Monday: Hili dialogue (and Leon lagniappe)

November 2, 2015 • 5:01 am

Monday has come again, has come again, and in Virginia the chinkapins are falling. Professor Ceiling Cat (Emeritus) has a dicky tummy today (should I change my name to Richard Tummy?), and so I might rest a bit, meaning posting may be light today. I’ll do my best.  Meanwhile in Dobrzyn, Hili has been disturbed while sleeping with her hot water bottle:

Hili: What did you want?
A: Nothing, I’m just taking pictures.

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In Polish:
Hili: Co chciałeś?
Ja: Nic, robię tylko zdjęcie.

 

*******

And in Włocławek, Leon is helping Elsbieta hunt mushrooms from his comfortable perch. I guess he’s tired of the leash.

Leon: See what a beautiful mushroom I found for you?

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Lip-reading the first Democratic debate

November 1, 2015 • 2:30 pm

On August 23 I posted a hilarious lip-reading take on the first Republican debate, and now we have one from the Democrats. It’s pretty good, though I think the Republican one is a bit funnier. Maybe it’s my bias, but Clinton’s genital-shooting drawing can’t match Ben Carson’s song “One Wittle Wee-Wee”(4:12 here).

h/t: Blue

Krauss on entanglement

November 1, 2015 • 1:00 pm

Doesn’t the New Yorker need someone to write about evolution as well as cosmology? Once again, I’m both impressed by and jealous of Lawrence Krauss’s performance at that venue, and this week he writes about the new physics experiment that pretty much verified the idea of quantum entanglement and nonlocality. The piece, “Tangled up in entanglement.”

I like it when scientists rather than science journalists write about such things, for you know that at least they understand what is going on. (Don’t get me wrong: not all science journalists are ignorant of their subject: Faye Flam and Carl Zimmer are notable exceptions.). And Krauss does about as good a job as possible of explaining entanglement to the layperson. When I say “as good as possible,” I mean that entanglement is such a bizarre, counterintuitive concept that understanding it intellectually is not the same thing as fully grasping its bizarreness, which simply can’t be done in words.

I’ll leave it to you to read Krauss’s very clear description of the experiment, and why it doesn’t mean that we can send information at superluminal speeds. I’ll just put in one bit in which Krauss disses the misuse of quantum mechanics:

Entanglement is so spooky that it’s tempting, when thinking about it, to draw nonsensical conclusions. Deepak Chopra, for example, keeps implying that quantum mechanics means that objective reality doesn’t exist apart from conscious experience. The truth, however, is that consciousness is irrelevant to the act of measurement, which can be done by machines, or even by single photons. If consciousness matters, then the inner thoughts of the experimenter who operates the machines would also have to be reported when we write up the results of our experiments. We’d need to know whether they were daydreaming about sex, for example. We don’t. The machines can record data and print it out whether or not a person is in the room, and those printouts, which behave classically, don’t change when the humans come back.
Similarly, last week, the Pulitzer prize-winning writer Marilynne Robinson published an essay in which she challenges the nature and relevance of modern science. The essay argued that entanglement “raises fundamental questions about time and space, and therefore about causality.” She went on to say that this called into question the ability of science to explain reality as a whole. It’s easy to understand how Robinson arrived at this incorrect idea: when a measurement of one electron here can instantaneously affect the measurement of another electron on the opposite side of the universe, faster than the speed of light, it does seem as though causality has been thrown out the window.
Now I will predict—and I’m doing this without looking—that Deepity Chopra will already have attacked Krauss on his site. But forget the niggling and carping of the risible Chopra. What’s amazing is that nonlocality exists at all: that getting information about one electron a gazillion miles away form its entangled twin will affect the state of that electron instantly. This now appears to be the case, but I still can’t get my head around it.

The “coywolf”: a new species of canid?

November 1, 2015 • 11:00 am

At least three readers have pointed me to articles, one in The Economist and the other in Raw Story, arguing that a new species of canid, the “coywolf” (also called a “wolfote”) is emerging before our eyes as wolves (Canis lupus), domestic dogs, and coyotes (Canis latrans) all hybridize to form a distinct entity.

Such “hybrid speciation” is indeed possible, and has been seen several times in animals and many times in plants. (Wikipedia gives a good summary of the facts, and a longer treatment appears in Chapter 9 of Speciation, the book I wrote with Allen Orr. There’s also a short but useful paper by Richard Abbott and Loren Rieseberg, free online, here.)

