How the Coronavirus and Flu Are Not the Same

There has been much attention, too much in my opinion, comparing SARS-CoV-2 with Influenza B. SARS-CoV-2 and Influenza B are the specific names for the viruses in question when we generally short hand Coronavirus and Flu, there are many types of coronaviruses, including SARS, MERS, and some versions of the common cold (although most colds are caused by rhinoviruses). There are also multiple types of flu, including influenza type A, B, and C, although A and B are the most common. From here on out, I'll use Coronavirus and Flu as this is how most people and the media discuss them, but realize this is short-hand. (COVID-19 is the disease caused by Sara-CoV-2 and is not a pseudonym, much like AIDS is a disease caused by HIV.)

Both viruses are RNA viruses, their genetic material is RNA and this is converted into DNA after infection into a host cell. These viruses force the host cell to use this DNA copy to make all the proteins required to make new virus and to make complete RNA copies which will then be packaged into new viral particles before killing the host cell and infecting other cells and/or hosts.

Both Coronavirus and Flu cause significant respiratory illness. Indeed, SARS is an acronym for Severe Acute Respiratory Syndrome. These infections make breathing more difficult, in large part due to immune responses trying to keep you alive, but they also make a patient more prone to getting pneumonia, which can also kill you. These aspects of infection help explain why the elderly, immunosuppressed, and young are high risk groups (It appears that Coronavirus is not particularly lethal in the young, however data is still limited in my opinion.)

At first glance it looks like Coronavirus and Flu are similar. This could lead some, like an orange baboon, to directly compare them. If we do compare them directly, its easy to conclude that Flu is much much worse and its a plot by the universe to be concerned about Coronavirus. In the US, Flu infects 10s of millions, leading to hundreds of thousands of hospitalizations, and 10s of thousand deaths! Every year!!! To date world-wide, Coronavirus has infected over 100,000 people and caused about 4000 deaths. For non-viral comparison sake, car crashes kill about 40 thousand people in the US, comparable to the flu virus. Gin deaths are similar in the US.

Your basic Orange Baboon. From here, although I realize the image on the left is an infant orangutang and the image on the right is an actual orange baboon.

Since we don't shut down schools, concerts, etc for the flu and don't seem to care that much about vehicular deaths and definitely aren't willing to do anything about gun deaths, what is the concern about Coronavirus all about?

It's because because these comparisons are, at best, inadequate but more likely abysmal.

First, we need to consider what happens when someone gets sick with either virus. Maybe nothing both viruses cause symptomatic infections, although these patients can readily pass the viruses on to others who may not be so lucky. Next possibility is you get sick but not so severely that you go to the hospital. Hopefully you stay home and recover, but this being America, many people will have to go to work or are otherwise unable to rest because social safety nets are for commies, you know like every other developed country on the planet. More severe cases lead to hospitalization and of those a subset will leave the hospital in a casket. Here's one of the first places where Coronavirus and Flu differ. Roughly 2-3% of infected individuals will die of Coronavirus, aka leave in a casket, this number will likely change as more information is obtained (in other areas of the world because the US is wasting time and energy NOT testing even likely infected patients). However, the Flu leads to death in roughly 0.1% of patients.

Second, lets consider some other critical differences.

1. There's a Flu vaccine! That's right there's a vaccine against influenza, but somewhere between jack and shit for SARS-CoV-2, to be fair it's closer to shit than jack shit. Regardless of what orange baboons say, it will be a long time, at the earliest before, there's a vaccine. In fact, it may take many years before there's a vaccine. We still do not have anything close to a vaccine to HIV and we've been working on it since the 80s. The flu vaccine isn't perfect because it has to be developed before flu season begins so some years its more effective than others (if it were developed afterwards, it would be too late to be useful....hmmmm). To be clear, even when the vaccine doesn't match well, it still provides some protection and reduces mortality and severity, shortens length of illness, and reduces chance of infection. Also evolution matters and flu, much like other RNA viruses, I'm looking at you SARS-CoV-2, evolves quickly. This is why you should get a flu vaccine every year. By the time a Coronavirus vaccine is developed, in the best case scenario, most of the planet will already have been exposed.

