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)

A slight improvement

A recent debate among Muslims on evolution had a better outcome than most of the similar debates among Christians — they ended up laughing at the creationists.

The high quality of scientific and theological discussion exposed the shallowness of Islamic creationists, such as Harun Yahya. One of his acolytes, Oktar Babuna, presented his arguments from Istanbul, via the internet. He kept on pointing to fossils as evidence that species have never changed in history. He also discounted any historical changes in the DNA. Babuna’s arguments were countered earlier on by both Abouheif and Jackson. But he unintentionally served as a comic relief, when the audience realised that after several hours of discussion, almost all of his responses included the mention of “fossils”, irrespective of the topic of discussion.

Yeah, “fossils” is the only argument they’ve got, and it’s a bad one. Anyone who has browsed Yahya’s Atlas of Creation knows that that’s what it is: page after page of stolen photographs of fossils next to stolen photos of extant organisms, claiming that there has been no change at all in millions of years, therefore evolution is false.

So it’s actually good progress that they ended up finding Yahya absurd. In the US (the debate took place in London), we instead end up nominating the loons for high office.

But, not to be complacent…most of the discussion was about reconciling evolution with Islam, and they trotted out the usual tropes, from “God inserted Adam in the natural order” to “science only tells us ‘how’ things happen, and not ‘why'”, and claiming that “the miracle of Adam is preserved theologically” without recognizing that those positions are almost as laughable as Yahya’s and Babuna’s.

I also have to take exception to the editor’s summary of the article: “A high-quality debate of a sensitive topic did not disappoint, as all panellists bar one accepted the scientific consensus”. Nope. The scientific consensus is that there is no teleological imperative in evolution at all. The panelists accepted a phenomenological narrative of evolution, while implicitly rejecting the mechanistic underpinnings of the science.

It’s still progress, though. American fundamentalists aren’t even that far along yet.

Maybe the conspiracy theorists need to conspire together more?

Would you believe that there are Sandy Hook truthers, people who believe the murders at the Newtown schools were completely faked? Some of them are even college professors! They think it was a cunning plan by Obama to railroad through gun control.

On the other hand, there are conspiracy theorists who have a completely different idea.

My worst fear: Dozens of terrorist sleeper cells, with five or six men each, would activate roughly at the same time and attack designated schools across the country. I’d be at work, and I would be helpless to retrieve my children and keep them safe from maniacs.

I imagined further that, from a terrorist’s point of view, these attacks would have a dramatic, profound effect on our collective psyche: No parent would allow his child to return to school to long as they were not secure from violent, lethal attacks. Our economy and economic security wouldn’t just hiccup; it would collapse.

I have a request. Can we please give them all the guns they so deeply desire, lock them in a room together, and let them…settle…the issue?

What was that about his Catholicism again?

William Oddie, the Catholic writer for the Catholic Herald who writes about Catholic concerns, is very irate. It seems a popular celebrity recently died, and the newspapers were fulsome in their obituaries, praising his charitable works and his lifelong generosity, but almost none of them mentioned that he was a devout Catholic who attended Mass several times a week, and that he even had a papal knighthood.

But why not mention that an important part of his life was attending daily Mass? There’s a deep dedication in the life of a man who gives away 90 per cent of everything he earns and so tirelessly does all the other things he did. You’d think that an obituarist would want to ask a simple question: where did all that come from? It’s almost as though they couldn’t bear to accept that the answer was his Catholicism: even that Catholicism itself could ever be the source of actual human goodness.

There must be an anti-Catholic conspiracy in the media!

Unfortunately, the celebrity was Jimmy Savile, the fellow who was revealed to have been raping children for decades, “one of the most prolific sex offenders” in Britain.

I have to ask a simple question: where did all that come from? It’s almost as though Oddie couldn’t bear to accept that the answer was his Catholicism: even that Catholicism itself could ever be the source of actual human evil.

And say, doesn’t the careful omission of his religious background therefore represent a pro-Catholic bias in the media?

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.

Dating tips!

Rats, it’s too late. If only the girls had studied these dating tips back in the day, I might not have grown into the sullen, resentful, entitled git illustrated here.

dancing

driving

And my favorite…

deserve

There’s the root of the whole problem! Men deserve your complete and total attention at all times!


While we’re on the subject of how the wimminz ought to behave, I should mention the F00t’s new video, titled, “Do Hot Girls Have All the Advantages?” Yep, it’s about how women have an edge by just being pretty.

Let that sink in for a bit.

Oh, I wish I were pretty! Then there’s an interesting reply: Why Can’t Thunderf00t Be More Like Indiana Jones? Isn’t it interesting how we can overlook superficial attributes in a man, but they’re always prioritized in women? And how some people can look on this skewed perspective as advantageous for women?

Although, I have to say, I don’t expect the guy to look like Indiana Jones, but am just dismayed at how he’s looking more and more like Pat Robertson every day. Robertson recently fielded a question from a young viewer about how he was troubled that his father seemed to be growing more distant from his mother; his answer was basically that his mother just wasn’t pretty enough, which was why all the romance is leaving the marriage.


One more: misandric pants.