Whatever happened to Boyan Slat’s test?

Slat was the wunderkind who came up with an idea, using floating booms, to clear the oceans of floating plastic waste. He was mocked by all the scientists who actually knew something about the problem, but hey, this is science. Empirical results trump all. He ran a trial last summer, and if his scheme worked, you know we should all be writing apologies.

He tried a small scale (2 million euros!) test, in a patch of the sea that was calmer and more temperate than the Pacific, where he ultimately hoped to clear up the great Pacific garbage patch. Guess what?

It didn’t work, as expected. It was broken up after 2 months and didn’t collect any garbage.

Man, it sure would have been nice to have to write that apology.

Course Design: Blocking out the course

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Hola, amigos, it’s been a long time since I rapped at you, but I’ve been busy. I’ve been staring at calendars and juggling time in my head. I sort of had to gaze in horror at my spring semester schedule, and had to spend some time working on my other classes. Here’s what my weekly calendar looks like:

spr2017schedule

One thing is very nice: I’ve arranged to have Fridays wide open. That does not imply that I’ll spend every Friday in my PJs sipping Scotch — that’s when I’ll be catching up on grading and composing lectures for the coming week. But hey, it also means if anyone wants to invite me out to speak somewhere, I’ve got a 3-day weekend every week.

Other days are mostly gutted by my genetics and genetics lab courses, which will take up the bulk of my time. Those lectures are mostly already planned out and done, as I’ve taught this course every year for almost two decades now. There’s still a lot of work required there, and I have to keep that in mind when budgeting time for this course, Ecological Developmental Biology. Right away, you might spot the fresh horror involved in that class: it’s a 100 minute lecture course, twice a week, at 8am. Ack. I’ve got to be ready to go first thing those mornings, and I have to have a larger than normal block of material. Double ack: students have to be awake and alert.

So right away, I’ve decided that that’s too much for early morning attention spans. Each class is going to be broken in two, with a break in between. I’m going to bring in my tea kettle to class, and it’ll be enough time that if they want to run over to the next building and grab coffee, that’s going to be fine. Let’s be civilized about all this.

I’m also going to mix up my teaching style. I plan to give a lecture-style general overview of a topic from the textbook in the first half, recess briefly for coffee and tea, and then meet again for a more detailed, interactive discussion, using a paper from the primary literature as a nucleus for the conversation. That also sounds pleasant and civilized. There will be some exceptions to that, though.

This is the only course in developmental biology these students will have taken, so I feel some obligation to bring them up with the basics of the field. The first two weeks will be a crash course in development, hitting some key processes that they ought to understand before we dive deeper. So on my calendar I’ve blocked out the first two weeks to include short lectures in the history and philosophy of development, polarity, gastrulation, limb development, and craniofacial development. Again, brief overviews of those topics suited to early morning undergraduates, with time for discussion and interaction. Fortunately, Scott Gilbert’s Developmental Biology text is available for free on NCBI, so I can assign supplemental readings from that.

What about assessment? First day I’m going to give them 3 assignments.

  • Read Lewontin’s The Triple Helix. This is the philosophical backbone of the course, and we’ll be discussing it in class in the third week. This discussion will be driven by questions I will ask (I’m not giving answers), and I will put individuals on the spot to answer them. This will be a preview of the oral exam they’ll be taking at the midterm.

  • Each student will be assigned a week in human development, or a key organ system, and will give a 5 minute summary presentation in the third week. I’ll make available Langman’s Medical Embryology, which is the only source they’ll use. Again, this will be a warm up to a longer presentation they’ll give at the end of the term.

  • They’re going to be warned that they’ll be given half the class period in the last weeks of the semester to individually present and discuss a topic and at least one primary research paper. Start thinking and planning!

There, I’ve already wiped out a big chunk of the semester. First two weeks, a crash course in developmental biology. Third week, a group in-class oral exam on the topic of The Triple Helix, and a series of very short presentations by the students to summarize human embryology. And then I’ve blocked off the last month of the course for in-depth student presentations.

Other assessment-related assignments: in the 6th week, they’re to give me a proposal for their presentation, with a short annotated bibliography. In the 8th week, I’ll expect an outline of their presentation. There’s no time to waste, so it all starts early, and I’m going to be mean about deadlines. I know how students can procrastinate over semester long projects.

The 8th week is also set aside for one-on-one oral exams, a half-hour per student. There will be some general questions, and I’ll also give each student some customized questions, based on their project proposal. There will also be a few pointed nudges about their progress on their presentation research.

