Pages that I visit a lot.

2023-01-05

Images dumping ground

I just realised (well, re-realised) that Box links are damned all use for linking images inline into blog posts. Whereas images posted here at least acquire a displayable link.

Scratchpad for post-in-work

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Nope, WP can't process those links either.

Images pile

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add new images here 

Blogger wants double line-breaks for new-paragraph. Or what?

How I like my WP (word processor) set up.

2022-09-21

September Science readings.

September Notes Page

====================

Articles studied this September - some of which might go to Slashdot.
DART impacted
Doggerland Bathymetry
End of document

September science readings.

2/3 the way through the months, and I've not written a word, Even though I've got 4 things open on my desktop, and haven't touched ArXiv for most of the month.


NASA impactor "DART" hit it's target.

link

DART is a part of a mission to attempt to examine how efficiently an impactor (the DART body) transferrs momentum to the (probably) not-very-solid body of the asteroid's "moon". For many ideas about how to deflect bodies on a impact trajector with Earth, this is important data.

According to Hollywood, this will always work ; reality may differ from Hollywood [shock! horror!]. That is why the experiment has been carried out.

Doggerland Bathymetry

For people's information : a seabed map of the "Doggerland" region, countoured at 10m isobaths.

Yes, compared to the main part of the North Sea, it's shallow. But that's still not particularly shallow - the shallowest contour on this map is at 20m, around twice the area is enclosed by the 30m contour. That's about 10kyr ago in terms of post-glacial sealevel rise.

Note the "grooved" structure to the seafloor, which is regions of currently active tidal scour. Power cables, pipelines and turbine bases in areas with scour like this need extensive (i.e. expensive) armouring with concrete-filled sand bags etc to avoid the structures being undermined by erosion.

The "Silverpit" seabed structure (a fishing ground) is prominent between the Dogger Bank and the coast of Norfolk.


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2022-08-18

August Science readings

Articles studied this August - some of which might go to Slashdot.
Topic 01 Last July, Ammonia considered as a biosignature
Topic 2010 asteroids may be result of recent breakup
Topic Topic 03
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Not the most productive of months, nor Sept either, with me closing this page 21 Sept.


Last July - Ammonia, considered as a biosignature

https://arxiv.org/pdf/2107.12424.pdf Assessment of Ammonia as a Biosignature Gas in Exoplanet Atmospheres, Huang, Seager et al, ArXiv posting
Abstract -Ammonia (NH3) in a terrestrial planet atmosphere is generally a good biosignature gas, primarily because terrestrial planets have no significant known abiotic NH3 source. The conditions required for NH3 to accumulate in the atmosphere are, however, stringent. NH3's high water solubility and high bio-useability likely prevent NH3 from accumulating in the atmosphere to detectable levels unless life is a net source of NH3 and produces enough NH3 to saturate the surface sinks. Only then can NH3 accumulate in the atmosphere with a reasonable surface production flux.
For the highly favorable planetary scenario of terrestrial planets with H2-dominated atmospheres orbiting M dwarf stars (M5V), we find a minimum of about 5 ppm column-averaged mixing ratio is needed for NH3 to be detectable with JWST, considering a 10 ppm JWST systematic noise floor. When the surface is saturated with NH3 (i.e., there are no NH3-removal reactions on the surface), the required biological surface flux to reach 5 ppm is on the order of 1010 molecules cm-2 s-1, comparable to the terrestrial biological production of CH4. However, when the surface is unsaturated with NH3, due to additional sinks present on the surface, life would have to produce NH3 at surface flux levels on the order of 1015 molecules cm-2 s-1 (~4.5×106 Tg year-1). This value is roughly 20,000 times greater than the biological production of NH3 on Earth and about 10,000 times greater than Earth’s CH4 biological production.
Volatile amines have similar solubilities and reactivities to NH3 and hence share NH3's weaknesses and strengths as a biosignature. Finally, to establish NH3 as a biosignature gas, we must rule out mini-Neptunes with deep atmospheres, where temperatures and pressures are high enough for NH3’s atmospheric production.

This was brought to my attention by Slashdot user "burtosis" when I mentioned my interest in the multiple eutectics in the ammonia-water-CO2 system in the ~240 - 270 K temperature range, at modest pressures achievable with a less than Venusian atmosphere on a terrestrial planet. A number of people have pointed out the potential importance of the low density of ice compared to liquid water, possibly helping persistence of pre-biotic chemistry in water solution below a (seasonal) skim of ice ; another strand of thought is that, in such a "cold-Darwinian" "icy little pool" could to a degree bypass the "concentration problem" for (proto-)biomolecules by the zone-refining effect where minor contaminants are excluded on a growing crystal surface, and concentrate in the region ahead of the growing crystal. This industrially useful process could concentrate (proto-)biomolecules into small volumes of interstitial water between ice crystals, where reactions might take place at higher concentrations in the bulk. If you were to combine this scenario with, say, a hydrothermal spring's outlet pool on an early Earth under a faint young Sun, you could easily get a diurnal (possibly as little as 12 hours) cycle of chemical concentration, then re-heating and mixing, then re-concentration under ice ... which is a very good situation for processing lots of similar chemical reactions.

