twenty-two things tagged “covid”

“Crowded, Compartmentalized, Sticky, Spatially Inhomogeneous”

In college, I remember being blown away by a huge, physical map of metabolic pathways our Biochemistry professor once brought into class. It looked like this:

metabolic pathways

Here it is online. Kinda like a Google Maps of cellular reactions. It was impressed upon us that the interior of a cell (especially a eukaryotic one) is a really, really busy and tight and ‘goopy’ place: “crowded, compartmentalized, sticky, spatially inhomogeneous”. As that paper notes, this messy, “macromolecular crowding” helps your proteins fold properly (among several other factors.) This was a bit hard for me to appreciate since, up to then, I was only accustomed to images of cells from a light microscope or vastly simplified illustrations school texts.

I was somehow reminded of all of that after seeing some astounding paintings by Professor David S. Goodsell (Wiki, Twitter, Website). He calls the series “Molecular Landscapes.” Here are a few related to the pandemic we’ve been through.

SARS-CoV-2 and Neutralizing Antibodies, 2020

Art by David S. Goodsell

Acknowledgement: David S. Goodsell, RCSB Protein Data Bank and Springer Nature; doi: 10.2210/rcsb_pdb/goodsell-gallery-025. The painting was commissioned for the cover of a special COVID-19 issue of Nature, presented 20 August 2020, and is currently in the collection of the Cultural Programs of the National Academy of Sciences.

(Unknown Title)

Art by David S. Goodsell

Acknowledgement: Illustration by David S. Goodsell

Coronavirus, 2020

Art by David S. Goodsell

Acknowledgement: Illustration by David S. Goodsell, RCSB Protein Data Bank; doi: 10.2210/rcsb_pdb/goodsell-gallery-019. This painting depicts a coronavirus just entering the lungs, surrounded by mucus secreted by respiratory cells, secreted antibodies, and several small immune systems proteins. The virus is enclosed by a membrane that includes the S (spike) protein, which will mediate attachment and entry into cells, M (membrane) protein, which is involved in organization of the nucleoprotein inside, and E (envelope) protein, which is a membrane channel involved in budding of the virus and may be incorporated into the virion during that process. The nucleoprotein inside includes many copies of the N (nucleocapsid) protein bound to the genomic RNA.

SARS-CoV-2 Fusion, 2020

Art by David S. Goodsell

Acknowledgement: Illustration by David S. Goodsell, RCSB Protein Data Bank; doi: 10.2210/rcsb_pdb/goodsell-gallery-026. This painting depicts the fusion of SARS-CoV-2 (magenta) with an endosomal membrane (green), releasing the viral RNA genome into the cell cytoplasm (blue), where it is beginning to be translated by cellular ribosomes to create viral polyproteins. The painting includes speculative elements that are designed to highlight the process, most notably, multiple states of the viral spike protein are shown.

SARS-CoV-2 mRNA Vaccine, 2020

Art by David S. Goodsell

Acknowledgement: Illustration by David S. Goodsell, RCSB Protein Data Bank; doi: 10.2210/rcsb_pdb/goodsell-gallery-027. Messenger RNA (mRNA) vaccines developed for the COVID-19 pandemic are composed of long strands of RNA (magenta) that encode the SARS-CoV-2 spike surface glycoprotein enclosed in lipids (blue) that deliver the RNA into cells. Several different types of lipids are used, including familar lipids, cholesterol, ionizable lipids that interact with RNA, and lipids connected to polyethylene glycol chains (green) that help shield the vaccine from the immune system, lengthening its lifetime following administration. In this idealized illustration, all of the lipids are arranged in a simple circular bilayer that surrounds the mRNA and the PEG strands have both extended and folded conformations. In reality, the structure may be less regular, as suggested in the NanoLetters paper […]

Good Old Iowan Common Sense

As of the 4th of February 2021, and under its Governor’s wise, prescient, expert and data-driven leadership, Iowa ranks 47th in the nation for the number of vaccines administered 💯

Iowa has received 446,825 doses of vaccine and has administered 266,777 doses, or just under 60% of vaccines received, the CDC reported Thursday. The state has the sixth-lowest rate of administered vaccine per capita in the nation.

“We’re averaging about 60% in getting the vaccines administered and that’s not where we need to be,” Reynolds said. “We want to do better. We know we can do better.”

AP, “Iowa’s vaccination rate is 47th in the US

We certainly can. The number of COVID-related deaths in Iowa stood at 5,033 as of this date. The very next day, our fearless Governor signed a Public Health Disaster proclamation that, compared to its predecessor, ended mask mandates and removed all limits on public gatherings.

In time for the Super Bowl, of course.

All of these relaxations at this stage of the pandemic make about as much sense as wearing underwear constructed out of nails and thumbtacks. If anything, Iowa should be enhancing precautions during the next several weeks, as long as the colder temperatures and drier air may be driving greater transmission of the virus. What is the scientific justification for what Reynolds has declared in the emergency declaration? It’s unclear. Seems like someone may owe Iowa an explanation.

Bruce Y. Lee, “#CovidKim Trends After Iowa Governor Reynolds Lifts Covid-19 Coronavirus Precautions

Other the the usual bullshit conservative pabulum about freedom and small businesses and bootstraps and moochers and handouts, I don’t expect any explanation that makes sense.

“I want you to take a step back and COVER YOUR FACE”

I wish they would blare portions of Tom Cruise’s COVID meltdown at all grocery stores in my lovely state. Someone on /r/desmoines posted an anti-masker patriot at our Costco who could use this message.

I’m on the phone with every f–king studio at night, insurance companies, producers, and they’re looking at us and using us to make their movies. We are creating thousands of jobs you motherf–kers.

