Hillary Clinton to announce Presidential bid on Sunday

April 10, 2015 • 11:00 am

According to CNN, Hillary Clinton will throw her hat in the ring (is anybody surprised?) with a video announcement on Sunday:

Hillary Clinton is planning to launch her presidential candidacy on Sunday through a video message on social media, a person close to her campaign-in-waiting tells CNN, followed immediately by traveling to early-voting states of Iowa and New Hampshire to start making her case to voters.

The trip to Iowa, where a third-place finish in 2008 ultimately led to the collapse of her presidential aspirations, illustrates what aides say is a commitment to not take anything for granted in her second bid for the White House, even though she dominates the likely Democratic field in 2016.

Clinton has already filmed her campaign video, a person close to the campaign said, which outlines the central themes of her second bid for the White House. The message is intended to send a signal to Democrats that she intends to aggressively fight for the party’s presidential nomination.

A new epilogue of her book, “Hard Choices,” an excerpt of which was released Friday to the Huffington Post, offers a glimpse into why she is embarking on another presidential campaign. She writes about her new granddaughter, Charlotte, and calls for equal opportunity for her generation.

No Republican can field a candidate, at least right now, that can challenge her. Nor is there a credible challenger in her own party. I’m not a huge fan of Clinton, and although I think it’s time that we had a woman president in this country, I’d much rather it be Elizabeth Warren than Hillary Clinton. And indeed, Warren has been making the tiniest of noises that she may challenge Clinton. I’d favor that, for while I’d hold my nose and vote for Hillary over any Republican on this planet, I’d vote eagerly and gladly for Warren.

Sadly, I think that Warren could be too easily written off by the electorate as a “Massachusetts liberal,” something that would also doom John Kerry, another person I’d like to see in the running. (Kerry, of course, could also be branded as a “loser” for his defeat in the 2004 Presidential campaign, though I don’t see why a single loss is so damning.)

Frankly, I have little confidence that Clinton would be a good President, given her penchant for secrecy, her ties with the wealthy, her failure so far to articulate any vision that I respect, and—not her fault—the fact that she’ll face a Republican Congress. But is this the best the Democratic party can do?

How often do genes move between distantly related species?

April 10, 2015 • 8:45 am

Did you read Matthew’s post on the okapi yesterday? I hope so, because I’m worried, in view of the paucity of comments on science posts, that people are skipping them. Perhaps that just reflects the dearth of things that non-scientist readers have to say. I hope that’s the answer, for it takes about four or five times more work to do a science post than, say, an anti-theist post.

So I’ll try once more today. This is a genetics paper that came out a few weeks ago, but I haven’t had time until now to read it and summarize it. It’s on the phenomenon of horizontal gene transfer (HGT), whereby genes move between the genomes of very distantly related species. Examples include the include the absorption of bacteria by other species (that’s how the mitochondria originated, a theory suggested by Lynn Margulis; and these mitochondria, once free-living bacteria, contribute their genes to the absorbing organism); the transfer of pigment genes from fungi to aphids, which give the aphids a red color that may help hide them; and the transfer of several enzymes from bacteria to insects, which help the insects use new plants as food.

The phenomenon of HGT has been called “non-Darwinian,” since it simply wasn’t envisioned by Darwin or, indeed, even in the early days (ca. 1930-1940) of the “modern synthetic theory” of evolution.  But, contra some critics of evolution, HGT does not invalidate the modern theory of evolution. For the transfer of genes between distantly related species is simply a new source of genetic variation—like “normal” mutations—whose fate is still subject to whether the transferred genes are good or bad for the host. In the case of aphids, for instance, the acquired pigment genes rose in frequency in the pea aphid species by natural selection, but had they been deleterious they would have been eliminated.

This kind of gene transfer can occur in several ways: by eating of one organism by another, and then incorporation of that organism’s DNA into the genome; by infectious transfer of microorganisms followed by the same kind of incorporation; or simply by absorption of microorganisms into the body, as when rotifers rehydrate after they’ve become desiccated.

