Glyphosate turns out to be kind of a boring molecule

Glyphosate

Derek Lowe has a sensible article about glyphosphate, the herbicide otherwise known as Roundup. Glyphosate is scary: it’s a chemical, don’t you know, and it kills weeds, so who knows what it’s doing to your children and your cats; even scarier, some crops are being genetically modified to be resistant to glyphosate, and then proteins that protect against Roundup might end up in your cornflakes.

And now some people are raving that glyphosate causes autism, because of course every chemical compound that they don’t understand causes behavioral problems that we don’t like. We must have a scapegoat. It doesn’t matter that it has never been found to have an effect on humans.

An extensive scientific literature indicates that glyphosate is specifically not genotoxic, is not a carcinogen or a teratogen, nor has any specific adverse health effect ever been demonstrated to have been caused by exposure to or low-level consumption of glyphosate. It has little effect on non-target organisms other than plants; a contributing factor to this is that glyphosate inhibits an enzyme found in plants. This enzyme is not found in humans, other mammals, birds, fish, or insects.

The use of glyphosate on herbicide tolerant crops has proven problematic to anti-GMO activists since adoption of the technology promotes the switch to a chemical with a lower environmental impact quotient and lower toxicity.

Lowe explains the statistical nature of risk, and the cautious style of chemical classifications, that allows almost any chemical to be judged as risky to some degree, and feeds sensationalist misreadings. All the data really seems to be saying that it does nothing to animals, but let’s cover our bets and keep an eye on it.

I even have an anecdote about Roundup. We tried to see if it has any early teratogenic effects. The results are sadly unpublishable (for very bad reasons) so it’s safe to summarize them here.

We have a simple assay for developmental errors. Zebrafish pop out a bunch of eggs every morning when the lights come on, and we clean them up and separate them out into beakers, with about 100ml of water for 50 embryos. For our controls, we use fish tank water, the same stuff the adults are swimming around in. It’s got fish pee in it, bacteria, fungal spores, even tiny invertebrates (check your home aquarium water — would you drink it?). We use that because it does have some challenges for growing embryos, and provides a good background for comparisons — we lose 5-10% of the embryos, usually to fungal growth, in these situations.

I had a student who wanted to test local water sources for potential teratogens. So they collected jugs of water from nearby ponds and streams, which are rich with agricultural runoff. We then grew embryos in simple, unfiltered water from Lake Crystal, or the Pomme de Terre river, or nearby ponds, just to see if we had any preliminary effect worth pursuing. This is why we use crude tank water for the controls — those sources would also be complex and biologically rich.

Here’s the boring result: nothing happened. Fish grew happily in water from a shallow pond full of duck poop with an ethanol plant on one side and a dairy farm on the other, with no detectable disorders or effects on the rate of development. In fact, the pond water embryos were healthier in one sense — they had reduced mortality from fungal infections than embryos in tank water. Tentative explanation for that: tank water might specifically be a breeding ground for fungi that thrive on fish, or the fungi might be more sensitive to agricultural chemicals than the fish are. Anyway, it was a negative result.

Then we thought to push it, and see if we could get any deleterious effect from those agricultural chemicals, so I bought a gallon of Roundup at the hardware store, and we did a dilution series. Nope, nothing. We had embryos growing in a concentration of several percent glyphosate, and they didn’t seem to mind at all. We used concentrations that were approximately ten times what Monsanto recommends that you spray directly on your lawn, and the zebrafish didn’t care.

Now of course this was a limited and preliminary experiment. All we were examining was survival and basic morphology, and we were only looking at early developmental events, like gastrulation and neurulation and the earliest twitching behaviors, and we can say with some confidence that those were unaffected. We did not look at older animals, so if it were an endocrine disruptor (it isn’t) for instance, we wouldn’t know it. We also don’t have a test for fish autism.

I can also say that I wouldn’t drink glyphosate, but not because I’m afraid it would give me cancer. It’s because the straight stuff is kind of oily and smells nasty. So those stunts where people give Monsanto executives a glass of Roundup and dare them to drink it are really misleading — they’re not going to drink it because concentrated-just-about-anything is unpleasant.