One way is “diploid (or “homoploid”) hybrid speciation,” which is what’s supposed to be happening in the coyowolf. In that case, two plants or animals hybridize, and the hybrid undergoes genetic change via natural selection, a change that involves sorting out the different genes from the two parental species into a novel mixed genome. If this new genome has features that prevent its carriers from reproducing with the parental species (“reproductive isolating barriers”), it could form an interbreeding unit that would be considered a new species because its members mate only with each other, and not with the two parental species.

This appears to have happened in some fish, butterflies, and birds, as well as plants, but it’s not common. That’s because hybrids between existing species are usually at a fitness disadvantage, and also would likely be “mated to death” because a rare hybrid would be more likely to mate with one of the parental species in the area than to find other rare hybrids to mate with. Also, it’s unlikely that a mixed genome from two parents would undergo genetic change that could produce a genome producing reproductive barriers from those parents.

But that could occur if the new hybrid species has different ecological requirements from those of both parents. Such a difference might segregate the hybrid into a new area where the parents don’t occur, allowing it to survive and reproduce. After all, a single hybrid individual is not a species, which most evolutionists recognize as a population of interbreeding individuals that has barriers to gene exchange with other populations. A hybrid species, then, has to comprise a lot of individuals that breed with each other, but not very much with the parental species.

Indeed, new diploid hybrid species of plants often show unique ecological requirements that sequester them in a new habitat, and give them evolutionary “breathing room” to reproduce with each other, and evolve further changes that restrict gene flow from the parental species. The work of Loren Rieseberg and his colleagues on diploid hybrid sunflowers, some of which are restricted to extreme habitats like sand dunes, is perhaps the best example of this. Below is a photo of a new species of sunflower, H. anomalus (middle) which, as genetic analysis shows, formed after hybridization of the parental species (left and right). As you see, the new species also occupies a novel new habitat: sand dunes:

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Another form of hybrid speciation is more common: polyploidy. In such cases, new species form by hybridization of two distinct species, but the hybrid is largely sterile because the chromosomes of the hybrid fail to pair (this is a requirement for formation of gametes). But in some cases the semisterile can produce offspring in which its entire genome is doubled, so that each individual now has a full genome from each parental species. The chromosomes in such a “tetraploid” can pair properly, and it can be fertile.

This form of speciation, called “allopolyploidy,” still faces the twin problems of hybrid speciation: the need to form an interbreeding population, and the need for some kind of ecological segregation to prevent the new tetrapoloid from being mated to death with nearby parental plants, producing sterile “triploid” offspring that doom the hybrid to extinction. But this form of hybrid speciation is fairly common in plants. Using data from Sally Otto and Jeannette Whitton at the University of British Columbia, Orr and I estimated that roughly 7% of new speciation events in ferns and 2-4% of speciation events in flowering plants involve allopolyploid speciation. Why this kind of speciation is much rarer in animals than in plants is still unresolved, but there are various hypotheses you can find in our book.

That’s just background on how new species can form by hybridization between existing species. Now what about the coywolf?

The following information is taken from the Economist article and some genetic from Wikipedia (the Raw Story appears to be a condensed version of the Economist’s article). I’m going by that information since a scientific paper on the coywolf doesn’t seem to have yet been published.

  • Habitat destruction and the killing of wolves has been forcing coyotes and gray wolves (which are closely related: about 3.3 million years diverged) into closer proximity with each other and with human-owned d*gs, leading to hybridization between all of three canids and the production of animals with mixed genomes. Wolf-coyote hybridization is also promoted by the increasing rarity of wolves in the eastern U.S., so that they see coyotes as potential mates. (I call this the “prison effect”.) The fact that hybrids can include coyote, dog, and wolf genomes has been verified by genetic analysis.
  • About 10% of the coywolf genome comes from domestic dogs, 25% is gray wolf, and the other 65% is from coyote. I have no idea how variable this mixture is among coywolf individuals.
  • The “species” (we’ll get to whether it really is a species shortly) shows a mixture of morphological traits of coyotes and wolves. As The Economist notes:

“At 25kg or more, many coywolves have twice the heft of purebred coyotes. With larger jaws, more muscle and faster legs, individual coywolves can take down small deer. A pack of them can even kill a moose.

