Post #1477: COVID-19 non-trend to 4/4/2022. BA.2 dud. No flu. Inopportune 2nd COVID booster.

 

The U.S. remains at 9 new COVID-19 cases per 100K per day, unchanged from a week ago.  The different regions of the U.S. diverge, with continued new-case increases on the East Coast offset by declines in the South Central and Pacific regions.

That said, even though the U.S. curve hasn’t turned upwards, this is starting to look like every other inflection point on the curve.  As the individual regions go their own separate ways, the “strands” that form the graph appear to be unraveling.  Historically, that’s been a strong signal that the U.S. curve is likely to make a change in direction.

Continue reading Post #1477: COVID-19 non-trend to 4/4/2022. BA.2 dud. No flu. Inopportune 2nd COVID booster.

Post G22-009, the second-biggest waste of time in the U.S.A.

Traditional, unconditional, last-frost date

I had planted a few cold-hardy vegetables in my garden weeks prior to last weekend’s deep freeze.  I put in some snow peas, potatoes, beets, garlic, onions. 

It got down below 20F briefly on one of those nights.  I can now say that all of those appear to have survived, with just a bit of TLC.   That was in the form of capping the bed with radiant barrier, then adding a piece of plastic for air-tightness.  (See Post G21-018, or my just-prior garden posts.)

It’s no surprise that we had a freeze.  Our nominal “last frost date” is somewhere around April 22,so these plants were in the ground almost two months ahead of that.  Instead, the interesting thing is that I had two weeks’ warning that the freeze would occur.  The fourteen-day forecast accurately predicted that there would be a freeze that weekend, although the original forecasts understated the depth of that freeze.

This leads me to ponder the implications of reasonably-accurate long range weather forecasting and our “last-frost” dates.  Folklore guidelines (“plant peas on St. Patrick’s Day”) and science-based “last frost date” guidelines predate the era of supercomputers that make long-range forecasting possible.   Weather is still chaotic in the mathematical sense, and so not predictable at very long intervals, but we now have two-weeks-ahead temperature forecasts that are reasonably accurate.

I already rang the changes on this once, in post G21-005, Your 70th percentile last frost date is actually your 90th percentile last frost date.  What you typically see cited as your “last frost date” is the date on which, historically, frost only occurred after that date around 30 percent of the time.  But that’s an unconditional probability, as if you would plant on that date regardless.  If, by contrast, you check your 14-day forecast on that date, and refrain from planting if frost is in the forecast, then you’ll convert that to a 90th percentile last-frost date.  That conditional probability — chance of frost after that date, conditional on a frost-free 14-day forecast — gives you a much higher chance of avoiding a freeze after that date.

The upshot is that a reasonable prediction of the two weeks following the “last frost date” shifts the odds attached to that date considerably.  It’s actually a lot safer to plant frost-sensitive plants on that date, in the modern world, than it was in the era when no forecasts extended more than three days.  As long as you make that decision conditional on the extended forecast, and you’re smart enough not to plant if it looks like frost any time in the next two weeks.

At present, we’re creeping up on 14 days prior to our April 22 “last frost date”. And I’m pondering — just as an exercise in probability and statistics — whether that same math works 14 days in advance of the date. 

And I’m pretty sure it does.  If the 14-day forecast were completely accurate, then the conditional 70th percentile last frost date in this area would be April 9th.  No frost in the forecast through April 22 would mean that the conditional odds of frost occurring after April 9 would be the same as the unconditional odds after April 22.

That is, April 9 is our conditional 70th percentile last frost date.  If we have a decidedly frost-free 14 day forecast at that point, planting on that date bears the same risk of frost damage as planting blindly on April 22.

The only uncertainty there is in how accurate the 14-day forecast actually is, for daily low temperature.

Weather forecasts seem to be one of the few true ephemera of the digital age.  They are published, and then they are replaced with the next day’s forecast.  Nobody cares about yesterday’s forecast, other than those who have some deep professional interest in forecast accuracy.  Accordingly, where you can look up the actual weather 14 days ago, I haven’t yet located a database that lets me look up the actual weather forecast 14 days ago.

So that’s going to have to remain an unknown, for the time being, unless I want to try to compile the data, for my location, day-by-day, myself.  Or if I can find existing research that addresses this exact question of predicting a frost.  So I’ll just have to leave that as saying that if the 14-day forecast shows lows that are well above freezing, then you can probably move your traditional (unconditional) 70th percentile last-frost date up by two weeks.


