Microbiologists don’t need labs, apparently

All they need to do is visit student residences.

A student died after eating leftover pasta that had been left on his kitchen benchtop for five days.

The 20-year-old from the Brussels in Belgium became sick after eating leftover spaghetti with tomato sauce which had been prepared five days earlier and stored at room temperature.

Many thoughts are wheeling through my brain right now.

What kind of environment was this in that food left out for 5 days wasn’t covered in green fur?

Was it all furry with mold, and the student ate it anyway?

I don’t eat food that’s been refrigerated for more than a few days. How desperate was this person? What circumstances led someone to such a dire meal?

I don’t recommend this as an analysis tool, but how did it taste? Shouldn’t the first mouthful have been his first warning?

He became violently ill after eating it. Second warning. You’ve just done something incredibly dangerous.

I wonder how many student kitchens are greater health hazards than anything they might encounter in a microbiology lab. On second thought…I don’t want to know.

Students do not deserve death for poverty and carelessness. How about if we all recognize that what grows on our food and what we stuff in faces might be the greatest threat to our health and survival?

I swear to…who?

I am so glad that I don’t watch Fox News, but that other people suffer through it to let me know what they think is the latest threat to the Republic. It seems the newest change that has Republicans foaming at the mouth is a new oath.

The House Committee on Natural Resources has in the past used a witness oath that reads, “Do you solemnly swear or affirm that the testimony that you are about to give is the truth, the whole truth, and nothing but the truth, so help you God?”

The proposed new version will say, “Do you solemnly swear or affirm, under penalty of law, that the testimony that you are about to give is the truth, the whole truth, and nothing but the truth?”

If it helps them make up their minds, as a devious atheist with a scheming mind I could regard that “so help you God” clause as a loophole — God doesn’t help me, so the oath doesn’t apply. Also, you’ve just made me affirm a religious oath that I do not believe in, so by saying “yes”, I’ve already said a lie. A few more won’t hurt, then. And if my punishment for lying is hellfire, which I don’t believe in, then there is no compulsion here.

As Rob Boston points out,

The gang at Fox News might want to ponder the following statement: “A magistrate ought not to tender an oath to an unregenerate man … and cause him to take the name of God in vain.”

What left-wing Marxist said that? Actually, it was colonial-era religious freedom pioneer Roger Williams. Williams was a far-sighted man and a devout Christian to boot. Fox News could learn a thing or two from him.

Exactly. The Republicans already would consider me an unregenerate man, so why should I find that oath binding? It does have the benefit of giving us unregenerates an opportunity to spit in the face of their imaginary god, but otherwise, it doesn’t have much going for it.

Surprise! A billionaire’s favorite graph is one that justifies billionaires!

Wow. This is a capitalist miracle: extreme poverty is rapidly declining!

Except…what is extreme poverty? What about regular poverty? Is there something we could call moderate poverty? And, errm, where do those numbers from the 1800s and 1500s come from? Why is the 19th century represented with such a smooth, gradual improvement when we know that the lives of so many were ruined and suffering by colonialism (where does Rhodesia fit into this graph) and slavery? Those are charts that raise more questions than they answer.

Jason Hickel tries to answer some of the questions. The early numbers are guesswork, molded into the desired form, and the economic data are a case of applying an invalid metric to messy human reality.

What Roser’s numbers actually reveal is that the world went from a situation where most of humanity had no need of money at all to one where today most of humanity struggles to survive on extremely small amounts of money. The graph casts this as a decline in poverty, but in reality what was going on was a process of dispossession that bulldozed people into the capitalist labour system, during the enclosure movements in Europe and the colonisation of the global south.

Prior to colonisation, most people lived in subsistence economies where they enjoyed access to abundant commons – land, water, forests, livestock and robust systems of sharing and reciprocity. They had little if any money, but then they didn’t need it in order to live well – so it makes little sense to claim that they were poor. This way of life was violently destroyed by colonisers who forced people off the land and into European-owned mines, factories and plantations, where they were paid paltry wages for work they never wanted to do in the first place.

In other words, Roser’s graph illustrates a story of coerced proletarianisation. It is not at all clear that this represents an improvement in people’s lives, as in most cases we know that the new income people earned from wages didn’t come anywhere close to compensating for their loss of land and resources, which were of course gobbled up by colonisers. Gates’s favourite infographic takes the violence of colonisation and repackages it as a happy story of progress.

