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How evolution builds genes from scratch.

The news item I'll discuss in this post is this one: How evolution builds genes from scratch

I don't think I logged into Nature when I saw it, so I think it's open sourced.

A lot of my day to day work is involved in proteomics either directly or indirectly. I am therefore often required to think about protein isoforms, many of which arise from genetic differences in people and related organisms; there is little more fascinating than seeing those forms highly conserved throughout evolution in comparison to variable, and indeed, vestigial proteins and sequences.

A surprise of the discovery of automated gene sequencing that led to the result of the human genome sequence, as the subsequent gene mapping of many other species is how much "junk DNA" there is, some of which is artifacts of ancient viral infections in ancestors or ancestral organisms.

This news article suggests that new genes can sometimes arise from turning on "junk DNA."

Some excerpts:

PDF version
5-inch Arctic cod in hollows of ice floes in the Arctic Ocean
Some cod species have a newly minted gene involved in preventing freezing.Credit: Paul Nicklen/NG Image Collection

In the depths of winter, water temperatures in the ice-covered Arctic Ocean can sink below zero. That’s cold enough to freeze many fish, but the conditions don’t trouble the cod. A protein in its blood and tissues binds to tiny ice crystals and stops them from growing.

Where codfish got this talent was a puzzle that evolutionary biologist Helle Tessand Baalsrud wanted to solve. She and her team at the University of Oslo searched the genomes of the Atlantic cod (Gadus morhua) and several of its closest relatives, thinking they would track down the cousins of the antifreeze gene. None showed up. Baalsrud, who at the time was a new parent, worried that her lack of sleep was causing her to miss something obvious.

But then she stumbled on studies suggesting that genes do not always evolve from existing ones, as biologists long supposed. Instead, some are fashioned from desolate stretches of the genome that do not code for any functional molecules. When she looked back at the fish genomes, she saw hints this might be the case: the antifreeze protein — essential to the cod’s survival — had seemingly been built from scratch1.

The cod is in good company. In the past five years, researchers have found numerous signs of these newly minted ‘de novo’ genes in every lineage they have surveyed. These include model organisms such as fruit flies and mice, important crop plants and humans; some of the genes are expressed in brain and testicular tissue, others in various cancers...

...Back in the 1970s, geneticists saw evolution as a rather conservative process. When Susumu Ohno laid out the hypothesis that most genes evolved through duplication2, he wrote that “In a strict sense, nothing in evolution is created de novo. Each new gene must have arisen from an already existing gene.”

Gene duplication occurs when errors in the DNA-replication process produce multiple instances of a gene. Over generations, the versions accrue mutations and diverge, so that they eventually encode different molecules, each with their own function. Since the 1970s, researchers have found a raft of other examples of how evolution tinkers with genes — existing genes can be broken up or ‘laterally transferred’ between species. All these processes have something in common: their main ingredient is existing code from a well-oiled molecular machine...

...But genomes contain much more than just genes: in fact, only a few per cent of the human genome, for example, actually encodes genes. Alongside are substantial stretches of DNA — often labelled ‘junk DNA’ — that seem to lack any function. Some of these stretches share features with protein-coding genes without actually being genes themselves: for instance, they are littered with three-letter codons that could, in theory, tell the cell to translate the code into a protein.

It wasn’t until the twenty-first century that scientists began to see hints that non-coding sections of DNA could lead to new functional codes for proteins. As genetic sequencing advanced to the point that researchers could compare entire genomes of close relatives, they began to find evidence that genes could disappear rather quickly during evolution...

...Some of these genes-in-waiting, or what Carvunis and her colleagues called proto-genes, were more gene-like than others, with longer sequences and more of the instructions necessary for turning the DNA into proteins. The proto-genes could provide a fertile testing ground for evolution to convert non-coding material into true genes. “It’s like a beta launch,” suggests Aoife McLysaght, who works on molecular evolution at Trinity College Dublin...

The nice cartoon in the news article:

Interesting I think.

From bomb to Moon: a Nobel laureate of principles

When I was a kid, I used to spend a lot of time at Urey Hall on the UCSD campus. Urey, of course, is the discoverer of deuterium.

At that time of my life I didn't think all that much about Urey, which was my loss. (I was a stupid kid and am now a somewhat less stupid adult.)

Nature has a review of a biography of Urey, and I'm going to put it on my list of "need to read someday."

