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It’s not fair. The horrible wretched campus conservative newspaper gets shoved under my office door in multiple copies, and they threaten to sue me for throwing them out, but the local chapter of Queer Devil Worshippers for a Better Future come out with a newsletter, and I don’t know about it until I stumble across a copy in a dark hallway. I am so here for this. Here’s the letter from the Void Mother.

And here’s a sample article, “How to Ritually Consume Your Girlfriend in 10 Simple Steps” (Don’t worry, step 1 is to ask for consent).

The part about whispering into her belly button “Be the deviant and strange change you wish to see in the world.” Charming.

I hope all the parents of our students are also charmed and consider this a perfectly lovely way to live. It’s so much sweeter than the hatefests we get from the College Republicans.

Whisper Network vs. Old Guys’ Network

Theres been another development in the story of BethAnn McLaughlin. To recap: she’s a neuroscientist at Vanderbilt who also has a reputation for activism for women’s rights in science. She was up for tenure, which she was initially awarded, and then, in a peculiar maneuver, suddenly a second committee was convened to revoke tenure, something I’d never heard of being done before.

The shocking new development is that a member of the second committee was abruptly placed on leave a few months ago. Why? Because he’s accused of assaulting a graduate student! Furthermore, Vanderbilt had been sitting on this accusation for almost a year before deciding they needed to take action.

As of August this year, Vanderbilt University neuroscientist David Sweatt has been on leave while the university looks into allegations that he drugged and sexually assaulted a student at a conference, according to documents obtained by Buzzfeed News and published in a report yesterday (October 31). The school initially became aware of the accusations nearly a year before, in September 2017, but determined there were no grounds for action at the time.

“Nauseous in my kitchen reading this. Vanderbilt knew for 11 months Sweatt was dangerous and did nothing,” climate scientist Sarah Myhre at the University of Washington writes in a tweet about the Buzzfeed article yesterday. “Students and trainees – like lambs to slaughter,” she continues.

It was a tweet by Myrhe from August describing the allegations that prompted Vanderbilt to suspend Sweatt, Buzzfeed reports.

Here’s that tweet:

One has to wonder how this guy continued to get on committees that decided women’s fates while under this cloud of suspicion. I think there must be an Old Guys’ Network that gets activated when their privilege is threatened, and all we have to counter it is a Whisper Network.

Wheee! It was off to the emergency room with meee!

Yesterday, I stood up from my chair and nearly fell over. Then I started to walk, and it was like the world was heaving and swaying all around me, and I nearly fell a couple more times as I walked down the hallway, clinging to furniture and walls to keep myself upright. Something was clearly wrong; was I having a stroke? A brain tumor? The aliens had used their mind control beams to take over, making me all herky jerky? I told my wife that it looked like a trip to the emergency room was in order, especially since all the spinning and heaving was making me acutely nauseous.

We got a lift from our neighbor, Ted — yeah, not even fear of my brain imminently exploding will motivate us to pay the bill for an ambulance pick-up — and made it to the emergency room to discover that Saturday, 16 February, is the day everyone has an accident and the waiting room was packed. Fortunately, presenting as an old man pale and sweating and swaying gets you bumped to the front of the line. Sorry, chainsaw accident! Sorry, broken bone! Sorry, ebola victim! Old dude privilege, coming through!

It may have been the fact that I looked like an imminent font of projectile vomiting, which I was, and they wanted to avoid the mess. As soon as they got me in an examining room, it all came up. I’d picked the wrong day to experiment with trying my hand at spätzle in the kitchen, because that stuff looks like a horror second time around.

Anyway, I got diagnosed: Benign Paroxysmal Positional Vertigo, or BPPV. My inner ear is messed up. Apparently this is fairly common in us old people over the age of 60, and treatment is simple: I’m taking seasickness pills, which are already helping, and there are some easy physical therapies that can lead to the problem going away in a few days to weeks.

So right now, I’m just sitting quietly, no sudden moves, and the world is mostly motionless. I’ll try to avoid abruptly standing up or turning around to make you all suddenly jump up and get shaken around. Also, no spätzle.