When I've thought about possible (not necessarily Earth-like) conditions in which a chemical life-like system could develop, I've often considered this NH3 - H2O - CO2 as a useful pounterpoint to the general assumption of a water-based chemistry. (This does not mean that I think this happened on Earth ; I'm using it as a theoretical counterpoint to terrestrial water-based chemistry). I admit that I hadn't particularly considered the abundance of ammonia in planetary atmospheres - it's well known in the atmospheres of Jupiter, Saturn, Uranus ("George, don't do that!" ; I get fed up with the juvenuile wittering of people incapable of pronouncing that planet's name without adding a scatological joke, so I'll counter with Madam Joyce's cut-glass admonitions to her little star, George. Yes, it's a Herschel joke.), so I just assumed it is there. Maybe a mistake to just assume that. Ammonia is also reported as a (small) component of volcanic out-gassing.

The authors of this paper point out that around Sun-like stars ammonia is subject to UV photolysis, so my putative NH3 - H2O - CO2 atmosphere would probably need to be restricted to "red dwarf" (K, M, N spectral classes) stars. But since the interesting atmospheres would also need to be somewhat colder than Earth's (present) atmosphere, I don't really see that as a terrible constraint. Also, K, M, N dwarfs are the commonest types of stars, by a considerable margin.

These authors also point out that today there are a number of geochemical sinks for ammonia, largely involving photochemically-mediated oxidation by atmospheric oxygen. Well, it's certainly a point - but since oxygen itself is generally also considered a biomarker, and I've already "turned down" the UV dose by restricting myself to K,M,N dwarfs, I don't think it's a disabling point for a "atmosphere for discussion.

"Burtosis" did provoke me to think more closely about possible places for such an environment to exist. To get the right range of temperatures and pressures, without being on an "ice giant", I thought about the "ice balls" (minor bodies like Europa, Callisto, Ganymede, and possibly Pluto or Charon) which have substantial ice shells above (probable) watery oceans. If (and it's an "if" ; I'm world-building here, to look for non-aqueous solvent life-formation environments here, not necessarily being serious) the planet (minor body) produced or released significant ammonia by (tidal friction-driven) vulcanicity, then you might get the relevant mix of compounds to produce this "environment for argument" on the underside of the ice shell.

All in all, I think I'll continue using this as a counter-argument to arrertions that "origin of life needs liquid water". I'm perfectly happy that the example of life which we have (Earth's) originated using water as a dominant solvent. But that's an argument about "Life Jim, but as we know it!" ; but trying to extend the discussion to life generally, we also need to try to consider systems of "Life, Jim, but NOT as we know it". And this is an environment for argument about that. I'll continue to use it, but bear in mind the (purported) realtive paucity of ammonia as a nitrogen-containing species.

Several of the papers authors also made some discussion of a putative planet type with a deep nitrogen-hydrogen (H2O -N2) atmosphere, where putative life could "burn" hydrogen to ammonia using whatever biochemical counterpart of photosynthesis it needs to invent. That's an interesting world - they describe it as a "Cold Haber" world - and I might pilfer that idea too. (They cite it as "Seager, S., Bains, W. & Hu, R. Biosignature gases in H2-Dominated atmospheres on rocky exoplanets. Astrophys. J. 777, 95 (2013)" ; I'll have to get a copy one of these days.)


Extremely young asteroid pair (458271) 2010 UM26 and 2010 RN221

arxiv.org pdf 2208.06207.pdf Abstract - Aims. Extremely similar heliocentric orbital elements of the main-belt objects (458271) 2010 UM26 and 2010 RN221 make them the tightest known pair and promise its very young age. We analyzed the conditions of its origin and determined its age.
Methods. We conducted dedicated observations of (458271) 2010 UM26 and 2010 RN221 in summer 2022 that resulted in a high- accuracy astrometric set of data. Joining them with the previously available observations, we improved the precision of the orbit determination of both asteroids. We used numerical simulations backward in time to constrain the origin of this new pair by observing orbital convergence in the Cartesian space.
Results. Using a large number of possible clone variants of (458271) 2010 UM26 and 2010 RN221 we find they all converge in a narrow time interval around March 2003 having extremely tight minimum distances (≤ 1000 km) and minimum relative velocities (≤ 3 cm s−1). These conditions require to include mutual gravitational attraction of the asteroids constituting the pair for its age determination. Extending our model by this effect even improves the convergence results. We find there is more than 55% probability that the pair formed after the year 2000. However, quasi-satellite captures make the possible age uncertainty of this pair prolonged possibly to the 1960s. Still, this is by far the youngest known asteroid pair, a prime target for future astronomical observations.

Well, there's not a lot to say that isn't in the Abstract. That being what abstracts are for, after all.

The authors do grant that the precision of orbital calculations (and calculations of perturbations from all the other planets and asteroids) isn't enough to distinguish cleanly between an origin of the pair by fission of a progenitor body in 2003, versus fission of the progenitor as early as the 1960s followed by a period of unstable mutual orbit before reaching the point of orbital separation.

It's not as if we haven't seen this sort of thing before - a significant number of comets fragemnt into multiple parts, often but not always as the pass close to the Sun ; there's no particular reason to think it can't happen to asteroids too, as they are spun-up by effects like the Yarkovsky-O'Keefe-Radzievskii-Paddack (YORP) effect. Then there's the close-approach effect, as exemplified by Comet Shoemaker-Levy-9.



