Scamperings

As I'm recovering from covid, I've been trying to figure out when I can *stop* isolating. Specifically, how do I know when I'm no longer contagious? This is surprisingly difficult! I'm going to share what I've learned so far, and I'd love to hear about any papers you can find that add new information or contradict what I've found.

The challenges

The most likely protocol would be built around symptoms, tests, and timelines. But these are hard to rely on.

The first problem is that symptoms don't necessarily correlate with contagiousness. People are most contagious *before* their symptoms even appear, and symptoms can continue well after the virus is effectively cleared. (And of course asymptomatic cases can be *very* effective at spreading a virus.) Some symptoms are strongly indicative of what stage of infection the person is in. Fever is a strong indication of active infection, for instance, and anyone with a fever definitely should continue isolating. But others are less specific (such as coughing or fatigue), and those less specific ones kind of drag on, leaving a lot of uncertainty.

Another problem is that PCR and rapid antigen tests (RATs) detect viral fragments, not whole, live, infectious viruses. In the tail end of an infection, your body still has a lot of cells churning out broken chunks of virus that are basically harmless but that will give positives on these tests, so just going by positives may keep you in isolation for too long. PCR in particular is ridiculously sensitive. One interesting thing is that unlike RATs, PCR gives you quantitative information -- the number of cycles required before the test comes up positive (the "cycle time", or "Ct") can tell you about the relative density of viral RNA in the sample. But this information isn't necessarily available to individuals getting tested at a pharmacy, and it's not obvious what thresholds might be meaningful. The most accurate information you could plausibly get would be via culturing respiratory particles from an infected person and seeing if SARS-CoV-2 spreads in the culture. But this option is completely inaccessible except for specialized research labs, so at most this can be used to *validate* other approaches.

And finally, there's just a lot of individual variation in how long people remain contagious. Some people start testing negative after just 5 days, while others are still testing positive on RATs for 15+ days. People with compromised immune systems in particular can in some cases stay contagious for months, and that likely includes people taking immunosuppressive drugs. I also have some questions about the effects of paxlovid; when I took it, my covid symptoms almost completely went away, and then returned a couple days after the last dose. I'm sure it dramatically reduced my illness overall, but I have to wonder if it so thoroughly suppressed viral replication that it actually "reset the clock" and I should really count days from post-paxlovid symptom return, rather than from the original onset. (I wonder what would happen in a trial of a reduced dose of paxlovid for a longer period!)

New info

The paper I've found so far that appears most promising is Deisolation in the Healthcare Setting Following Recent COVID-19 Infection, a review article from 2024 in the journal Viruses. It has the goal of helping healthcare facilities establish guidelines for when to take patients out of isolation.

A word of caution on this paper: I'm not an academic, and I'm really not qualified to evaluate papers or journals, but I think it's worth noting that the organization behind this journal, MPDI, seems to not do a great job of filtering for quality. So it may be worth mostly using this review article as a source of citations to other papers, maybe in journals by less controversial publishers. I do like that this paper is from 2024, but... a lot of its sources are from 2020 or 2021, studying earlier strains of the virus. Something to keep in mind.

One of the most important bits of information here is that when viral cultures have been taken, they've generally indicated that 10 days is *roughly* the usual limit for contagiousness:

Viral culture observing for cytopathic effects and/or substantial increases in the viral load by RT-PCR remains the gold standard for detecting viable virus in respiratory samples. SARS-CoV-2 will not be isolated in the majority of specimens collected from patients with mild to moderate disease by days 8–11 post-symptom onset [20,22,24,32,33,34,35].

Their main recommendation uses a combination of symptoms, tests, and timelines:

Recommendation: In light of the above, for asymptomatic, mild, or moderate disease in non-immunocompromised patients, regardless of vaccination status, deisolation should be considered if the patient is asymptomatic by day five and has either a negative RAT or RT-PCR test on day six or seven. If SARS-CoV-2 RNA is detected by RT-PCR, but with a Ct value ≥ 30, a RAT should be performed and the decision to deisolate determined by the RAT result. In the absence of further testing, ten days of isolation should be observed (Table 4).

In the context of healthcare workers themselves deisolating and returning to work:

Ongoing lethargy and a lingering dry cough may, however, be expected and should not preclude return to work.