Hometown Klan

David Leppert

I’m browsing, as one does, and reading a bit of labor history, and the name of my hometown, Kent, Washington, comes up. I had to look, because I knew that town well — I’m familiar with the streets, the major buildings, my father’s family lived there for generations, and it always seemed like a dead quiet small town that was never going to come up in history. There’s nothing there! Banks and gas stations, a five-and-dime, a sporting goods store, lots of little business and residences, and when I was growing up, it was mainly a farming community. They grew a lot of lettuce and cauliflower.

So what do I find? The mayor of Kent in the 1920s (before my time, before my parents’ time, but my grandparents would have been kicking around then) was an Exalted Cyclops of the Ku Klux Klan. This wasn’t Mississippi, but Washington state, and apparently the KKK had a surge of popularity in the 20s, to the point where a KKK member could be elected to office and I guess we were known as a “100% Klan town”.

Notable Klan members elected to public office in Washington State include the Mayor of Kent, David Leppert, and Bellingham City Attorney Charles B. Sampley. Politicians who were likely members of the Klan include the Mayor of Blaine, Alan Keyes, and Wapato’s Director of Schools, Frank Sutton. Given that the Klan was a secret society, it is hard to differentiate Klan allies from Klan members, and it is likely that many other local elected officials in Washington state were Klan members.

Fortunately, their tenure was short and the Klan faded away fairly quickly, in part thanks to people who stood up against them.

Klan activity in the Valley reached its high point in mid-July of 1923. On July 14, the Klan held its first “Konvention” in the state of Washington near Renton Junction and initiated some 500 to 1,000 new members. A rally for the general public, complete with fireworks and multiple cross-burnings, was held that evening at Wilson’s Station four miles south of the park. The Kent Advertiser-Journal described “a monster crowd of thousands of people who came in between 2500 and 3000 automobiles to participate and witness the ceremony.” The Washington Co-Operator estimated that between 10,000 and 20,000 attended. The Globe-Republican, however, indicated that attendees were “attracted chiefly by curiosity and by the lingering suspician [sic] that an exciting clash might occur between Klansmen and representatives of Sheriff Matt Starwich’s office.” The state had a law forbidding public gatherings of masked persons except for masquerades and similar events. Before the rally, the Klan openly dared Starwich to enforce the law, and he insisted he would. The Klan backed down, however, and only wore the masks briefly. Seemingly, the dare was simply a publicity stunt and, if so, it worked. Starwich retaliated a month later by firing a deputy working on the Northern Pacific Railroad for taking part, commenting, “I won’t stand for any Klansmen being connected with my office.” Afterwards, reporting on the Klan dropped off sharply and activity quieted.

While they weren’t parading about in robes, though, they reflected a real problem in that community. People might have chastised the Klan, but at the same time, they’d later applaud internment of our Japanese compatriots.

Traditionally, the Klan has been portrayed as a violent, backwards-looking, and extremist organization that was part of the conservative mood that followed World War One. Recent works, however, emphasize that, for better or worse, the Klan was rooted in the mainstream of society, often attracted leading citizens in communities throughout the country, and championed popular causes. This was the case with the White River Klan. While it is difficult to discern why people in the Valley joined the Klan from newspaper accounts that we have available, Klan ideology clearly spoke to fairly common sentiments. For example, Prohibition enforcement was a major issue in Auburn politics and the Klan’s call for rigorous enforcement was not out of the ordinary at all. Similarly, there was substantial, mainstream, anti-Japanese sentiment. The state of Washington, not the Klan, passed Alien Land Laws to prevent Asian immigrants who, by law, could not become citizens from owning or renting land. When Klan organizers like Jeffries spoke out against Japanese immigrants, they found a receptive audience. Lastly, the sheer spectacle value of the Klan should not be overlooked. The Klan had a mystique surrounding it. People were curious about it and rallies provided entertainment. Most of those who attended meetings and rallies went because it was something to do and did not join, regardless of their feelings about Klan ideology.

