Hacking America, History of Information, History of Africa, William Shakespeare

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At this moment, there is a batch of very interesting and generally acclaimed books for sale really cheap in Kindle form in the US, that I suspect readers of this blog will be interested in.

A Year in the Life of William Shakespeare: 1599 by James Shapiro. Good reviews, but this is outside my area of expertise so I can’t say for sure, but it looks good.

Creek Mary’s Blood: A Novel by “Burry my Heart at Wounded Knee” author Dee Brown.

Africa: A History is an anthology that includes some older material, but all good. This is totally within my area of expertise, and I can say this book is full of classic writing by classic scholars. Not a light read. Edited by Alvin Josephy.

The Information: A History, a Theory, a Flood by James Gleick.

The Plot to Hack America: How Putin’s Cyberspies and WikiLeaks Tried to Steal the 2016 Election by Malcom Nance.

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No, Michael Moore did not make a documentary called “Planet of the Humans”

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That was some other guy. The recently released documentary “Planet of the Humas” was written by Jeff Gibbs and Directed by Jeff Gibbs. See?

No mention of Michael Moore there. This is a Jeff Gibbs documentary.

Michael Moore does have a lot to do with this production, though. He is the executive producer, and he seems to be promoting it. But it is not his baby. It is Jeff Gibbs’ baby. We don’t know how much Moore was involved, or if he’s even seen it. (Well, he’s probably seen it, but did he only see it after it was done?)

Why is this important? For a rather sad pair of reasons. Here they are:

1) Trusted, sincere, carefully done analysis from several different individuals shows us that Planet of the Humans is not a good documentary at all. It borders on dishonest (if not charging across that border several times) and while here and there in the film there is surely an important message or two, the messages are supported with information that is mostly bogus, biased, some kind of balderdash.

2) Many people love and respect Michael Moore and his work, and a large number of individuals have, in my experience, decided that since this is a Michael Moore joint, it must be fabulous, and it must be true.

So, I say this to you, Michael Moore fan: This documentary sucks, but it is OK that it sucks. This is a documentary by Jeff Gibbs, not by Michael Moore. So, it is OK to pay attention to the many voices of critique. Indeed, as my friend Adam Siegel asked me earlier today: “Who is the real victim here? Is Michael Moore a victim of his friend Gibbs’ poor work? Does he know how bad this is? Poor man,” or words to that effect.

Speaking of Siegel, he is the one on-line expert who has gone all meta over Moore. He has assembled a series of posts, the most recent (on top of the list below) being the most comprehensive but all are worth a look, that put together the panoply of critiques of Planet of the Humans. Go read:

Moore’s Boorish Planet of The Humans: An Annotated Collection

Planet Of The Humans: Moore Trouble Than It’s Worth

Distributor pulls Michael Moore’s (@MMFlint’s) #PlanetOfTheHumans due to truthiness & errors

For #EarthDay, Michael Moore (@MMFlint) releases fundamentally misleading film

Sometimes less is more. In this case, Moore is less.

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Piecing Together Human Anatomy In The Time of Covid-19

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Resorting to jigsaw puzzles?

Like science?

Then you are in luck! Try the new Dr. Livingston’s Anatomy Jigsaw Puzzles, based on art created by Mesa Schumacher, a Certified Medical Illustrator from Johns Hopkins University.

Dr. Livingston’s Human Anatomy Jigsaw Puzzles come in three volumes so far, a head, a thorax, and an abdomen. The maximum dimensions of each puzzle would make this a 1000 piecer for sure, but since they are not rectangles they run closer to 500-600 pieces. They are also not terribly hard. Some of the puzzle perimeters have a double edge: the actual edge of the puzzle, and the edge of the illustration (ie., skull) running close and in parallel, so that 12% or so of the puzzle practically does itself. Also, you can’t really be a good anatomical drawing and ahve the kind of vagueness that a harder puzzle tends to have. But that’s OK because you will want to do all of them in a short time anyway.

I believe there are plans to make a total of seven puzzles, but at the moment there are only the three mentioned above available.

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Do read “People of the Book”

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And I mention this now because it is dirt cheap on Kindle.

People of the Book: A Novel, by Geraldine Brooks, is one of my favorite books. The focal character is a book restorer, brought in to examine and work with a book that has an incredible recent, and ancient, history. Inspired in part by a real event, this book takes the reader through history and across Europe and North Africa. So cheap on Kindle you would be crazy to not get it.

Speaking of this author, Geraldine Brooks also has another book, Year of Wonders: A Novel of the Plague, about a 17th century village on pandemic lock-down. I haven’t read it, but I thought for some reason it might be worht noting.

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A Coronavirus (Covid-19) Vaccine

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There are no current vaccines for any coronavirus. I’m not comfortable explaining why that is the case, but I’m usually told that the actual killer coronaviruses (there are not many, most viruses of this kind are not big problems for humans) came and went too fast to “need” a vaccine.

This is not really true, since at least one such virus is endemic to a region, a continuous threat, but found mostly in domestic camels. There was a vaccine developed to address that virus, but testing was never completed, and deployment never happened, so we don’t know if it was really effective.

