May 4, 2020

Some Good News: Glycan Shielding on SARS-CoV2 Is Lower Than That of Vaccine Intractable HIV.

This morning I watched an online lecture by Scientists at the University of Southampton, on the subject of glycosylation in the "Spike Protein" SARS-CoV2 viruses. Glycosyl groups are small variable sugar polymers that are attached to amino acid groups in proteins. These glycans are very much involved in immune responses.

Only in recent years has it become possible to map and sequence these sugars using software to process high resolution mass spectrometry signals.

Anyway the lecture led me to a nice paper - it has yet to be peer reviewed - on the subject of the relative glycan density on proteins, in a paper published by two of the scientists who presented the lecture this morning.

It is here: Vulnerabilities in coronavirus glycan shields despite extensive glycosylation (Crispin, Allen, Seabright et al., BioRxiv, February 2020.

This preprint is open sourced; anyone can read it.

Viruses can exhibit "Glycan Shielding" which depending on the density of the glycans on the surface, can prevent the access by neutralizing antibodies that destroy the virus, giving immunity.

The high density of glycans on HIV is a big part of the reason that more than 30 years into the AIDS crisis, we still don't have a viable vaccine.

A graphic from the paper:




The caption:

Apparently the SARS-CoV-2 virus lacks this high degree of glycosylation. Although the molecule is reportedly highly glycosylated there are still potential weak spots that give hope that vaccine development will proceed faster than it has with AIDS.

As HIV shows, vaccine development is never a "slam dunk," but this bit of good news suggests that the development of a vaccine for this disease may prove somewhat less challenging than has been observed in that case.

May 4, 2020

The Historian Eric Foner: "Buchanan did not recommend drinking Lysol.

I confess that I have a certain fondness for these polls of historians ranking Presidents. In general I more or less agree with most of them, with the exception of the rating of U.S. Grant as a poor or mediocre President. I consider Grant to have been the second greatest President of the 19th century, after Lincoln himself. (Good luck with that, NNadir!)

Yesterday on CSPAN there was a discussion between Harold Holzer, a well known expert on Abraham Lincoln, Amity Shlaes, a Calvin Coolidge scholar, moderated by Brian Lamb, designed to market the new CSPAN book on the Presidents, beginning with the top (Lincoln) and working the way down. The discussion was held in FDR's New York City Residence, now owned by Hunter College. Ms. Shlaes argued that President Coolidge deserves placement among the top 5 Presidents because of his wonderful work on the economy and budget. (Good luck with that Ms. Shlaes!)

We can, of course, in general disagree with these rankings, but it does seem there will be one case pretty clear cut:

This commentary was in Bloomberg's this morning, comparing Lincoln and, um, Trump, since Trump smeared Lincoln simply by being near his memorial:

Trump and Lincoln Are Opposite Kinds of Presidents

It concludes with the comments of the famous historian Eric Foner, of Columbia University on worst Presidents, generally taken to be James Buchanan, Andrew Johnson, Warren G. Harding (Coolidge was his VP who assumed office when Harding died) and John Tyler, (and let's not forget Franklin Pierce.)

The Bloomberg article concludes with this comment on Buchanan vs Trump vs Johnson.

The bold is mine.

May 1, 2020

Since Republicans care a great deal more about fetuses than children or adults, maybe this paper...

...can be utilized to convince them to give a rat's ass insisting that we really shouldn't care more about haircuts and bars than people.

Second-Trimester Miscarriage in a Pregnant Woman With SARS-CoV-2 Infection (David Baud, MD, PhD1; Gilbert Greub, MD, PhD2; Guillaume Favre, MD1; Journal of the American Medical Association (JAMA), published on line April 30, 2020)

This woman's medical outcome is of course a tragedy, but Republicans seem to have a more narrow definition of tragedy than real human beings do, and perhaps this might drill through their thick heads.

April 30, 2020

The Global Disinformation Index:

I'm on the mailing list for the AAAS blog, and there was a chat today on the AAAS blog with Dr. Danny Rodgers of the "GDI," the Global Disinformation Index.

It advertises a "neutral" approach to statistically rate the credibility of information.

Dr. Rodgers biographical info (from the website) is this:

From the "live chat" a participant asked:



...to which Dr. Rodgers replied:



The site, in their "research heading" describes their methodology:



[link:https://disinformationindex.org/wp-content/uploads/2019/12/GDI_Index-Methodology_Report_Dec2019.pdf|Rating
Disinformation Risk: The GDI Methodology]

A brief excerpt:



I have only superficially evaluated this Index, but the concept strikes me as interesting and worthy of some more study to understand their approach.

