My investigation into engineering the covid virus

I have a good science background, but not particularly strong for genetic issues, and the origin of the covid virus is mostly a genetics question. A bunch of Americans, including friends of mine, are convinced the virus was engineered. One friend thinks it was created at the University of North Carolina. 

I didn't feel capable of evaluating the data, but I tried anyway and learned a fair amount along the way. One of my first attempts was asking Google AI some question (not kept), and it responded that RNA can't be precisely edited, so I thought that settled the issue. However I noticed virologists didn't consider the matter settled, so obviously I shouldn't decide based on one AI response. Back to the investigation I went. 

Gene editing medium - DNA or RNA?

It turns out that RNA isn't a great medium for specific genetic editing. It's not as stable as DNA, so most work is done on DNA and then transcribed to RNA, which is very typical genetic processing. RNA can also be reverse transcribed into DNA, which is less common but some tricky viruses learned how to do this and some tricky virologists copy the tricky viruses. Amazing stuff, right? 

So if a virologist wanted to experiment with coronaviruses of the SARS type, he would take one (and several are typed and readily available to scientists in the field), and turn it into DNA and then work on editing the DNA before turning it back into RNA. Then additional tests could be run on the newly created RNA. 

This sounds like scary Frankenstein-like hubris, but this happens in nature all the time. Not the DNA part (which is much rarer), but RNA getting smashed up, parts deleted, parts inserted, genes recombined, and general RNA sequences being mashed together in all sorts of ways. In nature, cells/viruses even try to repair smashed up RNA and introduce changes in the attempts. So it's not surprising that virologists try to do this too because they want to try to stay a bit ahead of the viruses when possible. 

So it's possible to engineer the covid-19 virus. But is that how it happened? The consensus among most virologists seems to be that it could be done and also it would be hard to tell if it was done. Signs of manipulation can be wiped out readily, so there aren't necessarily telltale signs. 

The inserted nucleotides

The biggest change in the transmissibility of the virus came from an insertion of 12 nucleotides that created a furin cleavage site in the spike protein of the virus. This is a protein on the surface of the virus that latches onto cells the virus is trying to infect. Latching on is one step, but more important in actually penetrating into the cell, and the furin cleavage site helps a lot in penetrating human cells. So this is the big mutation that made covid as bad as it was in 2019-2020. 

Some virologists have looked at the 12 nucleotides and considered it a smoking gun, obviously engineered. The majority don't appear to share that opinion, but it's enough of a debate to take it seriously -- not just wackos on one side of the question. 

So who has the stronger case? That's also a matter of opinion, and I actually developed an opinion. To me, it doesn't look engineered. It's a non-standard furin cleavage site, and I think a virologist would go with a standard model rather than trying something somewhat random. (The covid furin cleavage site is PRRA versus the standard R-X-K/R-R.) Also the nucleotides start in the midst of a codon (the 3-nucleotide triplet that encodes for a specific amino acid). This looks somewhat unlikely for engineering too because the real target is the change in the amino acids, not the codons themselves. The codons are just the means. As an analogy, when we write we don't swap out individual letters but we do swap out entire words with words being analogous to the 3-nucleotide codons. 

So that's my tentative conclusion, subject to change with new evidence.

My sources and what I learned

Three sources on CRISPR DNA editing showing how very specific it can be. 1, 2, 3. For RNA there aren't these tools, just some limited nucleotides replacement enzymes and less precise cut and/or paste. 

One proposal to NIH is considered by some to be a smoking gun because it proposes tinkering with coronaviruses genome especially the spike protein and adding cleavage sites there. The program, called DEFUSE, covered many additional areas of research too, but it wasn't funded. However some of the research may have been done with alternate funding. Overview here. More detail here. Full text of the proposal here; I found 'cleavage' to be most useful search term to get to the parts on engineering the spike protein. Nothing here showed the specific sequences to be tried. Another paper on engineering of chimeric (combination manipulated genomes) viruses to show that it's a standard procedure in viral research. A 500+ page collection of approved NIH research proposals just to hold on to a valuable link. This isn't pointed to as a smoking gun so I haven't looked extensively at it. 

Finally a batch of six papers about the specific nucleotide sequence and related material. Claim it was engineered. Detailed rebuttal of the claim explaining how huge a project it would have been. Claim that the furin cleavage site came naturally from another coronavirus. This paper is notable for the Q&A comments after the paper. The clearest explanation of the actual nucleotide sequence, written by a virologist some people think is complicit in engineering, meaning it could be a coverup. Very helpful timeline showing some of the controversial early discussions on the origin. Lastly an article on the natural mutations of the virus into the omicron variant to give a sense of how the virus can change naturally, which is what I think happened to create the original nasty covid virus. 

Image: nih.gov

Extras: Oh no, I wrote about this before and have no memory of it. I think I did a good job this time. 

Researching the Second Amendment

Was the second amendment intended to secure individual gun ownership rights? I decided to look into the issue myself instead of reading the viewpoints of others since they could be shading the evidence. I read the most relevant Federalist paper. 

I read some original state constitutions, several of which are explicit in guaranteeing private ownership rights. Here's a selection:

Pennsylvania: § 21.  Right to bear arms. The right of the citizens to bear arms in defense of themselves and the State shall not be questioned.

Ohio: The people have the right to bear arms for their defense and security; but standing armies, in time of peace, are dangerous to liberty, and shall not be kept up; and the military shall be in strict subordination to the civil power.

Georgia: Paragraph VIII. Arms, right to keep and bear. The right of the people to keep and bear arms shall not be infringed, but the General Assembly shall have power to prescribe the manner in which arms may be borne.

Virginia: Section 13. Militia; standing armies; military subordinate to civil power. That a well regulated militia, composed of the body of the people, trained to arms, is the proper, natural, and safe defense of a free state, therefore, the right of the people to keep and bear arms shall not be infringed; that standing armies, in time of peace, should be avoided as dangerous to liberty; and that in all cases the military should be under strict subordination to, and governed by, the civil power.