The question of “can there be a vaccine” and “do we develop an immunity to this virus” are related, and we still see the occasional panicked revelation that maybe humans don’t actually develop an immunity to this virus. Don’t worry, we do. If we didn’t the situation would look very different than it does now.

However, we don’t know everything we need to know about that immunity. We know that for this kind of virus, it is possible that a partial immunity develops in most but not all people, and that some people have a much stronger immune response than others. It is quite possible that we develop an immunity that lasts only a few years (for most people), and it is also possible that repeated exposures and/or vaccinations will build up a longer term immunity. These are all important questions, but they do not raise the possibility that we can’t be or won’t be immune to SARS-CoV-2 (the virus that causes Covid-19). Rather, they frame the issue of how a vaccine is actually deployed. We may see a world, in two years from now, where a Covid-stick is an annual event, but one that people take more seriously than they currently take the annual flu shot, and quite possibly, one that works better (SARS-CoV-2 and influenza are very different things).

There are several vaccines in development. In my experience tracking disease and epidemiology (I’m an immunologists or an epidemiologists, but both my wife and I play these roles in the classroom and she is actually a fellow in an immunology program for teachers), the assertion that “we’re close to a vaccine” is one of the Great Lies, which are “the check is in the mail” and two other ones.

But, there is hope, and it might be real hope, that there will be a vaccine, and there is even the possibility that it will take less time than the several years. It may even take less than the oft-cited but pretty much made up “18 month” time span.

A few takes current, add to comments your newer information if you have some:

April 14: Microneedle coronavirus vaccine triggers immune response in mice

Researchers led by Drs. Louis Falo, Jr. and Andrea Gambotto from the University of Pittsburgh have been working to develop vaccines for other coronaviruses… They adapted the system they had been developing to produce a candidate MERS vaccine to rapidly produce an experimental vaccine using the SARS-CoV-2 spike protein.

…a method for delivering their MERS vaccine into mice using a microneedle patch. Such patches resemble a piece of Velcro, with hundreds of tiny microneedles made of sugar. The needles prick just into the skin and quickly dissolve, releasing the vaccine. Since the immune system is highly active in the skin, delivering vaccines this way may produce a more rapid and robust immune response than standard injections under the skin.

When delivered by microneedle patch to mice, three different experimental MERS vaccines induced the production of antibodies against the virus. These responses were stronger than the responses generated by regular injection of one of the vaccines along with a powerful immune stimulant (an adjuvant). Antibody levels continued to increase over time in mice vaccinated by microneedle patch—up to 55 weeks, when the experiments ended….

April 14th: Johnson and Johnson claim a vaccine is imminent

Johnson & Johnson (JNJ) said on Tuesday it plans to begin imminent production of its trial COVID-19 vaccine on an “at risk” basis, as the coronavirus pandemic infects nearly 2 million people around the world.

Manufacturing “at risk” allows the world’s third largest pharmaceutical company to produce a product before its ultimate design is finalized and released to the public. The company plans to produce its COVID-19 vaccine in the Netherlands, and a facility it is updating in the United States.

“We’re manufacturing at risk to ensure that should the clinical development and the trials be successful, we are in a position to kind of flip the switch and ready to go, to create great access across the globe,” J&J CFO Joe Wolk told Yahoo Finance in an interview.

J&J began developing its vaccine for COVID-19 in early January with its European subsidiary Janssen Vaccines & Prevention B.V. It’s using the same biological platform Janssen uses in developmental vaccines for Ebola, Zika and Influenza.

During J&J’s first quarter earnings call, Chief Scientific Officer Paul Stoffels said the company is also negotiating with partners in Europe and Asia to produce the vaccine, and partnerships will be announced in the coming weeks.

“Our goal is to enable the supply of more than 1 billion doses of the vaccine globally,” Stoffels said.

April 14th: Two Pharmaceutical Giants Collaborating To Develop One. GlaxoSmithKline and Sanofi are joining up …

” in an unprecedented collaboration. It brings together two of the world’s biggest vaccine companies with proven pandemic technologies and significant scale, all with the aim of developing an adjuvanted COVID-19 vaccine.”

An adjuvanted vaccine is one that includes a compound known as an adjuvant that enhances someone’s immune response to a vaccine. In the partnership, GSK will be providing the adjuvant and Sanofi will provide the specific protein component of the coronavirus that will generate the appropriate antibody response.

“… we’re planning to start trials in the next few months,” Walmsley said. “And if we’re successful, subject to regulatory considerations, we aim to complete the development required to make the vaccine available in the second half of 2021.”

There is an earlier reported vaccine in development at Johns Hopkins.

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Enormous footprints found on cave ceiling

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This is not something you see every day. Footprints measuring up to 1.25 meters in length, were found on the ceiling of a cave in a karstic cave in southern France, on the Causse Méjean plateau. It is suspected that they were left by a kind of Titanosaur. Artists reconstruction of a Titanosaur walking on the ceiling is to the right.

