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NNadir

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Rare Carbon, Nitrogen, and Oxygen Isotopes Appear Abundant in a Young Planetary Nebula.

The paper I'll discuss in this post is this one: Extreme 13C,15N and 17O isotopic enrichment in the young planetary nebula K4-47 (Ziurys et al Nature 564, 378–381 (2018))

Some background:

Carbon has two stable isotopes, 12C and 13C; Nitrogen has two as well, 14N and 15N; Oxygen has three, 16O, 17O, and 18O.

All of the atoms in the universe except for hydrogen, a portion of its helium and a fraction of just one of lithium’s isotopes, 7Li, have been created by nuclear reactions after the “big bang.” The majority of these reactions took place in stars, with some important exceptions: Lithium’s other isotope, 6Li practically all of the beryllium in the universe, and all of its boron. (Lithium, beryllium, and boron are not stable in stars, and all three are rapidly consumed in them; they all exist because of nuclear spallation reactions driven by cosmic rays in gaseous interstellar clouds.)

For the uninitiated, writing a nuclear reaction in the format 14N(n,p)14C means that a nucleon, in this case nitrogen’s isotope with a mass number of 14 is struck by a neutron (n) and as a consequence ejects a proton (p) to give a new nucleon, carbon’s radioactive isotope having a mass number of 14.

In the case of carbon, the nuclear reaction just described has been taking place in Earth’s atmosphere ever since that atmosphere formed with large amounts of nitrogen gas in it. Thus a third radioactive isotope of carbon occurs naturally from the 14N(n,p)14C reaction in the atmosphere as a result of the cosmic ray flux from deep space and protons flowing out of the sun. However, since carbon 14 is radioactive and since the number of radioactive decays depends proportionately on the amount of atoms that exist, it eventually reaches a point at which it is decaying as fast as it is formed. We call this “secular equilibirium.” The long term secular equilibrium at which carbon 14 is formed in the atmosphere at the same rate at which it is decaying is the basis of carbon dating. (This secular equilibrium has been disturbed by the input of 14C as a result of nuclear weapons testing.) Even with the injection of 14C as a result of nuclear testing, 14C remains nonetheless extremely rare and for most purposes other than dating, can be ignored, except perhaps by radiation paranoids.


In the case of all three elements mentioned at the outset, the isotopic distribution in the immediate area of our solar system is dominated in each case by a single isotope: On Earth Carbon is 98.9% 12C; Nitrogen is 99.6% 14N; Oxygen is 99.8% 16O. The abundances vary only very slightly in the sun.

An interesting nuclear aside: 14N has a very unusual property: It is the only known nuclide to be stable while having both an odd number of neutrons and an odd number of protons. No other such example is known. Note the correction to this statement by a clear thinking correspondent in the comments below.

In recent years, I've been rather entranced by the interesting properties of the fissionable actinide nitrides, in particular the mononitrides of uranium, neptunium and plutonium and their interesting and likely very useful properties, and in this sense I've been sort of wistful over the low abundance of 15N in natural nitrogen. In an operating nuclear reactor, with a high flux on neutrons - in the type of reactors I think the world needs, fast neutrons - the same nuclear reaction that takes place in the upper atmosphere, the 14N(n,p)14C reaction, takes place. Thus the inclusion of the common isotope of nitrogen in nitride nuclear fuels will result in the accumulation of radioactive carbon-14. In this case, given 14C’s long half-life, around 5,700 years – much longer than the lifetime of a nuclear fuel – secular equilibrium will not occur while the fuel is being used.

Personally this doesn't bother me, since it avoids the unnecessary expense (in my view) of isolating nitrogen’s rare isotope, 15N, and because carbon-14 has many interesting and important uses already. Carbon-14’s nuclear properties are also excellent for use in carbide fuels, inasmuch as it has a trivial neutron capture cross section compared to carbons two stable isotopes and, without reference to the crystal structure of actinide nitrides and mean free paths therein, and without reference to the scattering cross section of the nuclide (which I don't have readily available), it takes 15% more collisions (for C14 to moderate (slow down) fast neutrons from 1 MeV (the order of magnitude at which neutrons emerge during fission) to thermal (0.253 eV) neutrons than it takes for carbon’s common isotope 12C. (Cf, Stacey, Nuclear Reactor Physics, Wiley, 2001, page 31.) Thus 14C is a less effective moderator, and thus has superior properties in the "breed and burn" type reactors I favor, reactors designed to run for more than half a century without being refueled, reactors designed to run on uranium’s most common isotope, 238U rather than the rare isotope, 235U, currently utilized in most nuclear reactors today. Over the many centuries it would take to consume all of the 238 already mined and sometimes regarded as so called “nuclear waste,” access to industrial amounts of carbon-14 might well prove very desirable for the purposes of neutron efficiency.

Anyway...

The dominance of the major isotopes of carbon, nitrogen, and oxygen in our local solar system and in much of the universe is a function of stellar synthesis. Most stable stars destined to have lives measured in billions of years, including our sun, actually run on the CNO cycle, in which the nuclear fusion of hydrogen into helium takes place catalytically rather than directly.

Here's a picture showing the CNO cycle pathways:



Six of the nuclei in this diagram are stable, the aforementioned 12C, 13C, 14N, 15N, 16O, and 17O. However only 3 of them occur in other pathways, 12C, 14N, and 16O. When a main sequence star is very old and has consumed nearly all of its hydrogen, the only nuclei left to "burn" is 4He. The problem is that 4He has much higher binding energy than its nearest neighbors, including putative beryllium isotopes. Here is the binding energy curve for atomic nuclei, the higher points being the more stable with respect to the lower points:



Helium-4's anomalous stability prevents the formation of the putative isotope Beryllium-8. Observation of this isotope of beryllium is almost impossible since it's half-life is on the order of ten attoseconds, and it cannot actually form in stars. This is why 12C is a critical element in the pathway to the existence of all heavier elements. It forms from the simultaneous fusion of three helium atoms, and exists because it is more stable than helium-4. This is exactly what happens in dense stars when they have run low or out of hydrogen and only have helium left to burn. Carbon-12 can fuse with helium-4 to form oxygen-16. In addition, it can fuse with residual deuterium (2H) under these circumstances to form nitrogen-14. (However, in the helium burning phase deuterium, which forms from the p(p,γ )d reaction, where d is deuterium nuclei, is also relatively depleted.) Thus the formation of these isotopes is independent of the CNO cycle. As a result, it turns out that after hydrogen and helium which together account for 98% of the universe’s elemental mass, oxygen and carbon are respectively the third and fourth most common elements. These four elements comprise 99.5% of the elemental mass of the universe. All other elements, with nitrogen included, turn out to be minor impurities in the universe as a whole.

The minor isotopes in the CNO cycle are actually consumed in stars in this model, and to the extent that they exist, they simply raise the catalytic rate of hydrogen consumption.

All of this is the “understanding,” at least.

According to the authors of the paper cited at the outset, however, there seems to be other things going on in the universe, places where these reactions and their effects do not dominate. The authors are studying, at microwave and other frequencies, a planetary nebula that is estimated to be only 400-900 years old.

From the introductory text in the paper:

The planetary nebula phase, which follows the asymptotic giant branch (AGB) track, marks the end of the stellar life cycle as the star ejects most of its mass and evolves into a white dwarf, a strong emitter of ultraviolet radiation. This radiation subsequently ionizes the ejected stellar material, creating a bright nebula. K4-47, a young planetary nebula with an age of 400–900 years9, is particularly interesting because of its kinematic structure. K4-47 has a highly collimated bipolar outflow, visible in the emission of vibrationally excited H2, as well as a hot central region traced by highly excited atomic lines such as [O III], as shown in Fig. 19,10. Furthermore, CO, HCO+ and CS have been observed at millimetre wavelengths in K4-47 by our group11.


From the abstract of the paper, touching on the unusual nature of what the authors are seeing:

Carbon, nitrogen and oxygen are the three most abundant elements in the Galaxy after hydrogen and helium. Whereas hydrogen and helium were created in the Big Bang, carbon, nitrogen and oxygen arise from nucleosynthesis in stars. Of particular interest1,2 are the isotopic ratios 12C/13C, 14N/15N and 16O/17O because they are effective tracers of nucleosynthesis and help to benchmark the chemical processes that occurred in primitive interstellar material as it evolved into our Solar System3. However, the origins of the rare isotopes 15N and 17O remain uncertain, although novae and very massive stars that explode as supernovae are postulated4,5,6 to be the main sources of 15N. Here we report millimetre-wavelength observations of the young bipolar planetary nebula K4-47 that indicate another possible source for these isotopes...

... These results suggest that nucleosynthesis of carbon, nitrogen and oxygen is not well understood and that the classification of certain stardust grains must be reconsidered.


