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.
In a cartoon called “The Tao of Tommy: Budding Apologist Edition“, Reader Pliny the in Between presents a self-aggrandizing version of the familiar (and flawed) Ontological Argument:
I think that the kid, though, is really “Billy,” a budding William Lane Craig. However, there’s an unstated premise in the argument: “my happiness must necessarily be instantiated in this world.”
From The Colossal comes a great post with amazing photos of pinned insects, and the method used to take them will surely interest the photographers in the audience.
First, a few photos, which are in much lower resolution than the original. Let me add that these pictures, taken by Levon Bliss, will be on exhibit at the Oxford Museum of Natural History from May 27 until October of this year. If you’re in Oxford, by all means see it.
First, a few photos:
This video tells you what you need to know about how they were made. Hint: they weren’t single images, but composites of thousands of them, taken by a camera that moves only a few microns between shots:
And a gif showing how they make large prints. Such images of course require that everything be in focus.
h/t: Jeremy
If you haven’t been living in Alma Ata for a decade, you’ll know about the classified 28 pages of the bipartisan Congressional report on 9/ll. These pages have been kept from the public, and nearly everyone else, for 13 years, as they probably implicate Saudi Arabia in the terror attacks. So far, the only people who have had access to the 28 Pages are members of Congress, who can read them in an isolated room—without taking notes. Congressional aides aren’t allowed as substitutes.
It’s not clear exactly what’s in them, nor how high in the Saudi government the accusations extend, but there is no longer a reason to keep them secret on grounds of national security: the excuse that’s kept them classified all this time.
There’s some information from people who have read them, however. As the Independent reports:
New York Senator Kirsten Gillibrand, who has read the report, and Senator Bob Graham, who co-chaired the joint congressional inquiry, both believe that the 9/11 victims’ families deserve to read the report before president Obama visits the Middle East on 21 April.
Mr Graham told CBS News’ “60 Minutes” show that the report outlines a network of people that supported the hijackers while they were on the West Coast and helped them to enroll in flight school.
Questioned on whether that network included the government, rich people and charities, the Senator replied: “All of the above”.
And from another report in the same paper:
Two Congressmen, both of whom have seen the secret document, are behind the bipartisan motion for declassification. Stephen Lynch, a Massachusetts Democrat, held that the report offers evidence of links between “certain Saudi individuals” and the terrorists behind the 2001 attacks. Walter Jones, a Republican, said it also sheds light on why President Bush was so opposed to publication : “It’s about the Bush administration and its relationship with the Saudis.”
Some of the relatives of 9/11 victims want to sue those Saudis who might be responsible, and the Saudi government has threatened economic reprisals towards the U.S. if Congress passes a bill allowing such lawsuits. Since the Saudi government knows perfectly well what happened, this is a bit worrisome. At any rate, sources in the Obama administration suggest that all or part of the redacted 28 pages may be released by the summer. It’s time to do this now, for the excuse that those pages “endanger U.S. security” is no longer credible. It looks really bad for a Democratic administration to perpetuate such a coverup.
I’ve posted a few times about Malia Bouattia (e.g., here), the new president of Britain’s National Union of Students. Bouattia appears to espouse a double standard towards Israel and Palestine, completely demonizing the former and excusing all execrable acts by the latter. She’s even justified the Palestinian “resistance” (code for “killing Israelis civilians”), arguing that it works better (at what?) than do nonviolent methods. Here’s one of her quotes I gave in an earlier post, incorporating the classic anti-Semitic trope of “Zionist-led media outlets.” Shades of the Elders of Zion!:
“The notion of resistance has been perhaps washed out of our understanding of how colonised people will obtain their physical emancipation…With mainstream, Zionist-led media outlets …resistance is presented as an act of terrorism.
. . . To consider that Palestine will be free only by means of fundraising, non-violent protest and the Boycott, Divestment and Sanctions movement is problematic… My issue is that whilst at time it’s tactically used, or presented as the non-violent option, it can be misunderstood as the alternative to resistance by the Palestinian people…”
Since Bouttia’s election, and subsequent strong criticism for her extreme anti-Zionist views, she’s been frenetically walking back her earlier statements, claiming she was misunderstood. I strongly doubt that: I think she’s trying to retain her position and build up a good reputation. We shall see.
I’m not sure who is interviewing Bouattia in the first video below, but that interviewer presses hard on Bouattia’s views. But the NUS President simply refuses to answer the question of whether Israel should be allowed to exist (the interviewer asks her three times and then gives up).
And then, when asked whether she condemns Palestinian violence, Bouattia says, “It’s not for me to condemn Palestinian violence.” Instead, she says she supports international law, claiming that people under that law have a right of self-defense when attacked.