Most of that lettuce and cauliflower was grown by Japanese families; my wife worked in those fields in the summer when she was growing up, and I worked in a nursery owned by a Japanese horticulturist throughout high school. They didn’t speak about it, but there was this poison soaking in our town from the time the Klan was thriving there.

I suddenly have a different perspective on my childhood home.

Here’s how you evaluate the scientific rigor of a field

Warning: it’s boring, tedious, hard work. There’s nothing flashy about it.

First step: define a clear set of tested standards. For clinical trials, there’s something called Consolidated Standards of Reporting Trials (CONSORT) which was established by an international team of statisticians, clinicians, etc., and defines how you should carry out and publish the results of trials. For example, you are supposed to publish pre-specified expected outcomes: “I am testing whether an infusion of mashed spiders will cure all cancers”. When your results are done, you should clearly state how it addresses your hypothesis: “Spider mash failed to have any effect at all on the progression of cancer.” You are also expected to fully report all of your results, including secondary outcomes: “88% of subjects abandoned the trial as soon as they found out what it involved, and 12% vomited up the spider milkshake.” And you don’t get to reframe your hypothesis to put a positive spin on your results: “We have discovered that mashed-up spiders are an excellent purgative.”

It’s all very sensible stuff. If everyone did this, it would reduce the frequency of p-hacking and poor statistical validity of trial results. The catch is that if everyone did this, it would be harder to massage your data to extract a publishable result, because journals tend not to favor papers that say, “This protocol doesn’t work”.

So Ben Goldacre and others dug into this to see how well journals which had publicly accepted the CONSORT standards were enforcing those standards. Read the methods and you’ll see this was a thankless, dreary task in which a team met to go over published papers with a fine-toothed comb, comparing pre-specified expectations with published results, re-analyzing data, going over a checklist for every paper, and composing a summary of violations of the standard. They then sent off correction letters to the journals that published papers that didn’t meet the CONSORT standard, and measured their response.

I have to mention this here because this is the kind of hard, dirty work that needs to be done to maintain rigor in an important field (these are often tests of medicines you may rely on to save your life), and it isn’t the kind of splashy stuff that will get you noticed in Quillette or Slate. It should be noticed, because the results were disappointing.

Results
Sixty-seven trials were assessed in total. Outcome reporting was poor overall and there was wide variation between journals on pre-specified primary outcomes (mean 76% correctly reported, journal range 25–96%), secondary outcomes (mean 55%, range 31–72%), and number of undeclared additional outcomes per trial (mean 5.4, range 2.9–8.3). Fifty-eight trials had discrepancies requiring a correction letter (87%, journal range 67–100%). Twenty-three letters were published (40%) with extensive variation between journals (range 0–100%). Where letters were published, there were delays (median 99 days, range 0–257 days). Twenty-nine studies had a pre-trial protocol publicly available (43%, range 0–86%). Qualitative analysis demonstrated extensive misunderstandings among journal editors about correct outcome reporting and CONSORT. Some journals did not engage positively when provided correspondence that identified misreporting; we identified possible breaches of ethics and publishing guidelines.

Conclusions
All five journals were listed as endorsing CONSORT, but all exhibited extensive breaches of this guidance, and most rejected correction letters documenting shortcomings. Readers are likely to be misled by this discrepancy. We discuss the advantages of prospective methodology research sharing all data openly and pro-actively in real time as feedback on critiqued studies. This is the first empirical study of major academic journals’ willingness to publish a cohort of comparable and objective correction letters on misreported high-impact studies. Suggested improvements include changes to correspondence processes at journals, alternatives for indexed post-publication peer review, changes to CONSORT’s mechanisms for enforcement, and novel strategies for research on methods and reporting.

People. You’ve got a clear set of standards for proper statistical analysis. You’ve got a million dollars from NIH for a trial. You should at least sit down and study the appropriate methodology for analyzing your results and make sure you follow them. This sounds like an important ethical obligation to me.

Are you thinking of trusting the internet?

Don’t. I stumbled across this on Quora, a site that seems to specialize in collecting uninformed questions from ignorant people, and allowing other ignorant people to provide misinformation.

You may notice that it has 513 views. It also had about 40 upvotes, meaning 40 people read this and came away thinking they’d learned something.