They describe in the body of the paper the molecules they find that allow them to identify the isotopes, from the vibrational frequencies of their rotations which are effected by these, the frequencies being effected by the masses at the atoms of which they are constructed. (In the paper the techniques for the sensitive detection of these frequency variations is described.)

Our millimetre-wavelength observations showed that K4-47 is rich in gas-phase molecules, including HCN, HNC, CCH, CN and HC3N11,13,14,15, as well as the isotopically rare molecules H13CN, HN13C, 13CS, 13CN, HC15N, H13CCCN, HC13CCN, HCC13CN and C17O, as shown in Fig. 2. These molecules were detected via multiple millimetre-wavelength rotational transitions, typically observed at wavelengths of 3 mm and 1 mm.


Figure 2:



The caption:

The molecule and the total angular momentum quantum number J corresponding to each rotational transition are displayed in each panel. The spectra are plotted in terms of intensity (T∗A), given here in millikelvin, versus velocity with respect to the local standard of rest (VLSR), in kilometres per second. The J = 1 → 0 transitions of all molecules were observed with the new ARO ALMA 12-m prototype antenna, whereas the J = 3 → 2 lines were measured with the ARO SMT or the IRAM 30-m. The spectral resolution is 1–2 MHz.


Some further remarks:

The presence of such molecules in K4-47 is unexpected. The molecular content of planetary nebulae has always been considered to be extremely low16 because the ultraviolet radiation from the emerging white dwarf is thought to photodissociate most molecular species that are prominent in the previous AGB phase. Furthermore, the detection of these chemical compounds indicates a carbon-rich environment, reflecting that C > O in the progenitor star17. Comparison of molecular column densities for HCN, HNC, CN, HC3N, CO and CS and their corresponding isotopologues results in striking C, N and O isotope ratios: 14N/15N = 13.6 ± 6.5, 16O/17O = 21.4 ± 10.3 and 12C/13C = 2.2 ± 0.8 (3σ uncertainties; see Extended Data Table 1). Chemical fractionation cannot explain these ratios, because the gas temperatures in K4-47 are too high (≥55 K). Although 12C/13C ratios as low as about 2–4 have been found in envelopes of red giants and J-type stars18,19, to our knowledge, the observed 14N/15N and 16O/17O ratios are the lowest found thus far in interstellar gas. Our observations of K4-47 suggest that there may be a new, undiscovered source of 15N and 17O.


A note on the rarity of this finding:

The only other astronomical object that resembles K4-47 is the enigmatic CK Vul8, which is currently characterized as a white dwarf merger8,25. This carbon-rich object has a bipolar outflow and a central ionizing source with T > 50,000 K, as well as a similar set of molecules, indicating8 12C/13C = 3.8 ± 1.0, 14N/15N = 20 ± 10 and 16O/17O > 110. The molecular content of both objects is at least 0.5M⊙ (M⊙, mass of the Sun)26. The outflow velocities of about 400 km s−1 in CK Vul, as traced by CO and HCN, however, are considerably higher than those in K4-47 (about 60–80 km s−1). Such velocities are too low to classify K4-47 as a nova shell (velocities of about 370–850 km s−1)27.

Aside from K4-47 and CK Vul, similarly low 12C/13C, 14N/15N and 16O/17O ratios have been found in presolar grains—small, 0.1–20-μm-sized particles extracted from meteorites28. These grains are known to predate the Solar System and originate in the circumstellar envelopes of stars that have long since died.


There is some discussion of the current theories of the origins of presolar grains, comprised largely of silicon carbide, thought to originate from "AGB" (Asymptotic giant branch) stars.

A graphic on this topic from the paper:



The caption:

The presolar SiC grains are identified as arising from J-type stars for the A+B-type grains (circled in purple), AGB stars for the mainstream, Y and Z types (circled in yellow), supernovae for the X and Si3N4 types (circled in blue) and putative nova grains (circled in green); figure adapted from figure 6 of ref. 28. Data for Y CVn and RY Dra are shown with red circles and for K4-47 and CK Vul with red stars. The plot suggests that at least some nova grains arise from extreme J-type stars. Stellar data are plotted with error bars that indicate the 3σ confidence level.


Some final comments from the authors before technical discussions of methods:

The 14N/15N and 12C/13C ratios that we observe for K4-47 and CK Vul place these objects clearly among the ‘putative nova’ SiC presolar grains, as shown in Fig. 3. Furthermore, the 16O/17O ratio in K4-47 matches well those measured in oxide/silicate presolar grains also attributed to novae30. These remarkable results suggest that the nova presolar grains actually arise from stars other than novae, perhaps explosive J-type stars that produce large amounts of 15N and 17O, which evolve into planetary nebulae, as represented by K4-47. It is noteworthy that presolar A+B-type SiC grains are thought to come from J-type stars (Fig. 3). The A+B grain population appears directly above that considered to arise from novae. Thus, the putative nova grains may be simply an extension of A+B grains—all created from J-type stars.


50 years after the "Earth-rise" picture from Apollo 8 gave us a sense of our planetary fragility coupled with its magnificence, the rise of intellectually deficient, self absorbed fools, of which the asinine criminal Donald Trump is just one example, has threatened all that lives on that jewel planet first photographed from the orbit of the moon.

One feels the tragedy.

But the universe goes on, and for me, in this holiday season, it is good to feel its eternity, the beautiful facts that have no reason to be found other than that they are beautiful. In the grand scheme, I'm not sure we matter.

I wish you the best holiday season, and the peace that I found in this little paper, and that I wish that you, in your own place and own way, will similarly find.






If the 25th amendment is not activated under these circumstances, it may as well not have been...

...written.

It reads:

Amendment XXV
Section 1.
In case of the removal of the President from office or of his death or resignation, the Vice President shall become President.

Section 2.
Whenever there is a vacancy in the office of the Vice President, the President shall nominate a Vice President who shall take office upon confirmation by a majority vote of both Houses of Congress.

Section 3.
Whenever the President transmits to the President pro tempore of the Senate and the Speaker of the House of Representatives his written declaration that he is unable to discharge the powers and duties of his office, and until he transmits to them a written declaration to the contrary, such powers and duties shall be discharged by the Vice President as Acting President.

Section 4.
Whenever the Vice President and a majority of either the principal officers of the executive departments or of such other body as Congress may by law provide, transmit to the President pro tempore of the Senate and the Speaker of the House of Representatives their written declaration that the President is unable to discharge the powers and duties of his office, the Vice President shall immediately assume the powers and duties of the office as Acting President.

Thereafter, when the President transmits to the President pro tempore of the Senate and the Speaker of the House of Representatives his written declaration that no inability exists, he shall resume the powers and duties of his office unless the Vice President and a majority of either the principal officers of the executive department or of such other body as Congress may by law provide, transmit within four days to the President pro tempore of the Senate and the Speaker of the House of Representatives their written declaration that the President is unable to discharge the powers and duties of his office. Thereupon Congress shall decide the issue, assembling within forty-eight hours for that purpose if not in session. If the Congress, within twenty-one days after receipt of the latter written declaration, or, if Congress is not in session, within twenty-one days after Congress is required to assemble, determines by two-thirds vote of both Houses that the President is unable to discharge the powers and duties of his office, the Vice President shall continue to discharge the same as Acting President; otherwise, the President shall resume the powers and duties of his office.


This "President" has never been able to discharge his duties as President.

He is also clearly guilty of "high crimes and misdemeanors,." as he is clearly in the employ of a foreign autocrat.

Is there one, or two, or three patriots left in the Republican party?

Anyone?

None?

A Bunch of Artists Working with Uranium Based Media Have All Died.

The paper I'll discuss in this post is this one: Palaeolithic cave art in Borneo
(Aubert et al, Nature 564, 254–257 (2018) ).

From the abstract:

Figurative cave paintings from the Indonesian island of Sulawesi date to at least 35,000 years ago (ka) and hand-stencil art from the same region has a minimum date of 40 ka1. Here we show that similar rock art was created during essentially the same time period on the adjacent island of Borneo. Uranium-series analysis of calcium carbonate deposits that overlie a large reddish-orange figurative painting of an animal at Lubang Jeriji Saléh—a limestone cave in East Kalimantan, Indonesian Borneo—yielded a minimum date of 40 ka, which to our knowledge is currently the oldest date for figurative artwork from anywhere in the world. In addition, two reddish-orange-coloured hand stencils from the same site each yielded a minimum uranium-series date of 37.2 ka, and a third hand stencil of the same hue has a maximum date of 51.8 ka. We also obtained uranium-series determinations for cave art motifs from Lubang Jeriji Saléh and three other East Kalimantan karst caves, which enable us to constrain the chronology of a distinct younger phase of Pleistocene rock art production in this region.


