Sunday, December 20, 2020

A range of emotions (count down to New Year pt 2)

 Let's be absolutely clear. I'm shattered emotionally. My inner being is being torn between screaming into the void WHAT DOES IT MATTER THAT WE KNOW ALL OF THIS SINCE YOU DON'T LISTEN and whisper softly "say good bye to the people/things you care about since they will not survive this".

It's difficult to explain how I feel looking at my diary from February, and also the entries from April where I state things like "come May 1st we will be on lock down in Memphis and it will be too late to stop the spread in the poor community where they can't work from home". And the April one stating "the USA will see a spread and deaths in the fall that people won't comprehend".

Not to mention the most heartbreaking one where I wrote in July estimating by my (negative yet apparently pretty accurate) predictions on how exponential spread would go in numbers in the USA and then the deaths to follow. Notably I was wrong as in even I were too optimistic on the speed for cases in September.

I did write a small comment to myself in August - the time I was quarantining in my hotel room in Stockholm and had to acknowledge that my emotions after going through the transAtlantic flight experience were pretty high and unstable. (That's something for part 3 since it will take longer to explain the absolute rollercoaster that went on inside my body for 30 hours while going from safe house aka home in a controlled space to a controlled hotel room via four airports with vastly disparate rules and actions.)

Anyway, my comment in August was that we would see the highest number of the year after Thanksgiving. That said, it's not rocket science so I won't pat myself on the back too much. And also that the uptick in cases after school and all the activities in Septebmer would lead into more cases in the fall.... and then thanksgiving.... and then hoping that the fact that cases were up would mean we didn't have to discuss Christmas. Here I was wrong, and I had put a note saying (probably too optimistic, people are great at rationalizing "not me and my family but everyone else is needing to do X, Y, K".

And then looking at my diary entries of Sweden in the fall "once the cold sets in". Yes, not difficult to predict that the cases were going up - yet difficult to read right now when looking at the numbers and knowing my family is so far away only reachable with international air travel.

Long and the short of it is this; it's extremely tiresome seeing a situation play out in front of your eyes - knowing that the people you love are in danger - because everyone seems to need to "experience the horror themselves" before acknowledging the situation.

The lack of understanding the full notion - I don't have to die from a car crash to know that I should keep seatbelt on and drive the speed limit. Again, IF it ONLY affected you when you make the stupid choice I wouldn't care as much (individual freedom and all) but when your choice of freedom puts MY life in danger, that's where I fricking draw the line.

(Right now, I'm not mentioning the vaccine and the people who don't want to take it. I'm too angry and you know, there's not enough vaccines to go around so if people say no to vaccines, that means I move up the line to get the vaccine faster.... and therefore I guess I should just accept your fricking freedom to say no? Another day I'll delve in why this argument is not a proper bioethical choice and not the right one for me.) 

For right now, I've spent 9 months actively not wishing ill on people who are in power and who have put too many people at risk and have been the cause of so many (unnecessary) deaths. I'm only human and there's a limit for my compassion at this point. That's what I am doing this Holiday season - asking for grace and compassion so when I come back after January 1st, I can stand to meet all these people around me who spout lies, confusion and hate regarding the vaccine and the virus. And with stand to meet, I mean I can meet them with a compassionate face and giving them love as my neighbour and turning the other cheek since there is NO other way out of this. I know that. 

Why? Because it's a fricking airborne infectious disease and it spreads between people regardless if I like or dislike them. And the only way it will stop killing and hurting people is if we get enough people vaccinated and keeping the infection rates down. 

And the only way to do this (if we aren't a dictatorship like China where they welded the doors shut) is to do the tried and executed way of telling people to stay at home, give them financial ways to do it, give them hope and add in incentives for companies to keep going - OH and GIVE them Vaccines for free to help!

It's not like I'm advocating for a mandatory vaccine to be able to fly on a plane, see hockey, visit grandmother in a home, have a job, going to a restaurant or sing in a church choir. Where I live, LAND OF THE FREE, this will not happen. But separate businesses will start enforcing these rules and it will be uneven, inequitable and lots of families and children will suffer. But let's not listen to the Infectious Disease experts.

You go with your freedom. Me? I will continue to give money and effort to the poor and my community. And I will live alone* in my house and Work From Home. Wear my mask to the few times I go to the store and live a good life without travel or friends over to party.

I will lose a lot of family and friends due to the virus. And that will make me sad. And most of all, kinda convinced that the world would be better with me as a dictator. (obviously a joke, please see the section of "trying to fricking cope with this PREDICTABLE year where nothing was stopped")

Part 3 of Count Down to New Year will be less bitter. See this as my one time venting and who knows how long this will stay. 

*with my bubble man 

Friday, December 18, 2020

Giving for others - Thankful for my blessings (countdown to new years pt1)

 I wrote a couple of things for Thanksgiving, but they seem fitting for my take on 2020 and how I've tried to handle the Covid situation. Let's say I'm going to do a couple of COVID 2020 DEBRIEF POSTS. That's how it feels right now.

I didn't even pay attention that I had written this post before. 

So, if you want to know the spcifics of what I'm grateful fore - go to the November post. I only have one (that's bad).

My ket point, and this was where I got stuck in "I'm not bragging but want to share and maybe you would like to do something similar" was when mentioning how much of my salary this year has gone to others/charity. I've given more this year than ever. Why? Partly becasue I have not spent any money on travel or restaurants. No theatre nor opera performance. I haven't been to an art opening and I haven't purchased any paintings, photo cards or any other things that I usually buy when going to local art galleries, vernissages, art festivals as such.

However, I have given to these things regularly during the year:

local theatre company

globally to Doctors without borders 

Kiva - microloans all over the world

Currently 5% of Gross income. Most of that money otherwise spent on travel, restaurants and experiences (and HOCKEY). Mainly this has been easy since I decided that if we didn't go out to eat, drink and travel - I could spend a good portion of that money on others who will be in need of it since clearly I could spend it before, so why shouldn't I spend it on people who need it now?

  • I've also tried "two birds with one stone" and purchased at least 12 races of virtual races for good causes (charity). This has been a way for me to keep motivated to get out of the house and walk/run when the weather was 100F in the summer, and to keep going when it turned more rainy and dark in the fall. (I am tempted to post a list of the races with photos of all the medals, yet I don't want to come off as a bragging person but someone who want to share happy things! It's been the beacon of entusiasm when it was 100F degrees outside, and it's been similar for running in the mornings in Nov/Dec when it's 37F in the mornings...... I'm no a morning runner....)
I'm not stating this to feel good about myself (only). It's been a help for me to find my footing in a world full of uncertainty and not being in control (apart from over my very tiny part of working from home reality). 

I said short and sweet, so I will stop here. If you have the opportunity of giving to someone else - local foodbank, a venmo for a friendly server, a virtual race that gives to opportunities for women in law (Ruth Bader Ginsburg race....) or anything else that goes to someone out there in need of support - please consider it this holiday season. If there ever was a time to use those "Christmas present money" on others rather than on some unused little gadget, now is the time.

Here are a few links to places where your money will do a lot of good:

local food bank - for me it's MidSouth Food bank:
Purchase to help trafficking women getting out and a new life:

I've also given to local Arts organizations to keep the hope that there will be theatre, opera and art as painting in 2021.

And any local organization that will help service people with tips, work and other normal things. We had a "server Go fund Me" pop up in April for all the laid off Servers in the city area.

Overall though, my thing for this Holiday Season is "Give to someone else additional to you and the gift recipient". This is of course said if the gift recipient is well off/not having a rough time with covid. 

For some of my family and friends this year, I give hard cold cash since that's the best gift they can get from me right now.

