NNadir
NNadir's JournalWho feels in this election like Jodie Foster in the dark near the end of "Silence of the Lambs?"
Electric Dreams/Follow Your Heart.
The apparent annual low at the Mauna Loa CO2 observatory was in the week beginning 09/20/20.
As I've indicated many times in this space, I somewhat obsessively keep a spreadsheet of the weekly data for concentrations of the dangerous fossil fuel waste carbon dioxide as recorded at the Mauna Loa Carbon Dioxide Observatory. I use this spreadsheet 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.
Generally I post about milestones, all of which are unfortunate milestones, since nothing effective at all is being done about climate change anywhere. On the right, climate change is met with denial of its existence; on the left, the supposition is that tearing up pristine wildernesses and lacing them with roads to service wind turbines made with oil based plastic, coal based steel, copper, neodymium, dysprosium is doing "something." It isn't. Neither is the questionable practice of generating vast amounts of future electronic waste to make solar cells, doing anything. (The chemistry of solar cells is about to get worse, not better, with the rise of lead based perovskite solar cells.)
The data, which is a physical measurement, and thus a fact, clearly shows the reality. Facts matter.
Each year, although the general trend is rising at an ever increasing and alarming rate, the data follows a sinusoidal trajectory, a wave recorded on a slightly non-linear (and increasingly parabolic) monotonically rising axis. This graph, from the Mauna Loa site, which I have reproduced here many times before shows how this looks:
Atmospheric CO2 at the Mauna Loa Observatory.
Earlier this year, I reported prematurely, several times, the annual peak in carbon dioxide concentrations, each of which was an all time record concentration, only to see a larger peak reached after a minor decline after the previous peak. The data was noisy, which is not entirely surprising. Temporary annual peaks were reached, only to be followed by brief declines, for the weeks beginning April 5, 2020, April 19, 2020, and May 3, 2020 before reaching the final maximum on May 24, 2020, which was a concentration 417.43 ppm. This figure will remain the all time record until late winter or early spring of next year, 2021, when 417.43 ppm will surely be surpassed before reaching an even more depressing maximum around May of 2021. This is, again, because we are doing nothing effective to address climate change other than to cheer for the destruction of wilderness, vast mining enterprises, many of which involve human tragedy, and cheering for so called "renewable energy," oh, and Elon Musk's electric cars for distracted and oblivious bourgeois types who don't want to hear anything about cobalt mines in the Congo region, as they rain on the "Green" parade.
History will not forgive us; nor should it.
There has been a lot of speculation and some wishful thinking that the Covid crisis would slow carbon dioxide accumulations. The folks at the Mauna Loa Observatory have a nice note addressing people who have been asking them about this:
Can we see a change in the CO2 record because of COVID-19?
The evidence for a Covid "slowing" might be represented by the fact that the 2020 peak, again, 417.23 ppm was "only" 2.04 ppm higher than the 2019 peak, which was recorded on May 12, 2019 as 415.39 ppm. Such a figure for much the 20th century would have been terrifying, but in the 21st, where we have lots of wind farms, it's rather um, encouraging, at least in the Overton window of carbon dioxide changes. It is worth noting that the record 417.43 figure was, however, 24.80 ppm higher than the figure recorded in the same week ten years earlier, 2010.
There have been eight times in all recorded history at Mauna Loa, going back to the 1960s, where the comparisons, week to week, with data recorded 10 years earlier, have equaled or exceeded 25.00 ppm, for a rate equal to or greater than 2.5 ppm/year. Five of them occurred in 2020, our wonderful Covid year, and the other three were in 2019, including the 2019 maximum, 415,39 ppm, which was 25.27 ppm higher than the figure for the same week of 2009.
Don't worry. Be happy. Elon Musk's Tesla stock is doing very well.
This brings me finally to the annual minimum for 2020: It was recorded on the week beginning September 20, 2020.
The value was 411.00 ppm.
In comparison to the annual minimum of 2019, which was recorded during the week beginning September 29, 2019 and was 407.96 ppm, it is 3.04 ppm higher.