Apparently, this is the oldest know art on Earth. Let's cut to the chase and take a look at the art from a figure in the paper:



The caption:

Samples LJS1 and LJS1A are shown. a–c, Photograph (a) and tracing (b, c) showing the locations of the dated speleothems (n = 2) and associated painting: a large in-filled reddish-orange-coloured naturalistic depiction of an animal shown in profile. Although the animal figure has deteriorated, we interpret it as a figurative representation of what is possibly a wild bovid (Bornean banteng). Panel c is an enlargement of the area marked by a black box in b. d, Profiles of the speleothem showing the micro-excavated subsamples and associated U-series dates. Photograph, L.-H. Fage; tracing, L. Huntley, based on previously published data6 and at www.kalimanthrope.com.


This art was discovered in a remote area featuring very challenging access:

Since the 1990s, thousands of rock art images have been documented in the karst caves of the Sangkulirang–Mangkalihat Peninsula in East Kalimantan, a province in the Indonesian portion of Borneo2,3,4,5,6,7,8,9,10,11 (P.S., unpublished observations) (Fig. 1). This remote and difficult-to-access region contains 4,200 km2 of karst outcrops9,12 that are formed of late Eocene to early Pliocene limestone13. The karst terrain is characterized by densely forested mountain chains and towering cliffs that reach heights of several hundred metres. The Sangkulirang–Mangkalihat Peninsula is adjacent to the edge of the Sunda Shelf—a continental shelf that descends to about 2,500 m in depth—and therefore even during low sea-level stands in the Pleistocene, the karsts were situated essentially at the southeastern tip of Eurasia (Fig. 1).


Don't worry about those "densely forested" mountain chains, by the way. We'll kill the forests soon enough, if not by logging, then by climate driven fire. Once it's cleared you'll be able to drive your Tesla SUV right up to them.

If, by the way, you actually want to review some of this oldest art on Earth, you should click on the link to the paper. The paper itself is behind a fire wall, but I believe the the supplementary Extended Data and Supplemental files are open sourced and you can take a look.

One may also learn about the chemical composition of these pigments in these files. In particular, one can learn the isotopic signature of the uranium, natural thorium, and thorium-230, the decay product of uranium-238. The ratio of the latter two and the distance from the secular equilibrium point: the point at which thorium-230 concentrations in a particular sample are decaying at the same rate as they are being formed. This distance from this equilibrium point gives the age of the sample. The concentrations of uranium are on the order of parts per million, and the thorium-230 on the order of parts per trillion. The lower decay products are probably not useful to look at, since the caves surely have been leaching radon gas since they formed.

Other common dating techniques using natural radionuclides are, of course, carbon-14 (which has moved from its previous equilibrium point owing to nuclear testing in the 20th century) and rubidium/strontium 87 for very old rocks. Certain lanthanides can also be utilized in this way, since many of the natural lanthanides contain significant amounts of radioactive isotopes.

Here, from the full paper's text is a description of these determination:

U–Th dating was carried out using a Nu Plasma multi-collector inductively-coupled plasma mass spectrometer (MC-ICP-MS) in the Radiogenic Isotope Facility at the School of Earth and Environmental Sciences, University of Queensland, following chemical treatment procedures and MC-ICP-MS analytical protocols that have previously been described32,33,34. Powdered sub-samples weighing 3–170 mg were spiked with a mixed 229Th–233U tracer and then completely dissolved in concentrated HNO3. After digestion, each sample was treated with H2O2 to decompose trace amounts of organic matter (if any) and to facilitate complete sample-tracer homogenization. Uranium and thorium were separated using conventional anion-exchange column chemistry, using Bio-Rad AG 1-X8 resin. After stripping off the matrix from the column using double-distilled 7 N HNO3 as eluent, 3 ml of a 2% HNO3 solution mixed with trace amount of HF was used to elute both uranium and thorium into a 3.5-ml pre-cleaned test tube, ready for MC-ICP-MS analyses, without the need for further drying down and re-mixing. After column chemistry, the U–Th mixed solution was injected into the MC-ICP-MS through a DSN-100 desolvation nebulizer system with an uptake rate of around 0.1 ml per minute. The U–Th isotopic ratio measurement was performed on the MC-ICP-MS using a detector configuration to enable simultaneous measurements of both uranium and thorium34,35. The activity ratios of 230Th/238U and 234U/238U of the samples were calculated using the previously published decay constants36. U–Th dates were calculated using the Isoplot Ex 3.75 Program37.


Beautiful analytical chemistry...

The pigments themselves are actually not uranium based by the way, except to the extent that the carbonates therein carried leaching uranium. The pigments, most of which are said to have a "mulberry" color were largely iron based.

The title of this post by the way, represents an abuse of language. This abuse is deliberate.

Uranium is a ubiquitous element, as common as tin. There are between 4.5 and 5 billion tons of it in the oceans alone. I offered significant detail on planetary flows of uranium - giving the references - elsewhere on the internet: Sustaining the Wind, Part 3, Is Uranium Exhaustible?

The very large source of uranium resulting in human exposure is from fertilizer, since uranium has a high affinity for phosphate. (Phosphate ores in Florida were once considered as uranium ores, until richer sources of uranium were found. These same ores are now dug to make fertilizer and the uranium in them is not removed; it would be too expensive to do so.)

The existence of uranium is the last best hope of the human race as the planetary atmosphere collapses owing to the ongoing catastrophe of climate change. Regrettably, fear of this element in the periodic table - it is a chemically toxic element, as is the natural arsenic found in many worldwide water supplies, most notably Bangladesh - prevents its use to save what still might be saved. It is worth noting that over the long term, especially in continuous recycling schemes that nuclear power can reduce the radioactivity of the planet.

Studies of approaches to make uranium available for all future generations have the added benefit of being able to remove uranium from dilute sources. This can serve to remediate any uranium contamination anywhere, where the health risks are unacceptable.

The absurd title here surely is of a type that, without the text to which it refers, might induce some of the types of hysteria one hears from time to time, for example the bathos focus on a few hundred Dine uranium miners in Arizona who worked in the 1950s to the exclusion of the 250 million+ people who died from air pollution since 1960.

The title is absurd here, because our focus is absurd, because we need to think critically.

Have a wonderful weekend.

A Discussion of the Intensity of El Nino/La Nina Events Under the Volatile Climate Conditions.

The paper I'll briefly discuss in this post is this one: Increased variability of eastern Pacific El Niño under greenhouse warming (Cai et al, Nature 564, pages 201–206 (2018))

There's a large number of abbreviations in the text: SST = Sea Surface Temperature; CP = Central Pacific; EP = Eastern Pacific; ENSO = El Nino Southern Oscillation.

From the introduction:

Alternating between El Niño and La Niña events, the ENSO affects extreme weather events, ecosystems and agriculture around the world1,2,3,4,5,6,7. ENSO events vary greatly8,9,10,11,12,13,14,15: the EP-ENSO is associated with strong El Niño events and weak cold SST anomalies, and is characterized by the maximum SST anomaly (the SST anomaly centre) being located in the eastern equatorial Pacific (the ‘Niño3’ region: 5° S–5° N, 150°–90° W); the CP-ENSO is associated with strong or moderate La Niña events and modest El Niño events, and is characterized by the SST anomaly centre being located in the central equatorial Pacific (5° S–5° N, 160° E–150° W). EP-El Niño events are the strongest and most destructive El Niño events. During such events, SST warming in the Niño3 region leads to flooding in southwest USA, Ecuador and northeast Peru, and to droughts in regions that border the western Pacific1,4. In extreme cases, the disruption includes substantial loss of marine life in the eastern Pacific, mass bleaching of corals across the Pacific and beyond2, and movement of the intertropical convergence zone7 and of the South Pacific convergence zone towards the equator5,16, inducing catastrophic floods and droughts across the Pacific region5,7. Because of these severe effects, determining how EP-El Niño SST variability responds to greenhouse warming is one of the most important issues in climate science.


Imagine that...

...Important issues in Climate Science.

It appears that computational modeling of these events has proven problematic and the authors set out to improve the situation by the use of sophisticated statistical analysis, principle component (PC) analysis and empirical orthogonal function (EOF) analysis.