Coyotes dislike hunting in forests. Wolves prefer it. Interbreeding has produced an animal skilled at catching prey in both open terrain and densely wooded areas.”

Here’s a picture of one; you can see more in the video below:

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  • “Coywolves” are common, and appear to inhabit areas that aren’t much frequented by their two parental species:

“Purebred coyotes never managed to establish themselves east of the prairies. Wolves were killed off in eastern forests long ago. But by combining their DNA, the two have given rise to an animal that is able to spread into a vast and otherwise uninhabitable territory. Indeed, coywolves are now living even in large cities, like Boston, Washington and New York. According to Chris Nagy of the Gotham Coyote Project, which studies them in New York, the Big Apple already has about 20, and numbers are rising.”

Now for the million-dollar question, at least for me: Is the coywolf a new species, as many articles have implied? Indented quotes are from The Economist; my own comments are flush left. To answer this question, we have to discuss what evolutionists mean by “species”, and of course there are dissenters.

Whether the coywolf actually has evolved into a distinct species is debated. Jonathan Way, who works in Massachusetts for the National Park Service, claims in a forthcoming paper that it has. He thinks its morphological and genetic divergence from its ancestors is sufficient to qualify.

But morphological and genetic divergence from ancestors is not sufficient, for there are many sterile hybrids that occur in nature that are morphologically distinct from their ancestors (they’re usually intermediate), and also genetically divergent (they have genes from two or more ancestors), but they’re not species because they don’t form an interbreeding population that is reproductively isolated from the parents. It’s the bit in italics from the last sentence that must be satisfied before we can affirm that coywolves represent a new species. This, indeed, is pointed out by the Economist:

But many disagree. One common definition of a species is a population that will not interbreed with outsiders. Since coywolves continue to mate with dogs and wolves, the argument goes, they are therefore not a species. But, given the way coywolves came into existence, that definition would mean wolves and coyotes should not be considered different species either—and that does not even begin to address whether domestic dogs are a species, or just an aberrant form of wolf.

We needn’t concern ourselves whether domestic dogs are a species, as they are an artificially selected variant of the wolf and their reproductive isolation isn’t tested in a purely natural setting.  But the fact that wolves and coyotes produce occasional fertile hybrids should NOT be taken to mean that they’re the same species, for that hybridization was very rare in the natural environment before humans began degrading it. Many “good” species, like the polar and grizzly bears, can hybridize when their habitat changes, which shows that they were good species whose reproductive barriers at one time involved ecological differences that kept them geographically segregated. When the environment changes, “good species” can become a hybrid swarm. As Orr and I argue in Speciation, the production of a few hybrids doesn’t completely negate the concept of a species, and many distinct species do hybridize occasionally, sometimes producing fertile offspring (this happens in ducks). But often hybrids are sterile, so species remain distinct, and even fertile hybrids might be inviable or have difficulty finding mates. (That’s the case for ducks, I think: hybrid ducks are unattractive to females of the pure species who have a search image for a proper mate.) The Economist goes on:

In reality, “species” is a concept invented by human beings. And, as this argument shows, that concept is not clear-cut. What the example of the coywolf does demonstrate, though, is that evolution is not the simple process of one species branching into many that the textbooks might have you believe. Indeed, recent genetic research has discovered that even Homo sapiens is partly a product of hybridisation.

“Species” is a concept invented by human beings, but that doesn’t mean they’re not real and meaningful entities. The concept of a “star” was also invented by humans! Remember that stars can sometimes fuse together, or destroy each other.

Homo sapiens, for example, is a meaningful entity, and, at least now, doesn’t blur into other primate species. We do have genes from Neandertals and Denisovans, but those were probably members of our own species, as the hybrids were fertile; they were equivalent to the subspecies of animals and places recognized by biologists. Indeed, both Denisovans and Neandertals are usually placed in the same species as modern humans: H. sapiens.

When you look at the birds in your neighborhood, you won’t find any difficulty placing any of them in its group: pigeons, cardinals, starlings, sparrows, house finches, and so on. If species weren’t in some sense real entities, nature would be continuous and different people would place species boundaries at different places. That doesn’t occur (see Chapter 1 of Speciation for a long discussion on the reality of species.) Further, studies have shown that in most groups, including plants, it’s not hard to identify discrete entities. Nature is simply not a continuum with the boundaries between “species” being completely arbitrary.

