by Melanie Phillips that analyzes the Gard case. She argues that the parents’ hopes may have been kept alive by the vociferous, bullying, and life-at-all-costs American Right:

But here’s the really wicked thing about all this. The parents were reinforced in their refusal to accept this tragic situation, and the whole court process pointlessly prolonged, because of the pressure largely emanating from activists and media on the American political right (along with right-to-life campaigners) screaming that a baby was about to be killed by a socialised health care “death panel” enforced by the British government. This campaign led the parents to believe that such pressure could change the court’s mind. And so the parents were reinforced in their refusal to face reality.

. . . I write a great deal about the ideological bullying of the left, the lies published by left-wing media and the inhumanity and irrationality of so much allegedly progressive thinking. But I have never witnessed such concentrated ignorance, arrogance, stupidity and unthinking cruelty as has been displayed by the American political right over the tragic case of Charlie Gard.

_________

 

The public outrage continues about my post on whether we might consider euthanizing newborn babies with terminal conditions who are suffering horribly. All the articles about it, most of them expressing shock and horror at the notion, have appeared on either right-wing or religious websites, which tells you something. I’ve also received pretty nasty emails and phone calls from people who can’t even bear to consider the idea of putting a suffering, soon-to-be-dead infant out of its misery (see here, and here).

Predictably, my evolutionary biology background is sometimes held responsible, as if my views come from a Darwinian idea that we should help natural selection along, because doing that is good. That criticism, based on the naturalistic fallacy, holds no water, as my views have nothing to do with evolution and everything to do with compassion and philosophy. After all, if I really believed that what evolution does is good and should be promoted, I should have had a passel of children. But I am childless, with the only “Jerry Coynes” being cats.

It’s also clear that the opposition to infant euthanasia is underlain by human exceptionalism: the view that while it’s okay to euthanize terminally ill and suffering adult cats and dogs, who can’t give consent, we can’t do that for suffering and terminally sick infants who also can’t give consent. Much of that exceptionalism comes from religion, but I will grant that some does not. But in what respects are humans qualitatively different from dogs, cats, and other primates? Well, we alone know that we’re going to die, and we also have an idea of futurity, so we look forward to the rest of our lives (well, most of us do). But those aren’t characteristics of newborns, so to me they don’t count as reasons why we need to keep a dying child alive but can euthanize a dying dog. And many human infants share with both adult and infant animals the ability to suffer, but adult animals often exceed newborns in their degree of rationality and sentience. So what makes humans different from other animals are not qualities present in newborns; these “exceptional” qualities appear later in development.

I’ll also grant that not all opposition to euthanasia of infants comes from religion: some comes from the disabled who put themselves in the place of an infant about to be euthanized. The other day I got an outraged call, for instance, from a woman with spina bifida, who accused me of wanting to have her “snuffed out.” But there are degrees of that impairment, and it’s not at all clear that such infants would always be put to death by parents, or that rational guidelines for euthanasia wouldn’t deem such infants as candidates for adoption. Further, one has to consider that those severely disabled people who are now grown up and can consider their situation wouldn’t even be in that position had they been given euthanasia as newborns. This is not an argument for euthanizing every sick or deformed infant, of course, but one has to take the parent’s willingness and ability to give care—often lifelong—to children with severe illness.

At any rate, all I’m proposing is that we should think about this issue, and suggest that it would be merciful in some cases to put terminally ill or severely deformed infants to death rather than allowing them to suffer. I see no point in allowing such suffering to continue when there is no point to it, and when the child is certain or almost certain to die soon.

The case of Charlie Gard in England, which Heather Hastie just discussed on her website, is one example. The infant, born in England about a year ago, began showing signs of illness, and it was discovered that he had a severe form of “encephalomyopathy mitochondrial DNA depletion syndrome” (MDDS), a genetic disease which causes progressive muscle weakness and brain damage.  It’s nearly always terminal, and in Charlie’s case it was certainly terminal. The infant was soon on both a respirator and feeding tube, and had brain damage exacerbated by seizures. His medical team, and then the courts, decided that Charlie should have only palliative care and that there was no hope for his survival.

An American doctor said he had an experimental treatment that might improve Charlie’s condition (see Heather’s post for more information), but it turned out that he didn’t, and the British courts didn’t permit the infant to be moved to the U.S. for this treatment. They further ruled that Charlie, who was by now deaf and had failing kidneys as well as an inability to breathe on his own, should be moved to a hospice-like facility and the ventilator withdrawn. That happened on July 27, and the next day Charlie died.

Note here that British courts ruled that a suffering and terminally ill child should be put out of his suffering by withdrawing breathing assistance. That is a decision to take action that has a predictable consequence: Charlie’s death. What is the moral difference between doing that and putting Charlie to death earlier with an injection? That’s illegal in Britain, but should it be?

Of course, Charlie’s parents wanted to keep him alive, and those wishes should be heavily weighed in such cases, but in the end the courts and medical team overruled the parents’ initial wishes, something I don’t think is legal in America. At any rate, had the parents wished Charlie to be euthanized once his terminal condition was known, I can’t see a rational objection to that which at the same time allows withdrawing respiratory aid.

