Saturday, May 23, 2020

Weekend Reading: The Thankful for a Long Weekend Edition

This week was probably the worst one for me since this all began. Nothing particularly bad happened, but I think the accumulation of extra work, extra things to do at home, loss of my usual coping strategies, and the background anger and sadness about how poorly we've managed the pandemic here in the US caught up with me.

We talked to my sister-in-law in New Zealand on Sunday (her Monday). It was her kids' first day back at school. They're back to fairly normal school, which is safe because New Zealand has their outbreak well and truly under control: they have long stretches with no new cases. There was one new case report this week, but it was associated with one of the known clusters. There are no cases that they can't trace the source of, so they are confident that they've notified all contacts and they're isolating.

On Tuesday, I read the CDC's guidelines for schools reopening here in the US. These are just guidelines, and each school district is going to have to work out what makes sense in their specific situation. But I think it is likely that my kids will not be going back to "normal" school when they go back to school. I think this will be the right choice, but I am very sad about it. Both of my kids had an outburst/meltdown about how school is right now this week. I can't argue with them. School right now is not good. Our district did a good job setting something up in a very short period of time. But this is not a good way to do school. I am sad for what we're asking our children to sacrifice, and sad to know that we'll have to ask for more sacrifices.

We talked to my husband's parents last night and also one of his best friends, who is in Auckland. They were all shocked to hear my report on how our county is doing - when I told them we're averaging 100-150 new cases a day, they thought that was for the whole of California, not just San Diego county. I haven't been tracking the numbers for all of California, but I just looked it up and we had more than 2000 new cases yesterday.

Meanwhile, people here are surprised when I tell them that my in-laws aren't under guidance to wear masks. There is no real reason for them to wear masks, because there is very little risk they'll run into someone who is infected.

Against that backdrop, I've been very busy at work, both because my own projects are busy and because I've been helping pick up some slack for some of the people whose childcare situations are more challenging than mine. And household chores remain more time, thought, and energy consuming than usual. I also feel like my local leaders are spending all of their efforts on how to open businesses, and not enough effort on providing people with guidance on how to safely do things that might help us emotionally, like see friends. This leaves us all to figure out what is OK to do on our own, with no official guidance. If you take that responsibility seriously (which I do), that is just more work to do.

So anyway, I was worn out and had a bad week. Luckily, I had planned to make this a four day weekend. I took yesterday off. I had a short to-do list to start the day and then I read in my hammock, went for a walk on the beach with Petunia, and picked up ice cream with the kids. It was a nice day. A couple more like it and I might start to feel less worn down! We'll see how the rest of the weekend goes.

Anyway, on to the links:

In the comments on last week's post, my friend Autumn asked if I had any good links for the effectiveness of cloth masks. I was in the midst of the crappy week I whined about above, so I didn't go look them up but promised to post some today. Here's what I have:

Bob Wachter, the UCSF doctor who has been doing daily Twitter threads with his observations about COVID-19 and other related information, took his thread about masks and converted it to a Medium post. There are links in there to the data on masks and also a reproduction of the graphic that shows an analogy to someone peeing on you (yes, really).  If you are only going to read one thing about masks, that's the one I'd pick.

Cleveland Clinic also has a nice summary of the evidence and the recommendation about masks.

And here is a Medium post by a researcher in Singapore about masks that I read a month or so ago. It was probably what convinced me that cloth masks were worthwhile, even before the official guidance here changed.

In reading all of these things, I think it is important to keep in mind that our best evidence right now is that most SARS-CoV-2 transmission is via droplets, not aerosols. (Here is an article from March that does a good job of explaining what that difference means.) Almost any face covering is going to reduce the amount of droplets getting out of your mouth, because droplets are relatively big. Medical workers clearly need PPE that can protect against aerosols, because there is evidence that some medical procedures can produce SARS-CoV-2 aerosols. People who have to work all day around other people (bus drivers, grocery store workers, etc.) should ideally get medical grade masks, and failing that I would spend some time research which cloth masks will do the best job of protecting against inward transmission.

The rest of us should think most about stopping outward transmission and can probably use just about any cloth covering as long as we're keeping our distance from others. My personal decision has been to look for masks that work well in the various situations we need them. I'm finding that what works well when I'm shopping isn't what works best when I'm walking on the beach, for instance.

Depending on what things look like in a couple of months, I may end up doing research on the best type of cloth to use in masks to protect the kids at school. But for right now, my focus is on experimenting with designs to find what styles work best for us all.

Speaking of which... here is what ended up working best for Petunia, whose ears were too floppy to hold a mask. I sewed two buttons onto one of her headbands. She wears the headband and loops the mask around the buttons. She can do that on her own, which makes this a better option than the mask extenders we tried because she needed help to get her mask on with those.

On this weekend's to do list: Order more stretchy headbands so that I can make her several of these.

OK, on to the other links.

Ed Yong wrote another great article on COVID-19, this time on our patchwork response.

I also found this Science article about the details hidden beneath the average R0 really useful.

I am concerned by the reports coming out about a Kawasaki-like disease in young COVID-19 patients. Washington Post has an article about the fact that they're seeing it in young adults as well as children and Science has a good article summarizing what we do and do not know about SARS-CoV-2 infections in children. Taken together, these two articles make me want us to be more cautious about reopening things. There is a lot we don't know and I think a lot of people are making assumptions about the safety of opening schools without first controlling the local outbreak that don't acknowledge the huge gaps in our knowledge.

Speaking of reopening things... my county opened up restaurants and retail stores. I have mixed feelings about this and we don't plan to change our behaviors with respect to restaurants or stores anytime soon. We'll do takeout and look for curbside pickup options.

Clearly, not everyone in my area is feeling so cautious... the county has already shutdown one establishment for violating the rules.

Here's what violating the rules looked like:

Meanwhile, we still can't go to most of our big public parks, like Mission Bay or Balboa Park. And I am really struggling to see why the official rules say it is safe to sit in a restaurant 6 feet away from people you don't know but not safe to sit on a beach 6 feet away from people you don't know. Maybe it is just that we don't have the resources to enforce the distancing in the big public areas, but can tell restaurants to enforce distancing? I don't know.