This prints date to the Bathonian age (ca. 168–166 Ma), which is near the middle of the Jurassic. Some of the tracks, found in three different trackways, are very detailed. And yes, it is possible (and not terribly uncommon) to erect a new species on the basis of footprints. In this case, the new species is Occitanopodus gandi, igen. et isp. nov.

The environment at the time is reconstructed to have been a lake, near the shore. I’ve only read the summaries, so I’m not sure of the exact context and orientation, but limestones from the middle Jurassic in Southern France are sometimes very tilted, so I suppose this could be an upside down (or at least, tilted over 90 degrees) layer. The find is some 500 meters below the surface, which counts as deep in a cave.

Moreau, Jean-David et al. 2020.
Middle Jurassic tracks of sauropod dinosaurs in a deep karst cave in France. Journal of Vertebrate Paleontology. Article: e1728286 | Received 29 Oct 2018, Accepted 13 Dec 2019, Published online: 25 Mar 2020.

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How to best use Zoom, Hangouts, Meet, Skype, and so on

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This is not a complete guide to how to use Zoom or similar face to face on line conferencing software. Rather, this is a list of pointers, many of which you would not get from the software’s manual (were there a manual). As far as I can tell, most people don’t know many of the things I cover here, but these are things that will make you a better Zoomer, Skyper, Meeter, Hangouter, or whateverer.

Give permission so you don’t need forgiveness later

When you start a meeting, you are often asked to give permission for the software to use your video and your audio. Some people get annoyed at this, but you need to know that this is feature, not a bug. You really do not want to grant permanent permission to any entity to have access to your video and audio.

Now that I think about it, you should probably be covering your camera with a Post-It Note between uses. But don’t forget to remove it when it is time to use it.

Massive muting avoids mutiny

The single biggest problem with multi-person on line conferencing is that people have no idea what sorts of noises they are making, and transmitting sometimes way too efficiently, over the microphone. Gentle tapping on the keyboard becomes pounding like the proverbial feet of the Russian Army. Moving something around on your desk can sound like the Concord take off. That one last time. And, most annoyingly, consider the times you turn your attention to the person in your room — your spouse, your kid, even your pet — and have a lengthy conversation with them about how you are out of toilet paper, or whether or not that last cookie is yours, or whatever. The entire group can hear you, mainly you, they stop, and they listen, and they wait and figuratively tap their feet. Because you forgot about the meeting and so you forgot to mute your mic.

A partial solution to this is to always have your mute on, until you need to speak (for more guidance see below). But then, remember to turn your mute back on when you do want to speak. Else, you’ll be yammering on and on and others will be interrupting you and acting like you are not even there and totally ignoring you! Then by the time you realize your mic was off the whole time, the conversation has moved on to the next inane thing. A YouTube video of that happening could be funny, though.

If you are running a meeting, pre-mute everyone, and remind them about their mic and what kinds of noises they make, unknowingly. Then, when someone joins the meeting late, take a moment to remind them as well (but see below for more information on that). Also, make sure to tell them how to unmute themselves. I had a recent meeting where one of the participants, a Zoom first timer, sent me an email asking to be unmuted near the end so he could add his two cents.

Consider getting an external microphone and using headphones. A good set of earbuds with a microphone, or if you like the DJ look, must go all the way and get a set of YouTuber headphones. Generally speaking, using headphones or earbuds will reduce the potential for feedback and other bad noises.*

You’re not going to like the way you look

I have a collection of screenshots of people Zooming that is totally hysterical but that I can’t show you our I’d lose friends and relatives. Just how many nose hairs does Aunt Betty have? I didn’t realize that Emanuel’s forehead was so interesting, but good thing it is because that is all I can see of him. My colleague Jane in Indiana is a demigod, I can tell because of the huge halo surround her body. Or is that just the giant window with the sun blaring through it in front of which she is sitting? I had no idea Ahmed’s face was so freaking big!

Lighting should be shining on you from your front, not from behind you. You want your camera positioned at your eye level or slightly above, pointing at your face, not some other thing in the room. Not just the top of your head. You don’t want the camera shooting up towards you with your head bent down looking at it. Just do that and look at yourself. See the quadruple chin? That is because your head has sunk into your neck because your laptop is on your lap, your screen pointing up at a steep angle so your built-in camera can get your face, but you are looking down your nose (nice nose hairs, by the way). Just stop that.

Sit in a chair. Have your laptop on a desk or table in front of you, probably on a book or two so that the camera is eye to eye with you. Make sure there is a gap between the top of your head and the top of the visible image of you in the software, and make sure your shoulders are visible, at least. Make sure the background is dark, foreground is light, and that what can be seen in the background is not something you don’t want people to see. Or maybe it is something funny or apropos, just not something that ruins either the image or your reputation.

Take a shower, comb your hear, wear a clean shirt. And, just in case you have to stand up for a moment, wear pants. Please.

Consider getting a separate free-standing camera (a web cam) that can be placed somewhere other than on the front of your laptop. You want a small tripod perhaps like this or similar. I suggest a Logitech Webcam, but DON’T BUY IT NOW. With everyone using Zoom all at once, webcams are the new toilet paper. They are sold out, but you can get a $50 one for $300 if you want. Just wait on that, but later consider it.

