Focus stacking!

Some people mentioned I should try focus stacking on my spiders, so I fumbled around and found some inexpensive software to do it, and gave it a shot. Here are a couple of trial runs (including some spiders I photographed in a single plane yesterday.

I’m just going to say…nice. Also easy. I always take multiple shots anyway, so I just do what I always do, maybe being a little more careful about centering each shot as identically as I can, and then dumping 4-8 photos into the software. I especially like how the juvenile in the third image turned out, letting me see individual hairs on the legs while not compromising the sharpness of the abdominal pigment pattern.

A few words about how I’m doing this: this is my Spider Studio.

It’s nothing fancy, as you can see. I’ve got a Canon body and a speedlite; I’m using my lovely Tokina macro 100mm lens, with a couple of tube extenders for extra magnification, and there’s also a big white diffuser there. I’ve got a bright LED panel to the left and back, and a simple clamp light with a full spectrum light on a jointed arm.

There are some colored papers on the bench top that I can use for backgrounds, but they don’t matter much with the big adults, who are usually hunkered down in a corner of their cardboard frame. The camera is stationary on a tripod, and I’m doing everything manually, focusing by holding the spider’s container in one hand and moving it back and forth, while in the other hand I’m holding a remote trigger and clicking away madly. The juveniles are contained in these clear plastic boxes, about 5cm square — I just pop off the lid, and there’s plenty of light from all around to illuminate the animal.

Hey, if handheld focus stacking is good enough for Thomas Shahan, it’s good enough for me. I was worried that I was going to need a fancy optical bench and something that would allow me to do precisely calibrated advancement of the camera focus, but nah, it turns out to be far easier than I feared.

I was also concerned because I’d seen all these finicky tutorials about using Photoshop or some other software to prep and align each frame, which was going to be tedious. Nope, don’t need that either: I found a program called Focus Stacker that does automatic alignment and assembles all the images into a single sharp result. It’s totally mindless, which I need: shoot a bunch of images with changing focus, drop them into Focus Stacker, and a few minutes later it presents you with the stacked image. I’m going to do this with all my spider photos from now on!

I’m going to have to disagree with you there, Snopes

You’ve probably heard about this Ohio law that dictates that teachers can’t penalize students for religious references in their essays and exams. Snopes thinks it’s harmless, and doesn’t affect the separation of church and state. I’m going to say that that is only true if you entirely ignore context and history and take every word literally. Here’s the law:

Sec. 3320.03. No school district board of education, governing authority of a community school established under Chapter 3314. of the Revised Code, governing body of a STEM school established under Chapter 3326. of the Revised Code, or board of trustees of a college-preparatory boarding school established under Chapter 3328. of the Revised Code shall prohibit a student from engaging in religious expression in the completion of homework, artwork, or other written or oral assignments. Assignment grades and scores shall be calculated using ordinary academic standards of substance and relevance, including any legitimate pedagogical concerns, and shall not penalize or reward a student based on the religious content of a student’s work.

It’s true, it does say “grades and scores shall be calculated using ordinary academic standards of substance and relevance,” but I have to ask…what is the purpose of this law? That’s how we calculate grades and scores now! Is there some mysterious network of teachers who have been using the frequency of “Praise Jesus!” comments in essays as an essential rubric? This is a law purportedly stating rules for STEM classes, where religious statements are irrelevant. Why do we need a law to set standards for religious statements?

Right now, if a student answers an exam question with the words “Praise Jesus” somewhere on the page, like a little doodle that they did in their spare time, I’d treat it exactly as I would if they sketched a picture of a dinosaur…as something to to ignore. However, if every other sentence in an essay was about Jesus (or dinosaurs — I don’t teach paleontology), I’d start marking it down for incoherence or irrelevancy. “Ordinary academic standards of substance and relevance” prohibit religious expression in most circumstances because we’re going to value clarity, brevity, and accuracy, so this law is redundant.

Except that what it’s really about is getting religion into the STEM curriculum somehow. It’s saying, “Don’t think of an elephant,” knowing that it immediately puts religious parents on guard to protest if their favorite creation myth isn’t discussed in biology class. This law was not written by someone concerned about the teaching of science, but by someone who wants to guarantee that theology will be brought up in science class.