***

The second useful paper I found was Duration of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infectivity: When Is It Safe to Discontinue Isolation?, from August 2020. (This was actually cited in the first paper, but with an incorrect title.) It has a table reviewing evidence around viral culture, PCR cycle time, days from symptom onset, and contact tracing. Note that some of the sources are for severe and critical illness, which you should generally expect to require longer isolation times than asymptomatic or mild cases. But overall it paints a picture of 10 days being a reasonable cutoff for mild/moderate cases (if tests haven't started showing negatives yet).

It's funny... at home I have 180 emails in my inbox, dating back to 2017 (but there are actually more unread, auto-archived from before that). The vast majority are from 2020 and 2022, curiously enough. And I have an ever-growing todo list. But at work I maintain Inbox Zero, or at least Inbox Rarely More Than Two, and there are extremely few tasks that linger.

I suppose the difference is in several parts:

- A number of the home emails are essentially tasks; at work, I would shove these into an issue tracker (and in some cases reply to the sender with a link to the issue I filed). I don't have a good "ticket tracker" at home.
- A lot of the home emails are "here's an interesting thing". Maybe I read the thing, maybe I don't. There's ambiguity: Is this something I should treat like I would on social media, where I at most leave a fave/upvote/heart/star and move on, or is it more like a conversation, where the person is expecting a response? When I have ambiguous work I have a very strong tendency to procrastinate, and so it sits there.
- In the case of my todo list... I don't have a manager at home! My boss is me. There's no undercurrent of "what if I don't perform well", so I don't have as much external motivation to get stuff done.

I'm curious in particular whether other people have found good solutions to the "I'm using my inbox as a todo list, badly" problem. Are there applications you use? Strategies?

Last week I was surprised and delighted to see a mockingbird beating the absolute tar out of what I think was a Manduca caterpillar. I don't bear any ill-will towards Manduca, mind you; it was just so unexpected. I didn't know anything ate those! The bird must have plucked it out of someone's home garden on that block.

I was also able to locate the nest -- very loud cheeping in a nearby tree. :-)

----

A neighbor was giving out some ham from Walden Local Meats, a Massachusetts meat-share program with good standards. (So this is from pasture-raised pigs.) It's "uncured ham", which apparently actually means "cured, but with less gross ingredients". I accepted, and now we have to figure out what to do with it. Ham has not been much a part of my life. It's too fatty for me to enjoy directly on a sandwich, but I fried up some thin slices and I guess that's basically the same thing as bacon. Amazingly tasty. The fat mostly comes out into the skillet, so we can fry up other stuff in that instead of using olive oil.

These days I also make "tempeh cutlets" pretty often -- slice two packages of it thin, then marinate in 2 Tbsp soy sauce, 1 Tbsp balsamic vinegar, and 20 drops liquid smoke until absorbed. Pan fry in copious olive and toasted sesame oil. Pretty incredible in sandwiches, especially with burger/hot dog condiments and sometimes cheese.

I made some last night and fried up the first couple in the pork fat. And you know, I think they actually weren't as good as the ones fried up on the other oils! That was a bit of a surprise.

----

Such drought here. A lot of trees have brown leaf margins. Many lawns are covered in brown grass, which I guess is good, considering; that means people aren't watering them. There are watering advisories in effect but this isn't a drought-prone area, so I don't know how well-publicized they are.

Two rain barrels continue to be sufficient, but I'm also starting to measure how much water is coming out of the dehumidifier. It looks like 1-2 gallons per day, which is honestly a huge amount. Again, a terribly energy-inefficient way to collect water, and it wouldn't be enough for hygiene, but that's enough to keep a couple of people in probably-OK-quality drinking water in an emergency where you have electricity but not water. I don't think it's actually enough for my garden by itself, but it's supplementing rainfall enough that I haven't had to use tap water.

----

The hopniss poked a tendril out of the pot the other day and just sort of sat there for a few days, but when I wasn't looking it shot a good 10-15 cm up. Maybe because I gave the pot a good soak. I'm looking forward to sitting with the plant and learning its shape and how it moves. Right now I wouldn't be able to tell hopniss from wisteria foliage, so I can't be sure whether I saw one in the wild or not a couple weeks ago. A little embarrassing.

