Rich and Strange Aeons

https://www.cnn.com/2023/05/29/health/human-metapneumovirus-explainer-wellness/index.html

Discovered in 2001. Causes about as many cases and misery as influenza and RSV. Little known.

Paper 1: https://twitter.com/ENirenberg/status/1496294352594915328 (summary, but also has direct link to PDF.)

bad news: antibodies decline a lot after 3 months.

good? news: that's not a covid vaccine thing, it's an immune system thing. Infection antibodies come from short-lived plasmablasts, that pump out a flood of antibodies, then die on schedule. Then you have long-lived plasma cells that trickle out antibodies, and memory B cells that will spawn more short-lived cells 4-6 days after a new infection, which is a lot better than the 2-3 weeks to get antibodies to a novel antigen.

good news: memory B cells increase over time -- 10x as many 9 months later, compared to right after the second covid dose.

bad news not in this paper: omicron can propagate in 2-3 days. By the time your B cells respond, you've infected people and *they've* infected more people. I've mentioned this before.

other news: unvacced, 28 +/- 15 days from first positive swab to first negative PCR test; 20 +- 9 days for vacc.


Paper 2: https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1009509
I've linked to this before, but it deserves a second pass. The key table is replicated here https://twitter.com/jmcrookston/status/1498877041105674240

The author says that all the viral diseases we develop lasting immunity against infection to, need to pass through our blood/lymph to transmit. I don't remember him spelling out exactly why, and I see two possibilities: one is that passing through the blood in itself exposes viruses to more of our immune system; the other is that passing through blood intrinsically takes longer than being able to transmit from respiratory cells alone. If I knew of any fast blood diseases or slow respiratory-only diseases, that would help differentiate the mechanisms. (Measles has a 12 day generation time; influenza may have 2 days, though other sources say 3.6. Wiki says typically 1-2 days.)

[Edit 2022-04-12: couple of money quotes:

"even natural respiratory infections with measles or variola (smallpox) viruses, famous for inducing life-long immunity to disease, do not prevent respiratory reinfection,"

"What polio-, variola, and measles virus share is dissemination from the initial infection site via lymph and (secondarily) blood as an obligate step in pathogenesis or transmission." ]

At any rate, since covid-19 has a generation time of just a few days, down to 2 for omicron, and does not need to pass through blood to transmit, we get the same result: lasting immunity to covid-19 infections is impossible. And people have done challenges with less alarming coronaviruses: "Human challenge studies established that seasonal CoV [coronavirus] reinfection with the identical strain can occur within a year after initial exposure, though typically with reduced shedding and milder symptoms."

Put another way, if the only thing between a virus and transmission is mucosal antibody levels, the virus will eventually transmit. As opposed to diseases like measles or polio where B and T cells must be crossed before transmission.


Seems to me that covid-19 is a "worst of both worlds" virus. It doesn't need the rest of our bodies to propagate, so it can transmit quickly and repeatedly, uncurbed by memory B cell responses. But thanks to the cell receptor it uses, it *can* randomly wander off to infect any organ of our bodies (vs. some cold virus that infected our noses but *stayed there*.) Influenza may also be such a virus (family)... and hey, influenza can be pretty deadly too.

On top of that, covid-19 has the killer app of suppressing initial innate immune response (something about blocking or inhibiting interferon production), which is why it has such a long pre-symptomatic infectious period, and probably part of why even partial NPIs (non-pharmaceutical intervention, masking and staying home and such) that failed to contain covid were able to crush flu and cold transmission.


And that's the virus that world leaders have decided we can just let rip, trusting entirely to our vaccines, despite not having a clear view of how much vaccines protect against long covid/blood clots/organ damage.

Dunno about you, but I'm still wearing respirators and not dining out.

What happens when you get a booster shot? Same thing as usual: B cells responsive to those antigens multiply, and diversify, randomly mutating in case they get a better fit.

So even if all your shots are against original covid, and you then get hit by Delta or even Omicron, some of those mutated B cells and antibodies may be responsive to the variant, and then your immune system will shift over and learn.