Another way to think of it is that this is a law about a peculiar non-issue. Imagine if Ohio created a law that said you cannot prohibit or penalize a student from engaging in discussion of Jack Nicklaus, golfing legend, in homework, artwork, or other written or oral assignments. Would this actually be a proposal to guarantee fairness in science teaching, or do you think it would be more of an effort to promote Jack Nicklaus? Or golfing. Or the lawmaker’s golf course.

We’ve also got decades of precedent where creationists like to nibble away, inserting references to their beliefs in all kinds of laws, and then standing back with an expression of incredulity that you’d find this harmless little acknowledgment of America’s Christian heritage at all offensive, but they’ll build on it and grow and grow the Jesus nonsense a phrase at a time into the law books. They’re patient and dedicated. That law is only the first step to expand religious bias into STEM classes, I promise you.

How did the so-called rationalist community become so gullible?

Here we go again. Remember that silly “Sovereign Nations” conference? An obscure organization — actually little more than a single crank with money — invites a couple of dubious atheist celebrities to a weekend in London to give a couple of talks. Sure, that’s a conference all right, by definition, and that’s how many currently respected atheist conferences had their beginning, but it’s not much of an effort to communicate and share ideas. What made it weird is that some people treated it as a distinctive mark of honor that conferred instant credibility on a particular narrow point of view. It didn’t help that Richard Dawkins praised it (at first…when he learned that organizer was a strange religious conservative, he back-pedaled.)

It’s happening again. In this case, two people I never heard of announced an atheist conference in England and immediately got an endorsement from Richard Dawkins. It’s called the Anti-Theism International Convention. They got some respectable people, like Maryam Namazie and Stephen Law and Aron Ra, and then…Lawrence Krauss. A gaggle of YouTubers better known for their opposition to transgender issues and support for Rationality Rules. Lurking in their unused video promos is Richard Carrier. I think I can already detect a bias here — this is just another reaction to #MeToo, trying to whitewash misogyny.

One of the organizers is someone named John Richards, the publications director for Atheist Alliance International. You know, the organization that recently hired David Silverman. By this time, the whole thing is reeking of sliminess.

But OK, they have the right to organize a conference, and I’m not going to oppose it. Please do go buy a ticket for £199 if this is the kind of thing that floats your boat. I’ll just mention that you’re being bamboozled. This is an impromptu money grab by a small group in a pretend organization that didn’t exist until this past July, when they created a Facebook page, a Facebook page that is practically empty of content and has no commenters. It’s an empty shell of an organization that seems to have been a spontaneous brain fart by a pair of obscure nobodies.

Again, that’s fine. That’s how big events get started, and they all have to get started somewhere. I’ll just point out that this one contains a heck of a lot of ridiculous claims.

One of their big things is a gala awards banquet, in which they’ll be handing out awards for “Atheist of the Year” and “Jesus Mythicist of the Year” and “Best Atheist Video of the Year”, etc. You can make nominations, if you’d like, but a panel of unnamed judges will make the final decision, and I suspect that all the winners will conform to the organizer’s somewhat regressive political leanings. Furthermore, the hyperbole will turn your stomach.

You’ve heard of the Oscars, Emmys and Baftas?

This is the Attys! (the Anti-Theism International Awards)

Yes, I’ve heard of the Oscars, Emmys and Baftas. The “Attys” are not exactly of the same rank. It gets worse.

The Atty Awards are probably the most prestigious Awards in the Atheist Community and winning a Atty Award will not only get you recognition within the Atheist Community, it will give you a chance to enjoy giving worldwide speaking engagements as well as Keynote presentations at many events around the world. The Awards will be presented by some of the most famous atheist on the planet and the winners will be invited to the VIP area of the after awards ceremony for photo opportunites and press talks.

These “Atty Awards” have not been given out before, are a new invention of this oddly new and nebulous organization, and they are already the most prestigious award an atheist can get? Wow. Winning one will get you worldwide speaking engagements? Really? I sure hope none of the winners proudly advertise themselves as recipients of an Atty Award, because it’s not going to impress. I think all it means is that John Richards likes you this year, and that and $3 will get you a cup of coffee from the Caribou stand in the supermarket in Morris, Minnesota.

