twenty-one things tagged “science”

The Schmidt Pain Index

This is the Schmidt Sting Pain Index, an eponymous and subjective measurement of the pain caused by bees, wasps, and ants (and other things in the order hymenoptera.) It ranges from 0-4. In Level Zero, you don’t feel any pain whatsoever; the stinger doesn’t even penetrate your skin. The humble and familiar honeybee will deliver a Level 2.

Schmidt describes Level 4, the absolute worst, as follows:

Bullet Ant

“Pure, intense, brilliant pain… like walking over flaming charcoal with a three-inch nail embedded in your heel”

“That really shuts you down. It really felt like a bullet. It was instantaneous, almost even before it stung me. It was absolutely riveting. There were huge waves and crescendos of burning pain—a tsunami of pain coming out of my finger. The tsunami would crash as they do on the beach, then recede a little bit, then crash again. It wasn’t just two or three of these waves. It continued for around 12 hours. Crash. Recede. Crash. It was absolutely excruciating. There wasn’t much I could do except be aware of it and groan.”

Tarantula Hawk

“Blinding, fierce [and] shockingly electric”

“A running hair dryer has just been dropped into your bubble bath”

“Like you were walking underneath a high-voltage electric line in a wind storm, a wind gust snapped the line, and it fell on your arm. You get 20,000 volts all at once cascading through your body. It’s pure electrifying pain. Instantaneous. Very clean and sharp.”

Warrior Wasp

“Torture. You are chained in the flow of an active volcano. Why did I start this list?”

Here’s Dr. Schmidt with a giant bug on his face.

Dr Justin O. Schmidt

Some quotes and that image are from this article he penned in Esquire (cached) where he touches upon why the pain profiles are different.

“Crowded, Compartmentalized, Sticky, Spatially Inhomogeneous”

In college, I remember being blown away by a huge, physical map of metabolic pathways our Biochemistry professor once brought into class. It looked like this:

metabolic pathways

Here it is online. Kinda like a Google Maps of cellular reactions. It was impressed upon us that the interior of a cell (especially a eukaryotic one) is a really, really busy and tight and ‘goopy’ place: “crowded, compartmentalized, sticky, spatially inhomogeneous”. As that paper notes, this messy, “macromolecular crowding” helps your proteins fold properly (among several other factors.) This was a bit hard for me to appreciate since, up to then, I was only accustomed to images of cells from a light microscope or vastly simplified illustrations school texts.

I was somehow reminded of all of that after seeing some astounding paintings by Professor David S. Goodsell (Wiki, Twitter, Website). He calls the series “Molecular Landscapes.” Here are a few related to the pandemic we’ve been through.

SARS-CoV-2 and Neutralizing Antibodies, 2020

Art by David S. Goodsell

Acknowledgement: David S. Goodsell, RCSB Protein Data Bank and Springer Nature; doi: 10.2210/rcsb_pdb/goodsell-gallery-025. The painting was commissioned for the cover of a special COVID-19 issue of Nature, presented 20 August 2020, and is currently in the collection of the Cultural Programs of the National Academy of Sciences.

(Unknown Title)

Art by David S. Goodsell

Acknowledgement: Illustration by David S. Goodsell

Coronavirus, 2020

Art by David S. Goodsell

Acknowledgement: Illustration by David S. Goodsell, RCSB Protein Data Bank; doi: 10.2210/rcsb_pdb/goodsell-gallery-019. This painting depicts a coronavirus just entering the lungs, surrounded by mucus secreted by respiratory cells, secreted antibodies, and several small immune systems proteins. The virus is enclosed by a membrane that includes the S (spike) protein, which will mediate attachment and entry into cells, M (membrane) protein, which is involved in organization of the nucleoprotein inside, and E (envelope) protein, which is a membrane channel involved in budding of the virus and may be incorporated into the virion during that process. The nucleoprotein inside includes many copies of the N (nucleocapsid) protein bound to the genomic RNA.

SARS-CoV-2 Fusion, 2020

Art by David S. Goodsell

Acknowledgement: Illustration by David S. Goodsell, RCSB Protein Data Bank; doi: 10.2210/rcsb_pdb/goodsell-gallery-026. This painting depicts the fusion of SARS-CoV-2 (magenta) with an endosomal membrane (green), releasing the viral RNA genome into the cell cytoplasm (blue), where it is beginning to be translated by cellular ribosomes to create viral polyproteins. The painting includes speculative elements that are designed to highlight the process, most notably, multiple states of the viral spike protein are shown.

