The lull before the storm

Good for me! I got all of the finals for all of my classes composed and sent off to the students (they’re all take-home exams). Now I’m all done with this semester except…all three of them are due on the same day, Thursday, which is just by chance the officially scheduled day for all of my class finals. Friday and this weekend are not going to be happy times for yours truly.

Until then, though, I’m kind of at loose ends. Four whole days with no class obligations hanging over my head, which feels very strange, and like there’s something wrong here. So I started getting ready for my spring genetics course, ordering flies, organizing my calendar, thinking about rewriting a bunch of my lectures, etc., etc., etc.

And just generally feeling like I’m heading into a savage storm a few days from now…

This cannot be tolerated: creationists lying about spider evolution

Oh dear. Oh dear oh dear oh dear. The Discovery Institute has turned it’s puerile, feeble attention to spiders now, and it’s as pathetic as you might imagine. It’s written by a guy, Eric Cassell, who felt it important to mention that he had an undergraduate biology degree, which he earned at least four decades ago, before committing to work in — take a wild guess — engineering, of course. Much as I respect many engineers and their work, it sure tends to breed inappropriate teleological attitudes in the brains of its practitioners.

This article, The Miracle of Spiderwebs, is typical of the type. First, talk about how freakin’ complicated spider webs are, then declare that they don’t understand how they could have evolved, which therefore means it could not have evolved. Never mind that spiders have been dependent on silk for their survival for 350 million years and there has been constant selection for more effective functionality, some old guy with negligible background in biology can’t understand it! Furthermore, it can’t possibly be because he’s an ignorant ass, he has to misrepresent the current science to make his case.

Despite great effort, humans have yet to produce anything functionally equivalent to silk. Through genetic engineering, attempts have been made to duplicate it without success. The main challenge is replicating the sophisticated and information-rich protein molecules found in the silk produced by spiders and other silk-producing arthropods such as silkworms — proteins that are nearly double the size of average human proteins. Smaller proteins do not have the strength or flexibility of spider silk. Given the advanced genetic and manufacturing technologies available today, it is remarkable that spider silk still cannot be duplicated. This illustrates just how advanced the engineering design of spider silk is.

No, he’s wrong. The silk molecules tend to be long, but not particularly “information-rich”, whatever that means. They are made up of long stretches of highly repetitive amino acid sequences, interspersed with special purpose regions. The strength comes from the repetition — they fold into crystalline bricks made of beta-pleated sheets. The length of each molecule is an obstacle to synthesizing them, of course, but there’s nothing magical or incomprehensible about the genes.

Rather, what makes them difficult to replicate is the silk production apparatus. The silk gland stores a large quantity of the fluid suspension of the silk molecules, but to make a silk fiber requires passage through a long duct that physically compresses and stretches the fibers as it extracts water and acidifies the environment, causing a controlled phase transition that makes the silk molecules align and precipitate to build a continuous fiber. That’s the hard part. It’s the gene (relatively easy) plus the specific mechanical and chemical processing that makes the silk. It is not at all remarkable that we can’t duplicate that process, but there’s nothing divine about it.

But that’s all there is to this article. Gosh, it’s amazing what biology can accomplish, says the guy who thinks it’s all about engineering.

Various spiderwebs, even among spiders of the same species, are far from identical. The most obvious reason for the differences is that each is tailored to its specific location. As the Goulds explain, “Every set of initial anchor points is different; the number of radii is contingent on opportunity; the beginning of the sticky spiral depends on where the longest several radii turn out to be. In short, each web is a custom production.” The Goulds postulate that spiders have a form of mapping ability that enables them to implement general design principles in a wide variety of circumstances. This is demonstrated, for instance, by spiders successfully making repairs to damaged webs.

And…? So…? The reason every web is a custom production is that nature is not uniform. A spider has an algorithm for navigating a variable environment: an orb weaver lays down radial lines from a central point to convenient anchor points, then walks a spiral, laying down sticky threads. The process builds a recognizable, functional sheet that varies depending on structures in the neighborhood. What is the miracle here?

