Welcome to DU! The truly grassroots left-of-center political community where regular people, not algorithms, drive the discussions and set the standards. Join the community: Create a free account Support DU (and get rid of ads!): Become a Star Member Latest Breaking News General Discussion The DU Lounge All Forums Issue Forums Culture Forums Alliance Forums Region Forums Support Forums Help & Search

NNadir

NNadir's Journal
NNadir's Journal
February 7, 2021

For Only the 3rd Time in Its Records, the CO2 Readings at Mauna Loa Are Above 417 ppm.

As I have remarked many times in this forum, and when I was writing there, the E&E forum, somewhat obsessively I keep a spreadsheet of the weekly data, reported at the Mauna Loa Carbon Dioxide Observatory, of carbon dioxide concentrations, 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 have noted many times, with sadness and regret, that we on the left are not free of such fear ignorance and dogma, although I wish we were. We cannot, with justice, attribute this outcome to Ronald Reagan, George Bush the first and second, and Donald Trump. We bear responsibility, no matter how much we pat ourselves on the back for our insane, and frankly, delusional worship of so called "renewable energy."

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

This is an amount that is larger than the GDP of India, a nation with 1.4 billion people in it.

It is obvious that all the money thrown at so called "renewable energy" did not work, is not working, if the definition of "working" reflects dealing with climate change. I, for one, am absolutely and irrevocably certain that even more money, tens of trillions of dollars, will not work if this is the goal, and not simply keeping the mining and semiconductor industries flush with money changing hands.

The reason is physics. The laws of physics are not determined by popular opinion, delusional or otherwise. They are independent of politics, and politicians ignore them at the peril of all humanity. The reason that so called "renewable energy" has failed, is failing and will always fail is the low energy to mass ratio associated with it, along with its intrinsic variability.

The data at Mauna Loa fluctuates with the seasons, a roughly sinusoidal curve whose axis is a quasi-linear (slightly parabolic actually) pretty much monotonically increasing line:



The annual maxima are usually seen sometime in May of any given year; the annual minima usually occur in September or October,

Here is the data from the Mauna Loa observatory for the week beginning January 31, 2021:

Up-to-date weekly average CO2 at Mauna Loa

Week beginning on January 31, 2021: 417.12 ppm
Weekly value from 1 year ago: 414.50 ppm
Weekly value from 10 years ago: 392.19 ppm
Last updated: February 7, 2021

This is only the third such measurement to ever exceed 417 ppm at the Mauna Loa observatory, going back to the 1950's. Weekly data points are available for the Mauna Loa CO2 observatory going back to the week beginning May 25, 1975, when the reading was 331.10 ppm. Last year, the annual maximum was recorded as 417.43 ppm for the week beginning May 24, 2020, and the week after, beginning May 31, 2020 recorded a value of 417.20 ppm.

In terms of the comparison with weekly measurements recorded 10 years ago, the difference recorded here, 24.93 ppm, is the 10th highest among all 10 year week to comparisons, out of 1891 such data points available in my spreadsheet.

There is considerable noise in these measurements. There has been a lot of speculation about the effect of Covid-19 on carbon dioxide accumulations in 2020, and it is possible that this year may show up as "lighter than usual" - at least for these times, although the trend in annual increases, since the first weeks of 2021 have been showing unusually mild increases over the previous year, averaging "only" 1.96 ppm higher than the same four weeks of 2020. Similarly the last 4 weeks of 2020, the weeks of December, the average was "only" 2.22 ppm.

I'm personally not mislead, since the average of all week to week comparators between weeks of 2020 and weeks of 2019 was 2.58 ppm, which, compared with values in the 20th century, is obscenely high.

Here is how the Mauna Loa observatory calculates annual increases:

The annual mean rate of growth of CO2 in a given year is the difference in concentration between the end of December and the start of January of that year. If used as an average for the globe, it would represent the sum of all CO2 added to, and removed from, the atmosphere during the year by human activities and by natural processes. There is a small amount of month-to-month variability in the CO2 concentration that may be caused by anomalies of the winds or weather systems arriving at Mauna Loa. This variability would not be representative of the underlying trend for the northern hemisphere which Mauna Loa is intended to represent. Therefore, we finalize our estimate for the annual mean growth rate of the previous year in March, by using the average of the most recent November-February months, corrected for the average seasonal cycle, as the trend value for January 1. Our estimate for the annual mean growth rate (based on the Mauna Loa data) is obtained by subtracting the same four-month average centered on the previous January 1. Preliminary values for the previous year are calculated in January and in February.

The estimated uncertainty in the Mauna Loa annual mean growth rate is 0.11 ppm/yr. This estimate is based on the standard deviation of the differences between monthly mean values measured independently by the Scripps Institution of Oceanography and by NOAA/ESRL. The annual growth rate measured at Mauna is not the same as the global growth rate, but it is quite similar. One standard deviation of the annual differences MLO minus global is 0.26 ppm/year.


Using this method of calculation, there were, in the 40 year period between 1959 and 1999 five years in which the carbon dioxide concentrations of the dangerous fossil fuel waste carbon dioxide increased by more than 2.0 ppm. In the 21st century, 13 out of 20 have exceeded 2.0 ppm increases.

However, the preliminary figure for the increase, perhaps calculated differently, linked on the data page at the Mauna Loa website shows the increase for 2020 as being 2.57 ppm.