SARS-CoV-2 mRNA Vaccine, 2020

Art by David S. Goodsell

Acknowledgement: Illustration by David S. Goodsell, RCSB Protein Data Bank; doi: 10.2210/rcsb_pdb/goodsell-gallery-027. Messenger RNA (mRNA) vaccines developed for the COVID-19 pandemic are composed of long strands of RNA (magenta) that encode the SARS-CoV-2 spike surface glycoprotein enclosed in lipids (blue) that deliver the RNA into cells. Several different types of lipids are used, including familar lipids, cholesterol, ionizable lipids that interact with RNA, and lipids connected to polyethylene glycol chains (green) that help shield the vaccine from the immune system, lengthening its lifetime following administration. In this idealized illustration, all of the lipids are arranged in a simple circular bilayer that surrounds the mRNA and the PEG strands have both extended and folded conformations. In reality, the structure may be less regular, as suggested in the NanoLetters paper […]

You Cannot Overcook Mushrooms

Note that you can certainly burn them. That’s not ‘cooking’, however. The key here is that mushroom cell walls are composed of chitin which is far more heat-stable by virtue of the structures it forms, compared to pectin which is what you’d find in veggies1.

In this video, Dan Souza explains all this and does something quite surprising when cooking mushrooms: He sautés the mushrooms in water to ‘collapse’ them prior to cooking them in just a teeny bit of oil (and the usual salt, pepper, butter, and herbs.) Amazing.

  1. You’ll also find chitin in the “exoskeletons of arthropods, such as crustaceans and insects, the radulae of molluscs, cephalopod beaks, and the scales of fish and skin of lissamphibians.” Leave it to fungi to be weird 😍🍄 ↩︎

Resolution versus Magnification

Was looking for a portable iPhone microscope and came by this one on Amazon. Doubted the “50x-1000x magnification” claim and landed on this video by Oliver Kim (here’s his channel on YouTube) on how to make sense of that feature.

The key idea here is to think of a microscope as a device that resolves hitherto unseen things. It’s simply not just a magnifier of small things our eyes cannot resolve. This is the difference between the 2x optical zoom on your iPhone versus the 10x you can slide it up to.

So I don’t doubt that the product on Amazon can do 50x, which is fine for my needs. I just don’t believe that the upper bound (1000x) can provide anything useful.

Hubble Ultra-Deep Field

One of my favorite things in the world.

Located southwest of Orion in the southern-hemisphere constellation Fornax, the rectangular image is 2.4 arcminutes to an edge, or 3.4 arcminutes diagonally. This is approximately one tenth of the angular diameter of a full moon viewed from Earth (which is less than 34 arcminutes), smaller than 1 sq. mm piece of paper held at 1 meter away, and equal to roughly one twenty-six-millionth of the total area of the sky. The image is oriented so that the upper left corner points toward north (−46.4°) on the celestial sphere.

Wikipedia (emphasis mine)

Here’s all that in video form

The best screensaver in the world using red-shift data

And a very high-resolution image (> 60MB). Wallpapers are available.

Our shit is so, so, so tiny.

There are over 100 billion galaxies in the universe. Simply saying that number doesn’t really mean much to us because it doesn’t provide any context. Our brains have no way to accurately put that in any meaningful perspective. When we look at this image, however, and think about the context of how it was made and really understand what it means, we instantly gain the perspective and cannot help, but be forever changed by it.

We pointed the most powerful telescope ever built by human beings at absolutely nothing for no other reason than because we were curious, and discovered that we occupy a very tiny place in the heavens.

Deep Astronomy

Not so sure about “instantly” gaining perspective but the rest about wonder and curiosity and our insignificant place the heavens still stand.

Why Hulls are Painted Red

TL;DW: This is “anti-fouling” that repels barnacles, algae, and mollusks by emitting “biocides”. This is desirable because they cause drag (think fuel) and structural damage. Red because traditionally some oxide of Copper.

Also this:

In nature bright colours serve as a warning and to stay away. Ships are very territorial and have even been known to attack people.

The Titanic and Climate Change

Stumbled upon this nearly three-hour, real-time, annotated simulation of the Titanic sinking. Late night1.

Which led me to James Cameron’s 2012 documentary Titanic: The Final Word, in which he assembles a group of engineers and historians to fix the simulation in the 1997 movie, which leads to this ‘final’ version.