We certainly do live in the world of disinformation, driven not just by Rupert Murdoch and Fox "News" but by many others as well. A successful system like this might well help raise a level of critical thinking.

April 30, 2020

Clinical Improvement in Covid Remdesivir Double Blind Study Is Not Statistically Significant.

This morning I'm seeing noise that Remdesvir is working in treating Covid patients.

Yesterday, the results of the first randomized clinical trial were published.

The results study were published yesterday in Lancet: Remdesivir in adults with severe COVID-19: a randomised, double-blind, placebo-controlled, multicentre trial.

(The publication is open sourced; anyone can read it.)

Here is the summary of the findings, for convenience:

A small benefit was observed, however it cannot be ruled out that this benefit derived from chance.

I wouldn't call the results "clear evidence" that this drug is a worthy treatment, unless I'm missing something.

April 30, 2020

Everything he touches... (CNN Headline)

Welcome to the worst economy ever

April 26, 2020

We May Have Hit The Annual Maximum CO2 Observatory at Mauna Loa Unusually Early This Year.

As I've indicated many times before, somewhat obsessively I keep a spreadsheet of the weekly data at the Mauna Loa Carbon Dioxide Observatory, which I use to do calculations to record the dying of our atmosphere, a triumph of fear, dogma and ignorance that did not have to be, but nonetheless our atmosphere is dying.

In my last post touching on this point, this one, I wrote:

The record set then, for the week beginning April 5, 2020, was 416.45 ppm, 3.78 ppm higher than the same week of the previous year.

If we look at the data from this week, and from last week (416,27 ppm) as well, we will see that both are lower than the figure observed on April 5.

Here is this week's data:

Weekly average CO2 at Mauna Loa



The difference for this week's reading compared to last year of the same week, 2.17 ppm is very close to the average of these readings in the 21st century, which is 2.16 ppm. The average for these readings for the 20th century, going back to 1975 was 1.54 ppm in comparison to the same week of the previous years.

I took a look at the data going back 44 years, to discover the earliest dates of annual peaks, and found that there were six times in the last 30 years in which the peak occurred in April, eight such years overall. April 5, if this date holds for this year, is the second earliest date, marking the beginning of a peak week, at which the peak has ever occurred. The earliest peak date was a peak set in April 4, 1999. It is effectively same week of the current observation owing to calendar fluctuations. The previous year, 1998, was until 2016, the record setting year for carbon dioxide increases, 2.93 ppm over 1997. Two readings in this decade, 2015 and 2016, superseded that record, both coming in at 2.99 ppm over the previous year. 2018 reached 2.83 ppm.

In 1998, the peak was reached on the week of May 24, 1998, when it reached the (then) disturbing level of 369.94.

In 1980, the peak arrived on the week of June, 1, 1980, the latest date recorded for such a peak. In that week, the peak value was 340.61 ppm. Except for some then obscure academics, including some who may have been aware of Arrhenius's prediction of climate change in the 19th century, no one probably thought much about that number.

Why, if it holds, the peak came so early this year is unknown. One may surmise that it is an effect of the severe restrictions placed on the car CULTure brought on by the Covid-19 catastrophe. We have been living with reduced access to our precious cars, as people always deign to inform me, without which we cannot live. Even with restrictions on our cars, it does seem to me that many of us are still alive, but perhaps that will change.

Another possibility is that as a result of climate change, spring is arriving earlier in the Northern Hemisphere, as carbon dioxide readings continue each year to decline through September before beginning to rise again. However a survey of the data shows that an April peak was observed as early as 1986, on the week of April 27, 1986, when the concentration of carbon dioxide was 350.71.

It is therefore difficult to say what this early peak occurred this year, only that it did.

At the Mauna Loa CO2 Observatory website the following is written about the effect of Covid-19 on climate change, which is a fair statement:



If any of these figures disturb you, don't worry, be happy. Cruise around the internet to find any of zillions of web pages talking all about how great solar energy is and how it will save the day.

It hasn't saved the day; it isn't saving the day; and it won't save the day, but it's the thought that counts.

Have a pleasant Sunday evening; stay healthy; stay safe.

April 25, 2020

The Greater, Ignored Plague, Disease and Water Use and Storage In India.

The paper I'll discuss in this post is this one: Household Water Storage Management, Hygiene Practices, and Associated Drinking Water Quality in Rural India (Sarah L. McGuinness,* Joanne O’Toole, S. Fiona Barker, Andrew B. Forbes, Thomas B. Boving, Asha Giriyan, Kavita Patil, Fraddry D’Souza, Ramkrishna Vhaval, Allen C. Cheng, and Karin Leder, Environ. Sci. Technol. 2020, 54, 8, 5062-5070).