Providing credible evolutionary explanations for the origin of silk and web design has proven problematic. Several theories have been proposed for the origin of both, but none have been generally accepted. Biologist and spider specialist William Shear concedes that “a functional explanation for the origins of silk and the spinning habit may be impossible to achieve.” One complicating factor is that the webs of some spiders that are more distantly related are nearly identical. Shear writes, “It appears probable that several web types are the product of convergent evolution — that is, that the same web has evolved in unrelated species that have adapted to similar environmental circumstances.” But as I will argue in Chapter 6, that is an unconvincing explanation for the origin of complex programmed behaviors.

For someone cited by a creationist, WA Shear sure has a lot of publications on the paleontology and evolution of spiders and other invertebrates. It looks like his work might have been mined to extract a misleading quote, and yep, he sure has.

That brief quote is taken from an article titled, “Untangling the evolution of the web,” and surprise, surprise, surprise, the creationist has left out the bulk of the context. I know, a creationist lies about the scientific literature? Say it ain’t so! But here’s the full and accurate quote from the paper. It starts, “A functional explanation for the origins of silk and the spinning habit may be impossible to achieve”, but then there’s a goddamn COMMA.

A functional explanation for the origins of silk and the spinning habit may be impossible to achieve, but the evolution of silk-spinning organs has been studied, and debated, extensively. Revealing evidence has come from the histology of silk glands — the details of their cellular construction — and from the embryological development of the spinnerets themselves. Histological evidence allows us to draw connections, or homologies, between silk glands in different spider groups, and embryology shows clearly that the spinnerets are paired abdominal appendages, with the silk issuing from modified setae, or hairs. So much information is available on the anatomy of the spinning apparatus, in fact, that the traditional view of web evolution rests heavily on a classification derived from the form and position of spinnerets.

This is one of those things about the creationist literature that makes me thoroughly furious: they unethically misrepresent and actively distort the work published in the credible scientific literature to pretend they are scholars. They aren’t. They’re liars. And they spin their lies out into collections of self-reinforcing nonsense. I note that the creationist here seems to think that convergent evolution is somehow an unacceptable explanation for the origin of multiple kinds of webs, and cites his own goddamn book, authored by a creationist engineer with no qualifications at all in this field, and ignores the fact that his source, WA Shear, goes on to give a summary of the evolution of diverse webs. That’s not a book worth reading, obviously.

Also, that Shear article contains a simple, clear illustration of the pattern of evolution that this creationist twit thinks can’t exist.

Phylogenetic tree shows how some families of spiders may have arrived at similar and different web designs. The Mesothelae are generally believed to have evolved first from the common ancestor of all spiders, followed by the Mygalomorphae and the “true spiders”, the Araneomorphae. The monophyletic hypothesis of orb-web origin (which is incorporated into this diagram) holds that the orb-web was invented by an araneomorph, the common ancestor of araneoid and uloborid spiders, that had a cribellum. The cribellum was acquired by a spider that was the common ancestor of all araneomorphs, including the araneoid superfamily and the uloborids. The araneoids lost the cribellum, and some araneoid families later lost the orb. Among the uloborids and their close relatives, the dinopids, are many species that have modified the orb.

But wait! There’s much more, all conveniently left out of Cassell’s stupid mangling of the article. We do have good models for the evolution of spider webs, all based on, as Shear notes, the evidence from taxonomy and histology and molecular biology.

Hypothetical pathways of spider-web evolution form a tangled web of their own, with the question of the orb’s origin, and its role as a possible precursor to other webs, at the center. In several cases it’s not clear which web is ancestral; it is possible that some aerial sheet webs preceded the orb web, whereas others developed from the orb. Pathways that are less likely are indicated by light-orange arrows; for some of them there is no direct evidence.

Oh look. Someone had the proper respect for the evidence and was happy to talk about the strengths and weakness of the support for their model, and it wasn’t Eric Cassel.

