I have landed

June 4, 2015 • 4:53 pm

The United Airlines flight was an hour late, they provide NO FREE SNACKS, and if you want to watch a movie during the four-hour flight to Vancouver, you have to pay $8! What a ripoff! I would have flown Southwest (free snacks, free bag check, friendly people) had they gone to Vancouver, but alas, I was stuck with Ripoff Airlines. At least I fortuitously received TSA Precheck status, so I breezed through security without even having to remove my boots, much less receiving the Ritual Goosing.

And at the other end, after waiting an hour in the Vancouver immigration line to show my passport (really, Candians?), Maryam Namazie and I, who arrived on nearly simultaneous flights, were met by a HUGE stretch limo, which was more like a rolling living room. One thing about the INR conferences is that they treat speakers really well, though I hate to think what kind of carbon footprint this left:

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Me at the other end (we photographed each other):

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I doubt that I’ll ever ride in a car like this again!

The next couple days should be a blast, for the INR conferences are well run, not overly crowded with events, so one can relax and chat with friends and attendees, and the noms are great.

Now if you’ll excuse me, I’ll spruce up and get ready for dinner at Vij’s Indian restaurant with Dr. Larry “Sandwalk” Moran. I will send reports on the talks and noms.

I noticed a Tim Horton’s in the airport for reference on my way to Toronto on Tuesday. What donuts are best now?

Time to talk about anything except the weather

June 4, 2015 • 2:00 pm

by Grania Spingies

Jerry said I ought to post the tweet I saw from @AstroSamantha yesterday, amusing for me because I live in Ireland; but possibly of no consequence to anyone else. I was aghast, as I really do not want to bore anyone to tears by talking about the weather of all things. Then he suggested that it might be time for an Open Thread anyway as he is currently on a plane and on his way to Vancouver.

Here’s the Tw**t. On a typical day, that sort of cloud cover stretches over Ireland. Sometimes it’s worse.

Hence this meme that was going around on Twitter too this week. So very, very true. And sad.

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On the subject of Neverland, has anyone actually read the book Peter Pan by J.M. Barrie, rather than the various Disney treatments of it? The book doesn’t extoll the virtues of childish imagination and spontaneity  quite as much as Disney would have us believe. Peter Pan is also self-centered, irresponsible and cruel – and a whole lot of fun at parties. He’s rather more complex and interesting than the rather flat daring hero that we see in the movie versions. Such, I guess, is the fate of all book to movie adaptations. Unless, of course, Peter Jackson can be persuaded to try his hand at it, in which case we might get a trilogy out of it.

Feel free to discuss anything you wish in the comments below.

H is for Hawk

June 4, 2015 • 1:00 pm

I can’t recommend highly enough the new book by Helen Macdonald: H is for Hawk.  It is up there with J. A. Baker’s The Peregrine as one of my favorite books about nature, but Macdonald’s book is very different. While Baker’s is about observing wild peregrines near his home, and is entirely lyrical writing about nature (with a barely detectable undertone of sadness), Macdonald’s tells three stories at once. After her father dies (her memories are one of the stories), Macdonald falls to pieces, trying to find solace in training a goshawk (Accipiter gentilis) to hunt.  She had previous experience in falconry, but not with the notoriously unruly goshawk (she names hers “Mabel”), which, unlike peregrines, hunts low above the ground.

Along with her story, and that of Mabel, Macdonald recounts the life of author T. H. White, best known for writing The Once and Future King. White, too, trained a goshawk, but also had a contorted existence, much of which Macdonald analyzes in the work. White was a closeted gay with sadistic tendencies, and apparently worked out some of these through hunting with a bird.

Macdonald’s prose is impeccable: her life, White’s life, and the doings of her hawk are keenly observed. I am not sure how writers do this, but she, like many of the great ones, has the ability to analyze her life as she lives it, and then describe her feelings in luminescent prose. Like a painter, she sees things and has feelings that simply aren’t available (or describable) to the rest of us. The book is deeply engrossing and wonderful. If it has one fault, it’s that she seems to try too hard to tie everything together at the end, which seems a tad contrived. But it’s one of the best memoirs—if you can call it that—I’ve read in years, and I think nearly all readers here would like it.

