Chris X Edwards

I'm always amazed when products for obsessive computer nerds to get their computers exactly how they want, do not support Linux.
2020-07-03 06:03
Similar to having a hammer and seeing nails everywhere: When you need a hammer and don't have one, everything looks a bit like a hammer.
2020-06-19 11:03
This mask stuff sucks for everyone but especially for deaf people. It would be interesting to check if deaf signers naturally infect less.
2020-06-18 18:35
Wouldn't it be more fun if everyone referred to the virus as Covfefe19? We could troll a certain narcissist into believing he discovered it.
2020-06-17 11:06
Can we shift irrational unemployment stigma to #LinkedIn for fatuously congratulating people for their new job of "Currently Unemployed"?
2020-06-10 08:51
Blah Blah
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Aftermath Of The Cytokine Storm

2020-06-05 07:11

Some precise number of days (which I know but will redact) before I turned 18, I know exactly where I was and what I was doing. That is because I could not quite legally gamble, yet I was in a casino in Las Vegas. On Christmas Day. I was doing a family thing for family connections that lived in Las Vegas. Visiting a casino on such a strange day is just something one can do if you don’t take traditional holidays too seriously and you happen to be in town coincidentally.

What single adjective would I use to describe the Las Vegas casinos on Christmas Day? Answer: Chinese. That was a while back, but I doubt things are too much different today. Think about it. Normal Christmas-celebrating Americans wouldn’t usually think to go to Vegas on such an incompatible major holiday. But it would be reasonable for normal Chinese people to happily take up the slack and cheap rates.

In 2019, exactly 8 days after flying and spending the day in airports (SAN, PHX, BUF — LAS on the way out!), I record my first written description of the illness that dominated my life this past winter. What day did I travel? November 28 - Thanksgiving Day. A day I chose because the rates (and I) were cheap — Americans do not like to travel the entirety of Thanksgiving Day. I have no idea if this is truly relevant, but it is certainly interesting to think about.

You know how my blog posts often maddeningly change topics a few paragraphs in? The change often looks like a radical departure, but I do actually try to keep a thematic strand connecting them. So here we go.

The Economist just posted a very interesting article called How SARS-CoV-2 Causes Disease And Death In Covid-19. The article says:

The immune response to a virus starts with infected cells producing a suite of signalling molecules called cytokines. Some of these tell other cells nearby to be on their guard against attack, thus stymying the virus’s ability to replicate itself. Others tell the immune system to come and put some stick about. Thus called to arms, the immune system launches both a prompt all-purpose response—inflammation—and a subsequent targeted counter-attack using antibodies and cells specifically programmed to attack both virus particles and the cells they have infected. Unfortunately SARS-CoV-2 seems able to interfere with the early steps of the immune response. It can apparently counteract the part that dampens replication in nearby cells. It may also enhance inflammation.

When inflammation gets completely out of control the body enters what is called a cytokine storm. Such storms drive the most severe outcomes for covid-19, including multi-organ failure.

Now take a look at this birthday greeting I wrote to a friend and former colleague who is a computational biophysics researcher and professor of pharmacology.

2019-12-29

I’m still struggling to get to my next birthday, still under attack by some kind of pathogen. … I’ve never had an illness like this as an adult. My guess is that it is a flu virus but it could be bacterial. I feel like it went from my lungs to my major meat muscles. Each day I’d get a new thing. For example, one day my tibialis anterior was hit with what runners call "shin splints". I’m very familiar with muscle pain from muscle wear and tear but it’s unnerving when there is no sensible cause. I set up a bike inside and riding that helped my leg muscles a lot. I think the main infection is mostly defeated and controlling secondary infections is indeed the important thing. I lost a lot of weight so I’m trying to eat as much as possible. That’s not easy since I have very little appetite. I’m also wondering if maybe my body is doing some silly overreacting, something like a cytokine storm. Of course, as you know, at that level it all becomes overwhelmingly complex.

cytokine.jpg

Reviewing these emails has helped me put together some other pieces of the puzzle. All spring long I’ve been cold. Especially my shins. I moved a down sleeping bag to my office to put on my shins thinking I was blocking a draft or something. I crawled around to see if a fan from a computer on the floor was blowing on my legs. I changed things around with my seating arrangements thinking maybe my circulation was being constrained by my chair making me cold (circulation problems are synonymous to me with being cold — and, yes, I am an expert). Then a few weeks ago the weather went from cool to insanely hot (90F/32C) overnight. My shins were still cold.

That was an "oh shit" moment for sure. My illness has really messed up my shins apparently. I am now aggressively rebuilding my shin muscles. Now that I’m focusing on them it’s clear, they’re not right at all. I’m a little nervous about other lasting damage. I’m sleeping about 30 minutes to an hour longer each day than I did at the same time last year (I always sleep the maximum amount my body will let me).

But I feel mostly ok. I have a near comically healthy lifestyle — if anyone is going to shake off problems that can be shaken off, it will be me. The excellent Ed Yong (whose book I reviewed) has a very interesting article in the Atlantic; it is the first I have seen which has been properly sympathetic to the brutal hardships of symptomatic survivors. The article is very scary because of this and strong hints of long term effects. You can see why I’m taking this all kind of seriously. And even though the infallible apolitical CDC has assured me — by fiat — that I did not suffer covid 19 because they did not notice the infection, I’m going to pay attention to covid 19 data and assume it is relevant for the functionally identical illness I did have.

