Chris X Edwards

Tim Berners-Lee's office thanked me for a pedantic typo correction on Sri Tim's main web page. That'll be the acme of my web dev activities.
2020-09-22 10:03
I guess real JS proficiency is the ability to make excuses for why `getMonth()` starts from 0. Hmm. `m=["Jan","Feb",..."Dec"][D.getMonth()]`
2020-09-15 09:23
Does any .com really want their jingle to be associated with the disgust+rage I feel when it interrupts Beethoven? #youtube #alex_delarge
2020-09-07 07:28
I love how the USmint.gov has a "loyalty program". Yes, I think we're all de facto members at this point.
2020-09-06 12:15
Silicon Valley is like the 1100000000 bytes RAM (ie 1.1GB from about:memory) needed to show me 140 bytes of text. That is how good they are.
2020-09-05 06:59
Blah Blah
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Oscilloscope Madness

2020-08-29 21:09

Sometimes I get a wild idea in my head - actually, I specialize in that. This week’s wild idea was that I need to learn more about oscilloscopes. I’ve been working on my electrical engineering notes and my newly appreciated ignorance about oscilloscopes was irking me.

Looking online for interesting resources that could educate me about the topic, I wondered if electrical engineers ever acquire electronics equipment the most honorable way possible: by making it themselves. I always found that the best machinists had a lot of tooling that they had machined themselves.

That sounded awesome. I had to give it a try and I ordered one. My expectations were reasonable. I figured it had about even chances to (A) be defective or missing a part, (B) fail because of some ineptitude on my part, or (C) actually work. At the very least, I expected that I would get some soldering practice. When it arrived, I set to practicing!

According to the instructions, a completed unit should look like this.

oscope-complete.jpg

However what actually showed up was this.

oscope-parts.jpg

Gulp! Some extreme attention to detail was required to make sure all the values were thoroughly checked and all components sorted. I actually used all of the functions on my multimeter for this project, several for the first time. Just knowing how to test transistors with my meter was worth $22.

Finally, after a lot meticulous work, I was ready to power it up. I did the preliminary assembly power checks and they came out good! Wow! I attached the display and powered it up and it was… iffy. After playing with it, I had seen it boot properly and sort of work and I had also seen it act completely rubbish. Hmm.

Carefully studying every connection, I found some dodgy soldering. I actually did all the resistors and capacitors with my beloved 25 year old gas powered soldering iron. Unfortunately, its tip was so worn that it wasn’t doing a great job. After fixing up some of that with a newer iron I discovered a single lead that I had missed — no solder at all. Oops. I fixed that and when I subsequently booted it, it came up fine and worked flawlessly! It was a euphoric feeling to pull off a correct execution and be so damn lucky.

Ok, cool. I built an oscilloscope. Uh, what now? What do I do with it? After playing around with it I got the very good idea to hook it up to a guitar. I just put the probes on one end of a 1/4" patch cable plug — other end on the guitar. Then I was able to see the sound waves. Amazing! So cool.

oscope-guitar.jpg

In this image you can see I’m holding down the 5th fret (note dot) on the E string which is an A (E - open, F - 1st fret, F# - 2nd, G - 3rd, G# - 4th, A - 5th). That A is actually the A440 pitch standard described in ISO 16:1975 used to standardize all of music to a certain pitch. Obviously if my guitar is in tune, the frequency of the sound wave should be 440. And you can see on the top left that it is reading Freq: 441.707Hz. You can also get a sense for the amount of voltage produced by a guitar pickup. Actually I have an unusual Yamaha SLG Series and I have no idea how its invisible magic pickups work — with nylon strings no less. But we can see that the voltage while this note rings goes between 16mV and -20mV, for (presumably) the Vpp (peak to peak?) of 36mV.

Although this would have been even more fun back when I had enviable eyesight, I’m still absolutely delighted with this project. I have learned a lot about a lot of different topics and have added a very powerful tool to my collection. What a cool little device!

UPDATE 2020-09-20

Having enjoyed that, I looked around for more such fun and found this signal generator kit. For only $12, I got to build this thing.

signal_gen.jpg

As you can see it does a nice job of giving my oscilloscope something to do. I think one of the main use cases for a signal generator (conceptually) is comparing this oscilloscope with a fancier, more accurate (?) one. But for now I’m just content that it generates square waves, sine waves, and the triangle waveform shown.