I read about the House discussion on the draft amendment. It contains a great deal of original info, but its viewpoint seems like it might be skewed in its emphasis on the Quaker issue. Here's a long article on early gun laws because that can show what they considered acceptable way back then. Yes, there were restrictions on crazy people. 

My current guess as of late summer of 2023? (Yes, there was a long delay in publishing this.) The second amendment is mostly about militias, how every state could and should have one, that the federal government shouldn't be able to ban state militias, and how they are to be militias of the populace at large. As for limitations on gun rights, that was like many issues--up to the individual state to decide. 

Image: American Rifleman

Extras. Massachusetts gun rights discussion.

Update 6/24/24. This article discusses in detail the SCOTUS decision allowing restrictions based on laws from 1800 and prior, if the laws are similar in these times. 

RFK Jr. is an anti-science, anti-vax nutcase.

This disqualifies him from being the US president. I don't have much interest in discussing pros and cons because the cons are very bad. 

This is how bad it is. Kennedy has knowingly lied when it comes to quoting scientists. He has ignored scientific evidence. He has pretended he isn't ignoring evidence. He is a zealot who hasn't stopped even when it has cost dozens of lives. That's behavior that I can't ignore, and there is no way I would support him. 

Here is the worst case I've read:

Kennedy also played a part in one of the worst measles outbreaks in recent memory. In 2018, two infants in American Samoa died when nurses accidentally prepared the combined measles, mumps and rubella, or MMR, vaccine with expired muscle relaxant rather than water. The Samoan government temporarily suspended the vaccination program, and anti-vaccine advocates — including Kennedy and his nonprofit — flooded the area with misinformation. The vaccination rate dropped to a dangerously low level. The next year, when a traveler brought measles to the islands, the disease tore through the population, sickening more than 5,700 people and killing 83, most of them young children.--FactCheck.org

Here's a longer listing of Kennedy's lies and misinformation, but I didn't need to read it. I was already so disgusted. 

Image: The Unbiased science podcast

Still more covid lies

I'm frustrated and unhappy with all the covid lies that I have to fight. In another forum with too many trolls, we have liars who pretend the vaccines were/are more dangerous than the infection. 

This is muddled by problems with reporting adverse effects. Some people have tried to bump up the reporting, and some healthcare professionals have tried to cover up some serious adverse effects. It's happening partly because of societal stresses where misinformation goes viral, and people make poor choices based on the misinformation. So rare problems aren't processed as rare, but as red flags meaning the government is lying to you and you need to believe someone like Alex Jones. 

A lot of people have made really bad risk assessments when it comes to covid and the vaccines. They've been so concerned about vaccine adverse effects that they didn't consider the possibilities of grave illness or death from covid. Maybe they also wrongly thought they could take ivermectin and that would handle it. Perhaps 2-10 out of each 1000 who thought this way ended up very sick, and therefore suffered a great deal based on a poor decision. (I don't know the numbers, and it would vary a lot by age and somewhat by location.) Vaxxed versus unvaxxed statistics have shown this in many places, and especially in Sept '21 through about March '22. 

Still, I've got one very persistent yahoo who claims the vaccines are very dangerous and I'm a horribly lying unethical person. I started look into what this erroneous claim was based on, and here are some of the sources I found:

• This conclusion is based on cherry-picking evidence, ignoring vaxxed vs. unvaxxed hospitalization and death rates, and concerns that the data has been censored and/or scrubbed. 
• It is possible to fool with the data and make it some much more innocuous than it is. Personnel can be encouraged to report or discouraged. Coverups are definitely a known phenomenon. But it's much harder to hide a large trend because there are many more people with the knowledge of the negative outcomes. 

So I reject the idea that the numbers are completely cooked. One observation I've had is that no hospital was overwhelmed with vaccine patients, but many were overwhelmed with covid patients. 

The yahoo seized on the issue of reporting of myocarditis. This is fair. It was downplayed to prevent people being discouraged or nervous about the vaccines. One report in particular was published and then withdrawn. The explanation is actually a non-explanation. It's claimed that data in the report was removed from VAERS, the US vaccine adverse effect reporting system. I found these sources with original matter from the article: Zenodo with a download; online full article, and another article on the same topic but with a reasonable balanced conclusion. The withdrawal article by Dr. Jessica Rose and the very questionable Dr. Peter McCullough, says this in the conclusion:

It  cannot  be  stressed  enough  when  referring  to VAERS  data  collected  in  the  context  of  the COVID-19  injectable  products  that  effective antiviral responses against the nCoV-2019 virus in the  form  of  both  cellular  and  humoral  immune responses  have  been  reported  in  peer-reviewed studies  [51–56].  Because  of  the  low  Infection Fatality  Rate,  indicating  effective  and  robust immune responses, it remains unclear why multiple experimental  mRNA  vaccines  have  been  fast-tracked through conventional testing protocols and are also being fast-tracked through production and administration  into  the  public.  With  repurposed drugs  like  hydroxychloroquine  and  Ivermectin showing extremely positive results in patients [57–68], it is also unclear why these drugs are not being more extensively promoted as effective tools in the fight  against  this virus.  What  is  clear  is that  the injectable  products  are  proving  unsafe  for  many individuals and inefficacious  in others.....

This conclusion downplayed the fatality rate and the strain on the healthcare systems, and wrongly stated that HCQ and ivermectin were showing extremely positive results. This paper came from antivaxx quack doctors. Sadly, there are quacks and charlatans in every line of work. Covid was been a bonanza for them. The political atmosphere has made it more likely that people take sides based on political affinity rather than sober evaluations of data. 

Image: Imperial College London

Extras. Another issue, and this is not a lie so much as a point of disagreement. Are vaccines more dangerous for those 0-39 than covid is? That definitely was and is an issue due to the adverse effects of the vaccines, and the inability to predict who will have a serious adverse effect. It was possible for a while that myocarditis from the vaccine was a bigger danger in that age group than covid itself. It was hard to be sure. One report showed that mortality in this age group briefly went higher for vaxxed vs unvaxxed (closeup here). However, when covid mutated and started infecting more people under 40, probably this question was settled toward vaccination, though perhaps only for certain years/variants. A number of people are probably glad they took the vaccine when the variant appeared. But prediction is difficult. 

