Curse you, Reginald C. Punnett

Yesterday, I gave my first year students a teeny-tiny quiz over the current unit in basic genetics. No biggie, I’d been hearing some troubling concerns from the class tutor that some of the students were struggling, so this was more of an assessment of how well they were grasping the simplest concepts in Mendelian genetics. Here, I’ll even let you see the entirety of the quiz: 5 questions, 2 points each.

You have a true-breeding diploid organism with the phenotype AB, and a second true-breeding organism with the phenotype ab. A is dominant to a, and B is dominant to b.

  1. What are the genotypes of these two creatures?
  2. You cross these two and obtain a clutch of F1s. What are their genotypes and phenotypes?
  3. You cross two of the F1s with each other. Predict what the phenotypes and their proportions in the next generation should be, assuming that Mendel’s laws apply.
  4. You cross one of the F1s with another organism that has the phenotype ab. Predict what the phenotypes and their proportions in the next generation should be, assuming that Mendel’s laws apply.
  5. You actually do the experiment in #4, you get the following results:
    AB: 35%
    Ab: 15%
    aB: 15%
    ab: 35%
    Interpret this distribution.

See? If you were a student who’d just suffered through 3 weeks of an introduction to genetics, you’d probably have absolutely no problem with this. If you’ve been teaching genetics for a few decades, you could answer this quiz in seconds, in your sleep, while standing on your head. I think that might be part of the problem, because this is stuff I can totally take for granted.

I gave the students 20 minutes. Most of them used the entirety of that time. I scored the quiz that afternoon, and was aghast: mean score was 2.7/10, high score was 8. Yikes. How…? Where have I gone wrong? These are smart, hard-working students, and they missed everything. Then I saw the problem. The quizzes were covered with…

PUNNETT SQUARES. Jesus. They tried to solve every problem with a 4×4 Punnett square, which is insane. Punnett squares are a tool for graphically illustrating the outcome of a cross. They are not tools for calculating the results. They are a terrible, slow, clumsy tool for doing that. The textbook is full of ’em, I think because they’re easy to draw and give the illusion of a comprehensive answer. I’d shown a few in class, because I had to explain what the textbook was showing them, but I always told them that Punnett squares were terrible and useless, but this is what they knew, probably from high school, and then reinforced by the text, and then I made the mistake of trying to explain what the book figures were showing, and they came away with the impression that this is what geneticists do. It is not. Mendelian genetics are dead simple. You can just treat each locus independently (and they’re trivial, you can memorize all the possible results if you can hold 3 frequencies in your head), solve for A, solve for B, multiply to get the answer for A & B.

Christ, they’re trying to mechanically brute-force a solution with 4×4 Punnett squares, and it’s a disaster.

I can’t blame the students, though, it’s all on me. I remember being their age and taking Dr Sandler’s genetics course at the UW, and struggling for the first few weeks, until suddenly the light bulb flicked on in my head and I saw how easy Mendel was, and then when he started layering on the advanced stuff, like segregation distorters and epistatic interactions (seriously, try solving those kinds of problems with a Punnett square — you might be able to assemble some kind of nightmarish diagram, but it’s not efficient. You can’t even do linkage with a Punnett square.), it was all just an easy arithmetic modifier added on to the basic concept. But then, Sandler was a brilliant teacher, I’ve got some catching up to do.

So how to deal with this problem…next week, I’m going to rewind and go back to the basics, review these elementary problems without Punnett squares anywhere in sight, and actively tell the students that Reginald C. Punnett was of the devil, put on this Earth to confound generations of genetics students. Then, over Christmas break, I’m going to back over my stored presentations and notes and edit out every mention of the P word. Maybe I should print one out so I can put it on the floor the first day of class and piss all over it — nah, some administrator would probably complain.

Then, you out there — yeah, YOU, high school teachers and textbook publishers — stop poisoning students minds with these abominations. I’ve never liked them, but I keep using them because they are traditional, and because the books and students come with them preloaded. Just stop it. They’re pedagogically bad. I’ve got to explicitly unteach them now.

