Sense/Anti-sense

First, I must remind everyone that billionaire Rupert Murdoch elbowed his way to the front of the queue to get the vaccine as soon as it was announced, and that all those blithering conservative on-air personalities on Fox News are required to be vaccinated, just to put this story on Fox News’ promotion of quacks in perspective. It lists ten of the COVID denialist and anti-vax and tepid apologists for inaction who have been featured on the network many hundreds of times. Names you should learn to recognize and scorn: Marc Siegel, Martin Makary, Nicole Saphier, Rand Paul, Brett Giroir, Janette Nesheiwat, Jayanta Bhattacharya, Harvey Risch, Scott Atlas, and Peter McCullough. They all have the title of “Dr”, but you should know that the majority of doctors disagree with these scam artists; Fox News has been carefully distilling the population of MDs to purify and isolate the most untrustworthy scum to selectively display on popular programs by even more reprehensible filth like Carlson and Ingraham and Kudlow. You don’t get a prime time opinion/bloviation slot on Fox if you hold a reasonable view of the science.

Contrast that with this genuinely excellent interview with Jonathan Eisen, a biologist at UC Davis. Eisen simply and plainly says what every biologist and informed citizen knows about SARS-CoV-2.

The Omicron variant is way more infectious [than Delta]. It’s horribly contagious. Even people who are boosted are still getting infected. [The vaccine] does not seem to provide a huge protection against getting infected. I think that’s part of why it’s spreading so fast—people who have been vaccinated and/or boosted have mistakenly thought they were not going to get infected, and so they were going maskless everywhere. But if you have five times as many people infected, that’s going to create havoc, and that’s what is happening in New York and the Northeast, where the hospitals are full. They’re already sending people away who have any other types of emergency or nonemergency health needs. I think we’re in for some tough times; that’s my prediction.

Exactly. This is what I’m expecting, too. It’s also what everyone who isn’t brainwashed by Fox News can figure out. So what should we do?

All the evidence right now shows that vaccines are incredibly effective in reducing the risk of severe illness and death from Covid. And this is true even for new variants such as Delta and Omicron, even though the vaccines were not specifically designed for them. One can reduce the risk of severe illness even more by getting a booster shot. This reduction in risk is very, very clear from all the data. The one issue with Omicron that is different than with other variants is that just getting the regular vaccine dose (e.g., two Pfizer shots) does not reduce the risk of severe illness as much as it did for other variants. In other words, to reduce the risk of severe illness or death, it seems that a booster is very important here.

This is what infuriates me. Everyone wants the quick fix, the easy treatment, the simplest, most painless way to prevent this disease, and science provides one: the vaccine. Go in to the clinic or pharmacy, poke, you’re done, death averted. And what happens? People who listen to Fox News whine, “I want an insta-fix, but not that one.” They’d rather dose themselves with hydroxychloroquine or ivermectin or bleach or betadine, treatments that don’t work, than take the medicine proven to work.

In a world with people who refuse the treatment that works, and other people who can’t, for other medical reasons, get the vaccine, what can we do to protect ourselves. That’s also easy. Wear a mask in public.

What I’m hoping is that people do a lot of behavioral intervention that can slow down the spread of the Omicron variant. It goes back to the whole “flattening the curve” thing from before, and there are many things we can do. If you’re in crowded indoor spaces, you can avoid doing things where you have to take off your mask—so, no eating. But even with your mask on, not all masks are created equal. There’s new guidance that has come out in the last few days that cloth masks just aren’t going to cut it against Omicron. They just do not, on their own, filter enough particles out to reduce your exposure when airspace is getting filled with virus. What you want is a KN95 or N95 mask.

Yes. Masks aren’t the imposition the whiny-ass-titty-babies of conservatism pretend they are. When I’m teaching, I wear them continuously all day long with no difficulty, other than that I’m generally soft-voiced and muffling me doesn’t help (I’m working on it by TALKING LOUDER with my teaching voice). I tried to order some N95 masks in time for spring classes, but right now they’re backlogged and horribly expensive, so I settled for N94…still expensive with slow delivery — I think they’re all coming from South Korea — but I’ll double-up with a cloth mask until N95s become more available, I hope. If they do.