In recent times the East Coast of Australia was devastated by vast fires; on the West Coast of the United States was similarly devastated. Record heat waves have been recorded around the world, and if one looks closely at death statistics, one can see that these heat waves kill people. Increasingly powerful hurricanes slam into population centers around the world, including the United States, causing billions upon billions of dollars in damage. The use of oil, natural gas, and coal has been rising throughout the 21st century, despite all kinds of delusional wishful thinking. Air pollution deaths vastly exceed Covid-19 related deaths, although much attention is paid to the latter and little to the former.
Yet, I'm told, frequently, by nominally liberal people - for me liberalism is involved in caring about human suffering wherever it exists - that nuclear power is "too dangerous."
Famously, the famous climate scientist, Jim Hansen, calculated that even while being vilified as "too dangerous," nuclear power prevented the dumping of more than 30 billion tons of the dangerous fossil fuel waste carbon dioxide and saved almost two million lives: Prevented Mortality and Greenhouse Gas Emissions from Historical and Projected Nuclear Power (Pushker A. Kharecha* and James E. Hansen Environ. Sci. Technol., 2013, 47 (9), pp 4889–4895)
Yet, it's "too dangerous" in the minds of some people.
Go figure.
Compared to what?
If we want to do something it will not be enough simply to defeat the racist, uneducated. uninformed, criminal currently living in the White House. On the contrary, it will take a good hard look at ourselves, and our own dogmatic beliefs, because we are decidedly not immune from ignoring facts.
Facts matter.
I trust you are having a pleasant and safe autumn weekend.
In new proposed Florida voting machines, pushing the red button is easiest.
Florida To Experiment With New 600-Lever Voting Machine
Driving through NE PA, Trump country, I saw a great anti-Trump sign.
It read, "Make Orwell fiction again."
It may be my favorite.
I also saw a quite impressive numer of Biden signs, quite impressive given the area.
I feel better politically than I have in years.
The Chairwoman of the SUNY Stony Brook Chemistry Dept Running Against a Trumper...
...for Congress.
This is a note in the high impact scientific journal Science: In New York, chemist Nancy Goroff is battling a Trump loyalist for a seat in Congress
It should be open sourced, as it's a news item.
An excerpt:
A physical organic chemist and longtime faculty member at Stony Brook University, Goroff will face off in November against Representative Lee Zeldin (R–NY), a lawyer seeking his fourth term. If she wins, Goroff would become the first female Ph.D. scientist to serve in Congress.
Running in a Long Island district that voted for Donald Trump in 2016 after twice backing Barack Obama for president, the first-time candidate is touting her scientific credentials.
“As a scientist, I look at things differently than the way politicians do,” Goroff says in one ad. Referring to the pandemic, she adds, “I’m running for Congress to use my science to lead us out of this crisis...”
...Along with many of her academic peers, Goroff stepped up those advocacy efforts after Trump took office in January 2017. She participated in both the Women’s March the day after his inauguration and the People’s Climate March in April, although professional obligations prevented her from attending the March for Science 1 week earlier. But she didn’t join the cluster of scientists running as part of what turned out to be a successful attempt by Democrats to regain control of the U.S. House of Representatives.
“I had just started as department chair [in January 2017] after stepping down as interim dean of the graduate school, and I was focused on how to make the university a better place,” she says.
Still, she didn’t like where Trump was taking the country, and she was also troubled by the growing power of social media to amplify false messages and distort civic discourse. In the aftermath of the November 2018 midterm elections, she says, “I felt that it was time to put in a full effort and try to be part of the solution...”
It was my privilege here in New Jersey to have a scientist as a Congressperson, Representative Dr. Rush Holt, until he retired. He was, by far, the best congressperson I have ever had in my entire life, and not just because he was a scientist, but because he was also an outstanding human being. I didn't agree with every position he took, but I always felt that his positions were considered and honorable. He was an (unsuccessful) pioneer in addressing the rising issue of election integrity when he was in Congress.
I grew up in Suffolk County, on Long Island. It's suburban redneck country, fairly right wing, although there is some potential for decency there, and a few times, I recall that Democrats actually won a few elections, not many but a few.