Real Progress In Autonomous Vehicles

2020-08-14 12:44

Regular readers may notice a decline in posts about autonomous vehicles. Rest assured, I’m bringing to light everything interesting in the field. The problem has been a conspicuous lack of anything interesting. There are only so many times I can say "They’re doing it wrong and will fail." But today some PR hype crossed my path that is actually on the correct trajectory so I wanted to highlight it.

Apparently the company behind this is the same one that recently canceled a giant project reimagining Toronto. They have some access to Alphabet and beaucoup Googlebucks which could be good or bad.

What’s somewhat unnerving to me is that I wonder if any of the people involved in this project understand why it is the correct approach. That sounds like a strange and pretentious thing to say, but note how all the press releases stress the connected aspect of this project; apparently CAVenue, their marketing name, stands for "connected autonomous vehicle". Here is their own press release saying that.

They seem utterly fixated on the wrong thing. They claim they are trying to "develop the world’s most sophisticated roadway" but that can not be true. What they hope to build will ideally be less sophisticated than any random road. No, I don’t care about the V2V distractions and great network coverage so people can adore their phones better. I’m talking about the brains here. Do you think their roads will match the sophistication of the sum total of human minds currently required to function on normal roadways? No. They will most certainly not do that.

But that’s just it. What we need isn’t a more sophisticated road. We need a less sophisticated road. Look at any of the PR shots of this thing. What is really going on that is profound and useful is what I call "idiot driver insulation".

idiotinsulation.png

That is the necessary and sufficient requirement to end human driving completely. We are not waiting on technology. We are waiting to do the simple things necessary to make the real problem not a problem.

I suspect that this move is shrouded in "connectedness" to distract the Silicon Valley people while real progress is made. The connectedness of vehicles is utterly irrelevant. Weather sensors, a perfectly good idea, are not essential. Platooning (as shown in the image) may one day be helpful for many reasons but so might teleportation. No, the real breakthrough here is simply clearing the road of idiot drivers.

If you’re following my logic here, then one question should come up: why not just build a light rail (like the kind my neighbors rightly complain about for the wrong reasons)? It is a good question and I think that the value proposition works today because the physics benefits of commuter rail are not as heavily leveraged as freight rail where steel on steel is important to energy budgeting.

I believe that autonomous cars running on a closed single corrider would still have some advantages. First is better on demand scheduling; with rail the granularity is an entire passenger car. Starting and stopping disadvantages rail but is easier for smaller shuttles and even very small transportation pods. It is also easier to integrate small freight shipments into the closed corridor. For example, how would Amazon send a couple of delivery vans down a light rail corridor? They can’t.

But the huge advantage and why I very much hope this project doesn’t hype-fizzle away is that this arrangement provides the launch pad for mixed mode cars. The reason you can’t sleep (alone) in your moving Tesla (or Cadillac for that matter) is because it is not on one of these roads. There are no other impediments. When people can choose a road where they can stop driving completely, I believe they will.

Sure, 99.999% of all other roads require the dangerous and tedious chore of driving, but if there’s one shining example of how it could be, maybe people will start to think differently about how every road might be organized. I certainly hope this will spark some discussion and thinking about the correct way forward.

If you really want to understand this news you can go back and revisit my 2016 post where I predict this exact development. Indeed, although we have finally managed to claw our way back to exactly where we were in 1997, in the world of autonomous vehicles, that is immense progress. Let us hope we don’t retrogress again.

The Good News, The Bad News, And The Ugly News

2020-08-08 15:50

The bad news is obvious, right? It’s everywhere. Plague! House arrest for everybody! Great Depression or Greatest Depression Ever?! Riots! A president who once savagely beat a puppy to death with a golf club. (Actually, I just made that last one up — but what is worse, that false "fact" or a president who doesn’t mind citing such flagrantly false facts? Feel free to make up your own "facts" about the president — he doesn’t care!)

Enough has been said about the bad news. I want to focus on the good news. Before that can make sense, however, we need to consider the ugly news — the news that makes no sense and is a muddled mess. Unfortunately, that has been literally all news about the details of this pandemic.

It starts with this.

The current coronavirus disease, Covid-19, has been called a once-in-a-century pandemic. But it may also be a once-in-a-century evidence fiasco.

At a time when everyone needs better information, from disease modelers and governments to people quarantined or just social distancing, we lack reliable evidence on how many people have been infected with SARS-CoV-2 or who continue to become infected. Better information is needed to guide decisions and actions of monumental significance and to monitor their impact.