To be sure, there is some blurring. There has to be when new species are evolving from different populations of a single species, or when there’s occasional hybridization, or when reproductive barriers are breaking down, as they seem to be in coyotes and wolves in some locales. All we can say is that speciation is a process, which can culminate in entities that are completely unable to exchange genes (“good species”), but that during that process, some entities can be more or less “species-like,” depending on gene flow. We will sometimes be faced with a judgment call, but very often, as with our own species or with lions, we aren’t.

There’s more information in this nine-minute clip, calld “Meet the coywolf,” from a PBS Nature documentary that appeared earlier this year:

What’s the upshot?  Given the information that coywolves seem to be semi-social and breed largely with other coywolves, that they seem to inhabit an ecological niche different from their parental species, and that they’re genetically distinct from either parent in possessing a hybrid genome, I’d say that the coywolf is going through early stages of hybrid speciation similar to that which occurred in the hybrid sunflowers. Before I’d call them a new species, though, I’d want to know how often they breed with either pure coyotes or domestic dogs, and how homogeneous the coywolf genome is . If they comprise a variety of diverse admixtures of coyote, wolf, and dog genes, so that their genomes haven’t become relatively homogenous among individuals, I’d be less inclined to call them species.

But, in the end, at this stage the question is a semantic one, for the coywolves do exchange genes with dogs and wolves, so they’re not what I call “good” species.

What’s more important is that we’re seeing, in the human habitat, a new form of animal emerging, one that, by combining genes from different species, has developed traits that allow it to exploit a new ecological niche. This is precisely what happened in the sunflowers that are now considered different species. So we may be seeing a case of speciation in statu nascendi—in the process of being formed. Only time will tell if coywolves will become so distinct, and so homogeneous among themselves, that they’ll deserve their own Linnaean binomial. Because of that, it’s premature for The Economist and The Raw Story to say that “a new species is emerging right before our eyes.”

Mr. Deity on the incompatibility of science and religion

November 1, 2015 • 9:30 am

Reader jsp sent me this new Brian Dalton video, “Science and Religion are Mortal Enemies (Part I)”, saying it was “right up my alley.”  In fact it is, as it emphasizes one big difference between science and faith—the value of doubt and questioning—that I discuss in Faith versus Fact. Dalton’s correct in saying that it’s too narrow to argue that these areas are compatible simply because much of science doesn’t challenge what’s in scripture (the Bible, for instance, says nothing about the Krebs Cycle or quantum mechanics). But what science does  challenge is the existence of deities and the “truths” arrived at by religious “ways of knowing.” The questions we need to keep hammering on when we talk to religious people about their beliefs are twofold: “How do you know that?” and “How would you know if you were wrong”?

This all seems obvious to me, but it rankles those who want to be down with both science and the supernatural—having their faith and eating it, too. But merely pointing out this palpable discrepancy, as I’ve learned to my chagrin, is taboo, for even many atheists and skeptics bridle at criticizing people for beliefs that are both foolish and unevidenced.

Since this is Part I, I’ll look forward to other parts forthcoming. In the meantime, you can contribute to Dalton’s “Mr. Deity” and “The Way of the Mister” clips at his Patreon site.

 

PuffHo calls out celebrities for “racist” Halloween costumes

November 1, 2015 • 8:15 am

I guess the newest way to ban costumes is to use the phrase “we are people, not costumes”. That, at least, is what the PuffHo says about the outfits of Kylie Jenner and Nicky Hilton (sister of Paris), showing their Halloween costumes that depict, respectively, an Eskimo (“Inuit” to most people) and an “Indian princess.” The article, written by PuffHo Entertainment Editor Stephanie Marcus, is called “Kylie Jenner and Nicky Hilton wore some pretty offensive Halloween costumes this year“. The article’s text is indented.

I wouldn’t have even known what the costume below depicts, but Jenner’s first Instagram photo on the site labels this “Eskimo”. The PuffHo text:

Well, there’s always someone who shows up to a Halloween party in a racist or offensive costume — this year it was Kylie Jenner and Nicky Hilton.

On Saturday, Jenner shared a video of herself decked out in her “Eskimo” costume that she wore to a party on Friday night. Never mind the fact that “Eskimo” is generally considered a slur, the Inuit and Alaska Natives are real people, not costumes. 