But is this just the second-biggest waste of time in the U.S.?

The second-biggest waste of time in the U.S.A. is doing something really well that doesn’t need to be done at all.  (I heard that in a time-use seminar I attended decades ago.)

In the fall, frost protection has some clear advantages.   The plants are already grown, the produce is already ripening.  Protection from an unexpected early frost is a matter of saving garden produce that would otherwise be lost.

But as I hustle about protecting my plants in the spring, it invites the obvious question:  Just how much am I gaining by planting these crops early? And to that, I will add not just planting early, but the whole process of starting seeds indoors, regardless of the planting date.

In reality, is this really just an example of the second-biggest waste of time in the U.S.?

Ultimately, while some plants may grow in the cold, they tend to grow slowly.  At some level, that’s just basic chemistry.  The rate at which a typical chemical reaction proceeds roughly doubles with every 10 degrees C of temperature increase.  Sure, plants will develop enzymes to speed those processes in colder temperatures.  But it doesn’t take a genius to notice that while they will grow, they sure won’t grow very fast.

What prompts this is my peas, which are now all of about 2″ high.  And it’s getting on close to a month after they went into the ground.  Is  that head start worth it, compared to simply waiting for the nominal last-frost date and planting them then?

In short, I’m beginning to suspect that my current setup — plant early, provide frost protection, but no greenhouse — might just be the least efficient of all possible worlds.  All the hassle of early planting, and (almost) none of the benefit.

Without a greenhouse structure (or poly tunnel, or similar) to warm the daytime air and soil temperatures, it seems like most of what I’ve done is to induce my plants to try to grow under inhospitable conditions.  And they are responding accordingly.

Back when I was a low-effort gardener, I seldom mucked around with any type of early planting.  I’d start seeds a couple of weeks before I planted them, just to be able to have a tiny visible plant to stick in the ground.  (And so, have better chance of survival for (say) tomato plants.)  But my opinion then was that the gains from very early planting were minimal.  Give it a couple of weeks, and the (e.g.) peas planted later in the year will have effectively caught up with those planted earlier.

As a result, I’m now wondering whether I’ve been taking all this early-planting advice from people who do early planting and have some type of greenhouse arrangement on top of those early plantings.  From what I’m observing so far, that would make a lot more sense than just sticking plants in the ground and protecting them from freezing as needed.

When I briefly Google for this topic, all I see is people touting the benefits of early planting.  In effect, a series of statements that you’ll get more out of your garden if you do it.  I’m not seeing any quantification of just how much more you get, from early planting alone (i.e., with frost protection but not a greenhouse or poly tunnel).

So, before I get any further caught up in this effort to see just how much I can push that last-frost date, and just how well I can protect those tender plants from frost, it seems like I need to assess the cost/benefit tradeoff.

I’ve proven that I can plant well in advance of that last-frost date.  I can do that very well, thank you.  But should I do that?  I don’t think I’ve really answered that question.  And, in particular, should I do that without some sort of setup to warm the daytime air and soil temperatures?

Maybe early planting without a greenhouse really is just the gardening equivalent of the second-biggest waste of time in the U.S.A.  Clearly, that needs to be the next thing I test.  For that, I need some sort of cheap, safe, low-effort greenhouse or poly tunnel.  One that minimizes the chances that I’m going to bake my plants to death.

So that’s the next thing on the agenda.  Replant what’s in my garden, one month after the original planting date. And work up a greenhouse covering that, as a lazy gardener, I can live with.

Post #1476, COVID-19, ditto. Plus, news of a wonder drug out of Australia.

 

Roughly 9 /100K/ day, roughly unchanged.  Rapid new case growth on the East Coast, rapid new case decline on the West Coast and South Central regions.

Data source for this and other graphs of new case counts:  Calculated from The New York Times. (2021). Coronavirus (Covid-19) Data in the United States. Retrieved 4/2/2022, from https://github.com/nytimes/covid-19-data.”  The NY Times U.S. tracking page may be found at https://www.nytimes.com/interactive/2020/us/coronavirus-us-cases.html

Australia is seeing a second Omicron wave, similar to that in the U.K.  Their current new case rate is about 20 times the rate in the U.S., and is still currently rising.