I think the bottom line is that making a claim about the deleterious effects of a substance requires actual data, and not cherry-picking suggestive and vaguely defined effects.

It also says that the file drawer effect is a problem. I suspect there have been lots of preliminary experiments that see nothing, and are abandoned as unpublishable, like ours. That effect is also complicated. You can’t tell me just to take the data we got and publish that, because it really was just a quick pilot experiment to see if there was something worth pursuing. It’s not just that a negative result is unpublishable, but that we didn’t see enough of an effect to make it worth our while to invest enough time and effort to make the results thorough and robust enough to even consider getting it into publishable shape. And thus science staggers on.

Mendel vs. Weldon, a pointless rematch

weldon

Classes are over, and that means I have more time to think…about my classes. So I’m on the lookout for ideas to improve my teaching, and gosh, look, Nature has an article on better ways to teach genetics. So I read it eagerly, and was left scratching my head. It’s a short news article, so it’s a bit thin on the details of how to teach genetics the way it recommends, but I’m also confused about how this approach would be useful.

The author, Gregory Radick, advocates teaching Weldonian genetics, rather than Mendelian genetics.

In a recent two-year project, we taught university students a curriculum that was altered to reflect what genetics textbooks might be like now if biology circa 1906 had taken the Weldonian rather than the Mendelian route. These students encountered genetics as funda­mentally tied to development and environment. Genes were not presented to them as what inheritance is ‘really about’, with everything else relegated to ignorable supporting roles. For example, they were taught that although genes can affect the heart directly, they also affect blood pressure, the body’s activity levels and other influential factors, themselves often influenced by non-genetic factors (such as smoking). Where in this tangle, we ask them, is a gene for heart disease? In effect, this revised curriculum seeks to take what is peripheral in the existing teaching of genetics and make it central, and to make what is central peripheral.

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“vagina bones”

vaginabones

Some gamer/anime fan complained about prudish censors painting out the vagina bones in his Japanese TV shows. I’ve dissected cadavers, I’ve gone through bone collections, I’ve even seen the genitalia of a real, live woman (I know! It was awesome!), but sad to say, while knowing about the pelvic bones in the general neighborhood, I’ve never seen bones in the vagina. I was about to laugh at this ignorant guy, but then…

I thought about it. It suddenly makes perfect sense.

What else would the teeth be attached to?

Clearly, the women of the world have been keeping a deep secret from not just your ordinary run-of-the-mill man-on-the-street, but also from all of the scientists. This conspiracy has to run terrifyingly deep. It has been incredibly thorough in hiding this basic fact from everyone. It was perhaps a little too thorough, making its one mistake in a little zealous editing of anime sexy babes, and the whole story has begun to unravel.

Thanks, gamers and guys obsessed with the authenticity of soft-core porn. You have opened my eyes to the Gynocracy.

What? The giraffe didn’t get a long neck by stretching?

Next they’ll try telling us the elephant didn’t get its trunk by a crocodile tugging on it.

The genomes of okapi and giraffe have been sequenced, and the signatures of specific genetic changes that are unique to their lineage have been identified. It looks like it wasn’t an act of will after all, but the accumulation of small changes over millions of years. Surprise!

This is an interesting comparison between long-necked mammals, short-necked, related mammals, and mammals as a whole that identified a number of genes that showed evidence of selection. The idea was to find the genes associated with a specific morphological change.

Using the average pairwise synonymous substitution divergence (dS) estimates between giraffe, okapi and cattle as calibrated by the pecoran common ancestor (27.6 mya), the divergence of giraffe and okapi from a common ancestor is estimated to be 11.5 mya.

Using the average pairwise synonymous substitution divergence (dS) estimates between giraffe, okapi and cattle as calibrated by the pecoran common ancestor (27.6 mya), the divergence of giraffe and okapi from a common ancestor is estimated to be 11.5 mya.