As Heather points out, Charlie’s parents eventually agreed that withdrawing life support was the right thing to do, but they were opposed by many Christians, including the Vatican. There were even death threats and abusive letters sent to the Great Ormond Street Hospital where Charlie was being treated.

This shows the degree of emotion that such cases arouse, and the resistance to withdrawing life support in even terminal cases. The resistance is even greater if one considers the possibility of euthanasia for a child like Charlie. I think it would have been more merciful for Charlie’s parents to at least have had that possibility. Suppose he had lingered for a day or two after respiration was withdrawn, gasping and fighting for breath before he died? How is that preferable to an injection that peacefully ends his life?

Well, the stories continue to accumulate explicitly or implicitly attacking my suggestion that euthanasia might be the most merciful choice in such cases. Here are a few articles, with excerpts below them (click on screenshots to go to article):


“Does Coyne really believe that we should treat humans like dogs and cats?” Dr. Richard Weikart, a professor at California State University and author of “Hitler’s Religion: The Twisted Beliefs That Drove the Third Reich,” wrote in a column for Evolution News.

“Ultimately, Coyne doesn’t think humans are any different from other animals, and this justifies euthanasia,” National Review columnist Jeff Cimmino wrote.

“Unfortunately, Coyne has a platform to teach students at a respectable university. One can only hope that his students see through and reject his misguided, poorly constructed arguments.”

I don’t even have a platform to teach students: I’m retired and am not allowed to teach any longer. You’d think Newsmax would at least check on this. And of course I’ve never even broached this topic in my introductory evolution course or any graduate or undergraduate course I’ve taught.

Comparison to Hitler’s program are rife, but there is not a chance in the world that any Western country would permit the kind of euthanasia that happened even at the beginning of the Reich’s extermination program. (No relatives, for example, were even asked, and were often lied to about what happened.)

Surprisingly, the Daily Caller‘s piece is straightforward reporting with no implicit editorializing:

Coyne cites Princeton University philosopher Peter Singer and argues that such newborns’ lives should be terminated not only with the withdrawal of care, but also via injection, provided the doctors and parents’ consent.

“After all, we euthanize our dogs and cats when to prolong their lives would be torture, so why not extend that to humans?” reasons the professor. “Dogs and cats, like newborns, can’t make such a decision, and so their caregivers take the responsibility.”

Coyne believes that religion distinguishes between humans, cats and dogs, deeming the former group “special.” He believes that “when religion vanishes, as it will, so will much of the opposition to both adult and newborn euthanasia.”

The Daily Caller News Foundation reached out to Coyne and the University of Chicago for comment, but received none in time for publication.

In contrast, the Right-wing National Review was outraged:

The evolutionary biologist, Jerry Coyne, writes a blog entitled, “Why Evolution is True.” One would think that by choosing that title, Coyne should restrict his discussions to questions of science that touch on questions and explanations about how and why life changes over time.  But Coyne — as many Darwinists do — takes the question beyond science, and extrapolates evolutionary theory into questions of morality, philosophy, and ethics. And now, he is promoting the propriety of infanticide. [JAC: I said NOTHING about evolution, and my views don’t derive from evolution at all.]

. . . Coyne’s odious advocacy is the logical outcome of accepting the following premises: That human life does not have unique value simply and merely because it is human, and; That eliminating suffering is the overriding purpose of society — allowing the elimination of the sufferer. Many scientists bemoan the fact that so many people refuse to accept evolution as a fact. Without getting into that controversy, perhaps they would be better off ruing the fact that ever since Darwin published The Origin of Species, so many of the promoters of that view also couple it with anti-humanism and a moral philosophy that was judged a crime against humanity at Nuremberg.

There’s the Nazi comparison again, as well as a gross distortion of my views. And note that this magazine, which I thought was respectable, avers that whether evolution is true is a “controversy.” Note to National Review: are you really going to argue that there’s some doubt about whether evolution happened? I wouldn’t dig my trench there were I you!

More excoriation came from the site of Milo Yiannopoulos, a man whose right to speak I’ve defended several times. And I defend his right to criticize me, even using a misguided and kneejerk rejection of euthanasia. The piece doesn’t say much, but does include some feedback from Twitter. I’ve included a few tweets.

Assisted suicide? That can’t even happen in infants!!!!  Here are some tweets:

I want to ask these people again: if you had an infant who was suffering with a terminal condition, and might live with that suffering for days or even months, and that death after suffering was almost certainly the outcome, why would you prefer it to suffer instead of ending its life swiftly and painlessly? What is the point?