A graphic touching on the subject:



The caption:

Nonlinear relationship between the first and second principal components (PC1 and PC2) of SST anomalies averaged over December–February (black dots; see also Extended Data Fig. 1) from five observational reanalysis products. Grey dots indicate monthly data. The nonlinearity is determined by fitting these monthly data with the quadratic function PC2(t) = α[PC1(t)]2 + βPC1(t) + γ. The red curve shows the same fit, but using the December–February average (black points). b, SST anomaly patterns associated with EP-ENSO in two models, highlighting the large difference in the longitude of EP-ENSO anomaly centres (132.25° W for CESM1-CAM5; 101.75° W for IPSL-CM5A-LR) that can occur between climate models. c, The parameter α determined using the monthly data versus the skewness of the E-index and C-index for all models analysed (symbols). This parameter is a measure of the contrast between the CP-ENSO and EP-ENSO and of the size of the skewness of the corresponding C-index and E-index. Models with greater |α| systematically produce larger negative skewness in the C-index and larger positive skewness in the E-index. The large black filled circles indicate the observed value αobs (dashed line; the mean of the five observational reanalysis products). The 17 models that produce |α| < |αobs|/2 (above the dash-dotted line) are denoted by stars and referred to as ‘non-selected’; the other 17 models are shown using various symbols and correspond to the 17 models that we select for further analysis. Details of all models can be found in ref. 29. The linear fits (solid lines) between α and the E-index or C-index are displayed together with the correlation coefficient R, slope and P value from the regression. d, e, Nonlinear relationship between the December–February-average principal components for the selected (d) and non-selected (e) models, with the red curves showing quadratic fits.


The statistical analysis involves all sorts of cool mathematics but this graphic cuts to the chase with modeling of the last century and this century, the one in which we bet the whole farm, well all the farms and all of the planet on the hope that so called "renewable energy" would save the day without interfering with our lifestyle including trips to our favorite restaurant. The statistical output is related to an "E-index" which refers to the relative amplitude of the El Nino Southern Isolation, and thus the size of the swings in the intensity of the destruction it causes Take a peak and weep:



The caption:

a, Comparison of the standard deviation of the E-index over the present-day (1900–1999) and future (2000–2099) 100-year periods in the 17 selected models. 15 of the 17 selected models (88%) simulate a greater variance in the E-index in the future period (red bars) than in the present-day period (blue bars); the two models that simulate a reduction in variance are greyed out. b, Number of strong EP-El Niño events (E-index > 1.5 s.d.) that occurred in the two 100-year periods. The multi-model mean is also shown in a and b; error bars in the multi-model mean correspond to the 95% confidence interval. The differences between the present-day and future multi-model-mean E-index (s.d.) and between the present-day and future multi-model-mean number of strong events are statistically significant at more than the 95% confidence level. The increase in EP-ENSO SST variance (E-index variance) generally translates to more EP-El Niño events for a given E-index intensity.


So called "renewable energy" didn't save the day, and clearly it isn't saving the day, and it won't save the day, but let's not let that change our minds about anything. It's not like data and results count.

While we tend to focus on California, its droughts, fires and floods, in terms of feedback loops the droughts in South Eastern Asia, owing to the carbon release associated with fires there are far more significant, since they involve rain forests. The worst such El Nino event there in the 20th century probably occurred in 1998, a remarkable year in the history of our destruction of the planetary atmosphere. In that year, carbon dioxide concentrations rose by an astounding 2.93 ppm in a single year! Well it was outstanding...

...We're doing a great job at solving the problem. 2.93 in a single year isn't such a big deal any more. In the whole 20th century we had four years, including 1998, that had single year increases greater than 2.00 ppm, this from 1958 to 1999, if I have my math right, 41 years. In the first 18 years of the 21st century, we've had 11 such years, two of which were greater than 1998. In 2015 carbon dioxide concentrations rose 3.05 ppm; in 2016 they rose 2.98 ppm.

(This data can all be found on the website of the NOAA carbon dioxide observatory at Mauna Loa.)

If you find any of this depressing, don't worry, be happy. Someday you might be able to afford to own a Tesla car, in which case none of this will be your fault; it will be the fault of those Chinese people who make the crap, you know, the Santa Claus place mats and inflatable plastic snowmen for your lawn, stuff like that, that you buy when you drive your wonderful Tesla car to the mall at Christmas time.

We wish you a Merry Christmas and a Happy New Year.

I hope your Christmas shopping is going well. Don't forget to pick up a "Sierra Club" Calendar.

Enjoy the coming solstice; it's only 8 days until the days start growing longer, which is great for all those wonderful solar cells in the Northern Hemisphere.



Wow. I just got my hands on the Farm Hall Transcripts, annotated by Jeremy Bernstein.

Just after World War II, all of Germany's nuclear scientists were captured by the Allies. The Americans and the British confined ten of them to a estate in Britain and recorded their conversations. The idea was to find out what they knew, and what they had done during the war in Nazi Germany to give Hitler an atomic bomb.

I personally had no idea that the transcripts of these recordings had been published, but recently learned that indeed they had been, well over 20 years ago.

The cast of characters is amazing, Werner Heisenburg most prominently, Max Von Laue, Otto Hahn, Carl Frederick von Weisacker, six others.


From Bernstein's Preface:


In practical terms, the Germans came nowhere near manufacturing an actual nuclear weapon during World War II. That being the case, why should the circumstances surrounding this non-event still arouse such passionate debate? I think that there are two reasons. On the one hand, many of the people who were involved in the successful development of the Allied nuclear weapons had serious moral misgivings, especially once they saw what the use of the weapon meant in terms of human misery. A sense of how these people felt was expressed by the Harvard nuclear physicist Kenneth Bainbridge, who immediately after the first successful test at Trinity, said to Oppenheimer, “Now we are all sons of bitches.”1 I mention these misgivings to show just how sensitive a subject this is for the people involved in the Allied program, some of whom are still alive and very articulate.

On the other hand—and this is where the debate begins—there is the version of this history promulgated by the German nuclear scientists after the war. Some of these scientists, a few of whom are also still alive, were also very articulate. Their version is built on the proposition that, unlike their American counterparts who actually constructed this “immoral” weapon, they, the Germans, took the moral high ground and “prevented” this weapon from falling into the hands of Hitler. In other words, they deliberately and consciously withheld their knowledge and expertise for the sake of some higher ethical purpose. If this were true, then these scientists, all of whom collaborated with the regime—some were members of the Nazi Party and some were not—could salvage something of their moral stature, which had been irreparably tarnished by their collaboration. They could claim that they functioned morally in an immoral regime,..

...At first sight, when confronted with such a maze of contradictory assertions and emotions, one might naively think that the way through would be to interview all the principals involved to see if one could not come to a consensus. As anyone who has tried to do this sort of thing soon discovers, however, memory often obscures fact instead of revealing it. The German scientists involved have told the same story over and over again for so many years that one wonders if they themselves now know what part of it is literally true and what part is invention. What is needed in situations like this are the contemporary documents—what people really said and wrote at the time—and not some post-facto, often self-serving, reconstruction. Ideal would be a recording, or a transcript of a recording, that would bring such conversations back to life...

...When I first saw these transcripts, soon after their release in February of 1992, I had something of the feeling that Champollion must have felt in August of 1808 when he saw a newly produced copy of the Rosetta stone—the key to the decipherment of the Egyptian hieroglyphics. Like Champollion with his knowledge of languages, I felt that if one knew enough about the subject matter, then by reading both the lines in the transcripts and what was between the lines, one could hope to reach into both the Germans’ state of mind and their state of knowledge as it was in 1945. What seemed to be needed here—the equivalent of the Coptic, Greek, and other languages Champollion needed to decipher the hieroglyphics—was a certain familiarity with the physics of nuclear weapons.

Although I was too young to have been at Los Alamos, I did get into physics in the late 1940s, when nuclear weapons loomed very large. When I received my Ph. D., in 1955, jobs in universities were scarce, and I thought seriously of employment at one of the weapons laboratories. To this end, I spent the summer of 1957 as an intern at Los Alamos, where I was exposed to some nuclear weapons technology and witnessed some actual testing in the Nevada desert. For the next two years or so I consulted at the Rand Corporation and at the General Atomic Company on problems that had a nuclear weapons component. Furthermore, most of my teachers, people like Bainbridge, Robert Marshak, Norman Ramsey, Victor Weisskopf and, later, people like Hans Bethe, I. I. Rabi, Robert Oppenheimer, Robert Wilson, Stanislaw Ulam and Robert Serber, had been at Los Alamos. I talked to them extensively about their experiences, and when I went to work at the Brookhaven National Laboratory I talked to Goudsmit on an almost daily basis. Indeed, when I started writing about science for the general public, a substantial part of what I wrote—profiles of people like Albert Einstein, I. I. Rabi, John Wheeler, and Hans Bethe—reflected this experience...



From the transcripts themselves...

Diebner: I wonder whether there are microphones installed here?

Heisenberg: Microphones installed? (laughing) Oh no, they’re not as cute as all that. I don’t think they know the real Gestapo methods; they’re a bit old fashioned in that respect.


As we now live under a completely immoral and clearly criminal government - although not one with the power that the Nazis had day to day over their citizens, this seems like a timely subject to read.