Ok, the savvy among you are already thinking, if there's a vaccine but still a shit ton of people die from Flu, why should I care about Coronavirus? Well, most people are not vaccinated for the Flu, maybe 50%, which is well below what is needed for 'herd immunity'. However, health care workers, doctors, nurses, EMTs, etc. are almost uniformly vaccinated against flu. Thus, they are much less likely to miss work because they have the flu, which means they are available to care for those who do get sick and require hospitalization.

2. We know the flu is coming! Look there's a reason you need a vaccine every year. As above its due to evolution. But here's the thing, for well over a hundred years we've known this is coming. Every single year. And as our medical personnel are kind of smart and know this is coming, they are prepared. Besides being vaccinated, hospitals and clinics generally have the resources available to handle the influx of respiratory illnesses that will show up during flu season. We know thousands of patients are coming in, so its factored into the medical care equation. Don't believe me, think this is some kind of plot conceived by the MSM? Ask yourself why do insurance companies, the epitome of capitalism in the US, prepare for these expenses every year? In the US, hospitals are generally revenue generating, at least for the wealthy, so why aren't they prepared for this change in hospital cases every year? The short answer is: they are prepared. They are prepared for flu, they are also prepared for other cases, like heart attacks and broken bones. However, they are NOT prepared for dealing with fundamental changes in the status quo.

Coronavirus is a change in the status quo.

3. Here's the problem if hospitals plan for X number of beds being occupied, even during flu season, what happens if more than X number of beds are occupied due to Coronavirus? What happens to any potential extra patients, like Grandpa with a heart attack? In the US, we live in a firm capitalistic society, if someone isn't making money then why bother. So hospitals don't have a bunch of excess beds for, just in case. Hospitals don't have extra doctors, nurses, or other staff sitting on the bench for, just in case.

TV medical dramas give a false sense of time frames in regards to infectious disease testing. One thing they do give reasonable service to is bed availability. If two school buses crash into each other, the local hospital cannot compensate with the increased patient load. This becomes the plot focus for episode this week. In these scenarios, patients are triaged and sent to other hospitals or patients left to wait for a team to be available to treat them. This is the drama of the episode. So what does this mean in the real world in the face of a pandemic?

4. If a small percentage of health service professionals, EMTs, nurses, doctors, get sick then everything fails. There are a finite number of nurses available to serve at a given hospital, there are only so many goalies available on game day (2 in fact). If the goalies get injured you are basically fucked. Yes there was this one game this one year that the team won, just saying. However, the reason this is notable is that most third string goalies never get in and when they do they fail.

If fewer medical professionals are available more people fail to receive adequate care, so these people get worse results. Furthermore, new cases get pushed to the back burner making the problem last longer. Also Grandpa who shows up with a heart attack is part of this queue.

5. This leads to the St Louis vs Philadelphia conundrum. (Not fair to either city.) During the flu of 1918, problematically called the Spanish Flu, Philadelphia took a Trump MAGA approach, not doing shit, and St. Louis took a more draconian approach of closing dance halls (clubs), schools, and other gathering areas. This this led to the 'flattening the curve' idea that is all over the nets.

From here

The gif is better in my opinion: Flatten the Curve

Basically the idea is that if exposure and infections are delayed, severe cases do not overwhelm the health care infrastructure. The bad part of this is infections occur over a longer period of time. The good part is that fewer people die! To be clear without flattening the curve, there's a much greater chance of people dying from Coronaviruse, but also Grandpa dying of a heart attack, because the health care system is overwhelmed. If doctors, nurses, and other staff are home sick they are not helping Grandpa out and there are not people on the zamboni who can come into the game successfuly.

We, in the US and most other places, are not prepared for pandemics. It's not our business model. However, by taking steps to mitigate the potential, and almost certain problems, we can respond adequately. To be clear people will die, people will get sick, there's no denying that. However, we can significantly reduce the number who die and get profoundly sick.

As an academic, a skeptic, and a realist I doubt we will succeed. Overall I think we are Philadelphia, not St. Louis.

Prove me wrong.