From bomb to Moon: a Nobel laureate of principles

I think the review is open sourced, but if it isn't, some excerpts:

The Life and Science of Harold C. Urey Matthew Shindell University of Chicago Press (2019)

After witnessing the 1945 Trinity atomic-bomb test, the theoretical physicist J. Robert Oppenheimer recalled Hindu scripture: “Now I am become Death, the destroyer of worlds.” Although this is often interpreted as admitting moral culpability on the part of the Manhattan Project’s scientific director, Oppenheimer remained a central player in the nuclear-weapons establishment until he lost his security clearance in the mid-1950s.

Harold Urey also worked for the Manhattan Project. But by contrast, the Nobel-prizewinning chemist distanced himself from nuclear weapons development after the war. His search for science beyond defence work prompted a shift into studying the origins of life and lunar geology. Now, the absorbing biography The Life and Science of Harold C. Urey by science historian Matthew Shindell uses the researcher’s life to show how a conscientious chemist navigated the cold war.

Shindell argues that Urey’s pious upbringing underpinned his convictions about the dangers of a nuclear arms race, and his commitment to research integrity. Urey grew up a minister’s son in a poor Indiana farming family belonging to a plain-living Protestant sect, the Church of the Brethren. Progressing through increasingly diverse educational environments, culminating in a PhD at the University of California, Berkeley, Urey became self-conscious about the zealousness of his family’s faith. He also found the path to a cosmopolitan, middle-class life.

In the 1920s, Urey was among a small group of chemists who collaborated closely with physicists. Working at Niels Bohr’s Institute for Theoretical Physics at the University of Copenhagen, he kept abreast of developments in quantum mechanics. There, and on travels in Germany, he met the likes of Werner Heisenberg, Wolfgang Pauli and Albert Einstein. But Urey decided he lacked the mathematical skills to make theoretical advances in quantum chemistry. Moving back to the United States, he started both a family and an academic career.

At Johns Hopkins University in Baltimore, Maryland, and later at Columbia University in New York City, Urey taught quantum mechanics to chemists, while setting out on the trail that led him to deuterium. In 1931, he discovered this isotope of hydrogen. Predicted on the basis of work by Bohr, Frederick Soddy, and J. J. Thomson, its existence had been doubted by many chemists and physicists. Urey’s identification won him the Nobel three years later. By this time, he had also co-authored one of the first texts in English on quantum mechanics as applied to molecular systems, the 1930 Atoms, Quanta and Molecules.

Urey’s continuing work on stable isotopes of other chemical elements, such as nitrogen and oxygen, led to important applications in biochemistry and geochemistry, including the pioneering use of isotopic labels to study metabolic pathways. Living in New York also led Urey to political liberalism. He became aware of the anti-Semitism affecting Jewish scientists, and the lack of opportunities for women scientists. A generous mentor, he shared his Nobel prize money with two collaborators, and split a grant he had been awarded with the young Isidor Rabi (who later discovered nuclear magnetic resonance)...

...The Second World War changed Urey’s life, as it did those of most physical scientists and researchers in many countries. His expertise in isotopes made him valuable to the Manhattan Project. Here, he eventually headed a massive team of scientists and engineers working on the separation of uranium isotopes using gaseous diffusion methods. However, he was ill-suited to the pressure of managing this technologically complex and cumbersome project, and Leslie Groves — the project’s overall director — regarded him with suspicion. Even before the war’s end, Urey became deeply disenchanted with working for the military...

...After the war, Urey used his laureate status to voice alarm about the prospect of nuclear warfare. He backed international control through world government as a way to control the military future of atomic energy. This was not a radical view in 1946...

...Over this harrowing period, Urey lost faith in the ability of modern secular society to manage the new threats of the atomic age. Although he had long abandoned his parents’ religion, he began to argue that Judaeo-Christianity was key to democracy. He attributed the success of science itself, with its commitments to honesty and credit, to religious ethics...

...In the late 1940s, Urey used his expertise in mass spectrometry to begin work in geochemistry, and then in planetary science. It was a way to escape the orbit of the nuclear weapons establishment (although he still advised the US Atomic Energy Commission). With chemistry graduate Stanley Miller, he tested hypotheses on the origins of life by Soviet biochemist Alexander Oparin and biologist J. B. S. Haldane, and successfully produced amino acids by sparking a solution of water, methane, ammonia and hydrogen. In 1952, Urey published The Planets, a chemical treatise on the formation of the Solar System...