Bright Side Of Life

2020-06-03 11:32

I’m proud that my cultural heritage can be helpful at this time. There might have been a translation error, however, because I’m not sure if the governor fully appreciates the sarcasm that is mixed in with the stoic nihilism here. Still, it put a smile on my face.

bright_side.jpg

Life’s a piece of shit
When you look at it
Life’s a laugh and death’s a joke, it’s true
You’ll see it’s all a show
Keep em laughin as you go
Just remember the last laugh is on you

And always look on the bright side of life!

X Marks The Loot

2020-05-25 01:21

I recently had an idea for a new video game mechanic. In many game genres, there is a common trope where the protagonist goes out into the world and does exciting action things which often result in surplus equipment or other valuables. You might kill a dragon which has a valuable set of scales. Or you kill a few enemy soldiers. In both of those cases the normal way the situation is handled is by giving the player the chance to "loot" the scene. But how can it make any sense to head back into town with a half dozen sets of weapons and full suits of armor, or a complete dragon hide? Staggering back thus encumbered might be plausible if that’s all you needed to do, but there will be obstacles, other monsters and other things to discover. You know, the stuff that makes the game have a plot.

Currently there are a few strategies to deal with this. One is to severely limit what you can loot from the set of what one would reasonably expect. Was everyone you just fought wearing socks? Yes? Yet the game is not going to let you loot socks. It limits things to just the salient weapons or even just some random items drawn from a loot table.

The other main strategy — and they’re not mutually exclusive — is to just let the player carry an absurd amount of stuff. Related to that is discounting how much items weigh. A champion of those strategies would be the deliberately fanciful Minecraft where players can carry nearly 10 billion kg! (I actually disagree with that analysis because I don’t assume nondestructive crafting in Minecraft. And a player can carry only 36 hats before collapsing under their weight. But the point of the analysis is still quite correct and illustrative.)

But what if you’re going for a game with maximal immersion and fidelity. I can not recall ever seeing this problem addressed realistically. How might a game do better with this problem?

I imagine an open world game like Skyrim or Borderlands or Fallout or Witcher3 or or Red Dead Redemption or even GTA handling this problem in the following way. Once a player encounters a situation where collecting an absurd amount of stuff is possible, they have the option to shuttle it to a cache, basically a hiding place. They then make a note of that on their maps.

How this works is that back in the village among safe and helpful NPCs, the player can then choose to sell these notes to various salvage operators. These guys are not professional dragon slayers. They are just professional movers of stuff. If you tell them exactly where to go and what to find — with assurances that the local monsters are all dead! — they can then make the implausible portaging plausible. Why bother bringing all this stuff back to town to sell, when the shopkeeper you’re planning to sell things to could also be handling the moving? You’re this world’s messiah — outsource a bit!

Geralt Should Hire A Sherpa

geraltsherpa.jpg

Besides making games less unrealistic, what’s cool about this mechanic is that it can have a lot of tunable elements which could be interesting for the player. For example, let’s say you come to town and tell a salvager that you have buried a chest of gold that you want to sell and reveal the general area it’s in. All of this can be done by selecting from a menu that is essentially your notes. At this point the salvager has to decide if he trusts you enough to go attempt to get your stuff. You could have a system where you build trust slowly. Maybe at first you can only hire shady itinerant movers who commonly set out after your gold and then disappear forever, maybe stealing your treasure or maybe failing and its still there waiting. Or maybe the earnest recovery effort is robbed by bandits or their ship is dashed on the rocks in a storm. These kinds of problems set up new missions where you, the hero, can go salvage the salvage operation or hunt down perfidious cheaters.

As you do more business, you might be able to pay, up front, someone in a permanent location to go fetch your stuff. They have a good reputation and will likely work to keep it. Eventually you are trustworthy enough that these professional salvagers will simply pay you coin for your notes and the transaction is complete — you have gold in your pocket from some lootable adventure without the clumsy impossible process of hauling that loot.

Khajiit Trader Says: Necessary Assets Ready To Go

khajiit-trader.jpg

You could imagine that different towns would have different reputations. You could trick some of these merchants if they aggravate you or you don’t mind burning your reputation there. They may charge more commission if the trip is long or requires visiting dangerous places. There can be a whole complex dynamic to work out optimal routes for multiple pickups, a famously tricky travelling salesman problem. They might even tell you that they could loot the cave in the elven ruins if it weren’t for the trolls that lived nearby — prompting you to go kill three stone trolls and add their loot to the shipping manifest. This would make it plausible to capture entire ships or wagons or cars and leave them for others to sensibly pick up and liquidate.

There might be interesting dynamics in how long it takes to get paid or take possession of the item back in town, maybe timed for correct leveling. You could have a system that allows players to basically act as scouts for some things; for example, they might come back and sell to a craftsman the general location of a crafting ingredient (e.g. mine’s ore vein or rare plant grove or animal sighting, etc). Or even "loot" entire buildings or towns by delivering to the right people the information that it is now safe to occupy.

You could hire trustworthy movers to go to your remote base and retrieve needed items from storage for some particular mission. A lighter version of this would be where the player has to haul all of the loot to major hubs which functionally act as railheads.

Maybe have different levels of caching. A poorly stashed hoard may be found by someone else by the time your mover arrives sparking all kinds of interesting tension. Maybe if this is a common problem the player can improve their odds by dividing the loot and performing multiple hiding operations. Maybe there could be a dynamic where poor hiding results in the mover not being able to find the loot; the loot is still there, but the mover is too annoyed to try again. Or maybe that problem doesn’t result from poor hiding but rather careful hiding!

By having a system like this, players can obsessively loot a place and yet the carrying weight limit can still be set at something sane. It opens the door for all kinds of intrigue. You can duly approve and appreciate all the junk items you’re taking from the battlefield sets without having them clutter your real working inventory. And if you come across an item that’s a keeper, but you can’t take it now, it can be handled later — by someone else!