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Skepticism will not fix its problems by denying their existence

Nature has a short news piece on the Horgan/NECSS spat. I’ve read several of the rebuttals now, and I’m not impressed: I can agree that Horgan’s talk was kind of scattershot, but let’s not go the other way and pretend that organized skepticism is a happy clappy land where all the issues are objectively evaluated and treated with the weight they deserve. There is a terrifyingly substantial number of skeptics who are rank assholes who hate anyone who introduces the concept of social justice into the organization; they are dominated by us privileged white guys, too.

Anyway, the reporter asked me to comment, and I’ve got teeny-tiny mention in the story (which is appropriate, it’s not about me), but since I sent him a longer argument, and I have a blog, I’m including it here.

Steve is correct that there has been frequent discussion about priorities. What he left out, however, is that the conclusion of such discussion has typically been to shout down anyone who argues that there are major social issues that ought to be on the skeptical slate, like war and racism, as Horgan mentions, and I would also add that feminism has been a hot-button issue. Novella is one of the more open people on these topics, so he sees a more benevolent skepticism than I do. I found the intolerance and narrowness of a great many skeptics so frustratingly oppressive, that I had to simply announce that I would have nothing more to do with the skeptical organizations, and stepped away from them as a waste of effort.

There is a fair amount of diversity in the skeptical movement. There are a substantial number of skeptics who buy into scientific racism, for instance, or are climate change denialists, or even, I’ve discovered, a few who believe in flying saucers. At least those latter people get laughed out of the movement, but the others have been dealt with by largely avoiding the topics, because they would bring on too much dissent. And when they do deal with them, they tread far more carefully than they do when addressing psychics or Bigfoot hunters.

On the other hand, Horgan commits the fallacy of relative privation. Bigfoot and chupacabra are silly topics, but as long as a significant number of people believe in them, they are part of the skeptical purview…and they also represent easy learning exercises, a kind of skepticism with training wheels. It’s just that too often, skeptics think they’re smart enough to dismiss UFOs, and then use that cockiness to also dismiss sexism or racism as equivalent. It makes for a very unpleasant environment for a lot of us.

Another concern that should have been brought up is skepticism’s treatment of women. You should definitely get a few women’s voices in your article. Karen Stollznow has had a less than happy experience with organized skepticism; Rebecca Watson has worked happily with Novella in the past, but has some general grievances with both the skeptical and atheist movements. They can tell you about another problem: that chronic harassers are tolerated and even rewarded within skepticism.

I would hope that rather than pretending all of Horgan’s objections are irrelevant, that the next meeting of NECSS makes an effort to include a few speakers who broaden the range and who gore a few dangerously sacred cows, not just the spavined beasts that make for light entertainment.

The best and the worst

Let’s start with the worst. Chuck C. Johnson did an AMA for Reddit. Read for the spectacle of fawning turdwaffles praising a racist, sexist, vile shitlord, and wonder what’s wrong with people in this country.

It’s in a pro-Trump forum, and you can tell that a certain squat-fingered orange troll doll has really given a voice to the nastiest elements in the US. You will feel despair as you witness swarms of anonymous people celebrating ignorance and hatred.

But then you can read Rachel Swirsky and feel a little better. She’s a writer who has been targeted by Theodore Beale and his minions, and they’ve once again tried to subvert the Hugo awards, in part because they are horrified that she wrote “If you were a dinosaur, my love”. I think it’s because they didn’t understand it, or at least kinda vaguely grokked that it’s a) dreamy and metaphorical, which they hate, and b) it doesn’t approve of beating up people for racist/sexist reasons, which they also hate.

So she wrote about the harassment campaign, and their hilarious ineptitude.

That’s where the Hugos come in. Since trolls gotta troll in order to justify their petty lives, they decided to troll the Hugo Awards. Want to know why? The same reason the neighborhood bully knocks over your Lego tower. They can’t figure out how to make one of their own. Using underhanded tactics, they nominated a “satire” of my work to the ballot, which the white supremacist posted on his own blog. As the publisher, he included a comment saying I should be killed. Sure, it’s phrased as a “joke.” But the dogs can hear the whistle.