...Urey became influential during the early days of NASA, formed after the 1957 launch of the Soviet satellite Sputnik, offering the agency persuasive reasons to prioritize exploration of the Moon over other bodies. In 1969, he analysed lunar rocks collected during the Apollo 11 mission, which supported his theory of the Moon’s common origin with Earth. He wanted the well-funded agency to test theories about the origins of the Solar System — experimentation beyond the reach of individual university scientists. Despite his influence, he was disappointed in this: NASA focused on crewed space exploration over questions of cosmogony.

Sounds like a cool book about a cool life, no?

Have a nice weekend.

The terrible day of the wisecrack.

From the Wikipedia entry on the life of Dorothy Parker:

Following Campbell's death, Parker returned to New York City and the Volney Residential hotel. In her later years, she denigrated the Algonquin Round Table, although it had brought her such early notoriety:

These were no giants. Think who was writing in those days—Lardner, Fitzgerald, Faulkner and Hemingway. Those were the real giants. The Round Table was just a lot of people telling jokes and telling each other how good they were. Just a bunch of loudmouths showing off, saving their gags for days, waiting for a chance to spring them... There was no truth in anything they said. It was the terrible day of the wisecrack, so there didn't have to be any truth...[61]

Dorothy Parker

Of course, things are much worse in the age of Twitter, the age of anti-thinking.

We are all in the Algonquin Round Table, and that is not a good thing.

Mapping 123 million neonatal, infant and child deaths between 2000 and 2017

The paper I'll discuss in this post is this one: Mapping 123 million neonatal, infant and child deaths between 2000 and 2017.

This paper is open sourced, and anyone who cares can read it in its entirety.

The argument is often made - and it's a very good one - that the carrying capacity of the planet for human beings has been exceeded now for many decades. Thus it might seem that an argument for saving the lives of children under the age of five while consistent with human ethics may conflict with environmental ethics.

I have long argued that this conflict is actually invalid. The countries with the lowest birth rates are precisely those where people are secure in their homes, have sufficient health care, shelter, food, and where the rights of women in particular are most actively supported. The problem of exploding populations is therefore, in my opinion, is actually an issue of poverty and human development.

This is precisely why I personally focus the overwhelming portion of my private scientific interests on clean energy, because without clean energy, we cannot eliminate poverty and advance human development.

From article 25 of the Universal Declaration of Human Rights, approved by the United Nations in 1948, but since honored more in breach than practice:

Article 25.

(1) Everyone has the right to a standard of living adequate for the health and well-being of himself and of his family, including food, clothing, housing and medical care and necessary social services, and the right to security in the event of unemployment, sickness, disability, widowhood, old age or other lack of livelihood in circumstances beyond his control.

Universal Declaration of Human Rights

Note that Article 25 is not about electric cars and McMansions with solar cells on the roofs. Modern liberalism differs from 1948 liberalism; I personally prefer the latter.

From the abstract:

ince 2000, many countries have achieved considerable success in improving child survival, but localized progress remains unclear. To inform efforts towards United Nations Sustainable Development Goal 3.2—to end preventable child deaths by 2030—we need consistently estimated data at the subnational level regarding child mortality rates and trends. Here we quantified, for the period 2000–2017, the subnational variation in mortality rates and number of deaths of neonates, infants and children under 5 years of age within 99 low- and middle-income countries using a geostatistical survival model. We estimated that 32% of children under 5 in these countries lived in districts that had attained rates of 25 or fewer child deaths per 1,000 live births by 2017, and that 58% of child deaths between 2000 and 2017 in these countries could have been averted in the absence of geographical inequality. This study enables the identification of high-mortality clusters, patterns of progress and geographical inequalities to inform appropriate investments and implementations that will help to improve the health of all populations.

From the introduction:

Gains in child survival have long served as an important proxy measure for improvements in overall population health and development1,2. Global progress in reducing child deaths has been heralded as one of the greatest success stories of global health3. The annual global number of deaths of children under 5 years of age (under 5)4 has declined from 19.6 million in 1950 to 5.4 million in 2017. Nevertheless, these advances in child survival have been far from universally achieved, particularly in low- and middle-income countries (LMICs)4. Previous subnational child mortality assessments at the first (that is, states or provinces) or second (that is, districts or counties) administrative level indicate that extensive geographical inequalities persist5,6,7.

