computer models – The Laughing Wolf

COVID-19 16Apr20

Yes, I took a few days off. First, most of the news on COVID-19, aka Winnie the Flu/Xi Flu/Chinese Flu/etc., was political in nature rather than science based. Second, a lot of the more learned discussion had to do with models, and much of the really good discussions on that would be “inside baseball” to most people. Short version remains, however, that the prime model used for policy is seriously flawed and even with corrections is not yet close to reality. Until it is, it should not be used for policy decisions in my opinion. Third, I needed a break and got some other things done.

Before I get to the main topic for today, two quick notes. It is good to see that what was previously taboo is now going mainstream. Back two months ago, if you talked about the safety problems at both labs in Wuhan and even appeared to entertain the idea it could have been a lab accident, you were guilty of spreading false information and could be deplatformed. I’m glad several of us did, and even more glad to see some more open discussion of those problems and the possibility this started in a lab.

This article asks another taboo question that needs full and honest discussion. Given that the Chinese economy is brittle and was already in trouble; and, that Xi seized the opportunity to expand monitoring even as troublesome people were disappeared and various cleansings expanded, it is not outside the realm of possibility that Xi decided to level the world economic field a bit and make the most of it.

The main topic for today, however, is a study being breathlessly touted in the media for saying it is futile to develop a vaccine (and with some other slams). No, no it does not say that vaccine research is futile. Not unless you selectively edit the quote.

“Based on the close relationship of SARS-CoV-2 to SARS, current vaccine and drug development for SARS-CoV-2 has also focused on the S protein and its human binding receptor ACE2 (7, 24). Thus, the observation in this study raised the alarm that SARS290 CoV-2 mutation with varied epitope profile could arise at any time, which means current vaccine development against SARS-CoV-2 is at great risk of becoming futile. “

Let’s break this down and take on some of the media talking points.

Point 1: Until it is peer reviewed, and other studies confirm (or refute) it’s findings, I don’t trust it. Number of reasons, including that early studies can be like early reporting: full of errors and sensationalism.

Point 2: A finding of the study is that a mutation of COVID-19 has been found in India. That mutation, if you go to line 282 in the paper, actually makes that version less infectious as it reduces the ability to bind to ACE2 receptors. Did you get that? The mutation is less infectious, not more.

Point 3: Unlike some other covids and other viruses, the rate of mutation in COVID-19 is slow. If you go to line 229, this paper confirms that and even goes so far as to note “A relatively stable genome of SARS-CoV-2 is a good indication for the epidemic control, as less mutation raises the hope of the rapid development of validate vaccine and antiviral drugs.” Hardly the breathless gloom and doom implied by various headlines and discussion.

Point 4: Going back to the discussion above, changes in the S protein may make vaccine development targeted to that protein (and the related ACE2 binding) futile. Not all vaccines, just that target.

There are some other interesting points in the paper, but again it has to be taken with caution for now. As other studies replicate or provide information, a better assessment can be made.

As I discussed in a previous update that discussed structure-based drug design, viruses mutate. It’s a given. Some mutate slowly, some like an ADD squirrel in a field of nuts. Some mutations make the virus easier to catch, some make it more deadly, others can change receptors, symptoms, and more.

The fact is, however, that quite a few of those mutations are evolutionary dead-ends. Too deadly, and people die before they can transmit it. Less infectious (as seems to be the case discussed here), again, it is a strain that could die out well before others.

The key to vaccine development for fast mutations is to find targets that don’t change, because when those change that strain dies out. There are always such targets, the trick is finding them and finding ways to target them.

In conclusion, don’t let the MSM wind you up or be your main source of info. When it comes to false information, they lead the pack.

Since the media isn’t going to say it, once again, COVID-19 is not Capt. Tripps. It is not the flu or a cold. Chill, distance, and use good hygiene. STOP THE PANIC!

Also, a reminder once again: if you are sick or think you are sick, DO NOT GO TO WORK OR TO VISIT PEOPLE. Stay the frack home. Don’t be Stupid, go to work/out, and insist on getting up close and personal to everyone you meet. Yes, Stupid is capitalized as I work with Stupid, who did just that. Don’t be Stupid.

If my posts are enjoyable, helpful, or otherwise a benefit, please consider hitting the tip jar. Any help is very much appreciated, especially as I’ve been off work without pay since 27 Mar.