What did you say, Private? It wasn’t private!

In Zoom, and this may be true in other software, there is a chat function that includes a “private” chat that is person to person. The point of this feature is to allow you to have a side-bar conversation with someone else and not distract the larger group. The point of this feature is NOT to have an actual private chat. It turns out anyone can see this private chat of yours, and this is a feature, not a bug. If anyone clicks on “save” in the chat box, both the “To everyone” conversation and the private conversations are now saved, and visible in that saved document. This is great for keeping meeting minutes. Or, blackmailing your friends and co-workers.

You shouldn’t be saying anything privately that you can’t say publicly anyway, but especially using the Zoom “private” chat.

Be like a Boyscout, but in a good way

Before using any meeting software, be prepared. Have a pre-meeting, and try to get everyone to join in. Maybe two meetings. And don’t expect your first meeting to go well, or to give everyone a fair chance to participate.

I have an analogy. For the longest time, only a few people knew how to drive, or ever wanted or needed to drive. Then, one day, everybody had to drive, so everybody got a car and a learners permit more or less on the same day. Chaos. There are some of us who have been using on line conferencing software on a regular basis, for years. To the rest of you: Welcome to our world!

Get a wing-person, or be a wing-person

For larger, or more complex, or more important meetings I recommend a two-leader approach. One person (in your organization this can be the secretary or communications committee chief, perhaps, whoever takes minutes) initiates the Zoom meeting (meaning, does the invites, sets it up, and acts as “host”). A second person chairs the meeting. The host is in charge of making sure that participants’ names are showing (if someone calls in, that has to be fixed by replacing their phone number with their name), and that everyone is muted, and that people are reminded to unmute and remute. The host force-mutes or throws off the meeting any participate who, probably through no fault of their own, is disrupting the meeting. Yes, folks, if suddenly you are talking to your spouse about the day’s plans and can’t manage to mute yourself, you should be bounced off the meeting, get an email from the host telling you why and welcoming you back.

There is another thing I think the people running the meeting can do, but I’ve not done this, so I can’t advise in detail. In Zoom there is a lobby, or waiting room that you can force people to wait in before being allowed into the meeting. It is very common for people to show up at a meeting late. They should be forced to wait in the meeting room until they have been given the guidelines and norms for the meeting. Otherwise you’ll have 80% of the participants doing everything right, and a too-large number (which is 1 or more) of participants talking to their dog and writing their thesis on a loud keyboard as they pretend to be in the meeting. Or sending scurrilous private notes to others. Or whatever.

Norms and Guidelines

By now this should be obvious, but in case not: At the beginning of each meeting, take a minute to go over a few norms and guidelines. Like, how to get permission to speak, if that is necessary, the muting rules, etc. Ideally, a five or six bullet point text file can be on hand and transmitted along with the meeting invite, and then also put on the chat box. But you will have to tell people that the chat box exists and how to get it. And, much of this can be done in the waiting room.

I hope this helps you, and I hope you add in the comments your own tips and tricks.

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Narnia, Lincoln and Tevis super cheap

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The chronicles of Narnia, to be read in whatever order you feel is correct (but there is really only One True Order), are now for a short time available for $1.99 each in Kindle form. This probably only applies to US buyers, but I don’t know that for a fact.

The Lion, the Witch and the Wardrobe (Chronicles of Narnia Book 2 BUT REALLY BOOK 1)

The Magician’s Nephew (Chronicles of Narnia Book 1 BUT REALLY BOOK 2)

The Horse and His Boy (Chronicles of Narnia Book 3)

Prince Caspian: The Return to Narnia (Chronicles of Narnia Book 4)

The Voyage of the Dawn Treader (Chronicles of Narnia Book 5)

The Silver Chair (Chronicles of Narnia Book 6)

In addition to this, a very special and engaging biography of LBJ: Lyndon Johnson and the American Dream

And this, which I’ve not read, but thought you might like to know is cheap:

The Man Who Fell to Earth

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How To Think About Immunity to COVID-19

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This is what immunity is not: You are an organism walking down the street, and you are immune to the rare virus squirrelpox. A squirrelpox virus is walking on the same sidewalk towards you. It sees you, and goes, “that one’s immune to me,” and quickly crosses the street, going nowhere near you. Beause you are immune.

This is what immunity often is: You have built up an immunity to a common cold virus. Somebody infected with that virus sneezes on you and now that virus is in you. It begins to reproduce and do its thing, and you develop cold symptoms. However, your adaptive immune system has seen this virus before, so it quickly mounts a defense, so even though you do get a cold, you fight it off quickly and in five days you feel fine.

Lots of times, though, immunity works like this: You have an immunity to a certain disease. Perhaps you had that disease earlier in your life and your adaptive immune system developed a strategy to attack this pathogen next time it comes around. Perhaps you got a vaccine that prompted your adaptive immune system to develop a strategy to attack this pathogen next time it comes around. The virus goes in you — the virus does in fact infect you, it does not “cross the street” to avoid you. But your body is so ready for it that the counter attack is fast and effective, and before you can either develop symptoms or start passing the disease on to someone else, your body’s immune system has literally killed it.