But what happens if you never do get infected? Antibody levels drop, and B cells get selected for specificity against the antigen your body actually knows about.

Which isn't Delta, or Omicron. If you've never seen Omicron spike protein, you literally have no reason to keep around B cells specific to it.

Which suggests the boosters really do have a temporary effect against variants, working just by restoring a diverse population of covid-ish antibodies, some of which might include the variants. But without exposure, you'll never keep B cells for those variants.

Which would mean Fauci is wrong about not needing omicron boosters. Sure, get a booster now, to benefit from that higher and more diverse level of antibodies, but in the long term you need an omicron vaccine to hope to prevent infection.

Or, if you live dangerously and don't think they'll make new vaccine types, get a booster and then go expose yourself while you're at peak resistance, so you body can learn from direct exposure.

I would love to be wrong, but this is where my lay knowledge of immunology takes me.

https://www.atlasobscura.com/articles/grapefruit-history-and-drug-interactions

Article via conuly.

* citrus genetics were weird and messy, if you didn't know that already.

* grapefruit is a feral hybrid discovered in Barbados, halfway around the world from Citrus Central.

* As you should learn if you don't know already, grapefruit has lots of drug interactions. Seems that's indirect: grapefruit disables stomach enzymes that normally break down most of an oral medication, so if you take the drug within 12 hours of grapefruit, you get much more drug than the prescription calls for. It can also disable some drug transporter proteins that bring things (like drugs) into cells, so in those cases you get less drug than expected.

* Tylenol is one of the drugs, though I'm not sure which class. I assume the second, from the lack of more strident recommendations not to mix them, because it's already too easy to OD on Tylenol.

* All the bitter pomelo derivatives have that effect, but you're "unlikely" to consume enough lime or sour orange for it to hurt, and I assume sweet orange doesn't have enough pomelo heritage, or didn't inherit the right genes.

Currently reading The Secret Life of Trees by Colin Tudge, not to be confused with the more recent The Hidden Life of Trees by a German forester.

What is a tree? The obvious popular, and functional, definition is a tall plant on a stick, outgrowing competition in a race for sunlight. The least interesting definition requires the stick to be made of wood[1], rather than herbal stems kept up by water pressure; I'll call that "woody tree". A more evolutionary definition of "trees proper" invokes secondary growth, and specifically the cambium, a sheath of cells around the trunk that generate wood on the inside and bark on the outside (xylem and phloem), contributing to growth outward as well as upward.

The tree lifestyle is one of the targets of convergent evolution, hit by Lepidodendron, tree ferns, some Carboniferous horsetails, various monocots.

The tree proper encompasses conifers (and their gymnosperm relatives, cycads and ginkgo) and most flowering (angiosperm) trees, which suggests their common ancestor was a tree, and also that the first flowering plant was a tree, despite the vast mass of angiosperms that have since shed all wood and tree-ness.

Flowering plants can be divided into primitive dicots, true dicots (eudicots), and monocots. The big distinction is that monocot leaves grow from the base, rather than the tip or edge; grasses are monocots, and having their growth region below the ground means they can survive grazing, which is part of why they've become so successful in the last 40 million years. There are five groups of monocot 'trees', none of which have the cambium of trees proper, so the first monocot must have been herby, with subsequent re-inventions of the tree lifestyle. Some of those have a form of secondary growth but not the cambium. Monocot trees include Joshua trees and palms.

[1] Lignified cellulose. Cellulose is floppy, having lots of lignin molecules in it makes for a rigid matrix that can stand up on its own.

When you look at the multicellular part of the tree of life, almost everything reproduces sexually. Not all the time -- some plants can self-fertilize, many plants can spread vegetatively, some animals are optionally parthenogenetic. But almost everything has sex as an option. Not all: there are some animal species that only reproduce by parthenogenesis. But they're all twigs on the tree of life, not lush branches, suggesting that this approach to reproduction doesn't last long. Why not? That touches on the question of why sex evolved in the first place, but a rather plausible answer is that it helps protect against parasites and germs, by mixing things up. Asexual reproduction looks like a good short-term genetic bet for the parent -- 100% of genes pass on! -- but yields a population of clones that can be scythed through by the parasite that figures out the key.

