Archive for April, 2020

DIFFERENT QUESTIONS

April 29, 2020

The other day, a woman called in to Doctor Radio wondering when there was going to be a cure for Covid-19.  Her voice was peremptory, as if this were something we should all be expecting by now.  Americans are impatient, and while I am impatient, I have inhaled a dose of reality.  I know there are many drug trials, at least a dozen, with results due anywhere from next week to late September. That’s good. What isn’t so good is that if we had any trial stopping event—like polio vaccine, which was so powerful the drug trial was halted and the vaccine being given—we might know that by now. Something that pulls someone off a ventilator overnight, or ECMO, or empties an ICU is a big deal, and I haven’t heard of that yet.  I don’t expect to.  

But, we have something now. One Remdesiver trial showed the time for half the patients to recover was 11 days with the drug and 15 days without. The death rate was 8% in the control group vs. 11.6% in the treated group.  That is a 31% difference with a p-value of 0.059. The time to recover was significantly shorter; the death rate statistically not significant (want p-value under 0.05, which is the probability if chance were operating and nothing else, we could have seen this result or one more striking), but with a larger study, I suspect we would see a value under 0.05, which is an artificial construct but generally used.  Study two compared length of time efficacy; 5 days’ treatment is as good as 10 days, good news. 

From Oxford, a genetically modified MERS virus vaccine stopped Covid in macaques, a control group of whom did not survive similar doses of the virus without the vaccine. This study needs to be watched. 

But for the moment, let’s look at reality: how quickly we are going to return to whatever will be normal.  And those last four words to me are key. Sports, concerts, flying, cruise ships, restaurants, road trips, and schools aren’t going to be normal for some time, in my view, a lot longer time than many think. I have cancelled two trips this spring; I don’t expect to canoe in September, and I am not expecting to see the eclipse in December. 

Certainly not on a cruise ship.

Some wonder whether it is worth getting the virus and getting it over with.  Given the number of anecdotal cases of young and middle aged people having severe disease, I don’t think that is a wise choice, especially if one has diabetes, is obese or smokes, which are not rare in society today.  I correspond with people overseas, and one in Asia told me the whole family just got clinical Covid.  Two have anosmia, mild in the scheme of life, but people complain bitterly about it.

There are additional issues with the virus either causing a coagulopathy, where the blood doesn’t clot, or attacks the blood vessels directly.  Coronavirus myocardial damage is known; coronavirus encephalopathy and involvement of the thalamus in the brain is known, and the virus been found in the kidneys.  One third on ventilators have significant kidney disease. That should bother anyone.  I sure don’t want that at my age.

We also don’t know whether there will be after effects of pulmonary scarring, congestive heart failure, or chronic renal failure. Again, I don’t want to get this virus. 

I look at a lot of numbers and have noted from the beginning that Washington State never had a big problem after the initial attack in the nursing homes.  I expected California to explode with cases like New York, but it didn’t. Florida had people on beaches, and it had cases, but not like New York’s. I have wondered whether the population density of susceptible people mattered, and I think it does. The media does mention that “cases are rising xx per cent,” but they are rising from a smaller number.  What is clear is the numbers of cases in the mid-continent haven’t yet started to fall, whereas they have on the east and west coasts.  That concerns me, but to say the numbers are rising at 10% a day means a doubling time of 7 days, and NYC started with doubling at 3 days and continued that way for awhile.  Oregon is going to allow elective surgery.  That makes sense, because elective surgery is often biopsies and fixing things that we all have come to expect with surgery.  I think social distancing worked; we need to remember that there is a two week delay when people start moving about before we will know if there are new infections.

For those who are saying we never had to do anything, that this virus wasn’t all that bad, keep in mind that the purpose of public health workers is to prevent things. We don’t have many cases of measles; if people vaccinated, we wouldn’t have any.  It’s not that measles is gone; it just doesn’t have a home here. We social distanced and we cut the number of Covid-19 cases.  Not enough, and the numbers are well past the number of deaths from influenza that people quote every year.  I suspect they will be more than 100,000, the low end of the original estimate. We are already 11,000 over the estimate for 1 May that I read two weeks ago.

The other issue is testing, an important catchword, and we need to also know how good tests are,  Recently several were checked; three were good.  It turns out, (proof below),  a test that is 90% specific (one has the disease, test is positive) and 95% sensitive (one doesn’t have the disease, test is negative) and the disease is relatively uncommon (5% of people), a positive test has a 50% chance of being false positive.  It is the difference between “if I have the disease what is my test?” and “I test positive, do I have the disease?”  The more common the disease in the underlying population, the more likely a positive test is true.  It’s why public health people did not require AIDS testing for wedding licenses. The disease was uncommon enough that a third of the positives were true and the other false. 

