A strange calm descends

It’s very strange. Classes start tomorrow, and I’ve got a tough semester ahead of me with both our core cell biology course and an upper level cancer biology course…and I freakin’ know what I’m doing. Syllabi are all laid out, my lectures are all planned, and I’ve got my first assignments loaded into the blunderbuss, ready to be fired out at the classroom. It’s like I’m organized or something, when usually I’d be bouncing off the walls, panicking at all the stuff I have to get done at the last minute. Is this what it’s like to be an old teacher?

So I’m going in to work this morning. I have to fuss over fish, and I do have one planned meeting with my new advisees, but otherwise, I think I’m going to tidy up a student lab, clean up my office (it looks like a library walked in and exploded right now), and sit back with a cup of tea. Weird.

I might get anxious because I feel too relaxed for the day before classes.

At least I’ve got that interview on Christian talk radio tomorrow, right before my first class, to get me jazzed up and wired. I don’t want to be too mellow when I start lecturing.

The Onion explains it all

The purported managing editor of CNN explains how they picked their top story in a fictitious opinion piece (which still rings very true).

There was nothing, and I mean nothing, about that story that related to the important news of the day, the chronicling of significant human events, or the idea that journalism itself can be a force for positive change in the world. For Christ’s sake, there was an accompanying story with the headline “Miley’s Shocking Moves.” In fact, putting that story front and center was actually doing, if anything, a disservice to the public. And come to think of it, probably a disservice to the hundreds of thousands of people dying in Syria, those suffering from the current unrest in Egypt, or, hell, even people who just wanted to read about the 50th anniversary of Martin Luther King’s “I Have A Dream” speech.

It’s all about the traffic, I guess, not the news…which any glimpse of CNN, Fox News, or the Huff Po will tell you.

I didn’t say anything about it because I was totally squicked out by the weird things she was doing with her tongue.

Just in time for my cancer class

In a few weeks, we’ll be having a discussion of the ethics of cancer research: what is a reasonable intervention in the case of a patient who has no hope of survival? And look at the interesting case that just appeared on my radar: two cancer surgeons who treated brain tumors by deliberately infecting them with bacteria.

Two UC Davis neurosurgeons who intentionally infected three brain-cancer patients with bowel bacteria have resigned their posts after the university found they had "deliberately circumvented" internal policies, "defied directives" from top leaders and sidestepped federal regulations, according to newly released university documents.

Dr. J. Paul Muizelaar, 66, the former head of the neurosurgery department, and his colleague, Dr. Rudolph J. Schrot, violated the university’s faculty code of conduct with their experimental work, one internal investigation concluded.

All three patients consented to the procedures in 2010 and 2011. Two of the patients died within weeks of their surgeries, while the other survived more than a year after being infected.

The premise behind their experimental procedure is probiotics, which immediately throws a warning on the play: there’s a lot of abuse of the concept out there.

Muizelaar and Schrot called their novel approach “probiotic intracranial therapy,” or the introduction of live bowel bacteria, Enterobacter aerogenes, directly into their patients’ brains or bone flaps. The doctors theorized that an infection might stimulate the patients’ immune systems and prolong their lives.

But there are some serious problems here. They didn’t have institutional review and approval of their procedure! That’s not a warning flag, it immediately calls the entire research into question and brings the ethics of the doctors under the microscope. You don’t get to do that.

And then there’s their logic. This is a disease with a median survival of 15 months. Their first patient died less than 6 weeks after the surgery, while the second lived for a year, which the report says “buoyed the doctors and seemed to bolster their theory”. That makes no sense at all — with so few trials they can’t possibly make that kind of assessment. Furthermore, their third patient died of sepsis.

At least it sounds like we’ll have something to talk about. That seems a paltry reward for three people’s deaths.

(via The Tree of Life)

If Dr. Phil is a fraudulent hack, is it OK to respect his opinions?

No.

This has been a brief example of easy answers to stupid questions. For the longer version, take a look at Dr. Phil’s recent excursion into JAQing off over rape, where he asked if it’s OK to have sex with a drunk girl.