Be good, be safe and do to others what you want done to you. I'll write the bitterness post soon.... ;)

Tuesday, November 24, 2020

Thanksgiving (in the USA)

It's not a regular Thanksgiving. It hasn't been a regular year. I'll be short and sweet, pointing out my main take away for this 5 day weekend from work that I am going to have.

I'm thankful for a couple of things;
  • First and foremost that no one in my immediate family has been killed by covid.
  • Second, no one of my friends has died of covid.
  • I have a couple of friends and family who have had covid, but aren't showing too many long term symptoms so far. I'm grateful for that too.
  • I haven't lost my job. And, even though I'm scared of jinxing anything, I don't think I am at risk for losing my job over the next 6 months either.
  • My lovely man hasn't lost his job either, nor being at risk.
  • Both of us have been able to work from home full time, we are lucky enough to have space so it's not one room for both of us.
  • I've given more to charity - both locally to the "server/service fund, local foodbank, the local arts and theatre company, and globally to Doctors without borders and Kiva - than I've ever done. Mainly this has been easy since I decided that if we didn't go out to eat, drink and travel - I could spend a good portion of that money on others who will be in need of it since clearly I could spend it before, so why shouldn't I spend it on people who need it now?
  • I've also tried "two birds with one stone" and purchased a couple (a dozen?) of virtual races for good causes (charity). This has been a way for me to keep motivated to get out of the house and walk/run when the weather was 100F in the summer, and to keep going when it turned more rainy and dark in the fall. (I am tempted to post a list of the races with photos of all the medals, yet I don't want to come off as a bragging person but someone who want to share happy things!)

I'm not stating this to feel good about myself (only). It's been a help for me to find my footing in a world full of uncertainty and not being in control (apart from over my very tiny part of working from home reality). 

It was extremely clear to me when I had the good fortune to go back to my home country in the summer to take care of my parents. After more than 3 months in an all controlled environment (my house and working from home) I got on a flight (well, three flights) and then entered a world where people weren't wearing masks nor felt it was necessary to quarantine after said flights. Needless to say, I had a rough first week. Lucky for me, and I do mean this from the bottom of my heart, I could stay all alone in a hotel room getting my bearings. I could go outside in the temperate summer and go running to alleviate some of my stress and anxiety. And then I got to spend three weeks with my aging parents. It was one of those times where we made memories and I felt like a good daughter and they felt like good parents.

I stayed at a hotel for over 30 days. And that didn't break my bank. (It was a lot of discount due to covid but still, being able to stay in a hotel for that long is a luxury. And I am thankful for that.)

I said short and sweet, so I will stop here. If you have the opportunity of giving to someone else - local foodbank, a venmo for a friendly server, a virtual race that gives to opportunities for women in law (Ruth Bader Ginsburg race....) or anything else that goes to someone out there in need of support - please consider it this holiday season. If there ever was a time to use those "Christmas present money" on others rather than on some unused little gadget, now is the time.

I will use my five days off work to contemplate my luck in life, my present day and consider my future and what I want with it. Lofty goals perhaps, but every journey begins with one step.

(and I will also try and not think and dread too much about my charity marathon run that has to happen week after Thanksgiving. Weather is looking like "the coldest it's been all fall" with temperatures starting in the high 20ies at night, and steady 30-40 during the day.....)

Sunday, October 04, 2020

testing negative and being non-infected with Covid - slight comment

I wasn't planning on doing this but after a few days of hearing news from all over the place (thanks to being involved with someone who listens to Fox and "christian radio", I've gotten a view from there as well as the European sector that I cover on a regular daily basis and then the NPR and "liberal media" we both listen to....).

Anyhooo..... since part of what I'll be writing here shouldn't be an issue on anyone - regards republican or democrat - since it is fact.

The facts are as follows:

SARS-CoV-2 replicates in upper lung or lower lung, but most often is detected in respiratory part of the back of the nose (nasopharyngeal part). 

The PCR tests are designed to find the RNA in the swabs that are put in our noses - or sometimes the back of the throat - and will pick up virus and parts of the virus to show detection when run through the test.

The quick test - is having a high degree of certainty when positive (that means there is presence of virus in you) but the degree of false negatives is pretty high. This means that the Limit of Detection (LOD) as I previously wrote about, will be higher than 0. There's also a pure biological reason that the rapid test is having a low detection level of people "who might be infected but test negative" since there virus need to replicate to a point of detection. None of the test on market - understandably so - can say that they know you are infected the same day or day after (or even up to day "before you have symptoms") - since there LOD is not as sensitive as that.

Short explanation is this: you meet your friend and hug them. They are infected with SARS-CoV-2 and breathe when they say "Happy to see you". You get some of that breath, and viral particles, in your breath that you take into your lungs/upper respiratory tract (back of the nose/throat). The virus is all happy getting cells to infect and starts getting to work.... that means multiplying.

Depending on how well the virus is multiplying inside your cells, the number of cells and number of viral particles and RNA in your system (cells in the nose/lungs, bloodstream or stool) will vary. That's why some people show "positive" on the testing after 2 days after exposure, or others don't show it until 10 days. Either of them could be sick, have symptoms, and get others sick - it's all individual. That's why the guidelines say 5-14 days for quarantine.

As I explained to my parents - both over 70 - when I went to see them. I had a high risk event when flying, and I said "I want to wait 10 days before meeting you outside" (I'd still wear a mask since I'm the potential spreader at that point). The key facts for me are the scientific articles that say "after 11 days of quarantine without symptoms from a high risk/positive covid19 encounter, 97% are non-positive") .

When I re-entered USA to go to home to my house, I lived in my guest room for 9 days  - monitoring my temperature and symptoms - since it was important to me not getting anyone else potentially infected, and then I got a PCR test on day 8 since if my flight was the potential spreader moment. The test would pick up me as infected after 8 days even if I was symptomatic due to the viral replication rate as reported.

I feel like this aspect has been lost in the discussion. The test will NOT pick up on you being exposed today, yesterday, day before yesterday and maybe not day before that. Why? Because there isn't enough virus in you to get a positive in the test. the Swab is only so good. The swab doesn't go everywhere where the virus might be. The amount of virus is not what the Swab need it to be to pick it up.

This is what's mentioned in the discussion as "wait to test until 4 days after exposure" and quarantine until then. It's also why "going to work every day without social distancing even if you test every day will keep you safe from potential infections" (since you don't know who met someone infected the night before since the test will show up as negative that morning after....). 

Everyone with a basic biology degree should know this. 

Anyone having an infectious disease degree or knowledge knows this. Anyone with a pandemic preparedness knows this.

That's why I'm so confused seeing the "Rose Garden Event" from last Saturday since people are not only kissing and huggin (outdoors), they are also gathering indoors without any social distancing. It's confusing on a Risk level, and on a "protection level"

The only conclusion I can draw from this is that; people in the WH really didn't think Covid19 was an issue from the President, not any of the people surrounding him, since otherwise they would've taken precautions like social distancing, mask wearing indoors and no people cheek kissing and then talking to the president.  

Again, I feel like repeating - "What do I know? I'm just a PhD in microbiology with a speciality of virology and pandemic".....

Sunday, September 13, 2020

World Childless Week Sep 14th-20th

From the website: 
"World Childless Week aims to raise awareness of the childless not by choice (cnbc) community. To help the community to find support groups that understand their grief and can help them move forwards to acceptance. It's for anyone who is childless despite their longing to be a parent because they have never been pregnant (for any reason), not carried full term or have suffered the sadness of a baby born sleeping. All our Champions and founder Steph, represent our audience. 

We are here for you through the year, we get louder in September"

Starting Monday is "World Childless Week" and I recommend anyone interested to click on the link here and go explore the community. There will be daily different topics and posts on the subject, and daily webinars.

