Hold the presses: maybe tardigrades don’t have so much horizontal gene transfer after all

December 4, 2015 • 10:30 am

About a week ago I discussed a new paper by Boothby et al. in the Proceedings of the National Academy of Sciences (US) with a stunning finding: the sequenced DNA of the tardigrade species Hypsibius dujardini showed that about 17% of its genome comprised sequences taken from distantly-related species—mostly bacteria. This was the most pervasive example of horizontal gene transfer (HGT) known in animals, though bacteria often have such high levels of HGT.

But maybe that conclusion was premature—or wrong. A new manuscript by Georgios Koutsovoulos et al. (reference and free download at bottom), posted at the website bioRχiv, suggesst that Boothby et al.’s results may have been due to contamination of their DNA sample with bacteria, and the level of HGT in this species may be much lower.

Do be aware, when evaluating the discrepancy between the two papers, that the Koutsovoulos et al. manuscript hasn’t been refereed: the authors simply posted a manuscript—presumably submitted to some unspecified journal—on a public website. But let’s compare them anyway. 

Although Boothby et al. argued that they cleaned up their sample to eliminate contamination, Koutovoulos seem to have taken more stringent precautions. And the sequencing of their sample, compared to the published sequences of Boothby et al., showed a very different result. First, about 30% of Boothby’s DNA appears to represent contaminant material.

Granted, their sample was a different isolate of the species (started from one asexually-reproducing female), but their culture and that of Boothby et al. were separated by only fifteen years of divergence, so it’s unlikely that the differences in DNA content result from different genetic constitution of the isolates. 

How much of the tardigrade genome is still composed of foreign DNA in the new species? We don’t know completely, but Koutsovolos et al. report that they looked at 23,021 protein-coding genes in the H. dujardini genome, and found only 36 genes that appeared to have a bacterial origin. That’s a proportion of only 0.16%—a far cry from 17%.

Koutsovoulos et al. also note that H. duardini is not known to undergo the drying and rehydration process known as cryptobiosis—a process that takes in lots of water from the environment, destabilizes membranes, and breaks DNA: an idea way to take foreign DNA into your genome. But if this tardigrade doesn’t do that—and I don’t recall Boothby et al. mentioning this fact, though they might have—then it makes it even less likely that the 17% HGT figure is correct.

As I said, the “replication” study hasn’t yet been published after peer review, so we’ll have to suspend judgment. Resolution of this problem will await the publication of the Koutsovoulos et al. paper, and, ideally, a third study (perhaps by Boothby et al.) with very stringent precautions. After all, the press had a field day with the 17% HGT figure, which truly was astounding; and, as Hitchens said, extraordinary claims demand extraordinary evidence.

And a postscript: the methods of both papers are above my pay grade, so read both if you’re in the field and want to judge the results.

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I get bizarre email: the death of atheism

December 4, 2015 • 9:30 am

This email landed in my box yesterday, and I see it as a novel way to denigrate atheism:

Dear Professor Coyne: Look at Europe and what do you see? The birth rate has fallen far below replacement level. European civilization is dying. When a country adopts atheism, its birth rate drops to zero and the country dies. That is why atheism is a failure as an ideology. It causes every civilization that adopts it to die. Atheism is the god that failed. Raising children is such an irksome duty that you cannot get people to do it unless you convince them that God wants them to do it. If I was a Muslim fundamentalist, I would say to you “Why should we want to be like you? Your civilization is dying!

Have a nice day.
Sincerely, [Name redacted to avoid embarrassment]

The gentleman who wrote this clearly hasn’t considered alternative hypotheses for falling birthrates, like MODERNITY. After all, the U.S. birthrate is still below replacement level, even though we’re the most religious of First World nations, and religious Brazil is also below replacement rate, as are Italy and Poland, two of Europe’s most religious nations. Before China adopted its one-child policy (now two-child, I believe), the population of that godless nation was growing rapidly.

Yes, the Middle East has a higher-than-replacement birthrate, as does much of Africa and southeast Asia, but is that due to their religiosity or their poverty (which leads to high child mortality), or both? Remember that many studies show a connection between higher religiosity and lower socioeconomic well being.

This is a prime example of how correlation (if one really exists her) might be misleading about causality.

For your delectation, he’s a figure from Wikipedia showing the fertility rates of various nations reported in 2015. Rates below 2.1 (children born per woman) indicate falling population (exclusive of immigration). Click to enlarge.