Some may object that this makes the game too complicated, like running a logistics business. But I’m afraid that fast travel wagon has already rolled out of the city gates. Have a look at this hilarious scene CD Project Red scripted into Witcher3 to troll people who run mods to give themselves unaccountable wealth.

Clearly players can enjoy such bookkeeping details!

Virus Epidemic For All

2020-05-23 22:53

An Illustrative Fable

Imagine you’re swimming in a small lake and some massive creature grabs your leg and mauls you with hundreds of sharp pointy teeth. You kick and thrash and barely make it to shore. "Holy shit! What was that!?", you would wonder as you frantically look for a tourniquet. After extensive reconstructive surgeries and weeks of healing you’d still really love to know what the hell could have done that.

Now imagine it’s a few months later, say March, and some old people who had gone for a swim in this popular lake have been found washed up on the shore dead, torn to pieces by some beast. Ok, that’s weird. Now the police department and animal control officers go to "thoroughly" search the lake. Nothing. Some more people get mauled, but only people who go swimming in the deepest water — the kids in the shallow beach area never have any problem. But clearly there’s something going on. The police and officials get more serious about it because now things are starting to look bad. Still nothing.

Now we’re hearing that because of "air travel" one of the river dolphins from the Wuhan Institute of Hydrobiology has gone missing. (By the way, that’s a real place where such things live; so slightly less imagining should be necessary. You’re welcome.) Ok, so now we’re thinking that yes, this could have been the work of a rogue cosmopolitan river dolphin, and, sure "air travel", whatever… why not? It’s got to be something, right?

River dolphins - do they look trustworthy to you?

riverdolphin.jpg

This is a busy swimming lake and people keep swimming in it because only a really small percentage of people have any bad experiences. Come on, who gets mauled by something swimming in a lake anyway? It’d be really bad luck, right? But now that officials are paying attention, yes, it does turn out that shark bite specialist surgeons are becoming overbooked for some reason related to this lake. It would seem that there must be a river dolphin in the lake! It all fits! Scientists set up monitoring cameras and finally, at the end of March, they catch a glimpse of it. It has been confirmed — there has been a river dolphin in the lake! The shark bite surgeons inspect some of their patients for river dolphin bites and it does turn out that a vague percentage of them may have been bitten by river dolphins! Because of such scientific analyses people are starting to worry.

This dolphin is trained to do tricks and therefore is good at hiding and very hard to catch. While professional dolphin humiliaters are summoned from Seaworld, the lake is declared a danger zone. Outside of their own homes, everyone must breathe through a snorkel and wear a pointy hat to approximate the snout of a dolphin (unless they’re buying fish of course). No one is sure if this is sufficient or necessary but it is decided that literally everything possible must be done — even the things that don’t exactly make sense.

My important question to you is this: when did this dolphin book his flight?

For most people the dolphin obviously arrived in March when everyone started talking about it and wearing the pointy hats. When scientists got photos of it, that made March seem "scientific". But is that a satisfactory explanation? If you had your leg mauled swimming in December, I’m going to suggest that you would have some different feelings. Sure, some people who got bit by a snapping turtle or scraped their skin on sharp submerged rocks may be over-imagining that they had been mauled by a river dolphin years ago the last time they visited the lake, but if you still have scars of hundreds of little teeth marks in your leg from December, you may feel that the March hypothesis leaves something to be desired.

It’s going to take a lot to convince you that this river dolphin wasn’t there when you got mauled. If videos of that specific dolphin doing tricks at a February show in China emerge on Tik Tok, that is still not the end of it. Even in that case where we have high-quality information exonerating the river dolphin in December, there is still something very important to say about the lake, something important that must be done once the dolphin is captured…

Keep looking.

Because that’s not your only problem is it? Either that river dolphin was mauling people in December, or there’s another lake monster doing naughty things.

Who Cares?

Why should anyone care? That’s a solid question. I personally care because I was mauled by something functionally identical to Covid19 in December and the official story is that it could not possibly have been related to the pretext for our current global calamity. I would consider it epidemiologically curious if I did have Covid19. However, it would have been a serious and interesting freak coincidence if I did not have it.

If I did not have it, clearly there’s something else out there that we may additionally want to freak out about. If you think Covid19 is scary, wait until you hear about Covid19 plus some other thing that will horrifically kill you!

I feel like I have insight into contracting and surviving a Covid19-style disease. (If that sounds especially interesting, see my other post where I go into too much detail about exactly what happened to me.) For example, I have heard no one hypothesize that having some external temperature stress could exacerbate the disease, but in my case I feel that is likely what happened. It definitely is worth considering and such information would have policy recommendation implications.

Also as a survivor of a serious Covid19-like disease, there’s another topic I’d love to address — no one ever talks about how to help the afflicted. These CDC guidelines on how to take care of "yourself" when you’re sick suck ass. They are, in fact, basically guidelines to keep you from passing it on. They are how to take care of others while you are sick.

This document says: "People with COVID-19 who have stayed home (home isolated) can leave home under the following conditions**:"

Fine but what about when the victim is losing a lot of weight and needs to buy some food and can barely stand? What was that disinfectant they were supposed to go acquire? How many times were they supposed to do spring cleaning every day?

What I would have said in December is, "See you in Hell!"

Seriously, to offer "help" to people who are knocking on death’s door by basically saying, "stay away from me you icky monster", is not help. How about some resources or tips on how to get food or take care of your family when you’re more than half dead?

What Is The Reality Of Covid19?