Progress in child survival also diverges across age groups4. Global reductions in mortality rates of children under 5—that is, the under-5 mortality rate (U5MR)—among post-neonatal age groups are greater than those for mortality of neonates (0–28 days)4,8. It is relatively unclear how these age patterns are shifting at a more local scale, posing challenges to ensuring child survival. To pursue the ambitious Sustainable Development Goal (SDG) of the United Nations9 to “end preventable deaths of newborns and children under 5” by 2030, it is vital for decision-makers at all levels to better understand where, and at what ages, child survival remains most tenuous.

A map:

The caption:

a, U5MR at the second administrative level in 2000. b, U5MR at the second administrative level in 2017. c, Modelled posterior exceedance probability that a given second administrative unit had achieved the SDG 3.2 target of 25 deaths per 1,000 live births for children under 5 in 2017. d, Proportion of mortality of children under 5 occurring in the neonatal (0–28 days) group at the second administrative level in 2017.

We live in a country where children are kept in cages for no "crime" other than their race. We are beneath contempt.

This is probably one of the most important scientific papers in terms of ethical import I've read in a long time, and I read a lot of papers.

Have a nice weekend.

Crosslinking ionic oligomers as conformable precursors to calcium carbonate

The paper I'll discuss in this post is this one: Crosslinking ionic oligomers as conformable precursors to calcium carbonate (Tang et al, Nature 574, 394–398 (2019))

The fastest growing contributor on this planet in the 21st century has been dangerous coal, followed by petroleum, which is likely to be exceeded in the next decade by dangerous natural gas. The next largest contributor, also accelerating, is land use changes. Following these, closely is concrete. (Much of the climate change cost of concrete is connected to heat, almost always generated by the use of dangerous fossil fuels. In theory, if not in wide practice it is possible for the use of concrete to by carbon negative, and some major advances along this line have been made, for instance Riman Concrete, but even Riman concrete requires heat to make. Nuclear heat is actually the only practical way to make concrete without dangerous fossil fuels, despite whatever cartoons you've read or even written about solar thermal plants. Solar thermal plants didn't work, they aren't working and they won't work to address climate change and they will never work to make concrete.

In the past several years, my vicarious interest in my son's education has led me to consider a concept called "polymer derived ceramics" in which is just what it sounds like, a polymer is, via process engineering (and generally heat) converted into a highly structured ceramic. This paper touches on that concept, at least in a loose way. Beautiful things, these, with all sorts of fabulous potential applications.

The abstract, which is open sourced:

Inorganic materials have essential roles in society, including in building construction, optical devices, mechanical engineering and as biomaterials1,2,3,4. However, the manufacture of inorganic materials is limited by classical crystallization5, which often produces powders rather than monoliths with continuous structures. Several precursors that enable non-classical crystallization—such as pre-nucleation clusters6,7,8, dense liquid droplets9,10, polymer-induced liquid precursor phases11,12,13 and nanoparticles14—have been proposed to improve the construction of inorganic materials, but the large-scale application of these precursors in monolith preparations is limited by availability and by practical considerations. Inspired by the processability of polymeric materials that can be manufactured by crosslinking monomers or oligomers15, here we demonstrate the construction of continuously structured inorganic materials by crosslinking ionic oligomers. Using calcium carbonate as a model, we obtain a large quantity of its oligomers (CaCO3)n with controllable molecular weights, in which triethylamine acts as a capping agent to stabilize the oligomers. The removal of triethylamine initiates crosslinking of the (CaCO3)n oligomers, and thus the rapid construction of pure monolithic calcium carbonate and even single crystals with a continuous internal structure. The fluid-like behaviour of the oligomer precursor enables it to be readily processed or moulded into shapes, even for materials with structural complexity and variable morphologies. The material construction strategy that we introduce here arises from a fusion of classic inorganic and polymer chemistry, and uses the same cross-linking process for the manufacture the materials.

An excerpt from the introduction:

Published: 16 October 2019
Crosslinking ionic oligomers as conformable precursors to calcium carbonate
Zhaoming Liu, Changyu Shao, Biao Jin, Zhisen Zhang, Yueqi Zhao, Xurong Xu & Ruikang Tang
Nature volume 574, pages394–398 (2019) | Download Citation