Infrequent HGT, then, doesn’t kill the theory of evolution, but expands it by showing that “mutations”—the raw material for evolution—can be acquired in a way we didn’t previously suspect.

Now if HGT was very, very common, then it would completely efface the evolutionary relatedness of organisms as seen from their DNA. If Drosophila species, for example, got genes repeatedly from microorganisms, and different fly species got different genes, then one might be completely thrown off by using DNA sequences to determine how related they are. You’d mess up your phylogeny by including horizontally acquired DNA from unrelated species in your tree-making algorithm. This was the basis of the infamous New Scientist cover that read “Where Darwin Went Wrong.” The “wrong” bit was supposedly that Darwin envisioned a branching bush of life, but HGT might mean that the branches were effaced by transfer of DNA from distantly related species, and we wouldn’t have easily defined bushes at all.

Fortunately for evolutionists, HGT isn’t that common—certainly not common enough to prevent us from reconstructing evolutionary relationships, as scientists recently did for families of birds (see here). Cries that “Darwin was wrong!” or “Evolutionary theory is disproven!” are simply wrong. The branching bush of life is still secure, though there are bits of bark that move between the branches.

A new paper in Genome Biology by Alastair Crisp et al. (reference and download below) is the first attempt to systematically find out how much HGT there is between three groups of metazoan organisms (nematodes, flies, and primates) and simpler ones (fungi, microbes, algae). What they did was perform genome scans of DNA sequences of species in all these groups, looking for those gene sequences in nematodes, flies, and humans that were far more similar to sequences in the other species than to more-closely related species of metazoans. For example, they could find a gene in one or several species of fruit flies that was far more similar in sequence to a gene in a bacterium than to any genes in other metazoans. That would imply that that gene had been transferred from bacteria to flies. (Another possibility is that the gene was not the result of HGT, but was present in the common ancestor of all of these species and was simply lost in all the non-fly metazoan species. But the authors used controls to rule out that possibility.)

The authors also divided up the genes that presumably moved by HGT into three classes, A, B, and C, differing in the assurance with which HGT occurred (i.e., the degree of difference in similarity of DNA between related and very unrelated species). “A” is the gold standard, with very high probability of HGT, while B and C have less assurance, but still probably still reflect HGT.

What Crisp et al. revealed was a moderate but not high frequency of HGT in two of the groups, and a low frequency in the other. The results suggest that there is indeed HGT, it’s not vanishingly rare, and that it can contribute to evolutionary change. But the level of HGT is not high enough to either efface phylogenetic trees or suggest that we revise evolutionary theory to say that genetic variation comes more often from HGT than from simple mutations in organisms.

The salient findings:

  • First, a refresher: primates have roughly 20,000 genes, fruit flies about 15,000, and the nematode Caenorhabditis about 11,000. You can see that there’s not much difference in gene number between these species: a result that surprised evolutionists and developmental biologists when the data first came out. Perhaps solipsistically, we humans seem a lot more complicated than flies, but don’t have many more genes. The difference may reside in how those genes are used, that is, in the regulation of a fairly constant number of genes.
  • How much HGT has occurred? In primates, the number of genes that have moved by HGT in classes A, B, and C are 32, 79, and 109, respectively. In Drosophila the numbers are 40, 25, and 4. In the nematodes it’s 68, 127, and 173, respectively.  There’s much less HGT in flies than in the other groups, but still the extent of HGT is only moderate in worms and primates: about 0.2%- 1.5%, depending on which species you use and what class of genes you want to count as acquired by HGT. That’s not enough transfer to constitute serious problems for making phylogenetic trees.
  • Most of the genes transferred to all three groups were those producing enzymes, which makes sense since they can confer immediate new functions on the recipient organism. Genes most often transferred affected the immune system, lipid metabolism, the modification of other large molecules, proteins produced when organisms are stressed, and antioxidant activities. This held across worms, flies, and primates.
  • Curiously, one gene that may have been transferred horizontally is the Landsteiner blood group gene in primates: the gene producing different antigens on red blood cells that give us type A, B, AB or O blood.
  • Finally, by placing the putatively transferred genes on the family tree of metazoans, they determined that gene transfer is both ancient and ongoing: HGT genes were acquired in both the ancient parts of a group’s phylogeny or in the more recent parts: say in the lineage of only one species of primate—which implies recent HGT since that one species diverged from other primates.