It’s very confusing. So, if I’m planning a cannibal meal, and a right-handed person eats my left-handed victim, does everything just pass through (great if you’re trying to lose weight!), or does it turn all my dinner guests left-handed?

Oh my god, I’ve been in Minnesota for too long

Because I started drooling and making strange guttural noises when I read this story of a remote-controlled 3-D printed snowblower. I was having these mind-blowing fantasies of sitting in my home office with a joystick, clearing my driveway while sitting in warmth and comfort.

(Turn the volume down, you don’t need to hear the awful cacophony of the soundtrack to this clip)

I don’t have a 3D printer, and I probably couldn’t afford the kind of model that would suffice for that thing, so why doesn’t someone come out with a pre-assembled version for sale? I’m not sure this one has enough oomph to handle the mountain ranges of snow that the snowplows drop across our driveway, but it could probably handle our sidewalks.

On second thought, maybe it would be nice to have one where I could just print up damaged parts as I need them. Our existing manual snowblower is currently laid up with a cracked gas tank, and having one I could fix on the spot would be so handy.

Behe’s polar bears

Michael Behe has a problem: he uses polar bears as an example of how “damaging” a gene can have an advantageous effect. As Nathan Lents explains:

Behe offers them as an example of how harming genes can help an organism and lead to adaptive evolution. Imagine an ancestor bear population that looked pretty much like brown bears. Then came some random mutations that reduced the production or deposition of pigment into the fur of the bears. This made the bears white and – voilà! – the bears acquired natural camouflage in snowy climates so as to better sneak up on their prey.

This seems like a pretty straightforward example and most people will simply take it at face value. Behe jumps from this example to his claim that this is all that unguided mutations can do. However, even in this apparently “pro-Darwinism” example, Behe exaggerates his claims and misrepresents what science has actually revealed. The evolution of polar bears was not only a matter of harmful mutations.

The first part is fine: there are all kinds of ways a genetic change can produce an adaptive phenotype, and downregulating a gene is one of them. It’s the second part that’s the problem. Behe leaps from a few examples to an assertion that this is a universal rule, which is not the case. Lents shows another example in polar bears.

Look at those polar bears, slurping down all those sugary soft drinks. It’s a little known fact that they’re using Coca-Cola to wash down their diet of fatty, blubbery seals, and they pretty much eat nothing but meat and fat, which, if any of us tried the Polar Bear Diet, we’d be dead of coronary disease in short order. It would be interesting to know how these animals cope with a diet high in cholesterol and fats, so Lents cites a paper that looked at the molecular sequence of apolipoprotein B (APOB), a protein that is important in the transport of fats in the blood, and compared it to that of brown bears. Surprise — the form found in polar bears is better at clearing fats from the bloodstream.

Substantial work has been done on the functional significance of APOB mutations in other mammals. In humans and mice, genetic APOB variants associated with increased levels of apoB are also associated with unusually high plasma concentrations of cholesterol and LDL, which in turn contribute to hypercholesterolemia and heart disease in humans (Benn, 2009; Hegele, 2009). In contrast with brown bear, which has no fixed APOB mutations compared to the giant panda genome, we find nine fixed missense mutations in the polar bear (Figure 5A). Five of the nine cluster within the N-terminal ba1 domain of the APOB gene, although the region comprises only 22% of the protein (binomial test p value = 0.029). This domain encodes the surface region and contains the majority of functional domains for lipid transport. We suggest that the shift to a diet consisting predominantly of fatty acids in polar bears induced adaptive changes in APOB, which enabled the species to cope with high fatty acid intake by contributing to the effective clearance of cholesterol from the blood.

Clearly, the authors do not expect the polar bear APOB to be “broken.” Rather, a bare majority of the amino acid changes are in the most important region for the clearing of cholesterol from the blood. In other words, these mutations likely enhance the function of apoB, at least when it comes to surviving on a diet high in saturated fats.

So APOB in polar bears isn’t broken at all. It does carry mutations relative to brown bears, but they haven’t resulted in reduced functionality at all — quite the opposite, actually.