No more Lance Armstrong

OK, we’re all done with professional bully, liar, and drug abuser Lance Armstrong, right?

The interview began with seven very effective yes or no questions, getting the central truths, the truths Armstrong has denied for so long, out of the way in a brutal incantation: Did you ever take banned substances to enhances your cycling performance? Yes. EPO? Yes. Blood doping? Yes? Testosterone, Cortisone, Human Growth Hormone? Yes. Was he doping for all seven of his Tour De France victories? Yes.

That Armstrong is a fraud who doesn’t deserve the millions of dollars he’s sitting on right now isn’t even a question anymore. The only real question is…is professional cycling roughly equivalent to professional wrestling on the hokum scale?

Blocked!

The good people at CFI have been getting spammed by the usual cranky suspects on twitter, so they have officially announced their policy for blocking people on twitter. It’s a good set of general rules, and is actually simple common sense: there are people out there who don’t recognize reasonable limits and use twitter for non-stop harassment. I personally am pretty liberal about blocking — with something like a hundred thousand followers, it’s fairly easy to get swamped with noise, and one person trying to dominate a conversation can really derail everything. As Fidalgo points out, “‘block and ignore’ is Twitter’s own advice about handling this kind of thing.”

There are six comments on the announcement so far. Would you believe every one of them is from a slymepitter whining bitterly about the policy? Yes, of course you would. When all they’ve got is “raw hectoring” and abuse to offer, of course they’re going to complain when someone declares that they won’t be listening to raw hectoring and abuse.

Catholic hospitals have ethics commissions?

But aren’t ethics in conflict with Catholic policy?

The latest case of Catholic callousness comes out of Germany, where a young woman was brought into an emergency center with signs of sexual assault; she had no memory of what had occurred and may have been doped with a date rape drug. She was treated by a Dr Maiworm, who then called the local Catholic hospital to arrange a gynecological examination, which ought to be routine. But that’s where it gets strange.

According to the paper, the doctor told Maiworm that the hospital’s ethics commission, after consulting with Cardinal Joachim Meisner, had decided not to conduct exams after sexual attacks, so as not to be in the position of having to advise on possible unwanted pregnancies resulting from the attacks.

Maiworm told the paper that the doctor did not change her mind, despite having been told that she had already written the woman a prescription for the morning-after pill. A colleague of Maiworm’s was given a similar explanation at another Catholic hospital in Cologne, according to the paper. Both hospitals are run by the Foundation of the Cellites of St. Mary.

The church is now claiming that it was all a “misunderstanding”, and that they don’t have a policy denying treatment to rape victims. But that still doesn’t explain why this woman was turned away and not given a routine examination.

I think the simplest solution for the future is to simply deny Catholic dogmatists any influence on medical decisions at all. Haven’t recent events been sufficient to conclude that they’re morally compromised?

It’s not just Louisiana

The contagion is spreading! Zack Kopplin has documented how vouchers abuse taxpayer investment in education in many places, not just Bobby Jindal’s corrupt little wanna-be theocracy.

Liberty Christian School, in Anderson, Indiana, has field trips to the Creation Museum and students learn from the creationist A Beka curriculum. Kingsway Christian School, in Avon, Indiana, also has Creation Museum field trips. Mansfield Christian School, in Ohio, teaches science through the creationist Answers in Genesis website, run by the founder of the Creation Museum. The school’s Philosophy of Science page says, “the literal view of creation is foundational to a Biblical World View.” All three of these schools, and more than 300 schools like them, are receiving taxpayer money.

Vouchers are nothing but a way to uncouple schools from a responsibility to meet educational standards, and the worst schools love ’em: they can get money for teaching garbage.

What I taught today: a little old-school history of embryology

This is an abbreviated summary of my class lecture in developmental biology today. This was the first day of class, so part of the hour was spent on introducing ourselves and going over the syllabus, but then I gave a lightning fast overview of the history of developmental biology.

Classical embryology began with Aristotle, whose work was surprisingly good: he approached the problem of development with relatively few preconceptions and fairly accurately summarized what was going on in the development of the chick. Most of this old school embryology is descriptive and was really a narrow subset of anatomy, but there were a few major conceptual issues that concerned the old investigators, in particular the question of preformation (the plan of the embryo is laid out in the egg) vs. epigenesis (the plan of the embryo emerges progressively). Aristotle, by the way, was on the right side of this debate, favoring epigenesis.

In the 19th century, development was seen as a progressive process that paralleled the hierarchical organization of nature — that is, developmental biology, what there was of it, was coupled to the great ladder of being. This is not an evolutionary idea, but reflects the view that there was a coherent pattern of greater and lesser development that was part of a coherent divine plan for life on earth. The German ‘Natural Philosophers’ pursued this line of reasoning, often to degrees that now look ridiculous in hindsight. In contrast, there were developmental biologists like Karl Ernst von Baer who wanted nothing to do with a cosmic teleology but instead preferred to emphasize observation and data, and simple minimal hypotheses.