•My Amazon Wishlist

As always:

If you suspect you have COVID-19 or have been exposed: call your state health department and work with them so that you can be dealt with in a way that minimizes the chance of spreading the virus to those helping you and to the general public. Can’t get them? Call your local department or see if your health service has online/telemedicine screening set up; or see if one who has will let you use it even if you are not in their network. Do not go out in public, and don’t go to an ER or other facility without calling ahead. Be smart.

Use the interactive graphic to keep track of things. Is COVID19 an epidemic? Yes. Is it a Pandemic? Yes. Is there need for panic? NO. HELL NO. Should you be paying attention? Yes. Hell yes. Should you be preparing? Yes, better late than never. And good luck finding/getting stuff.

Want to avoid catching COVID19 here in the U.S.? Wash your flippin hands frequently, wash them thoroughly every time you use the bathroom, then follow with hand sanitizer after every washing, use hand sanitizer liberally when you can’t wash on a regular basis. Cover your mouth and nose when you sneeze, and stay away from those who don’t. Also, keep your bugger hooks out of/away from your eyes, nose, and mouth. Do NOT shake hands with anyone, and avoid touching or being touched by strangers. Or your strange friends.

Avoid travel if at all possible. If you have to travel, or go out for any reason, use lots of hand sanitizer and go to full flu protocols. If you have to use a public restroom, take full precautions including using paper towels and such to handle faucets, doors,etc. Believe it or not, this was highly recommended before now, and major grocery chains have long told employees to use those practices to avoid getting or spreading colds, flu, etc. Not many actually do it, but…

If you own a business, make sure your employees know the above protocols. Have someone who refuses to wash their hands or otherwise follow the protocols? Talk to them, write them up, and if necessary fire them as they now pose a risk of infection to you and your customers. Extreme? Yes, but while the CDC and others are working to slow it down, odds are it is already here and could hit hard and fast. Prepare for the worst and hope for the best.

I want to reiterate that there is no need for panic, but there is a strong need to be alert, be informed, and be prepared.

Good Sources Of Information On COVID-19

Instapundit (no longer doing roundups, but great articles from Glenn and his team)

South China Morning Post (decent, some salt may be needed)

Business Insider (decent, even if they did fall for some lies about Trump)

New England Journal of Medicine

Additional link to Johns Hopkins

More to come

Local Independent Businesses That Need Your Support

Oaken Barrel (Twitter at @OakenBarrel)

More to come

Other COVID19/COVID-19/2019-nCoV articles:

COVID-19 13Mar20 The Game Of Loads And Vectors Gets Real For America

COVID-19 12Mar20

COVID-19 11Mar20

COVID-19 10Mar20

COVID-19 9Mar20 The Game Of Loads And Vectors

COVID-19 8Mar20

Heh

COVID-19 7Mar20 How To Do It Right If You Have/Have Been Exposed To COVID-19

COVID-19 What Am I Doing?

COVID-19 2Mar20

COVID-19 1Mar20

COVID-19 29Feb20

Quick Additional Thoughts On The Bureaucracy

Panic Is Off And Running

COVID-19 28Feb20 Reasons To Hope, Reasons To Fear

COVID-19 A Plea To The Politicians (And Media)

COVID-19 27Feb20

COVID-19 Breaking A Chain?

COVID-19 26Feb20

COVID19 The Situation In China Gets Even Weirder

COVID19 25Feb20

COVID19 24Feb20 Raising DEFCON

COVID19 23Feb20

COVID19 22Feb20

COVID19 21Feb20: Just Look At The Blooms Dear

COVID19 Update 20Feb20

COVID19 Update

Update & Quick Thoughts On Preparedness

Expansion On A Theme

Well Maybe I Was Wrong

Some Quick Thoughts On Coronavirus 2019-nCoV

Why Should You Be Prepared?

Keeping Alert

Coronavirus And Practical Preparedness

COVID-19 27Mar20

Where to start. Well, let’s start with the same thing as the last few days. If you are depending on the mainstream media for accurate and unbiased news, please stop. What you are getting from them is a deliberate attempt to create panic for partisan and personal gain. You are NOT getting good info. In fact, what you are getting is a threat to your physical health, your mental health, and your freedoms. The latest of far too many was an attempt to smear a hospital and create a climate of fear. There is no excuse for this. Period. Full Stop. Want to see more lies and distortions, go read this. You also need to read this.