The trends are clear enough from this bar graph on the Mauna Loa website:



Annual Mean Growth Rate for Mauna Loa, Hawaii

If any of this troubles you, don't worry, be happy. Head on over to our E&E forum and read all about how some bourgeois person over there has put solar cells on the roof of his or her McMansion, and is saving money which he or she can use to buy his or her Tesla electric car.

It doesn't do much for me, but maybe you're different than I am.

Have a nice Sunday afternoon.

February 7, 2021

Finally I get what the orange racist meant while saying "Make America Great Again."

It's a goal he may yet achieve.

He actually helped it to come about, by first taking a great country, the United States, and nearly destroying it, making it into a "shithole country," to use his locution, in order to serve his chief financier and owner, Vladmir Putin, so that a man like Joe Biden can come in, clean the country up and, in fact, make it great again.

A twisted path, but the very real one utilized by the ignorant racist orange buffoon.

February 7, 2021

A Very Brief Note on Following the Presence of Biofuels in Fossil Fuels by Radioactivity Mesurements

I'm catching up on my reading before focusing on a topic (later in the day) on the environmental behavior of plutonium at the Nevada National Insecurity Site, and came across this very cute and mildly interesting paper by scientists working (at Chevron) for the dangerous fossil fuel industry, an industry which I oppose (Chevron): Liquid Scintillation Counting Method for the Refinery Laboratory-Based Measurements of Fuels to Support Refinery Bio-Feed Co-Processing (Matthew Hurt, Josephine Martinez, Ajit Pradhan, Michelle Young, and Michael E. Moir Energy & Fuels 2021 35 (2), 1503-1510).

I'm not going to spend a lot of time writing about this paper, but here are a few cool excerpts about how the (disturbed) radioactive C-14 measurements, widely and famously used for carbon dating, apply to following the addition of biomass to dangerous fossil fuels:

With an ever-increasing need to reduce greenhouse gas emissions worldwide, there has been a regulatory push to start incentivizing the transition from traditional fossil fuels, such as crude oil, a high carbon intensity (CI) feedstock, to biologically sourced feedstocks that have lower CI.(1) To minimize costs while complying with the various government mandates, the goal for many in the petroleum refining industry is to utilize existing infrastructure.(2) It has been shown in a recent assessment that there is currently an abundance of low-cost biomass feedstocks that can be used to supplement crude oil to produce renewable fuels.(3) However, many traditional crude oil refineries are not equipped to handle a switch from 100% crude oil to 100% biological-based feeds because of process, catalytic, and metallurgical limitations of facilities.(4,5) To ease the transition from crude oil to bio-feeds and to comply with new regulations, some refineries have decided that the co-processing of bio-feedstocks into various reactor units in the refinery is the optimal way to proceed.(1,2,6) Co-processing bio-feeds, such as pyrolysis oil or vegetable oil, can be done in various locations, such as fluid catalytic cracking (FCC) and/or hydrotreating/hydrocracking units.(7?10) Recent pilot- and demonstration-scale studies using an FCC unit have demonstrated the viability of co-processing bio-oil with vacuum gas oil (VGO) in a refinery with FCC unit.(9?11) VGO is the distillation fraction of crude oil that requires vacuum to be applied to reduce the boiling point enough to evaporate the oil in the distillation column and typically has a boiling range of 800–1050 °F at standard temperature and pressure (STP). The Pacific Northwest National Laboratory (PNNL) conducted an assessment of all of the refineries in the United States on the flexibility of bio-oil co-processing capability using FCC, hydrotreating, or hydrocracking units and concluded that 95 out of 124 refineries have a total capacity ranging from 2900 to 232 500 barrels per day of VGO that could be used to co-process bio-feeds.(12)...

...14C is a radioactive isotope of carbon produced in the upper atmosphere through a neutron capture reaction by 14N atoms.(16) The production of 14C is relatively constant, with current atmospheric concentration changes due mostly to human activity either through the detonation of nuclear weapons (caused a spike in 14C concentration that peaked in the 1960s) or the excess production of CO2 through fossil fuel combustion (driving factor of current variation).(17,18) Living organisms take up all of the isotopes of carbon 12C, 13C, and 14C in the same proportions as they occur in the atmosphere for their life span.(19) For short-lived organisms, it can be assumed that the 14C concentration in the atmosphere is constant over the life span of the organism, which is a safe assumption for many fuel crops as they are typically harvested within 1 year of planting. It can also be assumed that crude oil has no 14C since the half-life of 14C is 5730 years, and crude oil is millions of years old.(1)
Commonly, refineries focus on running methods certified by the American Society for Testing and Materials (ASTM). There are currently two methods that are ASTM approved for the detection of 14C and are described in D6866 with the most recent version being D6866-20.


The authors note that the standard methods are expensive to run, and have a long lead time for turn around, and are not suitable for continuous processing, so they seek to find a fast convenient method that can be utilized as an in process control.