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Meanwhile, Nicky Hilton apparently learned nothing from the time her sister Paris attended a Halloween party at the Playboy mansion dressed as a “sexy Indian.” The younger Hilton sister also doesn’t seem to care that Native Americans and First Nations are real people with a real culture and therfore not a costume, because she turned up to the Casamigos Tequila Halloween Party on Friday night in this:

LOS ANGELES, CA - OCTOBER 30: Nicky Hilton attends the Casamigos Tequila Halloween Party Brought to you by Those Who Drink It at a private residence on October 30, 2015 in Los Angeles, California. (Photo by Amy Graves/Getty Images)
LOS ANGELES, CA – OCTOBER 30: Nicky Hilton attends the Casamigos Tequila Halloween Party Brought to you by Those Who Drink It at a private residence on October 30, 2015 in Los Angeles, California. (Photo by Amy Graves/Getty Images)

For more racist Halloween costumes you’ll want to avoid this year, next year and all future Halloween parties, click here if you don’t have the common sense not to offend people already.

“Racist”? That seems a bit over the top to me. And if you click on the PuffHo link in the sentence above, you’ll be sent to another site showing now-verboten costumes, including a skeleton, a salacious nurse (whose costume is said to “objectify the profession”), and a hobo (forbidden because it mocks the homeless). I wasn’t aware that hobos, nurses, and skeletons (supposedly mocking those with eating disorders) were “races.”

It’ll be even worse next Halloween, mark my words.

The “we are people, not costumes” trope is an overly glib way to protect a group from “appropriation,” and could be used to cast aspersions on almost anything. (Hobos, really? Do they even exist any more?) When I wear my Indian clothes—and I rush to assure you that I mean Indian as from India, not Native American—would a resident of, say, Delhi, tell me that Indians are people, not costumes, and I’m stereotyping the entire subcontinent? (Indeed, if I were to go trick-or-treating as an adult, I’d probably put on a nice kurta pajama. But now I must get my candy other ways.)

I have to say that while I do consider some costumes offensive, as I mentioned yesterday (e.g., blackface, and perhaps Mexican banditos), there’s a group of Cultural Enforcers, like Stephanie Marcus, who sniff around everywhere calling out what they deem “offensive.” It’s almost as if they’re touting their own ideological purity by this kind of sleuthing. Such Leisure Fascists, who are constantly signaling their own virtue, annoy me.

Readers’ wildlife photographs

November 1, 2015 • 7:30 am

Let’s start with a photo of an American kestrel (Falco sparvinus) taken by Stephen Barnard in Idaho. These are among my favorite birds, as they are adorable pocket-sized falcons. Stephen’s comment:

My feeders are this guy’s lunch counter.

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And reader Mark Sturtevant sent some nice aphids, a hemipteran that you’ve probably encountered if you grow plants. Mark’s photos show both their commensals (ants) and a predator. Remember that aphids are in the insect order Hemiptera: the “true bugs.”

Here is another installment of aphid pictures. First, aphids are well known to earn the protection of ants by providing a steady supply of sugary waste which is secreted from the little spigots on their abdomen. Now, I know as much about identifying small ants as I do aphids, but I suspect this ant belongs to the widespread species known as the winter ant (Prenolepis imparis). The aphid herd it is tending may be Uroleucon sp. I hope to be corrected in case I am wrong with this identification. In any case, the winter ant is so named since it is active even in cold weather.

1Aphids n Ants1

Next is another group of aphids (possibly also belonging to the genus Aphis) that is being well protected by what I am pretty sure are ants belonging to the genus Crematogaster. This ant genus is pretty easy to recognize with its distinctive ‘gaster’(which is the main part of the abdomen).

2-2Aphids n Ants

Of course there are many aphid predators and parasites. Here is a brown lacewing larva (Micromus sp.) which is sucking the juices from what I think is Aphis neri. While I was taking pictures, this little killer nonchalantly walked up to its victim and impaled it.

3Brownlacewing

Finally, syrphid fly larvae (species unknown) are also commonly seen to lurk among aphids. I do not know the reason for the dead aphids.

Although aphids are tiny, it is always good to stop and have a look at the happenings in an aphid colony. I have never failed to see some sort of drama.

4Syrphid