Source:  Johns Hopkins data via Google search

Because this is Australia’s first big COVID wave, we have no hard data on the likely seasonality (or lack thereof) of COVID in Australia.  The U.S. has seasonality on its side, as we head into summer, they are heading into winter.  But it’s not as if winters are terribly cold.  (e.g., typical August highs in Sydney are around 65F.)

Australia has had little bumps in their hospitalization rate for COVID-19 prior to this, but no huge run-ups in the new-case numbers.  And, for whatever reason, their case hospitalization rate is tiny compared to that of the U.S.   Currently, they have more than twice as many new cases per day, but the U.S. has more than five times as many people in the hospital with COVID.  The implication is that the Australia case-hospitalization rate for COVID-19 is about one-tenth that of the U.S.

In any case, on March 1 Australia added Merck’s oral anti-viral Molnupiravir to their formulary,  for high-risk individuals.  What caught my eye is that the most recent test of that showed that 100% of a sample of 92 infected persons appeared COVID-free after three days of treatment, compared to 78% of those given a placebo.  (Per this news reporting.)

The only reason to bring it up is the optics of that 100% figure.  It’s rare to see any treatment show up as 100% effective, in any mid-sized trial, of anything.  So that appears to be getting significant press in Australia of late, given their ongoing COVID-19 surge.

That said, while this one study seemed to show that this drug wiped out COVID-19, other studies have shown that it is less effective at preventing hospitalization than other approved anti-virals in the U.S. (reference).

So, YMMV.

FWIW, that’s one of three anti-virals currently approved or given an emergency use authorization by the U.S. FDA for use with COVID-19.  (Reference).  We seemed to have approved it for emergency use just prior to the Australians.

All of these antivirals have some fairly significant side-effects.  As a rule, sure, they muck around with viral DNA or RNA replication.  And they do the same for human DNA or RNA.  For example, this one isn’t approved for anyone under 18 because it affects bone and cartilage growth.

And yet, the trick with all of those is that you have to start the drug early.  In this case, the guideline is to start within five days of symptom onset.  So you have to make a judgement call regarding the likely severity of your COVID versus the likely severity of the side-effects of these COVID treatments.

I have not yet stumbled across data on how many U.S. COVID patients have been treated with these anti-virals.

 

 

 

Post #1474: COVID-19 non-trend to 3/30/2022

 

If you guessed that the U.S. has an average of about 9 new COVID-19 cases per 100K per day, AND that this is more-or-less unchanged from a week ago, then you’re today’s big winner.

Data source for this and other graphs of new case counts:  Calculated from The New York Times. (2021). Coronavirus (Covid-19) Data in the United States. Retrieved 3/31/2022, from https://github.com/nytimes/covid-19-data.”  The NY Times U.S. tracking page 3may be found at https://www.nytimes.com/interactive/2020/us/coronavirus-us-cases.html


Maybe our response shouldn’t be binary

The U.K. seems to have made a secondary peak now.   Note that their current rate is almost 20x the U.S. new case rate.  It’s not that Omicron hit them particularly harder than it hit the U.S.   Our peak rate was almost 250 new cases per 100K per day.  It’s that it never really went away there.  And now it’s back, as son-of-Omicron (BA.2).

Source:  Johns Hopkins data via Google search

And yet, the U.K.’s response to COVID-19 — and our response to COVID-19 — seems to be an either-or, yes-no approach.  Either yes, we’re in the middle of a pandemic, and precautions should be taken.  Or no, we’re over it, go back to exactly what you were doing before this all happened.  (Which is pretty much where the U.K is right now.)

And maybe that’s not the brightest approach.  Maybe some modest permanent changes might be more efficient.  Because maybe, just maybe, what we’re looking at for the forseeable future is a permanent change in the “disease environment”, for want of a better term.

Today’s Guardian has an insightful article about this.  Really, it’s about what “endemic” is supposed to mean. As opposed to what they are actually experiencing in Great Britain.

I think it’s well worth the five minute read.  Because, as I’ve said here before, I can’t quite get my mind around just how, exactly, Omicron/son-of-Omicrion is supposed to be come “endemic”, in the sense that the common cold is endemic.  And that article explains that quite clearly.

Omicron/son-of-Omicron is ridiculously easy to spread, compared to other endemic diseases.  The R-nought for BA.2 is estimated to be somewhere around 22, versus a typical value of 1.75 or so for seasonal flu.  But immunity seems to fade rapidly, re-infections are now common, and the existing vaccines are mediocre, at best, at preventing any new infection.  So, just like the flu, just because you had it last year doesn’t mean you can’t get it again this year.  Flu shot or no flu shot.