SUNY Stony Brook is a fairly decent university, not quite the UC Berkeley it was founded to be, but a pretty good school over all.
I wish Professor Goroff all the success in the world. May she succeed in her effort to win the election.
Synthetic connectivity, emergence, and self-regeneration in the network of prebiotic chemistry
The paper I'll discuss in this post is this one: Synthetic connectivity, emergence, and self-regeneration in the network of prebiotic chemistry (Wołos et al., Science 369, 1584 (2020) eaaw1955.
I was inspired to spend some time with this (full) paper by another post in this group, specifically this one: A New Chemical 'Tree of The Origins of Life' Reveals Our Possible Molecular Evolution (ScienceAlert) (Thank you eppur se muova!)
When I was a kid, planning an organic synthesis was largely a "seat of the pants" undertaking; one would look at a structure, and try to figure a series of disconnections that were available to bond formation using synthetic reactions of various types - the more you knew, the better you were able to plan these things - and one would talk to friends, advisors, bosses and also spend a long time in the library in the complex pathways to various leather bound "chemical abstracts" and their various kinds of indexes, find the relevant abstract, then search for the bound issue of the journal, only, often, to find that the particular paper was not the one you actually needed to accomplish the task. You'd work your way back until you had a plan using readily available starting materials.
Sometimes, your plan would actually work so far along the line, and you'd get ambitious and scale up, and then a flask would break, and boom...the pain...the pain...the pain...
You really had to think a lot in those days, and also consider the risks of wasting valuable materials.
You really had to think, and certain things had to be second nature.
Here's a problem, I pulled out of an old "exercise book," Ranganathan and Ranganathan, Academic Press, 1980, for problem 124. pg 42, on my bookshelf: The problem asked to propose a mechanism for the reaction that converted compound #4 into compound #10:
The paper, Chemistry of Santonic Acid. Oxidative and Reductive Modifications (Hortmann and Daniel, J. Org. Chem. 1972, 37, 26, 4446–4460) of course, gives an answer to the problem, a mechanism that seems quite reasonable, but the point of the exercise is to work it out yourself before being prodded by the paper.
Imagine someone asked you to make compound 10 with almost no information, other than what you learned in school? It's not too obvious...
This nice presentation, from K.C. Nicolaou shows classic "disconnection" thinking: [link:https://nicolaou.rice.edu/ppt_lectures/12_GERMANY_GENERAL.pdf|Total Synthesis of Natural Products of Biological
and Medicinal Importance]
It's been 30 years, maybe, since I planned a full synthesis; my career took a different path, but those were the "good old days." (Obviously not Lindsay Graham "Good Old Days" Up yours Lindsay.)
But when I was a kid, we used to go, like kids going to a big rock concert, to lectures by E.J. Corey, or D.H.R Barton, or Barry Trost, or K.C. Nicolaou or Roald Hoffman...
...sigh... Life is fun and then you die.
There are now, I'm sure a large number of computational programs to help design syntheses, and in fact, the paper referenced above, is about prebiotic chemistry, where the starting materials are simply the common "prebiotic" molecules spread across space. These programs probably use connectivity matrices of some kind or another - I don't know - my knowledge of programming is primitive at best, and to be honest, it's been decades since I thought about connectivity matrices.
I'm not sure if the link give more than the simple abstract or what is called the "structured abstract," to non-subscribers but the "structured abstract" has this conclusion:
Computer-generated reaction networks are useful in identifying synthetic routes to prebiotically relevant targets and are indispensable for the discovery of prebiotic chemical systems that are otherwise challenging to discern. As our network continues to grow by means of crowd-sourcing of newly validated prebiotic reactions, it will allow continued simulation of chemical genesis, beginning with molecules as simple as water, ammonia, and methane and leading to increasingly complex targets, including those of current interest in the chemical and pharmaceutical industries.
So there you have it...
The "structured abstract" includes this graphic:
The caption:
Computer simulation of plausible prebiotic reactions creates a network of molecules that are synthesizable from prebiotic feedstocks and establishes multiple unreported—but now experimentally validated—syntheses of prebiotic targets as well as self-regenerating cycles. In this schematic illustration, light blue nodes represent abiotic molecules, dark blue nodes represent molecules along newly discovered prebiotic syntheses of uric and citric acids, and red nodes represent other biotic molecules.