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2022-07-24

July science readings

Articles studied this July - some of which might go to Slashdot.
Not really science. A "Wittgenstein-ism"
A very fat neutron star
End of document

Had a holiday.

Done non-internet stuff. Better try to get back to some sort of normality.


A "Wittgenstein-ism"

(my quotes file)

Wikiquotes (last entry in the section from this book).

I picked up (from Prof Jerry Coyne, "Professor Ceiling Cat", at Why Evolution Is True (a website, not a blog, despite all appearences to the contrary) a nice little snippet from Wittgenstein, and dropped it into my "quotes" file.

German : Wovon man nicht sprechen kann, darüber muss man schweigen.
English : Whereof one cannot speak, thereof one must be silent.

I like it. A polite way of saying, "If you're unwilling to define your terms, STFU." I'll have to remember it next time there's a god-squaddy needing a slap in the arguments.


PSR J0952-0607: The Fastest and Heaviest Known Galactic Neutron Star

https://arxiv.org/pdf/2207.05124.pdf

The title is ambiguous - is "fastest" in reference to proper moton (across the "plane of the sky") or it's rotation? My first glance of the abstract says "rotation", but as I start making notes I think - "the forces that impart proper motion (an eccentric supernova explosion) might also be correlated with producing a rotational kick ; so could the two properties be correlated. Through an orientation factor to the plane of the sky/ line of sight, of course.

Abstract : We describe Keck-telescope spectrophotometry and imaging of the companion of the “black widow” pulsar PSR J0952−0607, the fastest known spinning neutron star (NS) in the disk of the Milky Way. The companion is very faint at minimum brightness, presenting observational challenges, but we have measured multicolor light curves and obtained radial velocities over the illuminated “day” half of the orbit. The model fits indicate system inclination i = 59.8 ± 1.9◦ and a pulsar mass MNS = 2.35 ± 0.17 Msol , the largest well-measured mass found to date. Modeling uncertainties are small, since the heating is not extreme; the companion lies well within its Roche lobe and a simple direct-heating model provides the best fit. If the NS started at a typical pulsar birth mass, nearly 1 Msol has been accreted; this may be connected with the especially low intrinsic dipole surface field, estimated at 6 × 107 G. Joined with reanalysis of other black widow and redback pulsars, we find that the minimum value for the maximum NS mass is Mmax > 2.19 Msol (2.09 Msol) at 1σ (3σ) confidence. This is ∼ 0.15 Msol heavier than the lower limit on Mmax implied by the white-dwarf–pulsar binaries measured via radio Shapiro-delay techniques.

No mention there of the "proper motion". Presumably that's too low to be measured (yet, given the arc since discovery), and unremarkable. The first line of the paper itself remarks on the short arc :

Pulsar PSR J0952−0607 (hereafter J0952) was discovered by Bassa et al. (2017) with a spin period of Ps = 1.41 ms, making it the fastest-spinning pulsar in the disk of the Milky Way.

That's an observation span of 5.2 years - not long for measuring a normal proper motion.

Justification : Table 1 gives the observation dates as MJD 58455.50562 to 59641.37420 (1,185.8 days, 3.25 years), and the Bassa (2017) reference notes it's "timing interval" as starting on MJD 57747.1 which extends the observation arc to 5.2 years.

Future observations are very likely (It's a prime candidate for timing variation studies, having both a very fast spin, and a conpanion to interact with and transfer angular momentum to), so we should get a proper motion eventually. Unless, of course, it's headed directly for us. That'll get the Chicken Little's crowing.

Oh, boring : this occurred to the paper's authors too. And they address it :

Since in addition their optical photometry suggests a large (> 5 kpc) distance, and timing data gave a best-fit (albeit low-significance) proper motion of ∼ 10 mas yr−1

What's the miss distance, for a 5 mas yr−1 proper motion at 5kpc? I make it about 1400AU (0.007 pc), which isn't terribly worrying, and that's assuming that the proper motion is half their "low significance" estimate.

I haven't worked out the travel time, but it's going to be in the millions of years. Let our (your) successor species worry about it.

All of which is good background - weighing NS is a fairly exotic occupation. But what's the paper about? Well, essentially, it's good old Kepler : find the orbital velocity of the bodies in orbit (using the "companion" star mentioned above), and their separation and period, and you can pull the masses of the bodies out of the equations. It's one of the main methods of weighing stars - and has been since the invention of spectroscopy which gives access to absorbtion lines in the spectrum and the radial velocity data (velocity in the line of sight). Very weell-established science, and if you "believe" in spectroscopy and Newton's gravitation, the results come out without complex modelling and points for argument.

But the interpretation of those results - where the NS mass interacts with the particle physics - that's more subtle. In theory, as the NS gets bigger, the central pressure geets higher, until the nuclear force is unable to keep the particles from collapsing to some higher energy state. But the presence of spin on the neutron star produces an apparrant centrifugal force (it's really just inertia, but it looks like a force) which acts to reduce the internal pressure in the NS. Which is why fast-spinning NS represent a close probe into how the pressure of NS matter (a proxy for the nuclei of normal matter) varies with the applied load.

From the orbital motions of the two components of this star-NS system, the mass of the NS is 2.35 ± 0.17 Msol, which is appreciably higher than non-rotating NS are thought to be able to reach.