Women in Science: an Example of Roadblocks

It's exciting times in our Medical School. We recently completed a Strategic Plan entitled Strategic Vision 2025 and we hired a new Dean. There are numerous problems at the university medical school, but these are off-set (in part) by the many strengths of the medical school.
Our new dean has embraced the Strategic Plan and had a Town Hall meeting this last summer to outline in broad terms 6 goals to be addressed in the next year (some are of course longer term goals, but can be started sooner rather than later). These goals line up well with those outlined in the Strategic Plan, although the Dean has put them in a context he finds most compelling.

The 6 goals are to:

1. Increase scholarship
2. Increase NIH ranking
3. Improve diversity
4. Merge the diverse health systems
5. Reduce medical student debt
6. Increase financial resources

In the format of a town hall, there was little time to get into specifics of how each goal will be reached. However, the two approaches to improve diversity were striking to me in their focus. First the issue of diversity is readily backed up with data, this can not be ignored as simply an issue of 'political correctness.' As a percentage of the state population, minorities are underrepresented in the medical school faculty as are women. Half the state population is female and, not surprisingly, half of the assistant professors in the medical school are women. However, there is a precipitous drop in the percentage of women being promoted to associate and full professor such that 30% of associate professors are women and 10% of full professors are women. 

This begs the standard question, why is there a discrepancy?

Two general answers to this question come to mind. 1, there is a problem with the women that are hired such that they are unable to be successfully promoted; 2. there is a problem with the administration that, at least subconsciously, fails to promote women.

During said town hall meeting two ideas were presented to improve diversity within the medical school faculty. First, we need to have more mentoring to improve the success of our female faculty. Second, we need to have workshops to facilitate female involvement in various collegiate activities.

These two ideas suggested one thing to me: the administration believes the reason women are not being promoted is because of the women.


I am a huge supporter of mentoring, for everyone, at all levels, but I wonder why mentoring is specifically pointed out here. Are women not being mentored, but men are? If so, then this is an administration problem not a women problem. Are the women we hire in special need of mentoring that the men do not need? If so, then this is an administration problem not a women problem, because we are clearly not hiring high quality well trained women. The same arguments can be made for the workshops. Maybe the men are getting this extra information in the locker room or over cocktails after work when the women are not around. Regardless, this is an administration issue and not a women issue.

What struck me at this town hall was the focus was on 'fixing' the women so they could be promoted, not 'fixing' the administration such that women were not overlooked and ignored.

I couldn't help but wonder what the women faculty in the audience of that town hall thought. Not growing up in an environment where I was implicitly considered lesser based on my gonads, I couldn't help but think they would be insulted. But maybe they are used to it.

'How It Works' via xkcd

The Changing Climate of Science in the USA (not a post on climate change)

UPDATE: If you are coming from uncommondescent.com please substitute the letter o for all letter u's to avoid 'the vapors'. Also, substitute Darwinius masillae anytime you see the word ENCODE so you won't miss the fucking point (to make things easy, you'll only have to make this substitution once).

One of my heroes: from here

I have seen a shift in the way science is being conducted in the United States. This shift still reflects of minority of the science being done, but it also represents the majority of the science being reported or disseminated to the public. In short, it appears to me that the pendulum has swung from favoring rigorous science to favoring and rewarding what I will call 'splash' science. To be clear this struggle between rigorous and splash science is not new nor different than in previous generations. Nor is all rigorous science not splash and vice versa. However, I think in the US the pendulum has swung dramatically to the splash at the expense of the rigorous. This change in trajectory is not surprising as funding has constricted immediately following a massive expansion. There are too many mouths at the trough and they are competing for those few morsels of grain.

More and more, scientific research is being sold on its revolutionary impact and not on its scientific merit. Of course 'impact' sounds much more important than 'merit'. Hell, important and impact both begin with the letter 'i' so there must be something to that. It seems much more science is being sold as 'paradigm shifting,' 'completely unexpected,' 'novel' (the only one that is true, but only in the trivial sense), or 'needing to rewrite the textbooks.' In these cases, it's also 99.99999999% bullshit (e.g. ENCODE).