I think this story illustrates some of the challenges for my region: San Diego hospitals are taking COVID-19 patients from Imperial County because their hospitals are getting overwhelmed. Why are their hospitals getting overwhelmed? It is a rural county without a lot of hospitals, and Americans living in Mexico are coming home if they get sick. El Centro, CA is right across the border from Mexicali, which is the capital of Baja California. There were stories here early on interviewing Americans living in Rosarito (a beach town not far south of Tijuana) who essentially said that was their plan: Stay in Mexico unless they got sick, in which case they'd cross the border.

I found this essay about why evangelicals are pushing for a faster reopening really interesting.

This essay about women on Tik-Tok figuring out how to satirize Trump is also really good.

This is a really succinct statement of what we gain from contact tracing beyond being able to isolate people who may be infected:

This made me smile:

I love this:

Mr. Darcy was RICH:

Here's your weekly rabbit:

Have a good weekend, everyone!

Saturday, May 16, 2020

Weekend Reading: The Tempers Fraying Edition

I am on the fourth day of a headache. It recedes sometimes, but keeps coming back. On Wednesday, it was what I call an "almost migraine" - I was feeling woozy and getting cold in addition to having a headache, both of which are signs that if I didn't go back to bed I'd probably end up with a full migraine. Thursday was better, but Friday morning the almost migraine was back. This morning, it is just a garden variety headache again.

I'm not sure what triggers these. The best guess is probably hormones. I have mostly figured out how to handle them so that I don't lose too much work time, but the combination of feeling behind on the things I need to do and the headache itself makes me short-tempered. Which is why I had a stupid argument with my husband on Thursday night about the fact that I was the one filling out the paperwork for our aftercare, like I always do. (And I do mean always: this was my ninth straight year of filling these same forms out.) They had only given us one day notice on when the submission period would start, and in general you need to get the paperwork in on the first day of the submission period to be sure of a spot. Who knows if that will be the case this year, but we wanted to submit on Friday and so the paperwork had to be done Thursday night.

Anyway, I slammed my clipboard with my to do list down on the table in a fit of pique that I am ALWAYS the person who fills out the paperwork, not realizing that my phone was on the table under some other papers. And that's how I cracked the screen on my phone. It cost $200 three years ago, so it was not a catastrophe that I broke it, but it was annoying. I decided to buy another $200 phone and got the exact same phone I'd just bought for Petunia earlier in the week, the Samsung A10e. I ordered it Thursday night, it was delivered yesterday, and I am almost done setting it up. So I guess as "stupid things I did to myself because I was angry" things go, this one wasn't too bad. The old phone was starting to need to be charged multiple times in a day, anyway.

This did make me realize, though, that we need to rebalance some of how we split up tasks to take into account the way life is right now. I am usually the one who figures out processes to make life work better and Mr. Snarky is the one who does a lot of the maintenance chores. Neither of us loves these tasks, but they fit our strengths well and it has been a fairly even split in time and annoyance. Until now. His stuff is still about the same as it was before all of this started, and he has even commented on how nice it is to be able to go out and do some gardening after lunch most days. My stuff, on the other hand, has increased at least 10-fold. I have figured out new ways to get groceries, what extra things we should order to be prepared for whatever is next (multiple times, since "what's next" keeps changing), what our mask processes should be (e.g., where we store them, when we wash them - only if we've come within 6 feet of someone else or we wore them a lot, what to do about the fact that masks won't stay on Petunia's ears, etc.), how to help the kids stay in touch with their friends, how to help Petunia keep doing art classes, and more.

I keep thinking I have everything sorted and we can just run with our processes, and then things change again. I don't think I would have been so angry about the aftercare forms if I didn't have the headache, but I probably still would have been cranky. There is just so much to do and I am tired.

But you didn't come here to read my whining. You came here for links! Here's what I have this week:

You maybe saw the picture of the man at the grocery store in a Klan hood. That was in Santee, which is a suburb of San Diego. It has long had a reputation for racism and intolerance, so much so that it has the nickname of "Klantee." This article in my local paper explains the history and also the way that many of the people living there now are trying to change things and build a more inclusive future.

I found this personal essay about the lure of conspiracy theories very insightful.

The Washington Post interviewed some public health experts about what they think is safe and what is risky. It is a good read.

Also very good: the blog post from a UMass biology professor named Erin Brommage about what we know about the risks right now. It has been all over the internet, including in the comments to last week's post here, so you've probably already read it. But if you haven't, it is good.

One of the cool things about Talking Points Memo is that long time readers will often write in with "front lines" sort of reports. There are two reports that posted this week that I encourage you to read: one from a manager at a grocery store and one from an American living in New Zealand.

I follow both the Wellington and Auckland Zoos on Instagram, and also Zealandia, a bird sanctuary near Wellington. They are all opening up now as New Zealand continues loosening its restrictions because they have the outbreak under control. We're hoping to call my in-laws this weekend to hear how that's feeling for people in the country.

It has been a but weird following how things are going in NZ. The country has about the same population as San Diego county, so in some ways we can directly compare. But as a country, NZ can impose strict quarantines on people coming in. San Diego county can't do that. It is clear we're still getting visitors from other parts of the state. The local newspaper interviewed people from Orange and Riverside counties on our beaches the first weekend they were open. We're also getting visitors from other parts of the country. Pumpkin has been playing a game in which she looks for each state's license plate in alphabetical order. She got Vermont in February and has been stuck on West Virginia. She got it this week, walking around our neighborhood. We've never seen that car here before. We also see plates from New York, Louisiana, Nevada, Iowa, Washington, and South Carolina. Some have been here a long time, but some are new.

There are also still people crossing the border with Mexico - both legally and illegally. That is a complex topic I'm not going to go into today. My point is just that the patchwork "let the states and counties handle the response" approach we have taken in this country due to the failure of Federal leadership has some serious limitations. No one is going to be able to have a New Zealand-like response because no one has the ability to control new arrivals like New Zealand did.

We need a national plan. We don't have one. Ezra Klein's piece laying that out is infuriating, but really worth your time.

In comparison, here's a nice write-up of what New Zealand got right in its response.