This is a tragic setback, because what my plan for the course was saying is that I start next week on the developmental biology unit, my favorite stuff, and now it’s getting bounced back two weeks, and is going to get slammed up against the end of the term. I’m going to blame Punnett.

Always label every bottle

One of those things every lab person knows: label everything. Write down what’s in it, and also the date it was made. At least the person responsible for this followed the rule.

Several vials labeled “smallpox” have been found at a vaccine research facility in Pennsylvania, the US Centers for Disease Control and Prevention said Tuesday.

“There is no indication that anyone has been exposed to the small number of frozen vials,” the CDC said in a statement emailed to CNN.

“The frozen vials labeled ‘Smallpox’ were incidentally discovered by a laboratory worker while cleaning out a freezer in a facility that conducts vaccine research in Pennsylvania. CDC, its Administration partners, and law enforcement are investigating the matter and the vials’ contents appear intact,” the CDC added.

“The laboratory worker who discovered the vials was wearing gloves and a face mask. We will provide further details as they are available.”

You don’t need intent to kill us all, when stupidity and neglect is sufficient.

Ta-Nehisi Coates always provides a good start to the day

Even if it is a little depressing. Here he comments on a book by Tony Judt.

I had never read so merciless a book. Tony had no use for pieties—no tolerance for invocations of a “Good War” or the “Greatest Generation.” Power reigns in Postwar, often in brutal ways. Tony writes of Jewish survivors of the Holocaust returning to Poland only to be asked, “Why have you come back?” He introduced me to intellectuals, such as François Furet, forced to reckon not just with Stalin’s crimes but with a discrediting of a “Grand Narrative” of history itself. “All the lives lost, and resources wasted in transforming societies under state direction,” Tony writes of this reckoning, were “just what their critics had always said they were: loss, waste, failure and crime.” Early in Postwar, Tony quotes the observations of a journalist covering the ethnic cleansings that characterized postwar Europe. The journalist self-satisfyingly claims that history will “exact a terrible retribution.” But, Tony tells us, history “exacted no such retribution.” No righteous, God-ordained price was to be paid for this crime against humanity. The arc of history did not magically bend. It was bent, even broken, by those with power.

That resonates with me, too. There is no trajectory of history in evolution, either, just a story we tell ourselves after the fact. There’s nothing but chance and a directionless, generation-by-generation stumbling, with no goal but survival, and afterwards the survivors pat themselves on the back and pretend it was destiny that they made it.

It’s also why I have no sympathy for Pinkerisms. It’s all retrospective coronations all the way down, self-defeating reassurances from the so-far successful that the status quo will carry us forward into a glorious future. It never works that way. Every advancement is the product of a battle by those who say “Not good enough!” and who strive to do better.

And sometimes the better don’t make it anyway.

Problem solving!

Teaching is a whole new world nowadays. I faced three different problems today.

One of our sports teams has been exposed to COVID-19, and they’ve been quarantined and can’t come to class.
Solution: I’ll be recording my lectures for a while and passing them on to the affected students. Also, we’ve been working through some genetics problems, so I’m forwarding those for them to work on in their isolation chambers.

A student had a serious family crisis and had to miss the last exam, and is panicking over it.
Solution: For them, I’ll pretend that exam never happened, and their final grade will be based on the average of four exams, rather than five, like the rest of the class. The exams are cumulative so it’s not like they won’t be evaluated on part of the class.

One of my international students has been abruptly drafted into the military service for a certain Eurasian country, and is flying away from the US prematurely.
Wooo. I wouldn’t want to be in that situation. Solution: I am arranging to email them a take-home final exam so they can get credit for the course, and I hope come back to finish up their degree.

I’m thinking now that I actually have it pretty easy. My job is to make everything as smooth and doable for the students who don’t have it so easy.