Not the societal reaction to it; right or wrong, that is going to be a colossal mess. No, what is the reality of Covid19, the infection, in real life? Well, obviously I can’t say because I had exactly all of the symptoms in December. But I can can say exactly what it’s like to have a functionally identical disease. When you get Covid19 I’m told that you are likely to present the following symptoms.

  • Fever (83–99%)

  • Cough (59–82%)

  • Fatigue (44–70%)

  • Anorexia (40–84%)

  • Shortness of breath (31–40%)

  • Sputum production (28–33%)

  • Myalgias (11–35%)

That information is from this CDC web page.

By the way, "anorexia" is the symptom anorexia, which just means that getting enough to eat becomes problematic, not the full eating disorder thing. Sputum is stuff you’re likely to cough up when your respiratory system is sick. And the only other symptom with a fancy medical term is myalgia which is simply obfuscatory doctor talk for "muscle pain".

But don’t rest yet.

Here is a different list from the CDC (from 2020-05-14 with order preserved):

  • Cough

  • Shortness of breath or difficulty breathing

  • Fever

  • Chills

  • Muscle pain

  • Sore throat

  • New loss of taste or smell

In December, because I suffered all of these exact symptoms, I looked for what malady they likely imply. Only once Covid19 found me (and everyone else) did I have a perfect candidate. If you know of an illness that is exactly like Covid19 and valid in Western New York or Southern California at the end of 2019, do let me know.

Were there any other interesting symptoms I had that are not on this list? Nothing major really. The things I would add are the following.

  • Loss of mental acuity, but that is directly related to hypoxia ("shortness of breath"). I’m lucky to have recreationally played with that one (without drugs! e.g. at high altitude, freezing temperatures, sunstroke, anaerobic sprinting, et al.) and I am good at handling it.

  • Hypoxia is also related to the numbness in my fingertips. That second CDC list does mention both of these items under "When to Seek Emergency Medical Attention". (They say bluish lips or face - that’s related to bluish fingers, cyanosis that can accompany serious pneumonia — they weren’t blue but I did describe numb fingertips before learning all this.)

  • I also had an ear infection at the end of the ordeal. That was unnerving because I couldn’t hear out of my left ear for a while. That did thankfully clear after a couple of weeks.

  • Reading the record today I was reminded of little red spots on my chest and back. I’m a middle aged guy and I still get acne, so my skin isn’t the most easygoing in any case. These little red spots were almost too small to notice and they went away quickly. Still, I must mention them for completeness as a symptom I’ve not heard about.

Let’s consider symptoms I did not have because I think that’s just as interesting.

  • Some sources vaguely mention diarrhea but it is not a hallmark symptom. I did not have any such problems.

  • Likewise my stomach was fine. I wasn’t hungry in a profoundly pathological way, but it was not from nausea or the kinds of things people must mean when they say "stomach flu".

  • One of the official symptom lists includes sore throat. I don’t have strong memories of that being a serious problem but I do remember some level of throat irritation. It was just overshadowed by much more serious problems. With all that coughing, this symptom seems almost redundant.

  • Congestion. My sense of smell broke, but not simply because my nose holes were blocked. At the end once the main symptoms were receding I did have a bit of congestion but nothing out of the ordinary really.

The loss of smell, or anosmia, was a very strange symptom. I went from eating 500g of chocolate per week to temporarily not liking chocolate. Thankfully that recovered! A lot of my food preferences were completely messed up. It might be wise for the CDC to add "sensation of taste" even though it is ultimately related to smell.

I feel like reports are pretty solid that anosmia is idiosyncratic to Covid19. Yes, other viral infections can do this, but it appears to be unusually common with Covid19 victims. This infectious disease researcher, who suffered a serious case of Covid 19 himself, says…

Loss of sense of smell is kind of a unique symptom. It’s not present in everyone. But if I have a patient call me and say, I don’t feel good and I’ve lost my sense of smell - until proven otherwise, they have COVID, there’s no question about it.

Here is a short paper about the loss of smell in Covid19 patients, written by people at UB just down the street from me.

Not Just Me

I’m not alone here. There are a lot of people who are hearing about Covid19 and thinking to themselves, ah, well that perfectly explains my very strange mystery illness.

The NYT wonders if maybe C19 was earlier than commonly supposed.

By the time New York City confirmed its first case of the coronavirus on March 1, thousands of infections were already silently spreading through the city, a hidden explosion of a disease that many still viewed as a remote threat as the city awaited the first signs of spring.

Hidden outbreaks were also spreading almost completely undetected in Boston, San Francisco, Chicago and Seattle, long before testing showed that each city had a major problem, according to a model of the spread of the disease by researchers at Northeastern University who shared their results with The New York Times. … "We weren’t testing, and if you’re not testing you don’t know," Dr. Heguy said. The new estimates suggesting that thousands of infections were spreading silently in the first months of the year "don’t seem surprising at all," she said.

There are other signs that the outbreak was worse at an earlier point than previously known. This week, health officials in Santa Clara County, Calif., announced a newly discovered coronavirus-linked death on Feb. 6, weeks earlier than what had been previously thought to be the first death caused by the virus in the United States. … In mid-February, a month before New York City schools were closed, New York City and San Francisco already had more than 600 people with unidentified infections, and Seattle, Chicago and Boston already had more than 100 people, the findings estimate. By March 1, as New York confirmed its first case, the numbers there may already have surpassed 10,000.

Here’s another one in USA Today citing some of the same researchers.

The Mount Sinai study looked at 90 SARS-CoV-2 genomes from 84 confirmed COVID-19 cases in its health system in New York and found "multiple, independent but isolated introductions mainly from Europe and other parts of the United States from January through early March 2020," the researchers wrote.