Lest you think that New Zealand is some sort of perfect society.... here is a creepy story about a Subway worker abusing the access to contact information given to him due to the epidemic response. Everybody talking about having lists of who visits restaurants, etc., as we start to reopen should be thinking about the potential for abuse and how we can protect against it.

Derek Lowe continues to publish excellent explanatory pieces at In the Pipeline. I'll link to his Q&A about vaccines and monoclonal antibodies both because it is very good and because I encourage you to search for the comments from "Mammalian scale up person" for a dose of reality about the challenges ahead once a good monoclonal antibody is found and validated. In the Pipeline has A LOT of readers in pharma and biotech and his usual commentariat is unusually well-informed. It is one of the few places where I always at least scan the comments.

I am pointing you to Mammalian scale up person's comments not because I don't think we could overcome the challenges described, but because doing so is going to take a level of Federal leadership (and international coordination) that we're not getting right now. Add this to the things that are at stake in the November election.

Also, the fact that a vaccine is almost certainly farther away than the optimistic "18 months" we keep hearing doesn't mean that we're doomed to stay isolated until then. If we can get cases down to the level where good old-fashioned contact tracing followed by isolating contacts is feasible, then we can get more things back with less risk. I feel like we're doing a really poor job of explaining that to people.

And we should be wearing masks. Making that a partisan thing is one of the worst things that has happened in our response. Here is a video from a professor explaining what his computational model shows about the impact of near universal mask-wearing on transmission. Their model indicates that 80% of people wearing masks by about day 50 of an outbreak, we can significantly reduce the size of the outbreak. For those of us who are living under stay at home orders, if we mask up as we exit those orders we can help keep the case numbers flat.

This case study from Canada is striking - a symptomatic COVID-19 patient on a long international flight wore a mask and no one else on the flight got infected.

It is frustrating that the early advice from the WHO and CDC was against mask use, since that added to confusion. But one way to look at it is that our sacrifice in staying at home for the last two months bought time for the research and discussion needed to change the thinking on use of masks. We now know more about how to reopen some things more safely.

Here's a reminder of yet another reason to be cautious: SARS-CoV-2 infection appears to be linked to an increase in Kawasaki-like disease in children. This is very worrying.

Which is why I think I also need to share this tweet:

In better news, Gilead is taking steps to scale up availability of remdesivir.

Stat News had a very good summary of the key takeaways from the Senate hearing about the COVID-19 response. Read the first takeaway: our leaders are too optimistic about vaccine development. They're looking for an easy out. We need leaders who are putting together a plan for the reality of a long haul instead.

And now the things that are helping me through right now:

This article about a 1000-year-old mill in England starting back up to address the flour shortage is wonderful.

Last night, Mr. Snarky and I watched some of the recording of the livestream Jason Isbell and Amanda Shires did in support of their new album. It was set up so that they could see the people watching them on Zoom, and they interacted a bit. We talked a little about how people are finding ways to make connections and community happen right now, and how seeing that is one of the nice things about this time.

Along those lines, if this isn't real, I don't want to know:
In other interesting music we watched last night, there were two songs from LA-based bands about this moment in time that we really liked and thought captured the feeling well:

First up, OK Go, a band that is most famous for its elaborate videos. Stay long enough to see the best use of a toy piano in a music video:

"Everyone alone all together on the precipice" is a great line.

And next The Regrettes, who have the best band name ever:

These cats have social distancing figured out:

Here is your rabbit of the week:

Happy weekend, everyone!

Saturday, May 09, 2020

Weekend Reading: Here We Still Are Edition

It was a busy work week, particularly yesterday, which frankly kicked my butt. Petunia slept in which made me a little late getting to my computer and I'd barely finished my emails when I started 3 straight hours of meetings. I'd expected an hour break in the middle, but 10 minutes before my 9 a.m. meeting finished, someone sent me a message asking me to join a 10 a.m. meeting, and I already had an 11 a.m. The 11a.m. was a particularly intense meeting - we're gathering requirements for a new project with one of my customers, and the system we'll create will be used by two groups that do similar work but in different stages of the drug discovery process. Anyone familiar with drug discovery knows that this means the two groups have different tolerances for standardizing their workflow. (In general, the earlier in the drug discovery pipeline the work is, the more variable the workflow.) Their management wants them to merge their processes and we'll provide a system to support that. I can tell that their processes are similar enough that we can do it but extracting the common requirements is more challenging than usual, particularly since one group is suspicious of what they're being asked to do.

So anyway, I finished that meeting at noon pretty drained... and then had to rush around to get things set up for Petunia's 12:30 art class. She is enjoying the classes on Zoom, but can't completely set up for them on her own.

I ate my lunch answering questions from one of my colleagues via our chat tool and then somehow it was almost 2 p.m. and I was only on the second item on my to do list for the day. My husband came back in from the bike ride he'd taken after lunch wanting to tell me about possible rollerblading spots he'd found for me and I had to tell him I couldn't talk about it right then. Of everything I've had to give up since March, it is my Friday routine I miss the most. In the midst of a stressful Friday like yesterday I couldn't handle talking about what I could try to put in its place.

I think I need to find a time to take advantage of the fact that we're allowed to walk on our beaches!

Anyway, on to the links:

First up, something NOT about coronavirus: I started this Ezra Klein interview with Pramila Jayapal on my drive down to pick up art supplies for Petunia (via curbside service!) and finished it on a solo walk I took one evening. It is a really good conversation about the realities of the current situation in Washington and how progressives can get and wield power. If you don't want to listen to the podcast, here is an excerpted transcript.

Laura McGann's careful, detailed piece about reporting on Tara Reade's allegations is essential reading.

And something only somewhat about COVID-19: Caitlin Flanagan's beautiful essay about living with cancer.

If you'd like to be depressed about a different problem for a change: The lockdowns have cut world emissions... but not by enough. This really illustrates the limits of individual behavior changes in fighting climate change.

This is a really good interview with Peter Piot, a virologist who was one of the discoverers of the Ebola virus and has spent his career fighting infections diseases... and who caught COVID-19.