OK, I’ll sweeten the deal. I’m giving out the Morris Award for the Most Lost Atheist of 2020 to the first godless person to hit me up at the Willies Supervalu. I’ll even pay for the cup of coffee. Keep the cup, because I’m sure it will get you prestigious invitations to worldwide speaking engagements.

Post-prandial #SpiderSunday

The spider colony wasn’t very lively today. Everyone is still bloated from that waxworm feast last week, and even when I threw flies right into their webs they wouldn’t move — they just sat there, at best they might waddle a bit and desultorily wave a claw at such mundane fare. They now expect more. I promised them mealworms for tomorrow, but no, this is not enough, they have acquired a taste for larger prey.

“Bring us man-flesh,” they whispered.

I countered by telling them that in their current state, they weren’t going to be able to run down a baby, let alone a college freshman. They waddled towards me and hissed, which wasn’t too scary. They look like barrage balloons with a couple of feebly waving legs underneath. Like this:

Look at that! She’s not in a state to scamper at all. She’s huge.

Also pretty. Parasteatoda has these mottled rings of pigment in shades of black and brown, not at all flashy, but subtle and elegant. With abdomens so distended, they’re easy to admire, too. (by the way, the white circle top right is scrap from a hole punch, so you can estimate the size.)

They’re also marvelously variable. Here’s another Parasteatoda with an abdomen that looks like it was made up as an abstract mosaic. If you stare at it long enough you’ll see patterns. I’ve got my eyes open for one with Jesus’s face.

Right now I’ve got a bunch of full-grown adult females that are mostly immobilized by their gluttony, and then a largeish collection of juveniles in the incubator. I’m hoping to upgrade some of them to the larger cages soon — probably over Christmas break — and then I’ve got to introduce males to these young virgins. The Parasteatoda babies really are babies, tiny little spiderlings, that will take a little longer. Meanwhile, the next generation of Steatotoda triangulosa are coming along.

I’ve also got a few S. borealis, but I’m not sure I want to expand their numbers, since the Parasteatoda and S. triangulosa ought to be enough to keep me busy. On the other hand, S. borealis is so goth, with their blackish-purple bodies and gray racing stripes.

They also grow to a larger size. I may have to keep a few around looking badass.

Confirmed: We are the baddies

This is the tale of a “heroic” Navy SEAL, Edward Gallagher.

The investigation report said several members of the platoon told investigators that Chief Gallagher showed little regard for the safety of team members or the lives of civilians. Their mission was to advise Iraqi forces and provide assistance with snipers and drones, but they said the chief wanted instead to clear houses and start firefights.

He would order them to take what seemed to be needless risks, and to fire rockets at houses for no apparent reason, they said. He routinely parked an armored truck on a Tigris River bridge and emptied the truck’s heavy machine gun into neighborhoods on the other side with no discernible targets, according to one senior SEAL.

Chief Gallagher’s job was to plan and oversee missions for the platoon, but platoon members said he spent much of his time in a hidden perch with a sniper rifle, firing three or four times as often as other platoon snipers. They said he boasted about the number of people he had killed, including women.

Photos from the deployment that were stored on a hard drive seized by the Navy show the chief aiming sniper rifles and rocket launchers from rooftops in the city.

Two SEAL snipers told investigators that one day, from his sniper nest, Chief Gallagher shot a girl in a flower-print hijab who was walking with other girls on the riverbank. One of those snipers said he watched through his scope as she dropped, clutching her stomach, and the other girls dragged her away.

Another day, two other snipers said, the chief shot an unarmed man in a white robe with a wispy white beard. They said the man fell, a red blotch spreading on his back.

Before the 2017 deployment, Chief Gallagher ordered a hatchet and a hunting knife, both handmade by a SEAL veteran named Andrew Arrabito with whom he had served, text messages show. Hatchets have become an unofficial SEAL symbol, and some operators carry and use them on deployments. Chief Gallagher told Mr. Arrabito in a text message shortly after arriving in Iraq, “I’ll try and dig that knife or hatchet on someone’s skull!”