Van Bakel told the Times that his team identified seven distinct lineages of the virus circulating in New York.

"We will probably find more," he added.

Without early testing and then sequencing of the virus, though, public health officials weren’t able to know where the virus was coming from and who could be at risk before it grew to its current levels, Heguy said.

"Every single case of strange pneumonias here in New York, they could have been testing earlier and then do immediately the contact tracing," she said.

Heguy said continuing to collect data and build out a larger sample size will be a next step in the research. Scientists are also hoping to understand the clinical implications of the different strains of the virus. Sequencing the virus' genetic information now will also help in case a second wave were to occur, she said.

This Reuters report is also very suggestive.

A French hospital which has retested old samples from pneumonia patients discovered that it treated a man who had COVID-19 as early as Dec. 27, nearly a month before the French government confirmed its first cases.

In that article, a doctor foolishly entertains the idea that this may have been "patient zero" in France. To me it seems ridiculously unlikely. That’s like finding a 6e6 year old hominid fossil and assuming you must have found biblical Eve because that’s really old!

Counter Argument

Here are some scientists who think they’ve done sufficient science (checking mutations and assuming the rate is constant per time). And maybe they have and their methods are sound. Still I thought of some pointy questions for them.

  • One problem is if they see a second line that they can’t tell is a sequential mutation or just that such mutations are more likely (perhaps because they are benign). Sort of like two distinct populations of people could get a genetic resilience to alcohol, not because they’re in communication or descending from each other, but because it promotes success.

  • It seems a big assumption to assume mutations are constant. Maybe that’s ok though. They say "about two mutations per month".

  • What’s the error rate on correctly transcribing the sequence? Surely it must be something. And there must be self-checks that would be much less likely to happen from gradual mutations. I get the feeling that the error rate could be as high as 3 in 29811, C19’s genome size. See the above point about 2 mutations a month and think of how long we’re talking about here.

  • This may be effective methodology for very well established cases and outbreaks, but there could have been entire outbreaks where no one cared. Clearly that was true in my case whatever specific pathogen I had. (Still no one cares!) It is quite reasonable to consider whether there was a much more massive outbreak among relatively healthy people (one that reached all over the world) before it finally got into nursing homes and vulnerable populations in a noticeable way (where dying frequently is normal).

Without better controlled data and source material, this seems like a just so story. But I understand that so does the other hypothesis that this pathogen was in the wild before people realized it explicitly by name. It will be interesting to see if the hypothesis in this work holds for subsequent data.

Here is a report from my local WNY county which expresses surprise that a decent number (actual quantity strangely unspecified) of antibody tests showed a low percentage of infection.

Earlier this week, Erie County Executive Mark Poloncarz told us 92% of the community has tested negative for antibodies at this time.

There are a lot of unknowns here. For example, maybe it was 90% of the population had the antibodies at some point but they wear off.

[The Erie County Health Commissioner] also says we’re still learning more about antibodies, including if they even provide more immunity for those who test positive and for how long.

Conclusion

My goal here was to put my personal situation and observations down in writing so I can stop thinking about them. One of the following things is true.

  1. Covid19 was far more prevalent in the USA in 2019 than previously assumed.

  2. There is some very nasty other thing that is every bit as bad and scary as Covid19 out there unaccounted for that was in WNY in 2019.

  3. I am ridiculously unlucky to get a Covid19-style epidemic of one.

As with most medical facts, the surest thing you can say is we don’t know.

UPDATE 2020-06-01

I mentioned that a potential false positive symptom I experienced was red skin bumps on my chest and back, about sternum level. I had not heard of this as a symptom but listed it because my written record reminded me of it and I wanted to be complete. Now I find this short report at the NIH’s Pubmed which seems to echo my experience.

Conclusion: Infection with COVID-19 may result in dermatological manifestations with various clinical presentations, which may aid in the timely diagnosis of this infection.

It further singles out my presentation as exactly compatible with the findings.

Majority of lesions were localized on the trunk (66.7%, 50/72)…

Again, let me stress that if the CDC wishes me to not have had Covid19 by fiat, that’s fine, but clearly we then have some additional major disease going on too that needs to be addressed.

UPDATE 2020-06-05

Another post, this one with some more observations and some long term effects.

UPDATE 2020-06-18

A mayor in NJ publicly asserts he had a Covid19-style illness in November 2019.

A slightly different origin story from a phylogenetic research group at Cambridge. Still pretty confusing/confused.

UPDATE 2020-06-18

A BBC article about a study of Italian sewage samples from 2019-12-18 shows genetic traces of the virus.

Virus Epidemic For One

2020-05-23 22:47

Here is a good photo of me illustrating my baseline health in 2019. I am visiting San Diego and because it is the main activity I miss about the geography itself, I rode a bike to the top of Mt. Soledad. At least four times. The last time was on 2019-11-27.

soledad.jpg

Less than 10 days later I was in the poorest state of health of my entire life, as close to dying of natural causes as anyone ever has been who ultimately recovers on their own. Normally I would be horrified to complain or seem like I was complaining about any untoward ill-health. And I am not complaining now! Or fishing for sympathy or whatever it is that normally motivates people to complain/brag about their maladies. But because of the Virus That Broke The World, obviously everyone is much more interested in novel coronavirus symptoms than they’ve ever been before and ever imagined being.

I am hoping that this account can possibly be helpful in discussions about that other virus, which official people assure me, I could not possibly have had. My recollection of events was challenged even as they happened and time has naturally made them even fuzzier. I thought it would be interesting to review any writing I had from that time where I share interesting and relevant details about my ordeal. It turns out that my personal email was rich with statements which clearly illuminate my situation.