Bacteria and archaea evolve fast enough to keep up with each other and with viruses, perhaps... and, also, they have their own forms of gene transfer: conjugation (like sex), or transformation (uptake of plasmids, say.) (A side note: modern GMOs are thus less unnatural than you might think; genes jump around, even between multicellular animals, and GMOs are made via 'natural' techniques.)

There is one big exception to the "all twigs" statement: the bdelloid rotifers, a clade of 450+ species that have apparently been asexual for 25 million years. How do they pull it off? I'd thought maybe their cuticles were tough enough that they thoroughly kept out viruses and such, unlike anything else. But The Tangled Tree by David Quammen gave a better explanation. As freshwater plankton, they've evolved to survive drying out and being rehydrated. And it's not that they're really good at preserving their DNA through such stages; rather, they're decent at repairing the damage after rehydration. 'Decent' meaning that in the process they may incorporate foreign bits of DNA.

...they found at least twenty-two genes from non-bdelloid creatures, genes that must have arrived by horizontal transfer. Some of those were bacterial genes, some were fungal. One gene had come from a plant. At least a few of those genes were still functional, producing enzymes or other products useful to the animal. Later work on the same rotifer suggested that 8 percent of its genes had been acquired by horizontal transfer from bacteria or other dissimilar creatures. A team of researchers based mostly in England looked at four other species of bdelloids and also found “many hundreds” of foreign genes. Some of the imports had been ensconced in bdelloid genomes for a long time, since before the group diversified, while some were unique to each individual species, and therefore more recently acquired. This implied that horizontal gene transfer is an ancient phenomenon among bdelloid rotifers, and that it’s still occurring.

...biologists suspect that such drying-and-rehydrating stresses cause bdelloid DNA to fracture and leave cell membranes leaky. Given that they’re surrounded in their environments by living bacteria and fungi, plus naked DNA remnants from dead microbes, the porous membranes and fracturing could make it easy for alien DNA to enter even the nuclei of bdelloid cells and to get incorporated into bdelloid genomes as they repair themselves. Let me say that again: broken DNA, as a cell fixes it, using ambient materials, may include bits that weren’t part of the original. If that mended DNA happens to be in cells of the germ line, the changes will be heritable. Baby rotifers will get them and, when the babies mature, pass the changes along to their own daughters. Thus a bacterial or fungal gene can become part of the genome of a lineage of animals.

Some animals such as frogs and caterpillars really do freeze solid; he describes being able to tap a frozen caterpillar on the table, before thawing and reviving it. Such animals have adaptations to encourage freezing in body cavities, while keeping ice crystals out of cells.

One moth in the high Arctic spends most of the year frozen, eating growing a bit in the short thaw period, and repeating this for years before finally finally moving from the larval stage.

A lot of it is really about dehydration. Some African moth larva can lose 92% of its water to survive the dry season; in this state, it can survive being dipped in liquid helium! He describes adding water as "instant insect."

A couple of Heinrich's chapters end on an annoying note: he seems depressed by practical studies, extolling the spiritual uplift of pure research without any practical application. I'm all for the quest for knowledge, but you don't have to put down practicality like some pre-cryptography number theorist... He also has vague moral concerns about human cryonics.

I gave to this book to G in 2003; I just re-read that exact copy. It's a neat book about... I'm not sure how to summarize it. The first chapter is about standard cube-square scaling laws as applied to animal size, and why elephants are shaped differently from antelopes. But most of the rest of the book is about warm vs. cold bloodedness, to which scaling is one but not the only issue. Were dinosaurs warm blooded, or something in between; why there aren't more 'in between' animals; why warm bloods dominate large fauna on land and in the oceans; why cold bloods dominate rivers and are (or were before humans) prominent in Australia.