The expensive method, which was used for calibration:

All samples were sent for analysis to the Center for AMS at the Lawrence Livermore National Lab (LLNL), Livermore, CA. The facility has extensive prior experience testing fuel type samples and was involved in a previous AMS interlab study analyzing biofuels.(35) The LLNL AMS facility analyzed the samples according to ASTM D6866-18 Method B.(36) Using the 14C to 12C ratio, the data was reported in raw percent modern carbon (pMC). The raw pMC was then corrected using the 13C to 12C isotopic ratio measured by isotope ratio mass spectrometry (IRMS) instead of the results collected by the AMS for more accurate results. Choosing the correct reference year is very important to generate the most accurate results as the atmospheric concentration of 14C is slight changes over time.(36) The reference year of 2018 was used to correct for atmospheric 14C concentration for when the plants were grown; the 2018 pMC correction is 1.005 in accordance with ASTM D6866-18.(36) The data was further corrected by running a laboratory-supplied pure petroleum diesel sample, since previous studies showing blank correction help with accuracy.(35)


The cheap fast method using ambient radioactivity:

LSC was performed using a Hidex 300 SL automatic liquid scintillation counter super low-level system with active guard and temperature control modules. The samples were prepared by mixing 15 mL of the sample with 5 mL of Ultima Gold F scintillation cocktail and analyzed for 5 h. The counter was set to count between channels 100–400 to help maximize the signal-to-noise ratio instead of using the full 14C range between channels 5 and 650. The triple mode was used to reduce background noise further. The triple mode only counts photons that hit all three detectors at the same time; this is a unique feature of liquid scintillation counters that contain three photomultiplier detectors. Currently, Hidex liquid scintillation counters are the only commercial LSC instruments having three detectors. Once the samples are mixed, they are placed into the autosampler for a minimum of 1.0 h before running to minimize the chemiluminescence of the sample.


According to the conclusion of the paper, it worked quite well:

The goal of this study was to find a method to measure biocarbon content by 14C analysis that can easily be incorporated into a refinery laboratory, which yields comparable results to AMS, and has biocarbon detection limits between 0.53 and 0.72% depending on sample type. The use of a liquid scintillation counter with TDCR capabilities allows this to be achieved by removing the traditional and tedious sample preparation procedures. For these experiments, the use of a Hidex 300 SL LSC with a 5 h analysis time yielded data with an excellent correlation to AMS. As the absolute error for LSC increases with an increase in biocarbon concentration, method repeatability was calculated for two separate ranges, 0–20 and 20–100%. The calculated repeatability values are the method detection limit for each of the sample sets. For LSC results, the repeatability was calculated to be 0.72, 0.53, and 0.67% biocarbon, respectively, for the gasoline, diesel, and jet fuel standards, for the samples below 20% biocarbon, and for the samples above 20% biocarbon, the repeatability was 1.33, 1.41, and 1.33%, respectively.


Although I oppose fossil fuels, I believe that a possible means to keep some essential self propelled vehicles, rescue vehicles, farm machinery, transport trucking, using thermally reformed biomass (as opposed to fermented biomass such as ethanol as currently produced). This suggests, therefore some useful information, especially to detect cheating by the addition of dangerous fossil fuels after a regulated dangerous fossil fuel phase out, which is urgently necessary.


February 7, 2021

It has always been an American political genius to follow a disastrous Presidency with a great one.

Although I was very pleased to support President Biden, I wondered, at his age, if he was going to have in him to be that kind of President.

Clearly, I need not have been concerned.

It's out of FDR; it's out of Lincoln, and indeed Obama.

February 6, 2021

China opens its 50th nuclear reactor.

Hualong One Reactor Now Operating in China (Darrell Proctor, Power, February 1, 2021.

The first of two new reactors at a nuclear power plant in China has entered commercial operation, becoming that country’s 50th operating reactor, according to the China Nuclear Energy Association (CNEA).

Hualong One is a third-generation pressurized water reactor, developed by China National Nuclear Corp. (CNNC) and China General Nuclear Power. It is the fifth reactor now operating at Fujian Province’s Fuqing Nuclear Power Plant. It began commercial operation on Jan. 30 after being connected to the grid on Nov. 27 of last year. Construction of the reactor began in 2015...

...“This marks that China has mastered independent third-generation nuclear power technology following the United States, France, Russia and others,” CNNC said in a statement on the company’s official WeChat account. The Hualong One units are designed with power generation capacity of 1,161 MW, with a 60-year lifecycle.

CNNC has touted Hualong One as a reactor in which about 90% of the equipment used, including all elements of the core, was made in China. “We must not only export our own nuclear power but also build it according to our own standards, so that we can’t be controlled by others,” chief designer Xing Ji said in a statement...

Coal-fired power accounts for about two-thirds of the country’s generation mix. China capped total coal-fired generation at 1,100 GW last year, though the country still has hundreds of coal plants in its development pipeline.

Net-Zero Carbon Goal

...President Xi in September 2020 announced the country had a goal to cut its net carbon footprint to zero by 2060, but analysts have said coal-fired power is important to the country’s economic recovery after the coronavirus pandemic.


China has built most of its 50 reactors in the 21st century, after a "pause" for Fukushima for "safety." This is amusing: Pretty much every day in China, more people die from air pollution than have died in entirety of the 60 year history of nuclear power operations worldwide.

China's annual death toll from air pollution was reported in 2015 as being 1.6 million deaths per year:

The contribution of outdoor air pollution sources to premature mortality on a global scale (Lelieveld, J., Evans, J., Fnais, M. et al., Nature 525, 367–371 (17 September 2015)

Figure 1: Mortality linked to outdoor air pollution in 2010.
From: The contribution of outdoor air pollution sources to premature mortality on a global scale



The caption:

Units of mortality, deaths per area of 100 km × 100 km (colour coded). In the white areas, annual mean PM2.5 and O3 are below the concentration–response thresholds where no excess mortality is expected.