All we have to do next is end the pandemic, all other health problems, and end war, and teaching will get easier.

Please avoid the term “paradigm shift” unless you’ve got something really surprising

Am I missing something here? Here’s an article with the grand title of “Researchers propose expanded evolutionary concept”, which declares that we’re going to have to expand and rethink our understanding of evolutionary theory. “Oh really?” I thought, but I read it with an open mind, expecting some dramatic new phenomenon to be explained. I was a little disappointed to find it was about ramets.

Don’t get me wrong, ramets are interesting, and the paper’s content is fine, if maybe a little overhyped. Ramets are an asexual kind of reproduction, fairly common in plants, where runners sprout shoots that develop into individuals — a familiar example is aspen trees, where a clump of trees, even a whole forest, may consist of clones of a single source individual, each tree born of the original source root system, spawning more roots that generate more ramets that expand the clone.

The paper makes the good point that these organisms aren’t constrained by Weisman’s barrier, which postulates that there is no exchange of heritable variation from the soma to the gonads, which we animals take for granted. If your fingers were irradiated, producing a new collection of mutations in those tissues, it won’t matter to future offspring because those cells don’t contribute to sperm and egg. That would all change if you were able to sprout clonal copies of yourself from your fingertips, like these ramets, because then those irradiated digits would have a way to reproduce independent individuals. It would also be hard to type with all these finger-fetuses growing from my hands.

So in organisms with the ability to propagate from somatic tissues, somatic mutations are a mechanism for generating new variations. That’s the story here.

Evolutionary consequences of somatic mutations when they enter the germline.
(A) In most animals, the Weisman barrier between soma and germline prevents transfer. However, germline determination occurs late in plants, fungi, and some basal metazoans. In the hydrozoa, for example, stem cells differentiate into germ cells throughout the life of the colony. In others, trans-differentiation of soma into germ cells may occur. Thus, as somatic mutations accumulate, some may enter the germ line. Once in the germline, somatic mutations are recombined into different genetic backgrounds during meiosis similar to germline mutations. This reduces linkage between potentially deleterious mutations, which otherwise would lead to increasing genetic load. (B) Multilevel selection may also speed up adaptive evolution by providing a first filter of negative selection at the level of cell populations. However, the success of adaptive somatic genetic variation (SoGV) depends on whether they occur in stem cells and the specifics of how new modules arise. Homogeneous modules each arising from single mutated stem cells may compete with each other at the within-genet level and be subject to selection.

Yes, fine, this is an important phenomenon, but is it really new? Does it require bold new changes to evolutionary theory? In my head, I’m quite aware that asexual species can still evolve and acquire new traits, and that is perfectly compatible with the evolutionary principles I understand. There is often an erroneous bias in humans to assume that all populations reproduce sexually, like us, and that somatic tissues can’t propagate from cuttings, like us animals, but evolutionary theory isn’t blinkered in that way. Why is phys.org announcing we need an “expanded evolutionary concept” to account for this? We don’t. This could just be phys.org over-hyping something, as they tend to do.

But no, it’s actually in the paper itself. Oh no, it’s the dreaded paradigm shift.

Evolutionary biology has made tremendous progress in explaining the emergence and maintenance of sexual reproduction despite the two-fold costs of sex. Here, we addressed the flip side of the coin, namely, how do a large number of species cope with extended phases of asexual reproduction that, according to conventional wisdom, precludes the emergence of genetic and phenotypic diversity and hence, adaptive evolution? With empirical data increasingly confirming earlier conceptual work, it is now timely to suggest a paradigm shift that acknowledges the evolution of modular species at multiple levels. Cell lineages evolve within ramets, which in turn are forming asexual populations featuring a mix of mosaic and fixed SoGV. Both of these levels of variation and selection are, in turn, nested within sexually reproducing populations of genets that are corresponding to the ‘classical’ level of individuality in population genetics of unitary species, leading to potentially complex pathways of adaptation that merit further study.