That was back in March. Plenty of time for everybody to start to figure out what sensible data looks like. And yet, it never came! Every day there would be some fatuous headlines like these:

The Johns Hopkins Coronavirus Resource Center interactive map is a complete joke, gormlessly hinting that Germany is twice as dangerous as Indonesia.

jh.png

Another grand example of terrible data is the CDC. Check out their CDC COVID Data Tracker.

cdc.png

The default that comes up is "Total Cases". What is so stupid about this? Imagine a prolific creator of false facts using this "data" to "manage" the pandemic. First of all one can have fewer "total cases" by simply nerfing testing. But a really accomplished false fact artiste would say something like, "COVID-19 cures most natural causes of death! Just look at how the population is thriving under the therapeutic influence of this wonderful virus. Which was my idea by the way." Go on, look at that "data" in the CDC chart and tell me how that claim can be refuted. It can’t.

That’s the ugly news. I feel like I have been watching an endless game of Numberwang.

But I have seen a glimmer of hope! Let’s turn now to the good news.

Back in March, some rando on the internet — who also happens to be a faculty member of the University of Cambridge’s Risk and Evidence Communications unit — wrote a sensible article about How much normal risk does Covid represent? The answer, summarized, was that your risk of dying pretty much doubled.

The way I would explain that is to imagine playing Russian roulette with a six-shooter that had two bullets instead of one. If your gun had 800 chambers (equivalent odds for a normal person in their 30s), going from 1 bullet to 2 wouldn’t be quite so problematic. Note that everybody’s gun gets smaller as they age.

My real point there was that article way back in March was the last example of good data considered sensibly that I have seen during this entire mess — until today.

I feel too financially insecure to afford The Economist, but I do get their email newsletter and sometimes their content is not paywalled. Today they tipped me off to this unusually clear and cogent resource.

Stare at this and soak it in and you’ll understand what is wrong with all other sources.

The first thing to notice is they’ve cut through the bullshit of bullshit testing. The last time I saw such a muddled testing situation was either standardized academic testing or maybe even IQ. Testing sensibly for Covid pathologies and dangers is even worse than normal CYA medical diagnostics. This data from The Economist understands that and moves on to what can be sensibly inferred about the situation.

If we stop and ask ourselves what we care about, number one on the list is not getting killed. So The Economist asks the simple question, are we getting killed more than normal? Don’t worry about why. It could be people dying of asbestosis because masks are hard to acquire for construction work. Doesn’t matter. Step one is to answer the question - is there a problem? And The Economist’s methodology is so simple that it’s actually plausible. They simply look at how many people used to die and how many people are dying now and see how/if that has changed.

That’s so simple, but really it is a relief to me that someone is looking at this in a way that is not deeply flawed to the point of being meaningless. They even have a nice Github repo with all their data and scripts if you’d like to quibble with their methodological details. (For example, I would make minor adjustments based on natural changes of population, but really, not strictly necessary to appreciate these numbers as better than anything we’ve seen thus far.)

It is "good" news in the sense that it is of good quality. It is also good in the sense that it looks pretty good. I am not terrified by this data.

At first I misunderstood the "Absolute" setting on the graphs to mean they were like the fatuous CDC data. But really this data is much more useful. It is not showing absolute deaths - which no one really cares about. It is highlighting the validity of testing statistics. The difference in Covid-19 attributed deaths and real deaths is directly measuring the effectiveness of the testing programs. They are frankly not as abysmal as I thought — though I live in NY where, like NJ, Spain, Holland, Italy, and non-WEIRD nations, it is pretty abysmal.

It’s interesting to note the negative rates after the spike. The article cautions that some of this more recent data may just reflect reporting lag. My intuition is that many victims were probably close to death anyway and there were less people to die in June if they had their exit schedule moved up to May.

neg.png

Reports of a "second wave" seem pretty overblown. Again, could be reporting lag, but this data isn’t terrifying me. It’s looking like people got sick, like they do when something is going around. All the vulnerable and unlucky people got it, and it doesn’t really have much more room to cause trouble. That could be a very wrong guess, but this data, real actual data that is not meaningless, is in no way contradicting that assessment.