5% prevalence of disease


Test PositiveTest NegativeTotal
Disease positive (has it)45550
Disease negative47.5902.5950
Total92.5907.51000




This is sensitivity of 90% (45/50) and specificity of 95% (902.5/950).  Positive test has (45/92.5) or 49% chance of being a true positive, even when the specificity and sensitivity are both 90% or more.

Same with a 20% prevalence in the community would make false positives only 18%.

So, I wear my mask, take my walks, and wait. 

Maybe next year we will do a lot more, but not soon.  We don’t yet know for sure whether people are immune to the virus after having had it or can get it again. There is a bit of national denial in thinking that sports will start soon. They won’t until or unless there is a vaccine or an anti-viral better than Remdesivir. Additionally, we don’t know what it will take to get a vaccine, or whether a vaccine will even be effective, let alone for how long and what side effects are present. People want something, but vaccines can backfire and overstimulate the immune system, which is a huge problem with this virus.  Indeed, many medicines are in trials to see if they can turn down the immune system.  In the meantime, beware of those who are pushing strengthening our immune systems.  Stay in good health and let your immune system take care of you.

We are finally doing random sampling in various cities to get a sense of how many asymptomatic infections are present.  The evidence we had from China was that few were asymptomatic.  That is not true. We need more information about relative risk, not that 2/3s of the deaths are over 70 but what the risk of a 70 year-old or more, without chronic disease, surviving. That’s a different question.  We need to give the risk to people in various decades of life with and without chronic disease as to what their risks are—to be asymptomatic, to avoid hospitalization, to avoid ventilators, and to avoid death.  

If public health professionals are doing their job, people will complain that they were too strict. 

It’s nice to be still alive to complain.

THE JOYS OF CURIOSITY AND COUNTING

April 25, 2020

I miss hiking.  I miss snowshoeing, my last one five weeks ago now, when I soloed into Arrowhead Lake in the Diamond Peak Wilderness with nobody out there.  I knew I would not be going any time soon, and I fondly remember that special day.

Snowshoe tracks on Arrowhead Lake, Diamond Peak Wilderness March 2020

I am fortunate enough to be able to go out and walk, and nearby Alton Baker Park, straddling Eugene and Springfield, has miles of trails in meadow, oak savannah, and riparian zones.  I  cross Alton Baker to get to stores by the UO, and I’ve walked the entire 16 mile river bank loop on both sides.  Occasionally, I do a loop from Knickerbocker Bridge to Autzen Bridge and back through the park coming home.  It is about 4 miles and goes along the Willamette and then the canoe canal.  For the first week, I did my usual walks that I had done before.  

Then I decided to add more distance, going further downstream to the deFazio Bridge.  Because it is spring, I started counting the number of different wildflower species I saw.  I have a good app from the brother of noted trail writer William Sullivan.  For the past two years, I have used the app and a few other books to identify well over 150 species of wildflowers on my hikes over the course of the season.  I almost hit 200 last year.  In the park, I could usually hit 20, and one memorable day got near 30.  

Mind you, many of the wildflowers are weeds, but many of them are pretty, and I’m a non-native here, too.  I started by walking through a neighborhood over to the parking lot by Autzen stadium, past Cuthbert Amphitheater, where I have seen a couple of concerts, down to the duck pond, and the center of the 1 to a billion solar system model, and then upstream along the river to Knickerbocker Bridge and back home.  It is somewhat more than 5 miles and fairly quiet.  There are interesting birds, too.  Two of us are making an analemma at local noon throughout the year near where the big “Sun” is. I get to see rushing water leave the duck pond to go to the Willamette, then the Columbia, and finally the Pacific.  Or the atmosphere.  

But I couldn’t have imagined what I was going to see in the way of flowers.

With wildflowers, like birds, or stars, observing is quite simple: you look, if you don’t know what something is, you try to find it in a book or ask somebody, and eventually, if you see it a lot you know what it is, and after a while know its habitats. What you need is curiosity more than anything else, and I was lucky enough to have a lot instilled in me when I was a kid.  It ranks up there with reading as one of the greatest gifts I’ve received.  In Tucson, I did birding on my neighborhood walks, being called the Bird Man, and 20 species in a day was great.  The Christmas Bird Count included my neighborhood, and then I would push 30 species. I found that telling the difference between a pyrrhuloxia and a female cardinal was easy, whereas earlier I thought it impossible.  Verdins had different calls, depending on the time of year; we had rock wrens in the neighborhood and I heard an occasional canyon wren, in addition to the ever-present cactus wren, the state bird. I am very auditory; I remember people by their voice rather than their face, and I do birding the same way. I may not see a spotted Towhee, but I sure can tell when I hear one.  Lately, however, I have been spotting them more easily.  It’s practice and knowing what to look for.