She’s right there, but some of the Palestinian violence construed as “self defense” is as much (or more of) a violation of international law as are Israel’s actions, including the rampant car and stabbing attacks on Israeli civilians, the firing of rockets into Israel, aimed at civilians, from civilian areas in Gaza, and so on. What’s legal under international law is Palestinian resistance against military installations, soldiers who are armed, soldiers in combat and so on. Killing women, children, civilian men and even soldiers asleep on a bus (yes, a Palestinian teenager did this as well), whether through suicide bombing or stabbing, certainly violates international law. Is Bouattia ignorant of that?
Now Israel’s behavior, particularly under Netanyahu, has been execrable, showing no movement toward the only possible solution: a two-state solution with withdrawal from the West Bank. One can also make a case that occupation of that area is a violation of international law. But Bouattia is blaming only one side, uttering the disingenuous weasel words, “It is not for me to condemn Palestinian violence.” What does that even mean? Who should condemn it if not her—particularly since she’s so willing to condemn Israel?
I will give this woman a chance as NUS President: perhaps she realizes that she has to be more conciliatory as an NUS leader (see second video below). But statements like that give me no confidence in either her sincerity or her leadership ability. Yes, her views will appeal to the bulk of her student constituents who despise Israel, but her justification for Palestinian “resistance” against Israeli civilians (some of which surely disagree with their government’s policy), and her use of the code word “Zionist”, make me wary:
Here’s a video of a debate between two students about her views, taken from Daily Politics on April 25. The president of the Sheffield University Student Union claims that Bouattia has suddenly become more open-minded and more willing to listen to all her constituents, but the interview above casts doubt on that.
On the Channel Islands, 12-70 miles (20-113 km) off the Pacific coast of southern California, live six subspecies of the Channel Island Fox (Urocyon littoralis), a dwarf species that is a close relative of the gray fox living on the mainland (U. cineroargenteus). Genetic data suggest that these foxes have been isolated from the mainland species for about 9000 years, possibly brought to the islands by Native Americans who may have considered them sacred “spirit animals.”
Four of these subspecies are officially endangered, as their population sizes are fairly low—probably due to attacks by golden eagles and infection with canine distemper. They’re all holding on, though, and conservation efforts are increasing the population size. For now we don’t have to worry much about them.
These are adorable little animals, fully worthy of being Honorary Cats™. In contrast to the mainland species, whose individuals weigh between 8 and 15 pounds, these foxes have become dwarfed, weighing, according to a New York Times article by Carl Zimmer, as little as 2.3 pounds. For comparison, an average, non-obese house cat weighs between 6 and 10 pounds, so these foxes weigh about a third as much as a normal cat (or a fifth as much as Hili)! Subfossils show that the foxes were fully dwarfed by 7000 years ago, so it took only about two millennia for the small size to evolve.
Here’s a photo:
Many animals that invade islands become dwarfed (“island dwarfism“), and for reasons we don’t fully understand. I suspect it has something to do with a dearth of food: if you’re big, you’re going to require lots of food to survive and reproduce, and may do better if you have genes for small size. But there are other explanations (see the link). Another example of the phenomenon are the famous dwarf elephants—shorter than a human—that lived on islands in the Mediterranean during the Pleistocene. (Curiously, the Channel Islands also harbored dwarf mammoths.)
And here’s a video showing their size and the adorableness of one subspecies, along with a description of how biologists are trying to save it. Do watch it, as it’s a good summary of the subspecies’ situation.
I’m bringing up this species because it’s the subject of a new paper by Jacqueline Robinson et al. in Current Biology (reference and link below, I don’t think there’s a free download). The paper shows that all six subspecies lack genetic variation; in fact, one of them is the vertebrate having the smallest amount of genetic variation ever observed. This finding belies the common conservationist notion that low genetic variation is always a warning that a species is endangered. And that notion itself comes from evolutionary theory: without genetic variation, you can’t respond to selective pressures such as new diseases, environmental changes, and so on; and if those pressures sufficiently reduce mortality or reproduction, a species with very low genetic variation might go extinct.
Here are the islands sampled:
The researchers did full-genome sequencing of every animal (something we only dreamed about two decades ago), and did it on one fox from each island, except for two foxes from San Nicolas Island as well as one mainland gray fox. Here’s the phylogeny of the foxes taken from that molecular data. The two foxes from San Nicolas were almost genetically identical, which I’ll discuss below. One thing this phylogeny shows is that the Channel Island fox subspecies are all more closely related to each other than to the Gray Fox putative ancestor. What that means (unless there was gene flow between island fox populations) is that all the island foxes descend from a single ancestor that got to one island, and then spread to the other island. If each island was colonized independently by a gray fox migrant, you wouldn’t get a phylogeny that looked like this:
The remarkable finding of this study was the extremely low genetic variation in all these subspecies, particularly in the San Nicolas subspecies, which had the lowest genetic diversity observed in any outbreeding (sexually reproducing) species. The authors call this phenomenon “genomic flatlining”, part of the paper’s title.