Echolalia is the practice of repeating yourself or others without meaning, often thought as a sign of psychiatric symptoms, senility, for example, among old people.

And then, of course, there is a process of repeating one's self for emphasis, as when nothing meaningful gets through until it is, or nearly is, too late. (Think of the then old man Winston Churchill whining that the Nazis might be, um, bad people in the 1930's, when he was largely ignored.)

As the poet Amari Baraka put it in one of my favorite pieces of verse:

...as a day will repeat its color, the tired sounds run off its bones...

I am old and the sounds that run off my bones are tired sounds...and I repeat myself, and whether what I write is senile echolalia or a warning issued in the hope it is not entirely too late is not for me to judge, but for any interested reader to judge, if there are interested readers: I am infinitely more obscure than Winston Churchill was in 1938 and everything I say, whether it is echolalia or otherwise, will die with me, obscure.

One of the tired sounds I repeat is that so called "renewable energy" is a grotesque failure if the reason for embracing it was in any way connected to addressing climate change. This should be clear from the simple reality that climate change has not been addressed. It is getting worse, not better.

In 1976, a guy named Amory Lovins, then 29 years old, wrote this piece of unreferenced appalling drivel on the subject of Energy and the Environment: Energy Strategy: The Road Not Taken? in a social science journal, Foreign Affairs. The claim made in this intellectually appalling text, that so called "renewable energy" and energy conservation would save the world has become "The Road Most Taken" in attempting to address climate change: Many hundreds of thousands of scientific papers have been written on the subject of so called "renewable energy," the research funded by rich sources of grants, and as some people on this website never tire of pointing out, wind farms and solar cells are enormously popular, if entirely ineffective, bourgeois conceits.

Since 1976, Amory Lovins, who is now 73 years old has been engaged in echolalia, having become famous for writing the aforementioned piece of appalling drivel, declaring himself the Chief "Scientist" of an ignorance factory called the "Rocky Mountain Institute," inviting people to tour, for a fee, his obscene (but very energy efficient) McMansion in the very, very, very upscale community of Snowmass, Colorado, just down the road from the hip, hip, hip, hip skiing community of the "Stars," Aspen. Amory Lovins' echolalia has been to repeat, "as the day repeats its colors," the hip, hip, hip mantra that energy conservation and so called renewable energy will save the world. He makes a lot of money doing this, but he still asks you to contribute money to support his "genius."

In my opinion, he was senile - or at least uneducated - at the age of 29, since the subject of conservation and energy had been discussed in predictive terms that actually involved accurate predictions, based on data as opposed to handwaving, by the British economist William Stanley Jevons. His famous theory is known as "Jevons Paradox" which states, simply that the more efficiently a resource is utilized, the more of that resource will be utilized.

I repeat myself, "as the day will repeat its color..."

Here is what I wrote about Amory Lovins theology back in 2014, since I am not really a modern liberal who thinks that liberalism involves supporting huge wind farms in pristine wilderness, including offshore wilderness, and electric cars laced with cobalt mined by enslaved children in Congo, but I am an old liberal, inasmuch as I care about poverty, like Lyndon Johnson, like FDR and his remarkable wife, Eleanor Roosevelt:



Current Energy Demand; Ethical Energy Demand; Depleted Uranium and the Centuries to Come

..."as the day will repeat its color"...

Here is another thing I repeat frequently:

The amount of money "invested" in so called "renewable energy" in the period between 2004 and 2018 is over 3.036 trillion dollars; dominated by solar and wind which soaked up 2.774 trillion dollars.

Source: UNEP/Bloomberg Global Investment in Renewable Energy, 2019

Then I point out, "as the day will repeat its color" that this expenditure on so called "renewable energy" took place on a planet where more than 2 billion people lack access to even primitive sanitation using this link from the organization, recently maligned by the US's Chief Ignoramus, the World Health Organization:

Lack of sanitation for 2.4 billion people is undermining health improvements

To step outside of echolalia briefly this 2015 link has an update: WHO and UNICEF launch updated estimates for water, sanitation and hygiene



Then I point out, "...as the day will repeat its color..." that these billions of dollars that have been spent on so called "renewable energy," exceeds the entire GDP of India, a nation with 1.35 billion people in it, for everything Indians do, eat, educate themselves, build shelters, factories farms and drink.

This, I guess, brings me to the paper referenced at the outset of this repetitious diatribe. From the introductory text:



The authors toured rural Indian villages, where they conducted surveys and then sampled the drinking water of the people they surveyed and ran microbiological tests for fecal pathogens. Some excerpts of their procedures:



The documentation also included details about how the water was stored, covered or uncovered, and how it was delivered, by ladle, for example. The scale of the documentation can be seen in table 1 in the paper, which reports on the findings of homes with contaminated water:



Some graphical results from the paper:



The caption:



Some sample pictures of storage systems observed:



The caption:



The findings of risks in the sampled water:



The caption:



Some longitudinal data:



The caption:



The data speaks for itself, doesn't it?

