I’m still plugging away at my genetics course, and will be until May — so get used to me plopping in these long academic tutorials 3 times a week. You can ignore them, my students can’t.
I’m trusting that the students now have solid foundation in basic Mendelian genetics, so now it’s time to start cutting the mooring ropes so we can drift off into more complex and difficult waters.
Very exciting, but unfortunately this week’s lab video is largely about the glamorous side of lab life: washing glassware. Also about looking up stuff in databases. But maybe in another week we’ll get those F1 results!
Yet another lecture video. I’m still having a few tech problems — the camera died on me about 45 minutes in. I know what went wrong, though, so next time will be perfect!
Here’s the next step in our genetics lab experiment, crossing brown-eyed and scarlet-eyed flies.
What will the hybrid F1s look like?
I’ve been teaching non-stop all day, and boy are my brains tired. I end this exhausting day by dumping today’s genetics lecture on the world.
I should probably go to bed soon.
I can see my future now, for at least the next four months. I have committed myself to record all of my lectures so the students have asynchronous access to the course content to maximize flexibility in case pandemic catastrophe strikes, so what I’ve got to do is:
There are always glitches. Last week, the audio recording of the lecture was unlistenable, so I had to re-record the whole thing. That was better (but far from perfect) today. Today, though, the in-class technology threw up a whole bunch of problems — nothing worked until I called in IT to fix it, so I lost over 10 minutes to annoying problems. I intensely dislike the way the university has configured the AV in our classrooms.
So anyway, here’s today’s lecture. It’s about chromosomes.
I learned two things from this peculiar article, DNA Testing Forced Me To Rethink My Entire Racial Identity: that there is a terrible undercurrent of self-loathing among some black people, and that there is a pervasive over-emphasis on genes vs. culture. The latter I already knew, the former I guess I should have known.
The story is that the author, whose last name is Garcia, always assumed she was Hispanic, even though her family had no hint of Hispanic culture and didn’t even speak Spanish. Then, they took genetics tests. Shock, horror, they were just…black Americans.
The Garcias are led by a pair of oddball patriarchs who could give Clark Griswold a run for his money: my father, Joe, 71, and his brother, Tony, 68. My dad and uncle identify culturally as African-American — they were raised by a black woman from rural Maryland. But according to the family history, their father was of Mexican-Indian descent, hence the last name.
Note that important point: they identify culturally as African-American. Why would you think a genetic test would trump your lived experience?
Well, last summer, Uncle Tony sent in his DNA sample for my niece’s school project, and what ensued was a chain of existential group texts and conversations involving all the Garcias, former Garcias, and anyone married to a Garcia.
My uncle’s ethnic breakdown identified him as more than 70 percent African and 20 percent European.
“No Spanish! Not one drop!” texted my cousin Tony, an attorney in Baltimore and Uncle Tony’s son, referring to the fact that we apparently had no Mexican roots. As if we’d all missed that part.
What do they think it means to be Mexican? There is no such thing as genetically Mexican: the people of Mexico are incredibly diverse, with no one unique genetic signature. If that 20 percent European didn’t include any Spanish loci, and there were no Native American indications, then yes, it is unlikely (but not impossible) that they have Mexican ancestry. But so what? They are who they are, with their own distinct family history.
They did their own research, non-genetic research. They talked to their family, and found out about the author’s paternal grandfather.
“I once overheard my mom and dad say Uncle Joe was a wanted man,” said another new cousin, Marie Shakoor, 71. “He was wanted under the name Will Worthey, and that’s why we think he changed his name to Joe Garcia.”
My cousin Tony said our grandfather exhibited classic escapist behavior, which supported Shakoor’s theory.
“If you’re trying to change your name and your identity, you’re typically trying to evade law enforcement,” Tony said. “Choosing to be Mexican-Indian may not have been our grandfather’s first choice, but it may have been the better option.”
Now that’s interesting and genuine, maybe a little unsavory, but it’s real. The genetic test was irrelevant. Again, who you are isn’t just an assortment of alleles, it’s the cultural influences that shape you far more. Tracing your genetic lineage is just one component of your identity, and probably not the most important part.
Then the story gets a little disturbing, when we find out why the author thought it was so important.
At first, I was in disbelief. What about all those people who came up to me on the streets of New York City and started speaking Spanish? They never doubted for a moment that I was Hispanic. And I had always killed it in Spanish class, seemingly because I had Latino blood coursing through my veins. Accepting that I wasn’t a Garcia felt dangerously close to abandoning my identity.