From the introduction:
Allchemy’s “Life” module uses 614 reaction rules (“transforms”) involving C, O, N, S, and P elements, grouped within 72 broader reaction classes. Inclusion of these rules in our set is contingent on the existence of literature-described examples that document their execution under generally accepted prebiotic conditions...
The authors, however, dodge the elephant in the room, chirality:
The authors begin their task by running the alchemy program for two hours on a "standard laptop computer," using a network of reactions that involved only carbon, hydrogen, oxygen, and sulfur and which limited the molecules "discovered" in silico to those with a molecular weight of less than 300 Daltons. This generated tens of thousands of molecules, 82 of which were "biotic," which they define as consisting of the following classes of molecules: "...amino acids and peptides, nucleobases and nucleosides, carbohydrates, and metabolites..."
Again, to beat a dead horse, lacking chirality, the molecules are only weakly "biotic" in nature as I see it, and remain so without the spontaneous generation of chirality through either kinetic or other means.
In this paper, the captions are rather long and pretty much tell much of the story:
Fig. 1 Biotic and abiotic molecules in the networkof prebiotic chemistry:
The caption:
Another graphic:
Fig. 2 The network’s molecular content and synthetic connectivity.
The caption:
The authors note that the elimination of some classes of reaction classes does not necessarily preclude arriving at the full or nearly full set of biotic molecules as a generated in the full sized class reactions, whereas removing sets of reaction classes has a fairly profound effect on the the number of abiotic molecules generated.
Interestingly, the software is said to find new pathways to biotic molecules.
Fig. 3 Examples of known and newly identified syntheses within the network of prebiotic chemistry.
Now it gets interesting, because was is discussed is an abiotic example of something that characterizes many metabolic processes, cyclic reactions, the most famous of which is the citric acid (Krebs) cycle.
Reference 10 is this paper:
Synthesis and breakdown of universal metabolic precursors promoted by iron. (Muchowska, K.B., Varma, S.J. & Moran, J. Nature 569, 104–107 (2019))
And finally, there is the issue of catalysis, which, to return to a point I made earlier, may include asymmetric catalysis.
We first discuss the finding that compounds created within the network can themselves act as catalysts of additional chemical reactions, all operative under prebiotic conditions, thereby substantially expanding the accessible prebiotic chemical space. To show this, we queried the network for known organocatalysts or bi- and tridentate metal chelators capable of binding metal cations present on primitive Earth [e.g., Cu(II), Zn(II), and Mn(II) (40)] and also used in modern organometallic catalysts. Figure 4A lists eight such catalysts enabling different reaction types and collectively more than doubling the size of the network. All of these reactions were previously carried out under prebiotic conditions (41–48), but their relevance to OL was unnoticed.
Fig. 4 Chemical emergence in the network of prebiotic chemistry.
The caption:
IDA here is imidodiacetic acid, which is a derivative of the simplest amino acid, glycine, a "Siamese" glycine if you will. This molecule is an excellent chelator of metals, and as such, can coordinate metals which may act as catalysts.
The cyclic reaction detailed in the next figure, includes IDA in its pathway.
Fig. 5 Emergence of self-regenerating cycles within the network of prebiotic chemistry.
The caption:
The final piece of the puzzle is lipids, which of course make up cellular membranes, both for cells themselves and for intracellular organelles.
The caption:
Finally, the third class of emergence was the formation of surfactant molecules capable of spontaneously forming vesicles that could potentially house reactions and systems such as those described above. As illustrated in Fig. 6A, straight-chain saturated fatty acid and ?-hydroxy acid surfactants can form through repeated four-step cycles of aldehyde homologation. Breaking the cycle, the last step of fatty acid synthesis, may then occur via nitrile or thioamide hydrolysis to carboxylic acid. The aldehyde homologation cycle was proposed by Patel et al. (8) as a prebiotic method to make hydrophobic amino acids, but its straightforward extension to fatty acid surfactants was not noted in that report. In another and synthetically much shorter approach, peptide surfactants with variable glycine or alanine tails and aspartic acid head groups are available within only a few synthetic generations. Previously, such peptides had been synthesized by modern, nonprebiotic synthetic methods and had been shown (in the context of nanotechnology, not OL research) to form nanotubes and nanovesicles (64).