Were VAERS reports being ignored? Possibly. 

Quack doctor Peter McCullough faced the music when a certification board revoked his certification due to his false statements about covid and the vaccines. They gave him quite a spanking.

The suggestion that excess mortality was due to vaccines is given a gut punch in this article. Weekly data shows excess deaths matching the lines for covid deaths, not vaccination roll-out, supporting the more reasonable assumption that covid or delayed treatment of other diseases was the primary cause of excess mortality. A controversial paper about excess mortality was retracted two years after publication. 

Update 8/4/26. RFK Jr. is still spreading many lies about covid and the response. He downplayed how severe the spring 2020 surge was in NYC by saying some ICUs in the city were empty. Were they? I looked it up and found this in wikipedia:

Due to rules constraining transfers and preventing 911 calls from going there, [the USTA field hospital] remained mostly empty as at least three COVID-19 patients quarantining at home died and nearby hospitals exceeded capacity. USTA also had its own ambulances it could not use to pick up transfers due to exclusivity agreements between hospitals and ambulance companies. During the peak of the COVID-19 pandemic, private hospitals had spare beds while some public hospitals were unable to offload enough patients to stay within normal capacity, unlike during Hurricane Sandy, when patients were actively balanced across the region. Reference.

Scientists and others argue about the origin of covid-19

This is fun. Normally it would only be a discussion among scientists doing expert research in virus evolution. However it seems like lots of people get into the game because of the huge global effect and the distrust of government authorities, scientists, and people in general. 

I have a good science background, but not much that will help me with virus genetics or the questions of whether covid-19 was engineered in some ways. Of course, nature itself is a great accidental engineer. A few genetic changes, some recombinant mix-ins, and lots of biological bodies to pass it all around, and many things can happen to a virus. 

But did people (in China) fool around with coronoviruses and make covid-19? Would there be telltale signs of human fiddling? I can't answer that based on my experience. Nor am I getting that information from scientific articles. I can believe that splicing leaves signs, but nothing confirms it. 

Some of the information in clearer forms:

Evidence that covid-19 isn't engineered. 

The furin cleavage site in covid is very unusual. However furin cleavage sites aren't uncommon, but maybe none is quite like covid's. A study on a bunch of furin cleavage sites. I'm not sure if it's relevant and what it means.

Then there are some government reports. A very long report from a senator on origins. Assessments from the US Director of National Intelligence in 2021 and 2023. 

There are also reports about experiments conducted at Wuhan Institute of Virology, but it's hard to say that they clearly indicate anything. Talk about recombinant virus experiments, etc. aren't by themselves proof that the actual covid virus was from WIV. We'd have to know the details of the genomes, wouldn't we? But none of it seems clear right now, and China has reason to cover up any information and make it murky. 

Perhaps these experiments will be clarified sometime. Speculation swirls in the meantime, including about this proposal for research and its mentions of furin cleavage sites on pages 13 and 41.

One thing I strongly believe. Intelligence investigations aren't going to tell us the origin. The strongest information isn't going to come from spies, intelligence analysts, or congress people arguing about gain of function. It's going to come from scientists and their discussions of the evidence in genomes and blood samples. So if scientists aren't leading the discussions, I'm going to discount the information. 

Image: American Chemical Society

Extras. Vanity Fair covid article based on intelligence, not genome. Timeline of covid origin. Claim that origin is wild, based on genomic evidence.

Covid updates and articles

Publishing another post that's been sitting around. Good links here. 

The year in covid - 2021. Lots of people got vaccinated. There were a few scares with the vaccines, particularly rare blood clots from the Johnson&Johnson (very rare), and heart inflammation (myocarditis), mostly in younger men (somewhat rare). Summer brought a wave of the delta variant. Vaxxed people had some breakthrough cases, but few hospitalizations or deaths. Stupid red states like Texas had a ton of hospitalizations and deaths. And the anti-vaxxers remained dubious even with all the real-life info. The omicron wave started in November and surged fast, wiping out a lot of Christmas and New Year's plans. It was very contagious, but having a recent booster turned out still be quite protective. My family all got booster by December, so we had no covid cases here. 

Now the links:

An article about how masks protect. 

But the best explanation has come from private communication with an acquaintance with a PhD in molecular biology and decades of experience in pharmaceuticals and drug testing. He writes how masks are very helpful even though viruses are so small, 

A respiratory droplet contains water proteins, glycoproteins, salt, and if someone is infectious, SARS-VoV-2 virus.

When they very rapidly evaporate, what gets left behind is a hydrated particle of proteins, glycoproteins, salt, and virus.

It's not naked virus. It is much larger than the cold virus, although still small enough to remain airborne.

And yes, those droplet nuclei can pass fairly easily through a mask. I pointed that out of my original extended reply to you. That's why masks do a poor job of protecting the person wearing them.

But the point is that masks do quite a good job of trapping large respiratory droplets at the source, before they have a chance to evaporate into airborne droplet nuclei.

That's the point. Respiratory droplets get caught at the source before they have a chance to evaporate into droplet nuclei, which remain suspended in the air, and are quite effective at infecting other people.

The heartache of being a covid doctor. How huge the omicron wave was.  What it was like in Kansas City. 

Excellent resource. The report from the independent panel reviewing the Pfizer vaccine test data. Loads of info, like how many subjects were hospitalized. 

So the big ivermectin guru, Dr. Pierre Kory, got covid even though he was following his preventative protocol. Why he didn't change his advice--bias, of course.

Image: pewtrusts.org

The most important issues from the trial of Derek Chauvin

With my healthcare background, I can observe signs that other people might not notice. I've seen a movie where an actor had a moment of real intense emotion, causing his face to flush and forehead veins to pop. So I used these skills to see what I could observe in the videos of George Floyd's death. But I dearly hoped that the prosecution would bring in experts to do this and explain in detail what was happening in those final minutes. 