Overall, the numbers of people who are childless might surprise you - depending on where you are in your life and who you are friends with. At the moment, on average 1 in 5 women reach midlife (45 years old) without any children. In Germany it's as much as 1 in 3. There's a choice of words when it comes to talking about "being without children" and that I like to bring up since it gives a little more nuance to the concept.
  • Some are childless by choice (childfree) - implying that it is voluntary and by choice
  • Some are childless by infertility - tried to have children but didn't succeed either on their own with a partner or with IVF/fertility treatment
  • Some are childless by circumstance - the group that is considered to be the biggest one, and for which there is no "explanation" or rather a quite long list of potential options ranging from "never met someone with whom to have children" to "being with someone who didn't want children and then break off that relationship and then being too old" or other options. If you are interested, there is a list "50 ways not to be a Mother" in the book "Living the life unexpected" by Jody Day found here
For many of us who aren't in the childless by choice category I would say that there are a lot of times when it feels like you are the one who needs to put on a brave face and a smile - and often ignore all the "oh so private commentary regarding my choice or not" that comes along after the question; "do you have children?" has been uttered. 

(I usually say "No, unfortunately not" as I'm tired of hearing "oh, you decided to go have a career instead" or other rationalizations that have been thrown in my face too many times.)

Personally, I would say that some of the comments that I find the most demeaning have to do with parents stating - and often times this happens in work settings, leadership classes or other discussion groups - that "once you have children you realize how important it is to care for others" or "once you have children you become a an adult since you have to take care of someone else" and other short phrases that are thrown around to stated that "they didn't become an adult until they became a parent - however that might not be the universal truth"....

Anyway, I am not going into the Four Yorkshiremen territory (Monty Python) but if something, I would like all you parents and couples who haven't started trying for a baby yet - please consider that not everything in life plays out as one would've wished. And that there might not be a "simple explanation". Or even an explanation at all. That "just have a baby" might not be as straight forward as "boy meets girl, boy and girl have sex, girl gets pregnant, boy and girl have a healthy baby".

It's more talked about today, and maybe even within some sports communities like NHL where a few hockey players the last couple of years have been very honest and vocal about their miscarriages and baby tragedies. If nothing else, the sheer number of how common it is for a detected pregnancy to not proceed and reach week 22 or even later (miscarriage/still birth), is one of the things I wish I would've known earlier and would have been discussed in sex ed in high school. 

Or that it isn't a "simple as something wrong with the woman leading to issues" or other old stories from historic times where fertility is very much linked with male success and female definition of being a real woman = motherhood. That dinner party with my close women friends where it turned out that 75% had had one miscarriage....

As always, it's easy to see the world through one's own lens. All we can do is hope that a lot of us remember that everyone is embarked on a different journey through life, and that with humbleness, friendship and caring for others - we can find friends we didn't knew we had or learn new views from. And communities that support us through different times and obstacles that we might not have thought we would encounter when we started out life journey.

Be kind to each other.

(my post from last year can be found here)

Friday, August 28, 2020

TLDR; remember situation today was intentionally created

TLRD (too long, didn't read) is a great acronym for when things get carried away in explanations and then in the end of a long rant you want to make it easier to grasp "what is it I wanted to say".

I really had planned writing about #covid19 and how international travel has made me be very tired lately.

However, as with best laid plans, they aren't where you end up. I'll write about the covid19 things later. For tonight I feel that I want to clarify something that's been eating me up when listening and being asked to comment on current situation in the USA.

As an immigrant in the USA, living for over 13 years in the South of USA, I feel that I have gathered a lot of information and insight into things that I barely grasped when moving.

I grew up in an intellectual family in Sweden. Lots of reading, lots of politics, lots of knowledge of history. My formative years were times discussing South Africa (apartheid), the Palestine-Israel conflict, USA in Vietnam, colonial powers in general (France and Algeria for example) and Chilean (really several South American countries) dictatorship. I thought I had grasped quite a lot as a protected white native Swede. As one does when reading and meeting a lot of people and discussing on a theoretical level.

However, as usual, when living in the place where things happen - you grasp a different angle. You are forced to encounter situations that you never thought would happen (especially not when you perceive yourself as "knowing"). And most of all, you learn to be humble to a degree that is leaving you with only a few choices. One of them is "I will listen to and accept the reality that these people describe to me is their reality".

And that's what happened when I moved to the South.

I realized after half a year living in the South that something was off. What? Well, at starters I didn't - at the time - feel that my reality was that different from living in Sweden. (In hindsight, which is as we all know 20/20, that's a given red flag that something is strange..... ) My city where I lived was demographically very different from the Sweden city I grew up in.

To make it easy; my home city was easily 90% white, my new city was over 60% African-American. Despite this, the bars and restaurants (and church and work) where I hung out were probably at least 80% white. Or at least "as similar to my home town that I didn't feel that it was too different".

This gave me pause and made me question a few things. Mainly where I was hanging out, why this was and if there was something else on how this was happening.

(side note; it was like this partly because at the time I hung out with other white immigrants at the places they showed me, and then some other places where "middle-class/affluent" people frequented.)

After a few more years in the South I had gathered anecdotal evidence that I'm "passing as an American, specifically a white American woman" and that this fact opened a lot of doors for me. Note, the doors that opened were also where people greeted me as "you're not a real immigrant" since it was perception I spoke English as a native language in my home country Sweden (we speak Swedish), and I am a Christian, and - of course - being white.

However, that's not the point of this blog post. The points of this blog post are to link to a few articles that explain fundamental historical facts that has made the situation we are in today. Where African-Americans and People of Colour (PoC) are more likely to get shot, get arrested, get non-invited for interviews, get looked upon with distrust etc.

It's too long (as I mentioned in the beginning, it's a long story) for me to be succinct.

I mainly want you to know one fact I've learned after all this time living in the South.

It's intentional politics that have gotten us where we are. It's intentional to hinder non-whites and non-wanted people from voting. From owning their own homes. From having the thriving neighborhoods that once were. From excluding a lot of the history about this from schools and public education. (Like the fact that schools in Oklahoma didn't include the Tulsa Massacre in 1921 in the public school curriculum until this fall in 2020 (and who knows how that will happen now with covid).)

The reconstruction after the civil war, the backlash, the Jim Crow laws and the Civil Rights Movement and voting rights. And that are the voting rights that are hot contested in the USA today. It's not like in Sweden, and other EU countries, where you are automatically registered to vote on your 18th birthday - no action required. Nope, there is a process to get registered to vote, and on top of that the voting day is a regular work day with complications to get time off if you aren't a salaried worker.

And the fact that USA system, while it is a lot based on income and that there are a lot of poor white people as well, is based on a right that was for a very long time classifying a non-white African-American as 3/5 of a person. And that the District of Columbia being classified a district and not a state, therefore not having representation in the House of Representatives, is stemming from the fact that there was only "State representatives from real States, and slaves and servants" living there, and since the State representatives and their aides had voting in their home states - there was no need for the other people to have voting/representation rights.

To me, there is no way to see all these historical facts and not draw the conclusion - this is not "natural" this is a "created, systematical way of excluding people that are not wanted".

At the bottom are some links for further reading. There are many many more. And if you ever come by Memphis - the National Civil Rights Museum is a must. It'll take you more than 3 hours to go through it and you will still learn more things afterwards. There is a lot to take in. And it will not be easy. It is difficult things to see and understand.

Final comment; "If not now, when?" There is no waiting. It will be painful to acknowledge that regardless of your own intention or wanting, if you are white - there is a huge burden to take on and work on making things right and just. Nothing else to say or make excuses. It's something we just have to do. And it starts by listening to other peoples' experiences and acknowledging that there are a lot of things we have to change. Now.