Despite much world wide attention, it is clear that the famous and much discussed bogeyman at the Fukushima reactors destroyed by a natural disaster did not account for 1/1,000,000th as many deaths as air pollution in China kills each year. Most of the deaths associated, in fact pretty much all of the 20,000 deaths from the earthquake that destroyed the reactors were attributable to drownings from seawater associated with the Tsunami as well as collapsing buildings, thus proving that coastal cities are "too dangerous" and need to be phased out.
February 5, 2021

PPPL's Science on Saturday: Public Perception of Science: Lessons from a Dead Sheep

PPPL's science on Saturday lecture tomorrow morning by Dr Alan Ruben and is entitled Public Perception of Science: Lessons from a Dead Sheep

Dr Ruben's Profile is here on the AAAS website: Adam Ruben

Adam has written the monthly science humor column “Experimental Error” for Science Careers since 2010. He received his bachelor’s degree in molecular biology from Princeton University, where he won the Gregory T. Pope ’80 Prize for science writing, and his Ph.D. in biology from Johns Hopkins University, where he was simultaneously an adjunct faculty member in the Expository Writing program.

Adam performs stand-up comedy and storytelling, and he has appeared on the Food Network, the Weather Channel, Discovery International, and the Travel Channel. He currently co-hosts Outrageous Acts of Science on the Science Channel. He is the author of Surviving Your Stupid, Stupid Decision to Go to Grad School and Pinball Wizards: Jackpots, Drains, and the Cult of the Silver Ball.


Sign up here:

Science on Saturday, on Zoom

Almost always the talks are fascinating. Although, the Princeton Plasma Physics Lab is an National Physics Lab, the talks, while often involving physicists, also include, biologists, geologists, chemists, social scientists, oceanographers, climate scientists, etc.

They are hosted by the charming and fun Dr. Andrew Zwicker, head of science education at the lab, who also moonlights as the Democratic NJ Assemblyman in the NJ Legislature.

In previous years, the talks were held at PPPL with a very nice social hour before hand featuring coffee, donuts (great donuts!) bagels and interesting conversation.

As a result of Covid, the talks have moved to Zoom, they are now accessible around the world. They are held at 9:30 am EST, with a Q&A session after the talks ending usually by 11:30. The talks themselves are about an hour generally.

Check it out!
February 5, 2021

What...Reunification Videos...Reveal About the Trauma of Separated Children.

WHAT VIRAL REUNIFICATION VIDEOS REVEAL ABOUT THE TRAUMA OF SEPARATED IMMIGRANT CHILDREN



If for nothing other than this, Miller and Trump deserve to be hauled before the Hague:

A Guatemalan mother falls to her knees as her seven-year-old daughter walks through the door. They've been separated for 55 days, and the mother is completely overcome with emotion. She embraces her child, rocking her and rubbing her back, openly weeping and speaking to her daughter in Spanish. When she pulls back, the child's face appears somewhat frozen, but she clearly has tears in her eyes; her mother wipes her face with the tissue she has been clutching.

This video from CNN is just one of many that have gone viral in the past couple of months, showing immigrant children and their parents' first reunification after months of separation as a result of the Trump administration's "zero tolerance" policy. Something that is strikingly uniform in each of the videos is the frozen, non-emotional responses of the children as their parents weep over them. One video shows a devastated mother whose toddler continues to crawl away from her as she tries to talk to him and pick him up.

Even to a layperson's untrained eye, these reactions appear to be confirmation of the significant trauma mental-health experts warned would happen as a result of separating children from their adult caregivers.

Karen Johnson, senior director of trauma-informed services at the National Council for Behavioral Health, says that what we're likely seeing in these children's responses is a protective numbing or disassociating. Weeks- to months-long separations have an impact on a child's brain, Johnson says, "which speaks to the urgency to make sure that children do not spend one hour longer than they need to separated from their parents..."



January 31, 2021

Speculations on Covid-19 Vaccine Production Bottlenecks.

The paper I'll discuss in this post is this one: Optimization of Lipid Nanoparticle Formulations for mRNA Delivery in Vivo with Fractional Factorial and Definitive Screening Designs (Kevin J. Kauffman, J. Robert Dorkin, Jung H. Yang, Michael W. Heartlein, Frank DeRosa, Faryal F. Mir, Owen S. Fenton, and Daniel G. Anderson
Nano Letters 2015 15 (11), 7300-7306)

Recently on this website, I described how I cheered up my doctor by relaying to him "war stories" from the scale up of HIV protease inhibitors in the 1990s, of which I am a "veteran" of sorts. It's here: I hope I cheered my doctor up.

This morning I attended a (Zoom) lecture by an astrophysicist at Princeton University Professor Cristiano Galbiaiti who works on neutrino and dark matter detectors which rely on highly purified gases, who used his expertise and knowledge of them to rapidly design a new ventilator that was cheap, easy to manufacture, and proved to be highly effective for the treatment of Covid-19. It obtained the fastest approval, from conception to patient use, of a new medical device by the USFDA, 45 days.

It is an example of how "impractical science," the discovery of neutrinos in space, allows for "practical" innovation, much as the 1960's space program allowed for the development of small portable computers, on which many of us now rely.