I’ll also note that Cassel is relying on a generalist article from 1994 which incorporates little of the evidence from modern molecular phylogenies. He didn’t understand the 27 year old article, there’s little hope he could grasp a modern analysis, in which the details of evolution have been strengthened. Here’s an example from 2012, Early Events in the Evolution of Spider Silk Genes:

Spidroin gene tree is based on a ML analysis of the carboxy-terminal encoding region with gaps coded as binary characters and monophyly of some groups constrained (see Methods). Numbers next to nodes and terminals correspond to numbers in supplementary Tables S1 and S2 showing support values, alternate rootings, and continuous character data. Spidroins are colored according to the taxonomic group from which they were characterized: purple = Mesothelae, blue = Mygalomorphae, green = Araneomorphae. Gray squares indicate duplication events inferred by reconciliation. Hash marks on branch indicate arbitrary shortening of branch for figure quality purposes. Brackets indicate clades with the following abbreviations: AcSp = Aciniform, TuSp = Tubuliform, PySp = Pyriform, MaSp = Major ampullate, MiSp = Minor ampullate, Flag = Flagelliform.

A more fundamental challenge for those seeking to provide a detailed, causally credible explanation for the origin of silk and spiderweb architecture is the number of genes involved in producing silk, and the complex genomes of spiders. After decades of failed attempts to provide a causally adequate explanation, one can be forgiven for concluding that we have no compelling reason to assume that a step-by-step evolutionary pathway to such an information-rich substrate actually exists. And as we will discuss later, there are now some positive reasons to consider that such information-rich systems have for their source something other than a purely blind material process. Here, suffice it to say that the behaviors and functions associated with both silk and web spinning exhibit many characteristics of human engineering, and engineering of a very high order.

Repeat after me:

Complexity is not evidence of design.

Complexity is not evidence of design.

Complexity is not evidence of design.

Also repeat after me:

My ignorance is not evidence of design.

My ignorance is not evidence of design.

My ignorance is not evidence of design.

Biologists have provided causally adequate explanations for the origin and evolution of diverse spider webs, Mr Cassell is simply intentionally and maliciously ignoring them, and further, lying about the content of the scientific literature to make a claim that arachnologists are as ignorant as he is. He’s also logically contradictory.

If, Given the advanced genetic and manufacturing technologies available today, it is remarkable that spider silk still cannot be duplicated, how can you then turn around say that webs exhibit many characteristics of human engineering, and engineering of a very high order?

In about an hour, I get to teach my last lecture of Fall 2021

Yes! Almost done! I get to dismiss the class, and then move on to … composing the final exam, and then grading the exams next week. And then getting ready for Genetics in the spring.

I won’t be saying goodbye to the students, though. They’re mostly 2nd year students, and this is a small university, so we’ll all be seeing each other again (cue groans from the class who are struggling with the material right now.)

That is so Chuck

In my mailbox today, I found a copy of the University of Oregon Biology Newsletter — I’m sure the publications department at my alma mater will be pleased to know that at least one of their alumni actually read it, even if, admittedly, I just give it a quick skim before filing it away in the recycling bin. This time, though, I was surprised to find an article titled “On Being a New Postdoc in the Bill Cresko Lab”. The title wasn’t surprising, since that’s the kind of thing you expect to find in a newsletter, but the author was kind of unexpected. It’s by my grad school mentor, Chuck Kimmel!

Although I still want to keep a toe in the Institute of Neuroscience (ION), I’m delighted to announce that Biology Professor Bill Cresko in the Institute of Ecology and Evolution (IEE) here at UO has graciously accepted greenhorn (Bill’s term) me to join his lab as a postdoctoral fellow. Postdocs are typically young scientists just out of graduate school. However, I am an 81-year-old Emeritus Professor, working in the Department of Biology for over 50 years. Most of that time I’ve been a member of the ION, studying neurodevelopment in zebrafish, a species that my ION colleagues and I have promoted as a model organism for biomedical research, and that is now used in hundreds of science labs. Bill is a mere baby in comparison: He’s been in the Department of Biology for less than half the time I have. Still, he enjoys worldwide recognition for his work on evolutionary genomics and evolution of development. Now that I’m in Bill’s lab, the fish species of the moment is not the zebrafish, but the threespine stickleback, with which Bill has worked since his days as a graduate student.