Fig. 6 Biomimetic routes to surfactants and additional pharmaceutically relevant scaffolds.
The caption:
The authors consider, in conclusion that their work may not only assist in approaching the intellectually satisfying question of the origins of life, but may well have practical import as well.
I voted. It feels good to get it done, even if my son is going to "cancel my vote."
One of my happiest memories as a child is when my parents would drive back from voting - they always took me along - and my mother, a swing voter, would tell my father that she "canceled his vote," by voting for the Democrat.
In the good old family tradition, my oldest son announced he would be "cancelling my vote."
All three of us here at home, and the son away who will be voting in PA, are voting straight Democratic for all candidates, from Biden/Harris on down, but I voted against all three ballot initiatives on the NJ ballot, including the one that would legalize marijuana.
I don't believe that people should go to jail for possessing, smoking or even (privately) growing it, but I don't want legal pot stores here.
My son was a little upset with me and gave me the "alcohol is worse than pot" lecture that one hears, and while I'm not sure that the premise of that argument is wrong, I retorted that pancreatic cancer is worse than breast cancer, but this doesn't support an argument to make breast cancer easier to get. (To my knowledge, he has never smoked pot, but I don't want to make it easier for him to try.)
(He didn't like that.)
But the important point is that both my wife and dropped our ballots in the special drop boxes NJ has distributed, and there's two more votes for Joe and Kamala, and for the rest of the Democratic ticket, and two more to go from my family, my vote cancelling son and my "no pot on the ballot" son in PA.
I feel great!
Editors of the prestigious scientific journal Nature endorse Joe Biden!
Nature has been very active recently - for a very clear reason - in encouraging scientists to get political. Now there's this, another unprecedented US Presidential endorsement from a major scientific journal, following NEJM:Why Nature supports Joe Biden for US president.
On 9 November 2016, the world awoke to an unexpected result: Donald Trump had been elected president of the United States.
This journal did not hide its disappointment. But, Nature observed, US democracy was designed with safeguards intended to protect against excesses. It is founded on a system of checks and balances that makes it difficult for a president to exercise absolute power. We were hopeful that this would help to curb the damage that might result from Trump’s disregard for evidence and the truth, disrespect for those he disagrees with and toxic attitude towards women.
How wrong we turned out to be.
No US president in recent history has so relentlessly attacked and undermined so many valuable institutions, from science agencies to the media, the courts, the Department of Justice — and even the electoral system. Trump claims to put ‘America First’. But in his response to the pandemic, Trump has put himself first, not America.
His administration has picked fights with the country’s long-standing friends and allies, and walked away from crucial international scientific and environmental agreements and organizations: notably, the 2015 Paris climate accord; the Iran nuclear deal; the United Nations’ science and education agency UNESCO; and even, unthinkable in the middle of a pandemic, the World Health Organization (WHO).
Challenges such as ending the COVID-19 pandemic, tackling global warming and halting the proliferation and threat of nuclear weapons are global, and urgent. They will not be overcome without the collective efforts of the nation states and international institutions that the Trump administration has sought to undermine.
On the domestic front, one of this administration’s most dangerous legacies will be its shameful record of interference in health and science agencies — thus undermining public trust in the very institutions that are essential to keeping people safe...
...Joe Biden must be given an opportunity to restore trust in truth, in evidence, in science and in other institutions of democracy, heal a divided nation, and begin the urgent task of rebuilding the United States’ reputation in the world.
I'm quite sure it's open sourced, and the full endorsement can be read at the Nature website.
The outcome of world history very much depends on this election. As the job of the scientist is to engage with reality, to analyze it, to report it, and indeed to predict outcomes, these actions by the premier journals of the scientific community are of paramount importance.
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