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An interesting discourse on the biological marine sulfur cycle.

The paper I'll discuss in this post is this one: The metabolite dimethylsulfoxonium propionate extends the marine organosulfur cycle (Kathleen Thume, Björn Gebser, Liang Chen, Nils Meyer, David J. Kieber & Georg Pohnert, (Nature Volume 563, pages 412–415 (2018))

When I was a kid, one of my first professional successes in the lab involved the hydrophobic amino acid methionine, which is one of two of the 20 proteogenic amino acids (21 if one counts bacteria) for which genetic codons exist. Methionine is one of two members of this class which contains sulfur, the other being cysteine.

The role of cysteine, a thiol, in proteomics is spectacular, since its oxidative interaction with other cysteines in proteins is responsible for disulfide bridges without which many proteins would be useless, lacking the requisite geometry, and almost equally important, its role in metal co-ordination at catalytic centers of very important proteins. Methionine, a thioether rather than a thiol is far more rare in proteins, although it is important in the transfer of methyl groups in biological interactions and it has recently been discovered that interactions with the π systems in phenylalanine, tyrosine and - who knows - histidine also serve to stabilize protein geometry. Bacterial methionine biosynthesis (Ferla and Patrick, Microbiology (2014), 160, 1571–1584).

I am also interested in the chemistry of sulfur, because my generation failed all future generations by turning out planetary atmosphere into a vast waste dump for the dangerous fossil fuel waste carbon dioxide, and I am always thinking about ways that future generations can clean up our mess, and do so with a functionally destroyed resource base consisting almost entirely of our solid phase garbage dumps. One path to removing carbon dioxide from the atmosphere is to essentially reverse combustion by making the source of carbon materials - now made from dangerous fossil fuels - carbon oxides obtained by the thermal reformation (gasification) of waste (or problematic) biomass, using nuclear energy as the primary energy source. These technologies are being widely explored but a consistent factor that engineers must address is the fate of heteroatoms in biomass like potassium, sodium and, relevant to this discussion, sulfur.

Finally the paper cited at the outset of this post caught my eye because I always wonder about the environmental fate of common laboratory chemicals - one of which is dimethylsulfoxide - a wonderful solvent with wide use - and also because of my interest in stable charged organic species that play a role in a rapidly developing area of chemistry, ionic liquids.

So the paper itself:

From the abstract:

Algae produce massive amounts of dimethylsulfoniopropionate (DMSP), which fuel the organosulfur cycle1,2. On a global scale, several petagrams of this sulfur species are produced annually, thereby driving fundamental processes and the marine food web1. An important DMSP transformation product is dimethylsulfide, which can be either emitted to the atmosphere3,4 or oxidized to dimethylsulfoxide (DMSO) and other products5...

So it turns out that DMSO, which is used in some products for joint pain, is a normal biological species, present in the oceans on what may be a million ton scale. (I had a neighbor - to whom I stopped speaking years ago - who called me up to ask me if he could sue his employer because they asked him to work with this chemical, but that's another story.) That makes me feel better about all the DMSO I've used - or asked scientists working for or with me to use - in my career, for solvation, Swern oxidations, blah, blah, blah...

From the introduction to the paper:

The marine organosulfur cycle is fuelled by small sulfur-containing zwitterionic osmolytes that are primarily produced by planktonic algae. The main metabolite of this class, DMSP, is produced in the impressive amounts of 2 petagrams (2 × 109 tons) sulfur annually1. Cellular DMSP serves important physiological functions in marine algae that include, but are not limited to, acting as an osmolyte, a cryoprotectant and an antioxidant6,7. Enzymatic lysis of DMSP by DMSP lyases in bacteria and algae yields acrylate and dimethylsulfide (DMS)8. Volatile DMS is the main source of organosulfur in the atmosphere; and with an annual flux of approximately 30 teragrams of sulfur3, DMS has been proposed to affect cloud formation and regulate climate4. Dissolved DMSP arising from exudation, grazing, viral lysis and cell mortality serves as substrate for marine microorganisms7,9,10. In surface waters, substantial quantities of dissolved DMSP and DMS can be detected, but often the concentration of dissolved DMSO exceeds the concentration of each of these two species5,11. DMSO is mainly produced from bacterial and photochemical DMS oxidation12, but algal sources of DMSO may also be important13 The marine organosulfur cycle is fuelled by small sulfur-containing zwitterionic osmolytes that are primarily produced by planktonic algae. The main metabolite of this class, DMSP, is produced in the impressive amounts of 2 petagrams (2 × 109 tons) sulfur annually1. Cellular DMSP serves important physiological functions in marine algae that include, but are not limited to, acting as an osmolyte, a cryoprotectant and an antioxidant6,7. Enzymatic lysis of DMSP by DMSP lyases in bacteria and algae yields acrylate and dimethylsulfide (DMS)8. Volatile DMS is the main source of organosulfur in the atmosphere; and with an annual flux of approximately 30 teragrams of sulfur3, DMS has been proposed to affect cloud formation and regulate climate4. Dissolved DMSP arising from exudation, grazing, viral lysis and cell mortality serves as substrate for marine microorganisms7,9,10. In surface waters, substantial quantities of dissolved DMSP and DMS can be detected, but often the concentration of dissolved DMSO exceeds the concentration of each of these two species5,11. DMSO is mainly produced from bacterial and photochemical DMS oxidation12, but algal sources of DMSO may also be important13. Common pelagic bacteria use monooxygenases to oxidize DMS to DMSO14, a process that may serve as an energy source15. Here we report on the identification of the zwitterionic metabolite DMSOP, which is widely distributed in phytoplankton and also produced by marine bacteria. This metabolite is the substrate of a previously undescribed marine pathway for DMSO production (Fig. 1) .

It's probably now time to just look at the pictures the authors use to describe their "zwitterionic" species. (A zwitterion is a molecule that possesses, in the same molecule, both a positively and a negatively charged ion. The important physiological molecule carnitine is an example of a zwitterion.)

A picture:

The caption:

DMSOP and the transformations labelled with red arrows extend the established marine sulfur cycle. DMSOP is produced in eukaryotic microalgae (green) as well as in bacteria (purple). Bacteria metabolize DMSOP and therefore contribute to the marine DMSO pool. The established DMSP-based part of the sulfur cycle is indicated with grey arrows. DMSP is formed by marine algae and bacteria. It is then cleaved by algal and bacterial DMSP lyases to DMS and acrylate (not shown). The subsequent biological and photochemical oxidation of DMS to DMSO, sulfate and other products can occur within algae, bacteria, in the seawater and the atmosphere.