That raises two questions :

  1. what will happen as the NS accretes mass (and angular momentum from the companion ; will the NS implode under it's own gravity or will the increasing rotation continue to support it?
  2. or, will the NS (with it's relatively weak magnetic field) transfer (rotational) angular momentum to the companion star, slowing the NS rotation, increasing the internal pressure until the NS reaches the point that the nuclear forces cannot support the core against the pressure and ... something happens.

Whichever way it goes, getting baseline data now, then watching (for 100 years, or 100 million years - that's a third major question) is possibly a quicker way to probe the finer details of particle physics and nuclear forces than building a particle accelerator large enough (which may be somewhere between the size of the Moon's orbit, or Pluto's orbit). A most fascinating system. Is there an emoticon for Nimoy Spock's eyebrow-raise?

So, what are the critical points for a Slashdot article?

  • Who - an international group of astronomers (except they're not - all at California institutions ; not going to guess at nationalities)
  • What - identified the most massive known NS (to date).
  • Where - Data collection using the Keck telescope in Hawai'i, specifically the LRIS - Low Resolution Imaging Spectrograph - a low-light spectrograph that can acquire good quality data for faint objects.
  • When - Dec 02 2018 to Mar 03 2022 ; fairly fast on the paper-writing!
  • Why - the physics of neutron stars, particularly rotating ones, probes exquisitely into areas of particle energy (specifically, hadronic/ quark-based particles) which we can't approach with terrestrial particle accelerators. The interplay between the static mass of a large neutron star and the (effective, "centrifugal" force) support that the NS material gets from it's rotation allows us to examine the behaviour of the nuclear force in paramter space we can't directly access. Effectively, a spectroscope on a large telescope can perform observational experiments where the whole of CERn cannot reach.
  • Should we be worried - no, it's set for at least a 1400 AU miss, and that not for a million years or more. Someone Elses' Problem - if your Peril-o-matic Sunglasses have darkened, get a warranty repair.

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2022-06-05

June ArXivery

Articles studied June 2022 - some of which might go to Slashdot.
Biological Homochirality
Other things happened.
End of document

June science readings.

Maybe I'll get back to something "productive" now. I think Uncle Roger (deceased) would approve.

Biological Homochirality and the Search for Extraterrestrial Biosignatures

https://arxiv.org/pdf/2205.01193.pdf

Eny Fule Noe that the homochirality of biological molecules is a really important topic in O(s)OL studies. Homochirality is probably essential in biochemistry, because of the concentration problem -if you don't control chirality of reactions, then every chiral centre (which are inevitable in molecules above a fairly low complexity threashold) will approximately halve your reaction efficiency.

Is it important to biochemistry? Ask any thalidomide victim (the sedative is harmless ; flip one chiral centre and you get the teratogen.

Chirality is mentioned in almost every discussion of amino acids and proteins, because amino acids other than glycine (the simplest) has at least one chiral centre. It's also important in sugars, because most sugar monomers have one or two chiral centres, in addition to any introduced in the polytmerisation. Unsurprisingly, chirality is important to getting proteins to fold up into the "right" shape.

This paper examines evidence for homochiral enantiomeric excess (of L- over D, or of D- over L enantiomers) exists beyond Earth, elsewhere in the Solar system, in the "local neighbourhood" (galactic arm, galaxy group - what do they mean?) or in the wider universe.

This short (8 pages) paper seems to be an introduction or a summary for a forthcoming book on the subject, but the publication isn't named.

The big question is, would the detection of a robust homochirality signal by remote (spectroscopic, probably) means be a robust biosignature?

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2022-05-02

May Notes Page

Articles studied this month - some of which might go to Slashdot.
Left over from April Renumbering Of The Antikythera Mechanism Saros Cells, Resulting From The Saros Spiral Mechanical Apokatastasis
Diurnal variation of the surface temperature of Mars with the Emirates Mars Mission: A comparison with Curiosity and Perseverance rover measurements
The origin of Earth’s mantle nitrogen: primordial or early biogeochemical cycling
A numerical approach using a finite element model to constrain the possible interior layout of (16) Psyche
The possible formation of Jupiter from supersolar gas
End of document

May science readings.

What didn't I get to in April.
ReferenceLinkDiscussion
The Planetary Science Journal, 3:92 (11pp), 2022 AprilLarge-scale Volcanism and the Heat Death of Terrestrial WorldsConsiders the likelihood of near-simultaneous LIPs (Large Igneous Provinces) on Earth, and their possible consequences. Which could be a way that Venus hit it's greenhouse runaway while Earth hasn't - yet.
arXiv:2204.10832v1Longitudinal Variation of H2O Ice Absorption on MirandaA number of "small bodies", particularly those tidally locked to a larger body, have obvious accumulations of dark ("tholin") mareial on one aspect, but not on others. This has been seen previously for 4 of the main satellites of Uranus, but not for Miranda. Remembering, of course, that the Uranian system hasn't been visited since Voyager.
Mediterranean Archaeology and Archaeometry Vol. 21, No 2, (2021), pp. 107-128 Renumbering Of The Antikythera Mechanism Saros Cells, Resulting From The Saros Spiral Mechanical Apokatastasis The Antikythera mechanism is always good for commentary. This work looks at the symmetry of the mechanism to suppress the effects of post-manufacture damage. They come up with a new proposed date for the calibration of the mechanism - and hence maybe it's manufacture. Yeah, I think I need to look closely at this one.