So money is a convenient proxy for real wealth, which is land and resources and labor, and using it as a metric conceals the fact that a few people have seized most of the real wealth, and masked their theft by doling out pittances to the displaced billions.

As if that isn’t enough, “extreme poverty” is an arbitrary parameter chosen to hide the ongoing grand larceny by people like Gates. It had to be set extremely low so that you wouldn’t see what’s actually been happening.

But that’s not all that’s wrong here. The trend that the graph depicts is based on a poverty line of $1.90 (£1.44) per day, which is the equivalent of what $1.90 could buy in the US in 2011. It’s obscenely low by any standard, and we now have piles of evidence that people living just above this line have terrible levels of malnutrition and mortality. Earning $2 per day doesn’t mean that you’re somehow suddenly free of extreme poverty. Not by a long shot.

Scholars have been calling for a more reasonable poverty line for many years. Most agree that people need a minimum of about $7.40 per day to achieve basic nutrition and normal human life expectancy, plus a half-decent chance of seeing their kids survive their fifth birthday. And many scholars, including Harvard economist Lant Pritchett, insist that the poverty line should be set even higher, at $10 to $15 per day.

So what happens if we measure global poverty at the low end of this more realistic spectrum – $7.40 per day, to be extra conservative? Well, we see that the number of people living under this line has increased dramatically since measurements began in 1981, reaching some 4.2 billion people today. Suddenly the happy Davos narrative melts away.

You know, if Bill Gates set a Universal Basic Income of $3 a day, he could set “extreme poverty” in the US to zero. What a triumph! I’m trying to imagine what I could do on $3 a day. I know I could live cheaply on a diet of rice and beans for that, but, well, just my mortgage is 10 times that, and it was -36°C this morning. Forget about owning a car. Or having electricity. Or getting sick. Right now, on an income considerably greater than that, one debilitating illness could wipe me out.

Shorter Bill Gates: Relatively fewer people are dropping dead in the streets of starvation or cholera today, so therefore concentrating billions of dollars into my hands is good for everyone.

Should he have done more?

Here’s an interesting problem in bioethics: a person knows the field, and has an appropriate response to an individual making a serious ethical lapse, but he doesn’t report it to other authorities. Should he have?

He Jiankui, the Chinese researcher who used CRISPR techniques on human embryos, shared his ‘success’ in emails to Craig Mello, a Nobel-prize winning biologist, who then replied a few times with regret.

“I’m glad for you, but I’d rather not be kept in the loop on this,” Mello wrote, according to the AP.

“You are risking the health of the child you are editing… I just don’t see why you are doing this. I wish your patient the best of luck for a healthy pregnancy.”

“I think you are taking a big risk and I do not want anyone to think that I approve of what you are doing,” wrote Mello, who didn’t reply to a request for comment from the AP.

“I’m sorry I cannot be more supportive of this effort, I know you mean well.”

Good for Mello that he was immediately aware of the problematic nature of the research. I think my response would involve a lot more ALL CAPS sentences and a heavy use of exclamation points, and probably some profanity, but then, I’m not a Nobel-prize winning scientist. I would have also said confidentiality be damned, and contacted a swarm of other scientists and the major scientific societies and given the heads up, with a suggestion that everyone ought to be prepared to make a statement on this kind of genetic manipulation when it finally goes public. Maybe Mello did make some quiet notifications to a select few, the article doesn’t say, but it does mention this:

Mello didn’t go public with the revelation – and stayed on as an adviser to He’s company until news broke about the controversial experiment.

Yikes. He’s company. Because of course every biomedical advance must be coupled to a mechanism for extracting profit from it. That’s a great big fat bioethical problem lurking under everything.

I would have guessed Tom Brokaw was one of us…he isn’t

I just heard that interview with Old Tom Brokaw in which he exhibited that common disease in the journalism profession, that attempt to sympathize with bad people to the point you lose sight of the fact that they are, in fact, bad, and you begin to share their views (see also Jonathan Haidt, who is not a journalist, but has acquired a terminal case).

And a lot of this, we don’t want to talk about. But the fact is, on the Republican side, a lot of people see the rise of an extraordinary, important, new constituent in American politics, Hispanics, who will come here and all be Democrats. Also, I hear, when I push people a little harder, “Well, I don’t know whether I want brown grandbabies.” I mean, that’s also a part of it. It’s the intermarriage that is going on and the cultures that are conflicting with each other.

I also happen to believe that the Hispanics should work harder at assimilation. That’s one of the things I’ve been saying for a long time. You know, they ought not to be just codified in their communities but make sure that all their kids are learning to speak English, and that they feel comfortable in the communities. And that’s going to take outreach on both sides, frankly.