This map of when people in different parts of the country stayed at home is fascinating. My husband and I kept replaying it last night - we were surprised by how dark our region was even on March 1. There has been a lot of talk about the difference between NY and CA in this epidemic, and I wonder how much comes down to the different colors on that map on March 1. We were in no way under a stay at home order on March 1 - but we wonder if the outbreaks in Seattle and Northern California influenced people's behavior. I also wonder about the impact of what our Asian American population may have been hearing from friends and family in Asia. Along those lines: this article about the different outcomes in the Corona and Flushing neighborhoods in Queens is interesting.

Smartphone data shows that when Georgia opened up it got an influx of visitors from neighboring states. There are several counties in California that have not had big outbreaks and are pushing to open up earlier (or just doing it in disregard of the state orders). This article should give them pause. If you open, people will come. Some of those people may be infected, and now you have another outbreak.

This story about how people have died from COVID-19 in Florida is heartbreaking, but worth your time. So is the Faces of COVID Twitter account.

This Greg Sargent piece about Trump's focus on the appearance of normalcy is very good. One thing that scares me is the way mask-wearing and staying home are becoming partisan actions. I'm not talking about the state decisions to open or not, I am talking about the individual decisions of people about whether to wear a mask, go get a haircut, or go to a restaurant.

I see people pointing out that the Trump administration has no actual plan for restarting the economy, since they have no plan for the level of testing and contact tracing that would be needed to make people feel safe going about various activities. But I worry that they do have a plan: make going out to restaurants, etc., a marker of partisan identity so that a large number of people do start going out even though the best data we have indicates that is risky.

We don't really know how that will turn out. The available data about how SARS-CoV-2 transmits and our basic understanding of how respiratory viruses behave indicates that there will be an increase in infections. But we don't really know how big, because there is a lot we don't know yet. I worry that some in the White House and other Republican power centers are gambling on the increase in cases not becoming so large that it can't be ignored.

There is also a racial aspect. As Adam Serwer points out, once it became clear that in many places the epidemic is disproportionately sickening Black and brown people, some people stopped taking it so seriously. This is reprehensible. It also betrays a fundamental lack of understanding of how a respiratory virus transmits. As these people push for service businesses to open, the privileged people whose ability to work from home kept them safe so far will visit those businesses and start to become infected. Even those of us who continue to avoid restaurants and the like need to buy groceries... and some of us will get infected, too. It certainly won't be the first time our racism has hurt the entire country (evidence our current President....) but it is depressing nonetheless.

I know that some of the push to reopen is coming from real economic pain. I am also perhaps more sympathetic than many to the people who are just frustrated and bored with the situation and want to go back to doing the things they enjoyed. But I offer this tweet as warning:

We would do better to turn our energies towards addressing the suffering, both catastrophic and trivial,  in ways that minimize viral spread. One tragedy of this moment is that no one seems to have the bandwidth to do that because the inept White House response has created a situation where everyone has to spend their energy solving the same basic problems: how to get PPE, how to get tests, how to ramp up contact tracing... there is not enough time left to think about the ancillary but in the end equally important problems.

In science news:

Here is a small but encouraging study on using interferon beta in a combination therapy for COVID-19.

Ed Yong wrote a good piece about the reports of a "more infectious strain" of SARS-CoV-2. The short version is we don't have enough data on the mutation at the center of that story to say much about it.

Here's a good Twitter thread on the subject:

And as Derek Lowe explains, there is no reason to think that the mutation will interfere with any of the vaccines or therapeutics currently under development. It might turn out to matter - we don't know a lot of things yet! - but it is not something I'd waste time worrying about right now unless I were working on a vaccine or antibody project. This mutation has been known for a long time, so the scientists working on those projects have almost certainly thought about whether it is likely to impact what they are working on.

Also, yes people who get COVID-19 do seem to have immunity to it. What we don't know yet is for how long:

On to the things that made me smile:

Check out this girl Irish dancing to Megan Thee Stallion.

If you learned the Fifty Nifty United States song in school this will probably bring back memories as well as make you laugh:

The Ministry of Silly Walks in SLO!

Always look on the bright side of life....

They are beautiful dogs... but this is funny:
This thread is delightful:

So is this baby. Watch to the end for full effect!
Beautiful art:

Also beautiful:

Here is a beautiful bird:

Penguins go for a hike!

My favorite bunny picture of the week:

Happy weekend, everyone!

Saturday, May 02, 2020

Weekend Reading: The Mostly Hopeful Edition

Last night after dinner, we all got in our car and drove to the neighborhood my husband and I lived in before we had kids (Pacific Beach). We found a parking spot not far from the beach, put on our masks, and walked down to the beach to see the glowing waves.

We're having a particularly good bioluminescence show here right now. If you aren't familiar with the phenomenon, it is caused by a bloom of phytoplankton in the water. We get these blooms from time to time, but can't predict when. The waves glow when they break, and you can get cool effects in the sand. During the first bioluminescence event I ever saw (back in grad school!) if you walked in the wet sand, you left glowing footprints. It was magical. We didn't get glowing footprints last night, but we could make the wet sand glow briefly by dragging our feet through it.

We all had fun watching the glowing waves and playing in the sand. It was also nice just to be out as a family again. For the most part, just the grownups have been going out, and just to go do the shopping.

Most other people at the beach were wearing masks and trying to keep their distance from other groups. Our beaches only opened on Monday, and there isn't supposed to be any standing around or lounging on the beach. People were standing in little groups to watch the waves and take pictures, but I only saw one couple sitting on the beach. There were police present, and I suppose they would have intervened if it looked like people weren't following social distancing rules.

We're lucky that this bloom didn't happen two weeks ago, when none of us would have been allowed on the beach to enjoy it! From my informal survey of friends and colleagues, I think that the opening of the beaches for surfing and running/walking is a really big deal to us. We all got a little scare on Thursday, when a memo leaked indicating that the governor was going to close all beaches because there had been large crowds at several Orange County beaches last weekend. Instead, he closed just the Orange County beaches. I believe there is a legal challenge underway on that. Whatever the merits of that order, I think it may have given San Diegans extra incentive to follow the rules our county and city officials have put in place. We don't want to see our beaches close again!