In the late 19th century, developmental biology split into two directions. One was a dead end; Ernst Haeckel basically lifted the explanatory framework of the natural philosophers, replaced divinity with evolution, and tried to present development as a parallel process to evolution. Von Baer had already demolished this approach, and despite a few decades of popularity Haeckelian recapitulation died as a credible framework for studying evolution in the early years of the 20th century. The other direction developmental biology took was Wilhelm Roux’s Entwicklungsmechanik, or experimental embryology. This was an approach that largely eschewed larger theoretical frameworks, and focused almost exclusively on observation and experimental manipulation of embryos. It was a successful discipline, but also divorced mainstream developmental biology from the evolutionary biology that was increasingly influential.

As examples of Entwicklungsmechanik, I discussed Roux’s own experiments in which he killed one cell in a two-cell embryo and saw partial embryos result, an observation that fit with a preformationist model, but more specifically a mosaic pattern of development, in which patterns of development were encoded into the cytoplasm or cortex of the egg. Those experiments were seriously flawed, however, because the dead cell was left attached to the embryo, and could have deleteriously affected development. The experiments of Hans Driesch were cleaner; he dissociated embryos at the four cell stage, cultured each blastomere independently, and discovered that each isolated cell developed fully into a complete, miniature larva.

Driesch, unfortunately, interpreted these results to imply that there was an entelechy, or guiding intelligence outside the embryo, and that the only conceivable explanation was the existence of purpose behind embryology. This was also a dead end; the modern explanation for the phenomena is that they regulated, that is, that cells determine their fate by interacting with one another, rather than some kind of cosmic plan. And that’s really going to be a major focus of this course: how do cells communicate with one another, how are genes regulated to set up coherent and consistent patterns of gene expression that produce the organized cell types we find in an adult multicellular plant or animal?

That set up the next lecture. Entwicklungsmechanik, while representing a solid and productive research program, quickly reached its limits, because what we really needed to examine were those patterns of gene expression rather than trying to infer them from observations of morphology. The big breakthrough was the melding of developmental biology and molecular biology — most of the modern developmental biology literature focuses on examining interactions between genes. So on Wednesday we’ll get another fast overview of the molecular genetics research program, and a bit of evo-devo.

Slide thumbnails (PDF)

The death of Aaron Swartz

Many of you already know that Aaron Swartz, an online activist, committed suicide earlier this week. I didn’t know much about him, but now I’ve learned two things.

One, he was a victim of depression. I’ve never experienced this personally — at worst I can say I’ve been sad and stressed at time — but let’s be clear about something: depression is something altogether different. Swartz wrote about his depression, and got across a little bit about what it actually feels like. This is good communication.

Your face falls. Perhaps you cry. You feel worthless. You wonder whether it’s worth going on. Everything you think about seems bleak – the things you’ve done, the things you hope to do, the people around you. You want to lie in bed and keep the lights off. Depressed mood is like that, only it doesn’t come for any reason and it doesn’t go for any either. Go outside and get some fresh air or cuddle with a loved one and you don’t feel any better, only more upset at being unable to feel the joy that everyone else seems to feel. Everything gets colored by the sadness.

At best, you tell yourself that your thinking is irrational, that it is simply a mood disorder, that you should get on with your life. But sometimes that is worse. You feel as if streaks of pain are running through your head, you thrash your body, you search for some escape but find none.

Two, I’m outraged at the criminal abuse by the justice system that exacerbated his problems. The man was hounded to death, threatened with long prison terms by MIT and JSTOR, the journal archive service.

Aaron’s death is not simply a personal tragedy. It is the product of a criminal justice system rife with intimidation and prosecutorial overreach. Decisions made by officials in the Massachusetts U.S. Attorney’s office and at MIT contributed to his death. The US Attorney’s office pursued an exceptionally harsh array of charges, carrying potentially over 30 years in prison, to punish an alleged crime that had no victims. Meanwhile, unlike JSTOR, MIT refused to stand up for Aaron and its own community’s most cherished principles.

You might be wondering what awful crime he committed that justified arresting him and confronting him with a 50 year prison sentence: he downloaded scientific research articles and then made them available to others (Wait…apparently, he didn’t even share them, but just downloaded them via MIT’s protocols). Uh-oh. I’ve done this…just not on the scale of Swartz’s efforts. Swartz was committed to Open Access.

This is the problem: not that Swartz opened the door to scientific research, but that we’re laboring under an antiquated system of scientific information storage that privileges profit-making over open access to the results of publicly-funded research.

Did you have to remind me?

I wake up this morning to discover Doonesbury telling me stuff I already know.

newsem

Yep, classes start for me tomorrow at 8am. I have a lighter load than the grueling mess last semester, and I also get to teach my fave class, developmental biology. No new paradigms this time, though — I think it worked fairly well the way I did it last time, with a mix of once weekly lectures and lots of class time dedicated to discussion and analysis. I’ll also be compelling my students to set up blogs and write about science publicly, so I’ll occasionally be linking to a lot of student work.