When scientists use the term endemic, they mean something that a) is present in the population, and b) doesn’t flare up into huge outbreaks.  We also think of it as implying something relatively mild, but the Guardian points out that (e.g.) tuberculosis and malaria are endemic in much of the world, and those most certainly kill a lot of people.

Well, take a look at Great Britain.  Official policy now treats BA.2/son-of-Omicrion as if it’s endemic, but it currently meets none of the criteria.  The U.K. hospital system is once again under strain from the volume of admissions for COVID.

So if I had one takeaway from the Guardian article, it’s that maybe we’re just not quite getting our minds straight about this.  Everybody wants to return to the pre-COVID world.  But that world no longer exists.

Right now, seasonality is in our favor.  BA.2 or not, this is the time of year when conditions favor a reduction in spread of most or all airborne viral diseases.  It’s the end of flu season.  All other things equal, it ought to be the end of COVID season.

If we manage to get through BA.2, and into the summer, are we really just going to declare victory and pretend that this is all behind us, and nothing has changed?  Yeah, probably, I’d guess we’re going to try to do that.

But I can’t quite get my mind around what a nice, politely-behaved endemic Omicron is supposed to look like.  As the Guaradian points out, that’s probably a myth.  It certainly looks like a myth for Great Britain, right now.

Basing policy on myth is generally not a good idea.  But what set of rationally-thought-through permanent changes are we planning to implement?  Sure looks like none, to me.  E.g., at what new-case level would a Federal mask mandate on public transportation be re-instated (assuming it’s ever lifted)?  Nobody can even ask that question without getting slapped down.

Which means that, in effect, we’re hoping there will never be another outbreak.  Which really means that, with each new outbreak, we’ll just be winging it again.

Right now, COVID-19 presents less risk of hospitalization and death, for a vaccinated and boostered individual, than seasonal flu does.  So, right now, nobody needs to think about the most ration response in the event of another outbreak.  Which means that right now would be the right time to have some rational discussion about some forward-looking public health policy in this area.

Next time, maybe it would be better if our public health show was more scripted, and less improv.

Post #1473: COVID-19 non-trend to 3/29/2022

 

The U.S. still stands at 9 new COVID-19 cases per 100K population per day, roughly unchanged over the past seven days. That’s not due to a uniformly unchanging situation across the country, but to offsetting effects.  Rapid new-case increases in the Northeast are being offset by equally rapid continuing declines in the Mountain and Pacific regions.

Continue reading Post #1473: COVID-19 non-trend to 3/29/2022

Post G22-008: Plastic cloche surprise, not all plastics are created equal.

 

Background

In my last experiment, I showed how well a Ball (mason) jar worked as frost protection.  In the coldest part of the night, the inside of the jar stayed 10 degrees F warmer than the outside.  I thought that was exceptional performance for a lightweight uninsulated glass container.  My explanation is that the glass traps long-wave infrared.  And so, this works for the same reason that my radiant-barrier frost protection works.  It prevents the garden bed from radiating heat energy off into space.

Long-wave infrared absorption would explain why glass worked well but polyethylene sheet was a near-total failure.  A sheet of ordinary window glass will absorb about 86% of long-wave infrared, and reflect the rest.  Polyethylene, by contrast, was reported to be almost completely transparent to infrared.

Accordingly, where a glass jar works well as a garden cloche, I figured that a plastic jar would not.  And that’s what I tested last night.


Never let facts get in the way of a good argument.

There’s just one problem:  Different plastics have different infrared absorption spectra.  And it took me a while to track that down.

Using Wein’s Law, the spectrum of radiation emitted by my 50 F garden subsoil would peak somewhere around:

  • 10 microns (micrometers) wavelength
  • 10,000 nanometers wavelength
  • 1000 waves per centimeter.

Those are three ways of saying the exact same thing.

So I wanted to find out how different plastics behaved with respect to long-wave radiation somewhere in that vicinity.  That’s where most of the power from the upwelling long-wave radiation from the garden bed will be concentrated.

I never did find exactly the data that I wanted.  But I came close.  And, as it turns out, polyethylene’s absolute transparency in that region of the spectrum is the exception among plastics, not the rule.