A picture describing some of the techniques they used to find out about DMSOP:

The caption:

a, Chromatographic profile of zwitterionic metabolites from a P. minimum culture, separated using ultra-high-pressure liquid chromatography (UHPLC) with detection by electrospray ionization mass spectrometry (ESI-MS). The total ion current is shown in grey. The metabolites glycine betaine (GBT, cyan), dimethylsulfonioacetate (DMSA, orange), DMSP (black) and gonyol (blue) were assigned according to a previous study16. The ion trace of DMSOP, red, is shown at a tenfold magnification. b, Synthesis of authentic (labelled) DMSOP. c, Mass spectrum and tandem mass spectrum (inset) of DMSOP with characteristic fragments. d, UHPLC profile monitoring m/z = 151 of an extract of P. parvum (solid line) and the same extract treated with synthetic DMSOP in roughly equal amounts (dashed line), the experiment was repeated three times with varying concentrations of synthetic DMSOP to confirm co-elution.

Biosynthetic pathways:

The caption:

a, High-resolution mass spectrum of DMSOP obtained from P. bermudensis incubated for 24 h with 13C2-labelled DMSP (Fig. 2). The peak labelled in red represents 13C2-labelled DMSOP, the natural DMSOP isotopes are shown in black (see also Extended Data Table 3). b, c, DMSO release (concentration (c) given as mean ± s.d.) of the bacteria Sulfitobacter sp. and R. pomeroyi incubated with 1 µM DMSOP. P values directly over bars indicate significant difference from t = 10 min of the same treatment, P values over brackets indicate significant difference between treatment and the control without DMSOP addition. n = 4 independent biological replicates for 24 h, n = 3 for 10 min and 5 h, for statistical details see Methods.

From the conclusion:

Our results demonstrate that the ubiquitous zwitterionic metabolite, DMSOP, contributes to the marine DMSO pool and may partly account for DMSO in marine algae13. In light of our findings, a functional role of DMSP as an oxygen acceptor is probable and could explain numerous observations of DMSP regulation under oxidative stress. Algal and bacterial DMSOP biosynthesis and its bacterial degradation to DMSO represent a previously undescribed pathway for DMSO production, extending our current paradigm of the marine sulfur cycle beyond the established biotic and photochemical pathways through DMS oxidation

Esoteric things like this are actually very important, particularly in light of the disturbance to the sulfur cycle represented by the rapidly increasing use of dangerous fossil fuels as we all wait, like Godot, for the grand "renewable energy" "revolution" that never comes.

I wish you a very pleasant weekend, and hope your Thanksgivings plans are proceeding nicely.

Science candidates prevail in US midterm elections.

I had the privilege of having a Congressperson who was a scientist - Rush Holt - until he retired. Before being elected to Congress, Dr. Holt was the Assistant Director of the Princeton Plasma Physics labs.

While I didn't always agree with everything he said or did, overall he was a magnificent congressperson, the best Congressperson I ever experienced by orders of magnitude, which is not to say that his replacement, Bonnie Watson Coleman is a bad Congressperson, only that Rush Holt was the best, by far.

He should have been our Senator, but didn't come close in the only race he entered; won by Corey Booker; Rush wasn't flashy, just solid, decent, extremely intelligent, thoughtful, concerned with justice, open, helpful and responsive.

(For the record, the worst Congressperson I ever had was Randy "Duke" Cunningham, who happily went to prison directly from Congress.)

My tempered joy aside, it appears that our new congress will include several scientist/legislators. From Nature:

Science candidates prevail in US midterm elections (Jane J. Lee,
Amy Maxmen, Jeremy Rehm & Jeff Tollefson Nature 563, 302-303 (2018))

The results of the political experiment are in. At least 11 candidates with backgrounds in science, technology, engineering or medicine won election to the US House of Representatives on 6 November — including several who had never before run for political office.

They include Elaine Luria, a US Navy veteran and nuclear engineer in Virginia, and Chrissy Houlahan, a former business executive with a degree in engineering, in Pennsylvania. Illinois saw wins by registered nurse Lauren Underwood, a former senior adviser to the Department of Health and Human Services, and clean-energy entrepreneur Sean Casten, who has degrees in engineering and biochemistry.

The four — all Democrats — are among roughly 50 candidates with science backgrounds who ran for the House in 2018, sparked in part by opposition to President Donald Trump. Fewer than half of these novice politicians made it past the primaries to the general election, but many science advocates are already looking to the next campaign cycle.

“I’m feeling good,” says Representative Bill Foster (Democrat, Illinois), a physicist who has pushed to increase the number of scientists in elected office. Foster, the only current member of Congress with a science PhD, is excited about wins at the state and local levels by candidates with backgrounds in science, technology, engineering or medicine (STEM).

I am personally pleased to see a Democratic nuclear engineer elected, which is why I bolded her discipline in the excerpt above. If I have any difficulty with my fellow Democrats, it is with those who promote what I regard as our creationism, anti-nukism, which marks us a climate change hypocrites, too prevalent in the party to which Nobel Laureate Glenn Seaborg proudly belonged - he headed the AEC when most of our life saving nuclear infrastructure was built - is finally going the way of other anti-science stuff one hears, anti-vax, anti-GMO, etc., etc, that have also represented poisoned wings of our party.

We have no hope, absolutely no hope, of addressing the most severe environmental crisis experienced by human civilization without nuclear energy. I'm glad someone's there who can understand this.

If there's any civil lining on the reign of the orange naked emperor, it is that his attacks on science have raised awareness among scientists of what the stakes are, a new dark and poisoned age, or an age in which knowledge and intellect triumph.

Congrats to our new STEM scientist/congresspeople.

2018 World Energy Outlook: Solar and Wind Grew by 11.24% in 2017; Gas by "Only" 3.32%!!!!

We're Saved!!!!

Right? Right?

I have before me a PDF of the World Energy Outlook for 2018, which was released by the International Energy Agency yesterday.

I also have opened a PDF of the World Energy Outlook for 2017, which I have discussed in many threads in this space.