As it happens, a clearly insane criminal in the White House now has access to nuclear weapons on a scale that no one in 1945 could imagine.

It should make for some fascinating reading on the off hours...

Refractive Lens for Extreme UV Radiation Discovered.

The paper I'll discuss in this post is this one: Extreme-ultraviolet refractive optics| Extreme-ultraviolet refractive optics (L. Drescher, O. Kornilov, T. Witting, G. Reitsma, N. Monserud, A. Rouzée, J. Mikosch, M. J. J. Vrakking & B. Schütte, Nature 564, 91–94 (2018) )

Lenses for focusing extreme UV light - just short of x-rays in energy - do not exist. One can imagine many applications for this capability, for instance in materials etching, welding and other processing, spectroscopic investigations of the structure of matter, cancer and other surgeries (should the focusing be refined enough - hard to see here since the lenses are gases) and regrettably, as no discovery is free of possible sinister use, weapons systems.

The introductory text tells the story better than I can:

Refraction of light is omnipresent in nature, where it forms the basis for the functionality of the human eye and the observation of a rainbow. It is exploited in many applications in the visible, infrared and ultraviolet spectral regions. For instance, refractive errors of the eye are corrected by glasses or contact lenses, and optical microscopes enable the magnification of small objects or structures. In the context of laser physics, refractive lenses are extensively used to focus or (de-)magnify laser beams. Dispersion and deflection of light by optical prisms is used to compress or stretch ultrashort laser pulses.

When Röntgen discovered X-rays in 1895, he attempted refraction experiments using prisms and lenses8. Because he observed no significant deflection of the X-rays, he concluded that refractive lenses were not suitable for focusing X-ray radiation. A century later, a compound refractive lens consisting of a lens array was nevertheless developed for the hard X-ray regime, assisted by the comparably low absorption in this spectral region. Compound refractive lenses are used to focus X-rays emitted from modern synchrotron9 and free-electron laser facilities10,11. They have been applied for hard X-ray microscopy12, for X-ray nanofocusing13 and for the investigation of crystal scattering14, as well as for coherent diffractive imaging of nanoscale samples15.

Refractive elements have so far been missing in the extreme-ultraviolet (XUV) range but are highly desirable. For instance, refractive lenses could be used to focus XUV pulses without changing the propagation direction, thereby providing considerable flexibility. The use of specially designed microscopic refractive lenses has been proposed16,17. However, the need to use very thin lenses with a sophisticated design, owing to the strong absorption of XUV radiation, makes practical implementation challenging.

Here, we demonstrate that control over the refraction of XUV pulses can be achieved by using gases instead of solids. We exploit the fact that close to atomic resonances, the refractive index n has a dispersive lineshape, as depicted in the top part of Fig. 1a.


The authors utilize gas jets to focus the XUV beams using density gradients in the gas pulses. Since (in this case) the gases are monoatomic noble gases, they cannot be damaged by the energy that is contained in extreme UV radiation, as is the case with solid phase lenses.

If interested, take a look at the pictures.

Figure 1:



The caption:

a, Top, dispersive lineshape of the refractive index in the vicinity of an atomic resonance. Spectral components at photon energies below the resonance (n > 1) are indicated in red, components at energies above the resonance (n < 1) in blue. Middle, experimental configuration, showing an XUV pulse (violet arrow) that crosses a gas jet (black arrow), which has a density gradient in the vertical direction (orange arrow), at right angles. Bottom, deflection of an XUV pulse propagating below the centre of the gas jet. b, Angle-resolved spectrum of a broadband HHG pulse measured in the absence of the gas jet. The angular divergence of the XUV beam in the vertical direction is reflected in the spatial distribution along the vertical axis. arb. units, arbitrary units. c, The same spectrum after propagation at a distance of 0.3 mm below the centre of a dense He gas jet (generated using a backing pressure of 10 bar) shows clear signatures of refraction. Spectral components with photon energies below the 1s np resonances of He are deflected upwards, whereas spectral components above these resonances are deflected downwards. The deflection angles are largest close to the 1s 2p resonance and decrease for higher resonances, owing to the decreasing oscillator strengths. Above the ionization potential of He (at 24.58 eV), the XUV radiation is strongly absorbed. Owing to ageing effects, the sensitivity of the detector was reduced in regions where the undisturbed HHG spectrum is recorded (as in b) compared with regions where the deflected XUV radiation is observed. This makes the deflected XUV radiation appear more intense. d, Simulation of the XUV refraction in an inhomogeneous He gas jet, taking into account 1s np resonances with n = 2, 3, …, 8. The simulation indicates that for a backing pressure of 10 bar, a gas jet with a peak density of 9 × 10^19 atoms cm−3 (corresponding to a pressure of 3.7 bar at 300 K) was achieved in the interaction zone.



Figure 2:



The caption:

a–c, Angle-resolved XUV spectra after propagation at a distance of 0.3 mm below the centre of a He gas jet, for backing pressures of 1 bar (a), 3 bar (b) and 9 bar (c). d, The average deflection angle as a function of the photon energy for backing pressures of 3 bar (corresponding to a peak pressure in the interaction zone of about 1 bar; cyan solid curve) and 9 bar (orange solid curve). Here the vertical scale on the left axis applies, as indicated by the upper arrow. For comparison, the calculated refractivity (that is, n − 1) at standard temperature (273.15 K) and standard pressure (1 bar) is plotted on top of the deflection results (blue dotted curve). The vertical scale on the right axis applies, as indicated by the lower arrow. Note that the calculated refractivity is proportional to the pressure. The brown dotted curve shows the calculated refractivity multiplied by a factor of 3.


Image 3 (focused XUV radiation):



a, Spatially resolved spectrum of unfocused XUV radiation at 20.2 eV (corresponding to the 13th harmonic). b, c, The divergence of this harmonic is altered after propagation through a He gas jet (see inset of d), as shown for backing pressures of 6 bar (b) and 12 bar (c). d, Comparison of the vertical beam profiles using backing pressures of 0 bar (blue curve) and 12 bar (red curve). The inset shows the pressure-dependent spot size, where the error bars reflect the uncertainties in determining the spot sizes. e, Spatially resolved spectrum of radiation at 14.0 eV (corresponding to the ninth harmonic), which is close to the 3d and 5s resonances of Ar. f, Focusing of this harmonic is achieved by an Ar gas jet at a backing pressure of 2.5 bar. g, When further increasing the backing pressure to 4 bar, an increasing beam size is observed, because the Ar lens focuses the XUV beam between the gas jet and the detector. h, The vertical beam profiles for Ar backing pressures of 0 bar (blue curve) and 2.5 bar (red curve). The inset shows the pressure-dependent spot size, where the error bars reflect the uncertainties in determining the spot sizes.


Fig. 4: Simulation of the XUV focus:



The caption:

a, Simulated focus in the vertical direction as a function of the photon energy following propagation of an XUV pulse at 14.0 eV (1.9 mm FWHM diameter) through an Ar gas jet with a peak density of 2.2 × 1019 atoms cm−3 (corresponding to a pressure of 0.9 bar at 300 K). Because of chromatic aberration, the XUV spot size depends on the photon energy. b, Spot size as a function of the Ar gas density for XUV pulses with a bandwidth of 160 meV (black curve) and 2 meV (red curve), showing minimal spot sizes of 74 μm and 40 μm, respectively. c, The chromatic aberration is reduced for photon energies that are further away from the resonance. This is shown for the example of an XUV pulse at 20.2 eV (2.4 mm FWHM diameter) that propagates through a He gas jet with a peak density of 1.1 × 1020 atoms cm−3 (corresponding to a pressure of 4.3 bar at 300 K). d, Spot size as a function of He gas density for XUV pulses with a bandwidth of 240 meV (black curve) and 2 meV (red curve), which exhibit minimal spot sizes of 28 μm and 20 μm.


The authors conclude:

In conclusion, we have presented a method to deflect and focus XUV pulses by using the inhomogeneity of a gas jet placed in the way of an XUV beam. Our results enable the transfer of concepts based on refractive optics that are widely used in other spectral regions to the XUV regime, including microscopy, nanofocusing and the compression of ultrashort pulses. XUV gas-based lenses have several advantages, including their high transmission, deformability and tunability (by varying the gas composition, the gas pressure and the gas jet geometry)...

...Refractive XUV gas-phase lenses can be designed for photon energies between 10 eV and 24 eV by carefully selecting appropriate atoms or molecules for different photon energies. In the future, this range might be extended to higher photon energies by developing lenses that exploit refraction in an inhomogeneous plasma consisting of highly charged ions and electrons.


Esoteric, but interesting.

Have a pleasant day tomorrow.

The Molecular Biology of Methicillin Resistant Staphylococcus Aureus Involves Sugar Chemistry.