Links to read:
Segregation myth - Richard Rothstein This is a GREAT explanation and video interview of the systematic idea behind suburbs among other things
NY Times 1619 project 
Role of Highways in America - The Atlantic
Highway protests - Facing South
Reconstruction era - black congress members
Breaking up slave families

Monday, July 27, 2020

Safe back to school? as a swede and microbiologist in USA

There's a few times more that others when I get more attention. I remember the last pandemic - swine flu 2008 - when a bunch of friends (and not so close friends) from high school and uni contacted me to ask "should we give our kids the new vaccine?". My answer, starting with a disclaimer asking what their pediatrician said and why/if they trusted the MD whom they went to consult about their children with, was that I am pro-vaccines in general - against virus especially - and that I would take the swine flu vaccine when it was offered since I deemed it safe.*

In general, that's what I do; I defer to the experts and then I offer my point of view and what I will do and what I recommend my family to do. All in the same idea as the saying when I was a child "do as I do, not only what I say".

So, last week was a flutter of emails, texts and phone calls from a number of coworkers and friends asking "what do you think about going back to school? Is it safe? In Sweden they had school all through spring!".

I think the answer requires a multipoint explanation. I had a twitter thread the other day where I worked through some of the key points. (That thread started with a reaction of how some data is presenting as comparison between days and that there is no thought on having consistency between groups when comparing them. I'll write a separate post of stats, need to be consistent and attention to detail.)

Anyway, the thread can be found here

The relevant tweets for my this blog post start with number 5. It has to do with statistics ( percentage, likelihood, distribution) and then actual numbers.
In short, a lot of epidemiology concerns population based research, trends and breaking down distribution in larger cohorts. It doesn't really say much about one singular case. It is about distribution and likelihood, percentages and other general numbers that for many people is hard to understand when drawn to a single case.

I mean some of this is almost like explaining the likelihood of winning the powerball... (1 in 292,201,338) which is quite ridiculous and people still play it since "there's a chance to win". Yet same people might have a hard time accepting they have a 1:2.5(41%) of getting cancer after age 60 and not worry too much about that. Let's not get into the likelihood of getting SARS-CoV-2 virus in community spread without any mitigation technique like mask or physical distancing (like sports practicing like normal, indoors in teams).

To get back to point. A lot of these questions last week were directed at me since I am a Swede. My family is in Sweden, a lot of my friends are there and I live in the USA so I have "knowledge from both worlds". In this pandemic there's been a lot of polarizing news (some true, some not) and one of them has been the constant comment about "Sweden's experiment" (let's not get caught up in the fact that the whole world are doing some kind of experiment here and there, or the "United States of America's experiment"). Two parts that have been reported pretty heavily were that Sweden didn't close their schools in the spring, and that the country didn't have a lock down.Let's start with facts:

  • Sweden moved high school and universites to online only in March/April.
  • Sweden kept elementary and middle schoold open the whole time before summer break.
  • Sweden kept daycare open the whole time, and kept it during summer break.
  • While Sweden didn't have a mandatory lock down - there is no provision in the law during peace time to do this from congress - a lot of people worked from home, didn't travel, kept children at home, didn't visit grand parents and so on. (side note; Swedes are pretty good at following so called "governmental recommendations" as well as having a relatively big amount of single households in the country -world leading)

However, it's part of this fact checking that Sweden didn't see vast community spread outside of specific suburbs of Stockholm. And that the majority of people who have died so far have been people over 70 who lived in nursing homes/elder cares. It's a tragedy in itself, and should have been prevented.

Why am I mentioning this? Well, simply because I would say that the evidence in April looking at the metrics on who was infected, hospitalized and in ICU pointed at that there was a large group of "people over 60, definitely over 70" who were mainly affected of the virus. Other groups were showing low incidences.

However, like all epidemiologists (and some microbiologists) know there is that thing of "incidence bias". In short terms; as you look, you shall find. (how you test will bias the results you look at)

How many young adults were tested in the spring? How many people were really infected? How many people who had no symptoms were tested? (I bring this up since that's another group that has been shifting in interest the longer the pandemic and data gathering have been going on.)

There is this thing with incidence and drawing conclusions. It's fairly safe to presume that if a large group ends up in hospital during an outbreak - it's a high likelihood that that group is more susceptible than the rest of the population. It is sometimes "simple things" as "the people who have eaten at one restaurant", sometimes "an overabundance of people who are older".

However, it doesn't mean that the groups that aren't found in the hospital are safe. It means that they are either safe OR the outbreak hasn't touched them in large enough numbers for them to get sick. Depending on the numbers, the distribution of sick people might change, and the numbers of sick will people will change.

These details, as well as knowing the difference between an isolated outbreak, an ongoing epidemic and a move to a raging pandemic.... that's why I listen to experts. It's complex to break down all these parameters into bite size morsels of information that people can and want to digest. It requires trust with diseases specialists who work with this everyday. And most of all, it requires an understanding that whatever the data shows in the beginning of an outbreak/pandemic will most likely change with time and amount of people getting infected and that it is crucial to stay nimble, gather more information and reanalyze the results.

Anyway, to make a long story short. Looking at the facts of infection rate and age groups in the USA today it's pretty clear that

a) there's ongoing community spread in a lot of counties (% positive of tested over 10% in a conservative view)
b) actual numbers of infected children, youth and younger age groups are going up
c) there's been fatalities in the groups "under 25", even in "under 17" - which wasn't the case in EU
d) the situation in USA today (in various counties/states or as a nation) is not comparative to the situation in Sweden in the spring
e) the situation in USA today (in various counties/states or as a nation) is not comparative to the situation in EU at the moment where countries are opening up and preparing for school

I don't feel that this complex conversation is taking place - at least not in a bigger context as "the situation in the USA right now is completely different from the EU situation". (I know, northeast are looking more like EU and keeping the numbers pretty good with their continuing partial lock down and limited openness.) I have had a lot of various emotions about this, especially since there are so many things that could be done to mitigate and stop the spread.

Alas, I ended up writing this blog post to put words to my frustration. 

The final point. There is still time to do things to stop this virus from spreading. To be inconvenienced for another time in order to mitigate the spread and give us less infected, less in hospital, less lingering effects from people who have been infected. 

Why is this so important? Because if there is something that drives me completely bonkers right now is the statement "the virus will go away someday [so we don't need to do anything extra]".

(I am sorry about the caps lock) 


The ONLY way we would've eradicated it would've been to quell it completely before it spread into an endemic virus. If it was a "truth" that viruses go away "after awhile" we wouldn't have as many diseases, rare and all, that pop up every so often. 

There's been documented two viruses that have "gone away"; SARS-1 and Small Pox. (First because of effective lock downs and controls, with a virus that was highly deadly. Second because of a world wide joint effort of mass vaccinations and travel bans without showing proof of vaccinations.)

We haven't even eradicated measles even though we have a vaccine since 1970 (and a better one since 1986), and it affects and kills children. Just asking a simple question; if we haven't been able to eradicate a disease that is that deadly and horrible to children - what makes you think that SARS-Cov-2 "will just go away"? There's got to be a solid plan (including distribution of a made efficacious vaccine - this is for another post)

I'll stop since this post is too long, too upset and touching on a lot of different things. Let me know in the comments if there is something I should elaborate or remove. Thanks for reading and being there. 

*there were a number of younger Swedes and Finns who got bad side effects from the swine flu vaccine. It was, over all in hindsight, impossible to have anticipated these side effects. It was about 200 children in Sweden and about 100 in Finland if I remember correctly. Out of a combined population of 13 million at the time. It's difficult to know how this part would've been discovered in the way "we" establish vaccines to be safe in this day and age. Most safety trials require relatively few, and then in the Phase III part of the trials - the more rare side effects are gathered as informational. Still though, it was a huge break in trust and it effected them in a life altering way.

Wednesday, July 01, 2020

dealing with accidental death

It's been a weird couple of days. Well, to be honest - maybe it's more about it's been a weird couple of weeks and months where the "normal" has been exchanged to something new and uncertain, a lot of new experiences that aren't what we all are  used to, or even know what they mean.