I’m actually pretty impressed that a lot of states really are not seeing anything like what New York and New Jersey saw. Look at Wisconsin or Idaho or Missouri.

wiidmo.png

I would actually say that the danger for them is greater. It’s greater because to my thinking they have not had the full force of the pandemic come and hit their vulnerable populations yet.

One could make the case that this shows that protective measures, lockdowns, and hygiene theater are working. I’m not sure if there is enough data for that by, say, comparing Sweden with Switzerland. But this kind of data could tell us exactly what works. It’s not testing as I had previously imagined. Testing is almost as elusive as a vaccine; let’s just rule sensible tests out and focus on real and obvious effects.

What really works is simply tracking deaths promptly and accurately like any 21st century society should be doing anyway. With sensibly tracked deaths, accurate studies to gauge the efficacy of various measures are actually plausible, even using "natural" experiments with different sides of the state line doing different things. It would be really helpful to see these plots with the same plots superimposed from other flu seasons and outbreaks.

As one of the early adopters of Covid-19 I can tell you that if you get it, it’s no picnic. (I am feeling a bit better than last month, thanks.) But this data is not only good in the sense of not being stupid; it’s good because it doesn’t show an impending apocalypse. It’s exactly data like this that we need.

UPDATE 2020-08-10

A perceptive reader sent me this NYT article from late May: Putting The Risk Of Covid-19 In Perspective. It tries to focus on the comparative risk side of things. That would be valuable and correct if there was sufficient data to support such aspirations. Note what this article uses for data.

Using data from the [CDC], New York City experienced approximately 24,000 excess deaths from March 15 to May 9, when the pandemic was peaking. … …using the C.D.C. data, Michigan had approximately 6,200 excess deaths during this same time period.

Note he’s not comparing those directly but using excess deaths — the only metric we really have right now — to go on to put the risks into perspective. Excess deaths is finally some data that makes sense.

Virus Update And Cure Strategies

2020-07-13 11:40

Although bad haircuts are a widespread side effect of the current pandemic, it is not hard to recognize this guy even with a mask on.

boris.jpg

That of course is a guy who is famous for three things (besides his hair). The third is being prime minister of the UK and the second is being a famous Brexit wanker. But his most famous fame is being one of the most notorious victims of COVID-19. Whatever your feelings about him, I think we can all agree that Boris Johnson was hospitalized in mid-April because of a severe case of COVID-19. So here’s what I want to know.

Why is he wearing a mask now?

Besides privacy/anonymity, masks can have two functional objectives. The first one, the normal and obvious one, is to keep bad stuff away from you, like when you’re sanding fiberglass. Interestingly, in pandemic times, this is not why masks are encouraged. For airborne disease control the idea of masks is a second objective, keeping the wearer from expelling and spreading infectious particles.

Are we worried that The Right Honourable Mr Johnson is a threat to our health? Are we worried that he will spread some infectious agent that will inflame the pandemic? Do we think that two months after suffering the most unambiguous case of COVID-19 possible that he is still an infectious threat?

Or, is Mr. Johnson looking to the first function of protective masks and trying to keep himself from getting infected again with C19? Either way, I would suggest that if this strategic thinking is valid, we are into some serious zombie apocalypse scenario.

Of course I bring this famous case up to highlight one of the most obscure cases of COVID-19 — mine. It turns out that I’m not too fond of wearing masks even when sanding fiberglass (though I do my best to do so). But having to wear a mask in the limited public outings I’ve had in the last 4 months has been especially tiresome. Why? Because it impedes breathing. Not a problem for a high volume athletic oxygen furnace like me, right? Not so much these days.

I’m still cycling about 100km a week but I can feel the damage. I had mentioned reduced circulation in my shins but that was really just the most noticeable problem. I’ve done a lot of work to strengthen my shins and they feel ok today but still not full strength. But as in December there has been a wave of problems targeting many different subsystems, just much more mild. Right now my thighs are covered in bruises, both left and right — I have no idea why. Last week I had unnatural leg muscle pain for no explainable reason. When I wake up in the morning my arms tingle with paresthesia (aka limbs "falling asleep"). I also have an ear infection, just like I did at the end of my illness previously, but other ear now; the second ear infection of my life. And my breathing is not at full strength. I can become winded just climbing the stairs. When riding I can feel the loss of capacity. I’ve been saying that it feels like I’m living at 2000m or 3000m, depending on the day — about the altitude of HAPE, a mountaineering sickness, which has some very similar symptoms to C19. It’s all pretty tiring.