On the morning of May 4, 2017, Iraqi troops brought in an Islamic State fighter who had been wounded in the leg in battle, SEALs told investigators, and Chief Gallagher responded over the radio with words to the effect of “he’s mine.” The SEALs estimated that the captive was about 15 years old. A video clip shows the youth struggling to speak, but SEAL medics told investigators that his wounds had not appeared life-threatening.

A medic was treating the youth on the ground when Chief Gallagher walked up without a word and stabbed the wounded teenager several times in the neck and once in the chest with his hunting knife, killing him, two SEAL witnesses said.

Yes, there was an investigation. He was acquitted of multiple murders and was punished by being demoted one rank. That was it. This so angered the brave men and women who want the right to gun down young girls and old men that they lobbied hard to have this petty punishment dismissed, and they won: Donald Trump gave him a full pardon and restored his previous rank.

The man is a monster, as are many of his fellow SEALs. I’ll make an exception for the SEALs who were so outraged at his behavior that they brought him up on charges. Only now he’s back in business, tainting the honor, what’s left of it, of the military.

What is that guy going to be like if he ever returns to civilian life?

So, the Royal Family…what a piece of work, eh?

I listened to a bit of the interview with Prince Andrew and a couple of things leapt out at me as off. Just reekingly wrong.

After the interviewer recounts the story of Virginia Roberts, that they dined and danced together, went to a party hosted by billionaire sleaze and convicted pedophile Jeffrey Epstein, that he took her upstairs, and that he then had sex with her, and his reply is that he had “no recollection of ever meeting this lady.” You know, if someone confronted me with an accusation that I’d attended a billionaire sex party in Belgravia and took a specific woman into a bedroom to have my wicked way with her, my first reaction would be to indignantly state that I have never done any such thing, not to deny the identity of the woman I did it with. So can I take it as given that he was sexing up strange women so heedlessly that he had no idea who they were?

Also, he was hanging out in New York with a convicted pedophile because it was “convenient” and “the honourable and right thing to do” where the honourable thing to do was get foot massages from young Russian women and troop around with an assortment of youthful ladies — so many that he can’t remember them individually — for four days. This is a standard for dignified behavior of which I have not heard before. I’ve been doing everything wrong, I guess.

I’ve also missed out on the definition of “party”.

Andrew denied that there was a party at the residence or that he spent much time with Epstein away from their Central Park stroll.

He also said he was not aware of the presence of underage girls at the house, stating that Epstein’s house was like a “railway station,” so he could not comment about who was coming in and out.

Now he’s apologizing for behavior “not becoming of a member of the royal family”, which is remarkable. This is the family of Racist Prince Philip, Squidgygate, Prince Charles’s extramarital affair, Fergie’s toe-licking, and Andrew attending a party wearing a swastika armband, the family that has inherited billions scavenged from the British people, all for the onerous task of performing ribbon-cuttings and hosting parties. He must have done very bad things if he feels he let that family down.

I’ve always figured the royals were the UK’s version of The Jersey Shore.

Can spiders die of over-eating? Asking for a friend

I found one of my Texas S. triangulosa, Jacinta, in her cage this morning, lying on the floor next to a completely drained and shriveled waxworm, unmoving. I nudged her, and she was lying bloated in a puddle of bodily fluids, dead.

This is not good.

So, like the title asks, can spiders lack self-control to the point that they’ll suck prey dry until they rupture? I may be treading new medical frontiers here.

Eye of newt, toe of frog, might as well fling some tardigrade genes into the cauldron

I have to love speculative science — it’s in my contract as a popularizer — but I also like solid, well-established science and the cautious determination of incremental advances in our knowledge. Looking at both ends of the continuum and everything in between sometimes exposes some very poorly thought-out leaps in people’s assumptions, though, and then it’s also in my contract that I have to be grumpy and point out the flaws. This morning I’m feeling my grumpy side.