And that's the backlog sort-of addressed.

Renumbering Of The Antikythera Mechanism Saros Cells, Resulting From The Saros Spiral Mechanical Apokatastasis

Mediterranean Archaeology and Archaeometry Vol. 21, No 2, (2021), pp. 107-128

The Antikythera mechanism has substantially deformed in it's time under the ocean (original density of the bronze (about 8.87 g/cc ; current density about 3.4 g/cc ; sides aren't straight ; the mechanism disintegrated after eing brought to the surface and drying out - this is why marine archaeology puts finds straight into salt-water tanks on surfacing, and takes years to clean them). Pins, straps and machined-out grooves further complicate the stiffness of the structure, throwing direct measuremnts of the structure into some doubt. The authors propose that considerations of symmetry in the external and internal design of the mechanism might help resolve or resuce ambiguities in the mechanical analysis, to try to work out which Saros cycle the mechanism was intended to start predicting eclipses at. Unfortunately they don't give a specific date- but do add the constraint that the readout spiral starts with a month which includes a solar eclipse and the second half Saros starts with a lunar eclipse. Which probably means a series of possible start dates, 223 synodic months apart. How much ofan advance that is, I'm not sure.

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Diurnal variation of the surface temperature of Mars with the Emirates Mars Mission: A comparison with Curiosity and Perseverance rover measurements

arXiv, for MNRAS

A fairly simple one this one - there are several thermometers in various places on Mars. Having a radiation thermometer ("EMIRS", one of the less strained astronomical acronyms) in space, in a simpler environment, allows comparison between these multiple measures, for a more global picture (exactly like the effect Earth Observation Satellites (EOS) have on terrestrial environmental measurements.

Any surprises? There is a small difference between the temperatures seen by EMIRS (from high, covering a large area around the rover) and the MEDA instrument package on Mars 2020 (viewing the immediate proximity of the rover), during night time observations. The difference varies between 10 and 20 Kelvin (compared to instrument precisions of 1-3 K). The proposed explanation of this diffference is that the rover's drivers choose a less rocky, less rough route for it to travel along, while the satellite observes a wider area, including the rockier areas, with slightly less heat retention than the area around the rover. Well, maybe, maybe not. Time and argument will tell.

The paper introduces - to me - the Mars Climate Database (MCD) - which are at http://www-mars.lmd.jussieu.fr/, and allow you to get time- or location- constrained sets of up to 4 of about 50 parameters. Worth noting. Here is the weather (at time of writing) on Olympus Mons.

"Fun", for a very specific type of "fun".

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The origin of Earth’s mantle nitrogen: primordial or early biogeochemical cycling

link

Hmmm. Interesting. So, the Earth has a lot of nitrogen in it's atmosphere, and it is an essential, often a limiting nutrient. But there is about as much nitrogen in dissolved in the mantle as in the atmosphere, and nitrogen doesn't have a high solubility in magmas (from experimental data) ... so how did the nitrogen get into the mantle? Two options are examined - that the nitrogen is primordial - pre-dating the current arrangement of Earth and atmosphere - or that the nitrogen has been introduced by subdction of nitrogenous sediments. Which needs the nitrogen to be in mineralised forms, as a likely product of biological nitrogen cycling. Very early biological cycling.

Plain Language Summary

Nitrogen (N) is the main component of Earth’s atmosphere, and essential for life. The atmospheric N content influences Earth’s climate and capability to retain its surface water. Primary biological production is limited by bio-available N as well as phosphorous on modern Earth. It has been recently recognized that Earth’s interior contains N comparable to that found in its atmosphere, and thus its origin is important for our understanding of Earth-life co-evolution. We modeled N partitioning in Earth’s molten stage and long-term cycling after Earth’s solidification. Two scenarios are proposed from our modeling. One is that Earth’s mantle acquired its modern N content in the earlier stage due to an excess amount of N Earth accreted, which was later lost to space following asteroid impacts. Another is that Earth’s mantle acquired N via subduction of N-rich sediments, which requires the sedimentary N burial rate on early Earth comparable to the modern value sustained by biological activity. The two scenarios can be tested with future analysis of the geochemical record of surface and mantle N.

Good plain language summary. More journals should try something like that (like PNAS's "Significance" statement).

How much nitrogen is in the early mantle will influence - a lot - the nitrogen levels in the atmosphere, and with it the degree of greenhouse warming (di-nitrogen, N2 itself is not a greenhouse gas, but by bulking up the atmosphere it broadens the IR absorbtion bands of other gasses, enhancing their greenhouse potentials. That holds for water vapour as much as CO2.) subducting N on modern Earth has δ15N ∼ +6‰ [...] Thus, efficient subduction should lead to 15N enrichment in the mantle. Carbon-bearing deep mantle diamonds have been found to host N with almost exclusively positive δ15N values, which might be consistent with an origin from subducted oceanic sediments. However, MORBs (Mid-Ocean Ridge Basalts - in the slim chance that anyone other than me reads this.) on the other hand have less positive δ15N values (typically, ~-5‰) which is generally taken to imply that the mantle contains a significantly negatively enriched N reservoir. But the authiors seem to blow hot then cold on this question. A little later they say (my emphasis): The N isotopic ratio of initial mantle is from −40 to 0‰ as found in enstatite chondrites. We note that such low δ15N values have been reported for some rare diamonds from Earth’s mantle, which possibly record the signature of Earth’s N source (Palot et al., 2012). To my mind, that implies that they don't think that the typical mantle composition is as negatively enriched as that. Which is odd.