Anyway, I do have some things for you to read this weekend:

If you read only one thing, make it Ed Yong's latest piece about the pandemic, in which he explains why there's so much uncertainty about everything. As I mentioned in my last post, I think that living with this level of uncertainty is hard on a lot of people (it is hard on me!) and this piece does a good job of explaining why we can't have more certainty, which may help people figure out how to make decisions in this uncertain time.

My second choice would be David Frum's helpful explanation about why Mitch McConnell has been talking about letting states go bankrupt. Honestly, this might be the most infuriating thing I read all week, but it is important.

There were a lot of things written about remdesivir and what we know about the results of the NIAID trial of it. Derek Lowe does his usual stellar job of explaining it all. Since his post was written, the FDA announced emergency authorization for the use of remdesivir in severe COVID-19 cases. I assume additional trials will be done now to figure out how best to use remdesivir. A lot of people really want to see trials earlier in the disease, because that is typically when antivirals are most effective. Administering remdesivir early will be hard in most cases, though, because it is an IV drug. My opinion is that the way around that issue is to do the trials of early use in skilled nursing homes, which have been particularly hard hit by this epidemic and in which it should be possible to reliably administer an IV drug. Honestly, I think we should investigate whether it would be beneficial to administer remdesivir prophylactically in any group care situation in which there is a confirmed case of COVID-19, similar to what is done with Tamiflu and flu outbreaks (here's the CDC guidance on that - search on "antiviral chemoprophylaxis" to find the relevant info).

But we have a limited supply of remdesivir. Gilead has been working to increase supplies for awhile, but this is not an easy undertaking. STAT has a good writeup of the manufacturing efforts. I suspect we'll have limited supply of remdesivir for awhile. The people figuring out how best to use that supply know more about infectious disease treatment and clinical trial design than I do, so we'll just wait and see what comes next for that drug, and hope that more effective drugs come along as soon as possible.

Doctors are also learning more about how best to treat COVID-19 patients. Here's an article from the University of Chicago about using high-flow oxygen cannulas instead of ventilators.

New York has provided some data about which pre-existing conditions were most common comorbidities in patients who died from COVID-19. Asthma is surprisingly low on the list. That data made me feel better about my personal risk (my only relevant pre-existing condition is asthma).

Meanwhile, different areas are starting to experiment with what can be reopened. I am glad I live in a place that is taking a slow and deliberate approach to reopening, both because that just feels safer to me and because I hope it allows us to gather some actual evidence about which activities are relatively safe and which we should continue to avoid. Other states are moving faster. I don't think we really know how that will turn out, but this article describes how some people feel about it in Georgia. (Spoiler: worried.)

Here's California's plan for reopening. We're in Stage 1, starting to edge into Stage 2.

And here's a writeup about Washington state's plan.

I've mentioned the discussions about why New York City and Seattle had such different coronavirus outcomes. There was a long write-up in the New Yorker arguing that it was because the state of Washington and Seattle let the scientists lead the response.

I am trying to read obituaries of the people we've lost to COVID-19, to keep the numbers from making me numb to the tragedy. This one for Cesar Quirumbay hit me particularly hard.

David Roberts at Vox argues that we should electrify the postal fleet. I found it to be a convincing argument!

Now for some things that made me smile this week:

I love the flamingos out and about at the Denver Zoo. This was my favorite take on it:

Apparently, when someone asked Dr. Fauci who should play him in the movie, he jokingly said Brad Pitt. Brad Pitt obliged:

I knew before I looked that this had to be in Australia:

Also me:
This is beautiful:

This thread about Rebecca Black made me happy. So we went and listened to some of her recent music last night and it is pretty good!

I love this:

Prince Edward Island is taking the bear hunt idea seriously!


Happy weekend, everyone! I think our trip to the beach last night will be our only outing, but the weather is nice and my hammock calls to me....

Wednesday, April 29, 2020

Life in the Time of Coronavirus, Snapshot #4

We've settled into a pretty good work and school from home routine here. This is not optimal, but it is doable for us and for that I am grateful. The kids and I go for a walk pretty much every day - Petunia skips some days, but she's coming more often now. She's picked out a favorite house a couple blocks over and likes to walk by and visit it. We all like looking for new teddy bears in people's windows and pretty flowers in their front gardens. The hardest part of this routine is scheduling - between my work calls, the kids' school calls, and some Zoom tutoring Pumpkin is doing for younger kids it can sometimes be hard to find a 30 minute block of time for our walk. We usually manage, though, and have only had to postpone the walk to after dinner a couple of times.

Some days are better than others, of course. Tuesday, work really wore me down. I had a Zoom call with a friend after dinner, and struggled to explain why, exactly, work wore me down. It was a mix of several different frustrations I think, of which the extra difficulties created by working from home were only a small part. I think the bigger problem is that my usual ways of letting go of work annoyances are blocked to me and I haven't really found good replacements. I need to work on that because I honestly expect to be working from home for at least another couple of months and probably longer. (That doesn't mean I expect the stay at home order to be unchanged, but I have the sort of job that is easiest to do from home and I think people like me will be asked to keep working from home even as other things open back up.)

Today, I woke up with a headache and ended up taking some ibuprofen with a big glass of Propel and going back to sleep for an hour. I'd arranged to donate my small supply of N95 masks (bought as preparation in case of high smoke during fire season) to San Diego county's PPE donation center so even though I started work late, I had to take a break around 9 a.m. to go do that. I had been planning to make a Target run tomorrow. Our toilet paper supplies were getting a bit lower than I liked and toilet paper is the one thing I haven't figured out how to get delivered.  Since I was going out already, I checked Target's website and saw several types of toilet paper in stock at my local store. So after I dropped of the masks, I went to Target.

I got toilet paper, but it is a brand I've never heard of, not one of the brands the website said was in stock. I got to the store before 10 a.m., and there were 10 packs of toilet paper left on the shelf. I took one pack with 12 rolls in it. I think Target is limiting quantities you can buy, and even if they weren't it would have felt wrong to take more. This extends our toilet paper runway to 6-8 weeks, and presumably sometime in that period we'll be in a store that has toilet paper again.