The focus on cases and deaths is not helpful, to put it mildly. It is disingenuous at best (but makes breathtaking headlines), and it makes for bad analysis. Polymath on Twitter makes a good case that looking at composite data for the entire U.S. is not a good idea. I agree, and present the case that we need to be breaking it down further. Each state needs to be examined on its own, and within that each state should be looking at county/regional data hard.

Why? It shows trends, clusters, and other data that makes it easier to plan responses, ensure logistics of needed materials, and ensure other resources get to where they are needed most.

Which gets to the other issue we need to be discussing: How do we get America back to work. A one-size-fits-all approach is not the best approach, and will destroy both the American economy and our freedoms. What is needed is a response proportionate to each location. A rural area or even cities where the spread is minimal do not need to be on the same level of lockdown as an area with significant spread. You change things as the data warrants. This needs to apply not only at the state level, but at each county and even within counties.

Expect this to be fought tooth and nail by some. Far too many politicians are grabbing all they can to make things the way they want them to be, rather than what the Constitution says should be. Don’t believe me? Just look at the number of governors, mayors, and others who are using this as an excuse to ban gun and ammo sales, or take other actions to further radical political agendas. Lots to see out there.

In fact, if you want to see the true Evil, take a look at Nevada governor Sisolack , Michigan governor Whitmer, and (no surprise) His Majesty’s Governor Northam, the Earl of Blackface. Each of these has chosen to ban or severely restrict the use of hydroxychloroquine and chloroquine for reasons of politics, not medicine. Yes, I do consider that Evil, not evil, as they are willing to kill the citizens of their states for personal and political gain. They may or may not hate you, but they are willing to help you die. In my book, that’s murder. The law may well say negligent homicide, and if any die or are permanently harmed by the lack of treatment, they may find official immunity does not cover them from such charges and related civil actions. They need to be held to account for this before someone does die. If you live in that state, do you really want to have as a leader someone willing to put politics ahead of the lives and safety of those you love?

Nor are they alone. Look at NYC, where the mayor and top leaders deliberately encouraged actions — in the face of warnings from experts at the CDC and elsewhere — encouraged behaviors that guaranteed a catastrophic outbreak in NYC. There are other, similar stories around the country where elected leaders have put their personal and political gain ahead of the lives of their fellow Citizens, people they have sworn to serve (and protect). Congress, state, local. Again, do you really want to have as a leader someone willing to put politics ahead of the lives and safety of those you love?

Now, on to models which is a hot topic after yesterday’s news. Frankly, I’m disappointed with some I know who are both smart and educated in regards their comments about models and the use of same. Add to the list of those who say: it’s the flu, it’s going to kill us all, this was a Chinese bioattack, it’s all Trump’s fault, those that say we should never use computer models again for policy decisions. People who say any of these things are stupid, and you are probably better off without them in your life. Done right, computer models can be a very useful tool. Then again, like all statistics, they can be used to lie.

Dr. Birx has some thoughts on the subject, and on the media use of misleading (cough, lies, cough) models and statistics. They are well worth the time to watch and listen.

As noted previously, models are only as good as the data that goes in them. The GIGO law still applies today, and will always apply. That said, even flawed models can be useful if used properly.

For every model, there are usually four basic runs: best case, worst case, median, and mode. Running a model to get those four shows a range of outcomes. It helps define the limits of the problem, and with smart analysis, the model itself. With the range defined, you can drill down to get a better understanding of how different responses or other actions (such as different spread rates, death rates, etc. in this case) change outcomes. You can also identify critical areas to explore in more detail.

As noted before, if you are a leader facing a crisis be it a dam breaking or a pandemic hitting, you need good info on best case, worst case, median, and mode and you need it fast. While you hope for best case, you plan and act for worst case in order to get something closer to mean or median if you can’t be sure of getting the best case outcome. You have to depend on the experts to get you the data needed to make the right decisions.

In the case of our response (and it is worth noting that according to Johns Hopkins we were the best prepared nation in the world for a pandemic, thought that does not mean we were as prepared as we should have been, we weren’t.), one of the top experts was wrong with his models and our elites were off doing other things rather than their prime and critical job in the years leading up to this. And, yes, you will find the same thing, even more so, at the FDA and CDC. It is not just a problem with the NIH. There are many lessons to be learned and applied once this is behind us.