Great, yes, I agree, multiple levels of selection, somatic mutation can contribute to genetic diversity, there’s nothing wrong or surprising about that. But where’s the “paradigm shift”? What’s the part that can’t be accommodated by our current understanding of genes and phenotypes and populations? Come on, people, tone down the exaggeration.

Unless there’s something I am missing here, which does happen. I may be a bit of an animal-chauvinist, so it feels awkward to have to remind a plant-person that evolutionary theory can handle bacteria quite well, so the peculiarities of our multicellular models aren’t necessarily going to require radical renovation of the whole idea.

The Nobel acknowledges global warming, again

This year’s physics Nobel goes to Syukuro Manabe, Klaus Hasselmann, and Giorgio Parisi for “for the physical modelling of Earth’s climate, quantifying variability and reliably predicting global warmings” and “for the discovery of the interplay of disorder and fluctuations in physical systems from atomic to planetary scales” and for giving us something more to talk about in our Saturday podcast.

And yet, there are still people — Republicans, mainly, who I will grudgingly admit are still “people” — who deny the science.

Let’s be fair, though. There are also a lot of Democrats who are dragging their heels and refusing to do anything but the bare minimum they can get away with.

Molecular neurogenetics gets the nod from the Nobel committee

The Nobel in medicine this year goes to David Julius and Ardem Patapoutian for their work in identifying the receptors that transduce heat and touch into signals in the nervous system.

So now you know the proximal sensors that are activated when you hug someone, or when you nibble on some ghost pepper. It’s TRPV and PIEZO channels!

Now they just have to figure out what’s going on in the central nervous system when those channels are triggered.

Reminder: I’m answering questions at 11am Central time today

Today I’m going to answer some patron/reader questions:

• Viruses replicate? Does that mean they mutate in infected people, too?
• Given the choice between a vaccine that stops spread but does nothing to reduce lethality and a vaccine that allows spread but eliminates lethality, what would be a better strategy for us?
• Hey, what about that old germ layer theory? It’s 205 years old, is mesoderm still a thing?

I’ll also try to answer any other questions that come up.

For a grand finale, today is the day I nuke my Facebook account. It won’t be too exciting: click, click, click, click, click, click (etc.), it’s gone. At least, it better not be exciting, I won’t be too happy if the Facebook police show up at my door.

Iä! Iä! Teilhard de Chardin fhtagn!

I knew it. For years I’ve seen the “dinosauroid” trotted out as an illustration of how dinosaurs could have evolved, if only that little space rock hadn’t messed up their progression. To me, it was symptomatic of a deplorable strain of teleological thinking in biology, and I thought it was totally bogus from the first glance.

Why would anyone think a coelurosaur would gradually converge on an anthropoid form? So much of our morphology is a consequence of variations in our ancestors — ancestors that would not have been shared with dinosaurs. Yet here is this imaginary beast with ape-like details. How would it have acquired those?

Darren Naish has tracked down the history of this bizarre mannequin, and I am totally not surprised: we can blame Teilhard de Chardin, who had a pernicious influence on Dale Russell, the scientist who built it.

I’m confident that another factor contributed to the construction of the dinosauroid, but it’s something more controversial than everything discussed so far and is also harder to establish with any degree of certainty. I think that Dale Russell’s specific personal views on the nature of the universe and the position of humans within it played a role in everything that happened.

We know from the recollections of his colleagues that Dale Russell was religious, with an active spiritual life committed to Catholicism. We also know from statements made by Robert Bakker and others who discussed religion with him that Russell was fond of the ideas of Jesuit priest and palaeontologist Teilhard de Chardin (Campagna 2001, p. 7, Noble 2016, p. 41). Chardin (1959) argued for a directionality in evolution, that humans represent a point close to (but not at) the pinnacle of evolution, and that a humanoid stage was inevitable for those organisms approaching evolution’s final stage. Add to this the fact that Russell stated in correspondence his idea that “the human form might be a natural target for selective pressures” (as Russell wrote to anthropologist Noel Boaz in August 1984), and his implication – made several times in interview – that humans (and, by extension, other humanoids) are not simply additional animals (Russell 1987, p. 130, Psihoyos & Knoebber 1994, p. 252). We’re talking here about what’s been called the ‘inevitable humanoid proposition’, a concept often linked both to religiosity and to an anthropocentric view of the universe.