Wait wait wait…you can do that? Anyone want to take on a 65 year old grad student? I wouldn’t mind rewinding the tape for a bit.

This is typical Chuck, though. When I was in his lab, I remember he’d occasionally flit off to some other lab for a while and then he’d come back with new questions and new techniques and all the grad students and post-docs would groan because now we’d have to learn new stuff and we were still trying to figure out the old stuff and we just wanted to graduate. I guess that’s how old professors stay young, though. Gotta keep on the move, gotta get exposed to fresh ideas all the time.

I notice he’s still working on fish, though. Maybe when he turns 90 he’ll be ready to take a look at spiders.

Only purebloods will escape the curse of the vampire!

Oh boy, it’s getting intense out there. I discovered the latest absurdity via David Futrelle, and I encourage you to read it there rather than giving the original source the traffic, but I just had to mainline it myself and read it on Natural News. Whoa. What a rush. This is total pseudoscientific insanity.

Only PUREBLOODS will survive the vaccine / radiation holocaust being unleashed against humanity… the spike protein in vaccines causes genetic DISINTEGRATION
(Natural News) Today’s podcast is a bombshell that needs to be understood by anyone hoping to survive the vaccine holocaust, because it’s really a “genetic bomb” against humanity.

The vaccine, by suppressing the natural DNA repair mechanism in the body — known as NHEJ, or Non-Homologous End Joining — makes people highly susceptible to devastating, cancerous mutations even when exposed to very low levels of ionizing radiation such as sunlight exposure or mammography. With NHEJ suppressed by the spike protein, the body can no longer repair its damaged DNA, and cells mutate out of control, devastating the entire body and bringing about genetic disintegration of the organism.

The study documenting all this was published in the MDPI journal “Viruses” and was carried out by scientists at Stockholm University, Sweden:

https://doi.org/10.3390/v13102056

The study shows that NHEJ efficiency collapses in the presence of the mRNA covid vaccine spike protein:

Oh, look. Mike Adams includes a link to an actual paper in the actual scientific literature. I’ll come back to that, but for now, enjoy chaos and madness. He’s on a roll.

Importantly, once the beings on a planet are widely injected with the covid vaccine, globalists can unleash a nuclear accident (or nuclear terrorism) to distribute radiation across the planet. Even a low level of cesium-137 exposure (or strontium-91, iodine-131, etc.) will unleash a wave of deadly cancers among those who have been vaccinated. While normal, healthy people can repair the DNA damage caused by low levels of ionizing radiation exposure, vaccinated people can barely conduct the repairs (they have roughly a 90% suppression of DNA repair).

Thus, cancer rates will skyrocket among the vaccinated, and when they die, the deaths can be blamed on cancer rather than the vaccines. So this binary weapon arrangement also allows vaccine-pimping globalists to escape blame for the vaccines. It covers up vaccine deaths by categorizing them as cancer deaths.

All they need is another Chernobyl, Fukushima or nuclear explosion somewhere in the Northern hemisphere — almost anywhere — and the winds will spread the radioisotopes across half the planet, achieving the low levels of ionizing radiation necessary to turn vaccinated people into cancer-ridden mutants with accelerated deaths.

Those vaccinated individuals who aren’t killed by the cancers are very unlikely to be able to produce viable offspring due to DNA damage of sperm and egg cells.

Interestingly, once it becomes obvious that vaccinated individuals cannot tolerate sunlight without suffering genetic mutations, they will shun daylight and become creatures of the night.

In cultural mythos, vampires are creatures of the night who suffer instantaneous disintegration when sunlight touches their skin. In reality, the disintegration will take much more time, but it’s a similar idea:

Covid vaccines + sunlight = genetic disintegration.

Only purebloods will be able to reproduce, so the future of humankind belongs to those who reject mRNA vaccines
Those who reject covid vaccines are known as “purebloods.” They are the only ones who will be able to maintain genetic integrity for generations to come, which means the future of the human race belongs to those who reject covid vaccines. (People who take spike protein / mRNA covid shots are winning the Darwin Award…)

According to God, via the Old Testament, the blood is where the life exists. Your body manufactures two million red blood cells each minute, and these are manufactured in your bones. This is why Genesis says Eve was made from the rib of Adam. The bones are where the DNA exists to manufacture blood, the essence of life, and to find the genetic pattern that describes the biology of a new being.

A person who suffers genetic mutations in the blood is diagnosed with leukemia, essentially blood cancer. This is a disintegration of the genetic integrity of their blood manufacturing templates, put simply, and no mammal is viable in the long run when the genetic integrity of their blood is destroyed.

Yet this is exactly what the vaccines will accomplish when accompanied by low-level ionizing radiation exposure. Stated again:

Spike proteins + Ionizing radiation = DNA mutations / loss of genetic integrity

Those who took the spike protein injections are already experiencing accelerated growth of cancer tumors. This is being widely reported among naturopathic doctors and analysts. While it is possible that DNA mutations might be halted through an aggressive nutritional detox program and a lifetime of anti-cancer lifestyle habits, most people are in fact leading pro-cancer lifestyles via their toxic foods, toxic personal care products and toxic indoor living environments. Most people are vitamin D deficient on top of that, meaning they are essentially “cancer factories” even before spike protein injections came along.

Thus, we are about to see an explosion in worldwide cancer due to covid vaccines. This will really accelerate in 2022, and we will easily see over one million cancer deaths in the USA during 2022 (although the data won’t be available until 2024, most likely). Over the next decade (2022 – 2032) we will likely see tens of millions of cancer deaths in the United States.

Any radiation release by globalists will only accelerate these numbers and cost more lives. (That’s the goal of the globalists.)

Meanwhile, those who took the mRNA spike protein injections will be giving birth to mutated babies who lack genetic viability, even if they survive their own mutations. Currently about half the human population has taken covid jabs of one kind or another, which means the depopulation globalists may have already achieved their goal of destroying fertility / genetic viability for a significant portion of the human race.

The die-off has now begun. This winter, cancer deaths will explode across America, and they will skyrocket for the next decade in those who were gullible enough to be injected with deadly spike protein bioweapons. Get ready to see a tidal wave of cancers in America, Europe, Australia, Canada and every other nation where gullible people have committed vaccine suicide.

It’s going to be a real “We’re coming for you, Neville” moment I guess, with waves of tens of millions of Americans mutating and roaming the cities by night, draining the blood of the unvaxxed before dying of horrible deformities. And he got all that out of reading one scientific paper?

His mistake, though, was to include that link to “SARS–CoV–2 Spike Impairs DNA Damage Repair and Inhibits V(D)J Recombination In Vitro”, because I was able to read it and see there was nothing about vaxxed vampires or the coming cancer vampire apocalypse. It’s not even about the effects of vaccination, although it does speculate that there is a possible concern about certain kinds of vaccinations. What it’s really about is looking for an explanation of the prolonged and serious possible after-effects of coming down with COVID-19, the natural disease, not the vaccination. You know, for many people, COVID-19 is more than an episode of flu-like symptoms that you recover from — sometimes it can cause debilitating, long-term effects that last for months, maybe years, possibly for a lifetime. What’s going on there? The paper suggests one possible cause.