I'm grateful that I'm part of a team at my place of worship where we contact and talk to people who are terminal and their relatives.
I'm grateful to work in a place where we experience death and have people around who help with the process and help support the acceptance of the grieving process.
I'm grateful to use my experience with unexpected death, and suicide, in my circle of friends and acquaintances for something good as in at least I don't shy away of talking about it, or being there when someone else experience it.
I'm grateful that I have friends and acquaintances who have explained their experience with virtual funerals and memorials, especially in this covid time (it's such an odd, new concept that turns a lot of the old traditional ways upside down)

This is all to say that I'm grateful that I have been thinking about death and what I would like my relatives and friends to deal with, and that I think and hope I'm doing something good for people who are in this situation.

However, as everyone who knows, it's a different situation when you know the person in question. And it's never easy to deal with a friend taken away too soon, too fast, who has her whole life ahead of her.

It's one of those things though, so typical me, that when it happened - and people around me who didn't know her - said "I'm so sorry for your loss". I didn't know what to say. It's part of that I don't feel that it is my loss per se. It's her parent's loss. It's her partner's loss. It's the best friends' loss. It's the universe's loss. But it's not mine as a personal only loss. Only when I have unpackaged this I've realized that it's partly a language thing, partly a need to de-personal the loss. I want to answer them "It's all of our loss, cause she was a fantastic force and would do may great things".

I heard from a friend in the morning, she is dead. I was startled and I cried. I started with the negotiation with grief steps and got a fair bit on them. My issue? (As always) it's when you have to vocalize it to others. That's when it becomes real. That's when you have to handle the fall out and the others' feelings. And your own. When you have to tell others; "they are dead". There is no negotiation of that. And there is emotion from the other person. And you get to face that. For good or bad, you have to face your own feelings in that moment.

And yes. It is my loss. I will miss her. I will miss her laugh, stories, shared happy times with me and with others. She was such a joy and a great scientist. And such a wonderful person. She had a huge heart. And she wanted to make it possible for others to succeed in science, regardless of where you came from. She was a member of SACNAS and her friends there told wonderful memories of her. And she made the work day a brighter place with her laughter and her voice.

And in this covid times, I will have to get over the fact that we hadn't been in the same space since midMarch when campus closed down. It will be difficult understanding she is really gone, I will not see her when going to her lab space, the cell culture hood she used, or that she will pick up the phone - they way we have communicated the last couple of months.

I wish this was a better written post - a well written one to her memory. Maybe in the future I will be able to do her justice in an eloquent post with her wisdoms. Or I'll amplify her eulogy when it happens. But for now, I would like to simply say -

I miss you. You were such a great person to have around and you made life just a little brighter. You were brave and loud and so caring for people around you and for people you didn't even know when you went to the US-Mexican border to interpret for the people needing help. And that you were compassionate enough to allow me to feel that I helped, even if it was only with money and not physically being there since I don't know Spanish and I'm not a physician. You gave me courage and heart to keep on trying to help people around me. And you told me you wanted to be like me when you grew up. I joked it off since I didn't know how to deal with it - but I pulled up the texts and you said it several times. I will never forget you. And I will be an even better person in the future, the person you wanted to be, making you proud. Thank you for letting me getting to know you and being touched by your being.

Monday, June 15, 2020

PCR, serotesting, population level detection - what does this mean for me?! (covid19)

After more then three months of living in a pandemic, everyone is tired of it. It doesn't matter if it's living in a lockdown where people weren't allowed outside, or a country that sort of didn't mandated isolation for more than risks groups but every country has seen either extreme lockdown, massive death or lockdown and some death.

A few buzz words (describing mitigation techniques) have been floated during this time. I think that there are a fair amount of misunderstanding when using a lot of these words/techniques - compared to what they mean in a epidemiological setting. And since I have spent a fair amount of my time last three months discussing, explaining and listening to my friends and family telling me what limitations are involved with "testing", I would like to write a post about them (might have to be several).

First, a difference between tests. Two tests are mentioned a lot; PCR and serological (antibody). PCR test will indicate if there is RNA from the virus inside of a person.
Serological (antibody) will show if the person has developed antibodies against the virus (and therefore can not be sick again from the same virus). That is "the person has already 'seen' the virus".

Both tests have details attached to them that most people wouldn't know or care about. My primitive opinion is that people shouldn't really need know these details since FDA/EMA/country's each agency that approves test should know these details and only approve according to high standards. It might be obvious that I have an issue with how tests have been approved since I made this sentence in italics.

To evaluate biological tests for diagnostics there are three things to remember (there are a lot of others but these three are fundamental for how to view the test accuracy and validity - big words to say "does the test work well"):

  • Sensitivity (how likely is a negative test to be really negative)
  • Specificity (does the test detect the right thing that it's looking for)
  • Limit of Detection (LOD) (related to sensitivity however slightly different and especially when talking about a whole chain of things together)

Before I go through these parameters, let's throw in another caveat with tests in general - especially since it goes hand in glove with these three fundaments. A test result should for all intent and purposes be seen as a probability and not a certainty. The golden and easy example for everyone to talk about is pregnancy tests. Those are, even if they are really really good, still a question of probability and certainty. The easy thing - the great thing - with pregnancy tests are that they measure one hormone (hCG) that only exists if the woman has a growing fetus inside. Then the test becomes only the question of "how low of a level of hCG can the test detect" (LOD). That's usually made into an equivalent of an average level of hCG at certain number of days after implantation, which is why tests have "early detecting, 5 days before period" (very low amounts of hormone can be detected) or "detection as early as first day of missed period" (a decent amount of hormone can be detected). If only all tests could be this clear cut.

With virus and PCR there is another issue that isn't much talked about outside the world of virus and microbiology. The fact that "just because RNA is detected doesn't mean that there is an infectious virus present". Dr Raciniello has described this on his blog a long time ago (here). The main take home message is "just because you find RNA, doesn't mean you find a virus particle that can infect." Further making it complicated, it will also depend where in the infection phase the person is, and what was investigated". It's been clear looking at published aggregated case studies from hospitals in regards to Sars-cov-2  virus is the likelihood of a positive test at different times in the infection within a person. The amount of virus, more specifically the amount of virus loose in the body available for detection and reinfection, varies a lot during the infection. There is a lot of virus day before symptoms show, there's evidence that 4 days after first symptoms there is more likelihood of testing positive. Combining the points (existing RNA but not active virion) seem to support the findings that 30 days after first symptoms, even if a positive PCR test, doesn't mean shedding (spreading) infectious virus. Brings back to the idea "it's a probablity, not a certainty". Also why hospitals where patients test negative on PCR but have distinctive 'glass lung' on CT are treated as covid19 positive.

(Side note for extra points; there is an assay that virologists use to evaluate virus load based on "plaque forming units" pfu which is dead cells that a virus have infected and killed, and that would give a "how many viruses who can infect exist in a sample" <- .="" p="" virions="">

All this is more than a 5 min simple read, and I apologize for even trying to cram a lot into a hopefully half-interesting blog post, I'm trying to explain why it's more complicated than "positive serotest" and "negative PCR and you're not sick" while not getting caught in the weeds.

So, back to the Sensitivity, Specificity and LOD.

When you take a PCR test - especially for an RNA virus - there is alway an overall chance/risk it will end up as a negative if you fail running the test itself. Why? Because the test is looking for a detection of something that will have to be going through at least 3 steps where the actual RNA might disappear before showing up in the test results. That's why there's always a control sample run together will all the real samples to make sure that all the steps worked out.