I don’t ever want to see it again, ever! And if you don’t do it you’re fired, if I see you do it again you’re f–king gone. And if anyone in this crew does it – that’s it, and you too and you too. And you, don’t you ever f–king do it again.

That’s it! No apologies. You can tell it to the people that are losing their f-ing homes because our industry is shut down. It’s not going to put food on their table or pay for their college education.

That’s what I sleep with every night. The future of this f–king industry! So I’m sorry I am beyond your apologies. I have told you and now I want it and if you don’t do it you’re out. We are not shutting this f–king movie down! Is it understood?

If I see it again you’re f–king gone — and you are — so you’re going to cost him his job, if I see it on the set you’re gone and you’re gone.

That’s it. Am I clear?

Do you understand what I want? Do you understand the responsibility that you have? Because I will deal with your reason. And if you can’t be reasonable and I can’t deal with your logic, you’re fired. That’s it. That is it.

I trust you guys to be here. That’s it. That’s it guys. Have a little think about it. . . [inaudible].

That’s what I think of Universal and Paramount. Warner Brothers. Movies are going because of us. If we shut down it’s going to cost people f–king jobs, their home, their family. That’s what’s happening.

All the way down the line. And I care about you guys, but if you’re not going to help me you’re gone. OK? Do you see that stick? How many meters is that?

When people are standing around a f–king computer and hanging out around here, what are you doing? And if they don’t comply then send their names to Matt Spooner. That’s it.

The Joke

Trump has been saying the pandemic has been totally under control since January, and said it would just “go away” in February.

He reiterated this in March as the virus surged, and insisted we had “perfect” tests that anyone could get after reports of faulty tests. He said he wanted pandemic-related shutdowns to end by Easter so churches could be “packed” while claiming Hydroxychloroquine would be a miracle cure for COVID-19.

In April he continued to promote Hydroxychloroquine without evidence and suggested we could inject disinfectants or use UVC light inside the body to kill the virus, and right up through May Trump was discouraging the use of masks and refused to require them anywhere, with him and Pence famously flouting requirements at hospitals and factories. Trump also claimed he was taking Hydroxychloroquine as a prophylactic against the disease. At this point they were even planning to dismantle their own COVID-19 task force.

In June they were still insisting it was under control while fighting the FDA’s revocation of authorizations for Hydroxychloroquine, and denying that there was a second surge happening. They instead blamed the high infection statistics on there being more testing, and Trump suggested slowing down testing to improve the stats, noting he does not joke.

Rolling into July he still insisted he had things under control, claiming they had done an incredible job, as the White House nuked a trove of data previously available through the CDC while Trump was still hyping Hydroxychloroquine and his son was temporarily suspended from Twitter for continuing to spread disinformation about it.

Even in August, Trump claimed COVID-19 was totally under control, and the ~150k dead with a simple “it is what it is,”, and reiterated that the virus would go away all on its own. He finally encouraged the wearing of masks, but ignored all guidelines during his nomination acceptance speech at the Republican Convention.

In September Trump was saying that COVID-19 hurt “virtually nobody”, and openly disputed the CDC’s own claims about the effectiveness of masks.

In October Trump got COVID-19, and while still undergoing treatment, went on a quick spin around the hospital to wave to his supporters outside. He was discharged to the White House after only three days, posing for photo-ops without a mask. At this point White House officials finally concede that “we’re not going to control the pandemic.”. This would be the last time the COVID-19 task force would formally meet.

Since then Trump has pretty much avoided any and all public appearances except to complain about the election. November marked the point where a quarter of a million Americans had died of COVID-19. There are now more people dying each day of COVID-19 than died in the terrorist attacks on 9/11/2001 or in the Invasion of Normandy.

That’s the joke.

/u/kichigai (month highlights mine)

Idiots Out Walking Around - II

Informed Choice Iowa is a group that “unites Iowans seeking to preserve their medical freedoms.” They are “pro-science” folk that count “ex-vaxxers”, “selective vaxxers”, “non-vaxxers”, and “vaxxers” among their members. I’m guessing that this list doesn’t include a single practicing physician.

And here’s them celebrating their freedoms, by which they mean a blatant disregard for the science they claim to love and the Iowans they claim to serve. Need confirmation but I hear that eating at least two tubes of toothpaste is on the agenda for their next idiot congregation.

Here’s a local news story about this superspreader event.

On Masks

Bill Burr on The Joe Rogan Experience:

BURR: I don’t want to start this bullshit. I’m not gonna sit here with no medical degree, listening to you with no medical degree, with an American flag behind you smoking a cigar, acting like we know what’s up, better than the CDC. All I do, is I watch the news once every two weeks - I’m like, “Mask or no mask? Still mask? Alright, mask!” That’s all I give a fuck about. I don’t care. I just love how wearing a mask became like this fucking like soft thing that you were doing… like being courteous…”

ROGAN: It’s for bitches1.

BURR: Why is it for bitches? That’s just so stupid.

ROGAN: (Fakes weak cough)

BURR: Oh God you’re so tough with your fucking open nose and throat and your five o’clock shadow. This is a man right here! A man doesn’t wear a mask.

Rogan’s immediate response somehow reminded me of the “infantile phallocentric Nietzscheanism that is destroying modern human culture” from one of my favorite articles.

  1. Here’s something of a guide to his podcasts. ↩︎

COVID-19 Map

Found this map when Googling “coronavirus india”. Looks like it’s maintained by the WHO and is pretty up-to-date. They have a daily update page.

At the time of this writing, there are 110,029 confirmed cases, with 3,817 deaths in 105 countries. China, South Korea, Iran, France, and Germany account for 95% of the total number of cases and in that order.