The preliminaries and assessment are covered. What about the meat of the course, structured around Gilbert’s Ecological Developmental Biology? I’ve had to make some hard choices here. I can’t teach the whole text — as it is, I’m hitting the students with a lot of reading, and I’m already expecting that I might have to cut back on a few of my plans. I also don’t want to just teach what’s in the textbook, but will be providing papers that they’ll have to read and understand and discuss in class. What that means is that I’m doing something heretical: I’m not using the lovely material on evolution and development at the end of the book, chapters 9-11. I had to cut somewhere, and I figure enough of that will seep through in my general attitude in the course. I’m also holding it in reserve: it always happens that a student or two drops the course, especially since they’ll get early feedback on their grades, and I might just be able to fit in a little at the end, if student presentations don’t eat up the whole month. I may also steer a few of those students towards the evolution material.

I can tell them in the syllabus that the assigned readings and topics will be:

Week 1: The Triple Helix
Week 4: Chapter 1, Plasticity.
Week 5: Chapter 2, Environmental Epigenetics.
Week 6: Chapter 3, Developmental Symbiosis.
Week 7: Chapter 4, Developmental Physiology.
Week 8 will be the oral exam week.
Week 9: Chapters 5 and 6, Teratogenesis and Endocrine Disruptors.
Week 10: Chapters 7 and 8, Aging and Adult diseases, and Cancer.
Then a long block of student presentations on topics that interest them.
Week 15: if students haven’t eaten up all the time in the course, Chapter 10, Developmental Regulatory Genes.

Doesn’t that sound like fun? Intense, maybe, but you can’t learn without a little pain and effort.

Who knew fjords could be so dangerous?

If you’re looking for an entertaining movie on Netflix, my wife and I just watched Bølgen (The Wave) — it looks like the Norwegians (it’s subtitled) took the standard American disaster movie, stripped out the egregious stupidity and the exaggerated catastrophes, and made a good thriller about a realistic and major problem. It seems some of those scenic, steep-sided fjords have occasional gigantic rockfalls that can cause tsunami-like walls of water to go rushing down, destroying everything in their path. No volcanoes erupting in LA, no comets plummeting towards earth, no colossal earthquake that splits the planet in half…just a terrifying local danger and people trying to cope.

Once again, the Witherspoon assumes their biases are laws

The Witherspoon Institute has once again decided to dictate to us all about the proper, conservative approach to everything. This time, they take aim at National Geographic’s “Gender Revolution”: Bad Argument and Biased Ideology. Of course they’re agin’ them transgenders.

The January 2017 issue of National Geographic is dedicated to exploring what it calls the “Gender Revolution”—a post-Sexual Revolution movement that seeks to deconstruct traditional understandings about human embodiment, male-female sexual dimorphism, and gender. In an article titled “Rethinking Gender,” Robin Marantz Henig cites evolving gender norms as a justification for the Gender Revolution. But Henig’s argument is not only unpersuasive, it’s also based on a radical proposal about human nature that is at odds with both natural law and biblical anthropology.

I started reading this essay enthused about seeing their “natural law” and “biblical anthropology” arguments, both subjects I find to be nonsensical trash, and therefore ripe for mocking. To my disappointment, there is no biblical anthropology anywhere in it, and what ‘natural law’ arguments there are are sadly implicit, and just assumed. It reduces the whole essay to weak whining.

They have only one point to make, and it’s laid out in this one paragraph.

Indeed, this is the crux of the matter that plagues the transgender movement. It is based not on evidence, but on the ideology of expressive individualism—the idea that one’s identity is self-determined, that one should live out that identity, and that everyone else must respect and affirm that identity, no matter what it is. Expressive individualism requires no moral argument or empirical justification for its claims, no matter how absurd or controverted they may be. Transgenderism is not a scientific discovery but a prior ideological commitment about the pliability of gender.

The Witherspoon Institute, that deeply ideological organization, wants to argue that transgender people are wrong because they are ideological. But of course they are! So am I! So are they! If they want to claim that an “absence of scientific discovery” invalidates a whole personal and cultural phenomenon, they’re going to have to burn down the entirety of their archives, because nowhere, including in this essay, do they build a case for their ideology with science. In fact, this is the whole of their defense.

Accepting the claims of transgender ideology requires papering over one’s conscience and making a mockery of the “law written on the heart” that our bodies bear witness to in our complementary design.

They want to claim that there is a “law written on the heart” that makes the gender binary natural and proper and righteous — but they make no scientific (or biblical anthropological, which is fine, because I’d dismiss it) argument for that claim.

Here’s my proudly ideological argument against the Witherspoon’s biases.

The gender binary is a social construct: it is a set of behaviors and expectations for how people should conform within a society. It is built around biological predispositions which are real but not absolute; all we have to do is look at different cultures around the world and see that there different expectations in different societies. Real men don’t cry? Not always. Women are the sheltered, weaker sex? Not always. Men should always “pay” at the “restaurant” when they take a woman out on a “date”? I can’t even begin to unpack all the artificial cultural constructs built into that sentence. They are really trying to impose the standards of Victorian England on all of humanity, which is the kind of thing Victorians did all the time, but isn’t it about time we kicked that bullshit to the curb?