Eisen mentions also that he avoids big indoor events, even restaurants, and won’t fly, although he thinks if everyone on the plane takes reasonable precautions it’s probably safe. It’s just that too many people have been infected with the Fox brain-rot. Just glance at YouTube fights over masks on airplanes — people are getting into brawls in the aisles because they refuse to wear a mask. It’s nuts.

I avoid going out because I live in a county where practically no one wears a mask, ever. Even when our governor imposed a mask mandate, briefly, a lot of people ignored it, and our local business wouldn’t enforce it — and even then, half the population was incapable of figuring out that the mask covers your mouth and nose. It was good news when my university reluctantly decided to require masks and vaccines for all of our incoming students, but we’re a tiny island of common sense in an ocean of conservative denialists of basic medical facts.

We also need to worry about the long-term consequences of infection. Idiots like those talking heads on Fox News want to pretend it’s just a kind of flu, you get over it and carry on, but COVID has complications you ignore at your own peril.

That is one of my biggest concerns with this attitude of not worrying about Omicron too much because it might cause less severe symptoms. We know that long Covid is a problem for the other variants. It’s a big problem that is poorly understood medically, but is very clearly a real thing. These are real medical problems that people are having for months to now years after infection. Some people are saying everybody is going to eventually get Omicron, and that’s just the wrong attitude. We can make it so that not everybody gets it, and therefore reduce the risk of long Covid in too many people. We can’t just let it spread to everyone on the globe, because that’s going to be a medical catastrophe. Now is not the time to do nothing and hope for the best. It is the time to take measures while at the same time trying not to damage people’s lifestyles and lives and the economy.

Eisen’s is the kind of sensible voice we ought to have been hearing all along in our news media, providing accurate, honest information. I guess Rupert Murdoch knows that that doesn’t sell, unfortunately. And that’s why we’re screwed right now.

My new vicarious pleasure

I have discovered a subreddit called Abandoned Porn. This is very much my kind of porn : photos of old, crumbling, abandoned buildings. Very romantic. So tempting. I made a kind of Homer gurgle when I stumbled across it.

Imagine the spiders in there! I want to go exploring…this summer, I hope. I have to get over this annoying tendinitis (I can walk without pain now, I’m just at the stage of having to be very careful not to worsen anything), and then start casing a few joints in the region. Then, new spider survey! In empty buildings where a pandemic can’t bring everything to a screeching halt! I’m going to have to put this in my to-do list:

  • Get strong.

  • Wait for the snow to melt.

  • Rummage through the wreckage of ancient days.

I’ve got a couple of hardhats with helmet lights, and a collection of bright portable LED lights. I should probably get some nice steel-toed boots with good ankle support.

I should also stake out some sites that aren’t abandoned ruins for comparison.

Behold my mountain of digital papers!

All the final exams have been turned in, so now it’s time to sit my butt down and read them all. I’ve got two classes with about 25 students each, so here’s what I am to complete this weekend. These were all due on Friday, yesterday.

Comprehensive Final Exam for Fundamentals of Genetics, Evolution, and Development. This is the monster, 7 pages of questions in different formats that cover the topics in the title of the course and also a bit of the history and philosophy of science. FunGenEvoDevo is a first year overview course that doesn’t dig too deeply, but prepares them with the general background (there is also another intro course, Evolution of Biodiversity, that hits them with evolution again and also basics of ecology and systematics). I started on this one yesterday, and am a bit more than halfway through; I plan to finish it by this afternoon.

Lab Final for Cell Biology. Another longish exam, this one emphasizes basic quantitative skills they should have learned in the lab. So lots of questions about unit conversions, calculating concentrations, interpreting data, etc. For instance, they get some measurements of reaction rates, and they then have to calculate enzymatic Km and Vmax. There are a lot of parts to this one, too, but most of the answers are short, specific, and numeric, which are relatively easy to grade.

Required Final Essay for Cell Biology. Oh boy, this will be challenging. I gave them a paper to read (“How energy flow shapes cell evolution” by Nick Lane) and asked them to summarize it and relate it all to the content of the course. On this one, I demand high writing standards and coherence in addressing the subject, so we’ll see how that goes.

Optional Final Exam for Cell Biology. Another big ol’ comprehensive exam, but this one is optional for the students: whatever score they get on the final will replace their lowest midterm score. Everyone has a bad day, so this is their opportunity to vindicate themselves. It’s a long exam, but grading it might not be too bad — only about a third of the class has opted to do it.

So that’s my weekend! This is all I’m doing for a few days. I hope to get it all done by Sunday evening and get all those grades submitted to the registrar early.

Then on Monday I have one more class to grade, Biological Communications II, in which students spend the semester writing a 10+ page review paper under my tutelage, so I already have a good idea of what they’ve done — I just have to go over what is supposed to be the final polished draft of the paper. And then I’m ALL DONE!

I guess I better buckle down and get to work now.

10:45 Saturday: FunGenEvoDevo done! Grades submitted! Students mostly did OK, but a few of them may have learned that skipping an exam or two is a good way to fail a course.

3:45 Saturday: Lab final done! Starting on the required final essay.

1pm Sunday: Required lab final done! Now to polish off the optional final.

Resign yourself to the new normal

All of my final exams came due last night at midnight — they were all fortuitously scheduled for the last day of finals week — so I got to open my mailbox this morning to find an expected mountain of papers to grade. Oh joy. There goes my weekend. Also, my flies arrived late yesterday, so I’ve got to go in to the lab today and get the stocks set up for my spring genetics course. That course, by the way, is going to be taught entirely in person, because my university has been applying some gentle pressure on the faculty to pretend the pandemic is completely over and we can all go back to normal. To be fair, I really want to get back to normal, too, but I’m also realistic enough to know that what I desire isn’t necessarily what I’ll get. The university is not adjusting any of its policies to deal with the threat of the new Omicron variant, and is in fact loosening them. As usual, we’ll wait until a crisis is upon us and only then start changing things, too little and too late, to try and catch up to a disease that’s running ahead of us right now. And my university is relatively progressive compared to the western Minnesota community, and the Minnesota governor!

My next few days are going to be bogged down in work, and then my so-called Christmas “break” I’m going to be tied up in that magic word, preparation, for the next semester, which I’m required to take seriously, unlike the administration. Wouldn’t it be nice if I could submit my grades next week and then take a nap or play with spiders or you know, just relax, until 18 January, when classes resume? Nope, isn’t going to happen. Especially since I have a looming dread that this is going to be an abortion of a semester, that we’ll go in assuming an air of nonchalant normalcy, and at some point we’re going to get screaming panicky emails from the administration telling us the quarantine spaces are all full, the local hospital is full, the pandemic is spiking, change your class management and go into lockdown. I figure I’ve got to prepare for two classes, not just one, an in-person version and a remote version. Thanks, procrastinators on high!

And then Ed Yong has to come along and splash stinky reality all over me.

OK, I can’t blame him. I know this stuff, but hey, I’ve been trying to close my eyes and pretend it isn’t as bad as it probably will be. Omicron should open everyone’s eyes to the new normal, that because we refuse to do what needs to be done, we’re going to get new variants every year, and we’re going to have to learn to live with new levels of unpredictability.

America was not prepared for COVID-19 when it arrived. It was not prepared for last winter’s surge. It was not prepared for Delta’s arrival in the summer or its current winter assault. More than 1,000 Americans are still dying of COVID every day, and more have died this year than last. Hospitalizations are rising in 42 states. The University of Nebraska Medical Center in Omaha, which entered the pandemic as arguably the best-prepared hospital in the country, recently went from 70 COVID patients to 110 in four days, leaving its staff “grasping for resolve,” the virologist John Lowe told me. And now comes Omicron.

Will the new and rapidly spreading variant overwhelm the U.S. health-care system? The question is moot because the system is already overwhelmed, in a way that is affecting all patients, COVID or otherwise. “The level of care that we’ve come to expect in our hospitals no longer exists,” Lowe said.

Because we don’t know what is going to happen, we need more discipline, more cohesive action, more cooperative behavior in our communities. That’s not the American way!

The real unknown is what an Omicron cross will do when it follows a Delta hook. Given what scientists have learned in the three weeks since Omicron’s discovery, “some of the absolute worst-case scenarios that were possible when we saw its genome are off the table, but so are some of the most hopeful scenarios,” Dylan Morris, an evolutionary biologist at UCLA, told me. In any case, America is not prepared for Omicron. The variant’s threat is far greater at the societal level than at the personal one, and policy makers have already cut themselves off from the tools needed to protect the populations they serve. Like the variants that preceded it, Omicron requires individuals to think and act for the collective good—which is to say, it poses a heightened version of the same challenge that the U.S. has failed for two straight years, in bipartisan fashion.