So, you as a leader are dependent on those of critical expertise, who may or may not have any political or other biases and who may have little to no real-world experience. You go with what you have, do the best you can, and start correcting on the fly as you get better data. This is what has happened and is happening.

Right now, the issue is not the number of cases or the number of deaths. It is how many require hospital treatment, and more importantly how many will require advanced support. It is frustrating that there is not better data on this, and when I talked about breaking it down as far as we can, this is some of the most critical data out there. If you can project the local spread rate and the local required treatment rate and compare it to the available beds and support… This article takes a look at what states/areas are either at capacity or approaching it. It’s not definitive or hard data, but it’s a good start.

So, what to do? I hope the President will continue to do one thing above all others: cut loose the ingenuity and can-do attitude that is American Exceptionalism and free market capitalism. While government bureaucracy has time and time again hampered efforts at effective and efficient response to COVID-19, American businesses have time and time again worked miracles to meet needs.

We need ventilators. There are major companies lining up to make them. Even better, you have MIT developing a $100 model; and, you have James Dyson designing a new ventilator in 10 days and committing to building 15,000 of them as fast as possible. You have another company designing a device to allow one ventilator to help four patients at a time. There are a lot more stories like this out there. Rather than listen to or watch the media, go do a search and I think it will help your outlook.

You will also find stories where companies that still have manufacturing capabilities here are doubling down. 3M plans to make more than a billion masks by the end of the year. You will find the company that makes the swabs needed for testing (and a host of other uses) working overtime to meet demand and get ahead.

So, Mr. President, keep the bureaucrats at bay, replace the lockdown with a gradated series of responses, and let’s get cracking. Use the better data we are getting to analyze each area and decide what response is best for that area. As we do this, let’s look at what worked, what didn’t, what could have been done better (AARs are a good thing, so long as I don’t have to write them) and then use that as a starting point for the long overdue (and bitterly resisted) modernization, update, and refocusing of the CDC, FDA, NIH (and others, please) on their core missions. Let’s also look at the ineffective and unneeded regulations, burdensome laws, and other impediments to our nation and our economy and eliminate, change, and deal with them as needed.

Once again, COVID-19 is not Capt. Tripps. It is not the flu. Chill, distance, and use good hygiene. STOP THE PANIC!

If my posts are enjoyable, helpful, or otherwise a benefit, please consider hitting the tip jar. Any help is very much appreciated, especially as I’m now off for two weeks without pay.

•My Amazon Wishlist

As always:

I want to reiterate that there is no need for panic, but there is a strong need to be alert, be informed, and be prepared.

Good Sources Of Information On COVID-19

Instapundit (no longer doing roundups, but great articles from Glenn and his team)

South China Morning Post (decent, some salt may be needed)

Business Insider (decent, even if they did fall for some lies about Trump)

New England Journal of Medicine

Additional link to Johns Hopkins

More to come

Local Independent Businesses That Need Your Support

Oaken Barrel (Twitter at @OakenBarrel)

Shapiros

Greek Islands

Bynum’s Steak House

Pipe Puffer (cigar and pipe) regular hours for now

Schoolhouse 7 Cafe

WIBC’s list of local

More to come

Other COVID19/COVID-19/2019-nCoV articles:

COVID-19 13Mar20 The Game Of Loads And Vectors Gets Real For America

COVID-19 12Mar20

COVID-19 11Mar20

COVID-19 10Mar20

COVID-19 9Mar20 The Game Of Loads And Vectors

COVID-19 8Mar20

Heh

COVID-19 7Mar20 How To Do It Right If You Have/Have Been Exposed To COVID-19

COVID-19 What Am I Doing?

COVID-19 2Mar20

COVID-19 1Mar20

COVID-19 29Feb20

Quick Additional Thoughts On The Bureaucracy

Panic Is Off And Running

COVID-19 28Feb20 Reasons To Hope, Reasons To Fear

COVID-19 A Plea To The Politicians (And Media)

COVID-19 27Feb20

COVID-19 Breaking A Chain?