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Inorganic materials have essential roles in society, including in building construction, optical devices, mechanical engineering and as biomaterials1,2,3,4. However, the manufacture of inorganic materials is limited by classical crystallization5, which often produces powders rather than monoliths with continuous structures. Several precursors that enable non-classical crystallization—such as pre-nucleation clusters6,7,8, dense liquid droplets9,10, polymer-induced liquid precursor phases11,12,13 and nanoparticles14—have been proposed to improve the construction of inorganic materials, but the large-scale application of these precursors in monolith preparations is limited by availability and by practical considerations. Inspired by the processability of polymeric materials that can be manufactured by crosslinking monomers or oligomers15, here we demonstrate the construction of continuously structured inorganic materials by crosslinking ionic oligomers. Using calcium carbonate as a model, we obtain a large quantity of its oligomers (CaCO3)n with controllable molecular weights, in which triethylamine acts as a capping agent to stabilize the oligomers. The removal of triethylamine initiates crosslinking of the (CaCO3)n oligomers, and thus the rapid construction of pure monolithic calcium carbonate and even single crystals with a continuous internal structure. The fluid-like behaviour of the oligomer precursor enables it to be readily processed or moulded into shapes, even for materials with structural complexity and variable morphologies. The material construction strategy that we introduce here arises from a fusion of classic inorganic and polymer chemistry, and uses the same cross-linking process for the manufacture the materials.

Many materials are consolidated from their crystallized powders16, but their resulting discontinuous internal structures render them brittle with a poor ability to resist fracture17,18. By contrast, polymeric materials are ubiquitous in modern society, due not only to their varied properties but also to their ease of fabrication15,19. The polymerization strategy is superior to crystallization because of its efficiency and controllability. In polymer chemistry, covalent bonds have an important role in ensuring the linkage of small units. Although a few covalent-bond-based inorganic materials (for example silicone and silica)20,21 can be obtained as polymers, there is no general method for the preparation of such materials by crosslinking owing to the lack of investigation into ionic monomers or oligomers for this purpose. In the control of polymerization reactions, a capping agent is key22: capping can stabilize precursors, whereas de-capping can initiate polymerization. Analogously, we proposed that ionic oligomers could be stabilized by an appropriate capping agent. Capping based on hydrogen bonding was thought to be suitable, because most inorganic complexes contain oxygen. For example, triethylamine (TEA) can form a hydrogen bond with a protonated carbonate through its tertiary amine group. More importantly, TEA is a small molecule that can be volatilized at room temperature, and it was expected that this could initiate an expected crosslinking reaction.

The authors use triethylamine in a solvent, the solvent in this case being ethanol (which of course, unless the ethanol is recovered, makes industrialization questionable. The calcium carbonate is made by bubbling carbon dioxide through an ethanolic solution of calcium chloride. Mass spectrometry demonstrated the existence of calcium carbonate polymers from trimers to undecamers, with, for some reason, nonamers excluded. The structures were also studied by 13C NMR.

A figure from the paper:

The caption:

a, Left, scheme of the capping strategy and reaction conditions for producing (CaCO3)n oligomers; right, a photograph of gel-like (CaCO3)n oligomers. b, Mass spectra of (CaCO3)n oligomers with different Ca:TEA molar ratios. c, Liquid-state 13C NMR spectra of CO2 or the carbonates of (CaCO3)n oligomers with different Ca:TEA molar ratios in ethanol. d, Scattering plots of (CaCO3)n measured by SAXS. The red curve is the fitting result obtained using DAMMIF. I, scattering intensity; q, scattering vector. The error bar represents the standard deviation of twenty measurements. e, Pair–distance distribution function (P(r)) of the (CaCO3)n oligomers. The inset shows the shape simulation of the oligomer. Error bars represent one standard deviation, n = 20.

The fate of the chloride ions is not reported. This seems to me to be an important consideration, nevertheless this is an interesting paper.

Cross linking of the polymers is achieved by evaporating the ethanol and the triethylamine.

Another graphic:

The caption:

a, b, Molecular dynamics simulation of the evolution of the Ca–O (from carbonate) coordination number (a) and the average cluster size (b) from ions (Ca2+ and CO32− in the absence (black) or presence (blue) of TEA. c, A typical simulated CaCO3 cluster capped with TEA (an oligomer). d, In situ FTIR spectra during the drying of (CaCO3)n oligomers. e, The change in the coordination number of Ca–O during crosslinking. Owing to the uncertainty in the exact density during measurements, the blue and red lines are shown to represent the maximum and minimum coordination number of Ca–O, respectively. The black line shows the average coordination number. f, High-resolution TEM images of (CaCO3)n oligomers grown at different Ca:TEA ratios from 1:100 to 1:2. g, TEM images depicting the transformation of (CaCO3)n oligomers to larger structures during condensation.