Countriesbyfertilityrate.svg
Wikipedia adds this, for what it’s worth:
As of 2010, about 48% of the world population lives in nations with sub-replacement fertility. Nonetheless most of these countries still have growing populations due to immigration, population momentum and increase of the life expectancy. This includes most nations of Europe, Canada, Australia, Brazil, Russia, Iran, Tunisia, China, and many others. The countries or areas that have the lowest fertility are Hong Kong, Macau, Singapore, Taiwan, Ukraine andLithuania. Only a few countries have low enough or sustained sub-replacement fertility (sometimes combined with other population factors like emigration) to have population decline, such as Japan, Germany, Lithuania, and Ukraine.

Richard Posner decries the theocratic views of Justice Scalia

December 4, 2015 • 8:15 am

My colleague Richard Posner teaches at our law school, is a judge on the U.S. Court of Appeals of the Seventh Circuit, has repeatedly been mentioned as a candidate for the Supreme Court (he says he’s too old now), and is the most cited American legal scholar of the twentieth century. He’s also written 40 books, so is clearly an overachiever. Posner is generally characterized as a conservative, but that’s not an accurate label since he favors the legalization of both marijuana and gay marriage.

Posner’s penchant for leftish views was on show yesterday with an op-ed in the New York Times co-written with Eric Segall, a law professor at Georgia State. The piece, “Justice Scalia’s majoritarian theocracy“, decries the increasingly theocratic and loopy views of Supreme Court Justice Antonin Scalia. I give a few excerpts below (my emphasis). I hadn’t realized how anti-gay Scalia really was, though of course he’s a devout Catholic.

The Supreme Court has decided four major cases furthering gay rights. Justice Antonin Scalia has written a bitter dissent from each.

In Lawrence v. Texas, for example, where the court invalidated Texas’ ban on homosexual relations between consenting adults, Justice Scalia complained that: “Today’s opinion is the product of a Court, which is the product of a law-profession culture, that has largely signed on to the so-called homosexual agenda, by which I mean the agenda promoted by some homosexual activists directed at eliminating the moral opprobrium that has traditionally attached to homosexual conduct.”

He added: “Many Americans do not want persons who openly engage in homosexual conduct as partners in their business, as scoutmasters for their children, as teachers in their children’s schools, or as boarders in their home. They view this as protecting themselves and their families from a lifestyle that they believe to be immoral and destructive. The Court views it as ‘discrimination’ which it is the function of our judgments to deter. So imbued is the Court with the law profession’s anti-anti-homosexual culture, that it is seemingly unaware that the attitudes of that culture are not obviously ‘mainstream.’”

. . . In a recent speech to law students at Georgetown, he argued that there is no principled basis for distinguishing child molesters from homosexuals, since both are minorities and, further, that the protection of minorities should be the responsibility of legislatures, not courts. After all, he remarked sarcastically, child abusers are also a “deserving minority,” and added, “nobody loves them.”

. . . Obergefell [Obergefell et al. v. Hodges et al.: the gay-marriage case]  seems to obsess him. In a speech at Rhodes College in Memphis, he said that the decision represents the “furthest imaginable extension of the Supreme Court doing whatever it wants,” and that “saying that the Constitution requires that practice” — same-sex marriage — “which is contrary to the religious beliefs of many of our citizens, I don’t know how you can get more extreme than that.” The decision, he said, “had nothing to do with the law.”

The suggestion that the Constitution cannot override the religious beliefs of many American citizens is radical. It would imply, contrary to the provision that forbids religious tests for public office, that religious majorities are special wards of the Constitution. Justice Scalia seems to want to turn the Constitution upside down when it comes to government and religion; his political ideal verges on majoritarian theocracy.

The notion that our laws should somehow cater to “the religious beliefs of many of our citizens” is bizarre and scary—and, as Posner and Segall note, clearly violates the First Amendment to the Constitution, intended to protect minority faiths and nonbelief. And the comparison between gays and child molesters is reprehensible. Scalia’s statements bespeak someone so extreme, so marinated in faith, that he’s actually unstable—no longer able to judge judiciously. If judges could be fired, I’d say Scalia should get the pink slip immediately.

As an aside, Posner’s Wikipedia page describes his devotion to his Maine Coon cat, Pixie: I’ve previously featured on this site a photo of Pixie provided by judge Posner. I’ll show Pixie again, but go to the original post to see Posner’s notes on his beloved felid.

Two years ago The Daily Beast featured an interview with Posner, mainly about the way he writes. But among the Q&A I found this:

Tell us something about yourself that is largely unknown and perhaps surprising.