They want to argue that humans aren’t plastic, but are fixed by their biological natures. But we know that isn’t true, because we can see that human beings have thrived in a variety of different cultures without a necessary genetic difference in their makeup. Look at the United States — we have people living here who within the last few generations have come from Vietnam, Ireland, Laos, Nigeria, Peru, Sweden, Somalia, Iran, etc., etc., etc., and they have adapted, and in fact, the conservative American ideology requires that they must conform.

This is what people do. They adapt, they conform, they absorb the expectations of their surrounding culture, especially as children, and they also bring their past experiences into communities and shape their environments. The Witherspoon wants to reify masculinity and femininity to fit their ideological preconceptions, deny the reality of people’s identity, and they reject arguments against that kind of cultural imperialism because, they say, you can’t fit a person’s perception of their identity under a microscope. Well, you can’t fit Christian conservativism under a microscope either, yet you’re sinking a lot of money, time, and effort into propping it up.

Not everyone will be accommodating of your particular views. I am not comfortable, to put it mildly, with Christian conservativism — you don’t get to tell me that I am wrong in my identity, and that I must learn to love faith and oppressive authoritarianism. However, I am personally comfortable with my expected gender role — I have never questioned my conformity to maleness — but I am also capable of recognizing that not everyone else is, and that they would be as unhappy with a world that dictates that they must be a straight heterosexual man’s man as I would with a world that told me I had to participate in gay sex, and like it (although if I’d been brought up through childhood in that world where gender fluidity was more common, maybe I would…which I suspect is one of the ideas that horrifies the Witherspoon).

That the majority of people fall into one of the two broad, culturally accepted definitions of gender is not scientific evidence that these divisions are natural and necessary because, as I said, people are plastic and tend to conform to cultural norms. There have always been individuals who refuse or are unable to meet social expectations, even in Victorian England. The question is whether we punish people by demanding that their identity meet a narrow set of criteria, or whether we accept people for who they are and who they want to be. The former is a formula for widespread misery. The latter leads to greater happiness, although it does tend to piss off the authoritarian prigs who enjoy crushing the joys of others.

I have to confess to sharing a little bit of that latter attitude, because I would greatly enjoy crushing the totalitarian hopes and dreams of the Witherspoon Institute members.

I wouldn’t normally be telling you this

I want you to watch the O’Reilly Factor on Fox News, at 8pm ET tonight.

That ad in the NY Times protesting Trump has pissed Ol’ Bill off enough that he has invited a couple of the signatories on to be abused — unfortunately for him, it’ll be Carl Dix and Cornel West, so it might be an incendiary event, and a good time will be held by all.

I guess even I will watch Fox News tonight, much as it pains me.

Another example of why basic research matters

Scientists have been working on techniques to treat mitochondrial diseases, and one strategy is to create “3 parent” babies, where the mother’s defective mitochondria are replaced or supplemented in her gametes with mitochondria from another woman, and the gamete is then fertilized with sperm from the father. It works!

In September, reproductive endocrinologist John Zhang and his team at the New Hope Fertility Center in New York City captured the world’s attention when they announced the birth of a child to a mother carrying a fatal genetic defect.

Using a technique called mitochondrial replacement therapy, the researchers combined DNA from two women and one man to bypass the defect and produce a healthy baby boy — one with, quite literally, three genetic parents.

There is, however, a significant possibility of failure.

Earlier this month, a study published in Nature by Shoukhrat Mitalipov, head of the Center for Embryonic Cell and Gene Therapy at the Oregon Health and Science University in Portland, suggested that in roughly 15 percent of cases, the mitochondrial replacement could fail and allow fatal defects to return, or even increase a child’s vulnerability to new ailments.

The findings confirmed the suspicions of many researchers, and the conclusions drawn by Mitalipov and his team were unequivocal: The potential for conflicts between transplanted and original mitochondrial genomes is real, and more sophisticated matching of donor and recipient eggs — pairing mothers whose mitochondria share genetic similarities, for example — is needed to avoid potential tragedies.

This is not at all surprising, and shouldn’t be used as a reason to stop the research. This was expected. Anyone who has studied mitochondrial genetics — and I’m sure this is the case for these researchers as well — knows about dominant negative effects. There are known alleles in mitochondria that are negative, that is they are deleterious to the organelle, and are also dominant, that is, one copy of the of the allele can suppress healthy mitochondria in the same cell. We also know that mitochondria replicate independently of the cell, and that in some cases the defective mitochondria can outcompete and replace the healthy mitochondria. This is the case in, for instance, poky mutants in Neurospora, and petite mutants in yeast.

So, old news. It seems to make the popular press only when it looks like it might affect human beings, though, which is too bad, because awareness of the problem arose from basic cell biology, and will be best solved by experimental work in non-human organisms. Let’s see more funding for yeast and Neurospora and fruit fly and zebrafish research!