Luckily, there’s a hilarious silver lining. Because he and his followers are the kind of juvenile people who assume “gay = porn” (apparently, the word “gay” causes them to compulsively think of gay sex, which must be alarming for a homophobe), they also nominated a piece of porn about a dude who has sex with dinosaurs. It’s called “Space Raptor Butt Invasion” and it’s hilarious because the story’s author, Chuck Tingle, is some sort of subversive, queer, meta-fictional performance artist. Remember when Stephen Colbert hosted the white house correspondence dinner because no one bothered to do their leg work? It’s like that.

And she’s doing something more. If she reaches a certain level of donations on her Patreon account, she’ll write a parody story of her own. She has reached that level! But you should still donate, because she’s also going to give her first month’s awards to a charity that provides health services for LGBTQ people. It’s a good cause for a good reason, and it’ll also rankle the Chuck C Johnsons and Vox Days of the world.

But also, there are other rewards at other levels.

At $400, I’ll also release a silly version of “If You Were a Dinosaur, My Love” about cuttlefish. Because cuttlefish are bizarre and awesome. You know it to be true.

Yes. We know. So we should all support this story.

Kill the TSA

We’re flying to Korea this weekend, and I have more than the usual amount of travel anxiety. It’s not because of the flight, or because I’ll be spending a week in a foreign country — it’s airport security that I dread. We’re hearing about 3 hour plus wait times to get through the pointless, stupid inspections, and our flight is at a terrible time, 9:30 in the morning. Subtract 3 hours from that. Subtract another hour or two because of Old Man syndrome. Then realize that if we don’t get on the plane in time, we lose lots of money that we can’t afford, perhaps suffer the stress of a chain of missed flights, and worst of all, risk missing the wedding we’re flying to.

This article about the futility of TSA isn’t helping, either. We’ve known for years that the security measures at airports are pure theater, that they’re inefficient and wasteful, and that they simply don’t work. So why do we keep doing something that makes the problems worse?

We all know why: fear. All it takes is one incident to set bureaucrats to scrambling to find something they can do to pretend that they’re reducing the threat. Take off your shoes! 3-1-1! Next thing you know, it’ll be patriotic loyalty oaths before boarding, or something ridiculously arbitrary. No zippered clothing allowed! Shave yourself bald before coming to the airport! Dance, monkey, dance!

Also, watch this.

The heart-warming Poon/Tang case

It’s actually called that. This is the case of a wedding photographer who was sued by the groom, who was a bad lawyer, and it was informative to me in a couple of ways. I did not know that the occupation of wedding photographer was so hazardous — apparently, some people are really demanding and finicky about the little details around their wedding (sometimes, it seems, more so than they are about the marriage), and they’ll go after the photographer if the pictures are not sufficiently flattering. I wouldn’t know about that; at our wedding, we had some people with polaroid cameras wandering around informally. The pictures aren’t so great, but the marriage has been wonderful.

The threatening letter from the lawyer has to be seen to be believed. Here are some excerpts:

blusteringletter

I’ve received a few blustering extortion letters from attack-dog lawyers, but never anything as unprofessional and openly vicious as this thing — they usually try to keep the threats veiled and only vaguely unsettling. This jackhole just freely cranked it up to 11, to attempt to intimidate the photographer into settling.

But go read the whole thing. It has a happy ending with the lawyer having to go before the bar and defend himself. Some days, the bad guys lose.

Just another murder in Bangladesh

Another intellectual, a professor of English, Rezaul Karim Siddiquee, was hacked to death in Bangladesh for the crime of being an atheist. The twist here, though, is that he wasn’t an atheist at all.

But according to his daughter, Rizwana Hasin, 23, he was not an atheist.

Siddiquee participated in cultural activities and wanted to open a music school in nearby Bagmara.

“He loved music. A concept is growing in Bangladesh these days that those who are interested in music, culture, are not believers in religion,” she told CNN.

First they come for the atheists, an easy target. Then they go after the artists, the poets, the writers, the musicians, the poets because they love the world too much and are not sufficiently fanatical. Then the teachers and other educators. This is one way to change the culture to make everyone believe as you do: chop down everyone who isn’t as ignorant as you are.

The future Bangladesh of their dreams will contain only people who know how to pray and how to use a machete, nothing more.