If you member, in the early days of Covid, there was a huge shortage of ventilators, and the Canadian government, which funded the design and manufacture of the ventilators, ordered many tens of thousands of these new ventilators, which were delivered. The end result is interesting: There is now an oversupply of them, and the partners working on this project are now working to get Western governments to donate ventilators to Africa, where, predictably, ventilators are still in short supply.

I have to see my doctor again this week, and I decided to look into the manufacturing process of RNA vaccines, so I could further cheer my doctor up, with some more detailed insights into the manufacture of these vaccines, about which I have a sense of regulatory requirements, but not the actual details.

I am not currently in anyway involved in the manufacture of Covid vaccines, but I have had professional conversations about nucleic acid formulations, and have had other conversations relating to, and sometimes supporting, related "lipid nanoparticle" work, notably liposomes. Anything I say in this post will, however, be largely guesswork and should be taken with a grain of salt.

The HIV protease inhibitors are drugs that are considered "peptidomimetics" and they depended on access to certain amino acids as starting materials, in particular cysteine and phenylalanine (depending on the protease inhibitor in question). Since many chemical synthesis steps were involved in converting them into "isosteres" of peptides, these starting materials were unregulated commodity items required only to meet certain specifications subject to somewhat limited specifications.

What was involved was large chemical reactors, performing organic synthesis on a multi-ton scale, in some cases utilizing fairly dangerous reagents. (Phosgene was one.) Ultimately these were utilized to make the "API" - the active pharmaceutical ingredient, the protease inhibitor.

The situation with respect to the API of nucleic acid drugs is somewhat different, I expect.

Nucleic acids, such as DNA and RNA, are self replicating molecules of course, and so in theory, their production can (and does) proceed exponentially. This is the technology behind forensic and commercial (as in "23 and me" and related companies) "PCR" (Polymerase Chain Reaction) technology. It is the design of the nucleic acid that matters.

A nice overview of the design and some information about production of the API can be found in an open source article that is somewhat, but not, I think, overly, technical: The promise of mRNA vaccines: a biotech and industrial perspective. A cool feature of the design of these vaccines, with which I was unfamiliar, is the realization that they not only encode for the immunogen protein of the SARS-CoV-2 virus, the famous "spike" protein, but they also encode for some proteins designed to aid with the transcription of the RNA to generate the proteins.

I really can't say very much intelligent about the scale up of the API and potential bottlenecks, since these are involved more with biological systems than synthetic systems and I personally have far less exposure (mainly osmotic exposure) to these than I do to synthetic systems. I would imagine that the chief bottleneck might be having useful enzymes for transcription from the DNA parent the RNA, as well as nucleic acids themselves, although, as opposed to amino acids, which in living systems have 20 basic components (actually a few more because of "post translational modifications" ) there are only 8 nucleic acids in living cells, making separations more straight forward. I would imagine (but do not know) that these are synthetically available without isolation from natural sources (as are some amino acids) from ribose, deoxyribose (almost certainly obtained by fermentation) and the nucleobases which are readily available commodities lacking stereocenters. I know for a fact, that enzymes, including certainly the enzymes responsible for nucleic acid transcription are readily available from biological fermentation facilities. It is possible there has been some strain on these supplies, but basically a vast infrastructure exists.

So my guess is that the API's are not much of a bottleneck at all, beyond, it would seem, some industrial scale chromatography in at least some steps; I would imagine, perhaps, affinity chromatography, which is much, much cleaner than other types of chromatography, perhaps even at the level of solid phase affinity extraction. (These are all speculations; I have no information.)

My guess is that the real issue, the biggest bottleneck, is the formulating agents.

Nucleic acids are charged species, hydrophilic species, that is they are soluble in water and other polar solvents. All cell membranes, by contrast, are lipids, aka "fats." The basic rule that "like dissolves like" applies, which is why cells like blood cells are able to stay intact; their membranes are insoluble in water. Therefore the trick is to get the charged nucleic acids through the membrane, and into the cell. This requires amphiphilic lipids, which have hydrophobic properties on one end of the molecule, and hydrophilic properties on another end. The most famous of these are soaps, with which everyone is familiar.

In fact, the SARS-CoV-2 virus is coated with a lipid, and this is why soap, regular hand soap, is so effective at inactivating it, since it strips away the lipid layer on which the virus depends.

Fats are readily available from multiple sources, so much so that they have been utilized as fuels, biodiesel, in automobiles and trucks by the so called "renewable energy" industry, which has succeeded in destroying large swathes of Asian rain forest for palm oil plantations in part to make diesel fuel for German cars and trucks.

I want to be clear on something in this context, since I am about to discuss lipids, the amount of palm oil required to make the world supply of Covid vaccines (if palm oil is a basic source at all, which it may not be) will surely be trivial when compared to produce other commodities, including biodiesel and the palm oil utilized in foods. There is really no legitimate rationale for destroying the South Asian rain forests for commercial interests. The very special lipids that are likely utilized in Covid vaccines might have just as easily utilized corn oil as palm oil, since it is likely that the starting materials, saturated and unsaturated straight chain fatty acids are present in both sources, and perhaps other temperate zone agricultural products such as canola oil or soybean oil.

Anyway.

The lipids in question are amphiphilic, but they are very special lipids of a type, which are widely found in living systems, but which are also synthetically complex except by enzymatic routes.

To give a feel for the complexity of lipids beyond the straight chain fatty acids, here is a chart showing types of a class of lipids that are found prominently in skin, the ceramides:



Some of the lipids described in the paper cited at the beginning of this post are isosteric (similarly shaped) to sphingosines.