Luckily, the prosecution did put an expert on the stand to talk exactly about that. His name is Dr. Martin Tobin. I couldn't place his accent or manner of speaking, with its precision. It turns out that he's Irish, but has worked in the US for decades. (Not enough brogue, sadly.) 

His twin specialties are the physics and physiology of breathing and critical care of critically ill patients. He's observed many dying, and knows very well what it looks like. So he was able to observe and explain so much in the videos of George Floyd. 

First is that there is no doubt that Floyd died from not getting enough oxygen due to the police restraint on him. Chauvin was responsible for most of that fatal restraint. Floyd was pinned between the pavement and the knees for two officers. His arms were twisted behind his back, His neck was compressed. His left side was compressed. He was trying to draw breath through his compressed throat/trachea into his chest. Basically, he was constrained to breathing with his right lung and little power to expand it except on his right side. And drawing breath through his compressed neck. 

His intake of fentanyl wasn't a factor. He showed none of the signs of opiate overdose, that gradual slide into unconsciousness with reduced respiration rate. His respiration rate (breaths per minute) remained normal until his heart stopped. It's possible to see his last breath in this video at 17:22. 

With my background I was able to follow just about everything that Dr. Tobin talked about. Here is video of his testimony: part 1, part 2. 

A use-of-force expert testified for the defense, and tried to make a good case. However, the prosecutors managed to slice up some of his testimony because officers are required to reevaluate moment-to-moment and provide care as needed to those in custody. The prosecutors were well-prepared and discussed the placement of Chauvin's knees (using stills from the videos) and showing how the crowd wasn't vocal except for one person, nor was it advancing on the police. The video here. 

Image: news.sky.com

Extras. Another expert concurs with Dr. Tobin. The official autopsy report. What professional journalists report, in contrast to my idiosyncratic view. A key defense witness, an expert on restraint. The prosecution cross-examination, especially at 1:17:18, is masterful. Another key defense witness, a pathologist, is cross-examined with asphyxia being a major topic. 

Snopes fact-checks Floyd's criminal history. The jury instructions, directly from the judge, directly to the jury. 

A couple of links to body cam footage of George Floyd's arrest and death. Lane. Keung. Thao. 

Epidemic progression... past Easter

Hospitals are have now been slammed in several cities: Seattle, New York, Los Angeles, San Jose, Atlanta, and New Orleans. Nine states saw significant increases in deaths just today, which is a sign that the we are riding the death curve up to where it could get steeper due to lack of medical resources. This happened in Italy and Spain, and there's no reason to think it won't happen here. The nine states are: New York, New Jersey, California, Michigan, Florida, Louisiana, Georgia, Colorado, and Connecticut.

First-person accounts. In previous posts I linked to accounts from Italy (one, two, three) and New Orleans. This time I have accounts from Washington (older account but good details) and New York City (one, two). Another account from New Orleans. Video from an pulmonary specialist in New York City with practical tips to avoid infection.

We know from all these accounts that about 10-20% of those infected with the virus need hospitalization, so the hospital can jammed up beyond capacity. The virus might have a death rate of 5-10% of those hospitalized in ideal situations, but the death rate goes up to 8% or more in overloaded hospitals. In Italy, many people just stayed home and died there.

The hospitals in northern Italy got slammed about March 8, and the country instituted a quarantine. Eighteen days later and the death toll is still at a peak. There may be some relief after three weeks, which is the average time between exposure and death.

That means for New York City there probably won't see any relief until April 13... if New Yorkers were as blase about contacts as NY mayor DiBlasio was. (DiBlasio didn't close schools until 3/23.) Probably enough New Yorkers started being careful about contact by 3/14 that there might be a noticeable decline in deaths by April 4. But New York has a huge population that is a large reservoir for infection, so the peak may last many more weeks. The example of Italy is that we don't know how long to expect the peak to last.

All these shutdowns are so annoying--to those who want a strong economy going into the elections this fall. It's terribly inconvenient and unfair to have a pandemic spoiling the economy (and election chances). So some, including Trump, are suggesting that we get back to normal as soon as possible, pandemic be damned! Young people should go back to work and elders stay home (one suggestion). The recovered should go back to work. The exposed should go back to work if they aren't having symptoms. Maybe even the older should go to work and the young stay home.

All these ideas ignore some basic facts that can't be fudged. More exposures means more people getting infected, and passing it on. Most jobs are skilled, and absences mean that the workplace will be disrupted. The idea that people can continue working ignores that many will get sick, so soon the workplaces would be closing anyway due to lack of workers and patrons. It's hard to say how soon this would happen. The infection is more concentrated in cities at this point, but it's also inexorably spreading. So will medium sized cities in Ohio have too many sick in 4 weeks or in 8 weeks? We don't know. It's hard to explain why so many GOPers don't understand this--maybe happy-thinking is the mantra and endemic. One contrarian is Liz Cheney, but she doesn't have much of a voice.

So the upshot is that this pandemic, and the way this virus spreads, was always going to be highly disruptive unless it was contained extremely quickly. In the US, we missed that window, so we are taking the huge economic lumps for that. There is no avoiding it.

Image: omfif.org

Corona virus pandemic and the US bungled response

This is the biggest contagion of my lifetime. History is unfolding so it's important to pay attention. I have a lot of links below and I don't want to expend the effort to put them into a narrative. The big narrative is countries that handled the situation well versus those that didn't.

Countries like Singapore, South Korea, and Taiwan have handled the epidemic well, with good public health measures to prevent the wildfire spread. The US had a fairly long warning period, but it didn't have the political leadership to put together a good plan to sharply reduce the effect.

Some countries in Europe are in even rougher shape. Italy has had over 2000 deaths and its hospital system was overwhelmed.Today (3/16/20) it appears Spain is headed that way.

The US might be headed that way too. We were slow to identify carriers, don't have an aggressive testing and followup regime, and we have cases spread widely over the country. Perhaps we started some containment/quarantine efforts early enough to prevent an explosion, but we won't know for a few weeks. On 3/8/20, not many news outlets nor the government were closing down crowded venues to prevent the spread. Just 5 days later, many states had closed schools and banned gathering over 100 people.

