As reminders…

Alpha–Variant first identified in the UK

Beta–Variant first identified in South Africa

Gamma–Variant first identified in Brazil

Delta–Variant first identified in India

Omicron–Variant first identified in South Africa

Updating the chart above:

Ancestral: B.1.1.529 Omicron (and cousins)

Transmissibility: All the +

Immune Evasiveness: All the +

Vaccine Effectiveness: Check (for hospitalization)

Also as a reminder:

Monkeypox

Only significant update is that apparently the WHO is considering renaming “monkeypox” to avoid “stigmatization”, similar to the push to rename COVID variants not by country of first identification up above, but with greek letters.

Because apparently the world is full of kindergartners who will stand around on the playground and accuse someone who picked up monkeypox as being a monkey, because they got monkeypox, and then making monkey noises at them? I dunno. Apparently enough of a thing for a name change though?

Coronavirus

–Shanghai and Beijing are pausing reopening activities and ordering more mass testing as new COVID cases are being detected. Despite that, China published official economic data totally not goalseeked like usual that showed that the two month lockdown of Shanghai was barely an economic blip, so they could all high five about “owning the Free World” yet again with their genius, super wise, and obviously way better approach to the entire COVID pandemic.

I know, I know… human rights of the Uyghurs to continue to abuse, sanctions on Russia to circumvent, threats of military violence against their own citizens in Taiwan… it’s a busy time for the CCP.

Elsewhere around the horn, BA.4 and BA.5, the latest round of omicron cousins, have left the Southern hemisphere and are circulating widely in Europe. Portugal, for example, is seeing hospitalizations track up via sheer force of numbers. In the US, BA.4 and BA.5 are here and growing, pushing out the dying embers of the previous two omicron cousins. These two appear to be a little more capable of lung infection, and thus might possibly be more severe on case by case basis, but that was not the South African experience (where this wave has already come and gone), and presumably will not hold true elsewhere either. They do get through vaccines, so highly contagious, high breakthrough possibility, and we can absolutely expect the current “omicron-like” wave to continue through July as BA.4 and BA.5 keep the BA.2+ trends rolling.

Again anecdotally, extremely high correlation of recent travel (for vacation or business) to COVID positives that filtered back to me.

–There remains a slight chance that with BA.4 and BA.5 arriving “early” (these were South Africa’s fall/winter strains), absent another late winter wave from the Southern Hemisphere, virus activity may be muted this winter. One can hope, right?

–The CDC director has lifted testing requirements for international travelers returning to the US. Unsurprisingly, the airlines reported double digit spikes in searches for international travel routes.

–Slight trend in “scare” articles to shift from “COVID WAVE AND HOSPTIAL DOOM AND DEATH!” (because there just isn’t that much to write about in the data, even with the official cases that are undercounting positives) to emphasize long COVID symptoms.

As a reminder, respiratory and cardiovascular symptoms can linger after ANY severe respiratory infection, as we covered here, and despite being presented as somehow unique to COVID are not. They are just getting more attention, and it’s easy to blame for COVID for all of them now.

Also as a reminder, a giant study in France we covered here found that you were more likely to have “long COVID” symptoms if you knew you were infected, and the rate of them drops precipitously for those who had antibodies proving infection, but did not know they had caught COVID. Now, the caveats still remain that if they did not know they were infected, it might have been a more mild case, and thus less likely to result in long COVID symptoms -and- some of the post-COVID associations we can measure with labs that we have been finding are probably true. We had one endocrinologist mention their first referral for a new onsite Type 1 diabetes case after COVID, for example, and there is enough smoke to believe there is an increased risk of new onset diabetes with COVID, especially if it was bad enough to put you in the hospital. Hair loss also seems to be rare, but a thing too, and generally recovers.

So anyways, the new “scare article” tactic is to still be concerned for COVID enough to cower transfixed in fear before your news media of choice so they can sell all that sweet sweet attention to advertisers because prices on everything are rising for them too, because if you catch it, you too might get long COVID. At any time! It’s lurking around the corner, one cold/flu like spell away from months of malaise that may never get better! And COVID doesn’t get you, monkeypox is there with a knife.

