Juggling flies, fish, and students all week long


Time for another reflection on my mundane week of teaching. I know this is unexciting, but I’m trying to be self-aware about what I’m doing in the class.

I’ve already summarized some of what I did this week: we explored the meaning of “epigenetics”, and I made a big push to get them to think critically about the papers we’re reading. They’re supposed to be developing a topic they’ll explore independently, so I’ve had them doing library work to find a line of research they find interesting, and master the skill of extracting the key questions the work is trying to address. I’ve got a small stack of short papers that I’m going to read this weekend and we’ll see how well they can do that.

We also discussed symbiotic interactions in development, and next week the topic is other environmental effects. They are getting much, much better at opening up and talking at the miserable hour of 8am.

The other regular highlight of my week is FlyDay, when I have to scrub dead maggots and pupae out of fly bottles. I had to postpone FlyDay this week! Yesterday I was scheduled to meet with students and parents visiting the university to confirm their plans to attend, and I was all spiffed up in a nice suit, which isn’t the best thing to wear when one is flicking bits of chitin and gooey medium around. I went in early this morning to scrub bottles and get them cooking in the autoclave.

By the way, at that student meeting I was the official biology representative, and although biology is currently the largest major on campus, almost no one stopped by to talk to me. It might have been my terrifying glare, or my sciencey reek, but no: it was because there was a separate table for the pre-professional programs (pre-med, pre-vet, pre-dental, etc.). This is a minor peeve of mine: this is not 19th century England. You do not graduate from your public school education and go straight into medical school — no, here in 21st century America you get a broad-based undergraduate education first, and then you apply to med school. You should be thinking about your liberal arts education first, and in a couple of years we’ll start coaching you on how to get into those professional programs.

Oh, well. They ignore me now, but I know that I’ll get my claws on most of them soon — they’ll want all those bio classes to prep them for the MCATs.

I should mention that I am teaching another course beyond ecological development — I’m teaching a lab course on transmission genetics. They’ve been doing crosses with flies all semester long, and we’re getting to an interesting point.

The first half semester we’re doing a mapping cross, using recombination to estimate the distances between a couple of genes on the X chromosome. We’re using flies that are mutant for eye color (white, w), wing length (miniature, m), and bristle morphology (forked, f), and I’ve also got a few groups mapping body color (yellow, y), wing veins (crossveinless, cv) and forked, f; the latter are doing a pilot test to see if I want to add that cross to our regular repertoire.

The way this works is that they are given wild type and triple mutant flies. I first have them raise a new generation of the purebred stock, simply to get a little practice in sexing flies and basic skills in growing them. So they first do these crosses:

♀w m f/w m f x ♂w m f/Y

which produces bottles full of homozygous white-eyed, miniature-winged, forked-bristled flies, and

♀w+ m+ f+/w+ m+ f+ x ♂w+ m+ f+/Y

which produces bottles full of homozygous wild type flies.

Then I have them do a reciprocal cross of flies from the two bottles. These are X-linked traits, so it matters which strain is the mother and which the father, and I want them to see that. That is, they cross wild type females to triple mutant males, like so:

♀w+ m+ f+/w+ m+ f+ x ♂w m f/Y,

which produces progeny that are all wild type, both male and female (they all inherit the dominant wild type allele at all loci from their mothers). After they’ve scored the flies from this cross, we dispose of them all and don’t think any further about them.

They also cross mutant females to wild type males, like this:

♀w m f/w m f x ♂w+ m+ f+/Y.

That has the useful result that all the sons inherit w m f from their mother and a Y chromosome from their father, so they all express the mutant phenotype. The daughters, however, are all heterozygous, inheriting the mutant alleles from their mother and a wild type chromosome from their father, so their genotype is:

♀w m f/w+ m+ f+

Now the fun begins. Meiotic recombination in those flies will rearrange the +’s and -‘s in those chromosomes with a frequency dependent on their distance from one another — you’ll get less recombination between genes that are close to one another.

This week, they completed the reciprocal cross and got their heterozygous females and mutant males. Yay! That worked. They are now setting up a test cross to assess recombination frequencies.