  • Sensitivity is generally descried as how good the test is to find the true positives of what the test is looking for. That is to say, only the people who really have RNA from the virus should test positive when using the PCR test. Similar for the serotest (antibody), only people who have encountered Sars-cov-2 and developed those specific antibodies should test positive.
It also tells about the false negatives, which would the least good outcome. This since someone who tests with a PCR test, to see if they have virus and therefore might spread to other people, that comes back as negative might not keep safe distancing to people but move along closer so a false negative brings people safety when they really shouldn't have thought so.
  • Specificity is generally described as how good the test is to show true negatives of what the test is saying it looks for. To simplify, if you test for sars-cov-2 RNA it's important that anyone with any old cold doesn't show up as positive (the common cold is part of the coronavirus family and share some parts of the RNA with sars-cov-2). If you don't have the virus, you are negative when testing.
There are repercussions of this part failing as well since looking at serotests (looking for presence of antibody in the blood) and if this shows antibody titers but it's the wrong type of antibody (say, from the common cold) then the test will have a low specificity.
  • Limit of Detection (LOD) is the lowest concentration/level of test subject that can be detected in a sample. The reason for my addition to the list is that when it comes to certain tests, the LOD will depend on a number of different processes than "just the level in the blood/saliva" as is the case for a lot of samples. Again the pregnancy test as an example, pee on a stick. The hormone is in urine. The test is designed for levels that are found in urine (side note, the blood test is more sensitive and have a lower limit of detection). There is no part of the test that requires any manipulation/handling of the urine (or blood). However for a PCR test of an RNA virus - there are a lot of details involved. First of all, there is the base level of "amount of viral RNA present in the nose swab" that has to be present to be picked up on the swab. Then there are different ways to get the RNA (virus) off the swab, extracted into liquid and being able to even "run the PCR on" (PCR=polymerase chain reaction, a mix of stuff in a little tube to amplify what is in the tube from the start). And the limitations on how big of a volume was the RNA extracted into and how little was brought on into the PCR reaction etc..... 
I'm aware I didn't do a great job on the LOD discussion if nothing else I hope that I made it clear that it is complicated and also super important. Even if you don't know how to calculate this step - it should be super clear in the FDA approval process since the LOD will determine the limits of the usefulness of the test. 

All three of these parameters will decide if the test is useful. It will further determine if the test is useful on an individual or population view. Why this difference? Because of statistics. If the test is only to be roughly an estimate on where the population - a higher lever of uncertainty (higher possible wrong results) are more acceptable since stats work that many tests together with a fairly high certainty turns into an ok stats.

The same test can have a detrimental effect on an individual basis. As previously stated, imagine going for a PCR test to determine you don't have the virus before going to visit your grandmother. You get a false negative (you think it is negative), and then go visit grand mother. That's a huge risk. Similar with testing if you have antibodies (the serotest) and it comes back positive (you have antibodies). You then might start doing relaxing and not wash your hands as much as before, and then you get sick.

All of these parameters are things that I (we) anticipate and expect that the FDA (EMA/country of your living) have evaluated and deemed acceptable. However, it's important to remember that in this case of the pandemic - there were a lot of changes in the acceptance criteria for a lot of tests. In order  to get an Emergency Use Authorization (EUA) the documentation from companies were relaxed a lot and most of all, not required to clearly state the limits on the test themselves.

You can argue that there isn't time to go through rigorous testing and documentation in a pandemic with an unknown virus - and I would agree whole hearted that time is of the essence. However, I would say that these details, the basis of the validity of the entire test, are extremely important to clearly state. If nothing else exactly to use when calculating the results on a population basis since the errors will compound/become very different based on these base numbers.

From an individual point of view - I wouldn't take a serotest without wanting to know the exact specifications since I wouldn't know what to do with a positive test unless I knew the cross-reactivity number. And that's not even mentioning the issue what kind of levels (or types) of antibodies that might be protective against sars-cov-2. 

Friday, June 05, 2020

know it all - intentional or not?!

"She's so knowledgeable about all these things. I mean, I'm American and I didn't know that DC doesn't have a congress person or a Senator but she did and she's not even from here."

Welcome to "my musings when I take things as a backhanded comment but maybe it really isn't but I had a rough childhood and end up in a defense situation".

Obviously at this time - internal self reflections are a clear sign of something not great. I feel that I should write something about BlackLivesMatters, the protests, the killings by the police, the shooting of teargas, the riots, the looting, the general upheaval of the constitution of the United States of America if the Active military are patrolling or surveilling regular US cities.

However, encountering another one of these comments as written in the first paragraph brought me back to my childhood. The comment this time was voices after we had discussed the current situation in the country and mentioned the yellow paint of BlackLivesMatter on the DC street. And I had seen a video where that street close to the White House was renamed "Black Lives Matter Plaza" 

I had a small smile since I find these things (non violent yet clear statements for the public) very on point and something to point the finger at something that isn't quite right. It's easy to prove when someone is upset about something like this, to object they have to state their case and that means they have to state WHY it's upsetting. Case in point; in Iran the British Embassy was on Bobby Sands street and there was short period time that the Saudi embassy in DC was located on Khashoggi way.

Anyway, this is my long way into a shorter comment that DC is a District of Columbia and doesn't have state hood and not right as the "other states" of the USA (since it isn't a state). I pointed out that there is a person who can talk in the House of Rep but doesn't have a vote, and that they don't have a senator. Briefly touched on the idea that DC wasn't originally planned to have people living there to vote since they were either IN congress or worked FOR a person in congress but in any event they were signed up in their state they represented, and then there were "non persons" who built the White house etc.... (african americans 3/5 of a person deal)

And I understand that this is part of my issue - that I get uncomfortable when people drop those kind of comments since I don't know if it's to point out that I make them uncomfortable, or if I push too much or if it's simply a "wow you know a lot". I know that I automatically say "well, I don't have any kids so I have a lot of time to read" as an excuse.

Part of my time in school as a younger child was a lot about making fun of me for knowing a lot. And I know that I at that time was less smart on how I said things so I probably came off as a know-it-all. However, as a grown up - there are so many times when I've decided not to rock the boat and not offer an explanation or a fact on the topic of discussion. Why? Because it's really not liked a lot of times. And, like when dating or getting a report with people in power at work or networking, it's just best to be a woman with "just enough" brain and wit.

My issues are those times are more obvious when discussing something that might have a more complex background and leading to some faulty conclusion. And when these things arrive - I've made a decision to state my knowledge and see what happens. If nothing else, I can feel ok with having said something, and not argue away. That's not the key point.

However, it would be great to not feel like a freak knowing things that apparently other people don't know. I guess I have to work on how I say things (yet again). Luxury issues - that's what this is. Real issues - outside our windows every day. #blacklivesmatter

Tuesday, May 26, 2020

small filter - maybe slight venting?

I've been drafting these blog posts about "sensitivity and specificity", "difference between antibody test (serotests) and PCR (RT-PCR)" and "timeline of pandemics". They are all still in the works. I got sidetracked though. Not by something fun. Not even by my work, even though I've managed to have two hard deadlines and another coming up within a few days, but by fighting this feeling that "throwing pearls for swine isn't worth it".

Nownow, I know the mistake of the analogy. First off, my blog readers are few and a lot of you I kinda know over the years. So, not "random", and most certainly not appropriate to have an analogy to "swine" as in the saying. For argument sake, let's disregard the saying and move on with the post.

It might just be the notion that writing explanations and trying to make sense of what is going on in the world from a microbiology point of view would be a good idea IF the posts were read in good faith by someone who might learn and even change their way of thinking.

Alas, and here comes the tiredness and the reason for the crude analogy, there's been quite a few interactions with people who go at things in bad faith. And also that they are so firmly lodged in the "other camp" that they have no interest, no semblance of idea, to learn or listen to facts.