Where do the genes transferred into primates, worms, and flies come from? The authors provide this handy chart:

Screen Shot 2015-04-10 at 8.12.35 AM

The recipients are in the column to the left, the donor groups along the bottom. As you see, most genes come from microbes: bacteria and protists. This isn’t surprising because those organisms can transfer genes by either ingestion or infection.

The upshot is that we have a nice new finding, with some surprises—the ABO blood group genes still amaze me, and I’d like more confirmation—but a finding that hardly endangers evolutionary theory. And though I find the extent of HGT low, especially in flies, the authors do try to make a case that it’s rather high. As they note in the paper’s conclusions:

Although observed rates of acquisition of horizontally transferred genes in eukaryotes are generally lower than in prokaryotes, it appears that, far from being a rare occurrence, HGT has contributed to the evolution of many, perhaps all, animals and that the process is ongoing in most lineages. Between tens and hundreds of foreign genes are expressed in all the animals we surveyed, including humans. The majority of these genes are concerned with metabolism, suggesting that HGT contributes to biochemical diversification during animal evolution.

Well, technically “173” is “hundreds,” but I think the actual numbers I gave above, and the percentages of genes in a genome acquired by HGT, show that its prevalence is less than the paragraph above would suggest.

Nevertheless, it’s clear that we have a new source of genetic variation, and one that can contribute to adaptive evolution. But remember as well that the frequency of HGT transfer must be low, since such events must be rare, so we’re not entitled to say either that the number or commonality of HGT events is substantially higher than the number of genetic novelties produced by the more conventional process of mutations occurring within a species’ genome. This is why the branching bush of life seems, for the time, secure.

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Crisp, A., C. Boschetti, M. Perry, A. Tunnacliffe, and G. Micklem. 2015. Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes. Genome Biology 16:50, doi 10.1186/s13059-015-0607-3.

Readers’ wildlife photographs

April 10, 2015 • 7:30 am

For those of you who sent photos but haven’t seen them yet, don’t worry; I’ve saved everything, and am back in Chicago where the pictures reside. Today, however, we’ll have photos by two of our regulars.

First, Stephen Barnard of Idaho, who rarely sends mammals besides moose and his border collie Deets:

There was a family of River Otters (Lontra canadensis) in one of my ponds this morning. [JAC: yesterday]

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And his resident pair of bald eagles (Haliaeetus leucocephalus), Desi and Lucy (if you don’t know what their proper names mean, look them up). The eagles have apparently produced eaglets, but we haven’t seen them yet.

Lucy was calling to Desi to bring a fish for the babies, but he returned empty handed.

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And Diana MacPherson, for reasons beyond my ken, sent a chipmunk butt:

This chipmunk was sitting like this for hours. Bum of Eastern Chipmunk (Tamias striatus):
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Friday: Hili dialogue

April 10, 2015 • 4:53 am

It’s Friday, and we must all decide what seats we’ll take.  I have a week’s respite before I travel to South Carolina to go some talks, but the lagniappe is Southern noms and a chance to visit with Snowball the Dancing Cockatoo, the only single animal in the history of the world demonstrated to dance to a beat (see also here). Meanwhile in Dobrzyn, Hili is blackmailing people into giving her fusses!

A: You often sit on this corner of the desk.
Hili: Yes, because when people walk past they can pat me, and if they don’t I can bat them with my paw.