If you don’t want “brown grandbabies”, that’s simply racism. No matter what shade their skin is, they’re still grandbabies, and still your grandbabies.

If you don’t like intermarriage, that’s simply racism. Don’t pick who you love by their skin color, and don’t demand your children share your weird racist color preferences.

Demanding assimilation is just another way of rejecting differences. That’s simply racism. I see Hispanic people moving into rural Minnesota, and while they may initially struggle with the language, they’re adapting quickly and their children are fluent in English. How fast do you expect them to “assimilate” anyway? Are you expecting them to abandon pride in their family and their heritage, too?

I’ve looked into my family history, and I see a series of Norwegian farmers who settled in Minnesota, and then kept bringing in Swedish mail order brides every generation, almost as if they were refusing to assimilate and insisted on Scandinavian families, rather than melding with the American mongrels. My great-grandparents’ house was full of yellow and blue and knick-knacks in Swedish and Norwegian, and they spoke with a heavy accent that was the result of a lifetime in exclusively Scandinavian-American communities. Were they bad assimilators? Am I unamerican because I still like the Nordic foods of my childhood and still celebrate Swedish/Norwegian traditions?

I don’t even know what “assimilate” means in the minds of these people. Liquify and blend? Because that doesn’t happen. We are who we are. Hispanic people are adding a new strand to our communities, and the only reason they might tend to vote Democratic is because Republicans think like Tom Brokaw. He can go back to celebrating his “Greatest Generation” while ignoring how awfully racist and sexist that generation was.

Reagan Redux

Donald Trump has been telling this story about souped-up cars driven by bad guys who run the border with women tied up (with blue tape!) in the trunk, and finding prayer rugs in the desert left by terrorists. It’s all a lie. He’s making shit up. Where did it come from?

…there’s a movie called Sicario: Day of the Soldado, which was released last summer, and which included a woman being tied up with tape, smugglers driving vast vehicles, and officials finding prayer rugs in the dirt near the border.

Again, just so we’re all clear, the movie is real, but the story is fictional. The script was written by screenwriters, not documentarians. The plot of the film is made up, as are the characters and developments that unfolded on screen.

As Rachel added, “In a normal administration, it would be insane to suggest” the president of the United States saw stuff in a movie and maybe thought it reflected reality. And who knows, maybe it’s just a coincidence.

We’ve been here before with a president who can’t tell reality from fiction.

It was Reagan, you might remember, who told an annual meeting of the Congressional Medal of Honor Society about a World War II B-17 commander who elected to stay with a wounded crewman rather than bail out of his stricken plane. “He took the boy’s hand and said, ‘Never mind, son, we’ll ride it down together.’ Congressional Medal of Honor, posthumously awarded.”

Actually, Congressional Medal of Honor never awarded. There’s some dispute about where Reagan got the story. Some said it was from the 1944 movie “A Wing and a Prayer” while others cited a Reader’s Digest item. Whatever its source, Reagan’s account was not true.

We have a madman at the helm, and he’s forcing us to ride it down together.

Trump has to have been informed that his story is false. Next time he tells it, someone tackle him, put him in an ambulance, and take him to the nearest hospital for a thorough neurological examination.

I keep turning down these honors

Gosh, you’d think I’d welcome the attention. I just got a call from an apologetics group asking if I’d consider debating Frank Turek next fall. My answer:

“Debates are a tool to give bad ideas, like those of Frank Turek, an undeserved platform. No.”

He was a nice guy on the phone, but I’m done with being nice to creationists. Oh, wait, I was done with that 30 years ago.

Advice for new professors

I was there once. I remember working in a research position where almost all of my colleagues were white men, and then getting a job where I had to work with large numbers of diverse students, and it was a major change. Fortunately, I buckled down and paid attention to all those workshops on bias and seminars on effective teaching, and I started out with a relatively large amount of respect for students with different backgrounds. You may think that it’s all administrative make-work, and that you just want to get back to work in the lab, and that it is the job of the students to accommodate you if they want to learn at your feet, but that’s not reality. You are part of a community of learning that includes students, and every part of the machine must be respected and treated well.

Learn that, and you won’t make the career-wrecking mistake this assistant professor did.