The change came about because the situation in Italy exploded starting on 3/8/20. Luckily some people in the US paid attention. However a lot of conservative commenters I saw had reasons or excuses why people shouldn't cut back on their socializing. These included: it's only panic; don't be hysterical; what about the waiters who dependent on tips; this is no worse than the flu; and Obama handled the swine flu (H1N1) much worse. These contrary arguments irk me so much. They are stupid and will hurt or kill people if heeded. And they are based on nothing but partisanship and spiting the other side.

I'm hunkering down, everyone is working from home, we've cancelled our RSVPs to parties, and we're limiting our trips to stores. Luckily I realized the situation with certain supplies, and we have enough toilet paper on hand--bought on 3/8/20 before the hoarding started just one day later.

FINALLY, on Monday 3/16/20, Trump sounds like he gets there is an imminent crisis. The covid task force has a long press conference, and the experts are the people talking the most. Thank God there's an end to the denial. Both the New York Times and New Yorker magazine report that the change is due to a major report out of the UK concerning how high the death toll could be. The New Yorker report is more detailed.

The pandemic will affect so many lives and the entire world economy. Smaller than World War II, but possibly bigger than the 2008 recession or 9-11.

Image: euronews.com

Extras. Trump's misinformation machine. Drezner on Trump's incompetence and predictable consequences. Politico also discusses this with a lot of detail. Some of the failures of the administration. Administration hampered Washington state when they had known cases. Trump makes himself irrelevant. Governors move ahead without him. This might be another reason why Trump changed his tune. The House, Senate and administration can't write a bill. Oh well, they'll get to it eventually. Days later (3/17/20) and still no new bill.

Hong Kong and Singapore handled it much better. South Korea too, which improved after being badly hit by H1N1. The UK had a plan that they dropped. Act now before it's too late.

What China did to slow it down. Readable with plenty of data.

Fast worldwide overview. Hospitals in the west likely to be overwhelmed. Another overview. The dashboard I'm using. It's got daily new cases and new deaths which is info I really want.

Doctors in Italy give accounts. Focus on Italy and why it happened there. Summary of the situation in Italy. By March 7, there were approximately 550 people in ICU beds. The projection for March 20 to April 3 ranged from 900 to 14000. Yikes. More from Italy. More.

Scroll down to see graphic on which ages are dying.

Biogen company meeting that spread the virus. Ohio, with a Republican governor, gets honest and makes a painful guess about its situation. A brief overview of their plans.

Trump Jr. knowingly lies about Dems, again. What a weasel.

Update 3/18/20. A bunch of info from an ICU doctor in Seattle. The course of the disease and some of its quirks. What Fox News said then versus now. Fucking hypocrites. Trump's nonchalance. Trump finally starts to get it... after ignoring experts and the evidence but getting an intervention from Tucker Carlson. Oy vey. We're dependent on Fox News anchors doing the right thing. That's not good. Upon further research, I'm not sure Carlson had that big an effect. His meeting with Trump was 3/7/20. The tone started changing 3/13, with the biggest change coming on 3/16. So perhaps it was the projections from Britain.

A small Italian town stops it by doing 100% testing and lockdown. Not applicable to most of the US. For posterity, a typical daily news update. Will this Lancet report be born out? We shall see.

Update 3/23/20. Straight talk and no whitewash from NIH director. Warning signs that were missed, including those from a pandemic exercise. Trump isn't following through on defense authorization to direct industry to make needed equipment; governors are scrounging as best they can. Florida waited too long to shut down social venues. Trump touted a particular drug as a treatment, incorrectly. Turns out it's rather dangerous, not safe as he claimed. Bad details lead to bad outcomes. Trump and Fox News are already tiring of the lockdown and don't understand why it's important. Short attention span isn't good.

My predictions. There should already be a surge in hospital admissions but information is being held  tightly. On or around 3/26/20, we should have a surge in deaths, which will be reported. By 3/30/20, we should be seeing over 400 deaths per day in the US. This level of deaths will probably last at least 8 weeks. Since the level of deaths will be high, the lockdown won't be cancelled after the initial 15-day period.

Update 3/25/20. Two stories from ProPublica: how covid-19 is different from the usual winter pneumonia by an overworked respiratory therapist in New Orleans. Doctors are writing prescriptions and hoarding chloroquine, the medicine that may fight the virus. A slice of life with the pandemic--a nursing home in New Jersey with 94 patients evacuated. New Jersey is beginning a steep rise in deaths. NIH technical description of covid-19.

Update 4/6/20. I stumbled on an explanation for the run on toilet paper. It started on 2/26 in Hawaii with a message to stock up because of the spread of the virus. This might make sense if Hawaii doesn't have paper mills, and it seems (per a Google search) that maybe they don't. From Hawaii the panic buying migrated to Japan and Australia, then Europe and the US.

Trump rampages after impeachment acquittal

Acquittal of Trump was a foregone conclusion. I thought it would be a yawn--for me and everyone else. Trump apparently feels differently. He's on a tear firing people, smearing them in tweets (not unusual for him), and rooting out those disloyal traitors in government.

Trump fired Alexander Vindman and had him escorted out of the White House. And also hinted that the army would be investigating him and taking terrible vengeance. Well, the army seems to think differently, as they are a corps with rules and honor (two things Trump isn't acquainted with). Vindman will still have a job with the army, though probably a quiet low-key job. I doubt he'll end up in the brig. Ambassador Sondland was also fired--for not being the liar Trump needed him to be. Sondland can go back to running his hotel empire and be a poster child for saying no to a job in the Trump administration.

Then there was the scandal about Roger Stone, the unofficial Trump adviser and go-between to Wikileaks. The prosecutors' sentencing proposal was quite harsh, maybe 7-9 years or more. The DOJ quashed it and substituted a different proposal--a mealy-mouthed leave-it-to-the-judge request. The prosecutors protested and quit. Big brouhaha, but now (a week later) probably nothing will happen. Barr complained that Trump's tweets make his job impossible. Big headlines, but nothing happened on that either. Maybe Barr told him is was for public consumption, and the move was inspired by Trumpian strategy. That's my speculation for how Barr got away with it. In any case, Barr still appears to be very loyal and running interference for Trump while trying to keep up appearances.