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In Polish:
Ja: Często siadasz na tym rogu biurka…
Hili: Tak, bo jak ktoś przechodzi to może mnie pogłaskać, a jak tego nie robi, to ja go mogę pacnąć łapą.

 

Sexist ultra-Orthodox Jews continue to make trouble on planes

April 9, 2015 • 3:25 pm

Well, the New York Times has finally caught up to the prescient reporting of Professor Ceiling Cat, who has reported several times about the bad behavior of ultra-Orthodox Jews on airplanes (see here, for instance).  In their new piece, “Aboard flights, conflicts over seat assignments and religion,” the Times recounts what readers here have long known: in the past few months, those Orthodox religionists have delayed flights by refusing to sit next to women, which they claim is against their faith (they may, G*d forbid, actually touch a woman!). Flights have been delayed, passengers peeved at what is a sexist request, and there’s even been the spectacle of these Jews offering money to passengers to switch seats.

Several flights from New York to Israel over the last year have been delayed or disrupted over the issue, and with social media spreading outrage and debate, the disputes have spawned a protest initiative, an online petition and a spoof safety video from a Jewish magazine suggesting a full-body safety vest (“Yes, it’s kosher!”) to protect ultra-Orthodox men from women seated next to them on airplanes.

(Note: I’m looking forward to seeing that video!)

As the piece notes, it’s getting worse:

“The ultra-Orthodox have increasingly seen gender separation as a kind of litmus test of Orthodoxy — it wasn’t always that way, but it has become that way,” said Samuel Heilman, a professor of sociology at Queens College. “There is an ongoing culture war between these people and the rest of the modern world, and because the modern world has increasingly sought to become gender neutral, that has added to the desire to say, ‘We’re not like that.’”

Apparently in some cases the fear is not just “pollution” by accidentally touching a woman, but fear of temptation, the same fear that drives many Muslims to insist that women be covered.

Rabbi Shafran noted that despite religious laws that prohibit physical contact between Jewish men and women who are not their wives, many ultra-Orthodox men follow the guidance of an eminent Orthodox scholar, Rabbi Moshe Feinstein, who counseled that it was acceptable for a Jewish man to sit next to a woman on a subway or bus so long as there was no intention to seek sexual pleasure from any incidental contact.

. . . Mr. Roffe [a writer from Los Angeles] described his experience on a United Airlines flight to Chicago. When they started to board, he said, an ultra-Orthodox man stood in the aisle, refusing to move and delaying the departure for 15 to 20 minutes until another passenger volunteered to switch seats.

“My buddy who is Orthodox was saying this is a traditional thing — he doesn’t want to be tempted when his wife wasn’t there. And I said, ‘Are you kidding?’ This was just some woman flying to work or home and minding her own business.”

While many passengers refuse this requests—and I especially applaud the women who stand their ground—some people feel that they should move as a nice gesture to accommodate people’s faith:

Some passengers are sympathetic. Hamilton Morris, a 27-year-old journalist from Brooklyn, said he agreed to give up his seat on a US Airways flight from Los Angeles to Newark via Chicago because it seemed like the considerate thing to do.

“There was a Hasidic Jew sitting across the aisle, between two women, and a stewardess approached me and quietly asked if I would be willing to exchange seats because the Hasidic Jew was uncomfortable sitting between two women,” he said. “I was fine with that. Everyone was trying to be accommodating because on airplanes everyone is anxious about offending anyone for religious reasons.”

My own opinion is that it’s odious to go out of your way to afford respect to any beliefs that are sexist or misogynist, as these are. But others may feel differently. So here’s the question to readers: You’re on a plane, and an ultra-Orthodox Jew asks you to move so he doesn’t have to sit next to a women. (This could be asked to either men or women.)  Would you do it?

h/t: Greg Mayer

The lonely life of the reclusive okapi

April 9, 2015 • 10:56 am

By Matthew Cobb

Okapis (Okapia johnstoni) are the closest living relative of the giraffe (their lineages separated about 16 million years ago). They live in the rainforest of the Democratic Republic of Congo (DRC) in central Africa. Although their bodies are brown, their legs are striped like a zebra’s. They first became known to science at the end of the 19th century.

