twenty things tagged “biology”


They look like priceless brooches and are tremendously important to our planet.

A photo of diatoms through a microscope

Emphases mine:

Living diatoms make up a significant portion of the Earth’s biomass: they generate about 20 to 50 percent of the oxygen produced on the planet each year, take in over 6.7 billion metric tons of silicon each year from the waters in which they live, and constitute nearly half of the organic material found in the oceans. The shells of dead diatoms can reach as much as a half-mile (800 m) deep on the ocean floor, and the entire Amazon basin is fertilized annually by 27 million tons of diatom shell dust transported by transatlantic winds from the African Sahara, much of it from the Bodélé Depression, which was once made up of a system of fresh-water lakes.



These are fossilized crinoids found in Western Australia by Tom Kapitany. Crinoids are animals and belong to the phylum Eichinodermata which includes starfish and sea urchins (and they all have “pentameral symmetry”). This is all well and good but these things, in their fossilized state, look like so much like the sentinels from The Matrix I wonder if there was any inspiration here.

Crinoid fossils by Tom Kapitany

Sentinel robots from The Matrix

Here are a few more fossils

Crinoid fossil

Another Crinoid fossil
Source: Fossil Huntress

And their basic anatomy

Crinoid Anatomy

Steller’s Sea Eagle

The Steller’s sea eagle is one of the world’s rarest eagles. There are only around 4,000 left. It’s native to Russia and Japan. One was spotted in Maine and got bird watchers very excited.

“It would be like an elephant walking up out of Africa into Scandinavia,” Mr. Lund said. “Like getting a call that the Rolling Stones are playing in a field behind a warehouse in the next town over.”

Marion Renault, “This Eagle Is Very, Very Lost”, The New York Times

It also just happens to be an absolute unit of a bird at 20lbs with an 8ft wingspan 🔥🦅😍

Steller's Sea Eagle - 1
by Andres Vasquez Noboa

Steller's Sea Eagle - 2
Photographer unknown (source)

Steller's Sea Eagle - 3
by John Charles Putrino

Steller's Sea Eagle - 4
by Andres Vasquez Noboa

Dr. Lees said vagrancy, as a biological mechanism, could help migratory birds expand their ranges, a potential advantage as global warming redraws the contours of suitable habitat. Dr. Farnsworth said, conversely, extreme weather — which is anticipated to grow in frequency and intensity as climate change progresses — can also play a role in displacing birds by hundreds or even thousands of miles.

What’s next for the lone, pioneering Steller’s sea eagle? It could migrate along with native bald eagles down the coastline. It could find its way back to northeastern Asia. It could stick around Nova Scotia, as it is well adapted to the cold and seems able to survive there. It could die, out of range of its original flock.

“It’s like an avian soap opera,” Dr. Lees said. “We’re all rooting for it. Will it make it home? Or is it doomed to never see another species of its own in its lifetime?”


Peace Lily are Hard to Maintain

I have a dying peace lily. I’m a bit attached to it and don’t know that I’ll be able to save it. Searching the internet for any hope led me to this post (cached) which made me feel slightly better about my inexperience.

The first mistake is relying upon the plant’s visual cue that needs water: the leaves droop. But, as the post notes, this can happen when they’re both over and under-watered!

[…] This would be a good indicator of when to water, except that by the time things reach the point of laying flat, damage has been done: the roots die back slightly each time this happens, and if it happens often enough, it will eventually fail to come back at all.

[…] it’s difficult to get the watering just right. […] If it’s too wet, there’s a tendency for plants to rot where they sit, except that they do it in such a way that you don’t necessarily realize what’s going on. One day you go to pull off a dead leaf, and a whole rootless plant comes out. This will generally not be salvageable. To make things trickier, the plant (like a lot of other plants) responds to being too wet by – you guessed it – drooping, which would make an inexperienced grower think that it needs more water.

I think I ruined mine by transferring it to a larger pot, thinking I was ‘suffocating’ it in a smaller one.

However, it’s been my experience that, nine times out of ten, a peace lily with black leaf edges is suffering from root suffocation, either because its soil has broken down and compacted, or because part of the soil never gets to dry out. Especially in a very large pot, and especially especially in a plant that’s been overpotted (put in a pot that’s too large for the plant), and especially especially especially in a plant that’s in a very large pot, too big for the plant, with no drainage hole, the top of the soil can dry out while everything after the top three inches is soaking wet.

Contrary to marketing material, they are not easy beginner plants:

In the time I’ve been at Garden Web (since Dec. 2006), I’ve seen more people post about issues with their peace lilies than any other plant, no contest: too many marketers think that the only important thing about a plant is how much light it needs. It’s true that Spathiphyllum doesn’t require a lot of light; that doesn’t make it the best plant for you, any more than knowing Jennifer Anniston’s name makes her your best friend.

So what does one do?