I also got almost everything else on my list. There was no Fresca, unfortunately, and also no parchment paper (for baking). But both of those things I can try ordering from the grocery store, so we'll cope.

Our order to wear face coverings if we're coming within 6 feet of anyone goes into effect on Friday, but already most people were following it. For the most part, people kept their distance, too. It was not a fun shopping trip but it was far less stressful than the early trips I took to grocery stores. I think I'll be OK with doing more in person shopping now, but we'll keep trying to minimize it.

Anyway, that's a lot of words to say "we're coping OK and settling into a routine we can stick with for as long as we need to." That has been my goal - to make life in these weird conditions feel OK, so that we can deal with the uncertainty about when conditions will be less weird. In conversations with friends and in the online discourse, it seems that the uncertainty about how long we'll be living like this is really getting to people.

I get it. There is no way we're all going to live like this until a vaccine is ready.  The timeline for a vaccine is too long and people's resolve is already fraying. Or if their resolve isn't fraying, their nerves are, and they're struggling to see the point of what we're all doing if we're going to have to open things up without a vaccine, anyway.

There are three things I hold on to that help me NOT feel that way:

(1) My state and local governments are building testing capacity, and they're starting to work out how they're going to be able to do contact tracing at the scale needed to make an impact on virus spread. This means that even without a vaccine, we will have a safer way to open things up if we wait a bit longer. Yes, it would be better if we had a national strategy for this but that's not going to happen until January of 2021 at the earliest so I'll just be glad for what my state and county are doing. Epidemiology studies are also starting to come in, which will tell us more about what activities are riskiest so that we can make better decisions about what to open up and what to keep closed.

(2) I am not a doctor or an expert on critical patient care, but it seems to me from watching what happened in New York and Italy that there is a lot of value in keeping the hospitalization levels low enough to allow doctors to have plenty of time for each COVID-19 patient they have. I suspect this decreases the fatality rate. I am sure this decreases the strain on medical staff, and also on the people in the area. I am willing to put up with a lot to keep the hospitalization levels well below capacity in my area. If I ever start to feel impatient with the stay at home order, I think about this.

(3) Even if no vaccine is developed and we're all going to end up getting this virus eventually, I think that every day I can delay getting it improves my chances of a better outcome if I do get it. Clinical trials are underway - as we get more results from those trials, doctors will have a better idea of what drugs might provide a favorable benefit-to-risk ratio. Doctors are learning from what seems to work best for their patients and are sharing that information as quickly as they can. As drugs start to show promise, we'll need a strategy to scale up manufacturing and we'll need to figure out optimal dosing. This work is already underway for remdesivir, but it will take time to build up supplies of the drug to the point where anyone who needs it can get it (if it indeed turns out to be helpful).

These three things all feedback on each other, too - if we keep case numbers low, we need fewer contact tracers and less amounts of any drug that is useful. If a drug is truly beneficial, it can reduce the load on hospitals. If hospitals are not overloaded, doctors have time to try more things and learn more about what helps their COVID-19 patients. And so on.

So even with no defined end in sight, it is worth going as slow as we can on opening things up. A slow approach also lets us learn what things have an impact on case load. We have no choice but to run experiments on ourselves to find out what is safe, but if we open things up slowly, at least those experiments will give us useful information and not just a big spike in cases.

I do think we'll get a vaccine eventually, but that we'll be very lucky to have one in 2021. I don't look to a vaccine as the way out of what we're living through now. It may be the way back to something that really feels "normal" but we'll get to something better before then. We just need to remember why we're taking things slow and be as patient as we can be.

Saturday, April 25, 2020

Weekend Reading: The Beaches Are Opening Edition

Here we are, on another Saturday morning! It is going to be pretty hot here today - my phone says we're going up to the mid-80s today. It is the sort of day that would normally send people flocking to the beaches, but they're still closed. San Diego county has said that people can get back on the water for their favorite watersports starting Monday, and people will be allowed to walk and run on the beach if the cities that control the beaches permit it. Mostly, it seems like they will. Parking lots remain closed, though, which may help keep the crowds down.

Face coverings will be mandatory if you're going to be within 6 feet of someone else starting May 1. We don't wear masks when walking around our neighborhood because it is easy to stay 6 feet away from people - we just zig-zag to the side of the street with no one else on it, and in the case when three groups are passing at once someone goes in the middle of the street. Being able to do this is one of the benefits of living in a quiet residential neighborhood. Mr. Snarky and I took a walk yesterday evening and were commenting on how different it would be if we lived in one of the cooler parts of town with less space. As far as I know, San Diego hasn't closed any streets to traffic to make it easier for those folks. 

I will probably go for a beach walk at some point in the next few weeks, but not right away. I'll give everyone time to figure things out. Maybe first I'll go for a walk by Mission Bay, which I can walk to (although it will be a long walk). I will wear a mask if I head down towards the water. I think it will be easier to keep 6 feet away now than it was earlier on, because I think more people will also be trying to preserve their own 6 foot bubble - but it won't be as sparse as our neighborhood walks.

I think reopening our outdoor spaces is a good thing as long as we can keep from crowding. The  more spaces that are open, the easier to avoid crowding. According the announcement I linked to above, the county is hoping to have a plan in place to allow more outdoor recreation by May 1. My hope is that by having access to our outdoor spaces, we'll be able to handle keeping the indoor spaces closed longer. As more data on transmission comes out, it seems increasingly clear that the primary mode of transmission is droplets and the risky thing is to stay in close proximity to other people for prolonged periods of time. So I am in no rush to sit down for a meal at a restaurant or even to lay out a towel on a beach surrounded by lots of other people doing the same. But I think a walk on the beach, particularly if I time it to a less busy time, would be fine. And I've thought that for awhile - I didn't see the problem with Florida opening its beaches even while I think Georgia is setting itself up for a lot of pain by opening restaurants and bowling alleys and the like. 

But my expertise is not epidemiology or virology, so let's link to some of the new studies from actual experts!

Here's the study from China about the not yet symptomatic person who went to a restaurant and apparently infected people at both neighboring tables that were in the line of airflow (due to the air conditioner), but no one else, not even at the neighboring table outside the line of airflow.