Oh god, so many misconceptions…language isn’t transmitted via “Latino blood”. New York is a polyglot city, and culturally Hispanic people might speak their language to you because that’s how they’re comfortable talking. When I visited Iceland, strangers tended to address me in Icelandic — it wasn’t because they had a psychic understanding that I, too, was a native. Genetically, I’m also about 4% Neandertal, but I am culturally 0% Neandertal — I can’t knap a flint worth a darn and don’t have any of the words of their language flowing in my veins.
But to cringe even more…
The more I learned, the less I wanted to know. I had always liked being a Garcia. Growing up in a black community, where surnames like Smith, Brown and Jackson are ubiquitous, being a Garcia set me apart.
Perhaps more significantly, being a Garcia meant I could trace my roots to an ancestral homeland — albeit Mexico, not Africa. This was noteworthy when you consider that many African-Americans lost all ancestral ties as a result of slavery and the slave trade.
Slavers committed a great crime, breaking the chain of cultural transmission for millions of people, and denying human beings knowledge of families and tradition and customs. But why would you want to set yourself apart from your neighbors and friends who had similar family histories?
Maybe one great result of these genetic tests is that the author will stop trying to set herself apart from her community. An additional benefit would be if she’d also see the limitations of genetics, and take pride in who she actually is.
I had already known that the number of human chromosomes had been incorrectly reported as 48 (it’s actually 46), and that observers maintained that number for decades, seeing what they expected to see. I’ve used it as an example for years to tell students to clear their heads of preconceptions when making observations, trust what you see, and report your measurements as accurately as you can, because this tendency favoring confirmation bias can corrupt science surprisingly easily. It sounds like a relatively benign example: oops, early investigator makes a mistake counting chromosomes (I’ve done some chromosome work, it’s easy to do), and the initial observation gets perpetuated through the literature until superior techniques make the correct value obvious. Ha ha, don’t do that.
Now Dan Graur digs into the details of the mistake, and it turns out to be a goddamn horror story. There are more lessons here than I thought.
The guy who made the mistake was named Theophilus Painter, and he seems to have stumbled upwards throughout his career by being a terrible person.
The first horror: the specimens he used to make those initial chromosome counts were human testicles lopped off prisoners in an asylum. They were castrated for the crime of excessive masturbation. The methods discuss some grisly details I really didn’t need to know.
“The material upon which this study is based was obtained from three inmates of the Texas State Insane Asylum through the interest and cooperation of Dr. T. E. Cook, a physician at that institution. Two of these individuals were negroes and one was a young white man. In all three cases, the cause for the removal of the testes was excessive self abuse… The operation for the removal of the testes was made, in all three cases, under local anesthesia. An hour or two prior to the operation, the patients were given hypodermic injections of morphine in order to quiet them. This was followed by local injections of Novocain in the operating room. None of the patients exhibited any interest or excitement during the operation, nor did they show any signs of pain except when the vas deferens and the accompanying nerves were cut. One of the negroes went to sleep during the operation.”
Yikes. I guess mutilation of your patients was a routine practice in 1923. No big deal, Negroes don’t feel pain.
The second horror: as you might guess from the passage above, the whole affair was soaking in racism. Painter got the same erroneous chromosome count from all 3 of his victims, but always reported the count separately for his black and white subjects. There may also have been confirmation bias in Painter’s work, because more recent examination of his slides, which still exist, reveal that his methods were a cytological mess and it’s difficult to count chromosome numbers from them at all.
The third horror: Painter later got appointed to the presidency of the University of Texas because he was a reliably negligent creature who would happily turn a blind eye to blatantly discriminatory admission policies, and would allow segregation to continue.
Read Graur for all the details. I’m just dismayed that a point I’ve always used casually as an example of a simple error with long-term consequences is now going to have to be presented as a deeper point about bad science being used for evil. Oh, well, students should know how genetics can be misused for wicked purposes, and here’s yet another case.
It’s true: there are mistakes in Genetics textbooks.
You want to read a really good take-down of a bad science paper? Here you go. It’s a plea to Elsevier to retract a paper published in Personality and Individual Differences because…well, it’s racist garbage, frequently cited by racists who don’t understand the science but love the garbage interpretation. It really is a sign that we need better reviewers to catch this crap.