So, did the Earth's mantle get it's nitrogen inventory by primordial inheritance, or through biogenic nitrogen cycling? That's not clear.

One useful point is their discussion of how N solubility is related to oxidation state. Neutral N (as dinitrogen, N2) behaves similarly to Ar, an inert gas but in a reduced magma (reduced below the QFM buffer?) the N is present as NH4+, and can substitute for K+ in mineral lattices.

It's a modelling result, so highly prone to one's premises. That question about the reduction state of the Earth's mantle before the Great Oxidation Event of roughly 3.2 ~ 2.0 Gyr BP. and how soluble nitrogen was then. But without that, doe the nitrogen content of the mantle require a highly biogenic source of subducted N, very early in the Earth's history. Which isn't without precedent (the alleged carbon enrichment in Akilia's near-Hadean metasediments, for example), but is nibbling away at the fairly hard limit on the origin of life, as some time between the formation of the Earth, and the oldest fossils (trating Akilia's apatite-encased graphite as a fossil). You might stretch a point and look at the Moon-forming impact as the early bound, ut that only shifts borders by around 0.1 Gyr of a ~0.8 Gyr window.

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A numerical approach using a finite element model to constrain the possible interior layout of (16) Psyche

arXiv, no indication which journal it's intended for, or if it has been accepted.

So, why did this grab my attention? Probably it's that an awful lot of Musk-o-philes think it's an almost archaetypal asteroid - made of metal, big, lumpy, ideal for mining for "Precious Metals Measurless to Man" (to mis-quote Coleridge). It's what people want to hear, so it's what people hear. They don't want to hear that it comprises about 1% of the mass of the asteroid belt, which is reasonably consistent with other estimates of the abundance of metal-rich ("M-type" ; nothing to do with Star Trek) asteroids.

The paper is about modelling efforts to try to constrain the internal structure of Psyche, given the observations. It has metal on it's surface (spectroscopy tells us this, but radar reflectance also tells us that the surface is not entirely metals) ; it is not pure metal (iron meteorites have density typically ~7.5 g/cc (7500kg/m3 ; Psyche has overall density ~4.0).

The density data could be achieved by a rubble-pile structure with porosity of about 50% - but it would have remained malleable (temperature >~800K) until well after the bombardment intensity decreased below what would be needed to make so much porosity. Therefore the mixed composition (metals plus silicates) is the likely route to follow. That in itself raises a question - if the body is large enough and hot enough to be soft, why didn't large metal masses sink into the core? At which point, "ferrovolcanism" - the eruption of metal-rich magmas to the surface becomes a logical necessity.

We don't know the interior structure of Psyche - that's why there is an investigation mission somewhere between the drawing board and the assembly room - but people are working on models of it so that when more data comes in, the options can be rapidly narrowed down. Standard science - incremental advance, testing hypotheses against reality and discarding those that are wrong- Feynman would be proud.

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The possible formation of Jupiter from supersolar gas

arXiv, accepted for Planetary.Sci Journal

FTFA, More than two decades ago, the Galileo probe performed in situ measurements of the composition of Jupiter’s atmosphere and found that the abundances of C, N, S, P, Ar, Kr and Xe were all enriched by factors of 1.5–5.4 times their protosolar value. Juno’s measurements recently confirmed the supersolar N abundance and also found that the O abundance was enriched by a factor 1–5 compared to its protosolar value. So ... if Jupiter was formed from the smae gas as the Solar nebula, then 1 to [several] Jupiter-masses (MJ) of [H, He] material has been lost from Jupiter. Or, it was formed from a [H, He]-depleted region of the Solar nebula. But that "region of the Solar nebula" was probably most of the nebula, which is somewhat challenging.

Note that the abundances have been confirmed by two sets of measurements - from Galileo and from Juno - so it would take religious/ Trumpian levels of mendacity to claim the results are "fake news".

The results of modelling the inflow of dusts (and vapours when the dusts comes in too close to the Sun) from the "proto-solar nebula" (PSN) with the majority of the PSN (H, He) staying out in the vasty deep, but the condensed materials (dusts, then their vapours) settling towards the Sun by dynamic friction.

Their modelling shows that the right sort of composition of material occurs between the H2O and CO2 "ice-lines" (about 4AU from the Sun) between about 100 kyr and 300 kyr after solar ignition. Which is pretty early - compared to "planetesimal accretion models for the formation of the "terrestrial" planets, but people have always thought that most of the accretion of the gas giants took place very early, with the terrestrial planets (and "small bodies") forming as the giants exhibit their pas de deux of orbital evolution as the last of the nebula dissipates.

On the other hand, the necessary accretion timescales and rates are compatible with both core-accretion and gravitational-instability models for building a gas giant. This model doesn't help us decide which mechanism (or possibly, a third, but they're the two lead contenders by a considerable margin) occurred - or possibly both, in close sequence - but it does suggest that both are plausible.

Real Life &tm; intruded.

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Is Betelgeuse Shrinking?