The key point in this development is the concept of "ionizable lipids," which address the transport of a charged species, RNA, across the lipid membranes of cells.

(At this point, it behooves me to mention a post in this forum by our leader, pointing to the career of a famous lipid chemist in the early days of lipid chemistry: Watch for NOVA's rerun of "Forgotten Genius" in your area ... or watch it online ...

From the introduction to the paper cited at the outset:

Nucleic acids have tremendous therapeutic potential to modulate protein expression in vivo but must be delivered safely and effectively. Because the delivery of naked nucleic acids results in poor cellular internalization, rapid degradation, and fast renal clearance,(1, 2) lipid nanoparticles (LNPs) have been developed to encapsulate and deliver nucleic acids to the liver. Most notably, the field has seen orders-of-magnitude potency advances in the delivery of 21–23 nucleotide-long double stranded small interfering RNAs (siRNAs) due in part to the creation of new synthetic ionizable lipids and lipid-like materials.(2) Whereas some of these novel lipids were synthesized with rational design approaches by systematically varying the lipid head and tail structures (e.g., DLin-KC2-DMA, DLin-MC3-DMA, L319), (3-5) other materials were discovered by creating large combinatorial libraries of lipid-like materials (e.g., C12-200, cKK-E12, 503O13).(6-8) When formulated into LNPs, these amine-containing ionizable lipids and lipid-like materials electrostatically complex with the negatively charged siRNA and can both facilitate cellular uptake and endosomal escape of the siRNA to the cytoplasm.(6, 9) In particular, the ionizable lipid-like material C12-200 has been widely used to make siRNA-LNP formulations for various therapeutic applications in vivo to silence protein expression.(10-12)

In addition to the ionizable material, three other excipients are also commonly used to formulate LNPs: (1) a phospholipid, which provides structure to the LNP bilayer and also may aid in endosomal escape; (2, 13) (2) cholesterol, which enhances LNP stability and promotes membrane fusion; (14, 15) and (3) lipid-anchored polyethylene glycol (PEG), which reduces LNP aggregation and “shields” the LNP from nonspecific endocytosis by immune cells.(16) The particular composition of the LNP can also have profound effects on the potency of the formulation in vivo. Several previous efforts to study the effect of formulation parameters on siRNA-LNP potency utilized the one-variable-at-a-time method,(17, 18) in which formulation parameters were individually varied to maximize LNP potency; this approach, however, does not allow for examination of potentially important second-order interactions between parameters. Inspired by statistical methodologies commonly used in the engineering and combinatorial chemistry literature,(19, 20) we chose to utilize Design of Experiment (DOE) to better optimize LNP formulations for nucleic acid delivery. Using DOE, the number of individual experiments required to establish statistically significant trends in a large multidimensional design space are considerably reduced, which is particularly relevant for the economical screening of LNP formulations: in vitro screens are often poor predictors of in vivo efficacy with siRNA-LNPs,(21) and it would be both cost- and material-prohibitive to test large libraries of LNP formulations in vivo.

To demonstrate the application of DOE to LNP formulation optimization in vivo, we formulated LNPs with a different type of nucleic acid than siRNA. Recently, messenger mRNA (mRNA) has been investigated for therapeutic protein production in vivo, including applications in cancer immunotherapy, infectious disease vaccines, and protein replacement therapy.(22, 23) Unlike plasmid DNA, mRNA need only access the cytoplasm rather than the nucleus to enable protein translation and has no risk of inducing mutation through integration into the genome.(24) Because there are inherent chemical and structural differences between mRNA and siRNA in terms of length, stability, and charge density of the nucleic acid,(25) we hypothesized that LNP delivery formulations for mRNA may require significant variation from those developed for siRNA delivery...


The authors developed a combinatorial approach using chemical libraries (compounds modified and mixed in a controllable but different way) to screen lipid formulations.

There are many hundreds of papers on the topic of lipid particles utilized in nucleic acid drug development, but for this brief post, we'll just look at the pictures produced here, and return to figure one for further discussion:



The caption:

Figure 1. Formulation of lipid nanoparticles. Lipid nanoparticles (LNPs) are synthesized by the mixing of two phases: (1) a four-component ethanol phase containing ionizable lipid, helper phospholipid, cholesterol, and lipid-anchored PEG; (2) an acidic aqueous phase containing mRNA.




The caption:

Figure 2. Efficacy results of LNPs in Libraries A, B, and C. (a) Serum EPO concentration 6 h post-intravenous injection of 15 ?g total mRNA for each formulation in Libraries A and B, including the original formulation (data presented as mean + SD, n = 3). (b) A statistically significant trend of increasing serum EPO concentration was observed with increasing C12-200:mRNA weight ratio and with DOPE phospholipid for Library B formulations, independent of the other formulation parameters. Furthermore, a statistically significant second-order effect was observed between DOPE and increasing weight ratio, as indicated by the larger relative slope of the DOPE best-fit line compared to the DSPC best-fit line. (1 data point = 1 mouse) (c) Serum EPO concentration 6 h post-intravenous injection of 15 ?g total mRNA for formulation B-26 and Library C, which had similar formulation parameters as B-26 with differing C12-200:mRNA weight ratios. (Data presented as mean + SD, n = 3.)


EPO here, is one of the early protein drugs on the market, one that got Lance Armstrong and other athletes busted, the anti-anemia drug erythropoietin, which jacks up hemoglobulin in the blood. The idea here is to insert RNA into cells in such a way that rather than being produced in a reactor, it is produced within the blood itself. (I would imagine that tracing this would make anti-doping efforts somewhat more challenging.



The caption:

Figure 3. Efficacy and biodistribution of original and C-35 formulation with Luc mRNA. (a) Efficacy of original and C-35 LNP formulations synthesized with mRNA coding for luciferase in three organs of interest as measured by total flux from luminescence 6 h after intravenous injection of 15 ?g total mRNA. (Data presented as mean + SD, n = 3). (b) Representative biodistribution image of luciferase expression for original and C-35 LNP in seven organs as measured with an IVIS imaging system 6 h after intravenous injection of 15 ?g of total mRNA.




The caption:

Figure 4. Efficacy of original and C-35 formulation with siRNA. Efficacy of original versus optimized C-35 formulation made with C12-200 and siRNA coding against Factor VII (FVII) protein as measured by serum FVII levels 72 h post-intravenous injection of various doses of total siRNA. FVII levels were normalized with respect to PBS-injected control mice. (Data presented as mean + SD, n = 3.)


The experimental portion of the paper, by the way, describes the synthesis of the mRNA itself that was used in this study; it is very "PCR" like, an exponential growth system. Certainly some clean up is involved, but I suspect this is not a bottle neck.

mRNA Synthesis

mRNA was synthesized by in vitro transcription from a plasmid DNA template encoding the gene, which was followed by the addition of a 5? cap structure (Cap 1) using a vaccinia virus-based guanylyl transferase system. A poly(A) tail of approximately 300 nucleotides was incorporated via enzymatic addition employing poly-A polymerase. Fixed 5? and 3? untranslated regions were constructed to flank the coding sequences of the mRNA.


Now I'ld like to return to figure 1, which I repeat for conveninence, and make some comments.



Without having sourced it myself, I would imagine that cholesterol is easy to get from a variety of sources.

What are interesting are the other three molecules (which may represent classes of molecules in real cases or similar cases).

These I would imagine (and in one case, I know) are chemically synthesized in chemical reactors.

First the "ionizable lipid." There is an element of pseudosymmetry in this molecule, inasmuch as all the long carbon chains are C12, and are almost certainly obtained from lauric acid, the C12 fatty acid, which I know from experience is available in high quality from a number of sources. The core of the molecule is piperazine, the cyclic molecule in the center with two nitrogen atoms in the ring on opposite sides, also a commercially available reagent. Nevertheless, there is symmetry breaking inasmuch as the spacers in the two nitrogens on the piperazine ring have different spacers. This means to make the molecule, one must protect one (and only one) of the nitrogens, which is not entirely straight forward, or otherwise synthesize the ring in such a way that one nitrogen is protected, eliminating the advantage of using very cheap and readily available piperazine. My organic synthesis muscles are no longer strong enough to offer a route off the top of my head to the OH group that is one carbon removed from the amino nitrogens in those side chains, but I'm quite sure if one looks, one can find such a route.

Nevertheless, although very large reactors for making this "ionizable lipid" are certainly available under regulated ("GMP" ) conditions, this would be a bottleneck, if this particular (or a similar) "ionizable lipid" were utilized in formulating either the Moderna or the Pfizer vaccines.

The DSPC is a derivative of phosphocholine, which is found in many foods, notably eggs, and is fact found all over living organisms. In theory it can be made from one of the cheapest industrial chemicals there is, glycerol, a side product of the soap and biodiesel industries which is so cheap that people often dump it rather than sell it if they are far from a facility that uses it. The DSPC is a chiral molecule exhibiting "handedness" (being non-superimposable, like right and left hands). I'm sure that there are lots of enzymatic routes to making phosphocholine, but still, after one has it, one has to acylate the two oxygens with steric acid, also a commodity produced from things like palm oil, corn oil, canola oil...etc...etc. Still one needs a reactor to do this.

Finally there is there is "lipid anchored" "PEG," polyethylene glycol, which is also a derivative of phosphocholine, in fact, it is a derivative of DSPC. It is the PEG side chain that matters. The thing that disturbs me a little bit is the designation, at least in this paper, of a fixed length. PEG in most drugs - it is commonly used in many protein drugs to prevent their rapid breakdown in the body - is a polymer, and generally has a molecular weight distribution centered around a specific molecular weight, and also containing some molecules of higher and some of lower molecular weight. It is generally made by the polymerization of ethylene oxide (oxirane). I would hope that the formulations of the lipids in the vaccines do not actually in real life involve this restriction, since this would be problematic and represent a real bottle neck.

But even if it was...

One of the largest selling drugs in the world for many, many, many years was atorvastatin (Lipitor). It was discovered and initially developed at a company that no longer exists, Parke Davis. Here is the structure of atorvastin:



I was told a story about atorvastatin that I heard; it may or not be true. This drug was developed in the 1980's when industrial chiral synthesis was still somewhat problematic - it was a problem generally solved by the time HIV protease inhibitors came around - but early on it wasn't. I was told that Park Davis felt that atorvastatin would never be a big seller, because it was too expensive to make on an industrial scale, because of the seven carbon side chain with the two hydroxygroups on it, both of which are present as chiral centers. In the early days of scale up of the drug, the cost of the side chain was said to be over $1000/kg in 1980s dollars. I know people who were selling it for $800/kg in the 1990s.