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While we’re on goshawks, I’m combining this post with an old draft (I have nearly 900 drafts that I’ve never posted!) based on a piece about goshawks in March’s New York Times: “Nature’s fighter jets with flapping wings“. It shows the variety of flight paths that goshawks use to intersect with their prey, and there’s also a video, which I show below. The paper on which it’s based, from the Journal of Experimental Biology, can be found here (reference and link below), and I’ll let you read it for yourself. Here’s the video summarizing the authors’ findings:

Here’s a trained goshawk flying through holes of different size and shape. Notice how it uses its feet as support when flying:

Below is amazing video of a goshawk navigating through thick forest, taken with a camera mounted on the bird’s head. Goshawks are used to catch pheasants, rabbits, and other ground-dwelling prey; their hunting flights are short and often go through brush and forests:

Finally, here’s some classic goshawk hunting in Ireland. The hunters use a dog to flush the prey. Macdonald didn’t do that, but relied on either seeing the prey herself (Mabel was of course good at this when carried on a gloved hand) or flushing it while walking through the brush:

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Kane, S. A., A. H. Fulton and L. J. Rosenthal. 2015. When hawks attack: animal-borne video studies of goshawk pursuit and pre-evasion strategies. Experimental Biology: 218:212-222.

A miracle? Sawfish born of a virgin mother

June 4, 2015 • 9:30 am

It’s been known for a while that many species, including some vertebrates, can reproduce without sexual reproduction. But of course to observe this, one usually needs to keep animals in the lab and then see them produce offspring without ever having mated. But a new article in Current Biology by Andrew Fields et al. (reference below, abstract only at link) is the first report of vertebrates having done this in the wild.

First, a brief note. Biologists don’t really understand why animals have sex at all, for under most conditions an individual would leave more of its genes by reproducing parthenogenetically (without sex), than by reproducing sexually. If you bud off a diploid organism (one having all of your pairs of chromosomes) rather than producing an egg or sperm (having half your chromosomes) to fuse with another gamete, you leave an offspring having every one of your genes. Ditto if you simply produce an offspring from an unfertilized egg having all of your chromosomes rather than half.

If you have sex, however, you dilute your genetic contribution by half: the offspring has half of its genes from you, and half of its genes from your mate.

Thus, any gene that impelled you to reproduce parthenogentically would leave many more copies of itself than a gene that impelled you to reproduce sexually. In fact, it would leave twice as many copies, and would sweep through a population. The population would comprise only asexually reproducing individuals. This genetic deficit of having sex is called the “twofold cost of sex.”

But since the vast majority of non-microbial species have sex, why do they? They’re losing their genes by so doing. There must be a big advantage (at least twice that of being parthenogenetic) to explain the prevalance of sex.

There are several hypotheses, and some have empirical support; for example, the idea that reproducing sexually, by allowing you to mix your genes with those of other individuals, gives you a genetic flexibility to counter the evolution of other organisms, such as parasites, that are constantly adapting to parasitize you.  But the advantage of that must, again, be very large compared to the twofold cost of having sex. Another explanation is simply that an ancestral species did overcome that problem when evolving sexual reproduction, and once you reproduce sexually it’s just physiologically and developmentally very difficult to revert to parthenogenesis. (Humans, for example, can’t conceivably reproduce without sex—except of course for one mythical woman!)

One caveat: if you produce haploid offspring, having only half your genes (the equivalent of an unfertilized egg), then you gain no reproductive offspring (as far as I know). Such an offspring is genetically the same—as far as your evolutionary potential goes—to reproducting sexually, as each offspring carries only half of your genome.

I don’t think the public realizes that the fact of sexual reproduction is pretty much an evolutionary mystery—one of the biggest mysteries we have. But we do know that some organisms that normally reproduce sexually can revert to asexual parthenogenetic reproduction under some conditions. The paper by Fields et al. summarizes the data:

Facultative parthenogenesis — the ability of sexually reproducing species to sometimes produce offspring asexually — is known from a wide range of ordinarily sexually reproducing vertebrates in captivity, including some birds, reptiles and sharks. Despite this, free-living parthenogens have never been observed in any of these taxa in the wild, although two free-living snakes were recently discovered each gestating a single parthenogen — one copperhead (Agkistrodon contortrix) and one cottonmouth (Agkistrodon piscivorus).

It’s easy to see that if you can switch from sexual to asexual reproduction, it would be good to do that when population density is low, and you might not be able to find a mate. At least then you leave some genes. But if you can do that, why bother to ever have sex? Again, there must be some advantage of sexual reproduction about which we’re ignorant.