Paper : Systematic Change With Time In The Size Of Betelgeuse

Astrophysical Journal, 2009

I was tidying a corner of my hard drive earlier and found this paper. "Eny fule no" (well, at least, in my target audience, which is "me") that Betelgeuse was the first star to have it's size measured directly, using an interferometer bolted onto the top of the Mt Wilson "100-inch" telescope in the 1920s. Which was great. But one measurement is just that - one measurement. So, you repeat it (checking theat a new instrument is working, or if the diameter seems different at different wavelengths), because with one measurement, you have a data point, with two measurments, you have a disagreement, and with three measurements you are starting to understand any variation in the signal.

That thing about wavelength of observation may be slightly surprising, but when you think that Betelgeuse is itself a very red colour, and that spheres exhibit "limb darkening", it becomes less surprising that aparrent diameter is quite dependent o nthe wavelength you do your observation at.

The important point about the 2009 paper is that they performed multiple measurements over the years, but all at the same IR wavelength, so "apples are compared with apples". And they see a consistent change in diameter, which they fit a quadratic curve to. Quadratic, opening downwards. Which means, it's going to cross the "zero size axis" at some point in the future. I did a bit of mental figuring, then needed to work out the numbers, because apporximately Betelgeuse should be reaching "zero" size about now.

OK, people, I do realise that I'm extrapolating to about 7 times the original dataset's span. Not generally considered a good thing. But what the hey - with Betelgeuse still showing substantial, rapid brightness fluctuations, the prospect of it going out might excite the people waiting with baitéd breath. Doing the same quadratic (polynomial, order 2) fit as the original authors, and converting the dates from the paper to the standard Julian Day measure, to get this.

Re-plot of 2009 paper data, with equations.

The equations OOCalc churns out are on the printout, but aren't terribly important. Decent R-squared values though, over 0.9 for both. So, simplistically, the expected "zero diameter date range for Betelgeuse is 2030 to about 2040. Interesting. All terribly exciting.

I'd suspected that the imaging had just caught a part of a (very roughly) sinusoidal variation, and it just looked like a quadratic over that part of the cycle. I'm going to add the other diameter estimates into the data set. Firstly, there's the 1920 data, and that, in itself ought to hold a warning - a third-order (i.e. cubic) polynomial fits as well as a quadratic.

Let's see what I can find in intermediate data, to try to clarify that cubic/ quadratic question.

In 1973, a group used a TV camera to "speckle" the image of Betelgeuse and estimate it's diameter. That's in a visible waveband, so not directly comparable with the mid-IR data - but I'll compare them anyway. (Source : Astrophysical Journal, v181:L1-L4, 1973 April 1 (oh dear, an ominous date ; but I don't see much sign of jocularity ; I'll take it straight.) "Speckle Interferometry: Color-dependent Limb Darkening Evidenced On Alpha Orionis And Omicron Ceti"). They give several diameter estimates at different colour bands. The longest wavelength (closest to the mid-IR figures so far) size for Betelgeuse is (date 1972-09-09, wavelength 7190 Å, diameter 52 ±5 mas), so I'll plot that (JD 2441570).

Ohhh, that's lovely - really wrecks the correlation. The cubic fit for maximum diameter still drops to zero in the foreseeable future (and I've "improved" the 2extrapolating wildly beyond the dataset problem too - less than doubling the range of prediction. And some more data (Astron & Astrophys, v115, p253, 1982 July 20"The angular diameter of Betelgeuse.", using data from similar methods on other telescopes) gives two data lines (again, selecting the longest wavelength readings) of 1978-11-09, 7150±20Å 67±4 mas and 1979-02-22, 7730±84%Aring;, 62±2 mas. And I plot them up too, and it actually maintains the fit, if not at quite such good correlation coefficients. Although it doesn't really look like it, that fit for the maximum diameter (blue line) is actually a cubic curve, but it's so close to quadratic that the original author's choice is fully vindicated.

Well, I've found all the data I can. Or have I? I'm just referencing data from the 2009 paper. Has there been anything more recent? nothing significant I can find. It's a fun idea, that Betelgeuse is shrinking. It's probably nothing - just the reasonably well-known pulsation of some stars, particualarly big ones, possibly combined with shedding annuli of material from the surface and that evolving over time. But ... it would be fun if a bright star was to disappear from our sky. Much freaking out would happen.

(Is the "C.Townes" who keeps appearing in these references the guy who invented the maser/ laser? Would be a relevant field. ... Seems that it is.) Died 2015.

2022-04-20

DNA, RNA, chirality.

Biochemistry notes.
Slashdot discussion
Aside on optical microscopy
next Article Description
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"Eny fule no" that I've long been interested in OOL (Origin(s) Of Life). I think it even pre-dates the meeting I mentioned with Alan Cairns-Smith as a student, when he was promoting one of his books on his "clay life" hypothesis.

Well, I've just been having a conversation on Slashdot which has prompted me to improve my knowledge of biochemistry, because the question of chirality reared it's head again. (I hope any readers already know what chirality is, and why it is important in both biochemistry and discussions of OOL.)

This doesn't start at the beginning ; we'd been discussing, indirectly, OOL. See the discussion thread linked above. Slashdot has a fairly short window for discussion, before a thread is locked and archived. It also has a preview option (which too few people use, including me) because once you've posted, you can't edit or remove. (The admins can delete something, but very rarely do - it takes legal action.)

My comment to Immerman

I suspect that would be true even if the common ancestor was RNA-based.

Ummm, I think the UCGA bases in RNA are chiral - but I'd have to check. Hmmmm ...

The naturally occurring enantiomer of RNA is D-RNA composed of D-ribonucleotides. All chirality centers are located in the D-ribose. By the use of L-ribose or rather L-ribonucleotides, L-RNA can be synthesized.

Which rather implies that the bases themselves are not chiral. (I saw a mention that the purine group in RNA and DNA bases is made by metabolism of glycine - which itself is achiral.)

Adenine - achiral (just look at the structure of the molecule - no 4-radical carbons). I see an interesting note that "Both adenine and guanine are derived from the nucleotide inosine monophosphate (IMP), which in turn is synthesized from a pre-existing ribose phosphate through a complex pathway using atoms from the amino acids glycine, glutamine, and aspartic acid, as well as the coenzyme tetrahydrofolate." ... so the atoms derived from glutamine and aspartic acid must be from parts of the achiral side chains, not including the chiral amino acid centre. I also note that the highest turnover molecule in metabolism, ATP, is derived from adenine, and so by extension is achiral.

Cytosine - again, achiral ; look at the structure. Which also means that other pyrimidine derivative are achiral (unless you put in a side chain which itself is chiral). So that disposes of uracil too (the two can interconvert by amination/ deamination). Again, from Wiki, When found third in a codon of RNA, cytosine is synonymous with uracil, as they are interchangeable as the third base. When found as the second base in a codon, the third is always interchangeable. For example, UCU, UCC, UCA and UCG are all serine, regardless of the third base. Which is another clue towards the proposal that the original form of the DNA/ RNA/ "Preceeding Genetic System" may have had two-base-pair long codons, which added a third codon to the coding system when more than 15 amino acids were required by the metabolism. Not a universally accepted idea in OOL, but suggestive.

Guanine - achiral. Useless, but interesting factoid : "In 1656 in Paris, a Mr. Jaquin extracted from the scales of the fish Alburnus alburnus so-called "pearl essence", which is crystalline guanine. In the cosmetics industry, crystalline guanine is used as an additive to various products (e.g., shampoos), where it provides a pearly iridescent effect. " (Going through the process of writing these things down helps me get them to stick in my mental piling system.) Isn't crystallised guanine a common competitor in "pretty PPL/ XPL microscopic images" competitions?

Uracil - achiral again. This is the base that is found in RNA, replacing thymine, but I didn't know until now that it is actively removed from DNA strands : " Uracil-DNA glycosylase excises uracil bases from double-stranded DNA." (How does uracil get into DNA? see the note above about the deamination of cytosine.) Ah, this is interesting too, and very relevant to my interests in OOL : This problem is believed to have been solved in terms of evolution, i.e. by "tagging" (methylating) uracil. Methylated uracil is identical to thymine. Hence the hypothesis that, over time, thymine became standard in DNA instead of uracil. This snippet is worth piling away as well : Uracil-containing DNA still exists, for example in

  • DNA of several phages
  • Endopterygote development
  • Hypermutations during the synthesis of vertebrate antibodies.
. That's weird. as the saying goes, "who ordered that?".

Thymine - achiral. Nothing else particularly interesting, but a synthesis reaction described on Wiki leaves out a significant factor : "Patented 2013, the current method used for the manufacturing of thymine is done by dissolving the molecule Methyl methacrylate in a solvent of methanol." Odd capitalisation, but you probably have a few hundred grams of the compound around your house - it's the monomer of "Perspex" (under many names). Ye gods, it still shows that I spent 20 years living with a plastics chemist.

None of this is probably particularly interesting to you, but it has tickled some of my recurring interests in OOL matters. That chirality thing remains interesting. I'm probably going to have to read up on the chemistry of sugars, not just because of the thing about the spiral chirality of DNA being (by elimination) hosted in the deoxyribose backbone, not the bases. And as Molesworth and "eny fule no", biological sugars are as dedicatedly chiral as amino acids, but in the other sense (D- rather than L-). Which itself indicates that L-amino acids can produce enzymes that are perfectly happy to manipulate D- chiral molecules.

I'm going to file this post separately for my future reference.

- got hold of a biochemistry textbook . Revising my chemistry, with an emphasis on carbohydrates for the now, but I need to do some work on fats too. Noting that the "line" expression of carbohydrate structures (stretched along the carbon-carbon backbone) makes it easy to spot the chiral centres (the two off-backbone radicals are different ; this is a chiral centre [unless the two backbone segments are identical, which I don't think can happen in most sugars]).

Aside on optical microscopy.

I forgot to follow that thread (strand?) on PPL/ XPL. What do you call it when you illuminate a slide with PPL, but then insert the analyser parallel to the polarizer? You get a different set of interference colours (and not all petrological microscopes can do this), which are quite pretty. (I'm thinking of photos like this collection (of l-arginine crystals, particularly the contrasting nucleation rosettes and dendritic growths later in the article), but it seems my memory of particularly uracil and guanine being popular - lots of organic molecules are used.) Going back to the "polariser-parallel analyser" question, does it have a name? You're not looking at the ordinary vs extraordinary rays' path difference, but ... what? I really need to sit back at the microscope to work this out - probably with the plates to try some quantitative measurements.

next Article DNA/ RNA structure

https://en.wikipedia.org/wiki/A-DNA There are several different structures available to both DNA and double-strnaded RNA.

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