The data I will discuss here is collected from World Energy Outook 2018, Table 1.1 Page 38 and, for World Energy Outook 2017, Table 2.2 Page 79.

In each case, the data refers to the year before the title year, that is WEO 2018 refers to 2017's data; WEO 2017 refers to 2016. (In earlier editions of the WEO, the lag was 2 years and not 1 year, but reporting has apparently grown quicker.)

These tables give values in "MTOE," or "Million Tons Oil Equivalent." In my discussion, as my habit, all data will be converted to the SI unit the Exajoule, except of course, that wonderful "percent talk" used here by people who still believe that it was a good idea to bet the future of every generation to come, the climate, the planetary atmosphere on so called "renewable energy."

The tables break so called "renewable energy" into three categories, hydro, bioenergy, and "other," "other" referring to solar and wind primarily, with a little tidal and geothermal presumably thrown in. In the title of this post I have ignored tidal and geothermal - which I know to be trivial with respect to solar and wind.

In 2016, "other" renewables, again chiefly solar and wind, produced 9.42 exajoules of energy. In 2017, they produced 10.63 exajoules. In "percent talk" this represents the growth of 11.42% as described in the title. In terms of energy, the growth, which can be found by using an operator called "subtraction" was 1.21 exajoules. In 2016 dangerous natural gas produced 125.90 exajoules of energy; in 2017 it produced 130.08 exajoules. In "percent talk" this represents a growth of 3.32% as described in the title here. Of course, in absolute terms, dangerous natural gas grew by 4.19 exajoules.

In "percent talk," gas thus grew 100 * 4.19/1.21 = 345% faster than wind and solar combined.

Overall, world energy consumption grew from 576.10 exajoules in 2016 to 584.98 exajoules in 2018, or 8.88 exajoules.

World energy consumption thus grew 8.88/1.21 * 100 = 731% faster than solar and wind.

What I personally regard as the only sustainable form of energy on the planet, albeit an unpopular form of energy, nuclear energy, grew by 0.29 exajoules, or only 0.29/1.21 * 100 = 24% as fast as solar and wind.

The mistake of confusing what is popular with what is right is known as the logical fallacy of appeal to popularity or at other times the "Bandwagon Fallacy."

The example in the link just presented of the "Appeal to Popularity" fallacy is this:

A 2005 Gallup Poll found that an estimated 25% of Americans over the age of 18 believe in astrology—or that the position of the stars and planets can affect people's lives. That is roughly 75,000,000 people. Therefore, there must be some truth to astrology!

In the last ten years, 2.3 trillion dollars has been "invested" in solar and wind energy:

Frankfurt School/UNEP Global Renewable Energy Investment, 2018, Figure 3, page 14

This is more than the gross national product of India, a nation with 1.3 billion people in in it.

On the planet as a whole, 2.3 billion people lack access to any kind of improved sanitary facilities; but no one is going to spend 2.3 trillion dollars to change that, not while we can all dream of solar and wind powered Tesla electric cars.

For the Week Ending November 4, 2018 (Accessed 11/14/18) the concentration of the dangerous fossil fuel waste carbon dioxide in the planetary atmosphere as measured at the Mauna Loa observatory was 406.99 ppm. In the same week 10 years ago, the concentration was 383.80 ppm.

No one now living will ever see a measurement at this site of below 400 ppm again, no matter how many miles Bill McKibben drives in his Prius with a "350.org" bumper sticker on it.

We have not been saved by the 11.24% growth in solar and wind in 2017, and are not being saved by it, and no such "percent talk" announcements in the future will represent us being saved.

We are clueless.

Facts matter.

Have a nice day tomorrow.

A Device For Air Capture of Carbon Dioxide Which Regenerates at Waste Heat Temperatures.

Events in the United States and Brazil - and in fact, practically everywhere else on Earth - in the last few years assure that every living being on Earth is going to face increasing catastrophe from climate change.

Coupled deliberate indifference by politicians, again notable in the US and Brazil, is the idiotic and unworkable misplaced but popular faith in so called "renewable energy" - which is neither "renewable" nor sustainable - that is often incorrectly described as "doing something" about climate change.

We are doing nothing about climate change.

Future generations will need therefore to find a way to clean up our mess, and do so with far reduced resources, because in our contempt for all future generations, we have been consuming vast amounts of resources for quixotic things like wind turbines and electric cars, as well as a lot of other consumer junk.

To clean up our mess, the only option for these future generations from whom we've stolen, well, everything will be - and it is an incredibly difficult engineering challenge - air capture of carbon dioxide.

About 7 years ago, a controversial but much discussed paper on the energetics and thermodynamics of air capture was published, which at least put the challenge in perspective. It is here: Economic and energetic analysis of capturing CO2 from ambient air, (House et al PNAS, 108, 51 20428–20433, 2011). It drew a negative conclusion about the possibility of doing this, by exploring an estimations the costs of various technologies for doing this:

CO2 cost per ton (House PNAS 108 51 20428–20433 2011):

Advanced nuclear: $286/ton

IGCC CSS: $666/ton

Gas CC CCS: $388/ton

Wind (land): $369/ton

Wind Offshore: $598/ton

Solar PV: $1,030/ton

Solar Thermal: $686/ton

Biomass: $580/ton

Hydroelectricity: $299/ton.

It is possible to hydrogenate carbon dioxide to make gasoline. I covered this topic elsewhere (in a place where I was banned for telling the truth): How Much Gasoline Could Hydrogenation of ONE Coal Plant's Waste Produce?

Using a similar calculation of cost, I have calculated - using 2,4 dimethylpentane as the model gasoline compound - what the cost of the carbon atoms in gasoline might translate in familiar terms in the US, dollars per gallon. (Note this does not include the internal and external costs of producing hydrogen and thus is only a fraction of the real cost of gasoline would be in this case. These costs would be, respectively, using the figures above:

$2.32/gallon, $5.40/gallon $3.15/gallon $2.99/gallon $4.85/gallon $8.36/gallon $5.57/gallon $4.71/gallon $2.43/gallon.

The House paper has been criticized in the same journal on the grounds that the analysis relied on a narrow focus on technology.

Another paper in the same journal argued that air capture is essential; it MUST BE DONE.

I personally agree with the last paper's claim, if the future generations from whom we've stolen everything are to save anything left to be saved.