But on to the paper. The authors studied a very rare fish, the smalltooth sawfish (Pristin pectinata), a subtropical Atlantic and Mediterranean fish that is critically endangered.  Here’s one from Wikipedia described as being in the Georgia Aquarium:

Pristis_pectinata_-_Georgia_Aquarium_Jan_2006

They are big, sometimes over 7 meters long. But what the hell is that saw for? Wikipedia notes that it serves as a device to both detect and manipulate prey, as well as to defend itself (by slashing) when it’s attacked:

Recent studies have demonstrated, however, that the sawfish utilize their rostrum to both sense and manipulate prey.

A sawfish’s saw is made up of thousands of sensory organs that allow them to detect and monitor the movements of other organisms by measuring the electric fields they emit. The sensory organs, also called ampullary pores, are packed most densely on the dorsal side of its beak. This allows the fish to create an image of the three-dimensional area above it, even in waters of low-visibility. This provides support for the bottom-dwelling behavior of sawfish. Utilizing their saw as an extended sensing device, sawfish are able to “view” their entire surroundings by maintaining a position low to the sea floor.

Sawfish uncover sand dwelling crustaceans and mollusks, two common prey types, by using their unique anatomical structure as a tool for digging and grubbing about in sand or mud. The sawfish churn up the sea bottom with their exaggerated rostrum to uncover these hidden food sources.

Why are they endangered if nobody eats them? As Wikipedia again notes, “Smalltooth sawfish are extremely vulnerable to overexploitation because of their propensity for entanglement in nets, their restricted habitat, and low rate of population growth.”

While they’ve been observed to reproduce sexually in aquaria, the authors found, by studying wild sawfish, that they can also reproduce parthenogenetically. And they apparently do this in two genetic ways: producing haploid offspring (presumably unfertilized eggs that develop to adulthood) and diploid offspring (which may result from the fusion of two of the four products of meiosis, yielding a diploid egg that also grows to maturity).

How did they find this out? Not by observation, since they were dealing with wild specimens, but through genetics. They sampled 190 individuals captured off of Florida, and released them after taking a sample of either blood or tissue.

They analyzed 40 variable genes in each individual and looked to see if individuals had two copies of their genes (i.e. two different “alleles”, or gene forms, at these genes), or only one. In normal outbreeding, sexually-reproducing populations, individuals will often have different forms of genes at some loci (“heterozygous”), with some having the same form of a gene (“homozygous”). For example, individuals with AB blood type have two different alleles at the Landsteiner blood-group locus, while individuals that are O have two similar alleles.

The similarity of genes within each individual was expressed by an IR (“internal relatedness”) measure, which will be close to zero if an individuals’ parents are genetically unrelated (there will be a lot of heterozygosity in that offspring), but will be close to 1 if individuals are either haploid (having only one copy of each gene, so heterozygosity is zero) or if an individual’s parents are very highly related, as would occur after generations of intensive inbreeding (like brother-sister mating), something that is very unlikely in this fish.

Here’s what they found, with the histogram of IR values shown below the picture of the fish:

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Note that the graph is bimodal: the vast majority of IR values are low, but seven individuals (in box at right) had very high IR values. Two of these showed no genetic variation, while five had variation at only one or two of the 40 genes sampled. All of these high-IR individuals are female, as expected under parthenogenesis. (I don’t know how sex is determined in this fish, but if it’s like an XY system, the fish would have to be female because they’d be either XX or XO, since a parthenogenetic female parent doesn’t have Y chromosomes.)

The authors conclude that the two completely invariant fish were haploid, the result of parthenogenesis, which would be the first indication (see above) of a vertebrate reproducing successfully in the wild without sex. (I am taking the authors’ word for this; readers may know of some exceptions. (There are some fish that are parthenogenetic but require fertilization from a male, though the sperm serves a purely developmental function and its chromosomes are not incorporated into offspring.)

What about the five fish that were homozygous at nearly all genes, but variable at one or two? The authors interpret this as a result of parthenogenesis, too, but a form that produces diploid offspring. They hypothesize that this is automictic parthenogenesis: the mother was heterozygous at some of her genes, and when she came to produce eggs (this normally involves producing four haploid egg precursors, most of which—the “polar bodies”—degenerate before fertilization), two of those products fused to form a diploid egg. The two that fused were nearly genetically identical, since they were the fused products of simple cell division of a single haploid cell, but there might have been a rare “recombination” event with a non-identical polar body before this fusion.

So this vertebrate apparently reproduces occasionally without having sex. That would, of course, be adaptive in a species of low density, like this one, for it’s better to leave some of your genes than none.