An acquired or induced immunity can be called “100%” and it can be “life long” but it is never able to actually keep the disease out, and it is likely that few, if any, adaptive immune system build-ups last for the entire life of a person who lives a long time. Some immunity does not stop you from getting sick but does cause you to get better faster, and some immunity doesn’t last that long.

Much of the misunderstanding about immunity comes from the fact that our understanding of immunity comes from two distinct diseases: Polio and influenza. Polio vaccine is famous because its invention and deployment was historic and significant. Polio vaccine confers a strong immunity, one that is seen as life long and complete. Even this is not so simple, but if you believe what I just said about polio vaccination and immunity you would be in the ballpark. Influenza immunity is often discussed because it is at the center of the anti-vax debate, everyone gets the flu now and then (or so it seems) and the so-called “flu vaccine” is supposedly only “60% effective” or thereabouts, and thus, being imperfect, is the focus of rage on the internet as though it was a candidate for office.

If polio is an outlaw gunslinger in the old west, and the polio vaccine is Marshal Dillon, then influenza is all the underground crime organizations imagined in fiction and the flu vaccine is a competent but underfunded police agency.

When we say that the influenza vaccine is 50% effective in a give year in the US, as an example, what that can mean is that there are five kinds of flu circulating at various proportions in the population, and there are three kinds of vaccine in the shot you get; maybe two of those vaccines are nearly 100% effective in immunizing a person against two of the circulating influenza viruses, one of the viruses is untouched by the vaccine but doesn’t get you that sick, and one of the vaccines is for a virus that never really showed up, and the leftover viruses are the ones doing most of the damage. Or something along those lines. The outcome is, across the population, that the average vaccinated person in the population under consideration would have their chance of getting the flu if exposed is half what it would have been were they not vaccinated. So, 50% effective that year. Some other year these parameters may be very different, and the “vaccine” (a mix of different vaccines in one shot) is different. And, each vaccine may itself have a higher or lower level of effectiveness.

And that is the simple version of the story.

Immunity is not a folk concept. It is a medical concept. The fact that many people believe that immunity is the inability of a disease to affect a person, which is 100% wrong in every way, is not relevant to anything but people’s misunderstanding of the concept.

When we hear that there is a certain possible reinfection rate of COVID-19 in China or Japan, this does not mean that people don’t get immunity once they have the disease, or that COVID-19 has special powers. One health expert misstated that since we don’t know for sure what acquired immunity to COVID-19 looks like, we can’t assume that it is long term. That is balderdash. It is very likely long term (if “long” is years) because that is what normally happens. This statement is like looking at the first new car off the line of a new make and model and saying, “since we’ve never actually seen one of the drive, we have to assume there is a good chance none of these cars will work.” There may be a few recalls in the future of this make and model car, but it will work.

We can assume normalcy, we can assume biology to do what biology does. Bill O’Reilly does not know how tides work, but someone else does. Normally, adaptive immunity occurs, and lasts for a good time. Normally, immunity to certain kinds of viruses can be less than 100%, so there is some getting sick, and normally, a subset of people don’t develop much of an immunity because their own immune system simply fails at that task. COVID-19 will ultimately be found to match normal biological expectations, though we don’t know the details yet, and we won’t for some time. The fact that normal biological expectations do not form the basis of folk thinking about this disease, or pathogens and immunity in general, does not make Covid-19 a preternatural force, or an unknowable thing.

Still, remain hiding in your house until the all clear.

There is another level of thinking about immunity that I won’t go into detail about right now, but I’ll mention. We often, rightly, think of immunity at the population level, even though it does, truly, work at the individual and molecular level. Assume a particular vaccine, or exposure, typically provides ~100%) immunity in individuals. If 10% of the population have that immunity at the start, the disease will act like nobody is immune, as far as we’d be able to see. Often, natural (genetic?) immunity at low levels exist in a population, and can only be discovered by intensive research over a long time. If, on the other hand, 90% of the people in a population are ~100% immune, the disease may be so unable to get a foothold that it is like it isn’t there. The point is, the appearance of a diseases behavior seems to range from 0% (there ain’t none) to 100% (it’s everywhere!) on the surface, but this outcome is a function of a much smaller range of actual immunity values, like the 10-90% just noted, or more likely, closer to 0-70%. Putting this another way, a population gets very close to “immune” at the population level as the proportion of individuals who can’t get and pass on the pathogen rises over about half. This is called herd immunity. It will take several cycles of COVID-19 infection to achieve natural herd immunity, most likely, unless a vaccine is found. But once that happens, the disease is likely to stay around at low levels then occasionally come back and be menacing, but not as bad as it is now, on occasion.

So, let’s get that vaccine going!

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The Complete Scientific Guide to COVID-19

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… will be written in about three years from now. Meanwhile …

We labor under a number of falsehoods about how science works. Even scientists do. There are considerable differences among the panoply of scientific disciplines, and these are important enough that I would never trust the practitioners of one scientific discipline to, say, review research procedures or grant proposals from another discipline, by default.