I've been thinking about how one would grow starchy root plants in a no-dig manner. Carrots and beets can be pretty much pulled straight up, maybe requiring the soil to be loosened a bit first. Potatoes can be done totally no-dig by piling up mulch around them as they grow, so the base soil layer remains undisturbed; the tubers form in the soft mulch, not the firm soil. But sunchokes and hopniss probably don't work that way? My best thought is that you might be able to pull up the plants in the fall and bring some of the tubers up for harvest, and leave the rest int he ground for next year. It's still going to be disruptive, but not as disruptive to the soil structure as traditional digging.

We're in Virginia now, and nearing the end of our trip.

It's great being at my parents' place. The garden is wonderful, full of big healthy plants and innumerable insects and innumerable *kinds* of insects on every surface. And there are woods.

Woods

The woods are not the kind of woods I grew up in, despite being just a few miles away; those were older, more mature woods typical of the Blue Ridge foothills: Beech, maple, oak; various medicinal plants that I know; relatively open understory and thick canopy. A familiar smell. Hundreds of acres (belonging to the neighbors) to tromp through, with streams and fields. But the woods they have now are in a subdivision, and the red clay comes right to the surface; it must have been bulldozed some decades back, and is given over to invasives. The mature trees are tulip tree, pine, and Ailanthus (invasive), and choked with Oriental bittersweet, English ivy, stiltgrass, multiflora rose, porcelain berry (all invasive). The understory has a good amount of pawpaw, spicebush, and Carolina buckthorn among others, which we're hoping to encourage -- and keep from getting covered up.

My dad has been killing the Ailanthus with herbicide (downward hatchet cuts into the trunk, with glyphosate drizzled in) or fungus (blue oyster mushrooms spores in drilled holes) and there are now clearings opening up. Dangerous clearings, with trees unpredictably crashing down. Not a place to be on a windy day. Stiltgrass has spread through the clearings. I guess it could be worse? But there really does need to be something to replace the Ailanthus. When slippery elm and oak pop up in the garden, he transplants them out there, but the deer eat them, so they have to be caged. Some of the deer here will eat damn near anything, even holly sometimes. They're overpopulated. The regulations in this county apparently require killing antlerless deer (does, but also young males) before you're allowed to kill antlered deer, and that probably helps bring the population down, but I wonder if they should push a little further towards killing does. Maybe expand bow-hunting season, too? (Or reintroduce wolves. I can dream.) Anyway, the deer really aren't helping the effort to restore native plant populations, given their (understandable) preference for eating the native plants. But the reintroductions are working in some areas: Goldenseal, bloodroot, and wood anemone are pushing out into the woods, and I've been pulling bittersweet from the edges of that patch. Elusiveat has convinced me that this is the correct strategy -- it's not really worth pulling the invasives unless you're replacing them with something, and working the edges of expanding patches allows the native plants to do some work for you. Let the invasives compete with themselves in the worst areas; don't worry about that until the "front" reaches them.

I've thrown some inedible fallen fruits from the blueberries into the clearings. And I dug up some hopniss tubers that had escaped their planter box and buried them at the north edge of clearings after removing invasives. Maybe some will take, next year. Gotta keep throwing spaghetti at that wall.

Garden

The garden... oh the garden is gorgeous. 3000 sq ft, bark mulch paths and beds deep and soft with composted sawdust, a mix of perennials and annuals. Some things are in the garden just to keep them away from the deer and squirrels: Jerusalem artichokes, a persimmon tree, blueberry bushes, thornless raspberry and blackberry. (Multiple pints per day of berries.) The blueberries are under pond netting to keep the birds out, but the birds are free to have at the raspberries. Cardinals even made a nest in there. Squash, beans, tomatoes, peppers, sweet potatoes, various medicinals, some hopniss (groundnut), strawberries, kale, okra... My dad keeps the garden bare of weeds these days, which I feel mixed about; with the seed company and ~8000 sq ft of garden, the paths were often grass and weeds, and the planting areas allowed to cover over with chickweed and other weeds when fallow. It was a different kind of beautiful then, more wild. My own preference is to let certain weeds run unchecked to provide free salad greens, but I might feel differently if I had 3000 sq ft instead of a tiny front yard.