Common sense is important. If your plant is droopy and the soil feels wet, the plant is obviously not drooping because it’s too dry: don’t give it water. If the plant looks fine and the soil feels dry, the plant doesn’t need water just because the soil is dry: wait for the leaves to get a little limp first. Spathiphyllums are nothing if not good communicators.

And don’t worry about humidity. And use progressively larger pots. I think mine is too far gone at this point 😔

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 😍🍄 ↩︎

A Most Horrifying Description of Rabies by ZeriMasterpeace More Pasta

Rabies. It’s exceptionally common, but people just don’t run into the animals that carry it often. Skunks especially, and bats.

Let me paint you a picture.

You go camping, and at midday you decide to take a nap in a nice little hammock. While sleeping, a tiny brown bat, in the “rage” stages of infection is fidgeting in broad daylight, uncomfortable, and thirsty (due to the hydrophobia) and you snort, startling him. He goes into attack mode.

Except you’re asleep, and he’s a little brown bat, so weighs around 6 grams. You don’t even feel him land on your bare knee, and he starts to bite. His teeth are tiny. Hardly enough to even break the skin, but he does manage to give you the equivalent of a tiny scrape that goes completely unnoticed.

Rabies does not travel in your blood. In fact, a blood test won’t even tell you if you’ve got it. (Antibody tests may be done, but are useless if you’ve ever been vaccinated.)

You wake up, none the wiser. If you notice anything at the bite site at all, you assume you just lightly scraped it on something.

The bomb has been lit, and your nervous system is the wick. The rabies will multiply along your nervous system, doing virtually no damage, and completely undetectable. You literally have NO symptoms.

It may be four days, it may be a year, but the camping trip is most likely long forgotten. Then one day your back starts to ache… Or maybe you get a slight headache?

At this point, you’re already dead. There is no cure.

(The sole caveat to this is the Milwaukee Protocol, which leaves most patients dead anyway, and the survivors mentally disabled, and is seldom done - see below).

There’s no treatment. It has a 100% kill rate.

Absorb that. Not a single other virus on the planet has a 100% kill rate. Only rabies. And once you’re symptomatic, it’s over. You’re dead.

So what does that look like?

Your headache turns into a fever, and a general feeling of being unwell. You’re fidgety. Uncomfortable. And scared. As the virus that has taken its time getting into your brain finds a vast network of nerve endings, it begins to rapidly reproduce, starting at the base of your brain… Where your “pons” is located. This is the part of the brain that controls communication between the rest of the brain and body, as well as sleep cycles.

Next you become anxious. You still think you have only a mild fever, but suddenly you find yourself becoming scared, even horrified, and it doesn’t occur to you that you don’t know why. This is because the rabies is chewing up your amygdala.

As your cerebellum becomes hot with the virus, you begin to lose muscle coordination, and balance. You think maybe it’s a good idea to go to the doctor now, but assuming a doctor is smart enough to even run the tests necessary in the few days you have left on the planet, odds are they’ll only be able to tell your loved ones what you died of later.

You’re twitchy, shaking, and scared. You have the normal fear of not knowing what’s going on, but with the virus really fucking the amygdala this is amplified a hundred fold. It’s around this time the hydrophobia starts.

You’re horribly thirsty, you just want water. But you can’t drink. Every time you do, your throat clamps shut and you vomit. This has become a legitimate, active fear of water. You’re thirsty, but looking at a glass of water begins to make you gag, and shy back in fear. The contradiction is hard for your hot brain to see at this point. By now, the doctors will have to put you on IVs to keep you hydrated, but even that’s futile. You were dead the second you had a headache.

You begin hearing things, or not hearing at all as your thalamus goes. You taste sounds, you see smells, everything starts feeling like the most horrifying acid trip anyone has ever been on. With your hippocampus long under attack, you’re having trouble remembering things, especially family.

You’re alone, hallucinating, thirsty, confused, and absolutely, undeniably terrified. Everything scares the literal shit out of you at this point. These strange people in lab coats. These strange people standing around your bed crying, who keep trying to get you “drink something” and crying. And it’s only been about a week since that little headache that you’ve completely forgotten. Time means nothing to you anymore. Funny enough, you now know how the bat felt when he bit you.

Eventually, you slip into the “dumb rabies” phase. Your brain has started the process of shutting down. Too much of it has been turned to liquid virus. Your face droops. You drool. You’re all but unaware of what’s around you. A sudden noise or light might startle you, but for the most part, it’s all you can do to just stare at the ground. You haven’t really slept for about 72 hours.

Then you die. Always, you die.

And there’s not one… fucking… thing… anyone can do for you.

Then there’s the question of what to do with your corpse. I mean, sure, burying it is the right thing to do. But the fucking virus can survive in a corpse for years. You could kill every rabid animal on the planet today, and if two years from now, some moist, preserved, rotten hunk of used-to-be brain gets eaten by an animal, it starts all over.

So yeah, rabies scares the shit out of me. And it’s fucking EVERYWHERE. (Source: Spent a lot of time working with rabies. Would still get my vaccinations if I could afford them.)