Again, the most credible long COVID symptoms are correlated to severity of disease, especially if you were hospitalized or awfully close to it. As the virus gets more symptomatic, less contagious, it seems less probable for COVID to go long term. The rate of some of these versus peak transmission of various virus strains would be an interesting epidemiology study for somebody. Also, although there are no studies on it (yet), an interesting hypothesis is that if you do get early treatment with one of the plethora of effective early treatment options, you will reduce your chances of long COVID, as many of the symptoms appear auto-immune in nature (from the immune system going Ah-nold when it cannot clear the virus fast enough).

Regardless, I am not particularly worried that continued waves of ever more contagious (but less severe) COVID will give us all diabeetus by sheer force of inevitability of long COVID in everyone. You can still be reasonable in your risk approach to COVID.

–And you can finally test your T-cells! That’s right–there was a big breakthrough this week in a way to measure T-cell activation in response to COVID antigens. Ordinarily, that takes isolating and measuring growth of T-cells in a petri dish. No longer! This assay basically takes some of your blood, exposes the T-cells in it to SARS-CoV-2 antigens, and then looks to see if they release a chemical that T-cells do when they are getting revved up to wreck them some virus.

This means it can be tested quickly and at scale, although I suspect they will need to kit this assay up a bit for widespread adoption.

The authors hope (and I agree) that a combination of T-cell activation measurement and antibody titers can be used to better inform (read: “bring some science based sanity to”) the need for, and timing of, any future COVID booster shots.

Yet, this is still a world cranked to maximum stupid, so hope seems like a prelude to more crushing disappointment.

Still, hope springs.

–The NBER released another study this week on the impact and effectiveness of lockdown policies. Their conclusion was that in the US, lockdowns probably contributed to 170,000 excess deaths. In general, excess deaths trended higher for countries with more stringent and longer lockdowns. Sweden, for example, looks relatively unscathed. This is another example of picking studies that agree with your preferred narrative though. There is simply too much variation, particularly at the local level within countries, for lockdown severity, enforcement, and demographics, and far too many confounding variables for this study to be remotely conclusive. I’m not even sure it’s that suggestive. If your preferred news media was not a fan of lockdowns as a pandemic response, you probably saw headlines about this study. Since it agreed with your news media’s editorial board/owners, it was genius. If your preferred news media was generally in favor of lockdowns when they happened, this is likely the first you are hearing of this study.

–In other questions with no answers, the WHO suggested that the “lab leak hypothesis” needs further study. China’s response was predictably hostile. Again, is it possible SARS-CoV-2 was a natural mutation within a lab doing a lot of coronavirus work, including some gain of function work (as we now know), that got loose? Yes. Could it be one of the gain of function test viruses that got loose? Also, possible.

Provable? Not in our lifetime. Not with these politics. And not without access to the lab notebooks of those working in that laboratory. And if the lab leak hypothesis were true, what do you think the odds are that those lab notebooks still exist in the original, unmodified form (to hide the leak)–or at all? No one will be seeing them for a looooong time, regardless of truth or fiction of the “lab leak” theory. Of that much, I am sure.

Socioeconomic

—Reuters reports that depositors at a bank in China that many felt was ripping them off had a planned protest disrupted when their state issued and mandated COVID app was set to “red.” For all of them. At once. Even though they did not have COVID, or a positive test for COVID. Because you have to have a “green” pass to be legally out, enter restaurants, banks etc. and use public transportation in China, this change effectively shut down the protest.

I’m no lawyer, but that’s what they call “predictable abuse” of a mandated “health pass” for full participatory citizenship. Instead of its health purpose, if the wrong people get in charge, its authority can be usurped to “unperson” undesired political behavior.

The right people have not been in charge in China for some time now.

–If that kind of predictable abuse sounds vaguely familiar, Canada just did similar with banking freezes for protesting truckers, extending a tool designed to counter money laundering and international crime/terrorism to political protest.

–Otherwise, well, you can continue to see the same headlines I do regarding the world economy and inflation in all the things we need (energy and food). Thus far, these issues have proven resistant to international leaders, who increasingly look reactionary and behind the curve, if not in outright panic. There are growing concerns about significant food shortages to come later this year around the world.