Well, I’m a very big cat person. Used to like dogs, then I switched. I have a big crush on my current cat. I like animals generally. I’m very soft about animals. My cat is a Maine Coon named Pixie. What’s unusual about her, besides being beautiful and intelligent, but she’s affectionate. Very unusual in cats. She likes to give us nuzzles and be with us. Her little face falls if either of us leaves the house. She’s very social. She appears to recognize members of our families, kids and grandchildren. She’s a real sweetie. It’s one of the reasons I work at home a lot now. The nature of my work is such that I don’t really have to be in the office unless I’m hearing cases. I spend probably at least half the time at home working. Everything I need, I have with me or have electronic access to. One reason is that the cat wants us at home.

Check out that last sentence. What devotion (of the man, not the cat)!

Screen Shot 2015-12-03 at 2.25.27 PM
Pixie!

 Here’s Judge Posner with Pixie’s predecessor, Dinah (see the interview at Concurring Opinions):

Richard-Posner-and-his-cat

Readers’ wildlife photographs

December 4, 2015 • 7:30 am

I’ve unfortunately lost the email that came with these lovely photos by James Blilie, but since they’re fall and landscape shots, I don’t think we’re missing too much information. Perhaps he can comment (or email me) to fill this lacuna—especially the locations (as I recall, he lives in the state of Washington).

In the meantime, these photos can serve as an elegy for the summer past.

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While I’m posting unidentified photos, here are two photographs that I’ve saved under the rubric “Walkingmap CJ,” and again I can’t find an email with identifying information. I recall that the first shows a panorama in the Rocky Mountains, with the Continental Divide running from the lower left thought the valley in the middle, as well as some nearby lichens. If you contributed these photos, please add information in the comments or send me an email:


The Continental Divide

Lichens

Friday: Hili dialogue

December 4, 2015 • 5:15 am

It’s Friday—another week closer to The Big Nap. Once again I slept poorly and will have trouble braining, but, like Maru, I do my best. On this day in history, the first Burger King opened in Miami in 1954, the “Million Dollar Quartet “(Elvis, Johnny Cash, Carl Perkins, and Jerry Lee Lewis) had a jam session in Sun Studios in Nashville (1958; see the play if you can), and, in 1993, Frank Zappa died. Meanwhile in Dobrzyn, Hili has become a critic:

Hili: There are more and more words in these newspapers and less and less content.
Malgorzata: You might be right.
P1030654
In Polish:
Hili: W tych gazetach jest coraz więcej słów i coraz mniej treści.
Małgorzata: Możesz mieć rację.

Afternoon felids: Reader visits the cat pub, wins book; and Gus!

December 3, 2015 • 3:00 pm

As I mentioned earlier, I can’t brain today, so you’ll hve to be satisfied with persiflage.

And as I wrote earlier, I offered a free autographed copy of WEIT to any reader who visited the “cat pub” in Bristol and sent me a picture of themself with a cat and a pint. Well, reader Andy obliged, and I’ll be toting his book (with a cat drawn in it) to my Darwin Day lecture in London, where I’ll hand it over.

His notes and photo:

Please find attached a couple of photos of my trip to The Bag of Nails ‘cat pub’ in Bristol, previously mentioned on WEIT. Apologies for the slightly grainy nature of the photos as my phone is something of an antique!
I’ve only managed to capture 2 of the “kittens in training” (as the sign on the door stated) as some of the other kitties wandered off upstairs before I could photograph them (typically uncooperative 🙂
I also am holding a pint of ‘Elemental’, a rather fine brew. They also had an IPA and a Blackberry Porter which I shall test on future visits.
2015-12-01 17.01.43 (1)
I love it that the cats sit on the bar (the boxes are presumably a futile attempt at sanitation):
2015-12-01 17.08.40

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Second, we have an adorable new photo of Gus, the lovely earless cat of reader Taskin (his ears were frozen off when he was caught in a live trap in winter and not removed in time). Taskin adopted him and gave him a great forever home. Doesn’t he look like a polar bear?

IMG_3650 (2)

 

Alternative best headlines

December 3, 2015 • 12:30 pm

by Matthew Cobb

Yesterday we claimed that a headline involving frogs was the best headline in the history of the world. This piece of hyperbole was soon disputed on Tw*tter:

https://twitter.com/DrLindseyFitz/status/672149263627997184/photo/1

https://twitter.com/DougSaunders/status/672150534837571584/photo/1

The full story behind the frog headline:

https://twitter.com/wunderkamercast/status/672153379439689728/photo/1