Is this weakness half a year later scarring of some kind? Nerve damage? Vasculature damage? Immune system weakened? More live C19 virus attack? Reinfection? Hard to say.

My current guess about COVID-19, from personal experience, is most closely aligned with the thinking in this article which is well worth a read: Coronavirus May Be a Blood Vessel Disease, Which Explains Everything. I think that kind of idea is sinking in finally and I’m now seeing others pursue this possibility: It’s not just the lungs: The Covid-19 virus attacks like no other respiratory infection.

That’s my current situation — there are indeed long term effects. What can we do about it? Probably nothing for me personally, but for humans in general there are many different strategic approaches to defeating this disease. Let’s review my tiny opinions about each of them.

The first is a vaccine. To which I say good fucking luck. You can have no more than two of the following: developed soon; works; safe. This sensible article from a former CDC epidemiologist calls out all kinds of problems with the hope for a magic cure any time soon. It highlights a phenomenon known as antibody-dependent enhancement which

…causes some vaccine recipients, who nevertheless become infected by exposure to a pathogen, paradoxically to have more severe illness than if they had not been vaccinated at all. ADE has been observed for coronavirus vaccines in monkeys, pigs, cats, and in cultured human cells. It was also observed in children after a trial of a respiratory syncytial virus vaccine and after a mass campaign of a licensed dengue virus vaccine given to 830,000 children in the Philippines, resulting in withdrawal of the vaccine."

I just can’t help but think that the vaccine hope is a form of wishful thinking similar to "pharma is not predatory and these magic beans will magically cure my lifetime of poor lifestyle choices".

At this point C19 is a real pain in the ass, but so is HIV and ebola (actually now has a brand new vaccine after only 44 years!) and a lot of other diseases; why not come up with cures for them too? Because it is very hard to do and considerable luck is required.

What about "contact tracing"? Good idea, right? I side with Bruce Schneier who says correctly it is "just plain dumb". And he’s not even introducing any privacy concerns to the discussion. I like this barb at gormless Silicon Valley tech bros for their typical banality when solving any problem (Ans: a telephone app?). "To me, it’s just techies doing techie things because they don’t know what else to do." Australia’s experience is what I would expect: How did the Covidsafe app go from being vital to almost irrelevant?

What’s sad to me is that contact tracing is close to the right answer. This pandemic is not really a medical problem any more. It is an industrial engineering problem. Unfortunately the world’s industrial engineers are restrained in obscurity thanks to a terrible name for their profession. It has been extremely frustrating to see the terrible ad hoc industrial engineering popping up everywhere in response to The Virus. Suffering the virus itself was only slightly more demoralizing than the constant stream of fatuous reports featuring numbers of new cases lacking base rates! But a sensible application of some serious industrial engineering could cure this pandemic in a few weeks. Because very few people understand this, it will not happen. (I am delighted with the I.E. consolation prize — that this virus forced major grocery store chains to use single feeder lines. Yay! Should have done that decades ago!)

One problem that severely impacts the aforementioned industrial engineering cure is testing. Testing, if quick, accurate, and effective enough would itself essentially be a cure without fancy industrial engineering heroics. But it’s neither fast nor accurate, and thus not effective. People keep asking me, "Don’t you want to know if you have it?" Well, my symptoms were enough of a red flag positive test for me, but of course I’d love for some simplistic magic test to tell me something useful about this disease. But I have no faith in such things. I’ve seen all kinds of health security theater going on and these tests seem fraught with complexity. This resource is very expansive and hints at the diverse problems someone taking "testing" seriously will encounter. Tack onto that living in the medical third world and I’m not too keen to try my luck — you only need to read the title of this article to appreciate my misgivings: Two Friends in Texas Were Tested for Coronavirus. One Bill Was $199. The Other? $6,408.

Earlier some people were thinking that the warmer weather would tamp down the virus. That’s obviously not actually happening. People are out more, the dumb ones at political rallies even. Even if hot weather was helpful, it’s looking pretty strongly like air conditioning is not great for controlling the virus. When the AC industry lobby is worried about that we probably all should be.

How will this pandemic end? Consider the difference between these two scenarios: A. The disease is running amok and no one realizes there’s a problem. B. People are aware there is a virulent disease that is quite deadly to a certain demographic. It is possible that all the reduction we’re seeing is because we once had A and now we have B. I think that has been the single biggest factor in controlling things. My money is still on luck mysteriously causing this to simply go away for reasons that medical research will be too underfunded to understand. Like previous pandemics! At some point we will run out of susceptible potential victims.