I just want to say that I think I planned everything perfectly. That test cross will be ready to score next week, which is the week before spring break, which means we’ll have the data for all the calculations before they leave, and when they get back, I’ll be able to lead them through all the theory. It also means I’ll be able to purge a lot of fly bottles and get them scrubbed up over the break (you can tell already that I have glamorous plans for my short vacation). Trust me, though, this is good — there have been semesters where, due to student error, the flies haven’t been ready, and then my spring break is spent maintaining 120 bottles of student flies.

It also means we can launch into the next experiment as soon as they get back: we’re going to do a complementation cross between two eye color mutants, brown eye (bw) and scarlet eye (st). If I’ve got this one all timed out correctly, we’ll be getting F2 results of crosses between heterozygotes for both loci a week before the end of classes.

Now you know. I choreograph fly sex for my convenience.

Next up, I have to choreograph my schedule. It turns out I have been summoned to Howard Hughes headquarters on 8 March and 18 April, which punch big holes in my planned lessons, and which I hadn’t accounted for in my syllabi. I’m going to have to juggle lectures and exams and rearrange the order of various things in a big way this coming week.

Where did these people go to college?

These remarks by Betsy DeVos at CPAC are revealing. It sounds like she, and the cheering crowds, have no idea what college is actually like.

The fight against the education establishment extends to you too. The faculty, from adjunct professors to deans, tell you what to do, what to say, and more ominously, what to think. They say that if you voted for Donald Trump, you’re a threat to the university community. But the real threat is silencing the First Amendment rights of people with whom you disagree.

Those are lies. What we want, at real universities, is for our students to question everything intelligently. I just gave my class an assignment to critically analyze a paper — to read it specifically with a mind to finding flaws and developing arguments and tests to evaluate its validity. That’s standard practice.

DeVos attended Calvin College. I’d really like to know what classes she took that failed to give her an education.

Historical zebrafish!

Way back in the dim, distant past, before YouTube and publicly accessible digital media, two of my friends, Don Kane, now at Western Michigan University, and Rolf Karlstrom, now at Amherst, made a video of zebrafish development. This was in 1992. It was on VHS tape. (If you don’t know what that is, ask your grandparents).

Then in 1996, a whole issue of Development was dedicated to zebrafish development and genetics, and they translated that tape into modern technology: a flip book. The top right corner of the issue featured one frame of the video, so you could flip through it and see a nice little timelapse. Like this:

Isn’t that quaint?

Sadly, I have not been able to find a copy of the flip book transported to the convenient medium of youtube (maybe I can find my copy of the file and upload it, but that thing was over 20 freaking years ago, so it may take me a while to excavate it), but at least there’s a version available via facebook, as facebook reminded me today.

I routinely make better videos than that one now, but it’s because I’ve got hi-res digital video cameras and fancy software — just remember that historical flip book was made off of VHS tape and edited by hand frame by frame. It’s really a vast improvement over the prior version, which was chiseled on slabs of sandstone and mounted in a row, so you had to run past them very fast to get the animation effect.

Also, the subject didn’t get much reward or glory, and probably ended up going down a drain in Eugene, Oregon.

Welcome to the American Police State

This is bad. This is really bad. American customs is now taking it upon themselves to make moral judgments on visitors to this country.

André says he was planning to visit his boyfriend, who was working in New Orleans. But when he was going through Customs preclearance at Vancouver airport last October, he was selected for secondary inspection, where an officer took his phone, computer and other possessions, and demanded the passwords for his devices.

“I didn’t know what to do. I was scared, so I gave them the password and then I sat there for at least an hour or two. I missed my flight,” André says. “He came back and just started grilling me. ‘Is this your email?’ and it was an email attached to a Craigslist account for sex ads. He asked me, ‘Is this your account on Scruff? Is this you on BBRT?’ I was like, ‘Yes, this is me.’”

Holy crap. They’re demanding passwords and browsing through the contents of your phone now? What ever happened to any right to privacy? I’m flying to DC in a few weeks. I think. I’m not giving them access to anything, so maybe I won’t be.

André made it through on that flight, after being humiliated and grilled and missing one connection, but on a second trip, he thought he’d be clever and delete those ‘incriminating’ apps from his phone. Two lessons here: they had recorded his passwords and had them ready to use next time he showed up, and nope, deleting stuff from your phone doesn’t work.