Cameron, in the documentary:

Part of the Titanic parable is of arrogance, of hubris, of the sense that we’re too big to fail. Well where have we heard that one before? There was this big machine, this human system that was pushing forward with so much momentum, that it couldn’t turn, it couldn’t stop in time to avert a disaster. And that’s what we have right now. Within that human system onboard that ship, if you want to make it a microcosm for the world, you have different classes, you know, you’ve got first class, second class, and third class. Well in our world right now you’ve got developed nations and undeveloped nations. You’ve got the starving millions who are going to be the ones most affected by the next iceberg that we hit, which is going to be Climate Change.

We can see that iceberg ahead of us right now, but we can’t turn we can’t turn because of the momentum of the system. Political momentum, business momentum. There are too many people making money out of the system the way the system works right now, and those people, you know, frankly have their hands on the levers of power and aren’t ready to let them go. Until they do, we’re not going to be able to turn to miss that iceberg and we’re gonna hit it. When we hit it, the rich are still gonna be able to get their access to food, to arable land, to water, and so on. It’s going to be the poor, it’s going to be the steerage, that are gonna be impacted. It was the same with Titanic and I think that’s why this story will always fascinate people. Because it’s a perfect little encapsulation of the world and all social spectra. But until our lives are really put at risk, the moment of truth, we don’t know what we would do.

  1. Speaking of… found this amazing model of the ship. ↩︎

Timelapse of the Future

Best thing I’ve seen this year. About as spiritual as it gets.

After an unimaginable length of time, even the black holes will have evaporated and the universe will be nothing but a sea of photons, gradually tending towards the same temperature, as the expansion of the universe cools them towards absolute zero. Once the very last remnants of the very last stars are finally decayed away to nothing and everything reaches the same temperature, the story of the universe finally comes to an end. For the first time in its life, the Universe will be permanent and unchanging. Entropy finally stops increasing because the cosmos cannot get any more disordered.

Nothing happens. And it keeps not happening forever.

😢 how beautiful is that? And black holes take a long, long time to evaporate

A black hole with the mass of the sun will last a wizened 1067 years. Considering that the current age of our universe is a paltry 13.8 times 109 years, that’s a good amount of time. But if you happened to turn the Eiffel Tower into a black hole, it would evaporate in only about a day.

And that’s after this happens

It will take hundreds of trillions of years for the first stellar remnant to cool completely, fading from a white dwarf through red, infrared and all the way down to a true black dwarf. By that point, the Universe will hardly be forming any new stars at all, and space will be mostly black.

BLN and I spoke about how we simply have no good strategy to attempt a comprehension of “hundreds of trillions” of years.

Cute Aggression

NPR on why many of us can identify with little Agnes:

The study found that for the entire group of participants, cuter creatures were associated with greater activity in brain areas involved in emotion. But the more cute aggression a person felt, the more activity the scientists saw in the brain’s reward system.

That suggests people who think about squishing puppies appear to be driven by two powerful forces in the brain. “It’s not just reward and it’s not just emotion,” Stavropoulos says. “Both systems in the brain are involved in this experience of cute aggression.”

The combination can be overwhelming. And scientists suspect that’s why the brain starts producing aggressive thoughts. The idea is that the appearance of these negative emotions helps people get control of the positive ones running amok.

“It could possibly be that somehow these expressions help us to just sort of get it out and come down off that baby high a little faster,” says Oriana Aragón, an assistant professor at Clemson University who was part of the Yale team that gave cute aggression its name.

– Jon Hamilton, “When Too Cute Is Too Much, The Brain Can Get Aggressive

Freeman Dyson on Richard Feynman

When we arrived we were introduced to Henry Bethe, who is now five years old, but he was not at all impressed. The only thing he would say was “I want Dick. You told me Dick was coming,” and finally he had to be sent off to bed, since Dick (alias Feynman) did not materialise. About half an hour later, Feynman burst into the room, just had time to say “so sorry I’m late. Had a brilliant idea just as I was coming over,” and then dashed upstairs to console Henry. Conversation then ceased while the company listened to the joyful sounds above, sometimes taking the form of a duet and sometimes of a one-man percussion band.


In the evening I mentioned that there were just two problems for which the finiteness of the theory remained to be established; both problems are well-known and feared by physicists, since many long and difficult papers running to fifty pages and more have been written about them, trying unsuccessfully to make the older theories give sensible answers to them. When I mentioned this fact, Feynman said, “We’ll see about this,” and proceeded to sit down and in two hours, before our eyes, obtain finite and sensible answers to both problems. It was the most amazing piece of lightning calculation I have ever witnessed, and the results prove, apart from some unforeseen complication, the consistency of the whole theory.

– Freeman Dyson, “Maker of Patterns” (via Nautilus)