COVID-19 26Feb20

COVID19 The Situation In China Gets Even Weirder

COVID19 25Feb20

COVID19 24Feb20 Raising DEFCON

COVID19 23Feb20

COVID19 22Feb20

COVID19 21Feb20: Just Look At The Blooms Dear

COVID19 Update 20Feb20

COVID19 Update

Update & Quick Thoughts On Preparedness

Expansion On A Theme

Well Maybe I Was Wrong

Some Quick Thoughts On Coronavirus 2019-nCoV

Why Should You Be Prepared?

Keeping Alert

Coronavirus And Practical Preparedness

COVID-19 26Mar20

There is huge news this morning, news that may or may not get the coverage it should, both in terms of quality and quantity. In some ways, it is not unexpected but is rocking the epidemiological community.

The reason I started doing these updates was that I did not think the story was getting the coverage it should. One of the things I do is look at data and spot patterns. I did not like the pattern I was seeing even before the mainstream media started paying attention. It was clear something was going on; that it was far worse than China was admitting based off what data could be obtained; and, it was also clear that China was flat out lying with the data provided. It didn’t take much of a dive into Chinese social media (or into commercial intel) to figure that out.

One of the first places I found that was taking it seriously and trying to model what was happening was the Imperial College of London. Their model(s) were one of the first efforts to identify, chart, and project and I, like many others, linked to them and used them in our analysis.

This morning, I awoke to the news that Neil Ferguson at the ICM has revised, yet again, the projections. This is the third pivot, and while a lot of people are going to be castigating him, I’m not yet prepared to. For while we knew the data from China was incorrect, it was all we had. The problem is, in any model, that when you put garbage in, you get garbage out. GIGO applies today as it always has. While I did consider his previous advice on herd immunity — a reaction plan quickly dropped by the government — was idiotic, it was to some degree understandable.

The short version for those that don’t follow the link: it’s bad, but both the UK and the US should have enough beds and capacity to handle what is to come. It will get very close in some areas, and a few may hit capacity, but the death toll will be much, much lower. Seriously, go read the article.

Here in the U.S., I suspect that NY and California are going to be our two major hotspots where this may not hold. The unconscionable actions of DeBlasio in NYC in the early days have made a bad situation catastrophic. Previous decisions by him and by Gov. Cuomo pretty much guaranteed they would not be ready to handle something like this. California, well, much the same boat. It is anecdotal for now, but the countries and areas that had tight government controls on, or socialized centralized government healthcare, have faired the worst. An interesting point for debate sometime soon.

This news is going to change our response as well. Again, I will point out that we had to plan for and initiate a response based on worst-case until we had enough accurate data to understand the situation. We are now getting accurate data in amounts that will allow that, though we won’t have a truly clear picture for weeks. However, we have enough to begin considering options while we watch what transpires between now and the end of the 15-day period.

Also, I will admit I was wrong about masks. I did not think they would be effective under the circumstances we thought we were facing. The fact is, there is now evidence that if everyone were to wear surgical masks (and if we had them for people to wear them), it would slow the infection rate down. Note: just wearing one yourself won’t do a lot of good. This will only work if everyone wears one. A bit of anecdotal data on this is here. Again, the problem there is that we would have to have them, and right now we don’t.

There is a lot to learn from what has happened/is happening. There needs to be some serious and intense debate about it, and we need to massively overhaul and update the CDC and FDA — including trimming out the major mission creep in both and returning them to their original and vital functions.

Again, ignore the media and the breathless fixation on cases and deaths. Do not give in to the panic they are trying to create. Yes, as noted before, cases are going to spike both because of transmission and the rapid expansion of testing, which will generate a false spike as existing cases are confirmed. Yes, sadly, people will die but the number is going to be far less than most other causes including the flu.

As I noted yesterday: “What are the numbers to look at? First, what is the number of patients requiring treatment in a hospital. Second, what is the number of people requiring treatment in an ICU? Third, what is the number of patients who require ventilator support? You might be surprised at the age ranges of those needing ICU and/or ventilator time, as a surprising number of them are NOT in the at-risk range.”

Once again, COVID-19 is not Capt. Tripps. It is not the flu. Chill, distance, and use good hygiene. STOP THE PANIC!

If my posts are enjoyable, helpful, or otherwise a benefit, please consider hitting the tip jar. Any help is very much appreciated, especially as I’m now off for two weeks without pay.

•My Amazon Wishlist

As always: