NNadir
NNadir's JournalScience History Punctilio: The Free Solvated Electron Was Discovered Before its Mass Was Determined.
I've been thinking a lot about approaches to defluorinate the very troublesome perfluoro acids and sulfonates, which are turning into some very serious environmental issues owing to their wide technological use and their chemical inertness - the latter accounting for their wide use. Being who I am, this interest is driven by a possible application for radiation. Maybe I'll write about all of this later this weekend.
It turns out that the active species for defluorination of fluoroalkanes in solution - specifically the troublesome case where they contaminate waster supplies, which they do, and which is becoming a real health concern - is the solvated free electron. In a bout of intellectual laziness, I have long assumed that the active species was the hydride or hydroxide radicals, but on checking my assumptions I was wrong.
Anyway, this all inspired me to read more about solvated electrons, of which I've been aware for most of my adult life, but about which I didn't think all that much. So to read about solvated electrons, I pulled up a nice little review paper, this one: The Hydrated Electron (Herbert and Koons, Annual Review of Physical Chemistry Vol. 68:447-472 (2017)).
It's open sourced, anyone can read it.
Anyway, a fun thing to do in chemistry is to dissolve an alkali metal like potassium or sodium in liquid ammonia which gives a beautiful chemistry. When I was a lazy kid, more interested in very strong bases for organic synthesis, I was more interested in the salts one can obtain by evaporating the ammonia, sodium amide, etc, etc, but the solution that forms is a solution of free electrons, not sodium or potassium amide salts.
The paper has this very interesting note that this fact discovered only a few years after J.J. Thompson proved the (postulated) existence of the electron, and several years before Millikan showed what the mass of the electron was in the famous oil drop experiment.
Here's the text from the cited paper:
To this end, Kraus measured the electrical conductivity of solutions of alkali metals dissolved in liquid ammonia, and already in the first of these papers (in 1908), he proposed that the charge carriers were “electrons surrounded by an envelope of ammonia” (6, p. 1332), i.e., solvated electrons, formed via the dissociation equilibrium Na⇇Na++e?. This inference seems all the more profound when one considers that the nature of the electron as the charge carrier in cathode ray tubes had been established only about ten years earlier (7), and Kraus's 1908 paper predates the publication of Millikan's oil drop experiment (8)...
OK, I'm a dork, but I find this very cool.
If one must be locked down, thinking about this kind of science history is better than watching reruns of the movie, The Stand based on Steven King's book.
I think so anyway.
I hope you'll have some fun this weekend.
The History of Atmospheric Nuclear Weapons Tests & Determination of the Life Span of Whale Sharks.
The paper to which I will very briefly refer is this one: Annual Bands in Vertebrae Validated by Bomb Radiocarbon Assays Provide Estimates of Age and Growth of Whale Sharks (Joyce Jia Lin Ong et al., Frontiers in Marine Science, Vol 7 Page 188 (2020))
This paper is open sourced and is available to the public at the link, so I will not excerpt it extensively but only offer a brief explanation of some background on what about historical nuclear testing involves determination of the age of whale sharks.
As many people know, carbon-14, the radioactive isotope of carbon occurs widely as a result of the high energy radiation flux flowing from the sun at a reasonably constant rate. Interaction of these high energy particles with the overwhelmingly dominant isotope of nitrogen, nitrogen-14, results in a nuclear reaction in which N-14 is transformed into C-14. The radioactive half-life of carbon 14 is roughly 5700 years, relatively short on a geological time scale. Thus were it not being created by natural processes, it would not exist on Earth.
A system in which a radionuclide that is decaying according to the (exponential) nuclear decay law while simultaneously forming at a constant rate - this is the situation in nuclear reactors - will reach a state where it will asymptotically approach a constant value where it is impossible for the quantity to increase beyond a point defined by what we call "The Bateman Equilibrium."
This situation, established over millennia, allows for the famous "radiocarbon dating" technique, since living things exchange radioactive carbon with the environment but when they die, this exchange stops and the concentration falls as the C-14 decays back to N-14.
However, beginning in the 1950's, the long established Bateman equilibrium was disturbed with the dubious practice of open air nuclear weapons testing, particularly with the development of thermonuclear weapons which utilized nuclear fusion triggered by fission driven implosions at extraordinary high temperatures. In these thermonuclear tests, the lithium in lithium deuteride is converted into tritium (early thermonuclear weapons used tritium directly) and fused in the following nuclear reactions: 6Li(n,? )3H and 2H(3H,n)4He. In the first, Lithium-6 absorbs a neutron to release tritium, and in the second, deuterium (hydrogen-2) fuses with radioactive tritium (hydrogen-3) to yield helium and a neutron. The neutron is an order of magnitude higher in energy than typical fission neutrons, the latter being produced in an energy distribution of between 1 to 2 MeV (million electron Volts), the former at a well defined energy of about 14.1 MeV. In air, these 14.1 MeV neutrons have a probability (nuclear reaction cross section) to produce carbon-14 when a nitrogen-14 atom is struck by a neutron and ejects a proton: 14N(n,p)14C.
Since open air nuclear testing stopped nearly completely in the 1960's, albeit after the awful Soviet "Tsar Bomba" test that briefly had a power output equivalent of nearly 2% of the sun's output, this spike put a time marker in all living systems that basically set the clock around 1963, when the final concentration of 14C in the environment was measured.
Each year 0.0122% of a sample of 14C decays back to 14N. Thus by measuring what percentage of C14 has decayed, one can know when the organism was alive. In the 57 years since 1963, 0.691% has decayed.
Thus with precise instrumentation to measure the amount of carbon 14 in a sample one can calculate exactly how long ago a living thing has formed, very precisely in fact since 1963 since the 14C ratio was measured then rather than assumed, as in pre-1963 carbon 14 ratios based on an assumed Bateman equilibrium depending on a consistent nuclear particle flux from the sun.
It has been speculated that the bones of Whale Sharks are rather like tree rings, that surfaces lay down in them in a regular time related pattern. However, proof was lacking. Since bones incorporate some calcium carbonate as well as calcium phosphate however, sensitive testing of the bones should show a distribution of carbon-14 to carbon 12 and 13 ratios that are age dependent, and tied closely to the spike that occurred in the decade before 1963, from the US "Mike" test, the first thermonuclear explosion in 1953 to the last test in 1963.
The authors found that it did, and that thus whale shark bones are like tree rings. From this it is possible to determine when a particular whale shark was born and when it died from its bones.
A brief excerpt from the paper, as a preface to opening the full paper, which is, again, open to the public:
It is critical that age estimates provided by otoliths and vertebrae are accurate, since uncertainty or underestimates surrounding these ages can lead to stock collapses of exploited species (e.g., orange roughy Hoplostethus atlanticus; Smith et al., 1995), or compromise the effectiveness of recovery programs for species that are threatened or endangered. For this reason, many studies have sought to validate the timing of the production of growth bands (Campana, 2001). A common approach is to tag individuals with a chemical marker such as oxytetracycline (OTC) that is laid down within an otolith or vertebrae. Individuals are released and when recaptured at some time in the future, the tag acts as a time stamp that allows the rate of deposition of subsequent growth bands to be determined. For large fishes and sharks that are relatively long-lived and difficult to tag and recapture, validation of annual banding patterns can also be obtained through an analysis of bomb radiocarbon in vertebrae. Above-ground testing of thermonuclear weapons in the 1950s and 60s increased the ratio of carbon 14 isotopes in the atmosphere that were then mixed into the ocean, passed up food webs and incorporated into marine organisms. As a result, the timing of the deposition of bands can be validated by comparing carbon isotope values within vertebrae, with an isotope baseline chronology of known age (Campana, 2001; Campana et al., 2002; Goldman et al., 2012).
The whale shark, Rhincodon typus, is a huge (up to 18 m length; Mcclain et al., 2015), highly migratory, filter-feeding shark found in all tropical and warm temperate seas (Compagno, 2001; Chen et al., 2002; Stevens, 2007). It forms aggregations in productive coastal areas and is a highly valued target for marine eco-tourism (e.g., Huveneers et al., 2017). However, the whale shark has recently been classified as Endangered (IUCN Red List; Pierce and Norman, 2016) and there is now an urgent need for reliable and accurate information on age and growth of the species in order to develop effective conservation and management strategies. At present, there is relatively little demographic data available, especially for large or mature individuals. Using X-radiography, Wintner (2000) analyzed the growth bands in whole vertebrae of juveniles that had stranded on the coast of South Africa to develop an initial growth curve for the species...
I am proud that this work was conducted in my State's State University system, Rutgers, the State University of New Jersey. (One of my sons is a Rutgers graduate.)
Have the best weekend you can under the circumstances.
Prediction of Metal Organic Frameworks for Vacuum Swing Absorption of Carbon Dioxide.
The paper I'll discuss in this post is this one: Prediction of MOF Performance in Vacuum Swing Adsorption Systems for Postcombustion CO2 Capture Based on Integrated Molecular Simulations, Process Optimizations, and Machine Learning Models (Thomas D. Burns,§ Kasturi Nagesh Pai,§ Sai Gokul Subraveti, Sean P. Collins, Mykhaylo Krykunov, Arvind Rajendran,* and Tom K. Woo,* Environ. Sci. Technol. 2020, 54, 7, 4536-4544.)
The extraction of molecules from very dilute streams requires in general two things, high surface area combined with a high "Kd" - "Kd" referring to the distribution constant, the ratio of the solubility of the molecule being extracted in one phase - the concentrating phase - to its solubility in the dilute phase. If the solubility in both phases is high, the extraction can still take place if a reactant in one of the phases is removed by converting it into another molecule, so that the equilibrium condition results in the continuous flow from one phase to another. In general, with some exceptions, this latter approach requires energy, since the concentration of any particular solute by extraction from one system into another requires overcoming entropy, what is generally known as the "entropy of mixing."
Along with the chemical wastes we have dumped on all future generations - as I often remark in this space - we have dumped entropy on them: It will require energy for future generations - if they can do it at all given the fact that we have also used up most resources - to clean up after the worldwide sybaritic party we've been holding for the last half a century or so.
"By the time we got to Woodstock..." (We never left; what a mess!)
A system that has the appropriate features for the removal of a very dangerous fossil fuel waste, carbon dioxide - which despite its perniciousness is still dilute (416 ppm as of this writing) - is the photosynthetic system of plants and microorganisms. As it is self replicating, it can obviously under the right conditions produce a huge surface area, and it can use this surface area to take up dilute energy, light, to create a continuous flow of carbon dioxide in two phases, either air and quasi solid leaves, or water and seaweeds and other photosynthetic organisms.
This process has been going on for billions of years. The low entropy existence of dangerous fossil fuels represents this process of equilibrium shifting taking place over a very long period: The "fossil" in "fossil fuels" is all carbon that has been captured from a dilute stream, in air and water over many hundreds of millions of years. We have released the majority of this carbon in roughly a century, with enormous consequences for life on Earth. ("By the time we got to Woodstock..." What a party!)
It is obvious that biomass, even without fossilization, can be used in technological settings to remove carbon dioxide from the atmosphere, via the intermediary of combustion. As practiced almost everywhere in the world, the combustion of biomass represents a huge health risk: Slightly less than half of the six to seven million air pollution deaths that take place on this planet involves the combustion of biomass.
This said, it is conceivable, although not to my knowledge widely practiced, to subject biomass to combustion cleanly, in a situation known as "oxyfuel combustion" where the combustion takes place not in air but in pure or nearly pure oxygen. Pure, or nearly pure production of oxygen is also feasibly carried out by thermochemical splitting of either carbon dioxide or water, the latter case being somewhat more familiar. The necessary energy for the thermodynamics of such splitting is available cleanly from nuclear energy. In this case, combustion of biomass in pure oxygen, highly concentrated gases rich in carbon dioxide, with - depending on conditions - some nitrogen oxides and some carbon monoxide, can be obtained. Theoretically this carbon can be captured and reduced to make value added products such as polymers, carbon fibers, carbon materials, and highly refractory, chemically resistant, and very hard metal carbides. These value added products sequester carbon dioxide, as does, to be fair, wood and fabric.
However even in concentrated streams of carbon dioxide separation of the streams is required. This is also true, more true in fact, if biomass is burned in air instead of pure oxygen.
The paper under discussion here refers to MOF's, "metal organic frameworks" which are just what they sound like, metals arranged in particular porous frames constructed with organic (carbon) molecules. The inorganic equivalents of these are well known, they are called "zeolites" and they play a huge role in chemical technology already, primarily as catalysts, but also in purification systems.
The authors here have used molecular modeling techniques and machine learning to try to identify MOF's that separate carbon dioxide with the highest energy efficiency.
From the paper's introduction:
Several technologies are being explored as energy-efficient alternatives to current solvent-based CO2 scrubbing systems. At the forefront are solid sorbent-based technologies that use porous materials within pressure and/or temperature swing adsorption (P/TSA) systems. Technoeconomic studies suggest that P/TSA technologies have the potential to substantially reduce the cost of carbon capture if the right solid sorbents can be found.(4) Metal–organic frameworks (MOFs), which are crystalline nanoporous materials that are constructed from inorganic and organic building units,(5,6) have attracted significant attention as possible sorbents. Due to the seemingly endless combination of building units that can be combined to construct them, a dizzying range of MOFs is possible such that they can potentially be tuned for any given application. Indeed, it is estimated that nearly 70 000 different MOFs have been synthesized and characterized to date.(7)
MOFs are often introduced as outstanding materials for postcombustion CO2 capture by highlighting a few targeted adsorption properties, such as high CO2 uptake capacity or CO2/N2 selectivity,(8?12) without a clear understanding of how these properties affect their performance in a real industrial P/TSA process. Large databases, some containing millions of hypothetical materials,(13) have been screened computationally via detailed atomistic simulations for their potential to be used as solid sorbents for postcombustion CO2 capture.(14?17)
If the phrase, "...industrial-scale CCS projects exist that capture and store more than a million tons of CO2 per year..." impresses you, it shouldn't. The fraction that "a million tons of carbon dioxide" represents of what we dump each year, roughly 35 billion tons, is 0.00003. All of the carbon dioxide capture and sequestration "industrial plants" on the planet are essentially useless.
Carbon capture involves "parasitic energy" losses which the authors call "PE." The authors note that the US DOE, a standard set presumably before the organization entered into the process of being decimated by one of the most stupid leaders the world has ever seen, has set a standard for the recovery of between 90% to 95% of the carbon dioxide in a gas stream.
The authors further write:
...In this work, we have screened 1632 MOFs and related materials with an advanced PSA process simulator that has been experimentally validated at the pilot scale using a four-step light-product pressurization (LPP)(34) cycle shown in Figure 1. This cycle has been shown to be the most energy-efficient cycle for postcombustion CO2 capture.(34) While a costing algorithm could be used as the objective function, there are large uncertainties in the costing of MOFs to estimate the capital expenditures. Hence, the goal here was to obtain high-reliability results at a scale where our models have been validated. Therefore, the process conditions have been optimized for each material to minimize the PE or to maximize the productivity while meeting the 95/90 purity–recovery targets (PRTs). The productivity of a material or how much CO2 the sorbent can extract per unit volume of the material per unit time is not only important for determining how much material is required for CO2 capture but also vital for determining the complexity of the VSA system required and more suitable yet essential considerations such as the capacity of the vacuum pumps that are required.
Here is a cartoon showing the outline of how a VSA (Vacuum Swing Absorption) system works. (It is similar to "Pressure Swing Absorption" systems which produce commercial streams of concentrated (nearly pure) nitrogen or oxygen (for portable oxygen supplies for medical use).
The caption:
The authors screen 1584 MOF's after eliminating those that required the use of rare or toxic metals or could not be industrialized by other means.
This graphic shows some results of their screening efforts.
The caption:
This table also refers to some results:
Another figure showing results for selectivity:
The caption:
Note that the scale on the abscissa is logarithmic, a value of "3" is 1000 times more selective than a value of "1".
And so on...
Excerpts from the conclusion:
...Advanced process simulations of a four-step VSA system, which have been validated at the pilot scale, have been integrated with atomistic simulations allowing for the screening of 1632 experimentally characterized MOFs for postcombustion CO2 capture. A total of 392 MOFs were found to meet the 95/90 purity–recovery targets, while a dozen materials, including IISERP-MOF2, UTSA-16 and zeolite NaA, were able to simultaneously achieve PEs <250 kWhe/MT CO2 and productivities greater than those of zeolite-13X. Although we have assumed a dry flue gas, a handful of MOFs have been reported, whose CO2 adsorption properties are nearly unchanged in high-humidity conditions.(19,55) In those cases, the results of these simulations remain applicable. For MOFs whose adsorption properties are substantially changed in humid conditions, the flue gas stream can be dried at an energetic cost estimated to be as low as 24 kWhe/MT CO2.(40) In total, 97 MOFs were found to have PEs <250 kWhe/MT CO2, which makes them highly competitive with advanced solvent-based scrubbing systems even when the cost of drying the flue gas is included...
These sorts of papers suggest the world can be saved. This is not to say that it will be easy or cheap and that it will not take extreme effort, particularly in a time of rising stupidity, but if we have left all future generations a physiochemical environmental disaster, at least we have left them with something, that something being insight.
I trust you will do your best to enjoy all that can be enjoyed under the circumstances in the coming days.
"...to love one another without even knowing it..."
To brush up on my French, I've been using this extra time to work on something worthwhile, translating - how appropriate is this - Camus's La Peste, the Plague...
It's been a kind of revelation. I was struck by this paragraph in the first chapter, having known and admired someone who died in these times, which stikes at me powerfully.
My translation:
Suddenly it seems so much more urgent not to squander the time we have left to live.
It struck me as a powerful thought, I felt compelled to reflect on it.
"...only this glimmer, and that is what always triumphs..."
Camus was just an incredibly evocative writer, seeing in just a few words, so deeply into us all.
New Record Weekly CO2 Concentration Record Set at the Mauna Loa Observatory 416.45 ppm.
Although I am dealing with some personal grief over the loss of a great friend and colleague in this crisis, the greater crisis before all humanity remains, I'm talking about the real big crisis, climate change.
Over the next few weeks, through some week in May I'll be recycling text related to this topic of setting new weekly records for the concentration of the dangerous fossil fuel waste carbon dioxide concentrations in the planetary atmosphere, just changing the numbers to accommodate the numbers associated with the records.
Recycling is good, no? So I've heard.
I did discover a new, and frankly very disturbing way to look at the data this week, which I'll discuss below.
Anyway...
As I've indicated several 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 is.
I had the naive wishful thinking notion that restrictions on automobile traffic with all of the worldwide lock downs would lead to a slowing of carbon dioxide accumulations. Something quite different has been observed with the most recent weekly data.
The data from the Mauna Loa Carbon Dioxide Observatory:
Up-to-date weekly average CO2 at Mauna Loa
Week beginning on April 5, 2020: 416.45 ppm
Weekly value from 1 year ago: 412.67 ppm
Weekly value from 10 years ago: 391.12 ppm
Last updated: April 12, 2020
This week's reading, 416.45 ppm is the highest weekly average ever recorded at Mauna Loa, surpassing the record set last week, which was 415.75 ppm.
As I often note in this space the readings are sinusoidal, superimposed on a steadily rising slightly less than linear axis, as this graphic, which I often reproduce, from the Mauna Loa website shows:
Every year, like clockwork, a new all time record is set in May.
Last year's (then) highest ever recorded value, recorded on May 9, 2019, was 415.39 ppm
The increase in this week's reading over the same week 1 year ago is 3.35 ppm.
As of this writing, there have been 2,304 such data points, readings, at Mauna Loa. This week's reading is "only" the 39th highest ever observed.
Of the top 50 such readings, 29 have taken place in the last five years, 36 in the last ten years, and 40 in the twenty-first century.
Noting that this weeks reading is 25.33 ppm higher than the reading ten years ago, I decided to look at the data in a different way than I've been looking at it previously. The ten year figure for change after all, takes out a lot of noise in the measurements. This year, in 2020 for instance, weekly increases have varied from a low of 1.47 ppm over the previous year (recorded on February 23, 2020, to a high a 4.28 recorded in the week beginning in the week of March 23, 2020, the 11th highest data ever recorded out of all 2,304 such data points.
I chose to look therefore at the highest 10 year changes represented in the weekly data.
There have been 7 weeks in which the ten year change was equal to or exceeded 25.00 ppm, recorded in all weekly data points since January 1, 2000.
All of them occurred since January 1, 2019. Four of the seven occurred this year, and we're only in April.
Of the top 20 of the ten year readings, 18 have occurred since January 1, 2019. All of the top twenty have occurred since April 15, 2018.
If the fact that this reading is 25.33 ppm higher than it was ten years ago bothers you, don't worry, be happy.
Head over to Daily Kos and watch a smug scientifically illiterate anti-nuke prattle on about the "'Shovel Ready' Green New Deal". The "Green New Deal" is a proposal to save the world with so called "renewable energy"
Maybe you'll feel better.
I won't.
My impression that I've been hearing all about how rapidly renewable energy has been growing since I began writing here in 2002, when the reading on April 14, 2002 was 375.14 ppm should not disturb you, since it is better to think everything is fine rather than focus on reality.
In this century, the solar, wind, geothermal, and tidal energy on which people so cheerfully have bet the entire planetary atmosphere, stealing the future from all future generations, grew by 9.76 exajoules to 12.27 exajoules. World energy demand in 2018 was 599.34 exajoules. Unquestionably it will be higher in 2019 and in 2020.
10.63 exajoules is slightly over 2% of the world energy demand.
2018 Edition of the World Energy Outlook Table 1.1 Page 38 (I have converted MTOE in the original table to the SI unit exajoules in this text.)
According to this report, the fastest growing source of energy on the planet in the 21st century over all was coal, which grew from 2000 to 2018 by 63.22 exajoules to 159.98 exajoules.
If you think that unlike you, I am worrying and not being happy, you can always chant stuff about how "by 2050" or "by 2075" or "by 2100" we'll all live in a so called "renewable energy" nirvana powered by the sun and tooling around in Tesla electric cars.
Talk about "how dangerous" so called "nuclear waste" is, even if has a spectacular record over half a century of not killing anyone, even as dangerous fossil fuel and biomass combustion waste, aka "air pollution" kills between 6 and 7 million people a year, every year, without stop, about 19,000 people per day, every day.
I may be too jaded to be comforted, having heard this stuff my whole adult life - and I'm not young - but you could try. It's not results that count, but good intentions.
I'm kind of cynical, I guess, because I know how stuff is made.
I'm interested in facts, not fantasies.
Facts matter.
And the fact, is that things are deteriorating, despite the fact that humanity has spent more than two trillion dollars on so called "renewable energy" infrastructure in the last ten years - more than the entire GDP of India, a nation with 1.3 billion human beings in it. I know it didn't work. I know it isn't working. I know it won't work.
I know, for example, that steel is made by reducing iron oxide with coal transformed into coke, by heating coal in coal fired furnaces. I know that the blind faith in tearing up pristine wilderness to make roads for diesel trucks to access wind farms with turbines on massive steel posts is as abhorrent to me as the construction of the Hetch Hetchy Dam in Yosemite was to John Muir when he founded the Sierra Club.
After the last Covid-19 patient on the planet has recovered, the much larger problem of climate change will still be with us.
History will not forgive us, nor should it.
My boss died last evening.
In my long life, he was, the most honorable man with whom or for whom I have ever worked, an exemplar of integrity and all that is good among human beings. I, and everyone who knew him, will miss him greatly.
The world, it seems, is emptying.
A Trial of Lopinavir-Ritonavir in Adults Hospitalized with Severe Covid-19
The paper I'll discuss in this brief post is this one: A Trial of Lopinavir–Ritonavir in Adults Hospitalized with Severe Covid-19 (in Cao, M.D., Yeming Wang, M.D., Danning Wen, M.D., Wen Liu, M.S., Jingli Wang, M.D., Guohui Fan, M.S., Lianguo Ruan, M.D., Bin Song, M.D., Yanping Cai, M.D., Ming Wei, M.D., Xingwang Li, M.D., Jiaan Xia, M.D., et al. New England Journal of Medicine, March 18, 2020.)
Lopinavir and Ritonavir are proteases developed to treat HIV in the 1990s. Although I was personally not involved in the commercialization of the latter, I was involved - fairly peripherally - in issues connected with its scale up through phase 2. I was not involved in any way in the successor compound, Lopinavir, although I was aware of its development.
This paper is open sourced, as are all publications connected with Covid-19 in the primary scientific literature. The point of bringing it up is to show how clinical trials are conducted. Please note the summary conclusions:
In hospitalized adult patients with severe Covid-19, no benefit was observed with lopinavir–ritonavir treatment beyond standard care. Future trials in patients with severe illness may help to confirm or exclude the possibility of a treatment benefit. (Funded by Major Projects of National Science and Technology on New Drug Creation and Development and others; Chinese Clinical Trial Register number, ChiCTR2000029308. opens in new tab.)
Note also this statement in the body of the text:
The first sentence in the latter excerpt, which I have bolded, would seem to suggest a positive result to someone who knows nothing at all about clinical trials and their supporting statistics. However, upon statistical analysis, the authors, all of whom are highly trained physicians, conclude that there is no significant difference.
This would have no bearing of course, on "Dr./Professor" Snake Oil Trump and his even more stupid son in law "Dr./Professor" Slumlord Jared, but it means something to scientists, even if Snake Oil Trump and Slumlord Jared having never been accomplished enough to have opened a science book in their pathetic criminal lives and thus might advise people to take these drugs based on a stupid reading of the first sentence in the last excerpt.
As I used to say on another website where I used to write, "Ignorance kills."
Stay healthy. Be safe.
A Back of the Envelope Calculation of the Mass of Carbon Dioxide in Earth's Atmosphere.
Disclaimer: It's not actually "back of the envelope;" it's "in the spreadsheet."
Last night I started to write a post about a paper published yesterday in the scientific journal ACS Sustainable Chemistry and Engineering on the subject of nature of lignins. Lignins are often discussed in the scientific literature as a source of chemicals, particularly aromatic chemicals, to replace those that are currently provided by the dangerous fossil fuel petroleum. Lignins are highly complex structural polymers found in all terrestrial higher plants in the form of "lignocellulose." They are readily available as a side product of the manufacture of paper, which is largely derived from cellulose extracted from lignocellulose, including the much now appreciated, in the days of Covid, toilet paper. (Save Trees: Bring on the bidets!)
In writing that post, which will come along separately at some other time; I found myself asking the question of how much carbon dioxide could be sequestered as products if we began to use lignin as something other than a combustible fuel (which is how it is largely utilized now), that is, began to use it to make industrial structural polymers and other industrial products. The next question I asked myself is how significant this much sequestered carbon would be. This led me to ask a question that somehow I've been overlooking for some time, which is "what is the mass of the carbon dioxide in the Earth's atmosphere?"
Currently the concentration of the dangerous fossil fuel waste carbon dioxide in the atmosphere, as of this writing, is about 416 ppm. This number is a dimensionless number that actually represents the mole fraction which is a representation of the average number of atoms in the entire atmosphere that are carbon dioxide. It means that if one were to physically count one million atoms in the Earth's atmosphere on average 416 of them would be carbon dioxide molecules and 999,584 of them would be something else, other molecules, nitrogen molecules, oxygen molecules, monoatomic argon molecules and so on. In order to extract these carbon dioxide molecules from air, we would still need therefore to reject 999,584 molecules in the process of collecting the 416 CO2 molecules, a prodigious task. Besides dumping carbon dioxide on all future generations in the orgy of consumption my generation undertook from the late 1960's to the current day, we also dumped entropy, which in many ways is a more serious problem, especially as it extends beyond carbon to pretty much every other element in the periodic table.
The average molecular weight of air is taken as 28.97 gram/mole. The mass of the Earth's atmosphere, taken from a widely referenced paper, The Mass of the Atmosphere: A Constraint on Global Analyses (Kevin E. Trenberth, and Lesley Smith, Journal of Climate, Vol 18, pp 864-875), is 5.148 zetagrams (5.148 X 10^18 kg). From these figures we can see that the number of moles of air on this planet is 177.7 Examoles of air. (1.777 X 10^20 moles). Since the fraction of these moles that are moles of carbon dioxide is 416 ppm = 416/1,000,000 = 0.000416 is follows that the number of moles of carbon dioxide is 73.29 Petamoles (7.329 X 10^16 moles). The molecular weight of carbon dioxide is 40.01 grams/mole. This means that the Earth's atmosphere contains 3.253 Exagrams of carbon dioxide. Translated into metric tons, this amounts to 3.253 trillion tons of carbon dioxide.
About 200 years ago, the world began to abandon so called "renewable energy" because most people while most people lived short miserable lives of dire poverty, even more so than today, and the world was running out of forests to destroy to provide wood for rich people as well as to provide scrapings for the poor. At that time, the concentration of carbon dioxide was probably somewhere in the neighborhood of 270 ppm. The fraction that 270 ppm represents of today's concentration is 270/416 = 0.646.
It follows that the amount of carbon dioxide that would need to be removed from the atmosphere to reach pre-industrial levels is 1.15 trillion tons.
If we take 1820 as the year that the coal industry really began to take off because of the invention of the steam pump to drain coal mines so children could labor in them without drowning, we see this process of utilizing dangerous fossil fuels to avoid the poverty associated with so called "renewable energy" we can calculate that the average addition per year since 1820 was on the order of 5.76 billion tons per year.
In 1820, one could be excused for thinking this was a good idea. Atomic theory was still in its infancy (and not completely accepted), the nature of light was only partially understood and its relationship to energy even less so; indeed the concept of energy itself was largely esoteric and was a subject primarily of academic and not general interest.
However, since 1959 fairly precise records for carbon dioxide concentrations have been kept at the Mauna Loa carbon dioxide observatory, when mean the concentration of carbon dioxide was 315.97 ppm, we can see that since 1959 the concentration has risen by nearly exactly 100 ppm. From the above numbers, we can see that the amount of carbon dioxide dumped in the age of baby boomers, that awful generation to which I belong, amounted to about 782 billion tons of carbon dioxide. This means the average amount of carbon dioxide dumped since 1959 was 12.8 billion tons per year.
For perspective, we are now dumping, according to the most recent figures, about 35 billion tons per year with another 8 to 10 billion tons per year additional arising from land use changes, the conversion of wilderness to farm land, the conversion of farm land to suburbs with shopping malls and McMansions, the conversion of wilderness to strip mines etc, etc, etc...ad nauseum...including the conversion of wilderness to industrial parks for wind turbines that have had zero success in addressing climate change, are having zero success in addressing climate change and will continue to have zero success in addressing climate change.
Things are getting worse, not better.
If you're a baby boomer like me, don't worry, be happy. Just go on prattling about how wonderful wind farms and solar cells and Elon Musk's cobalt laced electric cars are. Don't forget to throw in illiterate comments about how dangerous nuclear energy is, neglecting of course to compare it do anything else in terms of destructive power; destructive power, I note, that unlike the mindless assumptions provided by your fervid imaginations about nuclear energy, that is actually being observed rather than imagined in the case of the unaddressed and continuously rising use of dangerous fossil fuels.
None of this is your problem, you'll be gone soon enough. It is the vast problem on an unimaginable scale for all those millennials you like to condescend in your bourgeois nobility and in fact, for every generation after theirs.
I'm a dissident, by the way, with respect to my views on the millennial generation. From my perspective, I expect great things from them, but even they do not prove to be a "greatest" generation as I expect they will, they could hardly be worse than we were.
History will not forgive us, nor should it.
A Commentary on Our Government in the Scientific Journal Science.
Science is one of the premier scientific journals.The full text of this "in depth" commentary is here: United States strains to act as cases set record
It speaks for itself, but here's an excerpt:
To limit the damage, Trump on 29 March announced that federal recommendations to practice physical distancing would remain in place at least through the end of April, dropping his much-criticized push for a faster return to business as usual. In the meantime, officials across the nation are scrambling to find enough ventilators, protective gear, and supplies for hospitals overwhelmed with COVID-19 patients—or about to be (see graph, below right). Many state governors ratcheted up restrictions intended to slow the pandemic, imposing stay-at-home orders that some said could last into June.
Despite such actions, the U.S. pandemic response remains a work in progress—fragmented, chaotic, and plagued by contradictory messaging from political leaders. “We don't have a national plan,” says epidemiologist Michael Osterholm of the University of Minnesota, Twin Cities. “We are going from press conference to press conference and crisis to crisis … trying to understand our response...”
A "Cryptic Epitope" to SARS-COV-1 Also Binds to SARS-COV-2: A Key to Vaccine Design.
The paper I'll discuss in this post is this one: A highly conserved cryptic epitope in the receptor-binding domains of SARS-CoV-2 and SARS-CoV. (Meng Yuan1,*, Nicholas C. Wu1,*, Xueyong Zhu1, Chang-Chun D. Lee1, Ray T. Y. So2, Huibin Lv2, Chris K. P. Mok2,†, Ian A. Wilson1,3,†, Science, April 3 2020.)
I am logged in under my subscription, but I believe all Covid-19 related papers in the scientific literature are open sourced.
Some brief simplifications of what is in the paper: Most proteins are very large molecules, containing many hundreds of amino acids. The bulk of these do not conduct the "business" of the protein, although they may and often do play other roles such as signalling when a protein may be activated or deactivated.
The actual place where "business" is conducted is a short sequence of amino acids within the protein that is called the "epitope." They may be as small as a few amino acids long, but seldom comprise all that much of the protein's overall sequence. Drugs are often designed so as interfere with this functional "epitopic" region. Many blood pressure medicines, for example, interfere with the epitopic region of the ACE2 target of the SARS-Covid virus. (Clinical trials exploiting this area for potential Covid treatments is planned at the University of Minnesota for Covid patients not requiring critical care.)
It appears that antibodies in a patient who recovered from SARS-CoV-1, which also interacts with SARS-CoV-2, which is very good news indeed. It means that much of the work on earlier SARS viruses may be utilized in exploring both treatment and vaccine opportunities.
An excerpt from the text:
CR3022, which was previously isolated from a convalescent SARS patient, is a neutralizing antibody that targets the receptor-binding domain (RBD) of SARS-CoV (4). The immunoglobulin heavy chain variable, diversity, and joining (IGHV, IGHD, and IGHJ) regions are encoded by germline genes IGHV5-51, IGHD3-10, and IGHJ6, while the light chain variable and joining regions are encoded by IGKV4-1 and IGKJ2 (4). Based on IgBlast analysis (5), the IGHV of CR3022 is 3.1% somatically mutated at the nucleotide sequence level, which results in eight amino-acid changes from the germline sequence, whereas IGKV of CR3022 is 1.3% somatically mutated resulting in three amino-acid changes from the germline sequence (fig. S1). A recent study has shown that CR3022 can also bind to the RBD of SARS-CoV-2 (6). This finding provides an opportunity to uncover a cross-reactive epitope.
A graphic from the text:
The caption:
(A) Sequence alignment of SARS-CoV-2 RBD and SARS-CoV RBD. CR3022 epitope residues are colored cyan. ACE2-binding residues are colored magenta. Non-conserved epitope residues are marked by asterisks. (B to E) Interactions between the non-conserved epitope residues and CR3022 are shown. Amino-acid variants observed in SARS-CoV are in parenthesis. SARS-CoV-2 RBD is colored in cyan, CR3022 heavy chain in orange, and CR3022 light chain in yellow. Residues are numbered according to their positions on the SARS-CoV-2 S protein sequence. (B) While SARS-CoV-2 has an Ala at residue 372, SARS-CoV has a Thr, which introduces an N-glycosylation site at residue N370. (C) The potential location of N370 glycan in SARS-CoV RBD is indicated by the box. CR3022 is shown as an electrostatic potential surface presentation. (D) P384 interacts with T31, S96, and T100 of CR3022 heavy chain. Ala at this position in SARS-CoV would allow the backbone to adopt a different conformation when binding to CR3022. (E) T430 forms a hydrogen bond with S27f of CR3022 light chain. Met at this position in SARS-CoV would instead likely insert its side chain into the hydrophobic pocket formed by Y27d, I28, Y32, and W50 of CR3022 light chain.
The letters are codes to conveniently list each of the 20 amino acids coded by the DNA of eucaryotic cells. (Bacteria have 21 coded amino acids, including selenomethionine with the other 20.) For example, Y is tyrosine; N is asparagine; and W is tryptophan.
There is another paper that addresses more broadly the evolutionary differences between a wide array of Corona viruses, this one:
[link:Structure, Function, and Antigenicity of the SARSCoV-2 Spike Glycoprotein|Structure, Function, and Antigenicity of the SARSCoV-2 Spike Glycoprotein] (Walls et al., 2020, Cell 180, 1–12)
A graphic showing amino acid sequences that have evolutionary changes from one another as well as the conserved sequences is this one.
The caption:
(A) Entry of MLV pseudotyped with SARS-CoV-2 S, SARS-CoV S and SARS-CoV-2 Sfur/mut in VeroE6 cells. Data are represented as mean ± standard deviation of technical triplicates.
(B) Entry of MLV pseudotyped with SARS-CoV-2 S or SARS-CoV-2 Sfur/mut in BHK cells transiently transfected with hACE2. The experiments were carried out with two independent pseudovirus preparations and a representative experiment is shown. Data are represented as mean ± standard deviation of technical triplicates.
(C) Sequence alignment of SARS-CoV-2 S with multiple related SARS-CoV and SARSr-CoV S glycoproteins reveals the introduction of an S1/S2 furin cleavage site in this novel coronavirus. Identical and similar positions are respectively shown with white or red font. The four amino acid residue insertion at SARS-CoV-2 S positions 681-684 is indicated with periods. The entire sequence alignment is presented in Data S1.
(D) Western blot analysis of SARS-CoV S-MLV, SARS-CoV-2 S-MLV, and SARS-CoV-2 Sfur/mut-MLV pseudovirions. See also Data S1.
I did see some literature on the apparently conserved PRRA in this graphic sequence indicating that it was mutated in Covid-19, but I may have been mistaken, since I generated that sequence on my own from the RNA sequence and may have scanned that paper too quickly.
Some of this may be arcane to non-scientists, but it is significant. I will be pleased to answer any questions anyone may have to the best of my ability.
The world scientific community is on the case.
I wish you good health.
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