We’re not ready for omicron. How about pi, and rho, and sigma, and phi, and…we’re going to run out of Greek letters long before this is over. Oh, wait, “over”? It may not ever be over, at least, not until the recalcitrant and deluded are all dead. I was letting my guard down after I got my third booster, but I’m going to have to look forward to my fourth, and fifth, whatever it takes (at least we run no risk of running out of numbers), and I’m going to have to be less cocky. He says, while preparing to abandon isolation and spend 16 weeks in a classroom.

First, the bad news: In terms of catching the virus, everyone should assume that they are less protected than they were two months ago. As a crude shorthand, assume that Omicron negates one previous immunizing event—either an infection or a vaccine dose. Someone who considered themselves fully vaccinated in September would be just partially vaccinated now (and the official definition may change imminently). But someone who’s been boosted has the same ballpark level of protection against Omicron infection as a vaccinated-but-unboosted person did against Delta. The extra dose not only raises a recipient’s level of antibodies but also broadens their range, giving them better odds of recognizing the shape of even Omicron’s altered spike. In a small British study, a booster effectively doubled the level of protection that two Pfizer doses provided against Omicron infection.

Second, some worse news: Boosting isn’t a foolproof shield against Omicron. In South Africa, the variant managed to infect a cluster of seven people who were all boosted. And according to a CDC report, boosted Americans made up a third of the first known Omicron cases in the U.S. “People who thought that they wouldn’t have to worry about infection this winter if they had their booster do still have to worry about infection with Omicron,” Trevor Bedford, a virologist at Fred Hutchinson Cancer Research Center, told me. “I’ve been going to restaurants and movies, and now with Omicron, that will change.”

I guess I’ll be self-isolating at home from now on, except every day when I go in to work.

Omicron might not actually be intrinsically milder. In South Africa and the United Kingdom, it has mostly infected younger people, whose bouts of COVID-19 tend to be less severe. And in places with lots of prior immunity, it might have caused few hospitalizations or deaths simply because it has mostly infected hosts with some protection, as Natalie Dean, a biostatistician at Emory University, explained in a Twitter thread. That pattern could change once it reaches more vulnerable communities. (The widespread notion that viruses naturally evolve to become less virulent is mistaken, as the virologist Andrew Pekosz of Johns Hopkins University clarified in The New York Times.) Also, deaths and hospitalizations are not the only fates that matter. Supposedly “mild” bouts of COVID-19 have led to cases of long COVID, in which people struggle with debilitating symptoms for months (or even years), while struggling to get care or disability benefits.

And even if Omicron is milder, greater transmissibility will likely trump that reduced virulence. Omicron is spreading so quickly that a small proportion of severe cases could still flood hospitals. To avert that scenario, the variant would need to be substantially milder than Delta—especially because hospitals are already at a breaking point. Two years of trauma have pushed droves of health-care workers, including many of the most experienced and committed, to quit their job. The remaining staff is ever more exhausted and demoralized, and “exceptionally high numbers” can’t work because they got breakthrough Delta infections and had to be separated from vulnerable patients, John Lowe told me. This pattern will only worsen as Omicron spreads, if the large clusters among South African health-care workers are any indication. “In the West, we’ve painted ourselves into a corner because most countries have huge Delta waves and most of them are stretched to the limit of their health-care systems,” Emma Hodcroft, an epidemiologist at the University of Bern, in Switzerland, told me. “What happens if those waves get even bigger with Omicron?”

Ha ha, I know! Nothing! Nothing will change! The people in charge will keep pushing everyone to go back to work, the media will amusingly report without condemnation on all those assholes protesting against basic hygiene, and Republicans will be passing laws against accurate information and public health measures.

And then I die because I can’t get healthcare from a system clogged with people on ventilators who refused to get vaccinated. I’m calling it now.

I’m eager to try out my new toy!

I got a new Christmas present for myself.

If you don’t know what it is, I explain it fully over on Patreon, for the benefit of the supporters who donated money to enable this purchase. I also explain some of my research plans there.

I’m sure some readers here will be able to instantly recognize it — it’s not that exotic — and the rest of you can entertain us all with wrong answers.

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.)