“They went through my computer. They were looking through Word documents,” André says. “I had nude photos of myself on my phone, and they were questioning who this person was. It was really humiliating and embarrassing.”

“They said, ‘Next time you come through, don’t have a cleared phone,’ and that was it. I wasn’t let through. He said I’m a suspected escort. You can’t really argue with them because you’re trapped,” he says.

“Don’t have a cleared phone.” Jesus fucking christ. I despised the TSA already, but this is criminal, fascist, and simply vile.

We’ve taken the first step in deconverting the Pope

It’s kind of a backhanded compliment — atheists are a little better than crooks! — but I guess it’s moving him in the right direction.

Christians who exploit people, lead a double life and get involved in “dirty business,” scandalize the church, Pope Francis said in a sermon Thursday in Rome. In fact, it might be better just to be an atheist.

“And so many Christians are like this, and these people scandalize others. How many times have we heard — all of us, around the neighborhood and elsewhere — ‘but to be a Catholic like that, it’s better to be an atheist.’ It is that, scandal. You destroy. You beat down,” Francis said, according to Vatican Radio.

I’m charitable, too. I’m willing to admit that many Catholics are, in fact, better than child-rapers.

Heretics must be erased

Creationists have a big problem: reality contradicts their beliefs. They are all in a situation of having to deny reality to some degree, but the question is…how much? Do you just go full on crackpot and declare that all of science is wrong, and that you just have to realize that God created everything with the illusion of great age? That’s tempting, but might be too great a reach for some. Better still is to deny the interpretations that conflict with your fable, and recast all the evidence in light of the Bible. That allows you to claim science supports your views while rejecting the science, which is a neat trick.

But there are multiple alternative ways to do that! Creationists have focused on two major problems with Biblical geology. One is the age of the Earth; the Bible makes it sound like our origin is relatively recent and human, while all the scientific evidence says its ancient. Another related problem is change: geology documents all kinds of upheavals, from seashells on mountaintops to warped strata in the rocks to the slow accumulation of sediments. That sure sounds like we need a lot of time to accommodate all that change.

One popular strategy was to shove all those ancient changes into a long period of time outside the scope of the Bible: yes, the Earth is old and there was a lot of irrelevant chaos over vast periods of time, but the Bible isn’t talking about that — it’s about God’s relationship to humankind, so it fast forwards through all the stuff about God’s relationship to dust, gas, and rocks. This was probably the most popular explanation at the end of the 19th and in the early 20th century.

You may notice, though, that that rationale is no longer in vogue, even if it is just as compatible with the Bible as anything can be with that mess of contradictions. Instead, most creationists push a peculiar alternative.

The Earth is young. And all those geological changes occured during one cataclysm mentioned in the Bible, the Noachian Flood.

This is why modern creationists are obsessed with the flood. This is why Ken Ham spent all that money building a giant fake ark: The Flood (and the Fall) are their giant excuse. Geology and biology are all about change…well, hey, the Bible has you covered! It’s just that all that changed occurred in one year.

It’s a weird and very specific idea, and not a necessary one at all. Where did it come from?

We know exactly where it came from, and so does Ken Ham: he credits one book, The Genesis Flood, by Whitcomb and Morris. All you have to read to understand the ‘science’ of Answers in Genesis or the Institute of Creation Research is that one book. It was incredibly influential and set the dogma of creationism in stone. All the modern creationists acknowledge its importance.

But where did Whitcomb and Morris get this idea? We know the answer to that, too. We know exactly who the most influential creationist in the period from the Scopes trial in 1925 to The Genesis Flood in 1961 was: it was George McCready Price, who was both fanatical and prolific in promoting his crackpot ideas about Flood geology. Read The Creationists by the historian Ron Numbers; he’s thorough in describing the efforts of fundamentalist Christians to rebound from the debacle of Scopes, and George McCready Price is everywhere and central in their attempts to recover some credibility.

One catch: Price was a heretic. He was a gosh-darned Seventh Day Adventist, and he was always praising the visions of their prophetess Ellen White and working SDA doctrine into his accounts.