If you don’t like reading about other people’s medical problems (I’m with you there) or you don’t feel my personal life is worth a lot of reading (it is my blog after all) then feel free to skip this one. If however, you’re interested in my life, this is definitely one of the most interesting things that has happened to me. Let’s review the historical record.

2019-11-28

The day after my last ascent up Soledad, I was in airports/airplanes all day, Thanksgiving Day, returning from a visit to SD.

2019-12-06

My wife leaves for a routine visit to her family in SD. Something isn’t perfect with my health, but nothing worth mentioning. With some rest I expect to feel fine.

2019-12-07

Instead of the deliberate rest I remember explicitly planning, I get a surprise opportunity to have some work done on my (job-related) boat. This prevents me from sleeping in and I end up standing outside chatting with the guys doing the work for 3 hours in 32F/0C weather. That’s standing outside doing nothing physical which is actually harder on the body than being active. I knew I wasn’t feeling full strength the day before, but this is where I think things took a serious wrong turn.

2019-12-08

Because my wife is away, I have a nice written record which provides detailed insights. I write to her…

I hope you’re feeling ok. I am definitely fighting off a tough illness. I got out of bed today at noon and now, 1830, I’m going to head back to bed. I’ve had severe chills all day and I’m wearing my outdoor winter gear and my robe! I’m super unsteady and clumsy. My lungs want to cough, but it hurts too much for that. I could barely eat anything. Ug. Tough day.

The next few days I’m really out of it with no written record. I am completely alone in the house and time goes by in strange ways as I spend almost all of my time sleeping. I’m having serious fever issues. I made a change to my bedding format because despite being around 60F/15C in my bedroom, I was sweating so much that the polyester comforter could not vent the moisture fast enough. I remember doing that because I liked the format change well enough that it is still that way now.

2019-12-12

Despite not having enough snow to ski I report that I barely managed to shovel the driveway, something I usually find easy and enjoy doing. Later, I write, "I did laundry. And now I’m very tired." Usually my lifetime of athleticism adequately provides for folding clothes!

I write to my dad…

I’ve been very sick for the past 5 days or so which is a novelty for me. This one’s a strange one. No food tastes good; I’m losing about a pound a day. My fingertips go numb. I can hear my eyelids. Each follicle of hair on my scalp seems somehow individually in mild pain. I’m wearing my outdoor gear all the time inside now and just can not be warm. I’m clumsy and have poor balance. All terrific fun! Still it clocks in at 3rd place behind real pain like dislocating your shoulder. And of course I can laugh this stuff off to my grave thanks to migraines spoiling the scale for any pain related phenomena.

Writing to a friend asking me for help with something…

I personally am unlikely to help at the moment. For the first time in my memory I have some very bad pathogen — worst since I had mumps at age 8 in Iran.

In retrospect — worse than mumps.

2019-12-13

Despite taking me to a doctor precisely zero times for illness the entirety of my early life (including mumps), my dad was actually concerned enough about what I described that he recommends I think about professional help. I allay his fears by demonstrating his apprehension of doctors has been duly passed on. Maybe amplified.

This illness is not a big deal. It’s annoying to lose so much time, sure, but I’ll live. This ailment is nowhere near as bad as whatever would be required to see a doctor. [I meant the hassle to just figure out US medical "care" which is prohibitively complex to me. I literally have no idea how to "see a doctor".] It’s a bit hard to take them seriously when their ROI R is questionable and their I seems designed to cause poor health. I’ll be fine though. Migraines taught me patience waiting for health to come back. I’m just thankful that it hit me right as [my wife is out of town] - so she neatly missed it.

I’ve had experience/practice with my thinking being compromised.

I’ve stopped [having fires in my fireplace] while sick because I am not touching my razor sharp axes until my clumsiness is quite gone. My metacognition is fine!

Here I’m concerning myself with what I can possibly eat that I will be able to enjoy enough to make up the caloric deficit I’m sensing.

I had an exhausting day which under normal circumstances would seem like I didn’t do anything. I walked to the [nearby] store and they did sell matches. I was surprisingly exhausted after that, like I’d just run, on foot, [20km] or something. After a nap, I actually went to Trader Joe’s where I amazingly not only remembered everything on my list, but thought of the things I couldn’t remember when making the list! I was interested in getting some of that horrendously delicious [chocolate] bark stuff that in normal times I feel like I could eat non-stop until I died of an overdose. But they didn’t have it. Fresh squeezed OJ was a gamble, but fortunately, its taste is not too badly corrupted in my system. I bought lots of bottle water. I guess I need to drink more so I will.

I knew I was very dehydrated from all the fever sweating. The matches were for the fireplace once I felt able to use an ax.

2019-12-14

I write to my mother in SD…

I meant to write earlier to say thank you for hosting me on my recent trip. But I’ve been attacked with some kind of lung infection that has kept me in bed pretty much this entire week. And it’s not letting up. I’ve lost about 5% of my body weight this week and if it keeps going down, that could get bad.

To my wife…

Well, still alive again today but really no change. I’m extra tired today, probably sorting out yesterday’s over ambitious activities [a short walk and shopping for food]. I’m pretty nervous that this will not be gone by the time you’re back. If I still have this I’m pretty sure you’ll conclude the best way to make me stop making the horrible coughing noises I can not not make is to just kill me. … Yesterday’s preliminary experiments suggested I could eat an entire tamale and so I’m going to do that now. I’m also going to try to make some lemonade. I’m very tired already just outlining the plan. Ugh.