How, you might ask, can you estimate the genetic diversity of an entire subspecies if only a single individual was sampled? We can estimate this because we can look at both copies of a gene in a whole-genome sequence, and if they’re identical in DNA sequence, that implies that the entire species is depauperate in genetic variation. After all, each individual has two copies of each gene—getting one copy from its father and one from its mother. If both copies are the same, that implies that the population as a whole is pretty much genetically depauperate, with every individual having the same DNA sequence.
The different subspecies, however, were genetically different from each other, as expected given their morphological and color differences.
The San Nicolas fox had an amazingly low diversity, with the two individuals not only being homozygous at most DNA sites, but the two individuals were, as expected, nearly genetically identical to each other. They were the equivalent of identical twins, or clones, as the whole population must be. The heterozygosity of this population (calculated as π, or nucleotide diversity) was about 0.000016, with, on average about only 1.6 DNA sites in 100,000 showing a difference between maternal and paternal genes.
Here’s a figure showing the nucleotide diversity of various outbreeding species, with asterisks next to the fox subspecies. Letters show other species, including some, like the cheetah, once suspected to be endangered because of low genetic diversity. Note that the X axis (nucleotide diversity) is on a log scale, and the bars represent 159 outbreeding species in total. The foxes are way low, with the San Nicolas subspecies off the scale. For humans the value of pi is about 0.001, not far from the Santa Catalina fox, and for the fruit fly Drosophila π is about 0.01.
The other finding from this survey is that the fox populations, with San Nicolas again in the extreme, have high numbers of DNA sites where the effect on the individual is putatively bad: these include sites where any new substitution will affect the protein sequence (usually for the worse), and loss-of-function genes, for which the island populations simply don’t produce a protein where they should. There’s no direct evidence, though, that any of these changes are deleterious to survival and reproduction.
All island populations showed elevated levels of putatively deleterious genes in the genome. Population-genetic theory shows that small population sizes can, though the phenomenon of genetic drift (random changes in allele frequencies due to sampling effects), increase the frequency of genes that are bad. The rule of thumb is that if the population size is lower than the reciprocal of the selection against an allele, the allele will act as if it had no effect on fitness at all, and could reach high frequency by genetic drift. For example, a gene producing a reproductive deficit of 1% (0.01) compared to its alternative would be effectively neutral in populations smaller than 100 (1/0.01). And drift was certainly a possibility in this species, since the level of heterozygosity, as well as direct observation in recent years, suggested that some fox populations were once down to about 10-100 individuals.
The upshot: Despite low population size, these fox subspecies are doing well, although conservationists warn us that such low levels of genetic variation can be harmful and promote extinction. It may be that the conservation efforts, combined with an environment that is fairly benign, ameliorate the effects of low genetic variation.
And did I mention that these foxes are tame? As Carl Zimmer noted in his piece:
“They’re like dodos,” Dr. Wayne [director of the study] said in an interview. “They have no notion of human fear. You can just put them in your lap.”
I’d love to do that!
_________
Robinson, Jacqueline A., D. Ortega-Del Vecchyo, Z. Fan, Bernard Y. Kim, Bridgett M. vonHoldt, Clare D. Marsden, Kirk E. Lohmueller, and Robert K. Wayne. Genomic Flatlining in the Endangered Island Fox. Current Biology, in press. doi:10.1016/j.cub.2016.02.062
Reader Alex MacMillan sent some photos of garter snakes, as well as a video he took. As you might know, garter snakes (and many others) overwinter underground in shelters called hibernacula, often congregating in large masses to shelter them from the elements during winter. Alex’s notes:
These photos and the video are of Eastern Garter Snakes (Thamnophis sirtalis sirtalis) emerging from a hibernacula which appears to be a water drain or pipe of some sort. This occurred in London, Ontario on April 16th of this year when we had a period of unseasonable warm (mid 20’s Celsius) weather.
After leaving the hibernacula T. sirtalis will form large mating balls as many males compete for a chance to mate with the larger females.
Snakes in a drain!
An emerging female:
His video:
Reader Anne-Marie Cournoyer has a daily standoff in her Montreal yard between a gray squirrel (Sciurus carolinensis) and a grackle (Quiscalus quiscula):
Almost every day this week, Petit Ami [the rodent] and Mister Grackle chase each other in our backyard. There is food in different places, but bothering each other for the same spot seems more interesting. Ahhh testosterone! I was lucky to catch them in action!
I didn’t really expect people to subscribe when I called yesterday for a Big Push to get subscribers over the magic 40K mark, but people responded, with over 150 subscribing. We now stand above the threshold:
Sadly, I couldn’t ascertain who was the 40,000th subscriber, but thanks to all you “amazing” people for following this “blog”.
Hili: Are you taking pictures when I need help?A: It will be a picture of a cat in need.
Hili: Robisz zdjęcia, kiedy ja potrzebuję pomocy?
Ja: Jasne. To będzie zdjęcie kota w potrzebie.
In Wroclawek, Leon shows some unexpected ingenuity:
Leon: When a cat wants to climb a fence he must weave it himself.
And in Winnipeg, Gus is blissed out in the Spring sunshine. Look at that face, too!