I spend a lot of my time here happily pulling invasives, harvesting crops, weeding, and picking bugs. The pest burden is considerable, and my dad has had to stop growing Cucurbita pepo entirely (yellow summer squash, jack o'lantern, acorn squash...) due to pickleworm and other pests. The local predators, parasites, and pathogens seem to have largely put brown marmorated stink bugs (BMSBs) in check, which is a huge relief, and Japanese beetles are no longer the total defoliators they used to be. Squash bugs are a perennial issue, and I collected probably 50+ egg masses over a couple days. (Persistently hunting and finding small things that do not want to be found is one of my sharpest skills.) I also learned that squash bug adults like to hang out on the cattle panel, and especially in the channel between the panel wires and the posts; we may put out some PVC tubes for them to "hide" in to more easily collect them. But there are always new pests. The squash lady beetle has moved in, and can do significant damage. I only found a few of those, and no larvae, which is odd. I'll keep looking.

Something new and exciting is that I spotted a zebra swallowtail, a butterfly I only saw once or twice as a kid. Their caterpillars basically just eat pawpaw leaves, and the adults are lovely large zebra-colored butterflies with some red highlights. I had told my dad about watching a cabbage white lay eggs on a horseradish and then being able to find the eggs later, which I suppose inspired my dad -- yesterday he spotted a zebra swallowtail laying eggs on his pawpaw trees. They tend to defoliate his trees, and the pawpaws are a bit of a project for him, with some anxiety about whether he'll get to the few fruits before the raccoons find them. In the past he has even sprayed the trees with pyrethrins to stop the defoliation, which I very much disapprove of, and find out of character for him. (They fully defoliate the small trees, which then recover, and only defoliate the large trees by about 1/4th. That seems like acceptable damage to me.) We went and looked for the eggs and managed to find them, and then I spotted a couple of caterpillars. I was a little nervous about showing them to him, but I think he's fascinated enough by them that he has formed a bit of attachment, and will be more gentle with them in the future. He's going out each day to look at them now and watch what the caterpillars do, and how the eggs mature. :-)

The other big excitement for me is the giant syrphid flies (dunno the species). Unlike the little syrphid flies I'm used to, these are *enormous*, maybe 3 cm long, looking like hornets. They love the massive elderberry bush out back of the garden (which produced a gallon of fruit last year) and my dad has seen one catch a carpenter bee. Apparently they also had a habit of hanging out by the brown marmorated stink bug trap and catching incoming stink bugs.

Edited to add: This year, almost no June bugs, although we're slightly earlier in the season. Far fewer of the really smelly, thin, millipedes in the house. Fewer skinks. No robber fly sightings. No live BMSBs in the house, and very few outdoors. The amaranth and cleomi, allowed to grow randomly in the garden as trap plants, show no harlequin bugs and very few cucumber beetles, although there's certainly defoliation from the latter.

Somewhere in the past days or weeks, Google started either bouncing email without a DKIM signature or is silently filing it as spam. (DKIM: DomainKeys Identified Mail, an anti-spoofing measure.)

If you receive email at a domain you registered, there is a good chance that recipients who use Google Mail are not receiving it. You'll need to ensure that you're getting a DKIM "pass" result that matches your domain name.

For example, I use Fastmail. GMail was indicating "DKIM PASS from messagingengine.com" (that's Fastmail's actual mail service) but was still rejecting my mail. Once I added the DNS records that Fastmail indicating I needed to add in their settings page for my domain, I instead started getting "DKIM PASS from [my actual domain]" and my mail started getting through.

(While DKIM is a reasonable tool and it's fine that Google is using this as part of their spam check, I suspect they're doing this strict version to try to solidify their position by further freezing out other mail providers.)

A good piece on international shipping and why it's all bollixed up right now, and is just going to get worse:

https://medium.com/@ryan79z28/im-a-twenty-year-truck-driver-i-will-tell-you-why-america-s-shipping-crisis-will-not-end-bbe0ebac6a91 (h/t siderea)

Note that this is specific to *ports*, which as I understand it largely affects international shipping. Domestic is less affected. There are still shipping issues domestically, but not as bad as the ports, since the ports have more restrictions and less capacity.