What’s also awful about that notorious tweet is that his twitter history shows what he’s doing: he’s trolling for story ideas for his ghastly little show. If you think that stupid question was bad, just imagine an hour of folksy Dr Phil trying to sympathize with a rapist who uses drugs to remove women’s ability to deny them.

Remember when TV was called a “vast wasteland”? That was in 1961. They hadn’t seen anything yet. If the FCC had seen Dr Phil coming then, they would have shut down all the networks on the spot.

Don’t you wish you’d chosen UMM?

Now that the academic year is starting, the Star-Tribune puts out a short summary of success at Minnesota colleges. We’ll use it next year to recruit more students.

The University of Minnesota, Morris stands out among the state’s public four-year institutions for generating more grads than expected at a good price. UM-Morris Chancellor Jacquie Johnson attributes that result to a tight-knit, supportive campus culture that allows the nearly 1,800 students to build strong relationships with faculty. One of every three students at Morris is either minority or international in origin. The school’s success with that diverse student population warrants examination and imitation.

Yay, us!

Well said

Read what Mano says about Glenn Greenwald. I will simply agree 100% with it.

One of our major problems in the US is that the journalists have mostly curled up and died, and we’re getting our news from lickspittles and news organizations shackled to both corporate interests and political favoritism. I appreciate someone who breaks out of that incestuous relationship.

All SF should be oceanic

Because that’s what we are and where we come from — and every cell contains a little ocean…a hot little ocean rich with complex contaminants and lovely energetic cascades. So I’ll share two wonderfully appropriate examples today.

NASA

NASA

Tonight at 8pm ET Jennifer Ouellette talks with JPL planetary scientist Kevin Hand about the new film Europa Report and astrobiology. You’ve all seen it, right? It’s a new independent movie that mostly gets the science right, with a scientific crew sent off on a long voyage to Europa to find out what’s going on in the gigantic deep ocean beneath the icy crust. Then it turns into a bit of a horror movie when they do find out. There were a few things that made me go “huh?” — why is the first major manned mission after decades of neglect going all the way to Jupiter? They seem to have an awfully easy time punching through an ice crust that has to be at least several kilometers thick. And shouldn’t the surface of Europa be as inimical to its deep-sea life as the surface of the moon would be to ours? — but I managed to suspend disbelief for most of it, which is a good sign for me, arch-nitpicky-nerd that I am.

You should listen in, it could be interesting. Or watch the movie, it is on iTunes.

The other thing is that while idling in Minneapolis yesterday I read Neptune’s Brood by Charles Stross. It had a wonderfully intricate plot about interstellar banking (!) but there were a couple of sciencey bits that tickled me.

One is that the characters are all “robots” — humanity is extinct, we purely biological organisms are called “Fragiles”, and our cultural descendants are all engineered. They defy our usual conventions about robots, though. They’re made of cells called mechanocytes, larger and more elaborate than our cells, but with similar properties of managing thermodynamic flows and forming structural elements. I approve. I think life is always going to be a compromise between rigid durability and flexible plasticity, and modular subunits is always going to be the best way to go for allowing repair and remodeling. So despite being machines, these beings have all the properties of human beings and so can be relatable protagonists.

It also makes them far more malleable. Brain functions are entirely modular and stored discretely in a way that allows them to be maintained independently of the body, so one way to do interstellar travel is to transmit your software at the speed of light to a distant star, where a new body of mechanocytes can be assembled. This requires building an infrastructure at the other end, of course, which can only be done by sending machines at some small fraction of the speed of light to the target first, which is why the story is all about interstellar banking — it turns out that you need a stable way to maintain debt over centuries, and interesting protocols to transfer capital between multiple star systems most of whose inhabitants will never physically meet.