One final interesting therapeutic approach is transfusions of antibody-rich blood plasma from COVID-19 survivors to inoculate against the disease. This article claims it is promising but mired in regulatory friction. I can’t say if that’s a sensible idea or not. But it does make me wonder… Who knows, maybe it might be smart for uninfected people to inhale deeply in the unmasked presence of strong antiviral producers like Boris Johnson. And me.

UPDATE 2020-07-19

In summary, progress since January 2020 has been impressive, but there is still so much more to learn. Are T cells protective and if so which are the key antigens and and cytokine effector programs to focus on? Are all T cell responses beneficial, or are some contributory to immunopathology and to be avoided? If it is indeed the case that antibodies are transient and T cell memory is more durable (though, how durable?), what can we learn about anomalies of T follicular helper-B cell interactions in germinal centers? In the short to medium term, we need to ensure that all of this T cell toolkit and knowledge is brought to bear on robust, comparative evaluation of the different vaccine platforms, their immunogenicity, efficacy and safety. Entering the next part of the battle, there are many thousands of people suffering the chronic aftermath of infection posed by chronic, so-called long-COVID cases, characterized by diverse symptoms including fatigue, joint pain and dyspnea. A more detailed understanding of the T cell immunology will be valuable in deciphering this pathogenesis.

At the start of the pandemic, a key mantra was that we needed the game-changer of antibody data to understand who had been infected and how many were protected. As we have learnt more about this challenging infection, it’s time to admit that we really need the T cell data too.

I’m citing this paper as a thoughtful excellent contribution to the topic. It is basically saying that simplistic thinking about the immune system is wrong. And I believe that sentiment is absolutely correct. But note the "and and" [sic] in the second sentence. My writing isn’t grammatical perfection but I’m not published in fancy scientific journals, i.e. peer reviewed and professionally edited. I don’t mean to carp but rather point out that we humans are fallible and even in the field of immunology, mistakes are made. Perhaps especially in that field? My point is that if we get a miracle cure it will indeed be a miracle.

UPDATE 2020-07-19

Some industrial engineering heroics finally shambling into action. It’s been very painful for me to watch this not happen for so long. Trump admin allows group Covid-19 testing.

UPDATE 2020-07-28

This short article asks, Can you get the coronavirus twice? They seem to conclude that it is possible but unlikely. They correctly make the logical conclusions echoing my concerns about the topic.

If [reinfection] can occur, that could undermine the idea of "immunity passports" for returning back to workplaces. And it would not bode well for hopes of getting a long-lasting vaccine.

Again, to summarize - either I have nothing to worry about personally or we’re all screwed.

UPDATE 2020-08-03

Still unclear about what an industrial engineering solution looks like? Here’s an example of the kind of thing that seems obvious to me but which has been clumsily avoided throughout this ordeal.

We construct network measures of nursing home connectedness and estimate that nursing homes have, on average, connections with 15 other facilities. Controlling for demographic and other factors, a home’s staff-network connections and its centrality within the greater network strongly predict COVID-19 cases.

UPDATE 2020-08-06

The ever excellent Ed Yong writes another superb piece.

This is about as gentle of an introduction to practical immunology as it gets and clearly addresses things I’ve been wondering about. In one sentence he hits upon the conundrum I’ve highlighted.

…concerns that people could be infected repeatedly, or even that a vaccine — many of which work by readying neutralizing antibodies — won’t provide long-term protection.

In other words, either people can’t get reinfected (well, easily anyway) or vaccines are not as useful as people imagine — one of the two, pick one. While that simple analysis is simple and not completely invalid, Yong does rightly spend the majority of the article correctly emphasizing that when it comes to immunology, it’s complicated.

UPDATE 2020-08-19

"Researchers have yet to find unambiguous evidence that coronavirus reinfections are occurring…"

My hypothesis here is that this disease affects people for a longer time than usual and can look like multiple infections as a result.

"This calls for some optimism about herd immunity, and potentially a vaccine."

It also makes me optimistic about personally avoiding the mystery preservatives found in vaccines. Of course the article did not even think to mention the fate of the zillions of people who have recovered — can we carry on with life now? Feel free to ask me to help deliver groceries to vulnerable populations. Etc. But no. That will go uncontemplated.

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.

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