Each time this gets reposted, there is a TON of misinformation that follows by people who simply don’t know, or have heard “information” from others who were ill informed:

Only x number of people have died in the U.S. in the past x years. Rabies is really rare.

Yes, deaths from rabies are rare in the United States, in the neighborhood of 2-3 per year. This does not mean rabies is rare. The reason that mortality is so rare in the U.S. is due to a very aggressive treatment protocol of all bite cases in the United States: If you are bitten, and you cannot identify the animal that bit you, or the animal were to die shortly after biting you, you will get post exposure treatment. That is the protocol.

Post exposure is very effective (almost 100%) if done before you become symptomatic. It involves a series of immunoglobulin shots - many of which are at the site of the bite - as well as the vaccine given over the span of a month. (Fun fact - if you’re vaccinated for rabies, you may be able to be an immunoglobulin donor!)

It’s not nearly as bad as was rumored when I was a kid. Something about getting shots in the stomach. Nothing like that.

In countries without good treatment protocols rabies is rampant. India alone sees 20,000 deaths from rabies PER YEAR.

The “why did nobody die of rabies in the past if it’s so dangerous?” argument.

There were entire epidemics of rabies in the past, so much so that suicide or murder of those suspected to have rabies were common.

In North America, the first case of human death by rabies wasn’t reported until 1768. This is because Rabies does not appear to be native to North America, and it spread very slowly. So slowly, in fact, that until the mid 1990’s, it was assumed that Canada and Northern New York didn’t have rabies at all. This changed when I was personally one of the first to send in a positive rabies specimen - a raccoon - which helped spawn a cooperative U.S. / Canada rabies bait drop some time between 1995 and 1997 (my memory’s shot).

Unfortunately, it was too late. Rabies had already crossed into Canada.

There are still however some countries (notably, Australia, where everything ELSE is trying to kill you) that still does not have Rabies.

Lots of people have survived rabies using the Milwaukee Protocol.

False. ONE woman did, and she is still recovering to this day (some 16+ years later). There’s also the possibility that she only survived due to either a genetic immunity, or possibly even was inadvertently “vaccinated” some other way. All other treatments ultimately failed, even the others that were reported as successes eventually succumbed to the virus. Almost all of the attributed “survivors” actually received post-exposure treatment before becoming symptomatic and many of THEM died anyway.

Bats don’t have rabies all that often. This is just a scare tactic.

False. To date, 6% of bats that have been “captured” or come into contact with humans were rabid.. This number is a lot higher when you consider that it equates to one in seventeen bats. If the bat is allowing you to catch/touch it, the odds that there’s a problem are simply too high to ignore.

You have to get the treatment within 72 hours, or it won’t work anyway.

False. The rabies virus travels via nervous system, and can take several years to reach the brain depending on the path it takes. If you’ve been exposed, it’s NEVER too late to get the treatment, and just because you didn’t die in a week does not mean you’re safe. A case of a guy incubating the virus for 8 years.

At least I live in Australia!


Please, please, PLEASE stop posting bad information every time this comes up. Rabies is not something to be shrugged off. And sadly, this kind of misinformation killed a 6 year old just this Sunday. Stop it.

On Consciousness

It is remarkable that mind enters into our awareness of nature on two separate levels. At the highest level, the level of human consciousness, our minds are somehow directly aware of the complicated flow of electrical and chemical patterns in our brains. At the lowest level, the level of single atoms and electrons, the mind of an observer is again involved in the description of events. Between lies the level of molecular biology, where mechanical models are adequate and mind appears to be irrelevant. But I, as a physicist, cannot help suspecting that there is a logical connection between the two ways in which mind appears in my universe. I cannot help thinking that our awareness of our own brains has something to do with the process which we call ‘observation’ in atomic physics. That is to say, I think our consciousness is not just a passive epiphenomenon carried along by the chemical events in our brains, but is an active agent forcing the molecular complexes to make choices between one quantum state and another. In other words, mind is already inherent in every electron, and the processes of human consciousness differ only in degree but not in kind from the processes of choice between quantum states which we call ‘chance’ when they are made by electrons.

Freeman Dyson


All Yesterdays is an exploration of things we know we will never know about “dinosaurs and prehistoric animals” . Jonathan Wojcik at has an excellent review of the book. Of particular interest: We know little-to-nothing about the creatures’ anatomies and morphologies because of missing soft tissue data. Here are paleoartists’ recreations of a cow and a swan:

Looked up a sperm whale’s skeleton and can’t imagine how lacking a recreation would be:


This article discusses the history and current state of paleoart. And this post is the ultimate TL;DR on the subject

As C.M. Kosemen explains throughout All Yesterdays, we really can’t ever know how much fat and other soft tissues contributed to the overall shape of dinosaurs since that’s the first thing to rot and shrivel tight against their bones and like even a sperm whale has a little skinny skeleton.

so like

how would we know?