Two weeks ago, I saw twenty species of wildflowers on a walk for the first time this year.  As I walked through the neighborhood, I saw a non-native pale blue violet growing outside someone’s yard.  By Autzen Stadium, I saw my first California poppy, and by the Science Center I saw the first camas of the year, a lovely five blue petaled plant.  I found a stretch near Frohnmeyer bridge where within 100 yards there were over 20 different species. I saw Hooker Fairy bells and realized the past couple of years I had misidentified a Woodland buttercup.  I went nearer the river and saw a Money plant, 4-pealed pink flowers. Larkspurs and Plumed Solomon seal were everywhere, along with Trilliums and Fringe cups.  Someone picked an Iris that I needed for my count, but a week later two more sprouted.  Near them were a cluster of Fawn lilies.   I learn more each year from the mistakes I have made.  Last year, I learned about salsify flowers, this year, I realized there were three kinds of geraniums with different sizes and leaves. I am picking up on grasses, too.  A few days later, I hit thirty species and ended the day with about 35. I figured that would be the top number. 

Camas

The app is great: I open it, make sure I have the right part of Oregon, the right week, and the right elevation. That decreases the flowers to about half, or 1800.  Wildflower (vs.  conifer, other tree, grasses, etc.) color, number of petals, size of blooms, whether leaves are alternate, opposite, apical or basal, the environment (Disturbed, alpine, rocky, riparian) bring the numbers down often to a dozen, sometimes to three or four. Then I can look at a map, read the description, and see if this is the plant.  

As the weather got sunnier, the counts rose.  I hit 40, then 45, and even 48, getting a sow thistle, Persian speedwell, and yellow oxalis in the last 20 yards, when I wasn’t expecting anything. That’s the other thing about observing; you have to always hope there is something there and at the same time be happy just to be looking and seeing what is there. Sort of like fishing.  I identified a Torlinga crabapple tree, then looked at my feet where I was almost standing in a patch of Lesser Periwinkle.

Today, I was musing how the single dogwood blossom I had seen for the past week had finally gone. For whatever reason, I looked up, which apparently I had not done, being more interested in ground blooms. There above me the whole tree was abloom. Fabulous.

Dogwood

A lot of times, I need to try different colors of the petals to make sure I am not missing something else.  I don’t identify everything but close to 90%.  I write them down when I get home and count them when I am out there.  I count a lot of things, always have, every day, often without thinking and often without knowing what I will do with the counts.  I watch the birds, too.  The other day, a Canada goose landed on the duck pond. As he landed, his feet extended and briefly, he was skimming the water like a water-skier, minus tow rope.  I had never seen that before.  There is a lot of interesting stuff in nature, but one has to look, and it helps if one both knows what one is looking for and at the same time, have the joy of looking for its own sake. One memorable morning in Nebraska, dancing cranes made the whole Platte River bounce for about 2 seconds.  I saw it myself.

https://michaelspinnersmith.com/2018/04/09/the-morning-the-platte-river-danced/

Canada geese young

This past week, I topped 50, then 52, reaching 56.  Some wildflowers are starting to fade. Oregon grape will be gone soon.  Someone picked the iris and the salsify, but I found another salsify near the river and two new irises have appeared.  The Wild roses are blooming now, and one of the plants I could not seem to identify turned out to be Miner’s lettuce.  That gave me 57 for today. And it was raining.

I’m looking forward to what I hope will be a chance to go back up Spencer Butte and this summer into the high country.  Trail work also means a chance to see new wildflowers.  But I am so happy I started looking where I hadn’t looked before.  

It’s remarkable what one sees.

Ladybug on English plantain
Fawn lilies
Plumed Solomon’s seal
Hooker Fairy bells
Red Columbine

DAYSRUNTOGETHER

April 7, 2020

As I began to write this, Bill de Blasio, the mayor of New York City, asked for a nationwide draft of doctors and other health care workers.

Ah, the draft.  I was number 56 in 1969; one brother was number 139; the other was a staff sergeant in the Marines at Da Nang. I ended up going to medical school, joining the reserves there, then spending two years’ active duty aboard the ‘Lou, the USS St. Louis (LKA-116), with two deployments to the western Pacific and having seen just about every country that bordered the Pacific north of the equator.  Just about.

The draft ended in 1973, so if I had not joined, I never would have had the experience of being a medical officer in an organization where medicine was not the top priority.  It had to be that way in the military, but ultimately that was the reason I left. But I never regretted my service. Not once.