One thing I’m considering doing differently…I might post summaries of lectures and discussion topics here, if time allows. Public exposure of all the stuff that usually goes on behind the doors of the classroom? I don’t know if the world is ready for that.

I’m including the syllabus for my developmental biology course. Just in case you think I’m totally slacking with just one class, I’m also teaching a course called Biological Communications, a writing course that tries to get students to read and write in the style of the scientific literature, and am also doing individual studies with 5 students.

I shoulda checked the reviews first

I watched the movie Red Lights last night on Netflix. The first part of the movie was strikingly familiar: it practically stole the life story of James Randi. There was the Peter Popoff exposé, the psychic surgery stunts, the usual whirl of frauds and fanatics, all under different names with different details, but the same general stories about exposing flim-flam. And then it had a marvelous cast: Sigourney Weaver, Robert De Niro, Cillian Murphy. The whole movie is following a good ol’ skeptical trajectory…and then, the ending. Oh, jebus, I have never seen a movie so thoroughly implode as this one did with that ending.

Stop here. Don’t read further, unless you want to know how it ends, because I’m going to give it all away. Completely. This isn’t just a spoiler, it is full disclosure.

[Read more…]

Every man thinks he’s Clint Eastwood

Sam Harris has really done it now. He’s stepped into the gun control debate with The Riddle of the Gun, and he’s taking the side of Wayne LaPierre of the NRA. And he’s also making a series of logic-defying assertions that have no credibility at all. I’m not even going to try to work through them all; this subject is clearly a bit of an obsession with him. But throughout, he takes a very personal and rather paranoid view of the world and makes it a justification for individual self-defense, which I think is his big mistake. For instance,

…if a person enters your home for the purpose of harming you, you cannot reasonably expect the police to arrive in time to stop him. This is not the fault of the police—it is a problem of physics.

Hmmm. If I’m on a crowded street, and the person behind me pulls a knife, I can’t expect the police to stop him in time, either — it is a problem of physics.

If the guy in the house across the street has a sniper rifle aimed at my bedroom window, waiting for my silhouette to cross his scope, I can’t expect the police to stop the bullet in time — it is a problem of physics.

If a disgruntled student rolls up to my front door in a tank, I can’t expect the SWAT team from Minneapolis to get all the way here in time — it is a problem of physics.

What I see over and over again in Harris and rabid defenders of gun ownership is something other than just merely seeing guns as a tool: it’s the cult of the rugged individual, the lone cowboy on his own in hostile territory, where the only recourse is to be quick on the draw. What’s the answer to any trouble? Why, you take care of it yourself, usually by killing the troublemaker. It’s a simple, quick solution that doesn’t require any thinking at all.

He takes a complicated problem — that an individual wants to do him great harm (something I have no trouble believing) — and reduces it to a simplistic scenario — the hostile bad guy is in his house, with a gun! — that can only be resolved by his personal decisiveness and training in firing right back at him.

Do I need to point out that in his scenario, he has already lost, no matter how well-trained he is with a firearm? He is having a gunfight in his home, with his family around him. Imagine yourself in your bedroom, pulling a pistol out of a bedside drawer, loading it, and calmly taking a few shots in the direction of the hallway, without the presence of an intruder to complicate and make even more dangerous the situation. This is not an action without consequences and without risk. But this is the preferred nightmare of the gun fanatics.

I prefer a multi-layered defense that relies on the cooperation of a community. I don’t want a gun put in my hands, because by the time the gun would be useful there have been multiple catastrophic failures of the whole system. An intruder should not be in my house. How about better locks, a security system, and regular police patrols in my neighborhood? An intruder should not be heavily armed. How about serious gun control that limits access to guns and monitors those who do have them? The intruder should not be vengefully gloating about the glory of shooting someone. How about changing the culture to stop worshipping gun violence, to stop thinking that killing an enemy resolves a problem rather than amplifying it?

I know already what response that will get: that it’s a starry-eyed optimistic dream. But what they won’t care about is that Harris’s dream of battling an evil-doer to the death with his well-practiced expertise in firing a gun is just as pie-in-the-sky, and that even in its most benign outcome, is still a horror and a nightmare.

This is my dismissal of the whole gun debate: that the answers the gun advocates propose all amplify the problem. The problem is the ready availability of guns and the willingness of self-righteous people (because, really, even the people gunning down school children are steadfast in their confidence that what they are doing is both right and necessary, as much so as the homeowner defending himself against a burglar) to resort to violent action to resolve conflicts. But they don’t bother to recognize that by the time deadly force is needed, it’s too late.

I promised I wouldn’t get sucked into a line-by-line dissection of Harris’s post. Fortunately, Eric MacDonald has exposed many of the logical fallacies in his argument, and Sean Faircloth has the facts and numbers that show his rationale is bogus.

I just want to emphasize that it’s a huge mistake to make the debate about the physics of the ultimate confrontation. The debate should be about how to make those gun-on-gun confrontations less likely.