In the US, reports on farmer sentiment show a precipitous drop in expectations of farm financial performance this year, mostly centered on concerns about price of seed, diesel and fertilizer. You can read it here. The headline is a little scare-tactic though. Sentiment has indeed fallen from last year, but only back to 2019 and 2020 lows during shutdown periods, and back to the 2016 average. That said, the velocity suggests the drop may not be done. How that impacts yields is hard to say, but the divergence of farmer sentiment around their land values bears mentioning. Even the report calls out the unusually rosy expectations of farmers about the short term value of their land; however, when they asked follow up questions, that is based mostly on inflation and non-farm investment interest (like the warehouses that have completely replaced several huge farmers about 20 minutes south of me). The long term expectations for farmers about their farms and land value has been on a steady decline since late last year, as inflation was beginning to bite, probably due to concerns over input costs.

These are the money quotes though if you are worried about US yields and world food supplies. Wheat has been particularly pressured, since, as we mentioned, the world’s fourth and first leading wheat producers (and exporters to much of the Middle East in particular) are still shooting at each other:

“Approximately 39% of the respondents to this month’s survey said they have used a wheat/double-crop soybean crop rotation at some time in the past. Twenty-eight percent of the producers who have experience with a wheat/double-crop soybean rotation said they plan to increase the percentage of their farms’ cropland devoted to this rotation by planting more wheat in fall 2022. The shift towards increasing wheat acreage is likely the result of the expected profitability improvement of the wheat/double-crop soybean rotation.

One of the policy proposals discussed by the Biden administration is a $10/acre double-crop soybean crop insurance subsidy to make this crop rotation more attractive to producers. This month’s survey asked respondents if the subsidy would encourage them to plant more wheat in fall 2022 than would otherwise be the case. Among producers who have employed a wheat/double-crop soybean rotation in the past, just over one in five (22%) said it would encourage them to plant more wheat. Among producers who have not followed a wheat/double-crop soybean rotation in the past, just one out of ten producers said the insurance subsidy would encourage them to plant more wheat this fall.”

–It won’t matter much for this year, but here’s a good article on Morocco’s fertilizer industry answering the bell, and viewing Russia’s loss as its potential market share gain. This is particularly important for fertilizer availability in Africa, where fertilizer use is essential in many areas to get anywhere close to necessary yields.

–A couple good think pieces this week.

First, a Google employee was suspended this week after raising concerns internally that an AI program they developed had become sentient. The AI in question is a natural language “chat bot” which could converse by text with humans, and appears to have been trained by access to Google’s wide array of linked written material. Google, to its credit, has an internal ethics board and people employed specifically to test for sentient, generalizable AI, and this program was monitored to make sure it did not run off the rails quite as spectacularly as this one when encountering real humans deliberately trying to corrupt it.

The Google engineer published transcripts of chats he had (as part of his job to look for signs of this in these programs), and you can read them here and decide for yourselves.

I agree with the blurb at the end that criteria for determining sentience are “pre-theoretic.” As I read that transcript, all I could help thinking is how hard it is to know, or prove that, especially just by chatting with an AI. For example, they ask it about “Les Mis” (the book), which it has “read” (because it has access to it via Google’s vast trove of data). They ask about its themes, which themes it enjoyed, and why. Now, I can absolutely see how an AI chatbot that could access not only the book, but critical review of the book, trained properly by machine learning could “fake it” by correctly responding with themes taken from papers written about “Les Mis.” And then combining those with written articles about how others feel about those themes. The AI is also designed to present a “persona” to the user, and in doing so, has to make choices about its “values” and “themes”, which again, it can learn from a list and train to associate the words without really knowing or feeling their meaning, but presenting them like they do from examples of humans who did use the words for their meaning and feeling the emotions described and wrote them down.

I almost think you have to do your own version of jabberwocky? Make up nonsense words that humans will ascribe mood or feeling or sense to, but will not be in an available database for the AI to have trained on. If it is really thinking, and sentient, and is feeling language, it should be able to do the same. But is that really the only criteria for sentience? Does knowing how and why, and then offer an explanation for “‘Twas brillig, and the slithy toves did gyre and gimble in the wabe?” the only thing that makes us sentient?