Ken Ham hates it when you link his theology to George McCready Price. He wrote an article denouncing the idea, stating that it was a false accusation that what we believe at AiG had its roots in the Seventh Day Adventist movement with Ellen White. No, no, those heretics had nothing to do with his obsession with the Flood!

At the same time, though, Ham acknowledges the indebtedness of the creationist movement to Whitcomb and Morris.

It is widely recognized today by both friend and foe that the modern creation movement—now growing steadily across America and other western nations—had its genesis in the early 1960s. But it happened in a somewhat surprising manner. First, it came through God using Henry Morris, a soft-spoken, bespectacled academician living in central Virginia. Second, the resurgence of the creation movement in modern times (a movement that had become relatively quiet since the Scopes trial of 1925) was launched not at a major rally led by Dr. Morris nor through any controversy in the courts or schools—nothing noisy whatsoever. In fact, the event was not even associated with the first chapter of Genesis and the account of creation.

The resurgent movement’s surprising trigger was the release of Dr. Morris’s groundbreaking book The Genesis Flood (coauthored with Dr. John Whitcomb). But what a stir that book created. The impact of this now-classic work was such that many church historians have concluded that Dr. Morris was a giant—perhaps unparalleled—in the battle for biblical inerrancy, as he defended the most-attacked book of the Bible. This unassuming scholar was to spearhead an international movement that was to shake the very foundations of the evolution establishment and, just as importantly, challenge the church to accept biblical authority from the very first verse.

All this is true. It doesn’t answer the question, though: where did Whitcomb and Morris come up with flood geology as a unifying concept? Whitcomb was a theologian, Morris was an engineer; neither were geologists. They had to get this idea from somewhere, and if you read The Genesis Flood and any of George McCready Price’s numerous tracts and papers, it’s obvious. Morris and Whitcomb were idea launderers. They took the flood geology of a Seventh Day Adventist and washed off the taint of Ellen White. And now Ham is in denial.

Oh yes he is! The gang at BioLogos (ooh, ick) looked into it. Poor George McCready Price and Ellen White have been mostly expunged from AiG’s history of creationism.

While conducting research for this column, I searched for Price’s full name on the AiG website, as well as a separate search without using his middle name (which found just one more article along with nearly 100 false positives). The result was unexpected, but revealing. AiG is a massive site devoted to almost every imaginable aspect of creationism, including a very large number of articles partly or entirely devoted to the history of the ideas and the movement. Yet my search for Price produced only nine articles—a remarkably small number, given the enormous role that he actually played in the history of creationism. Henry Morris’ name appears in more than 500 articles, with Whitcomb’s close behind. And, searching for Ellen White yields only three articles. Many other historical figures who didn’t really contribute to creationism come up far more often. Dozens of articles mention Robert Boyle, nearly 200 mention Johannes Kepler, and even more mention Isaac Newton. Now, there’s nothing odd about AiG showing much interest in great scientists from the seventeenth century, even someone like Newton who denied the divinity of Jesus, but the near absence of Price (and White) is passing strange.

Even better, they go to the earlier books of the Sainted Henry Morris, and guess what? Morris himself declares the source of his ideas about geology!

There are a few geologists, even today, who hold to some form of the flood theory. Probably the outstanding example is George M. Price, who is probably as conversant with the whole subject of historical geology as any man living. Because of his views, he has been subjected to a great deal of criticism and ridicule by orthodox geologists, but his wealth of accumulated facts and his incontrovertible logic have never been answered. Much of the material in this chapter is taken from his works.

It wasn’t just Price, either. Morris credits a lot of Adventists for his ideas.

In the bibliography at the end of that chapter, Morris listed four books and four articles by Price—far more than anyone else cited there. He also listed three articles by Adventist author Benjamin Franklin Allen and a very rare item by another Adventist (though not apparently of the Seventh-day variety), namely, The Flood: The Fact of History (1890), by Charles Totten, a military officer and Anglo-Israelite who probably originated the modern urban legend that astronomers have confirmed Joshua’s missing day. More than half of the twenty-three works, including eight by the man he identified as most important, were written by Adventists.

Oops. Not only can’t Ken Ham get the science right, he even distorts the history of his own worldview.

Poor George. He truly was a crackpot, and totally wrong about everything, but now he’s being carefully scrubbed out of all of the official state portraits of the creationist movement.