And after the latest couple of weeks sharing borders with conspiracy theorist, "freedom seekers" and "God & Trump will protect us and the virus will go away with the heat in June" - I have spent a lot of energy not saying what I think. Not stating rude things. Not making over the top faulty "I want this to be true" signs posting them all over internet or calling people names. (Like they have done.)

Why? Because I was raised to be a behaved person. I was raised to respect and accept other opinions than my views. I was raised that "be above such muck".

However, I was also raised to stand up for what I believe in.
And I was raised to protect the people who couldn't protect themselves.
To think about and consider the people who didn't have a voice in the society.
To NOT only think about myself.
To be alright with having some discomfort IF it meant others were protected and it saved others.
To NOT put myself first all the time but to be humble and considerate of others.
To do the best thing for all of us, not only the best thing for me and mine.

Some of these things have been easier than others the last few months. I won't lie.

"First, do no harm"
I'm not a physician but the sentiment would be something that I was raised considering regardless. Got to be honest though, my experience with bullies - and I'm afraid I have more than I would've liked - is that you can turn the other cheek a lot of times, and not stoop to their level and be the better person.

Sadly (?) though, I would say that there was some experience of an effective way to stop and that was "to stoop at their level" and intimidate back. Threaten as the bully was threatening. Strike a punch and they got scared and thought it wasn't worth it. And to be the bigger person if finding a bully in the younger peer group, bullying the younger ones.

I don't like the experience the violence and threat "solved some bullying". I'm old enough now to see that it works for specific occasions. And that it is situational, like a four year old knows that mommy will be more likely to give the candy in the store if threatened with a full on temper tantrum and screaming and all the noise.

I had some hope that we were above being four year olds as adults. Or that it needed to be "brought to your own family for you to care". I'm now contemplating that a lot. I find myself looking back at my grandmother's teachings of being a lady, while running a secondary commentary in my head "let's go outside and solve this the old fashioned way".

But most of all I have had to fight my thoughts of "maybe, just maybe it's going to have to be really bad for these people to understand the errors of their ways" - also known as Burn it to the ground.  It is a fairly common tactic in war after all (hello Russia in WWII and Germany on their Western front). Main issue is that there are A LOT of collateral damage. And again, the main issue here is that even if that would be a wakeup call for many "good faith" people, it wouldn't mean anything to "bad faith argument people". They see what they want to see. And collateral damage doesn't face them.

That means that the main thing getting hurt from that would be me and the collateral damage, and that wouldn't really help anything now would it?

Wash your hands.
It's helpful for vulnerable people (and you and others) if we keep social distancing.
Since we don't know everyone, if you are grocery shopping, in a closed space or on a public transportation, please wear a mask to save others like if you have the virus.
IF you feel sick, stay home and don't expose others.
It's the only way vulnerable people (and others like health care workers) will be able to go outside for the foreseeable future.

And also, if you still think this is a hoax - you are fooled by whatever outlet you watch, read or listen to. The virus and the consequences of being sick are real. And we don't even begin to know how being sick has affected people who have recovered.

Friday, May 15, 2020

interlude - canada geese

I mean, it's sort of a joke. Back in my home country (Sweden) we have a LOT of Canada geese. Especially congregating at the parks and places where we swedes would like to sit down and have picnics in the spring and summer. I might be slightly biased - as a young child, say 4 years old - I had a slightly less than terrific incident with regular geese (they are bigger and whiter than Canada geese but more tame and therefore less ferocious than wild Canada geese).

Anyway, it's funny for anyone else to notice that when I'm jogging around in my neighborhood during this "stay at home"/"stay safe" time in Covid-19, there is one new road that takes me to a ess than populated industrial area. I didn't know it existed before this "I need to find places to walk and jog since otherwise I will turn into more of a rotund person". However, I've explored a lot of places that are within a radius of 5 miles of my dwelling in the latests 6 weeks.

And there are these strange things like a congregation of Canada geese. Next by a road. Very little grass. And also, by another time when I went by, where there little alone cat used to hide.

Not sure what this means? Do someone feed the cat AND the Canada geese? Are the Canada geese going to eat the cat? (I don't think the cat can take on 5 Canada geese but sure, we could postulate I guess.)

Anyway, if anyone wants to leave a comment or email - feel free. I have a bunch of half made posts but I am trying to write them so that they are good (at least half decent) and not just venting based on the current situation in life and the world.

Here's a picture of the Canada geese. And yes, they are judging you. For sure! (the fifth one is one the street next to me on the left, outside of photo.)

Sunday, May 03, 2020

"let's wish the virus away" and other comments - from a microbiologist

The last couple of weeks (months if you are picky) it's been very clear to me that a lot of people are stating opinions and thoughts in regards to covid-19 that are not based on fact, nor knowledge. As I've been working from home and reading news, tweets, facebook posts and listened to a number of news shows and podcast - I've come to grow increasingly frustrated with a few very obvious limitations in what people really know in regards to viruses and pandemics.

This post is in no way covering all things that I would like to point out. It's mainly a try to state some of the bigger points that have been confused/forgotten/ignored/whathaveyou - in my opinion and knowledge as a trained microbiologist with training in viruses, bacteria and having been an active researcher at the time of the last pandemic (H1N1) where I was part of conferences and guideline preparations on what countries, companies and people could do to prepare for a situation that no one wanted to happen.

1) it's very important to remember that comparing countries - both in regards to "reported cases", "reported fatalities" and "actions suggested and legislation enforced" - are very different and difficult to compare to each other.
Example; one country only reports deaths in hospitals where the person have had a positive test for virus, another counts all deaths in a hospital where a person have been previously tested positive for the virus and people who died in nursing homes having a few symptoms associated with the virus.

2) the actions taken by various countries depend, not only on the way the various government have ability to enforce regulations, but also on when in a pandemic they encounter the virus that is spreading across the globe. If early, complete eradication might be possible, if later in the time line - mitigation might be the only opportunity.

3) reporting "positive tests" as a number on its own is not helpful unless presented in context of "how is testing done" and with numbers of "how many tests have been administrated". This is the long way of saying - know which part of population is being tested, how often and with which test.
Example; one country tests only people going to the hospital with symptoms, another country tests people who go to school regardless of symptoms.

4) as long as there is no vaccine nor treatment that will make an infected person better, there is no other option to stay healthy but not becoming infected. Any infected person will have to beat the infection on their own. Some people benefit from helpful interventions like ventilators, a lot of people don't necessarily get better as much as we would like from these interventions.

5) saying "it will go away" doesn't solve anything. The virus "will go away" when it is no longer present in the population by not having any more susceptible people to infect (either by everyone being immune due to earlier infection or by vaccination) or when we have successful treatments. This also implies that a lot of people will have become infected and either survived (immune) or not survived the infection (died) or a treatment has been found.
Example; very few infectious diseases have "gone away". Even when we have vaccines. They have decreased and for a lot of them they might "flare up" in a smaller part of the population and then we can successfully protect more people so they don't get infected. This is also where viruses are different from bacteria since for many of the infectious bacteria we have found an antibiotic that can treat the cause of infection. For viruses, viral infections, the only known "treatment" is a vaccine which technically is viewed as a prevention, rather than treatment, since you need to be vaccinated before being exposed to the virus and therefore avoid infection.

6) most airborne and droplet spread infections will be hindered by hand washing (the virus will not be present on your hands and therefore not spread when you put your hands in your face), wiping down shared surfaces you touch (with your hands) or by limiting the number of people you meet and talk, cough, hug, kiss or hand off infected stuff to.
Example; someone coughs in a room and droplets end up on a keyboard, you later touch the key board with your hand and then touch your face.... the virus spreads. If the keyboard is wiped down between different users, the virus will be removed/inactivated and the other user will not catch the virus on their hands.

7) masks limit the amount of virus particles you spread and that others spread to you when breathing/coughing. Proper mask handling is key for this to work. Improper mask handling will create a sense of false safety and therefore might increase the spread.