The paper I'll discuss in this post is this one: Methicillin-resistant Staphylococcus aureus alters cell wall glycosylation to evade immunity. (Peschel, Stehel et al Nature 563, pages705–709 (2018) )

A kind of mental block I've had over the years involves my understanding of the complex chemistry and biochemistry of sugars.

I've always found it hard, and tend to squirrel around it when it comes before me.

It's why I always love to read the introductory text of Gabius' The Sugar Code which I'm sure I've referenced before in this space.

To wit:

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…


H.J. Gabius ed. The Sugar Code, Wiley, 2009 pg 1.

That about sums it up. People don't think about sugars too much, because it's hard to do so...

(It's a great book by the way. I have to reference it all the time.)

One of the great - among many - challenges for future generations is antibiotic resistance. The extension of life span around the world is to a large measure the existence of antibiotics. My grandmother died at the age of 39 from a simple infection that could be cured today with a trip to the doctor, a prescription, and maybe 20 or 30 pills.

In order to address this rising crisis, it is useful to know how bacterial evolve to develop resistance to drugs, and, for that matter, natural antibodies.

This is why I found the paper cited above quite interesting.

From the introduction:

Novel prevention and treatment strategies against major antibiotic-resistant pathogens such as MRSA are urgently needed but are not within reach because some of the most critical virulence strategies of these pathogens are not understood8. The pathogenic potential of prominent healthcare-associated (HA)-MRSA and recently emerged livestock-associated (LA)-MRSA strains is thought to rely on particularly effective immune evasion strategies, whereas community-associated (CA)-MRSA strains often produce more aggressive toxins1,2. Most humans have high overall levels of antibodies against S. aureus as a consequence of preceding infections, but antibody titres differ strongly for specific antigens and are often not protective in immunocompromised patients, for reasons that are not clear3. A large percentage of human antibodies against S. aureus is directed against WTA5,9,10, which is largely invariant. However, some S. aureus lineages produce altered WTA, which modulates, for instance, phage susceptibility 7,11...


WTA is "Wall teichoic acid."

Teichoic acid, like nucleic "acid" is actually a copolymer.of a doubly phosphorylated acetylated aminosugar, galactosamine, and glycerol (or ribotol, an alcohol formed by reducing ribose.)

Here's a structure from Wikipedia:



The authors identified a protein called "TarP" that has close homology (27%) to a protein found in "normal" (not resistant) staphylococcus TarS. When they reinserted TarS into resistant strains, they found that they could restore susceptibility to antibiotics, as well as manipulate susceptibility to certain viruses.

I don't have a lot of time tonight, but here's some pictures and captions from the paper:



The caption:

a, TarP is encoded next to different integrase types (int gene) in prophages φtarP-Sa3int (with immune evasion cluster scn, chp, sak, sep), found in HA-MRSA, and φtarP-Sa1int and φtarP-Sa9int, identified in LA-MRSA. TarP variants in φtarP-Sa1int and φtarP-Sa9int differed from TarP in φtarP-Sa3int in one amino acid each (I8M and D296N, respectively). Both residues are distant from the catalytic centre. b, Complementation of S. aureus RN4420 ΔtarM/S with either tarS or tarP restores susceptibility to infection by WTA GlcNAc-binding siphophages, as indicated by plaque formation on bacterial lawns. Data shown are representative of three independent experiments. c, tarP expression reduces siphophage Φ11-mediated transfer of SaPIbov in N315. Values indicate the ratio of transduction units (TrU) to plaque-forming units (PFU) given as mean ± s.d. of three independent experiments. Statistical significances when compared to wild type were calculated by one-way ANOVA with Dunnett’s post-test (two-sided) and significant P values (P ≤ 0.05) are indicated. NO (none obtained) indicates no obtained transductants.


Some protein structures, teichoic acid structures, and some NMR's:



The caption:

a, Expression of tarP renders N315 resistant to podophages. Representative data from three independent experiments are shown. b, 1H NMR spectra reveal different ribitol hydroxyl glycosylation of N315 WTA by TarS (C4) or TarP (C3). The RboP units with attached GlcNAc are depicted above the corresponding proton resonances. Representative data from three experiments are shown. In-depth description of the structural motifs identified in the spectra is given in the Supplementary Information. c, Crystal structure of TarP homotrimer (pink, orange, grey) bound to UDP-GlcNAc (yellow) and two Mn2+ ions (lime green). The nucleotide-binding domain (NBD), acceptor-binding domain (ABD), and C-terminal trimerization domain (CTD) of the pink monomer are labelled. d, Views into the trimer interface (boxed in c). Left, polar interactions. Hydrogen bonds and salt bridges are shown as black dashed lines. The Mn2+ is 2.1 Å from each Asp316 carboxylate. Right, hydrophobic interactions, with the mutated residue Ile322 highlighted in red. e, Size-exclusion chromatography elution profiles. Based on calibration of the column, the TarP wild-type and I322E mutant proteins have estimated molecular weights of 138 kDa (n = 8) and 42 kDa (n = 3), respectively, in agreement with the calculated molecular weights of 120 kDa for a TarP trimer and 40 kDa for monomeric TarP.


A cartoon of interactions leading to the modified cell walss:



a, 3RboP binding site in the TarP–3RboP complex, with key amino acids shown (cyan). Asp181 is highlighted in red. The ribitol of 3RboP is coloured green and D-ribitol-5-phosphate units 1, 2 and 3 (RboP1, RboP2, and RboP3) are labelled. Hydrogen bonds and salt bridges are shown as black dashed lines. b, Ternary complex of TarP with UDP-GlcNAc and 3RboP. UDP-GlcNAc, Mg2+ and 3RboP are shown as full-atom models coloured yellow, magenta, and green, respectively. c, View into the active site of TarP. C1 of UDP-GlcNAc and Asp181 are highlighted with red labels. The arrow indicates how the C3-hydroxyl in RboP3 could nucleophilically attack GlcNAc C1. d, Comparison of the polyRboP-binding site of TarP with the corresponding region in TarS. Residues of TarP and 3RboP are coloured as in a. TarS residues are coloured violet and the two sulfates are labelled S1 and S2. Only residues of TarP are labelled, for clarity. Key TarP and TarS residues lining the polyRboP-binding site are shown at the bottom, with three identical (red) and one conserved amino acids (blue). e, Superposition of UDP-GlcNAc-bound TarS with the ternary TarP–UDP-GlcNAc–3RboP complex. UDP-GlcNAc and 3RboP bound to TarP are coloured as in b, whereas UDP-GlcNAc bound to TarS is coloured in cyan. Only the TarS residues are shown (coloured as in d), for clarity. The arrows indicate the C1 positions of UDP-GlcNAc in TarP and TarS.


Some immunology effects:



The caption:

a, TarP expression reduces deposition of IgG from human serum on N315 cells. The protein A gene spa was deleted in all strains. Top, human IgG isolated from three individual healthy donors (A, B, and C; n = 4); bottom, left, IgG from human serum enriched for RN4220 WTA binding (n = 4); middle and right, pooled human IgG from different suppliers (Abcam, n = 4; Athens R&T, n = 6). Results were normalized against wild type and shown as means with s.d. of n experiments. P values for comparison with wild type were calculated by one-way ANOVA with Dunnett’s post-test (two-sided), and P ≤ 0.05 was considered significant. Significant P values are displayed. b, TarP reduces neutrophil phagocytosis of N315 strains lacking protein A, opsonized with indicated concentrations of IgG enriched for WTA binding. Values are depicted as mean fluorescence intensity (MFI). Means of two dependent replicates of a representative experiment are shown. The other two representative experiments can be found in Extended Data Fig. 1g. c, TarP abrogates IgG response of mice towards WTA. For each experiment, WTA from N315 ΔtarP or ΔtarS was isolated independently. At least three mice per group were vaccinated and analysed for specific IgG at indicated time points after vaccination. Results are depicted as mean absorbance with s.d. Individual mice are indicated by colour. Increase in IgG levels was assessed by one-way ANOVA with Tukey’s post-test (two-sided). Significant differences (P ≤ 0.05) are indicated with corresponding P values. d, Vaccination with WTA does not protect mice against tarP-expressing N315, as shown for bacterial loads in kidney upon intravenous infection. No significant differences between groups of either five vaccinated mice or four mice for the alum control group (means indicated), calculated by one-way ANOVA, were observed.