These differences are even more significant outside of science itself. A common example is this one. A lay person evaluating peer reviewed research claims that a certain scientific conclusion can not be supported because there have been no double blind studies. That person may be unaware of the fact that almost no science uses double blind studies. This is a methodology used only in some areas of research. A study of earthquake hazards, genetic phylogeny of chickadees, or how long a particular virus lingers on a surface will not have a double blind methodology.

In some fields of study, a single idea will often be represented by a single major publication (sometimes a book) and will not be seen elsewhere unless it is being criticized. This is not common in the true sciences, per se, but this does happen in the peer reviewed literature. In other fields of study, a single idea may be addressed in hundreds of peer reviewed papers. In some fields of study, if a published peer reviewed paper presents a conclusion that is thought to be wrong, because of some flaw, the scholars in that field are expected to learn of this problem and thereafter avoid citing that paper. In other fields, when this happens, the paper is withdrawn from the literature after the invocation of complex rituals that might or might not involve the sounding of trumpets.

There seems to be two falsehoods affecting some of our thinking about COVID-19. One is the idea that a “study” or “publication” about some detail of the disease tells us something that we can take as fact. Yes, Covid-19 stays on a certain kind of surface for N days, therefore we can’t do X! That sort of thing. However, this research is, firstly, not peer reviewed. There may very well be no peer reviewed papers on COVID-19 at this time. This Pandemic has lasted less time that the typical peer review process takes. Maybe there are a few out there, but mostly, we are dealing with non-reviewed work, or work in review. This is good work, and important work, but it is more like a set of “emergency results” that address specific pressing questions in a provisional way.

It has been important to decide which of a small number of broad categories COVID-19 can be placed in, and the work on persistence on various surfaces has provided that rough and ready guide. There are pathogens that can find their way out of an exam room, go 20 feet down the hall, and infect a person sitting in a different exam room. There are pathogens that are so unlikely to infect another person that you practically have to lick the inside of their mouth five times to catch the disease. COVID-19 is in the in between category, where it sheds into the air and hangs around on surfaces for long enough that surfaces are found to have the virus on them. Is COVID-19 more or less surface-contaminating than, say, norovirus? Rotavirus? Nobody knows, because the research to determine that, and the publication array that would be necessary to lead to policy and recommendations about that, will take time. Someday there will be a study that looks at how much of the virus persists for how long on various surfaces, integrated with the other important question of how can the virus on a given surface actually infect a human, in order to allow for a realistic and useful statement about how to go about keeping a home, and ICU, an examining room, or a school relatively safe. COVID-19 has the potential to be the most studied pathogen in recent history, but not today.

So, that is the first fallacy: that a handful of quick and dirty, rough and ready, studies designed to get a clue about this disease constitute a well tempered and developed peer reviewed literature from which we can glean an accurate characterization of most o fhte important details of this disease. Nope.

One cost of this fallacy is the second fallacy, that we can evaluate models of either COVID-19’s behavior, or the efficacy of our reaction to it, based on a solid knowledge of the disease. That is backwards. We will eventually be able to evaluate ideas like “curve flattening” by understanding a lot about COVID-19, but that will happen after we have actually seen what various curve flattening efforts have done. A recent proposal that certain areas of the world may have seen a prior passage of COVID-19, causing some local immunity. One well meaning expert (not an actual expert) on social media responded that given the way COVID-19 operates, this is simply impossible. But that is backwards. The way we will eventually be able to describe how COVID-19 actually works is by observing it, measuring it, developing good explanations for what we see, strengthening and tempering those explanations by further hypothesis testing, replication, critique in the formal peer review process as well as the less formal but sometimes more important conversations at the conference-bar setting, and time. Time to just think. Then, we will be able to say things like “X is pretty much impossible because this is how COVID-19 works.” Now, we have an expansive void where some good theory and data will eventually reside, and the job of the scientists focused on this problem is to carefully and thoughtfully fill that void with what they come to know. To get a sense of how this works, read up on the literature that came out of the 2013 Ebola epidemic. Many key known things about the pathogen and its effects were not nailed down until months or years after the last patient was identified. These things take time.

I’m not an epidemiologist, but I play one in the classroom. Amanda and I teach a class on the immune system and epidemiology. Had I not gone into palaeoanthropology, I might have gone into this field. Excellent books on the topic include The Coming Plague: Newly Emerging Diseases in a World Out of Balance by Laurie Garrett (not current but mind-changing and foundational, includes some important forgotten history), Epidemics and Society: From the Black Death to the Present (Open Yale Courses) by Frank Snowden, and for a good textbook, Gordis Epidemiology.

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US Hummingbird Migration

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People in central or northern United States (excepting the Pacific Coast) need to get their hummingbird feeders ready, but don’t put them out until the birds are about to arrive! One of the more common mistakes people make with hummingbird feeders is putting them out too late. That’s like opening your lunch restaurant at 1:00PM. If you had a lunch restaurant that you could open, which you don’t. Another mistake is putting the feeder out, with the “nectar” in it, too early so the sugary liquid goes bad. That’s like getting the salad bar in your impossible lunch restaurant all ready the day before. Fake nectar doesn’t wilt, but it does go bad.