The chart below show the absorbance spectra of various common plastics, with the long-wave infrared region highlighted.   Note that the line for polyethylene is almost completely flat in that region.  It absorbs almost no long-wave infrared.   But PETE plastic, just below that, in fact absorbs infrared strongly right at the frequency where infrared from the soil will have its peak — wave number of 1000.

Source:  Figure 9, “Identification of black microplastics using long-wavelength infrared hyperspectral imaging with imaging-type two-dimensional Fourier spectroscopy“, Kosuke Nogo, Kou Ikejima, Wei Qi, et al., DOI: 10.1039/D0AY01738H (Paper) Anal. Methods, 2021, 13, 647-659

The upshot is that when I condemned all plastic for this use, I was too hasty.  Avoid polyethylene, for sure.  But, assuming the glass choche works as I have described it, PETE plastic ought to work reasonably well.  Not as well as glass, but certainly not as poorly as polyethylene.

As an odd little footnote, Mylar plastic — the kind used to make space blankets — is the same stuff as PET/PETE plastic — polyethylene terephthalate.


Results

Below is a photo of a quart Ball jar (right) and the thick-walled PETE jar that I’m going to test.  That was as close as I could get to the same size and shape as the Ball jar.  FWIW, the PETE jar originally held salad dressing.  You can see that it’s much thicker than (e.g.) a typical disposable water bottle or soda bottle.

 

When I tested that last night — two temperature loggers on a raised garden bed, one covered with the PETE bottle, one un-covered — sure enough, PETE works pretty well.  But not as well as glass.

At the very coldest part of the night, the PETE jar provided between 4 and 6 degrees F of protection, or about half the maximum protection observed for the glass jar.

The lesson here is that when I condemned all plastics for use in frost protection, I was too hasty.  Polyethylene sheet is a terrible choice, from the standpoint of trapping long-wave infrared.  But PETE’s OK.  Not quite as good as glass, but pretty close.

 

Post #1472: William and Mary COVID-19 trend to 3/28/2022

Source:  Data from William and Mary COVID dashboard, Virginia data from Virginia Department of Health file of case counts by age group.

W&M just announced a mask-optional policy for the Williamsburg campus.  It may be worthwhile to continue to track the weekly update, even though nothing much is happening now.

As you can see above, there was a slight uptick in cases for both the William and Mary campus and for the 18-24 age group in Virginia as a whole.

 

Post #1471: COVID-19 trend to 3/28/2022. Still scraping along the bottom

 

The U.S still stands at about 9 new COVID-19 cases per 100K population per day, unchanged from seven days ago.

Take that with a grain of salt, as an increasing number of states seem to be reporting their new case data at more-or-less random intervals.

Data source for this and other graphs of new case counts:  Calculated from The New York Times. (2021). Coronavirus (Covid-19) Data in the United States. Retrieved 3/29/2022, from https://github.com/nytimes/covid-19-data.”  The NY Times U.S. tracking page 3may be found at https://www.nytimes.com/interactive/2020/us/coronavirus-us-cases.html

Separately, the more-infectious son-of-Omicron strain (BA.2) is now the dominant strain in the U.S.  Which is great news, given that this has occured and we still aren’t seeing a European-style uptick in cases.Per the U.S. CDC’s COVID data tracker, BA.2 accounted for about 55% of new cases, for the week ending 3/26/2022.

If there’s any link between BA.2 and the regional patterns of increase and decrease shown on the chart above, it’s not obvious at a glance.

Source: CDC COVID data tracker

Cases are rising rapidly in the Northeast, which has a high proportion of BA.2.  Cases are falling rapidly in the Pacific region, which also has a high proportion of BA.2.  Whatever the impact of BA.2 is in the U.S., it doesn’t appear to be a prime driver of new case growth so far.

 

Post G22-007: The math of the mason jar cloche (corrected!).

 

Edit 11/10/2023:  On re-reading this, I think it’s wrong.  The estimate for the energy radiating into the opening of the mason jar seems right, but the analysis  fails to account for the energy radiating out of the opening of the jar.  The net radiant energy input is much smaller than what I calculate below. 

So now, the excellent performance of the mason-jar cloche is a bit of a mystery. 

Sure, it works in practice.   But does it work in theory?

My prior gardening post demonstrated that a standard Ball jar (mason jar) provides excellent frost protection, if used in a garden bed with relatively warm soil below the surface.

Now, let’s use a physics law, an insulating R-value, and a bit of math, and show that this works in theory. Continue reading Post G22-007: The math of the mason jar cloche (corrected!).