Let’s start at the beginning, with some nice work in tardigrades. Tardigrades are cool, obviously, and have a reputation as being tough customers who can survive all kinds of stresses that the environment throws at them. Freeze them, dry them out, throw them in outer space, zap them with radiation, and they can cope…at least, they cope far better than we do. Part of this ability is that they’re small and relatively simple, and being tiny and compact in itself is an advantage, but in addition, their cells have a sophisticated battery of proteins evolved specifically to enable them to handle stressful cellular situations without giving up and dying. It’s a sensible approach to take apart the tardigrade genome and puzzle out the genetic strategies they use to optimize cellular protection from stress, as Kunieda and others have done.

They scanned through the tardigrade genome looking for differences with other, less resilient animals, and found that sometimes that change involved deleting pathways that triggered stress responses. For instance, the genes in purple below are present in us, but missing in tardigrades.

Gene networks involved in the regulation of mTORC1 activity. Magenta indicates genes absent in the tardigrade genome and green indicates retained genes. The interconnected eight genes mediating environmental stress stimuli to downregulate mTORC1 were selectively lost, whereas all components involved in sensing and mediating physiologic demands were present.

This absence makes sense. It is desirable for our cells to kick the bucket when hit hard by environmental stresses; one kind of instance where this could happen is in cancer, where cells are in a poor physiological state, and it’s better for them to die and be replaced by healthy cells. Tardigrades, on the other hand, are already in possession of only a few tens of thousands of cells, and may be trying to cope with a systemic stress that affects every cell in their body, so this approach is not such a good one for them.

They also identified unique genes found only in tardigrades, such as this one, called Dsup, short for damage suppressor. This gene makes a protein that is associated with the DNA, and which has a high affinity for DNA; it’s also expressed in tardigrades with a high resistance to radiation damage. So, the immediate question is…is this protein responsible for radiation protection, and how does it work?

Since tardigrade cells have a lot of mechanisms for dealing with stress, and they want to just look at this one protein, the authors extracted the tardigrade gene and transfected it into a human cell line in order to determine its effects on a cell lacking all the other stuff a tardigrade cell provides.

They chose to use HEK293 cells (HEK is short for human embryonic kidney). A word of caution: these are cancer cells, not normal human cells. They are a popular cell culture choice because they proliferate readily in a dish, and are easily transfected with foreign DNA. They are hypotriploid — having nearly 3 times the number of chromosomes of a normal human cell — and contain adenovirus DNA that has turned them into madly dividing cancer cells. That doesn’t matter for the Kunieda study, though, since they just want to add a tardigrade protein to see what new properties it confers on the cells.

So they hit untreated HEK293 cells and HEK293 cells incorporating the tardigrade Dsup gene with X-rays, and found that the Dsup gene protected the chromosomes — they saw 40% fewer single-strand DNA breaks. They also saw that Dsup reduced the number of double-strand DNA breaks in these cells. They also did good controls, for instance knocking down Dsup expression in transfected cells, and seeing the protection going away.

Distribution of the numbers of γ-H2AX foci per nucleus is shown. Each dot represents an individual nucleus of a HEK293 cell (Control) or a Dsup-expressing cell (Dsup) under non-irradiated and irradiated conditions. ***P<0.001; NS, not significant (Welch’s t-test).
[γ-H2AX looks for phosphorylated histones that form around double-stranded DNA breaks]

Good stuff. Good fundamental cell biology. There’s a lot of work here, but that’s what you have to do to tease out the role of various components of the stress response.

But then it gets weird as it percolates up into the popular press. This was a focused bit of research designed to assess how tardigrades defend themselves against radiation that used a human cell line as a tool, and suddenly, that’s the newsworthy part of the work. It starts with a Nature news article — they should know better, and it does start with a relevant discussion of the work, and then we get the section where it just has to be explained how it could affect humans.

This makes the new paper’s findings “highly interesting for medicine”, says Jönsson. It opens up the possibility of improving the stress resistance of human cells, which could one day benefit people undergoing radiation therapies.

Wait a moment. Just think it through. You, a doctor, have a patient with cancer that you’re going to treat with radiation therapy. Do you really want to make their cells more resistant to radiation? Sure, their healthy cells, but if you’ve got a way to transfect healthy cells with Dsup that does not similarly help cancer cells, you’ve probably got better molecular tools to target cancer cells selectively than radiation anyway.

Then, the line that’s going to spawn a lot of crap, from Kunieda himself.