8) regardless of your political affiliation - the virus doesn't care about that - everyone in a society is susceptible to viruses (and other infectious diseases). Virus aren't sentient and therefore per definition "not smart" or "intelligent" or any other wording that's being used.

9) Actually, per strict biological definition a virus isn't alive since it can't replicate on its own. A virus needs to infect a cell to be able to replicate. That's why researchers make a distinction of "being able to replicate" or "infectious doses" and "RNA titers". Of course, this is detail that for much of the current (social and political) discussion isn't really relevant if it's not for the point that a test showing there is RNA present in someone doesn't automatically correlate to that person having a viable virus that can infect and then replicate (it's more likely than not that the virus titer indicates that there is a presence of virus being able to replicate - especially for this covid19 bullet point list that I'm writing here). For the sake of 99% of the conversation about covid19 though, this point is not key relevant since it's the weeds and details that many researchers take into consideration (mainly super important for the discussion of tests and their sensitivity and false negatives and false positives - see point 10).

10) the general understanding of what constitutes a "validated and confirmed biological test used in hospital setting/for medical purposes" is low. There are a lot of details going into validating a test. Two of the most important factors are sensitivity and specificity. The test needs to be specific enough to only pick up specific factors from the virus (microbe) in question to be positive. The test also needs to be sensitive enough to pick up factors even when in small quantities. There are more factors that are important but in general, I'd say these two factors are key when discussing "false negatives and false positives".
Example: currently there are a lot of antibody tests being deployed all over the world to investigate and confirm how many people have really been infected by SARS-CoV-2 (the virus that causes covid19). The antibody test need to be specific enough to ONLY give positive to people who have been infected by SARS-CoV-2 and not any other virus around. It also needs to be clear how sensitive it is - as in "how many antibodies/what level of immune response" will the test detect. This latter part is complicated since it's not known what kind of threshold is needed to be protected for future exposure nor what kind of immune response various individuals have had if they've been symptomatic or asymptomatic. (see, I'm in the weeds now... lots of details on the background on validation of these tests.)

11) microbiology, epidemiology and public health are specific areas of expertise where there are a lot of facts and previously collected knowledge that are helpful when determining what to do, when and how. There is a difference between non trained people and trained people in regards of this knowledge.

12) no situation is being helped by panic. Many situations involving "unknowns" and "large amount of people potentially afflicted" create panic reactions and knee jerk responses at the time they happen. This is why it's important to have a plan before a bad situation happens since then there is less second guessing or panic reactions but rather "following a plan previously vetted and laid out". Most health care workers have been trained in planned responses, so that when "panic situations" arise, the trained people don't panic but rather adapt well to the planned response and go through the situations many of us untrained people wouldn't handle as well. Trust well trained workers.

I'll stop here since I don't want to overthink or write more at this time. It's my vent and my thoughts and feelings. And hopefully someone who reads this will find it helpful. It was helpful for me to write it down. And possibly I'll make a blog post regarding number 10 - Validation of biological tests - later since I've created test validations under FDA (21 CFR part 11) and EU equivalent from EMA (EU Annex 11) requirements.

Saturday, April 25, 2020

WFH - or "being at home trying to work when crisis going on"?

It's been four weeks for me being at home and not being allowed to go to "campus" (my office). so officially I'm "Working From Home" - WFH.

One of the things that I've been dealing with is the fact that I was SO proud I never got a proper organized work from home station organized at home. (I'll have a disclaimer here - since I'm a "straight A person" this has been stressful. Don't get me wrong, last few years in my job I've worked "being off campus/off hours on weekends" but it's always been my work laptop on my dining table, for a selective period of hours.) It has NOT been in what I call "my room" where I do crafts, write my blog posts, skype with my parents on the weekends, write my short stories - in short; where I do my hobbies and feel like I'm in my personal space (as an introvert).

It's been a temporary space when I pen my laptop on the dining table in the mornings or perhaps the few days I've been at home the entire day working but not going into the office)l.


Well, sorry sweethearts. My "hobby/relaxing/lovely 'my' room" is turned into "my office". I have my work monitor, a set up with the keyboard, headphones and all the work papers and books that I brought with me from work with special approval. On one level I understand that I should feel grateful that I not only can work from home, and also that we have a full extra room that I can call "my room" - another part of me was very annoyed that "my" room is no longer "my" room rather than "my work room". It might not be an issue for a lot of people, but for me - it's clearly a new thing, and something I have needed to take some time adapting and accepting.

It's similar to what a colleague of mine mentioned last week. They talked to me about issues that have come up with employees who have a though time adapting to working from home - mainly since they are lab workers and do lots of lab work - with out lab, what do they do? And that they are fortunate to get a pay check anyways (my work place is paying everyone so far, no furloughs of full time employees, regardless of "being able to do work from home or not").

For me I've mainly been dealing with the idea that I could technically work at least 12 hours a day, every day. There's a lot of things I need to do that's only me doing and once I'm done, we are done. So, part of my anxiety is to focus on that I "will not" do the work in 3 days, but I will do it in 4 days since I'm working 8 hours a day from home.

Trust me, it's not that easy and clear cut for a slightly over-working, over-achieving type A personality like myself.

Another way of looking at this situation - especially when talking to colleagues who are at home with children and therefore feel guilty that they aren't doing great in either place, their younger kids are upset "mommy/daddy doesn't play with me", nor that they get enough done at work - is looking at it slightly differently.

It's not "working from home" as we usually know it. It's "being at home and trying to work in a crisis". Sometimes giving the right frame to a picture makes you see the details in a clearer light and giving you an added understanding to your emotions and actions.

Friday, April 10, 2020

dealing with anxiety (safer-at-home edition 1)

I ran into my old kickboxing trainer today. I would say he looked more surprised to see me than I him. He apparently thought I had left town. No idea why. Apart from that he was the one leaving and cutting all of us off. I almost said "you took the heavy bag I paid for when you scooted out, and I would've really enjoyed it in my home now in Covid19 times". Of course I didn't say that. Because that would be ... I dunno, unnecessary? It's been almost 10 years.

Still though, it brought back an old conversation I had with a therapist during my divorce (even more years ago). I talked about how I handled anxiety and that I had noticed 5 different outlets that might not have been the best options all the time.
In no particular order;

  • drinking (alcohol)
  • eating (oh chips, carbs are faves, but really - beggars can't be choosers)
  • getting into a fight (referring to verbal fights and slight screaming, since I wasn't a brawler)
  • having sex
  • working out (especially on a heavy bag with gloves, intervals so almost puking or sparring against someone bigger)
At the time, I was quite proud that I had moved away from the destructive ones and kept working out to keep calm and in control of feelings and stressors. This quarantine/safer-at-home deal makes it a little more complicated since I currently don't have a heavy bag at home. Sure, I have a few kettle bells and I jog/do intervals at times in the neighborhood. However, it's not the "all out endorphin looking kick" that I've chased over the years to mellow me out. 

I guess I know now that I have to up my milage (haven't done more than 6 miles since marathon in December) and start doing the horrid intervals/fartlek to see if that kicks in the "adrenalin get aways" and the endorphin kickoffs. It wasn't an issue in the fall when I averaged 22 miles a week (4, 3, 15 miles) when training for the marathon, and doing spinning intervalls and weights/boxing twice a week. Currently I'm more in the "walking 3-5 miles a day" and "jogging twice a week", but nothing over 6 miles (since I'm in my neighborhood and not the park where I used to go long distance running). It's not enough to keep the balance.

Why do I think about this?  Because the other options on the list aren't really great choices as outlets. And especially not as a grown up who should be honest with ones feelings and reactions - as I refer to myself right now. I know, it would be best if I learned to deal with anxiety as regular people. Now, what do regular people do when stressed??? (I really don't know. Please let me know)