...data...

..."as the day will repeat its color"...

As for that 29 year old kid referenced above who was not familiar with Jevons in 1976 but was declared a "genius" by some people who also hadn't read Jevons, and of course, by himself, he is now 73 years old; he was born in 1947, the age of the "baby boomer."

I am a baby boomer, profoundly ashamed of my generation and the way we so facilely latched on to what can only be described as silliness and delusion.

Our mantras about so called "renewable energy" did not work; they are not working; they will not work.

To my knowledge, there isn't data on the carbon dioxide concentrations in 1947, when Lovins was born, but the data at the Mauna Loa carbon dioxide observatory goes back to 1959, when the concentration was 315.97 ppm.

Less than 20 years later, the world would embrace the "conservation and renewable energy" Mantra Lovins proposed.

Here is the latest weekly data on the concentration of carbon dioxide in the planetary atmosphere as of this writing:



..."as the day will repeat its color"...

I do not know what world energy demand was in 1947 when Amory Lovins, but I do know what it was in 1973, just three years before he wrote his now famous drivel about so called "renewable energy" and conservation. It was 253 Exajoules, as reported in the 2011 World Energy Outlook.

..."as the day will repeat its color"...

In the most recent year that we have data, 2018, world energy demand was less than an Exajoule short of 600 Exajoules.

By the way, world wide, energy efficiency, has risen dramatically since 1976.

At times, we tend to focus on the income disparity of the United States, which is now sure to grow, as the right wing through inattention and manipulation has brought on what is sure to be a world wide economic depression.

..."as the day will repeat its color"...

As scientist who has echolalia dating back to 1976 uninfluenced by data is not actually a "scientist" at all, even if his title is "Chief Scientist" of an organization like say, "The Rocky Mountain Institute." Arguably, he is nothing more than the leader of a cult.

Hopefully, in this time of cults, political, economic, spiritual and otherwise, this emerging worldwide economic depression doesn't end like the last one did, with the worst war in human history.

One way to prevent that in my perhaps naive opinion is to consider that those people in India are human beings, just like people in Africa, in Mexico, in Canada, and, indeed the United States, that they matter, as all human beings worthy of being called human beings matter, because there is no justifiable reason that these people in India and in similar places should...



...while we obliviously wax romantic about our Tesla electric cars, wind turbines, and efficient refrigerators.

I might mention that one of the best and well known ways to sterilize water, and in fact, to remove some very dangerous pollutants is to irradiate it with ionizing radiation.

As the day will repeat its color, even in a time of the rising celebration of ignorance, I continue to believe, even as my life approaches its end, "the tired sounds running off my bones" that intelligence and decency can yet prevail.

I wish you health and safety in this spring weekend, and some measure, within the limits of our time, peace and happiness.

April 23, 2020

'A disaster': Roche CEO's verdict on some COVID-19 antibody tests

'A disaster': Roche CEO's verdict on some COVID-19 antibody tests

Roche is one of the leading companies in the world in the diagnostic field, and manufacturers equipment that meets the CLIA regulations for medical testing, a "go to" company.

I am not involved in any way in diagnostics, but I worked closely with Roche scientists in the early days of the AIDS crisis when people were dying without access to drugs. There was a quality problem with an intermediate that just bordered on the regulatory limits. The decision was not an easy call to make at all; again lives hung in the balance. People would die without that drug, quite literally. I however was very impressed by the professionalism and seriousness with which the Roche Scientific team considered the issue; and was impressed with how hard they worked to resolve the issue in a way that, um, saved human beings.

I mention this because one might hear in connection with this article, all kinds of stuff about big bad corporate people squashing little guys. I personally don't take it that way at all. I suspect the Roche CEO is being honest. Yes, he has skin in the game, but it is inaccurate and in fact, intellectually dishonest, to think that all Pharma executives are "in it for the money."

That's all I'll say on that score.

April 21, 2020

"From below, from basements, from cellars, from sewers they rose..."

As I've remarked a few times in this space, in this lockdown I'm translating Camus' La Peste (The Plague) from French into English, appropriate in these times.

I found this paragraph - presaging the coming human plague, where he describes massive numbers of rats crawling of from under the city dying - despite being grotesque, to be quite evocative and profoundly metaphorical, and in some ways, relevant, more than half a century after Camus's work was published, to the "rise" of Repuplicans in Washington.

My translation:

The original French:



The more things change, the more they stay the same, n'est pas?.