In the interim, I have often wanted a draft, and we likely would have been a lot more cautious about entering conflicts if we had one.  A lot of young men—now women—need a time in their lives when they have to follow orders.  A big reason we got out of Vietnam was that everyday America was taking part in the war. People in the military weren’t heroes then, other than the real ones who got “The Medal” or one of the Stars. When I returned home, nobody spat on me, but nobody treated me any differently, either. I was just a young man in the military.  Just about everybody had to do it, unless they had bone spurs or some other often minor condition.  

It was a couple of decades later before Veterans Day actually had meaning for me.  I realized I was a veteran, not something that had often occurred to me for at least 15 years after my service. Really.  

Now we are in a pandemic, with doubling times of deaths recently in the 3 day range, starting to lengthen now to 4-5 days, having doubled 14 times total as I write this, with only four more doublings before we hit 100,000.  You can see why 200,000 (one more doubling after that) is on the table. And NYC needs help, badly.

From what I see and hear, there are times I am tempted to pull out my old bag and go to volunteer, since I doubt there will be a doctor draft any time soon.  Even as out of date as I am, I could certainly screen, talk to families, answer calls (with my upstate New York accent), help with intubations, and probably a few other things.  

But that’s more romantic—and a lot crazier—than reality.  I would likely get in the way, probably get sick, not unlikely become a ventilator candidate, which I would refuse, and die alone, my last days becoming part of the problem I wanted to help, 3000 miles from home.  I’d rather do it here, but as of this writing, we have had our 10th doubling for cases (1024) and our doubling time is about six days. That doesn’t mean we can’t have a huge outbreak by June, but the doubling time is gradually lengthening. Our growth factor (new/prior day) is often under 1, which is good.

I’ve never been a hero, and I am not about to be a martyr, either.  We need to have a solid volunteer corps where people can immediately go to where they are needed, starting close to home. I might be good talking to families who want information.  When I practiced, I did not shy away from talking to families of dying patients.  I didn’t like it a good share of the time, I certainly didn’t get paid extra for it, but that was my job, and I made sure I did it.  I’ve been on both sides of the white coat, and I know how important it is to actually speak to a doctor about an ill family member.  But I doubt anybody will be interested. I am good at knowing when care is futile and when there is no ethical reason to continue, but many others know that just as well and are current.  

That leaves me one other spot on the left coast: the USNS Mercy. After all, I once served on a ship.  I know how to enter and leave one (if not in uniform one faces aft, where the flag is, then one faces the officer of the deck and requests permission to come aboard.) I know the numbering system on board, so if something is deck 2, frame 46, I know it is two decks below the main deck, port side and up forward to frame 46.  This is not rocket science.

I would have a place to stay, no worries about commuting, would be available for all sorts of duties.  After all, that stuff is not easily forgotten.  My hair is short, I line up my buttons with my zipper, I can say “Sir” easily, and most of all, I have this skill.

The Navy wants no COVID aboard the ship. That is impossible.  It will happen. And I recognize that.  But with hundreds of thousands of retired military in southern California, my ending up on the Mercy is not going to happen.

So, the days run together. I have lengthened my morning walk from 3 miles to 5, much along the Willamette River, which is flowing well if a bit low from another dry winter.  I wear a mask now—just a balaclava, so long as the mornings are cold—and count the number of wildflower species I have seen.  I hit 23 today, which is good for this time of year in a limited habitat. The towhees are zzzzttting, the scrub jays calling, with an occasional Steller being seen, cormorants are on one of the river islands, herons are close by, and there aren’t a lot of people out there.

It’s a good time for those few of us who dislike crowds.  I feel sorry for those who can’t be in large groups, especially because life may change after Covid.  I don’t know whether I will ever tutor again in person; I won’t be carpooling to the high country for hikes or for work parties on the trails.  But I spent my first year here not carpooling, and lately, I have been hiking alone, rather than with the Club.  Those are my best hikes, my best snowshoes.

Up in the high country, it will be quieter this year. The new requirements for trail reservations at some of the busier trailheads are not going to be rolled out as soon as planned. The trails may get a rest from the crowds this summer.  I worry about fire season, but if few are in the high country, that removes a large risk.  

Coming home after my walk, I spend time checking the numbers of the epidemic, seeing if I detect any changes. I also do some algebra problems on line and go to zooniverse and pick a couple of projects to help out,  My lap is open for a couple of the lap cats.

I would love to help, and maybe I will get a chance to, but unless things hit the fan big time here, I am best suited to take care of myself and be one less problem, one less case.

Milton’s Sonnet 19:

“…“God doth not need

” Either man’s work or his own gifts; who best 

 “Bear his mild yoke, they serve him best. His state 

” Is Kingly. Thousands at his bidding speed 

 “And post o’er Land and Ocean without rest: 

 “They also serve who only stand and wait.”

English Daisies
Following the CDC (a huge disappointment overall in these times) guidelines. Elections matter.