My son had been sick with a strange fatiguing illness when I visited SD. My mother in a different household also reports recent strange lung infections. Here I reply to her skeptically about the source of my illness assuming my temporally closer contacts might be more relevant. But at this point, who knows? It seems well established that in December 2019 a lot of people in the USA were more sick than usual in weird ways.

→ I also have been coughing up stuff from my chest. … Now [other person in household is] showing the same signs and symptoms.

Ya, [my son] seemed to think I was suffering from his illness too, but I do not think so. I was back home for days feeling fine and got sick after hanging around my colleague at work who had been quite seriously sick. He’s a tough hombre too who we were surprised to see lose a week to this.

You know something is off when I overlook a chance to use whom pedantically.

2019-12-15

Writing to my wife who is about to return, I first mention being worried about having the strength to shovel snow to get the car out to pick her up. Then I joke around about the grimness of the previous week…

It’s just too bad you can’t wait until I’m not half dead. You also must start working on your expectations. You can’t come back and say, "What the hell happened here?! This place is awful, like no one has done anything but awkwardly sleep in the bed since I’ve been gone." Because that is exactly what has happened. I stopped weighing myself but am still struggling to be calorie positive. I boiled some eggs tonight and eating one was not bad, a huge concession, I think, to the fact that I’m starving to death. I’m also quite worried about how much you will not love the horrible noises, which I can not stand to hear, which I must make or die. Yup, all night long!

2019-12-16

My wife returns, so I no longer am writing to her to tell her how I am. She can see first hand now and wisely starts sleeping in a different room. (My emails to her now are, ironically, us trying to win the exhausting fight to maintain health insurance. No, not to receive care — that’s a ludicrous idea — but merely continued coverage to avoid a billion dollar liability if something really bad happened involving cars + my bike.)

Email to a friend…

Sorry to be out of touch for a while. I’ve been uncharacteristically very ill. I’m not that good at flu/cold/pneumonia terminology because it does not really ever happen to me, but this last week, holy fuck, it happened to me! I’d like to say I’m recovering, but who the fuck knows? I could still have this in May. Or at my current weight loss pace, I’ll disappear by May. I usually get up and then after hacking and coughing and getting dressed and ready, I’m exhausted and ready to lie down again and rest. The day pretty much repeats like that. A good measure of how useless I am is that I can’t even play video games for very long. Now I kick myself for not learning how to "watch TV" as a modern person. I can’t even do that!

2019-12-18

My son arrives. Less activity in the written record. Most of my energy is spent worrying about finding enough food for him and me to eat. Thankfully, grocery stores and restaurants were open but after making whatever meal preparations were necessary, I was exhausted. He was not feeling completely healthy at this point either. He does know how to "watch TV" like a modern person so we do lots of that.

2019-12-24

This mail to my dad is the first recorded mention of the serious myalgia. First we get an idea of the general situation at this time…

I would not dare eat one [of the beloved holiday foods of my ancestral culture] anyway for many weeks since this pathogen has seriously messed up how things taste for me. I’m still fighting it but the chances of me surviving are much higher now. I can definitely see how a pandemic (e.g. 1918) can kill a zillion people in a hurry. It’s mostly on the run from my respiratory system and now has tried messing up the chemistry of my heavy meat muscles. I had some worry as it crept up my back (almost as painful as a migraine, but you can’t rest) but it mostly went for my legs where I can fight back. Thanks to the bike stand you have lent me, I was able to set up a "Pathogen Heater" and bake any imposter chemistry in my legs. In the last 24 hours it has lamely gone after my tibialis anterior muscles — this causes shin splints, something that while famously painful, is something I’ve been dealing with recreationally for decades. Again, burned some of that off on the bike. Feels great to be able to take the fight to the pathogen. Always an adventure to see what’s next on the hit list. I even had little red pox-like bumps (though not nearly so numerous or serious as, say, chicken pox, which I’ve had) on my chest and back as it messed with my skin chemistry. A tough thing has been the grinding pain making resting difficult and then I couldn’t get the Heater up to full burn because my lungs had been broken. And then it’s just dragged on and on. So many days wasted. So much of me wasted — I lost about 10lbs which I did not have to lose! Hopefully I’m coming out of the wraith world soon. I’m hopeful that my body has been laying good defenses for this kind of nonsense as we’ve made the grand tour through all my important subsystems. I figure if I can keep this shit at bay to every couple of decades (this is the worst I can remember) then it is probably acceptable that each recurrence will probably have half the chance of survival. But this one will not kill me. I will beat it. I believe very soon.

That’s a pretty interesting intuition about how being old produces a nonlinear susceptibility to dying from such an illness!

My dad then captures the essence of this blog post writing,

"That is really weird. Don’t you want to know what it is?"

He suggests I go to some medical service, the thought of which makes me ill for different reasons. And I offer my best guess at the time.

So my diagnosis is "some kind of virus, probably one of the many flu viruses". In theory I could get a "rapid test" (RIDT) but they’re not that accurate. … I picked up some flu virus (probably). I’m a very weird specimen with weird physiology. I am practiced at internal physiology battles. I am strong, especially in respiration (1918 flu strangely was especially harsh to the especially strong, but still, probably not a bad thing). … Now, if the situation radically worsens, say a bacterial infection wracks my lungs and I cough up too much blood, well, then some magic beans may be in order. Maybe some oxygen and other serious intervention. But I’m not to that point. No need to poke that bear with a stick just yet!

2019-12-25

At this point I’m fighting back — my idiosyncratic belief is that there are only ever two ways to cure any and all health problems: 1. rest 2. ride a bicycle. I knew that doing my normal matador routine with cars would quickly be fatal in the state I was in, but there was a solution — I set up a (stationary) bike inside. And so how was that DIY approach working out? Here I describe things on Christmas Day.