My personal opinion is that the dinosauroid was not, then, the honest experiment in speculative evolution that some authors have implied (e.g., Losos 2017; reviewed here at TetZoo). Instead, Russell had already decided that he wanted to showcase the possibility that human-shaped non-humans were ‘inevitable’, and that they might have a special place in the design of the universe.

Do not, under any circumstances, ever try to read Teilhard de Chardin’s Phenomenon of Man. I did, and it was the closest real-world experience to the horror movie trope of reading the Necronomicon aloud in a cabin in the woods. It contains damnable prose and arcane leaps of logic that defy rational thought. It is infuriatingly stupid.

You’re all going to try and read it now, aren’t you?

Before you throw yourself into that pit of madness, at least read Peter Medawar’s review. Be forewarned. Make sure you have a chainsaw and a shotgun near at hand.

What’s weird, though, is how so many discussions of this idea are gentle, almost apologetic in addressing Teilhard de Chardin’s and Dale Russell’s strange religious bias. Don’t take this stuff seriously — it’s Time Cube level of wrong, pure garbage in defiance of the scientific consensus with no evidence to support their interpretation. Worse, that delicacy in treating the teleological imperative has had some embarrassing influence — Carl Sagan’s worst book, The Dragons of Eden, was rife with it.

Also infected with the Teilhard de Chardin disease: Simon Conway Morris. The tentacles of that mad Frenchman extend everywhere, bringing insanity to all who view them.

A libertarian perspective on science funding

What a bizarre Twitter conversation. I have stirred up the Aubrey de Grey cultists who have been arguing at me that de Grey and his SENS foundation are doing great work and must be supported. When I ask why, there’s one point they constantly bring up: he recently got $25 million dollars of funding! Therefore, it must be worthy work.

If he’d received funding from NIH, then yeah, I’d be predisposed to suspect that there must be some core ideas that survived peer review by qualified scientists (peer review is not perfect, I hasten to add…it’s just better than no peer review). However, that $25 million came from some cryptocurrency donations called “Pulse Chain Airdrop, whatever that is, not scientific review, and all of the funding is coming from wealthy donors who have no scientific qualifications at all. So they’re trying to tell me that it is an unmitigated good that billionaires are supporting science — my concern is that this is about billionaires dictating what science gets done.

And then, this jaw-dropping statement:

As long as the scientists being paid to do the research are capable and knowledgeable, the scientific literacy of the funders themselves are pretty irrelevant.

Also realistically, the funders likely do understand the research on a basic level, otherwise, why would they find it?

Two points:

Scientists aren’t employees being paid to achieve a specific goal by a wealthy patron. This is a disastrous approach to funding science, especially since they admit that the scientific literacy of the people holding the purse strings is irrelevant. Right now science funding is weakly isolated from the ignorant with power; congress gives a block of money to scientific institutions that then determine by peer review how it is disbursed. Relying on authoritarian rich people to decide what science is worth pursuing is a huge step backwards.

I doubt the funders actually understand the research. Why would they fund it? Because some charismatic gomer promises them that their money will work to help them live forever. They don’t know how, but the con artists are good at babbling sciencey words. It is such a naive assumption that rich people only spend money on things they understand at a “basic level”, especially when you realize that Jeff Bezos is rumored to own a $400 million dollar yacht (at least, someone owns that beast). $25 million is a crumb, and for that, we want to allow billionaires to dictate what science should be done?

I think I spy a libertarian non-scientist who thinks expertise is irrelevant.