Kunieda adds that these findings may one day protect workers from radiation in nuclear facilities or possibly help us to grow crops in extreme environments, such as the ones found on Mars.

Oh jeez. This is where Live Science steps in and builds a fantasy of genetically modified humans colonizing Mars.

Will we one day combine tardigrade DNA with our cells to go to Mars?

Chris Mason, a geneticist and associate professor of physiology and biophysics at Weill Cornell University in New York, has investigated the genetic effects of spaceflight and how humans might overcome these challenges to expand our species farther into the solar system. One of the (strangest) ways that we might protect future astronauts on missions to places like Mars, Mason said, might involve the DNA of tardigrades, tiny micro-animals that can survive the most extreme conditions, even the vacuum of space!

This is what prompted me to dig into this line of research. I read this hypothetical, and my cortex immediately sneezed “Bullshit!” in an acute skeptical reaction, and I had to read further. It’s the combination of an imaginary Mars colony and an imaginary radical re-engineering of the human genome to produce customized genetic humans to labor under conditions of extreme environmental hostility that set me off. None of this is realistic. None of the evidence so far is at all adequate to justify this kind of speculation. There is only the glimmering of consideration for the ethical consequences of such experimentation, if it were even feasible. Is genetically modifying your offspring so they can more efficiently farm potatoes on Mars likely to be something they desire? Hey, though, it’s an opportunity to bamboozle a gullible audience with buzzwords!

One way that scientists could alter future astronauts is through epigenetic engineering, which essentially means that they would “turn on or off” the expression of specific genes, Mason explained.

I detest the casual abuse of the word “epigenetic”. I’m doing “epigenetic engineering” right now — my metabolism undergoes the usual seasonal shifts as we move into winter. You’re doing it too. Cells are constantly going to “turn on or off” the expression of specific genes as an expected consequence of basic biology. It sure sounds sciencey though, doesn’t it?

Alternatively, and even more strangely, these researchers are exploring how to combine the DNA of other species, namely tardigrades, with human cells to make them more resistant to the harmful effects of spaceflight, like radiation.

This wild concept was explored in a 2016 paper, and Mason and his team aim to build upon that research to see if, by using the DNA of ultra-resilient tardigrades, they could protect astronauts from the harmful effects of spaceflight.

This is where I get really irritated. See that phrase, “explored in a 2016 paper“? The “2016 paper” is the Nature news article I cited above. The only “exploring” of the concept is that one line from Kunieda, almost certainly prompted by a journalist prompting him to say something about the relevance of his research to humans, because they don’t understand basic biology.

Then there’s that bizarre claim about building upon tardigrade research to use tardigrade DNA to protect astronauts from radiation. It’s not a quote, so I expect the Live Science journalist just invented it to say some random something to justify the article, but I would just ask a simple question of whoever made it up.


What specifically is being experimented on to improve astronaut’s resistance to radiation?

I’m going to guess that the real answer would be nothing, at least not yet. Let’s keep on eye on those wacky basic biologists who are studying core processes in genetics and cell biology with work on weird organisms that aren’t humans at all, and hope that sometime in decades to come some methods will emerge that will be applicable to human medicine. But until then, nope, nobody is shooting up astronauts with magical tardigrade DNA.

I guess we have to kill all the superstar scientists now, too

A study of “star” scientists in biology discovers an unsurprising fact: their fields undergo a substantial change when they die.

In the first two years after a star’s death, publications in their subfields increased modestly. But as the years passed, breaking the numbers down by author showed a startling change: Papers by newcomers grew by 8.6 percent annually on average. At the same time, papers published by collaborators took a nosedive, decreasing by about 20 percent a year. After five years, growth from newcomers was so substantial, it made up for the deficit from the collaborators.

In other words, large swaths of these fields had essentially been turned over.

Strangely, the article doesn’t dwell much on the likely cause: funding. It doesn’t even have to be intentional, but reviewers and study sections at the funding agencies tend to be biased by the presence of those who have already been funded, and big labs will have an undue influence because they have so many former students cheerleading for their mentors. This stuff also affects hiring — if you come from a famous lab, you’re more likely to get interviews and jobs.

That’s always been my impression, nice to see the inertia of big-name biologists measured.