Besides Vindman and Sondland, there are other bigger purges starting, just like you'd expect with a dictator. Apparently you can't, as head of the intelligence services, tell Congress that the Russians are interfering again. Lose your job, do not pass Go, do not collect $200. Loyalty trumps truth, so there is a new acting head, and he walks the walk of loyalty. How many more people with insufficent loyalty and misguided honor will be fired? We'll see. It seems to me that I could turn this into blistering anti-Trump commercials come election time. Probably someone will do it, right? The somber narration practically writes itself:

[Voiceover] President Trump values loyalty to himself personally over everything else. Tell the truth about Russian interference--you're fired. Tell the truth about quid pro quo with Ukraine--you're fired...

FIRED!!!!!

Image: abcnews.go.com

Update 4/3/20. Trump fired the Inspector General who didn't quash the whistleblower complaint about Ukraine, but instead followed the law and informed Congress. He did this on a Friday evening during a pandemic crisis.

Weather-gate and Trump's stubbornness

Trump lies again and again. This isn't a surprise by now, but it's getting dumber. Trump made a mistake by saying Alabama was in range of a hurricane. Instead of correcting his mistake, or just letting it go, he doubled down repeatedly. It got too much media coverage because it was such foolish behavior. Even cowardly agencies under his thumb got involved.

It's hard to say what was the worst part of this unnecessary debacle. It wouldn't have been at all bad if it had ended with this (after Trump erroneously said Alabama could be hit):

[The] Birmingham office of the National Weather Service, in response to a flurry of calls and inquiries, issued a correction on Twitter, saying, "Alabama will NOT see any impacts from #Dorian." -- GQ magazine

But, nooooo, Trump couldn't let that stand. He couldn't admit even a tiny mistake. He had to blather (incorrectly) that Alabama had been a very likely target in the storm, including nonsense that there was a 95% chance of Alabama being hit at one point in the modeling. That was Trump being his usual fucking egotistical maniac self. 

Then Trump marked up an official weather service map to include Alabama. This is almost like changing the answer key on a test. Trump is so divorced from the truth that he'll pretend official information doesn't say what it says. And of course he used it as another skirmish in his war on the media, particularly CNN. 

This is all a game to Trump. The guy has no respect for truth or science, just for power. I'm absurdly eager for a break from this stupidity.

Wait, where did that black line come from?

Image: newshounds.us

Update 9/9/19. A number of officials in the weather/oceanic agency are loudly standing up for the scientists and accurate reporting and are pointing out how the mealy-mouthed communications supporting Trump are wrong. It looks like they are daring Trump to fire them. I don't think they'll be fired because it would be too obvious. How will Trump react? We'll see.

Update 9/11/19. An opinion column on this debacle with a some new info. The Secretary of Commerce ordered the support of the naked prez on pain of beheading, or similar. Sigh. Truth is not an option. 

Research into global warming and climate change

This isn't the first climate crisis I've researched. When I was in college, the threat to ozone was a hot topic. When the ozone hole was discovered, there was a consensus that the cause was a class of industrial chemical -- hydrocarbons containing chlorine and fluorine. I studied the scientific papers, and was surprised at how definitive the information was. The science was very clear and solid, so much so that an undergraduate could grasp it.

Luckily there wasn't a strong level of denial and stupidity about the findings. Many countries banded together to verify the science, and act responsibly by figuring out how to greatly decrease the use of the questionable chemicals. It was a case of rational response.

Greater complexity with CO2

In contrast, the questions about global warming have prompted huge levels of disagreement. People who barely know any science are passionate about it, sometimes for and sometimes against. Unlike the earlier climate crisis, the data doesn't seem so clearcut.

There have been fluctuations in climate throughout the history of the planet. The evidence of my lifetime is that my region is warming, and many other regions report the same trend. What is the cause? The growth of cities, change in the atmosphere, pollution - all of those seemed plausible, but that doesn't make them the actual cause.

It wasn't until earlier this year that I made a more determined study of the information. By this time I knew of other possible factors, including complex changes in weather patterns (so complex that I never grasped the mechanics of it). There is fairly solid evidence for a warmer period in the medieval period from about 900 - 1300 AD. It's also known (with good scientific data) that the sun can produce greater or lesser amounts of radiation, and that will affect temperatures on Earth. The amount of solar has been running lower than average, which is lucky for us. Had it been average levels, it probably would have added to the warming trend.

Three important FACTS

The warming trends I've seen in my life show on graphs of worldwide average temps:

Image: nasa.gov

There are questions as to how this data is gathered and massaged. I can't answer anything about that except to say that I'm not wrong about the trends I've seen, so I don't believe the earlier springs are a figment of my imagination or the result of shenanigans by scientists.

A second important data point in the increase in CO2 in the atmosphere. This is definitely true, since it would be easy to disprove if it wasn't. No atmospheric sampling has contradicted this finding, so let's accept it as undisputed.

Image: yale.edu

The mechanism of warming is complicated. CO2, water vapor, methane, and other gases are known to trap in heat. We experience this with water vapor (a humid place doesn't cool down at night as readily as a dry locale). Is it also true, as claimed, for CO2 and methane? I think it wouldn't be hard to verify this using standard techniques like mass spectrometry. I'm not a chemist, but this isn't difficult stuff to understand. Different chemical bond absorb and reradiate different wavelengths of light, blah, blah, blah. It's basic, and it's solid.

So, there are three solid points in the argument about global warming.

1. the demonstrated increase in global temps
2. the demonstrated increase in CO2
3. the likely mechanism of CO2 and methane with their known radiation profiles

How to ignore the FACTS

Climate change deniers tend to use these tricks:

1. They ignore that world wide temps are rising. This is a data-based fact.
2. They ignore that CO2 concentration in the atmosphere is rising. This is also a fact.
3. They pretend that climate/CO2 models must be very accurate or all of climate change is nonsense.