The paper is by Rushton, who polluted the scientific literature for decades, and Templer, published in 2012. It’s titled “Do pigmentation and the melanocortin system modulate aggression and sexuality in humans as they do in other animals?”, and you can tell what it’s trying to do: it’s trying to claim there is a genetic linkage between skin color and sexual behavior and violence, justifying it with an appeal to biology. It fails, because the authors don’t understand biology or genetics.
They’re advocating something called the pleiotropy hypothesis, which is the idea that every gene has multiple effects (this is true!), and that therefore every phenotype has effects that ripple across to every other phenotype (partially, probably mostly true), so that seeing one aspect of a phenotype means you can make valid predictions about other aspects of the phenotype (mostly not at all true). This allows them to abuse a study in other mammals to claim that human outcomes are identical. Here’s the key graf:
The basis of the pleiotropy hypothesis presented by Rushton and Templer hinges on a citation from Ducrest et al. (2008), which posits ‘pleiotropic effects of the melanocortins might account for the widespread covariance between melanin-based coloration and other phenotypic traits in vertebrates.’ However, Rushton and Templer misrepresent this work by extending it to humans, even though Ducrest et al. (2008) explicitly state, ‘these predictions hold only when variation in melanin-based coloration is mediated by variation in the level of the agonists at MC1R… [conversely] there should be no consistent association between melanin-based coloration and other phenotypic traits when variation in coloration is due to mutations at effectors of melanogenesis such as MC1R [as is the case in humans].’ Ducrest et al. continue, ‘variation in melanin-based coloration between human populations is primarily due to mutations at, for example, MC1R, TYR, MATP and SLC24A5 [29,30] and that human populations are therefore not expected to consistently exhibit the associations between melanin-based coloration and the physiological and behavioural traits reported in our study’ [emphasis mine]. Rushton and Templer ignore this critical passage, saying only ‘Ducrest et al. (2008) [caution that], because of genetic mutations, melanin-based coloration may not exhibit these traits consistently across human populations.’ This is misleading. The issue is not that genetic mutations will make melanin-based pleiotropy inconsistent across human populations, but that the genes responsible for skin pigmentation in humans are completely different to the genes Ducrest et al. describe.
To translate…developmental biologists and geneticists are familiar with the concept of an epistatic pathway, that is, of genes affecting the expression of other genes. So, for instance, Gene A might switch on Gene B which switches on Gene C, in an oversimplified pattern of regulation.
Nothing is ever that simple, we know. Gene A might also switch on Gene Delta and Gene Gamma — this is called pleiotropy, where one gene has multiple effects. And Gene Gamma might also activate Gene B, and Gene B might feed back on Gene A, and B might have pleiotropic effects on Gene Beta and Gene E and Gene C.
This stuff gets delightfully tangled, and is one of the reasons I love developmental biology. Everything is one big complex network of interactions.
What does this have to do with Rushton & Templer’s faulty interpretation? They looked at a study that identified mutations in a highly pleiotropic component of the pigmentation pathway — basically, they’re discussing Gene A in my cartoon — and equating that to a terminal gene in humans, equivalent to Gene C in my diagram. Human variations in skin color are mostly due to mutations in effector genes at the end of the pathway, like MC1R. It will have limited pleiotropic effects compared to genes higher up in the epistatic hierarchy, like the ones Ducrest et al. described. Worst of all, Ducrest et al. explicitly discussed how the kind of comparison Rushton & Templer would make is invalid! They had to willfully edit the conclusions to make their argument, which is more than a little dishonest.
It reminds me of another recent disclosure of a creationist paper that also misrepresented its results. This paper, published in the International Journal of Neuroscience, openly declared that it had evidence for creationism.
In the paper, Kuznetsov reportedly identified an mRNA from one vole species that blocked protein synthesis in a related vole species. That same mRNA, however, did not block translation in the original vole species or another species that was more distantly related. The finding, Kuznetsov wrote in his report, supported “the general creationist concept on the problems of the origin of boundless multitudes of different and harmonically functioning forms of life.”
I vaguely remember reading that paper and rolling my eyes at how weak and sloppy the data was — it was never taken seriously by anyone but creationists. I don’t recall the details, though, because it was published 30 years ago, and is only now being retracted, after decades of the author fabricating data and being so obvious about it that he was fired as editor of two journals in 2013. The guy had a reputation, shall we say. Yet he managed to maintain this academic facade for years.
Phillipe Rushton had similarly managed to keep up the pretense of being a serious academic for an awfully long time, right up until his death in 2012. He used his reputation to spray all kinds of fecal nonsense into the scientific literature, and that’s why you have to maintain a skeptical perspective even when reading prestigious journals.