Anyway, the oceanic part: a lot of the action takes place on a water world called Shin-Tethys (Stross on world building). People adapted by engineering new bodies, so many of the near-surface inhabitants are mer-people. Meh. Who wants to have a compromise physiology? But the cool thing is that the robot-people who live very, very deeply and mine dissolved radioactive minerals are…squid-people. Yes, my utopia has a fictional existence. Furthermore, these are altruistic collectivist squid people. Squid people with a plan.

“…we plan to establish a world completely free of money, a world populated by a new teuthidian humanity, with a society based on consensus, not debt, and respect for collective autonomy, not competitive commerce. A world where the word ‘free’ will not be needed because nothing will cost anything and everything will be attainable!” Her skin shone with the pearly luster of her enthusiasm for the radiant future of the communist squid-nation: “I’m going to bring about the Jubilee! For the squid-folk, anyway.”

Wow. I thought I was the only one who had those dreams.

Recommended. Read a book, watch a movie, or listen to an interview tonight, your choice.

Signs & portents

The Times has released their rankings of the world reputation for various universities. The news is rather depressing.

Overall, the US continues to dominate the rankings, with seven of the top 10 places and a total of 76 institutions in the top 200 – one more than last year and 45 more than any other nation. The UK has 31 representatives, followed by the Netherlands with 12.

But the US’ dominance of the rankings masks a picture of decline.

Although the US ultra-elite at the summit of the rankings have generally managed to consolidate their positions – with the Massachusetts Institute of Technology rising two places to fifth and the University of California, Berkeley moving from 10th to ninth – many more American institutions fell than climbed the table.

“If you only give a casual glance at the top 200, you’re likely to think it’s just a round-up of the usual suspects,” says Ruby. “Yes, many of the big names of US higher education head the list – the ‘super-brands’ still dominate, and they will continue to do so while they attend to core business and protect their image as elite research-based institutions.

“But when you look more closely, most of the flagship US public universities are slipping down.”

How can this be? Slipping? Us? I believe it.

And that’s exactly what’s been happening, according to the Center for Budget and Policy Priorities. Public universities and colleges in nearly every state have seen their state funding decline sharply. Nationwide, states are on average spending 28 percent less this year than they did in 2008, a decrease of $2,353 per student. As a result, colleges and universities have had to raise tuition, make changes that undermine educational quality, or usually both.

Not surprisingly, the changing position of American universities mirrors the larger political economy of the United States: a few “super-brands” at the top (which educate the sons and daughters of the world’s elite) continue to stay at the top while most of the others (which are supposed to educate the children of the American working-class) are falling behind, both nationally and internationally.

Meanwhile, our Republican masters will consider all this a good thing, and propose more cuts to put those eggheads in their place, and consider more demands to include religious dogma in our science classes, and replace objective sources of information with more right-wing think tanks that give them the answers they want to hear.

The right-wing corruption of the process of science continues apace

The thoroughly discredited Regnerus study has met another ethical challenge. The Regnerus study was a bit of hackwork that tried to demonstrate, using Science, that gay parents were bad parents. It was an ideologically loaded mess endorsed by right wing think tanks that had massive procedural problems, but the conclusions aligned with what the think tanks wanted, so they pushed it.

Here’s an example of the procedural problems. One man, Brad Wilcox, seemed to do everything.

It’s also been alleged that W. Bradford Wilcox, associate professor of sociology at the University of Virginia with former ties to the conservative Witherspoon Institute that funded the study, served as a reviewer. He also consulted on the study, according to documents made public by the University of Texas. Wilcox, who also serves on the journal’s editorial board, did not immediately respond to a request for comment.

That’s only the tip of the problem. It turns out that Wilcox initiated the study, arranged the grant from the Witherspoon Institute, was planning to run the study (but had to beg off because he was too busy screwing science in other ways), was paid as a consultant to the study, and then was one of the reviewers of the paper. I presume he also signed the standard statement on the review that he had no conflict of interest.

You know, in science we make a very big deal about faking data — it can easily cost you your career, and definitely devastates your reputation. Shouldn’t subverting the entire process of peer review and independent evaluation count as something even worse?