I went to bed last night and writhed in pain all night until I couldn’t take it any more. I finally got up at 0500 and did 30m on the bike. Went back to bed and could then sleep fine. Tonight, I’ve got 30m scheduled before bedtime. I just need to marshal enough calories but being able to ride that bike inside has been a huge help.

This is what I was doing to fight the serious muscle pain in my legs. I’m no stranger to serious leg muscle pain but I’ve never felt anything this severe.

2019-12-27

I’m feeling a lot better today. I think I’ve chased the pathogen out. If it’s not completely gone it will be soon. There are still some lingering strange things like I can’t look at close objects because if I position my eyeballs to look at something near, they hurt. That’s so weird, it’s almost funny. And I was sitting here and I realized my shins (those tibialis anterior again!) were freezing cold for no good reason. I now just need to recover from 3 weeks of being in the wraith world. But I survived this one.

2019-12-28

Recovering. Replying to my dad.

→ Glad to hear that the worst may be over. Quite an experience.

Indeed. I used to know in a statistical way that people did die from such things but now I know exactly how that could happen. But not this time!

2019-12-31

I feel better this morning than I have in about 3 weeks. Still that’s not great but encouraging. I was getting nervous about a secondary infection that was going after my ear. I had lost hearing in my left ear. … I feel like I just need to keep aggressively going after calories. If I can regain some strength I’ll be able to kick this mess out of my body for good.

The best I’ve got though is going to [a restaurant with normal American food] where I could relatively easily pick up 2500 calories and burning some pathogens on the bike. I always feel better after such a burn but the weight loss is an unnerving challenge.

It was frustrating that it was winter because my California solution to severe calorie deficit is simply ice cream.

2020-01-01

Feeling well enough to commit historical puns.

Ya, this serious illness thing is completely new to me. After a month of fighting it I think I’m starting to get on top of it. … If modern medical quackery (and agribusiness) continue to tragedy the commons of antibiotics, we’ll be back to [pre 19th century] levels of medical barberism pretty soon.

2020-01-05

However, my illness is finally starting to properly go away. In retrospect, it is more obvious to me now that I had pneumonia. A simple influenza infection shouldn’t last more than a month! That’s why my lungs were so damaged and filled with pink sludge. With lungs at 25% power, breathing is difficult. With that kind of hypoxia, my appetite went away and my brain stopped working as well as it normally does. Pretty much like altitude sickness. I was down around 61kg which is much too light for my frame. I’m now eating everything I can and looking a bit less skeletal. I can breathe properly and my health is coming back.

2020-01-07

My son goes back to SD.

2020-01-09

I lost a lot of weight and am now trying to eat as much as I can. My lungs were pretty beaten up. I either cracked a rib or tore some connective rib tissue from coughing and that’s still not healed. There were a lot of random bizarre problems that were caused by the pathogen or my overactive pathogen defense — things like sore eyeball muscles, couldn’t taste things properly, couldn’t hear in my left ear, etc. The attack systematically went through all my main muscle groups simulating various large athletic exploits (e.g. running a marathon) when I had actually done nothing. For example, one morning I might wake up with shin splints… The next day, it was the muscles in my feet. Etc. But I’m actually pretty good at having those muscles be pushed to the limits. I know how to sort it out. I mostly was trying to stir up my main meat muscles on a bike set up on a trainer inside. But with my lungs very weak it was hard to generate wattage. But it helped. I’m mostly back now. I’m back to work and I’m hoping I’ll be ready to bike to work by next week. I don’t want to push my luck though. It was definitely a surprising brush with non-invincibility.

2020-01-10

I’m still weak in the thermoregulation department. Wearing a puffy jacket (basically outerwear) right now indoors. And it’s not even cold outside!

2020-01-12

I’m pretty much over my illness. It’s pretty obvious in retrospect that it was pneumonia. That’s how you take a normal flu in a very healthy guy and drag that out close to death for over 5 weeks. But I outlived it. Now I’m just beat up and weakened by it. But I’m coming back! I was on the bike (inside) today long enough to actually generate enough wattage to be mostly naked and covered in sweat. That’s a big improvement over having thermoregulation problems and being cold all the time. I still have to be careful with that but reminding my body that generating heat is something I’m good at is a reasonable part of the recovery IMO. My lungs are starting to work at a reasonable level again. It was a pretty huge change to go from my normal high level of oxygen processing to that of a heavy smoker. I could barely climb the stairs! … I also have some rib damage [presumably from all the coughing] that is lingering as rib damage does. Sit ups are still very hard for me. But overall, I’m coming back. My thinking is back to reasonable levels (no oxygen to the brain isn’t the best for mental clarity).

Patent drawing for my new invention

c19test.png

2020-01-16

Here’s a good benchmark for my recovery.

Yesterday I just rode my bike to work for the first time in about 6 weeks (didn’t go in for 5 weeks!). (Last winter I rode pretty much every day.)

If going for a bike ride in the winter does not seem normal, remember that for me it is.

2020-01-17

I’m still very weak on the bike but I have resumed riding to work again. And my rib still hurts when I do sit-ups but I can do sit-ups again. My thinking seems to work as well as ever now too. Making progress.

And that concludes my personal story. It is obviously weird to have had an exact functional replica of the terror-inspiring Virus That Broke The World, but my pretty reliable written record does seem to indicate that’s how it happened.

With personal details about me now safely ignorable here, I am likely to continue commentary about the strangeness of this generally in another post. Which I have now written.

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