Are the authors correct in their presumption that they’ve detected asexual reproduction in parents simply by looking at an offspring’s genes? Given the bimodality of the graph above, and no sign of severe inbreeding in this species (in such a case every individual would have a high IR value), I think they’re right. This opens up the possibility, if you can survey many variable genes, of seeing how often asexual reproduction occurs in the wild, and whether, as expected, it occurs more often in low-density populations.

One thing I wished the authors would have done, which is likely difficult and probably impossible in this species, is to do a chromosome analysis of the cells.  Those putatively haploid individuals would have only half the normal number of chromosomes, while the diploid ones would have the normal number of chromosomes. This would have rendered their case airtight, but I still think that their conclusion is still pretty solid.

The only remaining question for this group is whether Mary could have reproduced this way—and don’t think that some crazy religionists won’t use this as an example of how a virgin can produce an offspring. The problem, of course, is that if Mary had reproduced this way, Jesus would have been either a female or a haploid intersex with an XO chromosome constitution, producing a short female with gonadal dysgenesis (rendering the individual sterile) and a webbed neck. (In this case the “H” in Jesus H. Christ could stand for “haploid”.) Since the New Testament mentions no such abnormalities, I conclude that, on genetic grounds, the Jesus story is a myth.

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Fields, A. T. et al. 2015. Facultative parthenogenesis in a critically endangered wild vertebrate. Current Biology 25:R446-447.

Readers’ wildlife photographs

June 4, 2015 • 7:45 am

As I wing my way to Vancouver, enjoy these photographs. The first set comes from Stephen Barnard in Idaho:

This is a juvenile Northern Harrier (Circus cyaneus). For about an hour I watched three of them and at least one adult (a male) raiding Red-winged Blackbird (Agelaius phoeniceus) nests in the potentilla (Potentilla) across the creek. It looked for all the world like the male was teaching them to hunt. Yesterday I saw a pair of harriers hand off a captured blackbird chick in flight. The blackbirds are very active and effective at defending against the harriers and it’s fun to watch their dogfights. They attack in gangs, at some risk. There’s probably kinship reciprocity going on. Even blackbirds have ethics. There are lots of  blackbirds because I feed them copiously.

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Reader Mark Sturtevant, a lep-lover, sent a lovely swallowtail:

I have some new pictures of local insects that might be worthy of the WEIT web site. This entry is of a black swallowtail (Papilio polyxenes), which had recently emerged from its chrysalis. It is the same individual that was seen last summer in WEIT.  I kept its chrysalis, along with other lep pupae, hidden in our refrigerator during the winter. More pictures of the other critters can come later.

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The 2nd and 3rd pictures were taken with a method that might be of some interest to the readers. I used a Canon T5i body with a basic 50mm prime lens plus an extension tube. I am relying on this inexpensive way to take close up pictures this season.

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I think the butterfly is saying ‘Oh Hai!’ in the 3rd picture:

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Thursday: Hili dialogue

June 4, 2015 • 3:46 am

Okay, it’s 3:45 a.m. and even for me it’s an ungodly hour. I catch a cab to O’Hare at 5, and so must be up now. I’ll be in Vancouver by noon at the latest, though, and will have time to rest (and share a fine Indian dinner with Larry “Genetic Drift” Moran) before the meetings start tomorrow. Meanwhile in Dobrzyn, it’s a religous holiday, and so we have a special Hili!

Hili: Not all roads lead to Rome.
A: That’s right, luckily, some roads lead home.

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In Polish:
Hili: Nie wszystkie drogi prowadzą do Rzymu.
Ja: To prawda, na szczęście, niektóre prowadzą do domu.
Hili lagniappe, with Malgorzata’s explanation:
This is Corpus Christi today which is a huge holiday in Poland. Andrzej posted a photo of Hili in a bishop’s mitre with the words: “In such a cap I’m always right”. And there is a caption over it: “Among humans a cap happens to be greater authority than reason. Corpus Christi, spill out homilies!”
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Bishop Hili

Two videos: banding peregrine chicks, and a cephalpod moves house

June 3, 2015 • 3:30 pm

As I head home to pack (well, I’m nearly all packed anyway), I’ll leave you with two animal videos. The first shows the banding of peregrine falcon chicks on the Verrazano Narrows bridge in New York, where they’ve clearly installed nest boxes. The parents are flying about, deeply disturbed, and the chick kicks up one hell of a ruckus:

And here’s an octopus moving house; or rather, it’s taking its coconut house along and changing locations:

h/t: Lauren, John