Some concluding remarks:

Protection against S. aureus infections is urgently needed, in particular for hospitalized and immunocompromised patients2,4. Antibodies can in principle protect against S. aureus, but their titres and specificities vary largely among humans and they are often not protective in immunocompromised patients3, probably in particular against S. aureus clones that mask dominant epitopes, for instance using TarP. Unfortunately, all previous human vaccination attempts with protein or glycopolymer antigens have failed, for reasons that are unclear24. Our study identifies a new strategy used by pandemic MRSA clones to subvert antibody-mediated immunity, which should be considered in future vaccination approaches. S. aureus WTA with GlcNAc at RboP C3 has been reported as a type-336 antigen, but was not further explored25. We found that tarP is present in type-336 S. aureus (Extended Data Fig. 1f). However, TarP-modified WTA is a very poor antigen and vaccines directed against GlcNAc at WTA RboP C3 or C4 may fail against many of the pandemic MRSA clones. The structural characterization of TarP will instruct the development of specific TarP inhibitors that could become important in combination with anti-WTA vaccines or antibiotic therapies...

...TarP is a new and probably crucial component of the S. aureus virulence factor arsenal26,27, highlighting the important roles of adaptive immunity and its evasion in S. aureus infections.


A note, which may or may not be all that easy to comprehend, from the front lines in confronting the growing antibiotic crisis with molecular biology.

Have a pleasant day tomorrow.

Pentavalent States Observed in Curium, Berkelium and Californium.

The paper I'll discuss in this post is this one: Pentavalent Curium, Berkelium, and Californium in Nitrate Complexes: Extending Actinide Chemistry and Oxidation States (Attila Kovács,*,† Phuong D. Dau,‡ Joaquim Marçalo,§ and John K. Gibson*, Inorg. Chem., 2018, 57 (15), pp 9453–9467.

The shape of the periodic table is actually a quantum mechanical effect. Every electron in an atom must have a unique set quantum configuration numbers, defined by it's primary shell number (which are represented by the rows in the periodic table), and then its suborbital, usually designated for historical reasons as s, p, d, and f, which are represented by its position in a column relative to the "steps" that appear in the table's shape.

In the periodic table both the lanthanides and actinides, the "f elements," appear in the boxes below the main group elements, and the discovery that the actinides, in particular, should go there was the recognition by Glenn Seaborg that they were "f elements" and not, as previously thought as "d elements" that begin with Scandium (Sc) and end with the synthetic element Copernicium (Cn), the "d block elements. The "d block" is actually broken by elements La-Lu (Lanthanum to Lutetium) and Ac-Lw (Actinium to Lawrencium). In fact the "f elements" should represent another "step" in the periodic table, but printing it in this way is logistically difficult since it would be difficult to print on standard paper without making the print too small to read, so they're put in boxes below the "main group" elements.

The heaviest element that has been isolated in a relatively pure form in quantities that are visible is element 99, Einsteinium. It seems theoretically possible to isolate, perhaps, albeit at enormous expense, a visible, if transitory, sample of fermium, element 100, since it is the last element formed by sequential beta decay, but I don't believe it has ever been done, nor will it ever be done. Generally fermium and all of the elements beyond are synthesized on an atom by atom scale in accelerators and are basically known from their decay products and the high energy radiation they produce.

The lanthanide elements, with a few important exceptions generally exhibit the +3 oxidation state, although a few elements like cerium (+4) and europium and samarium (+2) have other oxidation states, but they are all mostly characterized by +3 oxidation state, making their separations from one another somewhat difficult, meaning that their industrial chemistry, important in many modern devices, is at best environmentally suspect at best, environmentally odious at worst.

The chemistry of the lower actinide elements, including those that naturally occur if far richer. In fact thorium is almost always found in the +4 state, protactinium in the +5 state, and uranium in either the +4 or +6 state in the natural environment. For a long time, before Seaborg's discovery, these elements were thought to be "d elements" and in fact, thorium has chemistry much closer to zirconium and hafnium than say, curium, protactinium is more "tantalum like" than curium like, and uranium has many similarities to tungsten. (The presence of billion ton quantities of uranium in oceans only became possible on earth after oxygen appeared in the atmosphere, resulting in the somewhat more soluble +6 uranium oxidation state being formed by oxidation as opposed to the very insoluble +4 state. Uranium, and plutonium, but not generally neptunium, have well characterized +3 states, but thorium, protactinium, do not. (Uranium, neptunium, and plutonium all exhibit volatile hexafluorides (+6) albeit of decreasing stability in sequence; a fact of industrial importance; in the oceans and in certain fresh water supplies, uranium VI is present as the dioxo ion.)

In nuclear technology, the existence of multiple oxidation states among actinide elements greatly simplifies their separations from one another (but not necessarily from fission products), at least in the case where there are only trivial amounts of the transamericium elements, curium and berkelium and californium, all of which can be isolated in gram quantities, and in a the case of curium, kg quantities.

I personally always assumed that except for some exotic chemistry involving +2 states for curium at least, that curium, berkelium and californium most commonly exhibited +3 chemistry and that no higher states existed.

I was wrong.

From the paper cited above:

The range of accessible oxidation states (OSs) of an element is fundamental to its chemistry. In particular, high OSs provide an assessment of the propensity, and ultimately the ability, of valence electrons to become engaged in chemical bonding. Until recently, the highest known OS in the entire Periodic Table was VIII, such as in the stable and volatile molecules RuO4 and OsO4. The OS IX was finally realized in the gas-phase complex IrO4+,(1) but neither this moiety nor this highest OS has been isolated in the condensed phase.(1,2) The appearance of distinctive and otherwise inaccessible chemistry in gas-phase species, such as IrIX in IrO4+, is generally attributed to isolation of a moiety that would otherwise be highly reactive with neighbor species in condensed phases.(3) For example, gas-phase PaO22+, which comprises formally PaVI, has been synthesized, but it activates even dihydrogen to yield atomic H and PaO(OH)22+ in which the stable discrete PaV OS state is recovered.(4) In view of its gas-phase reactivity, there is scant chance of isolating PaO22+ in the condensed phase. Another example of a distinctively high OS accessible (so far) only in the gas phase is PrV in PrO2+ and NPrO,(5,6) this being the only known pentavalent lanthanide.

The early actinides yield ultimate OSs, from AcIII to NpVII, that correspond to engagement of all valence electrons in chemical bonding to yield an empty 5f0 valence electron shell.(7) After Np, the highest accessible actinide OSs, from PuVII to lower OSs beyond Pu, have one or more chemically unengaged valence 5f electron(s), as the nuclear charge increases and energies of the 5f orbitals decrease. The transition from chemical participation of all 5f valence electrons in ubiquitous UVI, to participation of only two valence electrons in prevalent NoII,(8) distinguishes the actinides from the lanthanides for which the relatively low energy of the valence 4f orbitals results in only a few OSs above trivalent.(9) The gas-phase molecular ions BkO2+ and CfO2+ were recently synthesized and their OSs computed as BkV and CfV, which was an advancement beyond oxidation state IV for these elements and extended the distinctive actinyl(V) dioxo moieties into the second half of the actinide series.(10) It is notable that the computed oxidation state in ground-state CmO2+ is not CmV but rather CmIII, which reflects the limited stabilities of OSs above III for the actinides after Am.(10)

A primary goal of the work reported here is to assess stabilities of OSs, particularly the pentavalent OS, of the actinides Cm, Bk, and Cf. These elements represent the transition from the early actinides that exhibit higher OS, including AmVI and possibly also AmVII,(11) to the latest actinides, Es through Lr, that have been definitively identified only in the AnII and/or AnIII OS. The meagre realm of OSs for the late actinides may not be entirely due to intrinsic chemistry because synthetic efforts for these elements have been very limited due to scarcity and short half-lives of available synthetic isotopes. Cm, Bk, and Cf are the heaviest actinides available as isotopes that are both sufficiently abundant (>10 μg) and long-lived (>100 days) for application of some conventional experimental approaches with relatively moderate procedural modifications.


The higher oxidation states were synthesized in the gas phase by the use of electrospray ionization (ESI) and detected in the mass spectrometer in which the ESI was performed.

The results of the spectra were verified by quantum mechanical computations using AIMAll Software

Some cool pictures from the paper:



The caption:

Scheme 1. Generic D2h, C2v, and C2 Symmetry Structures for AnO2(NO3)2–


Apparently this technique has also been applied to lanthanides, motivating this work:




Figure 1. CID mass spectra acquired at a nominal instrumental voltage of 0.5 V for (a) Ce(NO3)4–, (b) Pr(NO3)4–, (c) Nd(NO3)4–, and (d) Tb(NO3)4–. Elimination of NO2 is indicated by arrows. Sequential CID elimination of two NO2 is observed only for Pr(NO3)4– to yield PrO2(NO3)2–.


Mass spectra from the actinides:



The caption:

Figure 2. CID mass spectra acquired at a nominal instrumental voltage of 0.5 V for (a) Pu(NO3)4–, (b) Am(NO3)4–, (c) Cm(NO3)4–, (d) Bk(NO3)4– (with 7% isobaric Cf(NO3)4– from beta-decay of 249Bk), and (e) Cf(NO3)4–. Elimination of NO2 is indicated by arrows. Sequential CID elimination of two NO2 molecules from An(NO3)4– to yield AnO2(NO3)2– is observed in all five cases.