Very small animals are all cold blood, because warm can't eat enough and keep enough heat at that scale. Small animals are split; hiding is a good strategy, being warm has high costs, the world is more complex and has more niches at a small scale. Hiding doesn't work well for big animals, who are also driven to a simpler 2D world, so being ready for action has very high value and warm bloods dominate... unless food is so uncertain that you get long intervals of not eating, as in rivers or Australia.

Also river ecology is complex and poorly understood. Naked mole rats are practically cold blooded mammals, protected by their tunnels and living in very marginal areas, where the food tends to be a limited number of large roots. Ostritches used to span a wide area, like Greece, Moldavia, and China.

There's also discussion of how warm bloodedness evolved in the first place, given the high costs. Answer, we don't know, but there are a couple theories. One is that some ancient large animals in stable climates were mass homeotherms, with fairly stable temperatures even without working at it, so they optimized their enzymes to adapt to that (enzymes have narrow ranges of optimal performance; lots of organisms have more genes than humans probably because they needs lot of alternative cellular biochemistry), then when some branch shrank again, it was easier to invent warm bloodedness rather than re-invent a whole slew of enzymes.

The other idea is that boosted aerobic performance is beneficial by itself, and eventually some animals were boosted enough that they were significantly warm blooded as a side effect. This feels less elegant to me, but Lavers said it was favored at the time of writing.

The last chapter is on global mixing of species, thanks to human transport, and making a worrying analogy with the Permian mass extinction, which followed mixing (supercontinent) and global warming (massive volcanism, probably.)

Perspective of an ex-neo-Confederate.

Weekly church attendance by state.

Barcelona's plans for superblocks.  And Barcelona transit: crazy trains but hyperrational bus grid, with lines labeled as H2 or V5 ,for Horizontal or Vertical.

Paris turns the bus stop into major transit infrastructure.

Save a biker, use the Dutch reach in opening car doors.

Not sure if this is correct or just plausible, but words on why Europe, or cold climates in general, doesn't have many venomous animals.

The mythology of "Irish slavery".

Oil state prudence and sovereign wealth funds: Norway vs. Alberta, also a look at how Norway's fund invests. I liked the Albertan complaining that Norway is a relatively small country: yes, but it has more people than Alberta... http://www.theglobeandmail.com/report-on-business/international-business/european-business/norways-sovereign-wealth-fund/article25973060/?click=sf_globefb

Debunking the fear about EMPs http://foreignpolicy.com/2013/05/24/the-empire-strikes-back/

Portugal, optimal currency area, and labor mobility: fiscal union trumps labor mobility in importance. http://krugman.blogs.nytimes.com/2015/08/14/the-downside-of-labor-mobility/
Who cares about reserve currency status? http://krugman.blogs.nytimes.com/2015/08/12/international-money-mania/

First we export pollution to China via outsourcing, now they export it back to us via air movements: http://www.sgvtribune.com/environment-and-nature/20150810/air-pollution-from-china-undermining-gains-in-california-western-states

Trees and bus stop waiting time perception http://www.citylab.com/commute/2015/08/trees-can-make-waiting-for-the-bus-feel-shorter/401135/?utm_source=atlanticFB

How the US 'justice' system abuses bail: http://www.nytimes.com/2015/08/16/magazine/the-bail-trap.html?smid=tw-nytmag&_r=0

Vampire squid: not a squid. (Or vampire, durr.) http://www.washingtonpost.com/news/speaking-of-science/wp/2015/06/23/vampire-squids-arent-vampires-or-squids/

Real paleo diet might have evolved around carbs. Oops! http://www.nytimes.com/2015/08/13/science/for-evolving-brains-a-paleo-diet-full-of-carbs.html?smid=fb-nytimes&smtyp=cur

Privacy Badger, an EFF alternative to the supposedly more commercial Ghostery browser plug-in. https://www.eff.org/press/releases/privacy-badger-10-blocks-sneakiest-kinds-online-tracking