Thus I was entranced by a recent publication in one of my favorite scientific journals, this one: The Development and Validation of a Closed-Loop Experimental Setup for Investigating CO2 and H2O Coadsorption Kinetics under Conditions Relevant to Direct Air Capture (Jovanovic, Ng, and Yang, Ind. Eng. Chem. Res., 2018, 57 (42), pp 13987–13998.

I have convinced myself that the only sustainable option for providing the energy for this extremely challenging engineering task is nuclear energy, although I'm not convinced that the "advanced nuclear" House describes is really suitable for the task. Few details are provided directly in the paper about the kind of nuclear energy that constitutes "advanced nuclear" in House's paper, but I suspect it involves an electricity intermediate energy form, which, in my view, is unnecessary and wasteful. Carbon dioxide and water splitting by thermochemical means involves high temperatures, and high temperatures, although increasing thermodynamic efficiency, imply the rejection of heat to the environment. To the extent that this waste heat can be partially captured to do useful things, like say, capture carbon dioxide and release it in a concentrated form available for use, it can be environmentally attractive. Hence my interest in the Jovanovic paper where the regeneration of the absorbent occurs at a relatively low temperature, 95C, temperatures which would be relatively accessible for very high temperature nuclear reactors being utilized to either split carbon dioxide or water or both.

From the introduction to the Jovanovic paper:

Over the past decades, the emission of CO2 to the atmosphere has been increasing at an alarming rate. To mitigate the resulting adverse greenhouse-effect, significant effort has been dedicated to the sequestration of CO2 from large anthropogenic point-sources such as fossil fuel-based power plants.1 However, in order to reduce the CO2 concentration in the atmosphere to the target of 350 ppm,2 it appears necessary to also capture a part of the CO2 already dispersed in the atmosphere as a product of fossil fuel combustion in the transportation sector.3 Compared to the atmospheric CO2 removal methods such as afforestation, increase of cloud alkalinity, and promotion of phytoplankton growth in the oceans, it has been suggested that direct air capture (DAC) poses the lowest risk to radical ecosystem alteration.4 Furthermore, the success at efficient, large-scale CO2 capture from air may provide a source of a clean syngas exploiting process concepts under development for (i) combined CO2 and H2O splitting5 or (ii) reverse water gas shifting of renewable H2 6 that compete with the biomass gasification for commercially viable production of renewable transportation fuels.7

The paper is rather detailed and involved, but it may be useful to look at the pictures to get a feel for it:

The caption:
Figure 1. Schematic diagram of the CLDB setup. The sections outlined by the (blue) dashed and (green) dash-dotted lines represent the gas/sorbate supply manifold and the closed-loop test-rig, respectively. The (red) dotted lines indicate the gas flow direction during the adsorption experiments.

The caption:
Figure 2. (a) Disassembled and (b) assembled sample holder with the gas flow direction indicated by the yellow arrows and main components as follows: (1) PTFE gasket, (2) sorbent bed, (3) coiled stainless steel tube, (4) thermocouple, (5) upper flange, (6) KF clamp, (7) lower flange.

The caption:
Figure 3. Schematic of the tracer study setup.

The caption:
Figure 4. Comparison between the experimental and calculated CO2 mole fractions at the outlet of the tank assuming CSTR flow pattern. The zoom-in plots in panels b and c indicate error bars determined by the accuracy of the IRGAout.

IRGA stands for infrared gas analysis. CSTR = continuous stirred-tank reactor

The caption:
Figure 5. CO2 equilibrium loadings measured in TGA and CLDB setup under T = 35 °C. The solid line represents the Toth adsorption isotherm (eq 13) fitted to the TGA-determined equilibrium loadings.

The caption:
Figure 6. Effect of gas flow rate on the (a) CO2 and (b) H2O uptake profiles obtained with 30 mg of the sorbent under Tads = 30 °C, xCO2,0 = 1000 ppm, and RHads,0 = 50%. Larger fluctuations seen in Figure 6b are attributed to the inherently larger noise in xH2O measured with the IRGA.

The caption:
Figure 7. Sorbent bed temperature profiles recorded during the
experiments compared in Figure

The caption:
Figure 8. Amine-functionalized NFCs with the particle diameters of (a) 10 mm, (b) 4−5 mm, and (c) 1−2 mm

The caption:
Figure 9. Effect of sorbent particle diameter on (a) CO2 and (b) H2O uptake profiles obtained with 69 mg of the sorbent under ṅ = 0.074 mol· min−1, Tads = 25 °C, xCO2,0 = 6000 ppm, and RHads,0 = 50%.

The caption:
Figure 10. Sorbent bed temperature profiles recorded during the experiments compared in Figure 9. Note: the temperature of the dp = 10 mm particle was recorded with the thermocouple inserted into the sorbent particle while the remaining temperature sets were recorded with the thermocouple placed between the sorbent particles

The caption:
Figure 11. Leakage induced-relative errors of (a) CO2 and (b) H2O uptakes. The gray areas indicate the range of interest where adsorption kinetics are extracted.

Some excerpts from the text:

2.4. Data Analysis. The species j has an instantaneous adsorption rate rj (t) represented by the time derivative of the mass specific sorbate molar loading qj (t)

with qj (t) calculated from the temporal gas-phase species balance

where nj(t) and msorb represent the instantaneous sorbate amount in the gas phase within the closed-loop and mass of sorbent, respectively. The sorbate amount present in the gasphase can be determined using the ideal gas law if the sorbate mole fraction xj and the system pressure P, volume V, and temperature T are all known. Assuming the CSTR flow pattern in the tank and the plug flow through the reminder of the loop, xj is assumed uniform throughout the entire closed-loop. However, the pressure and temperature both vary within the loop due to the pressure drop in pipes, gas compression by the pump, and the lack of temperature control outside of the tank. To account for these nonuniformities in P and T, the closedloop was divided in several compartments as described in section S5 of the SI to calculate nj(t) as

where R is the universal gas constant and subscript “i” designates different compartments involved in the analysis. Note that the calculations of nj(0) and nj,(t) do not account for the exact same compartments, because the sorbate mixture bypassed the sorbent bed before the adsorption (see SI)...