However, climate change isn't nonsense because of the facts stated in #1 and #2.
Climate deniers are con men ignoring definite scientific data. However, #1 and #2 don't go away because they are liars.

They refuse to consider how harmful even higher levels of CO2 might be, or the bad effects of higher temperatures. Many won't even touch the biggest risk, which is a surge in CO2 when the permafrost melts. They won't face the very real risks. They won't face that it's not going to be possible to turn off the CO2 like you turn off a faucet. As a scientist, I can't pretend that these risks aren't real. Scientists are used to facing facts, whether we like them or not.

And really, are people unhappy with cleaner energy? Why would we be? I don't get why carbon-free energy wouldn't be a goal and something we do as much as feasible. It makes for a better quality of life.

This is the kind of gobbledegock from climate deniers:

And we're about half way to CO2 doubling since pre-industrial times now and what do we have? -- about .9C of warming, suggesting 1.8C for 2X Co2. But the science also states that CO2 constituters 9-26% of the GH-Effect, so it's only 9-26% of 1.8C in this case. The experts are full of beans. They are hoist on their own claims.

Risks, models, and uncertainty

One issue is now very clear to me based on my research. The carbon cycles on the Earth's surface, its oceans and its atmosphere are extremely complex. They are not thoroughly understood and quantified. We don't know how much CO2 a given body of water will absord, or a given forest. We don't know how much CO2 will be released from boggy lands in the northern latitudes as they warm up. These movements of CO2 are very large, and perhaps seem to dwarf the man-made CO2 pollution.

However, don't forget that CO2 in the atmosphere is clearly rising. If there are other huge point sources of CO2 creation on Earth, we would have found them by now and we could work on plugging them. But there aren't. The man-made pollution seems to be the source. To ignore this would be like ignoring a flat tire as the source of that strange noise when you're driving. Some may choose to ignore a clear source, but I don't because I don't ignore evidence that's right in front of me.

Because of the complexity of CO2 cycles on Earth and the interactions related to temperature, I don't trust that the various models of warming are accurate. However, their level of accuracy is not the biggest concern here. It's really only an excuse to ignore what is important, which is the risk of major changes in climate that can have devastating effects on almost all life on the Earth. The amount of possible damage shouldn't be ignored. It is unwise to do so. It definitely behooves real conservatives to be careful, and consider these risks. Real conservatives...

Extras. More on the medieval warming period with a bias against current concerns about warming. Models aren't accurate, but I've noted why that isn't the most important consideration. Trump buries and denies the report from US scientists... because facts don't matter.

The pause in temperature increases may be because the solar radiation was lower than normal due to a quieter solar cycle in the years 2006-20. Temperature versus solar activity clearly shows that temperature isn't currently correlated with higher solar activity. A more up-to-date graph of the solar cycles. 

CO2 levels for the past 800,000 years.

Update 2024. I looked up the trend since 1950. Here it is: Warming has been about 1degree C. CO2 + 112 ppm. Methane + 750 ppb.

This is not the best graph I've seen of temperature, CO2, and sunspots, but it's the best I can find right now. From a legit source -- an emeritus physics professor.

Image: L David Roper

Update 5/23/24. I found some cool tools for looking at temperature trends. Temperature trends with global, national, regional, city, and tons of other widgets. Fewer options, but focuses on anomalies. 

Update 6/9/2024. Found a link to a site with a large database about climate denial, including who funds it. 

Temperature and glacial trends for the last 500 million years. Yes, I'm also very interested in glacial periods. 

Good article about the carbon cycle. I'm inspired to estimate how much excess CO2 humans are pumping out. My initial calculation: 20 billion metric tons a year excess. This is based on 1ppm = 7.8 billion metric tons. We are currently increasing CO2 at 2.5 ppm each year. That's just the excess that ends up in the atmosphere. The claim that human production is miniscule compared to the throughput of the natural cycle--I have very strong doubts. I think the natural throughput might be only 5 times the human production. Possibly less. 

Here's a German physicist who makes videos to explain science to non-scientists. This is her capsule explanation for how we know human activity is changing the climate. Very clear, and what I tried doing myself. 

Temperature increase is 100% due to manmade greenhouse gases. A full analysis. 

Parking these two links with CO2 vs. temperature graphs. 400K years, 400 million years CO2 vs. glaciation.

Older webpage but so far the best explainer on the rapid climate changes in the recent glacial and interglacial period. The Younger Dryas et al. Good explanation for how living creatures handled changes in CO2 levels during earth's history. 

This graph shows the mean temperature fluctuations for the last 800,000 years. I'm keeping it handy to counter the denialist who claim that it's been much warmer in interglacial periods. No it hasn't-- just a bit warmer than now. 

Sources for energy, answering the question about how much coal, oil, natural gas, renewables, etc. 

Charges against Judge Kavanaugh

If one person comes out with a story about Brett Kavanaugh with a lot of gaps in the details and no witnesses, it's not too credible. When the count gets up to four people, it becomes more credible. Now there are over 8 people on the record with their names and what they witnessed. It includes drunkeness, aggressive behavior, and sexual aggression toward women. And that doesn't count numerous people who wouldn't release their names.

I find the charges against Kavanaugh plausible, but that doesn't mean much. It means he might well have been there and he might physically have been able to do the actions he's accused of. I don't believe arguments like 'it's not within his character' or 'she's so honest there's no way she's lying.' Those arguments aren't convincing to me unless I peronally know the extreme credibility of the character witness. Why? Because 'it's not within his character' has been said about too many serial killer, serial molesters, etc.

So the charges are plausible. It's also plausible that Ford is lying or mistaken. That's why the investigation is important. It's not going to be easy. Many people are not going to want to talk about their wild times in high school or college. If they're conservatives, as many of Kavanaugh's supporters are, they may not want to reveal his dirty past for political or tribal reasons. If they were friends, they may want to remain silent and loyal. That makes it hard for Kavanaugh to clear his name. The suspicions will linger. There's no way around that. It's an injustice built into suspicion, and it's impossible to remove it from people's brains.