2nd edition, 2011

Now admittedly and importantly, there are many studies that reveal unexpected results that lead to interesting and a variety of unexpected questions, which can themselves lead to new insights. For example, I sat in the audience at an American Society of Microbiology conference on Candida and Candidiasis where the phenomenon of white-opaque switching (a well known but poorly understood phenotype of certain Candida albicans strains) was directly and elegantly linked to mating (a process that, at the time, had recently been described but the biology nor the relevance was not understood). This was one of those 'HOLY SHIT!' moments that was amazingly cool, but also neither paradigm shifting nor required the rewriting of textbooks. In almost every single case these types of studies will not shift a paradigm nor require the revision of any textbooks. The results may be unexpected, but at most they will lead to the addition or significant revision of chapters in specialized topic books, such as the Candida and Candidiasis book from ASM.

It could be argued that inflating the importance of a study does not undercut the underlying data. But this argument is generally wrong at several levels. First, in order to emphasize the ephemeral, the actual suffers. In order to emphasize the ability to grow in high levels of arsenic, Wolfe-Simon focused on the bacteria using As in place of P in DNA and other macromolecules. The ability of the isolated bacterium to grow in such high concentrations of arsenic is interesting, but this was ignored to focus on the rewriting of textbooks on the structure of nucleic acids, which was wrong. Second, to push your paradigm shifting results, you have to actively ignore or overlook the contradictory data, even that data contained within your own work. Third, you have to discount and/or disregard the data, usually mountains of data, that led to the current paradigm in the first place.

These issues are what concern me most. This is not how I was trained as a scientist and is philosophically opposed to my understanding of the scientific process. In science, at least at the core, we try to prove ourselves wrong. We do not try to prove that X causes Y, we try to prove that X does not cause Y. When we obtain data that undercuts a paradigm, we do not write a fucking press release, we first consider how we fucked up the damn experiment! We do not identify the next great anti-cancer therapeutic target, we identify a protein that is required for uncontrolled cellular replication in a certain cell line under certain growth conditions in the lab.

If we as scientists, have truly identified a paradigm shifting result or established that the textbooks need to be rewritten, this will come out in the end. If we hoist ourselves by our own petard, then we have a problem. Think about this, when we push these boundaries of science as I see happening too often in publications and manuscripts I review, are we any different than the snake oil salesmen of yesteryear, or the person at the other end of the psychic hotline, or the politician that assess every problem to some simplistic social issue we already agree with.

We're scientists. We're better than this.

One of Our Own Hits the Big Time

H/T Sandwalk

Goodbye dear friend

Cupid at Lake Itasca. Age 12.

Yesterday was a hard day, today hasn't been much better. Yesterday I had to say good-bye to an old friend. A friend, a family member, of over fourteen years. It is with great sorrow that I say good-bye to Cupid our dog, companion, quiet supporter after all these years.

It was an otherwise quiet Christmas morning that Cupid entered my life. I was a graduate student in Tucson living with my fiance who has a passion for German Shepherd dogs (all animals actually). Several months earlier we had flown to Reno to breed Viva with a big black gorgeous German Shepherd called Boss, we also used this time as a vacation to see some of Northern Cal including Sacramento, wine country, and San Francisco. That was the time we got through Donner Pass just before it was closed because of the weather.

Viva was now noticeably pregnant and due in the next day or so. She went into labor around 5:00 in the morning Christmas of 1997 and the first pup came shortly thereafter. We had already been through a litter or two and realized this one was not going according to plan. It was taking too long between pups. So shortly after the time most parents are finally rolling out of bed on Christmas, we packed up Viva and, I think, 2 pups and headed to the nearby vet. We spent probably the next 8 - 10 hours celebrating Christmas there with the arrival of an occasional pup, talk about a Christmas present. We weren't at the vet's long before I proposed that if there were 9 pups in the litter, they be named after Santa's reindeer. The general approach was to use a letter of the alphabet and name all the puppies using that letter. But it was Christmas! This suggestion was approved and needless to say Blitzen, Comet, Cupid, Donner (I know), Vixen, Dasher, Dancer, Prancer, and Rudolph (the one nut wonder) arrived throughout the day. I could tell you stories about Blitzen and Vixen as puppies and young adults, but Cupid was the one who stayed in the family and stays in our hearts.