And, of course, many of these sites, as well as their readers, didn’t even consider the nuances and qualifications I discussed about the idea of infant euthanasia. Their attitude was this:

Readers’ wildlife photos

July 30, 2017 • 8:00 am

Reader Danish Meman sent some lovely photos, many in black and white, of animals in zoos. His notes are below, and I’ve given his IDs of the animals:

All of the photos presented here come from a larger set of photos taken at various zoos in the UK and USA. I know that people feel strongly about the existence of zoos and the treatment of animals within them, but I still think they serve a purpose. Most notably, they introduce adults and children to animals they might never get to see in the wild. For instance, I don’t have the resources or ability to venture to Africa to view lions and elephants in their natural habitats. Moreover, the best zoos are invested in conservation and education, which, hopefully, helps foster appreciation for the natural world and related careers.

As far as the photography goes I enjoy trying to capture the personality of these animals, which is why the majority of these photos are in black and white. I wanted to strip away everything else and make the animal the focal point of the viewer’s attention. My hope is for people to connect with the creatures in the photos and imagine a conversation, story or encounter with them.

In my case, I saw the animals live while taking these photos so I already have a story for each of them. For instance, I recall the African Elephant looking melancholy as it was led away from the crowds after being fed. Similarly, I remember how the chimpanzee smiled at the camera, at just the right moment, as it was playing with a flower.  By contrast, I think the personality of the birds is contained in the colors of their feathers and how they brighten their surroundings.

For those interested, all the photos were taken with a Nikon D7100 and 18-140mm Nikkor lens. Also, the photos were taken at the Colchester Zoo (England,UK), Edinburgh Zoo (Scotland,UK), Jungle Island (Miami) and the Miami Zoo (Florida,USA). I hope you enjoy the photos as much as I enjoyed taking them.”

African elephant (Loxodonta africana):

African lion (Panthera leo):

American Flamingo (Phoenicopterus ruber):

Black-and-White Ruffed Lemur (Varecia variegata):

Blue Throated and Scarlet Macaws (Ara glaucogularis & Ara macao):

Galápagos Tortoise (Geochelone nigra):

Green Iguana (Iguana iguana):

Indian Rhinoceros (Rhinoceros unicornis):

Koala (Phascolarctos cinereus):

Macaw (Ara sp.):

Meerkat (Suricata suricatta):

Red Panda (Ailurus fulgens):

Reticulated Giraffe (Giraffa camelopardalis reticulata):

Sun Conure (Aratinga solstitialis):

West African Chimpanzee (Pan troglodytes verus), female:

West African Chimpanze:

Sunday: Hili dialogue

July 30, 2017 • 7:00 am

Good morning! It’s Sunday, July 30, 2017, and all sane people are still in bed. The rest of us, well, we write about cats. It’s National Cheesecake Day, one of the finest desserts known to H. sapiens. I prefer mine plain, but will tolerate it with cherries on top (but nothing else). It’s also International Friendship Day, but that was founded (naturally) by Hallmark Cards, so let’s ignore it and celebrate our friends on, say, December 30 instead.

It was a terrible week for Donald Trump, and I hope all those people who voted for him are thinking twice. On top of that North Korea launched yet another ballistic missile, and soon they’ll be able to hit the U.S. with nukes. Professor Ceiling Cat predicts two years at max, and there’s absolutely nothing we can do about it.  Let us hope that Trump doesn’t start a war over this, as millions would die.

On July 30, 1619, the first representative governing body in the Americas met; it was the House of Burgesses in Jamestown, Virginia.  On this day in 1962, the Trans-Canada Highway was opened, and three years later Lyndon Johnson signed the Social Security Act of 1965 into law, establishing Medicare and Medicaid. OMG–socialized medicine! In the US! On this day in 1966, England won the FIFA World Cup, defeating Germany 4-2 in extra time. That, fifty-one years ago, was the last time England won, so for you Brits, here’s a recap:

Exactly five years after that, astronauts David Scott and James Irwin, on the Apollo 15 Mission landed on the Moon with the first Lunar Rover. “Falcon”.  And on July 30, 1975, Jimmy Hoffa disappeared from the parking lot of a Detroit restaurant, and was never heard from again–he was presumably whacked.

Notables born on this day include Emily Brontë (1818), Henry Ford (1863), Casey Stengel (1890), Henry Moore (1898), Peter Bogdanovich (1939), Patricia Schroeder (1940), and Paul Anka (1941). Those who died on this day include William Penn (1718), Otto von Bismarck (1898), Claudette Colbert (1996), Ingmar Bergman (2007), and Lynn Anderson (2015). Meanwhile in Dobrzyn, Hili is hankering again for fresh fowl:

Hili: Either I’m imagining it or there is a nest.
A: Yes, but it’s been empty for a long time.
Hili: I, too, was afraid of that.
In Polish
Hili: Albo mi się zdaje, albo tam jest gniazdko.
Ja: Tak, od dawna jest już puste.
Hili: Też się tego obawiam.
And your science lesson today: an insect that shows both Batesian mimicry and convergent evolution. This is not a wasp but a mantisfly, in the order Neuroptera along with lacewings and antlions. It’s not at all closely related to true mantids (e.g. the praying mantis), which are in a different order (Mantodea), but they’ve independently evolved a convergent pair of forelegs. And the color and appearance of this mantisfly mimics that of wasps, almost certainly to fool predators. Thanks to Matthew for finding the tw**t.