The mixing of the gas in the tank was assessed by imposing a continuous tracer input into the tank and then comparing the experimental CO2 tracer mole fractions at the outlet of the tank with those calculated based on the assumption that the gas in the tank was perfectly mixed (CSTR condition). As the experimentally observed uniformity of the gas temperature and pressure within the tank implied that

the tracer material balance for the CSTR condition, that is, assumption that the CO2 composition in the tank is uniform and equal to that at the tank outlet, reduces to

In eqs 4 and 5, ntank designates the total amount contained within the tank and subscripts “in” and “out” indicate the quantities at the inlet and the outlet of the tank, respectively.

From the conclusion:

This paper presents development of a closed-loop setup for dynamic CO2 and H2O coadsorption on amine-functionalized NFC under conditions relevant to direct air capture. The setup, based on a differential sorbent bed placed outside of a perfectly gas mixing tank, allows for measuring the coadsorption kinetics in the absence of external heat and mass transfer effects that are commonly encountered in thermogravimetric analyzers and packed-bed reactors...

...The setup presented in this work can be readily implemented to determine the adsorption kinetics on other sorbents developed for similar applications as well as kinetics of some gas−solid catalytic or noncatalytic reactions. The design and validation methodologies presented in this paper can serve as a reference for the development of batch experimental setups for measuring adsorption/reaction kinetics free of the intrusions by heat and mass transfer.

The turn of events surrounding climate change are depressing because, in my opinion, even many of the people who get remain hostile to the only viable solution which necessarily will involve nuclear energy, but also require huge advancements in chemical technology and chemical and materials science engineering.

I will be gone from this planet soon enough, and I do not really expect, at my age, that things will really get better, but if they do, the work performed and published here, and thousands of examples more like it, written by scientists working in relative obscurity and enduring some popular contempt, will lead the way.

That it exists makes me feel a little better.

Have a wonderful weekend.

When the worst President in US history was in office, a tall, lanky, fun guy lost a Senate election.

He ran because an insanely racist Supreme Court made rulings that tore the country apart.

He lost, relatively narrowly, to Steven Douglas, racist, because he held locally unpopular opinions, but his espousal of these opinions garnered national attention.

Two years later, he was elected President of the United States, replacing the man considered, at least until recently, to be the worst President in US history, James Buchanan.

I am, of course, referring to Abraham Lincoln, Senate loser in 1858, who came to the 1860 convention as everybody's second choice for President, with the exception of some party leaders in his home state, Illinois, where he was the first choice.

The rest is history.

Just saying...

In case you ever find yourself looking for a monograph on the physics of bubbles, here it is.

Some time ago in this space, I wrote about Lord Rayleigh, at the height of his fame pausing to write a paper about what happens when water boils in a kettle: I just stumbled into a very old paper by "Lord Rayleigh" contemplating water boiling in a pot.

Lately I've been wondering about the physics of bubbles, specifically an unusual case, the physics of a bubble containg metallic gases formed from one or two or more immiscible metals appearing in a viscous liquid phase of another metal. Three metals have extraordinarily long liquid ranges: Gallium, plutonium and neptunium, the boiling points of the latter two having not been subject to direct laboratory measurement but rather inferred by extrapolation of their vapor pressures. (A great deal of plutonium was vaporized in the planetary atmosphere in the late 1940's, all through the 1950's and through much of the early 1960's, with smaller amounts having been so vaporized in rarer cases thereafter: It's still here.)

In the case where we consider doing something practical about reversing currently observed degradation of the climate - not that popular opinion shows even a trace of interest in reality - this situation might be of extreme importance: In liquid plutonium (or liquid neptunium) actively undergoing fission several volatile or potentially volatile metal gases are formed as fission products, notably cesium, rubidium, strontium and barium, as well as several inert gases, xenon, krypton and in proliferation proof plutonium, considerable helium. All of these elements are insoluble in liquid plutonium. Although this same volatility represented the greatest risk associated with the events at Fukushima and Chernobyl - it is also certainly conceivable to technologically exploit this very same process to do certain things, which might well take too long to describe.

Anyway, it took me a long time to locate a general monograph focused specifically on bubble dynamics, but finally I found and obtained one. This is it: Acoustic Cavitation and Bubble Dynamics.

There's two whole sections on Rayleigh's work on bubbles. Here's an excerpt on section 2.1, "Rayleigh–Plesset Equation."

A typical cavitation bubble is filled with vapor and non-condensable gas such as air. The pressure inside a bubble is higher than the liquid pressure at the bubble wall due to surface tension [1, 2]. The surface tension (r) is the surface energy per unit area and is 7.275 10^(−2) (N/m) (= J/m^(2)) for pure water at 20 °C. For a spherical bubble with a radius R, the surface energy is 4σπR^2 because the surface area is 4πR^2...

The next section is on "Rayleigh collapse."

As an aside, my son had the grace to inform me that I've been mispronouncing Rayleigh's name my entire and overly long life by the way, as well as the pronunciation of Auger's name in "Auger electrons" since both scientists' work has relevance to his undergraduate research.

I appreciate that. I'm amazed no one ever corrected me on this score before, either because they assumed I was too stupid to correct or that they had pity on the fact that I was born in Brooklyn.

You may never have any interest in the physics of bubbles; most people don't, and I didn't for much of an overly long life, but in case you do, here's a shortcut to avoid spending as much time as I did to find a comprehensive monograph on the subject of bubbles.

Have a nice day tomorrow.

Open racists running for the school board in Hamilton NJ.

This is what we've come to with a racist President and a racist Congress working to legitimize racism:


Update on the annual death toll from air pollution.

There are certain links I just keep on file for use here when discussing the external costs - costs to the environment and to human health - of our continued and rapidly growing use of dangerous fossil fuels.

Here is the link I routinely produce whenever I'm discussing hot topics like, um, Fukushima and/or Chernobyl and/or Three Mile Island, none of which actually matter, on scale:

A comparative risk assessment of burden of disease and injury attributable to 67 risk factors and risk factor clusters in 21 regions, 1990–2010: a systematic analysis for the Global Burden of Disease Study 2010 (Lancet 2012, 380, 2224–60: For air pollution mortality figures see Table 3, page 2238 and the text on page 2240.)

The actual figures given in the table are:

For ambient (outdoor) particulate matter: 3,223,540 deaths in 2010, with the uncertainty expressed as a range, (2,828,854–3,619,148).