An okapi mother and her calf in the Okapi Wildlife Reserve in DRC. Taken from here.

These animals browse on plants growing in gaps in the forest caused by tree fall – this means that their food is relatively sparsely and randomly distributed around the forest. The precise number of okapis in the wild is unknown (figures vary between 10-50,000), but the overall trend is downwards (an estimated 50% decline in the last three generations). They are already extinct in neighbouring Uganda. As a result, the IUCN to have put the animal on its Red List of Endangered Animals.

The major problems for the okapi are, predictably, associated with humans – logging is destroying its habitat, and contact with humans is leading to hunting for bushmeat. Furthermore, illegal armed groups involved in elephant poaching, bushmeat hunting, illegal mining (gold, coltan and diamonds), illegal logging, charcoal production and agricultural encroachment, all make it difficult for conservationists to operate in the area.

Little is known about the ecology of the okapi because it lives in such difficult terrain. In the 1980s radiotracking of eight individuals suggested that they were solitary, with home ranges that were about 10.5 km2 for males, and 5.1 km2 for females. However, there is little solid evidence for how they live their lives, and how the sexes interact.

That has recently changed, with a new study by researchers in the UK and in DRC that looked at DNA extracted from 208 faecal samples collected in an okapi reserve (see map below). (In passing, hats off to the team for succeeding in this – a while back a student of mine tried extracting DNA from fresh howler monkey turds; we failed dismally.) Once the DNA had been extracted, they then looked at a short parts of the genome that they knew would show variability (these are known as ‘microsatellites’ in the trade). A total of 105 samples provided valid DNA.

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The team then did some fancy population genetics to draw a number of conclusions about the social system, the mating system and the dispersal of the okapis they were studying. (Another note in passing: many zoology students dislike both DNA extraction and population genetics – this study shows why both these techniques are important if you want to understand animals.)

Social system: the lack of overlap in genotypes found at the different dung sites suggests that okapi do not form social units, apart from mother-offspring and adult male-female pairings. There was no evidence of large social groups. This was expected, both from previous research, and from the behaviour of other animals that can be heavily predated (in the case of the okapi, by leopards). Because there was no indication of what is called ‘genetic structure’ to the population they sampled – that is, certain genotypes were not found more often in one area than another – the authors conclude that there are no physical obstacles to okapi moving around the region (see also below).

Mating system: The frequency with which the study picked up full and half siblings sugstes that okapi are genetically polygamous (each male will mate with more than one female) and promiscuous (this situation is typical of most mammalian species). However, varying population densities in different regions may mean that it is possible that in some areas males may defend a territory containing several females, although the team found no direct evidence of this.

Dispersal: evidence of dispersal/movement was hard to estimate because they found so few genotypes more than once (in other words, they did not sample the same animal very often – only 13 individuals provided two data points). One male was recorded twice, 25.5 km apart, but the average distance between samples, if this individual was excluded, was 0.337 km.

The conclusion is that the okapi is indeed a solitary beast. They are isolated for most of their lives, having social interactions only while a calf, or during mating. These beautiful animals, which always appear timid and slightly sad in zoos, are solitary and secretive. If we are not careful, the only place they may be safe is in a zoo.