When Cupid was a young adult, I moved away to start a post-doc in New York. Because we had some dominant personality and older German Shepherds, Im looking at you Fia and Dancer (different litter), Cupid seemed kind of hidden in the background. When I was home, she didn't run around screaming 'look at me! look at me! see what I can do!' like the others. In the pack hierarchy she was low girl on the totem pole, but she didn't cower or hide. She just blended. Maybe this has more to do with the little time I got to spend with the dogs during this time because I was only back every few months.

I lived apart from my family for a couple of years and then landed a position in Minnesota. I moved my stuff there from New York and headed to Arizona to get the family. We had lost the other dogs and only had Cupid left to make the trip with us. So, a moving truck loaded up the household items and furniture  and we took Cupid in the minivan with us. Cupid got to see Northern Arizona (again), Utah, Wyoming, South Dakota (where she visited Mt. Rushmore and saw the 'wild' donkeys), and finally Minnesota. All this and only 4 years old.

We rented a townhome for the first year we were in the Twin Cities area out in the boonies. Cupid spent her days hanging out there, but got long walks in the wooded areas around us each morning and afternoon. There were some commercial-industrial places that had large grassy areas and ponds, not to mention Otter Lake, nearby wildlife center, and the wetland area right next door. During the winter, we often walked on 'Squirrel Trail' which was a short nearby trail that surprisingly enough housed many squirrels. There were geese in abundance most of the year, and goslings some of the year. There were also deer more often than not. We almost lost Cupid early on when she decided to chase a flock of geese that flew over the road near the townhomes. We also had turtles running, well not running, around. One afternoon a turtle was scratching at our sliding door, I guess it was too lazy to go around the townhomes and wanted to cut through our place. Anyway my now wife opened the door so Cupid could say hi. I saw the turtle and shouted "Get Cupid back from" and didn't bother finishing because Cupid had just yelped and jumped back about 10 feet with a gash on her nose from the snapping turtle she was checking out. She kept a small scar on her nose from that encounter.

Cupid moved into the house we bought later that year and truly enjoyed having a private grassy backyard and deck to take sunbaths in. She also enjoyed her new job of keeping rabbits and squirrels on their best behavior as well as making sure the neighborhood cats, whose owners cant bother to take care of them, do not spend any amount of time in the yard hunting birds. This explains why the cardinals and blue jays always seemed to appreciate her.

At this point Cupid entered he professional career. She tried her paw as a sheepherder but decided early on that if she couldn't actually catch them, what was the point. She then moved over to tracking and showed some real potential. I remember one time we had traveled to Wisconsin with the tracking club and my wife, 7 or 8 months pregnant at the time, had just finished a long track that Cupid did awesome at. As they were walking back across this large field that was filled with all these divots, my wife disappeared into the grass, bounced right back into view saying "Im alright," and instantaneously disappeared into the next divot with the timing perfect for a prime time comedy. (Neither mother nor child, AFAIK, were harmed in the two crashes.) When they got back to us, Cupid was quite proud of her accomplishment on the tracking course, although I think I detected some ridicule at all us two legged mammals that have intrinsic issues with gravity.

Cupid was 6 when our son was finally born. The first night after he was delivered, I went home to take care of her and brought a blanket my son had been swaddled in for her to get used to his scent. I honestly had some trepidation about how the new arrival would go over. However, Cupid had no problems acclimating to him. She was the perfect grandmother. I would say mother, but anyone who has had a litter knows the moms are perfectly happy to bite, albeit gently, the puppies little heads when they get annoying. She often slept next to his crib and always checked his baby swing in the morning which was where he often slept.

Things pretty much settled down after that. There were frequent walks in the wooded area next to our house. (Its somewhat ironic that that area is being ripped up and replaced with houses starting this summer.) There were also many walks to the nearby lake with swimming and around the wetland across the street. She took on the habit of waiting until you were doing dishes or looking for something in the refrigerator and then stopping right behind you to see if she could trip you (Im pretty sure that was her way of rubbing in our faces that two-legged animals are more easily toppled).