For household (indoor) solid fuels (primarily "renewable" biomass but also some coal): 3,478,773 deaths in 2010; the uncertainty range, (2,638,548–4,386,590)

Ozone: 152,434 deaths in 2010, uncertainty range, (52,272–267,431).

The overstated precision in these figures is annoying, somewhat ameliorated by the error bars, but nonetheless, I think the data represented an excellent estimate.

I generally in my arguments rounded up to 7 million air pollution deaths per year.

The Global Burden of Disease surveys are an ongoing project funded by the Gates Foundation, and more recent figures have been published, but lazy person that I am, I haven't been using the more recent version.

The most recent full report from the Global Burden of Disease survey was published in 2016.

It is here:

Global, regional, and national comparative risk assessment of 79 behavioural, environmental and occupational, and metabolic risks or clusters of risks, 1990–2015: a systematic analysis for the Global Burden of Disease Study 2015 (Lancet 2016; 388: 1659–724)

The new report suggests that deaths from "renewable" biomass have actually fallen to 2,854,000 deaths per year from the previously reported figure from the 2012 study's report of 3,478,773 deaths. This improvement undoubtedly is tied to some success in the UN Global Sustainable Development Goals, which includes, among other things, improved stoves for indoor use by poor people.

It is surely the case that "development" has involved the displacement of indoor solid fuel combustion with the use of dangerous fossil fuels. If this offends you, I submit you are offended by reality. Even in the case where the change involves improved stoves with elaborate modern devices like, um, chimneys, the effect is still to move indoor pollution to outdoor pollution: The latter is suggested by an increase in the death toll related to outdoor particulate air pollution, which has risen to 4,241,000 deaths, as compared to 3,223,540 deaths reported in the 2012 study which refers to 2010.

Ozone deaths have risen to 207,000.

I can still round down to 7 million deaths per year. This is a holocaust every year, more or less, and every decade, more deaths than all deaths, combat, bombing, starvation, genocide etc than recorded in all of World War II for all countries involved.

We couldn't care less.

The death toll from what is sometimes represented as the only energy disaster to actually matter, particularly by people with their heads up their asses, Fukushima, does not appear in this list of causes of global mortality, probably on the grounds, realistically, that on scale, it doesn't matter.

Nuclear energy saves lives. Another bit I link often:

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)

I wish you a wonderful weekend and hope that you will vote next week. It has never been more important, with the possible exception of the 1864 election. My vote is already in, straight Democratic, although I had to abandon some principles to vote for one local Democrat, but did it anyway.

I wish I could vote, by the way, for the environment, rather than simply against racism, ignorance and fear, but I can't. Neither political party in this country actually gets it, though more on our side do than on their side do. It's small comfort but President Obama for instance, once appointed Steven Chu to be Secretary of Energy, a role in which he served with the great intelligence one would expect from a Nobel Laureate. Dr. Chu tried, but he didn't get there. Presidents Kennedy and Johnson essentially gave Nobel Laureate Glenn Seaborg effective cabinet rank.

I still can believe in hope and change. More serious than anything that happens on Tuesday though is the condition of our planet, whether anyone gets it or not.

Toward a sustainable materials system

I've been thinking all week about CO2 capture from air as a route for future generations to address our failure to do anything significant about the climate beyond praising even more consumer junk, like electric cars and solar cells.

I've been going over the aging, but still interesting - if controversial - PNAS House paper, Economic and energetic analysis of capturing CO2 from ambient air, (PNAS, 108, 51 20428–20433, 2011) poking around references and citations and I came across this short, non-technical and thoughtful commentary in a recent issue of Science; it's open sourced:

Global annual resource use reached nearly 90 billion metric tons in 2017 and may more than double by 2050. This growth is coupled with a shift of materials extraction from Europe and North America to Asia. In 2017, 60% of all materials were extracted in Asia, and extraction is expected to rise substantially in Africa over the next decade. Local extraction and processing helps to improve standards of living in the developing world, but also leads to important environmental concerns. Globally, materials production and consumption is coming up against environmental constraints in almost every domain, including species biodiversity, land-use change, climate impacts, and biogeochemical flows. Mitigating the impact of materials use is urgent and complex, necessitates proactive assessment of unintended consequences, and requires multidisciplinary systems approaches.

Materials consumption trends provide context to inform strategies for impact mitigation. Beginning in the mid-1950s, there has been a shift from biomass or renewable materials to nonrenewable substances, such as metals, fossil fuels, and minerals. Effective strategies for mitigating their impacts are different for high-volume materials with structural applications than for specialty materials with functional uses...

Toward a sustainable materials system Elsa A. Olivetti, Jonathan M. Cullen (Science 29 Jun 2018: Vol. 360, Issue 6396, pp. 1396-1398)

Well worth a read...

Interrogating the Development of Ant Castes with Interfering RNA.

The paper in the primary scientific literature I'll discuss in this post is this one: Social regulation of a rudimentary organ generates complex worker-caste systems in ants (Ehab Abouheif et al Nature Volume 562, pages 574–577 (2018))

I have a decent understanding of the molecular biology of proteins, including the remarkable nuclear proteins that choreograph the behavior the behavior of DNA, the highly conserved - because they're optimized across species - four histones of chromatin. Lipid chemistry is highly complex and important, but it's fairly easy to wrap one's head around it without too much effort; I've had to think about lipids a lot in my life time and seldom feel intimidated when I have to do so. Sugars, because of their complex stereochemistry and their large arrays of functional groups are often beyond me, but to the extent I have been involved with them, it's all been pretty much about N,O glycosylation of proteins, which sometimes plays a huge role in proteomics, but, well, I can generally get by by looking at the pictures and the schematics. I actually don't know too many experts in sugar chemistry because there aren't all that many synthetic sugar drugs, although there are indeed sugar based drugs on the market: In fact, one of the oldest drugs commercialized, digoxin, is technically a glycolipid. The absence of sugar drugs is probably a function of the difficulty of sugar chemistry. I'm always amused by this excerpt from a wonderful text on sugar chemistry, especially the lines I have bolded here: The Sugar Code that reads:

Teaching the biochemistry of carbohydrates is not simply an exercise in terminology. It has much more to offer than commonly touched upon in basic courses, if we deliberately pay attention to the far-reaching potential of sugars beyond energy metabolism and cell wall stability. In fact, then there is no reason why complex carbohydrates should shy at competition with nucleic acids and proteins for the top spot in high-density biocoding. On the contrary, sugars have ideal properties for this purpose, as will be concluded at the end of this chapter. In this sense, an obvious explanation why research in glycosciences (structural and functional glycomics and lectinomics) has lagged behind the fields of genomics and proteomics, also in the public eye, is 'that glycoconjugates are much more complex, variegated, and diffiailt to study than proteins and nucleic acids' [1]. What is a boon for decorating cell surfaces with a maximum number of molecular messages at the same time has been and still is a demanding challenge for analytical and synthetic chemistry

In other words, people shy away from sugar chemistry because sugar chemistry is hard.