And here's the study from South Korea about the call center floor, in which the cases are predominantly on one side of the building.

It is still early, and we have much to learn about this virus and how it spreads. But the evidence so far points to droplet not aerosol, and longer time period exposure over short contacts (e.g., sitting near an infected person at work, not just passing them in the hall). Based on this, I would not be in a hurry to surf (for those who don't live near a surfing area, surfers hang out on their boards not that far apart from each other for long periods of time, waiting to catch a wave), but since the surfers here have been some of the loudest about wanting back in the water I suspect we'll have data on this soon enough.

California's first COVID-19 death was much earlier than we thought. It now seems likely that both NY and CA had community transmission going on in February. Why did the two states have such different outcomes? There are a lot of plausible theories: differences in the particular strain that infected each area (NY was seeded from Italy, CA directly from Wuhan), difference in transit methods (plenty of Californians use public transit, but there are differences in degree of usage and also mode), differences in weather, and of course the difference in timing of the lockdown (a few days at the point on an exponential curve when it really takes off can be a very big difference). We don't know the reason and we probably won't know for some time yet. We may never know. I think the best thing to do is ignore the online shouting about this sort of thing and focus on what the actual studies are telling us about transmission and infection risks.

The reports coming out about strokes in young COVID-19 patients with seemingly mild cases are a sobering reminder of why we should go slow on reopening things.

We all really want treatments or a vaccine, but we should keep our expectations on when we might have those things realistic. Derek Lowe at In the Pipeline has a run down of the types of treatments that are possible and the timeframe in which they might be available.  I've linked to a similar summary from Matthew Herper before, but I think it is worth reiterating. Derek leaves out convalescent plasma, which is available now, albeit only by recruiting recovered COVID-19 patients to donate and so not in anywhere near the quantities needed to make it a common treatment. There are studies indicating it is effective starting to come out.

If a repurposed small molecule treatment proves at all effective (and we're probably still a month away from having meaningful data on the most likely of the bunch, remdesivir), there will be a big manufacturing scale up needed. Lisa Jarvis has a good write up of what that means.

Here's some promising vaccine news.

If you haven't seen the story about the Pennsylvania workers who slept at their factory for 28 days go read it. It will make you feel better about humanity.

This is a really good point, and I don't think it is just billionaires thinking that other people should have to go back to work while they continue to work from home.

This made me laugh:

As did this:

Here's something funny that is not about Trump:

This xkcd cartoon may be maximally funny only to bioscientists old enough to have done sequence analysis in a text editor... But it really made me laugh.

I think I linked to the Welsh weatherman who played the drums to his closing music... here is the utterly delightful follow up:

This is so cool. I'm sad we can't really go see the bioluminescence right now. But there will be other times.

Here's your bunny of the week:

Happy weekend! I'm planning to get my hammock out under the avocado tree and just chill. I hope you have something good planned, too!

Saturday, April 18, 2020

Weekend Reading: Another Week Edition

We made it through another week! Honestly, that's what I am focusing on right now: making it through each week. I know a lot of people say that the days all blend together and weekends don't feel like weekends, but for me weekends are definitely different from weekdays. There is no schoolwork to help with, and I shut my work laptop down on Friday evening and don't generally open it again until Monday morning. I still look forward to weekends even if I haven't figured out how to make the best use of them to recharge these days.

Yesterday at lunchtime I thought I might end up needing to work a little this weekend. I had a list of five things I had to get done before Monday and when I stopped for lunch I had done exactly one of them. I'd spent some time on Petunia's math assignment (including looking for something that had a weight marked on it that was less than 5 grams - I eventually found a tube of chapstick that did the trick) and some time helping on a project for a colleague who has bigger child schooling challenges than I do. These were the right things to do but I still needed to do the items on my list. Luckily, I had a burst of productivity after lunch. I had to stay at my desk a little longer than usual, but I still got to close down my work laptop for the weekend before I went to make dinner.

Anyway, let's have some links.

In self-promotional news:

In case you missed it, I wrote up the last trip my husband and I took before everything shut down. It was fun, but a little weird.

Also! Last week the latest Annorlunda book came out. Nontraditional is a wonderful collection of stories about the students Nan Kuhlman taught in a small town community college, and how they (and she) got second chances in life. This was a terrible time for a book release but once it became clear how terrible it would be it was too late to change the release date. I've really struggled to find reviewers for it which makes me sad because it deserves more readers. If you're looking for something to read, give it a try!

In coronavirus news:

Obviously, read Ed Yong's latest in which he tries to get us all to think realistically about what comes next.

Remdesivir has been in the news a lot this week. It is a small molecule made by Gilead that inhibits viral proteases polymerases (ugh sorry about that slip - I was still caffeinating when I wrote this). It was tried against Ebola without much use, but there is in vitro data indicating that it is a better inhibitor of the SARS-CoV-2 polymerase than the Ebola polymerase, which is encouraging. Here's a nice summary of that research.

Derek Lowe at In the Pipeline has a good summary of what the various leaks and signs about remdesivir tell us so far. Spoiler: not much. I can't find it now, but I also saw someone tweet out a notice from that the more informative trial with a placebo arm is extending the size of its treatment group. That often means that the effect size being seen in preliminary data is not large and therefore the trial team thinks they need a larger sample to get meaningful statistics. But we're all just reading tea leaves and we won't know anything until the trials actually report.

One thing that is a bit puzzling to me is that all of the trials seem to focus on relatively late stage disease - i.e., once a patient is hospitalized. I guess that might be because remdesivir has to be given by IV and hospitalized patients make that mode of delivery easier. But most of what we know about antivirals for respiratory illness indicates that they are most effective if given early (e.g., Tamiflu is most useful if given within 48 hours of the onset of symptoms) and there is encouraging data in monkeys based on early administration of remdesivir.  We are also sadly learning what populations of patients are most likely to progress to hospitalization and so I wonder if anyone is planning a trial in which those patients are treated with remdesivir early, with an endpoint of reduced hospitalizations.

But trial design is not my field of expertise and the people designing and running trials right now are not stupid. I assume this idea has also occurred to them and that there is a reason we're running the trials we're running.