It seems like this is a *great* time to refocus on getting what you need from the local economy. Food is pretty easy to get from local sources, here in New England, but also think about furniture, clothing, tools, etc. Electronics... is probably a harder one. Medicine, too. Not everything can be sourced locally; we have an international economy for reasons. And local commerce is still going to be affected by international shipping issues, in second-order ways. But something to keep in mind.

There's been some reporting recently of vaccines not protecting against severe infection as well as expected, based on looking at the number of hospitalized people who are vaccinated vs not. "60% of people with severe COVID-19 in the hospital had been vaccinated!" Here's an article explaining why this analysis is complete junk:

https://www.covid-datascience.com/post/israeli-data-how-can-efficacy-vs-severe-disease-be-strong-when-60-of-hospitalized-are-vaccinated

If you're familiar with Simpson's paradox, it's another case of that. TL;DR: Vaccination status is highly correlated with age, and if you actually slice up the cases by age, you see that efficacy against severe disease is 80–100%, depending on age. And yes, this is in the context of the Delta variant (or other current strains).

(But also see the article for some additional confounding factors.)

I brought _The Art of Fermentation_ by Sandor Katz with me on the Florida trip, and I've been reading it straight through (though I skipped the bits on alcohol fermentation, which I am largely disinterested in.) The book is somewhere between an encyclopedia, an ethnohistorical foods survey, and a how-to guide. It's very approachable.

Some general notes so far:

The main takeaway on fermentations involving lactic acid bacteria (e.g. yogurt, sauerkraut, and to some extent salami) is that as long as there's an anaerobic environment and sufficient carbohydrates, environmental lactic-acid bacteria will pretty much just take over and acidify and make something safe to eat. They're salt-tolerant, so salt helps them get a leg up, but it's not necessary, and you can often replace it with "backslopping" some of the previous batch in as a starter. (Salt is important for culinary reasons, though, including not allowing sauerkraut to get mushy.) I was startled at how many traditional fermentations are just "put the raw milk in the gourd" and food comes out a few days later. Milk in particular is ideal for this, and you see that in traditions all through Europe and Africa. It turns out that "aging like milk" is a bit of a misnomer -- unless the milk is pasteurized, in which case there's a bit more of a gamble.

However, just because it's safe doesn't mean it's tasty (to you). I've long been suspicious of how the variety of smells of cheeses is widely tolerated in American cuisine, but milk is only supposed to smell one way (a single very mild smell). It sounds like many of the times I've had "spoiled" milk, it would have been recognizable to *someone* in the world as a perfectly good dairy ferment, but that my upbringing has taught me to be disgusted by it (or rather, hasn't taught me to like it). As Katz points out, fermentation is a large middle ground between fresh and rotten. Some things are unambiguously rotten, but many are culturally relative. You just have to take your own society's word for it sometimes!

I also feel a little more vindicated in my willingness to eat "old" food from the fridge, trusting my eyes and nose and tongue: Molds are bad, brightly colored ones more so, and bad smells and flavors mean bad food. As far as I'm aware, I've never gotten food poisoning (although I also hear that's mostly a result of people not washing their hands in food harvesting and prep after using the toilet!)

===

Industrialization of traditional fermentation processes produces more *uniform* products, but doesn't really increase safety, and the flavors tend to be of only middling quality. The nutrition can also be reduced relative to the traditional methods. Both of these are because the industrial process uses one or more pure cultures on sterilized ingredients, rather than high diversity of species and strains you'd get from indigenous bacteria (those found on hands and ingredients). This is also why you can't really culture yogurt from storebought yogurt for more than a couple of iterations; the theory is that bacteriophages eventually kill of your cultures. Traditional yogurts use traditional yogurts as starters, and the diverse ecosystem of bacteria is more resistant to infection. Unfortunately, food regulators often don't understand this, and sometimes crack down on traditional fermentation; one salami-maker had to pay $100,000 to commission a study proving to the USDA that his methods don't allow _E. coli_ to grow. If he had succumbed to pressure, he would have had to use methods that make the same homogeneous salami that everyone else makes, rather than the exceptional products he was known for. And the use of pure cultures also inhibits home production and experimentation; if commercial yogurts used the historical Bulgarian cultures, I'd be able to make my own yogurt at home just by taking a sample of storebought stuff.