Although it may not be just her fault; that two other faculty members came to her to ask for help identifying wicked students who committed the egregious sin of speaking their native language suggests that there is a widespread problem at Duke University. I have two points to make about this remark: They were disappointed that these students were not taking the opportunity to improve their English and were being so impolite as to have a conversation that not everyone on the floor could understand. The first is that foreign students are going to get better practice in mastering English by listening to faculty in their classes, which are all in English, I ‘m sure, and by communicating with the majority native English-speakers in their community. Why are you seeking to hobble the ability of two fluent Chinese speakers to talk to each other? And second…why the hell do you think you have a right to listen in on the private discussions of students?

Also extremely dismaying is the implicit threat: they want to know the names of these students so they can deny them opportunities for internships or for work in their labs, and the department chair is amplifying that threat. This is completely unacceptable.

Megan Neely has resigned from her position as director of graduate studies in that program, which is entirely appropriate. No word on what happened to those nosy professors who wanted to blacklist a couple of students for a private conversation. It seems to me that this ought to provoke a major effort to get all the faculty in Duke Biostatistics into bias training, which will piss off a lot of them, but this is what happens when you neglect basic information on what ought to be university-wide standards for the people you promote to administrative positions. Apparently you all need to have your understanding of civil behavior refreshed.

Even old professors can royally fuck up and set a bad example for their colleagues, like this bozo:

Yes. Anxiety is a disability. I’ve had students force themselves to come into my offices, voices trembling and sweat streaming off their faces, because they’re terrified of authority (it’s not because I’m scary, I’m a teddy bear — they were somehow afraid of big mean old people generally). I’ve had students seize up and break down at the prospect of taking a test, even when they were competent on the material. Every university has policies in place to tell faculty what accommodations they must make for disabilities. They have ways of dealing with these problems. Every semester I’ll have two or three students who come to me with a note that says they’re not going to take tests in class — instead, I drop off exams at the library, where they have quiet rooms where they take the tests in a supervised but consistent and less stressful environment. This is a good thing. My job isn’t to make students suffer, but to make sure they comprehend the science I teach so they can succeed in subsequent courses and in their careers.

Also, don’t belittle students with disabilities.

The key thing to understand is that you are there to help students learn, not to create an obstacle course. When I teach a course in, for instance, ecological development, I’ll often include an assignment that involves public speaking in class — but if a student tells me that they’re totally wrecked at the thought, I’ll come up with an alternative that involves just as much work and allows them to demonstrate mastery of the material, because while public speaking is an important skill, it’s also not the primary subject of the course. Can you show me that you understand development? Good. I’ll recommend that they might want to take a separate course in communication in the appropriate department, or offer other options, like making a video for the class.

Maybe part of the problem is that people think they’re climbing a hierarchy and that they’re being given dominion over everyone with a lower rank, rather than that they’re joining a web of mutual responsibilities. Hierarchical thinking really does mess people up.

The most disturbing news yet

Insect populations are crashing.

“We knew that something was amiss in the first couple days,” said Brad Lister. “We were driving into the forest and at the same time both Andres and I said: ‘Where are all the birds?’ There was nothing.”

His return to the Luquillo rainforest in Puerto Rico after 35 years was to reveal an appalling discovery. The insect population that once provided plentiful food for birds throughout the mountainous national park had collapsed. On the ground, 98% had gone. Up in the leafy canopy, 80% had vanished. The most likely culprit by far is global warming.

Look at these numbers.

The Puerto Rico work is one of just a handful of studies assessing this vital issue, but those that do exist are deeply worrying. Flying insect numbers in Germany’s natural reserves have plunged 75% in just 25 years. The virtual disappearance of birds in an Australian eucalyptus forest was blamed on a lack of insects caused by drought and heat. Lister and his colleague Andrés García also found that insect numbers in a dry forest in Mexico had fallen 80% since the 1980s.

Data on other animals that feed on bugs backed up the findings. “The frogs and birds had also declined simultaneously by about 50% to 65%,” Lister said. The population of one dazzling green bird that eats almost nothing but insects, the Puerto Rican tody, dropped by 90%.

Lister calls these impacts a “bottom-up trophic cascade”, in which the knock-on effects of the insect collapse surge up through the food chain.

“I don’t think most people have a systems view of the natural world,” he said. “But it’s all connected and when the invertebrates are declining the entire food web is going to suffer and degrade. It is a system-wide effect.”

Exactly. We are part of a complex web of interdependencies, and it’s also a non-linear dynamical system. There’s a word for when parts of such a system show a pattern of failure: it’s called catastrophe. By the time you notice it, it’s too late to stop it.