There have also been some encouraging reports about repurposed drugs that target the "cytokine storm" that can occur in very sick patients. No trial readouts yet or even the sort of leaks and tea leave readings like we're getting on the remdesivir trials, but anecdotes coming out that some of the drugs may be beneficial.

I don't know if I posted a link to this before, but Matthew Herper published a good overview of the potential treatments for COVID-19 in March. If you'd like a better understanding of what treatments might become available, that is a good place to start.

I have seen a lot of angry tweets about the fact that we're all staying home to buy time and our government does not seem to be using that time to ramp up testing. I agree that is very frustrating, but better testing is not the only thing we're buying time for. We're buying time for more trials to complete so that we know which, if any, of the currently available drugs are beneficial. We're buying time for the efforts underway at various biotech and pharma companies to move other treatment options into the clinic.

Also there was some good news this week about swabs, which are one of the limiting components for a testing strategy. More validated swab materials and the less invasive swab collection method now approved by the FDA could both speed up testing.

So basically, we're all staying home to buy time for good science to be done. We want to accelerate things, but not rush them. We need to understand the detection limits of the tests. We need to know which drugs have a potential benefit that outweighs the risks from any side effects.  We need the vaccine safety trials to have time to complete. We need the science to be done and done well.

I thought it might be helpful to share one of the little things that has been helping me be OK with staying home:

My husband and I really enjoy the silly British quiz show 8 out of 10 Cats Does Countdown. We find the episodes on YouTube. Here's a randomly chosen episode. In searching for that I discovered that it might actually be available on Amazon Prime, too. I'll have to check that out.

But those shows are long and we don't always want such a long show at the end of the day. So we were happy when the YouTub algorithm alerted us to the existence of Jimmy Carr's Little Quiz of the Lockdown. It is a short nightly quiz and it has been a good way to unwind before bed. Here's a compilation of a week's worth of entries, but we tend to watch them one or two at a time.

And in other news... here are the things that made me smile this week:

This story is quite something:

Also a great story:

Look at these cute birds!


How cool are these flowers?

Here's your bunny of the week, from Carl Bovis who usually tweets wonderful bird pictures:

Happy weekend!

Saturday, April 11, 2020

Weekend Links: The Things that Made Me Smile Edition

Hello from my dining room table! Or, as I call it when our meeting schedules dictate that I move out here to work, the auxiliary office.

I've decided that today's post is mostly going to be links to things that made me smile this week, because it was a tough week and I would like to revisit the smiles! Our school district started up distance learning this week, albeit as a "soft launch" in which grades won't be affected by any of the work. My children were not swayed by that pronouncement, though, and so there has been some stress here at Chez Cloud about assignments that won't load, etc., etc. The kids also (reasonably) sometimes need something explained by a person and not a website. This seems to particularly happen with math, so I've been refreshing my memory of fractions (4th grader) and geometry (7th grader). I also learned about the difference between a population and a community so that I could help Petunia with her science assignment one day. This was complicated by the fact that all of the material she was looking at was in Spanish and I don't speak Spanish. Luckily, there were plenty of resources in English just a web search away....

But the time I spent doing 4th grade science and math and troubleshooting various technology issues was time I didn't spend doing the job that pays our bills. I am quite busy at my actual job because we sell and configure software for scientists and pretty much all of my customers are either 100% working from home or only allowed into the lab on a reduced schedule for essential activities. So they all suddenly have a lot more time to focus on their informatics needs and have been contacting me about speeding up their projects or adding new projects.

When I see the pictures of long lines of cars waiting for food bank distribution events or read about what people working in essential jobs are dealing with, though, I am reminded of just how lucky I am to have the problems I have. So after just a few general links, I'll post the things that made me smile.

First, here's a more well-rounded write-up of San Diego's distance learning launch in case anyone is curious to know more about it. I think the teachers and the district are working really hard to make this a good as it can be and I appreciate all their work.

This essay about why some voters might have preferred Joe Biden to the candidates offering big changes really resonated with me, even though my preferred candidate wanted to bring big, structural change. I was tired by the demands of this era before the pandemic hit. It is only worse now. I can see the attraction of the promise of four years to catch our collective breath.

The logistical failures Gov. Inslee points out in the interview described in this piece are so frustrating. I work in a very different sort of delivery project, but one of my most important jobs is to see the potential roadblocks and risks and have plans for how to work around them so that we can get to our goal. It is really frustrating for me to read about the failure of my government to do this basic task of project management. I know the federal government has people who are good at this sort of thing, but they have clearly been sidelined. We are all going to pay the price of that.

Derek Lowe has a good summary of the latest report on the results of compassionate use of remdesivir (Gilead's drug). The short answer is we still don't know much. Actual clinical trials should start providing results soon and that will tell us more. Given the timeline to get a vaccine it would be very, very good news if one of the repurposed drugs was actually beneficial. But we'll only know that if we take the time to do a proper study. Don't even get me started on the mess that has been made in the hydroxychloroquine situation.

I also saw a write-up of Pfizer's work for the first time. A lot of us in the industry have assumed (or even heard through the grapevine) that they were reactivating work on some leads they had developed during the SARS epidemic. While this isn't as much of an acceleration as repurposing a drug that has already been approved for other uses, it is still much faster than starting from scratch. Presumably they already have data about which compounds in their series have acceptable pharmacokinetic parameters and have learned some things about specificity and the like from their past work. Given all the layoffs and other turmoil at Pfizer (and other pharmas) in the intervening years, I wonder if the scientists who know this data best are still at Pfizer. I hope so. Here's a write up on Pfizer's various efforts that includes a discussion of the compounds that came from their earlier SARS work.

OK, now for the happy things.

This was the obvious song for this period in time:
But this one is pretty damn good, too:

I loved this:

Wait for it:

This is beautiful and amazing:

Also beautiful:

This, too:


I've enjoyed watching people on Twitter discover the existence of swamp rabbits:

I don't know enough botany to do this but it is a great idea!
I am really enjoying the things people are doing to help each other through this time:

Here's your weekly bunny:
Happy weekend everyone!