===

Meat and fish fermentation is more difficult because of the lack of carbohydrates -- there's no food for the safe bacteria, so putrefying bacteria have free reign. That's why salami has sugar added, and why fish is so often fermented with rice. (This is also why curing flesh requires so much more salt than preserving vegetables.)

Botulism used to be primarily caused by improperly prepared sausages (hence the name, from the Latin "botulus", for "sausage"). In the anaerobic, high water-activity, low acidity interior of meat, _Clostridium botulinum_ can thrive; traditional meat fermentation uses a combination of drying, salting, and souring to protect against this. In modern times, however, we get to enjoy the risk of botulism from canned vegetables as well! These vegetables would historically have been fermented instead, with far safer results. A special case is garlic in olive oil, which is *too* anaerobic; the safe thing to do is to ferment the garlic first, *then* use it for infusion. There was also a depressing note on Alaskan fish preservation -- traditional fermentation was done in grass-lined pits, but some people are switching to plastic and are getting botulism as a result of the anaerobic environment. Be careful of messing with traditions that work.

===

Many fermentations (or foods in general) are best done in a specific geographic and cultural context. For example, fermentations involving mold (e.g. tempeh, soy sauce, miso) are harder to arrange in a low tech way unless you live in a climate that is conducive to them, since the molds want access to air but *also* humidity *and* warm temperatures. Fish are easier to dry in a cool, dry, sunny climate. Meat is best preserved in cool, humid conditions, so slaughter and hunting are preferentially done at certain times of year. Many fermentations rely on local ingredients that are hard to acquire elsewhere, where preservation would be required for shipping and would destroy the important microbes on their surfaces. I would *like* to make my own tempeh, and it wouldn't be too hard, but I can't just get it going based on local materials. On the other hand, sauerkraut is ridiculously easy to make in New England; all I need is a cabbage, salt, a scale, and a jar (and ideally also a basement.) Those are things I already have. I'll likely do some experimentation with millet and lentils in fermented batters, such as dosa.

===

A good many fermentations are about preserving an abundance of food for the scarce part of the year -- sauerkraut, rakfisk, umeboshi. But others are primarily about developing flavors (wine, chocolate, miso), making the indigestible or toxic into something edible (some seeds), or reducing cooking requirements (many vegetables and grains, tough meat). In a few cases you get new forms entirely, like sourdough bread and carbonated beverages. These aren't exclusive, of course; soybeans in particular show up in almost all of these categories. Cheese certainly spans many of them.

I think my main interests are in "putting food up" during the harvest season with reducing cooking requirements a second, but I also delight in the wide variety of flavors. However, the latter more applies to fermentations I'm unlikely to do myself, such as cheese and mold/soy processes.

A couple days ago I was talking with a neighbor and she offered to do me a favor, which I didn't think I needed at the time. I declined, and then later changed my mind, so I gave her a call and left a message. I got a confused call back asking what I was talking about.

Turns out they're totally separate people! Now I need to figure out which of them does the rowing crew stuff, which is the one from Alabama, which one baked us that nice dessert that one time, etc. Ugh.

I'm usually only *moderately* bad at faces (and really quite bad at names), but this one really takes the cake.

We were out on the porch a couple days ago chatting with a neighbor when we heard crows making a fuss, which is usually a sign that some large, interesting bird is about. And sure enough, up flies a raven, pursued by crows!

The raven landed on bare branch of a tree across the street, with crows making close passes and even an impressive dive at it. It made some little croaking grunts and was soon joined by a second raven. The crows wandered off, which surprised me. Maybe they had succeeded at driving the ravens out of their territory.

This was one of the few times I've gotten a good look at a raven. They're quite impressive, and I was struck by how *small* the crows looked in comparison. (I don't know what kind of crow, other than I'm pretty sure they weren't fish crows since they didn't sound like squeaky toys.) Those big chunky bills are just lovely.

One of the ravens seemed preoccupied with a dead branch stump and jabbed at the bark with an open beak a few times, and I think may have taken a few whacks at it from the other side -- or, I realized today, that may have just been a vocalization of some sort. Most wonderfully, it also made a weird warbling call a couple of times. I don't really know how to describe it other than saying that it sounded like a series of musical notes, maybe along with a click. Certainly it was not the usual hoarse "gronk" sound.

We hear ravens once in a while but have only laid eyes on them a few times, so all in all it was quite a magical moment.