This text also suggests that the biochemistry of the nucleic acids is better understood because it's easier.

Well perhaps...

There are, now, a few drugs on the market that are in effect nucleic acids or modified nucleic acids, in particular anti-sense compounds. Also a major gene insertion product has been approved, Luxturna which cures a certain type of blindness with a single dose. By the way drugs which cure diseases have more economic difficulty than maintenance drugs like blood pressure pills and statins which only address symptoms or prevent - so long as they are continually used - disease. Luxturna represents an interesting ethical case, because I believe that a single dose - the only dose ever needed - to the eye costs close to a million dollars.

Anyone who has worked in a lab in a research capacity knows about the long path of training and education, long hours, disappointment after the acquisition of expensive and rare materials, the danger, the cost. I can only imagine the work that went into making Luxturna into a marketed product - the cost - the fear that the product would fail, the terror at looking at results and traveling to regulatory meetings. If one knows this, one finds that scientists deserve to be paid, but on the other hand, if someone is blind and can be cured of blindness, one also feels that it should be done for free.

(I don't have an answer for this conundrum, but I do know that tax breaks for shitheads like the orange President and his family at the expense of the rest of the world's population is criminal.)


On a superficial level, there is a beautiful simplicity to nucleic acids, with only five core building blocks in contrast to the 20 core building blocks of proteins (if one ignores post-translational modifications like the arginine -> ornithine or citrulline, etc, etc and bacterial codons for things like selenomethionine, phosphorylation, etc, etc and the aforementioned glycosylations.)

However, this superficial understanding conveys very little of the complexity of nucleic acid biochemistry; one of the great discoveries of recent times and applicable to the nature/nuture issue (or perhaps the "exposiome" ) is the marvelous complexity revealed in epigenetics.

This said, I have a very superficial working knowledge of these compounds and some of the experimental notes in the paper cited at the outset on ants inspires me to learn more - since there are parts of the nuts and bolts that I'll excerpt here that are clearly beyond me.

I don't know about you, but I find social insects, as problematic as some species are - yellow jackets and carpenter ants come to mind - fascinating. Before I knew any science whatsoever beyond the very primitive concepts discussed in elementary school in my time, I recall spending hours upon hours just watching sugar ants; sometimes feeding them just to watch them work.

The abstract of the nature paper refers to this wonder:

The origin of complex worker-caste systems in ants perplexed Darwin1 and has remained an enduring problem for evolutionary and developmental biology2,3,4,5,6. Ants originated approximately 150 million years ago, and produce colonies with winged queen and male castes as well as a wingless worker caste7. In the hyperdiverse genus Pheidole, the wingless worker caste has evolved into two morphologically distinct subcastes—small-headed minor workers and large-headed soldiers8. The wings of queens and males develop from populations of cells in larvae that are called wing imaginal discs7. Although minor workers and soldiers are wingless, vestiges or rudiments of wing imaginal discs appear transiently during soldier development7,9,10,11. Such rudimentary traits are phylogenetically widespread and are primarily used as evidence of common descent, yet their functional importance remains equivocal1,12,13,14. Here we show that the growth of rudimentary wing discs is necessary for regulating allometry—disproportionate scaling—between head and body size to generate large-headed soldiers in the genus Pheidole...

The authors explore the developmental molecular biology of the development of soldier ants pretty much from the very same genome of minor worker ants and for that matter, winged ants, queens and drones.

Soldier ants have big heads - and even if General Bonespurs in the White House is a long standing coward with an absurdly big head and thus is no soldier - in soldier ants big heads and powerful jaws are important in defending the colony from attack. The authors note that the soldier ants also have vestigial wings that minor worker ants lack and they explore the origins of this anatomical feature and its relation to big heads.

They do this by shutting off the expression of some genes by using interfering RNA on the messenger RNA produced by the DNA of the organism at different developmental phases. Interfering RNA is RNA that is complementary to expressed RNA and thus can interact with it forming double stranded (ds) RNA - as opposed to the functional single stranded RNA - thus blocking its ability to direct protein synthesis and ultimately function.

...We tested this possibility in Pheidole hyatti by targeting vestigial (vg), which in Drosophila is a selector gene that coordinates growth and patterning of wing imaginal discs and is necessary and sufficient for wing development18,19,20. Spatial expression of vg is similar in P. hyatti and Drosophila—in embryos vg is expressed in wing primordia and the ventral nerve cord, but in larvae vg expression could be detected only in the wing discs of winged castes and in the rudimentary forewing discs of soldiers (Fig. 2b–d and Extended Data Fig. 3a–o). We therefore used RNA-mediated interference (RNAi) to knockdown vg expression in soldier-destined larvae (Fig. 2a, red arrowhead)...

Some pictures from the text:

The caption:

a, Caste determination in Pheidole at three developmental switch points produces: winged males, winged queens, wingless minor workers and wingless soldiers. Points of experimental manipulation are indicated by coloured arrowheads: red, soldier-destined larvae; orange, bipotential larvae; green, male-destined larvae. JH, juvenile hormone. b–d, vg expression (purple) in larval wing discs of males or queens (b), minor workers (c) and soldiers (d). Black asterisk, absence of rudimentary wing disc. Scale bars, relative scale. e–f, Rudimentary forewing discs after yfp RNAi (control RNAi) (e) or vg RNAi (f). Rudimentary wing disc presence (white arrowheads) or absence (white asterisks). g, Comparing ratio of log(rudimentary forewing disc area (μm2)) to log(leg disc area (μm2)) (log(WD (μm2))/log(LD (μm2))) between control RNAi (n = 13) and vg RNAi (n = 16). The box plot shows mean (+), interquartile range (bars) and minimum to maximum values (whiskers); all points represent individual ants. Two-tailed Mann–Whitney U-test, U = 24, ***P = 0.0002. h, Wild-type minor worker and representative individuals treated with control RNAi or vg RNAi. i, Comparing slopes of control RNAi (n = 23) and vg RNAi (n = 35); analysis of covariance (ANCOVA), F = 38.1, degrees of freedom (d.f.) = 54, P < 0.0001. Experiments were repeated at least three times. j, Wild-type minor worker and treated individuals with either rudimentary forewing disc or leg disc ablated. Red asterisk, ablated leg. k, Comparing slopes of leg disc (n = 16) and rudimentary forewing disc ablations (n = 16); ANCOVA, F = 8.74, d.f. = 28, P = 0.0063. Image comparisons are to scale. Experiments were repeated at least twice. All regressions are x axis (log(body length (μm)) versus y axis (log(head width (μm)).