In order to make this work, you can use the Hummingbird Central Spring Migration map. Click here to visit it. This is what it looks like this morning:

hummingbird migration map, showing hummingbirds just staring to fly north of the southern coasts

Most people will not need a A Field Guide to Hummingbirds of North America, because there are not a lot of different species. But if you do, the Peterson guide is probably the best.

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COVID-19: Don’t Just Flatten The Curve, but also, do this….

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Is Washington State leveling off?

Are mainly Republican states seeing the greatest increases in COVID-19 infections (outside of New York)?

Is the NOLA effect an explainer of the the distribution of COVID-19 outbreaks?

What is the difference between flattening the curve and pushing the curve, and why is the latter what we need to be doing?

These and other questions….

Washington State is especially interesting because until New York muscled it out of the way, it was a US epicenter of Covid-19 infection. Over the last several days, the percentage increase in cases in Washington look like this:


Before getting too excited about that “4” we must digress to examine the “ever trust the last datum rule” in epidemiology. If you have been following the progress of COVID-19, you’ll notice that on many day — most days, really — the current situation always looks a bit rosy because the exponential rise in new cases is less for the most recent reading than for the previous readings. This is almost always an artifact of the nature of the data. Ignore the last day.

Having said that, it remains true that over the last several days the state of Washington’s new case number has not gone up as a percent of total cases. Washington is still in trouble, but measures being taken there may be helping.

It has been suggested that Republcian run states are going to have disproportionately more trouble from COVID-19 than Blue states, because Democrats pay attention to science and Republicans spend their days punching hippies and making liberals cry. This characterization of Democrats vs. Republicans is pretty much unassailable, but the effect on COVID-19 right now is a bit more complicated. Population size and density and other factors probably matter more, and it is possible that all the different virus related factors come together in the New York City Metropolitan area (which, to the surprise of Federal health authorities, includes about 10-12 counties, not four as they have been saying) to make that a hot zone no matter what.

Otherwise, the data, as shown in the following graphic which has a smudge on each state with the most rapid recent increase in COVID-19 infection, speak for themselves.

Sometimes, when data speaks for itself, it mumbles.

Not shown on that graphic because things are happening too quickly is the sudden and dramatic increase in cases, and deaths, in Louisiana. It thought that COVID-19 was active in that state during Mardi Gras. Contagious carnivalians were literally parading around on floats throwing the virus (on beads and such) to innocent revelers. There might have been some other forms of exposure. Right now, this morning, it appears that Louisiana has the second highest infection rate in the US, second only to New York and Washington, but possibly rising at a meteoric rate soon so surpass everyone.

And, of course, all those people who went home after Mardi Gras took it with them. I want to see travel to and from NOLA and other carnival sites mapped against infection outbreaks. Globally; Mardi Gras is only one carnival of many.

Flattening the curve is a nice idea, but there are two problems with it. First, it is probably very difficult to do unless cases are truly isolated prior to multiple infections. The idea of flattening the curve is to reduce R-naught, the number of people, on average, that are infected per infected person. Social distancing can help, but the only way to make a huge difference is to identify ill individuals very early in the course of their infection, and take them totally away from society. Social distancing does not do that enough. One can somewhat attenuate the curve, but mere social distancing is not going to do what happened in South Korea, Singapore, and China.

Moving the curve is somewhat difference. This involves recognizing that a spike will happen (though maybe a lower one than otherwise), but one moves the spike about two to three weeks ahead in time. Why? Because a given region probably has about 1/10th (or maybe in better scenarios, 1/5th) of the ICU beds needed to save most lives of the critically ill.

Flattening the curve is, explicitly, making the maximum infection rate low enough to duck under the bare of ICU bed number. Like this:

If the curve flattens a bit but fails at this objective, it was not flattening the curve, but rather, failing and losing to the virus. Like this:

Pushing the curve to later, which would probably reduce the amplitude of the peak but mostly result in the same huge increase in number of cases, allows the build up of ICU bed number. Like this:

That is what we are doing in Minnesota. We expect thousands of people to require ICU beds, no matter what happens. We are partly locked down, and increasing the lockdown on Friday. We are building new ICU facilities, apparently, at a sufficient rate to handle the eventual need.

Communities that are just flattening the curve, and that expect it to work, may run into trouble if they are not building out infrastructure now. We can argue about what the best approach is, but trying different methods in different states or regions is a hell of a way to test a hypothesis.

I learned yesterday that about 15% of the ventilators used in the US are made in Minnesota. We have about 2% of the population. So we’re good.

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COVID-19 Conversation: Updates and meanderings

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Spain has had a major surge in Covid-19 numbers. India has more people locked down right now than any other country. Trump intends to “open up” the economy by Easter. Fortunately he is powerless to do so. The best available information suggests that Covid-19 is not mutating much, suggesting that once a vaccine is developed, it can work widely and be more effective.

Things are bad in Iran. According to Arash Karami, “Iran’s confirmed corona cases is now 27,017 with 2,077 deaths. In the last 24 hours there have been 2,206 new cases and 143 deaths. In total 43 doctors and nurses have died from corona.”