I think Cupid was 8 when we learned she had degenerative neuromyopathy. This is a neuromuscular disease that seems to affect German Shepherds more than other large breed dogs. It causes the slow loss in muscle tone and function. With age comes interesting new growths, loss of hearing, and eyesight problems. This is also true in dogs. But the old girl got around just fine. She had to stop going up and down the basement stairs and for awhile I carried her up and down them so she could hang out with Alpha. As time went on, we started covering the wood floors with carpets because her back legs would slip too easily. Finally, last summer I built a ramp from the deck to the lawn so she didn't have to even use those steps.

During all this time she was basically happy and enjoyed being with the family, going for rides in the car, sun baths. But this last week she finally started having leg pain that we couldn't remedy. This had become a more recent problem, but would generally clear up after a nights rest. This time was different. I could see it in her eyes that this wasn't resolving, that it wasn't fun anymore, that the time had come. The vet was great and Cupid got to stay in the car for her final goodnight, she never was a fan of a Vet's office.

I do not believe in heaven or the afterlife like most people do when they say these terms. But Cupid was an important part of my life for over 14 years. Because of her I am not the same person I would have been if I didn't have Cupid. So I can honestly say that Cupid lives on in me. I can also say that in a way, since  I affect others, Cupid is playing a part in those interactions and maybe that's what the afterlife is or at least that's all it needs to be to me. So as tears wet my cheeks again I just want to say goodbye dear friend, I miss you.

Cupid: 12/25/1997 - 6/8/2011

Thoughts on Bin Laden

I can honestly say I am glad Osama Bin Laden is dead. In fact, I honestly believe that I could have given the order, putting US soldiers lives at risk, to potentially assassinate him. Could I have looked him in the eye, unarmed, and pulled the trigger myself? I would like to think so. if you can order someone else to do it, you should be able to do it yourself. But I do realize that it is not a trivial thing to take a life, not even a vile fuck like Bin Laden. (If he were armed, all bets are off. There's a big difference taking a life that is actively trying to take yours compared to assassinating someone.) I appreciate the decision Obama made to assassinate Bin Laden; I appreciate more the sacrifice the soldiers have made to carry out that mission.

Now that being said I am disappointed with fellow American citizens who celebrated Bin Laden's assassination. (For those who lost loved ones on 9/11, celebrate away, I would.) I remember when the towers came down, I was scheduled to give a seminar that day. While getting ready I heard that the first tower was hit and thought a pilot royally screwed the pooch (it's happened before). While watching the news the second plane slammed into the second tower, and the world changed. I remember not being able to leave the news for hours trying to figure out what was happening while in the back of my mind I'm thinking about having to give this stupid talk. Did I even want to go to the university? This may have been more poignant for me because I stopped working in NYC June of 2001, every day I took a bus from Union City NJ to the Port Authority Bus Terminal, to catch the A train to 168th St. I did go to work, keeping the news on the radio. Shortly after arriving, I received a call asking if I wanted to cancel my talk. Being the new guy on the block, I said I was ok to go, but was relieved when the decision was made to cancel it and close the university until some shit got figured out.

I was scared, not dramatically, but subtly because I did not know what was happening or why. Mostly though I was angry, I wanted payback. I wanted the perpetrators dead. I wanted answers and I wanted revenge. I remember the dancing and remember hating the woman in glasses. I got more pissed.



Osama Bin Laden is a maggot worthy of death. But why was that woman in glasses happy? Upon seeing that video, I would have ordered her assassination too. But FUCK, why were those kids dancing? I could simply take the viewpoint that these people are inherently evil but that seems stupid. Are those children evil? Maybe assassinating that woman isn't a reasonable response. Maybe these people have a perceived issue with the US and view this as some recompense. Maybe I don't know as much about the world around me as I think I do. Regardless, Bin Laden should be killed, his actions were not justified except in the mind of a madman.

So he is dead. Obama ordered his execution and the mission succeeded. No US soldiers were lost in the mission. It was a great success. So what did we do?



We danced.