The caption:

Manipulations are on soldier-destined larvae. Rudimentary wing disc presence (arrowheads) or absence (asterisks). a, b, Comparing rudimentary wing disc size after no inhibition (100% minor workers) (a) and high inhibition (100% soldiers) (b). c, Comparing ratios of log(rudimentary forewing disc area (μm2)) to log(leg disc area (μm2)) between 100% minor workers (n = 18) and 100% soldiers (n = 23). The box plot shows mean (+), interquartile range (bars) and minimum to maximum values (whiskers); all points represent individual ants. Two-tailed unequal variance t-test, t = 5.77, d.f. = 36.13, ****P < 0.0001. d, Wild-type minor worker and representative individuals raised by 100% minor workers or 100% soldiers. e, Comparing slopes of 100% minor workers (n = 24) and 100% soldiers (n = 35); ANCOVA, F = 36.55, d.f. = 55, P < 0.0001; x axis (log(body length (μm)) versus y axis (log(head width (μm)). Image comparisons are to scale. Experiments were repeated at least three times.

A nice cartoon:

The caption:

a, Interactions (arrows and lines) may be direct or indirect. Green arrows, activation; dashed green arrows, potential pathways to disproportionate scaling; red arrows and lines, inhibition; grey arrows, social interactions; grey circle, rudimentary forewing discs; grey boxes, wing gene network. b, Experimental manipulations (red) and controls (black) in P. hyatti. c, Wild-type C. floridanus workers29 (n = 179). d, Wild-type S. geminata workers30 (n = 239). Plots in b–d show log(body length (μm)) or log(scape length (μm)) on the x axis, versus log(head width (μm)) on the y axis. f, Comparison, to scale, of wild-type minor worker, large minor worker anomaly (XMW), wild-type soldier and supersoldier-like anomaly (XSD).

And now some experimental text that is frankly over my head, but inspires me to learn more - I've ordered several texts from various libraries:

Isolation of vestigial homologues

Forward: 5′-TATCCTTACCTKTAYCARACCC-3′ and reverse: 5′-GCTGACTATTCCAAAAGGARGG-3′ degenerate primers were designed based on a vestigial sequence alignment of Tribolium castaneum (XM_008201106), Apis mellifera (XM_001122002.4) and several ant species obtained from the Ant Genome Portal database (http://hymenopteragenome.org/ant_genomes/). P. hyatti RNA was isolated using TRIzol (Invitrogen) from a pool of embryos and larvae of different developmental stages. RNA was then reverse-transcribed to synthesize a cDNA library. PCR amplicons were ligated into the pGEM-T easy vector (Promega) and subsequently sequenced (MH683613) using Sanger sequencing at the Genome Quebec Innovation Centre at McGill University. To determine whether these vestigial sequences—including the TONDU/vestigial domain—are conserved, amino acid alignment was performed using Geneious Alignment on Geneious (R8), followed by manual alignment (Supplementary Fig. 2)...

...emi-quantitative reverse-transcription PCR of vestigial transcripts in P. hyatti
vestigial expression in wild-type terminal P. hyatti larvae was determined through the detection of vestigial transcripts using semi-quantitative PCR with reverse transcription (Extended Data Fig. 3 and Supplementary Fig. 1). The housekeeping gene Elongation factor 1 alpha (EF1a) was used as our reference gene because it has previously been validated as a reference gene for quantitative PCR with reverse transcription in social insects45. Therefore, EF1a was first cloned and sequenced (MH683615) from a P. hyatti cDNA library using the following degenerate primers: forward 5′-GATTCYGGCAAGTCGACCA-3′ and reverse 5′-GGAACTCTTGGAAAGCCTCAAC-3′. The PCR product was sequenced using Sanger sequencing at the Genome Quebec Innovation Centre at McGill University. To extract RNA, three minor worker larvae and three soldier larvae at the terminal stage were collected from a laboratory colony and total RNA was extracted from minor workers and soldiers separately. The tissue was disrupted using a TissueLyser (Qiagen) bead mill and RNA was extracted using the TRIzol (Invitrogen) RNA extraction protocol46, and then purified using the RNeasy Plus Kit (Qiagen). Minor worker and soldier RNA was treated with DNase I (Invitrogen) to remove genomic DNA before being reverse transcribed into cDNA using the Superscript III First-Strand Synthesis System (Invitrogen). The concentrations of total RNA and total cDNA were normalized between minor workers and soldiers before cDNA synthesis and PCR, respectively. The two cDNA libraries were used as PCR templates for the semi-quantitative PCR with reverse transcription of vestigial and EF1a. The P. hyatti vestigial PCR primers used were: forward 5′-TCCTTACCTGTATCAGACCCATC-3′ and reverse 5′-TGTCGATCTGTCGTCGTCCAA-3′, and the P. hyatti EF1a PCR primers used were: forward 5′-TCAGGACGTGTACAAGATC-3′ and reverse 5′-CAATGACCTGTGCAGTAAAG-3′. The PCR was performed using an annealing temperature of 56 °C with 31 thermocycles and four serial dilutions of the two cDNA libraries.

I'm an old man, but being old, and recognizing that there isn't much time left, I feel more and more urgency about finding things out.

Youth - and certainly my youth - as they say in a wonderful platitude that became a platitude by being true, is wasted on the young.

If nothing else, I've tried to impress that on my sons, and happily they both seem to get it, more or less.

A beautiful thing on a rainy Saturday.

Have a nice weekend.

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