Every chiral organic chemist in the world, both industrial and academic, looked at that side chain and figured that they could make a killing by making it cheaper; everybody in the world was going to get rich making it for $500/kg. Companies were founded on this expectation.

So many people exercised their genius to make the molecule cheaper that it ultimately became a commodity, and everybody was trying to undercut everyone else, because everyone's cheaper route made for an oversupply. I heard, that the cost of the side chain, before the expiry of the Park Davis successor company(ies) (ultimately Pfizer) the side chain was priced well under $100/kg, I heard $50, out of India and China.

So what's the story, morning glory?

Yeah, right now, there are bottlenecks, but they aren't going to last very long. Within a year, maybe sooner, these vaccines are going to be commodities, because, right now, there is clearly intellectual and almost certainly physical infrastructure to do it.

And that's a good thing. In the end, it will come down to logistics and little else.

Cheer up. We have a smart and energetic President who actually gives more than a rat's ass, vastly more than a rat's ass, as opposed to his orange predecessor, and we will beat this thing.

Some suggested further reading:

Martin A Maier, Muthusamy Jayaraman, Shigeo Matsuda, Ju Liu, Scott Barros, William Querbes, Ying K Tam, Steven M Ansell, Varun Kumar, June Qin, Xuemei Zhang, Qianfan Wang, Sue Panesar, Renta Hutabarat, Mary Carioto, Julia Hettinger, Pachamuthu Kandasamy, David Butler, Kallanthottathil G Rajeev, Bo Pang, Klaus Charisse, Kevin Fitzgerald, Barbara L Mui, Xinyao Du, Pieter Cullis, Thomas D Madden, Michael J Hope, Muthiah Manoharan, Akin Akinc, Biodegradable Lipids Enabling Rapidly Eliminated Lipid Nanoparticles for Systemic Delivery of RNAi Therapeutics, Molecular Therapy, Volume 21, Issue 8, 2013,

Dynamic PolyConjugates for targeted in vivo delivery of siRNA to hepatocytes
David B. Rozema, David L. Lewis, Darren H. Wakefield, So C. Wong, Jason J. Klein, Paula L. Roesch, Stephanie L. Bertin, Tom W. Reppen, Qili Chu, Andrei V. Blokhin, James E. Hagstrom, Jon A. Wolff, Proceedings of the National Academy of Sciences Aug 2007, 104 (32) 12982-12987; DOI: 10.1073/pnas.0703778104

Semple, S., Akinc, A., Chen, J. et al. Rational design of cationic lipids for siRNA delivery. Nat Biotechnol 28, 172–176 (2010). https://doi.org/10.1038/nbt.1602

Many, many, many more papers may be found by calling these papers up in Google Scholar, and clicking on the citations list.

I hope you will have a safe and enjoyable Sunday.

January 30, 2021

Has anyone here ever eaten a fruit called Durian?

I'm catching up on my reading, and I came across a paper titled thus: Food Waste Durian Rind-Derived Cellulose Organohydrogels: Toward Anti-Freezing and Antimicrobial Wound Dressing (Xi Cui, Jaslyn Lee, Kuan Rei Ng, and Wei Ning Chen, ACS Sustainable Chemistry & Engineering 2021 9 (3), 1304-1312).

It contains this text:

Durian is a fruit which is famous all over the world, especially in Southeast Asia as its name is “king of the fruits”. Durian is popular for its special flavor and high-quality nutrients, which could afford health benefits for the human body. However, less than a half part of the entire durian is edible, while the other parts (rind and seeds) are treated as food waste in the durian industry.(18) Durian residues (rind and seeds) are usually used in landfills or burned, which pose a serious problem to the environment and, in the meantime, are also a waste of the natural resource. Durian rind is composed of 31.6% cellulose, 15.5% hemicellulose, and 10.9% lignin in dried durian rind.(19) The content of cellulose in durian rind is larger than that in okara,(20) which makes durian rind a sustainable cellulose resource for hydrogel fabrication, and this can also help reduce the environmental pollution.


Famous all over the world?

Serious problem to the environment?

Never heard of Durian...

Anyone?
January 30, 2021

PPPL Science on Saturday: From studying the Sun, to searching for dark matter, to fighting Covid.

PPPL's science on Saturday lecture tomorrow morning by Princeton University Professor Professor Cristiano Galbiaiti giving a talk entitled: From studying the Sun, to searching for dark matter, to fighting COVID-19

Sign up here:

Science on Saturday, on Zoom

Almost always the talks are fascinating. Although, the Princeton Plasma Physics Lab is an National Physics Lab, the talks, while often involving physicists (as tomorrow's will), also include, biologists, geologists, chemists, social scientists, oceanographers, climate scientists, etc.

They are hosted by the charming and fun Dr. Andrew Zwicker, head of science education at the lab, who also moonlights as the Democratic NJ Assemblyman in the NJ Legislature.

In previous years, the talks were held at PPPL with a very nice social hour before hand featuring coffee, donuts (great donuts!) bagels and interesting conversation.

As with Covid, the talks have moved to Zoom, they are now accessible around the world. They are held at 9:30 am EST, with a Q&A session after the talks ending usually by 11:30. The talks themselves are about an hour generally.

Check it out!

Profile Information

Gender: Male
Current location: New Jersey
Member since: 2002
Number of posts: 33,517
Latest Discussions»NNadir's Journal