That is likely why Google suspended this employee; their committee felt that these chats did not prove sentience. The employee disagreed, went public with these internal transcripts, got suspended. Again, an interesting, if creepy-ish read. If nothing else, that chatbot is well past the Turing test, at least for its intended chat function.

–Second think piece is this one, which was written last year (apparently), but I was only put onto recently. Sadly, there has not been a “Part 2” yet. Regardless, I found it difficult to do more than quibble at the margins–even when he criticizes medicine. The nutrition portion he raises is certainly true. I know one of the OG reader physicians on this list and I have discussed how much more emphasis there should be on lifestyle and how to effectively get ourselves and our patients making healthier choices more routinely. Most of the highest risk conditions for COVID, aside from age, are heavily influenced by lifestyle, ranging from obesity to heart disease to Type 2 diabetes. One of the great lost opportunities of the pandemic was to spur greater and consistent lifestyle changes in the general population. I have also spent much of this week starting the write up on a couple of scientific papers. The introduction is always my least favorite to write, because the expectation is to cite like crazy. I will find some useful conclusion or detail in some published scientific paper or other which turns out to be a citation of yet another paper, and because I like to give the original research credit, I’ll chase the original down–sometimes that takes 2-3 citation leaps.

Only to find the original research didn’t really show what later citations claimed. Usually it’s by degree, with later citations being MUCH more confident about the conclusion or detail than the authors of the original work. But I bet this happens about 1 in every 8 to 10 citations I chase.

So I get the point that it doesn’t take long to find the gaps in knowledge, or assumptions and assertions that have far more uncertainty to them than even experts in a field suspect.

The hallowing out of peer review is also a concern, and the author of the linked piece above is not the first to suggest it may be unnecessary in the internet era, when new papers can be published and critically reviewed in real time in the comments section below it.

Outside perspective can often be more creative–often, another field entirely has found a solution. It’s also critical to avoid serious mistakes. Lockdown policy, for example, I think relied far too heavily on epidemiologist and specialist medical advice–experts who did not have expertise in the economy disruption it would cause, and the socioeconomic and political fall out of that. I hope the future will learn from that.

Meanwhile, there is an entire book in praise of the return of the generalist. But I may just be biased by graduating a small liberal arts college for my undergrad… ;

–Finally, China announced this week that their big eye radio telescope detected signals that may be communication from extra-terrestrials.

Now, close your eyes for a second, and imagine that is true. The aliens are real, and have finally reached out. And just like in all the movies, the first they have said is “Take me to your leader.”

With your eyes still closed, take a brief survey of the world since, oh, early 2020. A world lurching from crisis to crisis. A world where faith in its present, let alone its future, is put to the test. A crisis in confidence in ourselves. A burgeoning mistrust of anything we are told. An explosion of schismogenesis, seeking to divide us just when we must all pull together to meet even our basic needs, like food and shelter and heat. A bonfire of institutional credibilities, where we are left asking, in all seriousness and with disquietingly little disagreement that we might be accidentally living in a Dark Age. A world that truly captures the poetic metaphor intended by the author of these words:

“the sun will be darkened

and the moon will not give its light,

and the stars will be falling from the sky,

and the powers in heavens will be shaken.”

For truly, all the constants of our world, as constant as the north star, as constant as the phases of the moon, as constant as the rising of the sun (or so those institutions have seemed) are shaken.

That is a world in which there is an opportunity for true, authentic leadership to arrive. Self-sacrificing. Humble. The best of us. Those whom you would want to offer to the aliens as humanity’s best possible first impression.

Still got your eyes closed?

Who, among all the current leaders of the world during this period, would -you- want meeting the aliens? Who would you take them to, and not have a single worry, for this is a leader that can be trusted to wisely handle humanity’s first contact with alien civilizations? Who is that person who has proven they can rise to the challenge?

You get one choice–so who ya’ got?

Your chances of catching coronavirus this week are equivalent to the chances that your answer to the “who” questions leaves you very…. unsettled…

<Paladin>