Some calculated structures:



The caption:

Figure 3. Structures of CfIVO2(NO3)2– (top) and CfIIIO2(NO3)2– (bottom) in two perspectives and selected distances in angstrom from CASPT2/DZ calculations.


Results of density functional theory calculations for a curium oxonitride complex:



The caption:

Figure 4. Electron density map of CmO2(NO3)2– from DFT calculations. Charge concentration is indicated by yellow, while charge depletion is indicated by blue.


Molecular orbitals for the plutonium complex in this class:



The caption:

Figure 5. Characteristic molecular orbitals of PuO2(NO3)2– from CASPT2 calculations


The same thing for Berkelium:



The caption:

Figure 6. Characteristic molecular orbitals of BkO2(NO3)2– from CASPT2 calculations.




A text excerpt:

Of the various theoretical approaches, only the AIM model can characterize quantitatively the space between the bonding atoms. Therefore, we performed a topological analysis of the electron density distribution of the AnVO2(NO3)2– complexes in order to see how the density properties of the An–O bonds vary along the 5f row. We were particularly interested in the parameters of An–nitrate interactions, as they may provide a clue on the increasing bend along the actinide row. A graphical representation of the bonding paths, bond and ring critical points of AmVO2(NO3)2– is shown in Figure 7.


Figure 7:



The caption:

Figure 7. Bonding paths (black), bond (green), and ring (small red) critical points of AmVO2(NO3)2–.


Ionization energies:




The caption:

Figure 10. Actinide ionization energies in eV(79) (using corrected value for IE[U3+] as discussed above): (a) fourth IE; (b) fifth IE; (c) sum of fourth and fifth IEs. Dotted lines are approximate upper stability boundaries for (a) AnIV relative to AnIII; (b) AnV relative to AnIV; (c) AnV relative to AnIII.


Some remarks from the conclusion:

Comparison of experimental results for lanthanide and actinide oxide nitrate anion complexes suggested the AnV oxidation state as coordinated actinyl(V) moieties embedded in AnO2(NO3)2– for An = Pu, Am, Cm, Bk, and Cf, this being the first Cm(V) complex. The stability of oxidation state V in these AnO2(NO3)2– complexes has been confirmed by quantum chemical calculations. The relative stability of this oxidation state is particularly notable for Cf and Bk complexes, and therefore the AnIVO2(NO3)2– and AnIIIO2(NO3)2– forms have been explored and their lower stabilities with respect to CfV and BkV have been supported by both CASPT2 and DFT calculations. Whereas pentavalent Cf was expected to be stable due to a half-filled 5f7 configuration, the computations show that this configuration for CfVO2(NO3)2– is not octet with all seven 5f electrons spin-unpaired, but rather sextet with two of the 5f electrons spin-paired in a 5f1+ orbital.

The AnO2(NO3)2– complexes show interesting bonding features. While in the actinyl moiety the ionic character of bonding increases from Pu to Cf (in agreement with experience on several other actinide systems), in the An–NO3– interaction an opposite trend has been observed here. The increasing ionicity in the AnO2 moiety results in charge depletion around An making it more suitable as acceptor for charge transfer from the nitrate oxygens. The increasing covalent character from Pu to Bk ≈ Cf may be an important factor for the trend observed in the molecular geometries, i.e., a gradual bend of the NO3– ligands (described by the N–An–N angle) around An...


I'm well aware that this may all seem very "out there," and perhaps, in some quarters, generate remarks along the lines of "I couldn't care less."

I assure you though, whether you are inclined to believe it or not, or even if you despise the idea, that the chemistry of the actinides is critical, absolutely critical, to saving whatever is left to save of our rapidly deteriorating environment.

I wish you a rather pleasant Sunday.

Nobel Laureate and Nagasaki Atomic Bomb Survivor Osamu Himomura Has Died.

From Nature: Osamu Shimomura (1928–2018)

Growing up during one of the darkest times in history, Osamu Shimomura devoted his long and fruitful career to understanding how creatures emit light. He discovered green fluorescent protein (GFP), with which — decades later — biomedical researchers began to monitor the workings of proteins in living tissue, and to confirm the insertion of genes. For that discovery, he shared the Nobel Prize in Chemistry in 2008 with neurobiologist Martin Chalfie and the late Roger Tsien, a chemist.

Shimomura, who died in Nagasaki, Japan, on 19 October, was the first to show that a protein could contain the light-emitting apparatus within its own peptide chain, rather than interacting with a separate light-emitting compound. The significance of this discovery was that the gene encoding GFP could, in principle, be copied (or ‘cloned’) and used as a tool in other organisms...

...Born on 27 August 1928 in the town of Fukuchiyama, at the height of Japanese expansionism, Shimomura was the son of an army captain whose frequent postings abroad disrupted his child’s school education. Shimomura’s grandmother instilled in him the samurai principles of honour and fortitude. In 1944, with the Pacific War turning against Japan, he and his fellow school students were mobilized to work in a munitions factory in Isahaya, about 25 kilometres from Nagasaki. On 9 August 1945, he was at work when a blinding flash, followed by a huge pressure wave, signalled the dropping of the atomic bomb on the nearby city. He walked home under a shower of black rain. He later wrote that his grandmother’s quick action in putting him straight in the bath might have saved him from the effects of the radiation.

Without a high-school diploma, he despaired of finding a college place. Eventually, Nagasaki Pharmacy College admitted him in 1948. On graduation, he worked for four years as an assistant in practical classes. He devised research projects in his own time, and his professor obtained permission for him to do a year of advanced study...

...The luciferin paper brought an invitation for Shimomura to join the bioluminescence lab of biologist Frank Johnson at Princeton University in New Jersey. Three weeks after marrying Akemi Okubo in August 1960, Shimomura sailed to the United States, his travel paid for by a Fulbright scholarship...

...He discovered almost at once that it was activated by calcium (later, aequorin became an essential reagent as a glowing marker of calcium release). Shimomura, his family and his research colleagues spent 19 summers at Friday Harbor, collecting hundreds of thousands of jellyfish to obtain enough of the elusive material for a full structural analysis. Until a way of making genetically engineered aequorin became available in the 1990s, Shimomura freely shared his carefully harvested stocks with laboratories the world over...


Remarkable.

He reminds me of another Japanese scientist who labored in obscurity on a difficult project, investing heavily his own time, Shuji Nakamura (now at UC Santa Barbara).

One of my son's professors got his Ph.D. and did a post doc with Nakamura.

Nature Editorial for Scientists: Beware the rise of the radical right

The following editorial appears in the journal Nature, one of the world's premier scientific journals:

Beware the rise of the radical right

Academic freedom is on the hit list when radical politicians gain office — as they have done in Europe.

Some excerpts:

Hidden inside a 1970s office block close to London’s Waterloo station is a tiny organization that has helped tens of thousands of academics find sanctuary from conflict. Co-founded 85 years ago by the economist William Beveridge and physicist Ernest Rutherford, the organization, now called the Council for At-Risk Academics (CARA), enabled many notable twentieth-century scientists — including biochemist Hans Krebs and philosopher Karl Popper — escape the Nazis and settle at British universities. In recent years it has reached out to the Middle East and receives the largest volume of applications from Yemen and Iraq.

CARA and its counterparts in other countries exist because governments in the host nations value three of the pillars on which democracy rests: the rule of law, a free press and, as we explore in a Comment article, freedom of academic enquiry. If the British government were to decide not to support even one of these, CARA would struggle to carry on...

...Europe’s heads of government are biting their lips, and their reasons for doing so are understandable, even if European agreements or conventions are being violated. There is, of course, the principle of non-interference in the affairs of a sovereign state. But, in addition, the EU works through the collective solidarity of its member states. This is what has enabled the organization to enact progressive policies in climate change, anti-discrimination legislation and employee rights.

But collective progressivism breaks down when one-third of EU governments include political parties with scant commitment to protecting democratic institutions. Now that EU governments include parties who do not believe in the rights of people from minority groups, the consensus on climate change, or, indeed, academic freedom, it will become more difficult for the EU as a whole to either advance, advocate or protect policies in these fields...


I don't know why the editorial singles out Europe.

The United States - and now Brazil - are ruled by some of the worst examples of human beings the world has ever seen.

We will see if "the rule of law" can survive in the US. How history will regard it will depend entirely on whether the orange nightmare and his enablers see prison time or, better yet, die in prison.

The implications extend well beyond science, but at as we are realizing the climate catastrophe predicted years ago by scientists, more than science is at risk. It is the very future of humanity that is on the line.
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