Severe acute respiratory syndrome coronavirus 2 (SARS–CoV–2) has led to the coronavirus disease 2019 (COVID–19) pandemic, severely affecting public health and the global economy. Adaptive immunity plays a crucial role in fighting against SARS–CoV–2 infection and directly influences the clinical outcomes of patients. Clinical studies have indicated that patients with severe COVID–19 exhibit delayed and weak adaptive immune responses; however, the mechanism by which SARS–CoV–2 impedes adaptive immunity remains unclear. Here, by using an in vitro cell line, we report that the SARS–CoV–2 spike protein significantly inhibits DNA damage repair, which is required for effective V(D)J recombination in adaptive immunity. Mechanistically, we found that the spike protein localizes in the nucleus and inhibits DNA damage repair by impeding key DNA repair protein BRCA1 and 53BP1 recruitment to the damage site. Our findings reveal a potential molecular mechanism by which the spike protein might impede adaptive immunity and underscore the potential side effects of full-length spike-based vaccines.

I think someone got hung up on that last line, unfortunately, and then didn’t bother to read the whole paper.

Basically, what the work finds is that the viral spike protein itself does more than just form a tool for breaking and entering into a target cell — it can also act like a big clumsy spanner in the works, entering the nucleus and interfering with DNA repair mechanisms, and in particular, preventing the modification of DNA that normally happens in T cells to shape them to respond during adaptive immunity. However, note that what they’re concerned about is a consequence of coming down with full-blown COVID-19, not the response to the vaccine, so the night-stalking, tumor-ridden population of vampires is more likely to arise from the people who don’t get the protective effects of the vaccine. Oops.

Also, it’s got lots of caveats. They observed an effect on V(D)J recombination, which occurs in T cells of the immune system, but they admit that “no evidence has been published that SARS–CoV–2 can infect thymocytes or bone marrow lymphoid cells” — they saw it in their cultured cell lines, so it’s not improbable, especially since depressed T cell counts have been observed in COVID-19 patients. Maybe this is one of the mechanisms by which SARS-CoV-2 causes long-term harm to people, which tells me this is another reason to not get COVID-19: not only will it make you sick, and maybe kill you, and turn you into a vehicle for infecting the people close to you, but it can do long-term harm to your immune system. So get the jab!

Is the vaccination likely to cause these problems, though? No. The vaccine is injected into your muscles, where it can temporarily trick the muscle cells, not T lymphocytes, into making the spike protein and presenting it for immune system cells to recognize and trigger an immune response. The RNA vaccines break down fairly quickly, within days, so those cells don’t make the spike protein anymore, and the T cells never made the spike protein anyway. The vaccine is not going to do the same kind of widespread infection that the virus would.

But, to be cautious, they do suggest that their “findings also imply a potential side effect of the full–length spike–based vaccine”. Both the Moderna and Pfizer vaccines use RNA that encodes the full-length spike, which, if expressed in T cells for a long period of time, could actively suppress the DNA repair mechanism essential for the acquisition of adaptive immunity. Except, of course, that the vaccination doesn’t target T cells or persist for long, so this is a lesser concern than the actual damaging side-effects of coming down with the disease.

So get the vax, and meanwhile build up the defenses around your home to protect yourself from the rotting, disintegrating, vampiric purebloods who let the virus run rampant in their tissues, rather than getting a simple shot that would have prevented the virus from getting a grip on their T-cells.

(Nah, that won’t happen either. Mike Adams is just stoking the fears of his poor, gullible clients who will then buy his “nutritional detox program”. It’s all a scam.)

To an embryologist, everything looks a bit eggy

This is a nice micrograph of an ascidian egg. A very large egg.

That is definitely the sperm entry point there in the lower half, so it’s apparently a freshly fertilized zygote at this point.

Wait, no, that’s not an egg! It’s Jupiter! I wonder when it will start to gastrulate? I don’t want to be around when it reaches the tadpole larva stage and starts swimming away.

There’s a whole series of Hubble images of the outer planets. Uranus and Neptune are rather blurry, but a very pretty robin’s egg blue, which means obviously that when they hatch they’re going to start screeching to be fed, which will be a bit terrifying, especially when their mama flies back to the solar system.

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.