Yesterday, March 24, is the day Trump told us we would have zero cases of Covid-19 in the US. The actual number was 53,478.

I hear chest freezers are flying off the shelves.

Covid-19 is Partisan in the US

Example of the effects of social distancing on a symptomatic indicator of Covid-19, suggesting it is working well at least in some place.
The default behavior of the Covid-19 virus has almost the same pattern of spread and increase everywhere — exponential increase with a fairly high exponent, for a virus.

How different societies or regions attempt to “flatten the curve” seems to result in very different specific outcomes, but in several areas there has been real success.

It is probably true in the US that the federal response has been pretty much perfect, from the point of view of the Virus. Trump is treating Covid-19 much like he treats Putin. “What can I do for you, sir?” But fortunately, locally, it does not work that way.

Broadly speaking (with too few exceptions) Republican executives are literally supporting the virus in this manner. They want it to spike. Democratic executives are ordering serious responses and it is working to varying degrees. In states with Republican governors, Democratic (usually) mayors are responding despite what the Governors are saying, and that is working locally.

So, yes, Covid-19 response is partisan, and one of the parties is acting like a Death Panel determining that the aged, infirmed, and the less privileged be sacrificed for the benefit of the economy. The other party is trying to help. Republicans vs. Democrats.

The response in Congress is also partisan, but the Republican response is so awful that Democrats are winning out of sheer shame on Republicans. Plus at the moment, more Republcian Senators are down with the virus than are Democrats, so that seems to shift the balance of power.

In my own neighborhood, I’ve seen the Deplorable Housewives of Minnesota (yes, that is a thing) congregating in groups at the grocery store and loudly yammering about Nancy Pelosi and how she hates America, spreading viruses onto each other as they wander like a pack of hapless Gollumoids through the produce section.

(In the past the Senate Republican leadership has always been against remote voting. Now that it is in McConnell’s interest to have remote voting, expect his situational ethics to resituate.)

Bad News

The mother of NBA player Karl-Anthony Towns is very ill with Covid-19, as of this writing. Amy Klobuchar’s husband is in the hospital on O2 and quite ill. Minnesota’s Lt. Governor’s brother has died of complications of Covid-19. A minor youth in Los Angeles has died. Prince Charles has been diagnosed positive. There is a long list of famous people from Jackson Brown to Natalie Horner to Prince Albert II diagnosed. Terrence McNally dies of Covid-19. These folks happen to be famous, and the tends of thousands of non-famous victims do not exist on a lower plane. But having famous names across the spectrum of how people know them and what people think of them is, perhaps, to this pandemic what a set of really bad hurricanes is to climate change, if you get my drift.

Watching an interview with a former official from the Louisiana Health Department last night, we got two reminders. One is that Mardi Gras happened at just the right time and place to be a major incubator of the disease, and probably accounts for a lot of sick people. The number of cases in NOLA has skyrocketed. The other reminder: Official Atlantic Hurricane season starts June 1st, but actual hurricanes or tropical storms can show up in May. Gulf Coast and Eastern Seaboard hospitals and communities night have an interesting year.

Here is an interesting history of the N95 mask. An outtake:

In the fall of 1910, a plague broke out across Manchuria… “It’s apocalyptic. … It kills 100% of those infected, no one survives… within 24 to 48 hours of the first symptoms,” …

What followed was a scientific arms race, to deduce what was causing the plague and stop it. “Both Russia and China want to prove themselves worthy and scientific enough, because that would lead to a claim of sovereignty,” …

The Chinese Imperial Court brought in a doctor named Lien-teh Wu to head its efforts. … after conducting an autopsy on one of the victims, Wu determined that the plague was not spread by fleas, as many suspected, but through the air.

Expanding upon the surgery masks he’d seen in the West, Wu developed a heartier mask from gauze and cotton, which wrapped securely around one’s face and added several layers of cloth to filter inhalations. His invention was a breakthrough, but some doctors still doubted its efficacy.

“There’s a famous incident. He’s confronted by a famous old hand in the region, a French doctor [Gérald Mesny] . . . and Wu explains … his theory that plague is pneumonic and airborne,…and the French guy humiliates him . . . and in very racist terms says, ‘What can we expect from a Chinaman?’ And to prove this point, [Mesny] goes and attends the sick in a plague hospital without wearing Wu’s mask, and he dies in two days with plague.”

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Dune, Other Worlds, Cheap

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For kindle, Dune, cheap, at least for American customers.

Meanwhile, of possible interest: Other Worlds Than These by John Joseph Adams.

We can all imagine such “other worlds”–be they worlds just slightly different than our own or worlds full of magic and wonder–but it is only in fiction that we can travel to them. From The Wizard of Oz to The Dark Tower, from Philip Pullman’s The Golden Compass to C. S. Lewis’s The Chronicles of Narnia, there is a rich tradition of this kind of fiction, but never before have the best parallel world stories and portal fantasies been collected in a single volume–until now.

It is an anthology of some kind, I put it here because it looks interesting, but I’ve not read it. Have you?

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