If Christine Blasey Ford is lying, she figured out quite a cunning lie to tell. It's one that fits the pattern of Kavanaugh's partying. She's obscured details like where and when to make it harder to disprove. But she's done it in ways that are somewhat believable. I do have a couple problems with her story, which is her not remembering how she got to the house and how she left. Particularly not knowing how she left, I'm left wondering if she went back into the party. I wonder if she's leaving out details that which might undercut her story of how traumatized she was. It's also possible that she dissociated, and lacks the memory for that reason. Or there could be other reasons her memory is poor. I'm not an expert on memory, and I'm not sure anyone is expert enough to sort this out. Of course, a strong reason to conclude Ford hasn't fabricated the story is that she told her therapist and husband years ago, with therapy notes to confirm that. It's hard to fabricate a lie in advance.

This is one of those times when an infallible truth serum would be so helpful. I wish I could ask them both, and get the real story, not the one sorted and selected for the audience in the American public. But that's not possible, and we humans are such cunning animals. We aren't to be trusted. So what to do? We're left trying to make judgments in our imperfect ways. That's life.

Image: dailykos.com

Extras. This will be very long because I did a lot of research and want to save the info I found.

Transcript of Ford's and Kavanaugh's testimony. Julie Swetnick's sworn complaint. And another from another client of Avenatti. Decoding Kavanaugh's yearbook entry. Lots of references to sex and especially drinking. A letter from Kavanaugh to his friends about Beach Week, with lots of details and insider info. About Mark Judge's books.

Tucker Carlson and very sloppy argumentation. Weaknesses of Ford's story, and ignoring its strengths and supporting info. Biased assessment. As counterpoint, defending youthful mistakes--of privileged white guys, but not others.

Run down on two of the allegations. Rather complete at the time, so good detail. Private school culture at that time and place. Some sources fully identified. Also this article, which talks about gang rapes which weren't called gang rapes. A first-hand account by the author, so a named eye-witness. However, the parties are from the mid 1980s, so a few years after Kavanaugh graduated.

More people remembering Kavanaugh very drunk.  And more, with a follow-up. Others asked not to be named. A police report of Kavanaugh involved in a bar fight while at Yale, discrediting one of his character witnesses. Witnesses about Kavanaugh: Liz Swisher, Christine Keating, Lynne Brookes, James Roche, Charles Ludington, Elizabeth Rasor, Daniel Livan, Sean Hagan, Kerry Berchem, Kenneth Appold. Other named participants who should be thoroughly interviewed (which didn't happen) Mark Judge, Leland Keyser and Patrick Smythe. Also Renate Dolphin because she might have some very interesting stories to share.

A very critical analysis of Kavanaugh's testimony with numerous lies and evasions pointed out. Plus a companion piece on why Kavanaugh would be a harsh, rotten justice.

Inspired by Ford, a woman reveals her rape at a frat party many years ago. Is it fair for him to have to face consequences so many years later? Is it required that the survivor just let it go?

The very rigid rules for reading the FBI report, which forbids 'characterizing' the information. Looks like the FBI investigation is brief, limited, and a whitewash.

Update 11/5/18. A Republican consultant remembers being anger and aggressive at a conference meeting with Ken Starr. She's very disappointed with GOPers sweeping it under the rug.

History for Amnesiacs: What Mueller is investigating

The idiotic talking point among some conservatives is that the Mueller investigation is illegitimate, and was from the beginning. There wasn't any real evidence that deserved investigation. It's all been fake news and a conspiracy by the deep state. Many even call it a coup.

I read this so often that I made a list of the evidence that thoroughly justifies an investigation:

1. The Russians hacked the DNC and gave the hacked emails to Wikileaks, thereby affecting the election. It may not have changed the outcome, but it was an attempt to do so, and was criminal activity. 
2. The Russians hacked state voter databases. They probably hacked more than that too. 
3. Trump has had a lot of contacts with Russians over the years.
4. Many Trump advisers have had a lot of contacts with Russians.
5. Trump advisers had contacts with Russians during the campaign. Sessions didn't fully disclose this information.
6. Trump denied the meddling of the Russians and appeared ready to lift sanctions. 
7. Trump fired the FBI director who was overseeing the investigation. 
8. The fired FBI director recounted Trump asking for loyalty and for a pass for one of his former advisers.

That is plenty to warrant an investigation. The Mueller investigation should be happening, and should continue.

Some talking-point parrots trot out lawyer and presumed Democrat Alan Dershowitz as an ally. However, Dershowitz doesn't agree that there isn't evidence. He writes:

But there was plenty of evidence that Russian operatives had tried to interfere with the 2016 presidential election, and perhaps other elections, in the hope of destabilizing democracy. Yet, appointing a special counsel to look for crimes, behind the closed doors of a grand jury, was precisely the wrong way to address this ongoing challenge to our democracy.

Dershowitz follows up with this overstatement:

It [the Mueller investigation] has politicized our justice system beyond repair... In our age of hyperpartisanship, the public has understandably lost confidence in the ability and willingness of our leaders to separate their political views from their law enforcement decisions.

...Let Congress now appoint a nonpartisan commission to conduct a transparent investigation of Russia’s efforts to influence our elections. Let the special counsel suspend his investigation until the nonpartisan commission issues its report. If the report identifies crimes and criminals, there will be time enough to indict and prosecute. Right now, we need the nonpartisan truth, because we aren’t getting it from the special counsel.

Ahem, what is the evidence that Mueller isn't working on providing nonpartisan truth, also known as the truth?

 If anything, Congress has shown that it can't be trusted to seek and share the truth. Remember the dueling memos?

No, I'd much rather that Mueller continue. As for Dershowitz, I saw him described as a publicity whore hound. Wait, that's from 1989. I'm sure he's overcome that tendency by now.

Whatever. Mueller should continue, wrap up as soon as possible, and issue a detailed report of the facts.

Image: cnn.com