 

Reference: D. W. G. Stanton et al. (2015) ‘Enhancing knowledge of an endangered and elusive species, the okapi, using non-invasive genetic techniques’ Journal of Zoology 295:233–242

 

 

University of Michigan cancels showing of “American Sniper” after accusations of Islamophobia and triggering, substitutes showing of “Paddington Bear”

April 9, 2015 • 10:00 am

Today we have more identity politics, with the emphasis on “identity” rather than “politics.” This involves another college campus, the prestigious University of Michigan, which cancelled a showing of “American Sniper” after Muslim students—and probably many non-Muslim students—complained that the movie made them feel unsafe, was “triggering”, and perpetuated anti-Muslim stereotypes. As The College Fix reports (and it’s been substantiated by several other sources):

A scheduled movie screening of “American Sniper” at the University of Michigan was abruptly cancelled Tuesday after nearly 300 students and others complained the film perpetuates “negative and misleading stereotypes” against Muslims.

“The movie American Sniper not only tolerates but promotes anti-Muslim … rhetoric and sympathizes with a mass killer,” according to an online letter circulated among the campus community via Google Docs that garnered the signatures.

The signers were mostly students, but also some staff, as well as the Muslim Students’ Association and the president of Students Allied for Freedom and Equality, a Palestinian solidarity group at UMich.

The online memo, titled a “collective letter from Middle Eastern and North African (MENA) and Muslim students on campus,” accused the public university of “tolerating dangerous anti-Muslim and anti-MENA propaganda” by showing the movie, the highest grossing film of 2014.

Here’s the collective letter, which you can see at the first link (I wasn’t able to access the “online memo” link):

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The University caved:

“While our intent was to show a film, the impact of the content was harmful, and made students feel unsafe and unwelcomed at our program,” stated The Center for Campus Involvement, which oversees student activities and is run by university employees, as it announced its decision Tuesday on its various social media accounts, including Twitter and Facebook.

“We deeply regret causing harm to members of our community, and appreciate the thoughtful feedback provided to us by students and staff alike.”

University spokesman Rick Fitzgerald confirmed to The College Fix on Tuesday the movie was cancelled.

. . . “We in the Center for Campus Involvement and the UMix Late Night program did not intend to exclude any students or communities on campus through showing this film,” the center’s announcement stated.

“… UMix should always be a safe space for students to engage, unwind, and create community with others, and we commit to listening to and learning from our community in the interest of fostering that environment. … We will take time to deeper understand and screen for content that can negatively stereotype a group.”

The Center for Campus Involvement’s Facebook page indicated that the film would be replaced by, appropriately, “Paddington Bear“: the equivalent of showing triggered students videos of puppies and kittens.

The sad thing is that the students who objected didn’t have to go to the movie. In fact, everyone can find out what American Sniper is about from simply Googling. What they objected to was not seeing the movie, but having the movie actually shown on campus.  And they succeeded, thanks to a compliant group of administrators and students who don’t give a damn about free speech, for if anyone says that speech is “offensive”, we must by all means ban it.

American Sniper is a true story, and, though I haven’t seen it, I know it sparked a lively conversation about whether or not Kyle was admirable, about the ethics of his actions, and so on. That conversation will not take place at The University of Michigan. Should we also ban “Schindler’s List” or “Band of Brothers” because they show Germans engaged in mass killings, which could trigger both Germans and Jews? Should we ban “Triumph of the Will” by Leni Riefenstahl because it glorifies the Nazis, which it does in a very clear way?

There are in fact many movies showing bad people doing bad things. That’s what happens in this world. Regardless of what you think about Chris Kyle, students should have the opportunity to see the movie for themselves. If they think it will grossly offend or “trigger” them, then they shouldn’t go. But they have no right to control what other students will see.  I, for one, would welcome seeing Nazi propaganda movies, including those that demonize Jews, (in fact I’ve seen many of those movies) as a way of creating a conversation and learning about history.

These students should grow up; they have no right to not be offended. And the University of Michigan and those who cancelled the movie should be ashamed of themselves. They have abrogated the very mission of a good university: to challenge students’ views and make them think.

I look forward to the universities of 2040, in which all movies shown will be about bears, penguins, and puppies, and everyone always feels “safe.”