Some text about the results:

Centimetre-sized monolithic CaCO3 materials were obtained by the crosslinking of oligomers. The resulting bulk maintained the original morphology of the compact gel precursor (Fig. 3a). FTIR spectroscopy and thermal gravimetric analysis indicated the formation of pure ACC without organic residue (Extended Data Fig. 7a, b). Scanning electron microscopy (SEM) and TEM showed the structural continuity in the bulk (Fig. 3b–e), and the internal continuous and integral textures were confirmed by artificially creating a crack (Fig. 3c). At scales from nano- to micrometres, the fabricated material was fully dense and smooth with no porosity or cracks (Fig. 3d, e). A nanoindentation test revealed that the ACC sample (Fig. 3l, blue circle in Fig. 3m) had a Young’s modulus of 8.0 ± 1.6 GPa and a hardness of 0.33 ± 0.07 GPa; these values are greater than those of most plastic materials28.

Another picture:

The caption:

a, Photograph of monolithic ACC prepared from (CaCO3)n oligomers. b–e, SEM (b, c) and TEM (d, e) images indicating the continuous solid phase of the prepared monolithic ACC. The inset of e is the fast-Fourier-transform image of the sample. Typically, the image of a crack in monolithic ACC exhibits continuity from the surface to the bulk (c). f, Snapshot of monolithic calcite prepared from monolithic ACC. g, Polarized-light optical microscopy (POM) image of the prepared monolithic calcite. h, SEM image of a surface on crystallized monolithic CaCO3. i, j, TEM images of the inner bulk of crystallized monolithic CaCO3. The inset of j is the fast-Fourier-transform image of the sample. k, XRD pattern of calcite powder, geological single-crystalline calcite and the calcite sample produced from (CaCO3)n oligomers. l, Load–displacement curves of the ACC sample, calcite sample and geological single-crystalline calcite sample measured by nanoindentation. m, Ashby plot of hardness (H) against Young’s modulus (E) for the prepared CaCO3 (including ACC and calcite) and other materials. The upper left inset is an exemplary residual indent of the Berkovich diamond tip on the crystallized CaCO3. Ē, plane strain modulus.

ACC, is amorphous calcium carbonate.

Some discussion of possible applications:

A considerable advantage of the crosslinking of ionic oligomers is that the oligomeric precursors can be moulded into shapes to enable continuously structured construction (Fig. 4a–c). This in turn enables the engineering of single-crystalline materials, including additive manufacturing. The construction of calcite rod arrays by oligomer crosslinking demonstrates the practicality of the preparation of single-crystal materials with structural complexity (Fig. 4d, e). This method can even be extended to repair damaged single crystals. Calcite single-crystal surfaces in optical devices30 can be damaged by mechanical crashing, scratching or corrosion, which reduces their functional performance—in particular transmittance. However, (CaCO3)n oligomers can generate oriented calcite within nano- and micro-sized pits or ditches of the damaged calcites in order to recover their smooth surface (inset of Fig. 4d, f, g). The repaired region (Fig. 4h, i) had exactly the same crystalline phase and orientation as the bulk beneath (Fig. 4j). The images of the high-resolution lattice fringes from the calcite bulk to the repaired front (Fig. 4k) demonstrate continuous (104) facets without any break, confirming that the same crystalline structure was reproduced exactly

A graphic on engineering utilizing this technique:

a, Moulded CaCO3 with different dimensions and morphologies. b, c, Moulded CaCO3 with different patterns. The inset of c shows a single CaCO3 rod. d, Schemes for pattern construction on single-crystalline calcite (top path), and the repair of rough single-crystalline calcite to smooth calcite (bottom path). The insets show optical microscopy images of the calcite surface at different stages: native, corroded, and repaired. e, POM images of the patterned calcite rotated at different angles. f, g, SEM images of the repaired calcite (surface and cross-section, respectively). h, TEM image of a cross-sectional view of the repaired calcite. The different layers labelled 1, 2, 3 and 4 were characterized by selected area electron diffraction and high-resolution lattice fringes in j and k. i, EDS mapping of the repaired calcite in h, showing the repaired CaCO3 as well as gold nanolabels. j, Selected area electron diffraction patterns of different layers (1–3) of h with an aperture of around 170 nm in diameter, showing the same patterns from the bulk to the repaired surface. The red dots in 1 are the simulated diffraction pattern viewed along the <−4, 4, 1> zone axis. k, High-resolution lattice fringes at the different layers (1–4) of h, exhibiting the facets of (104) with exactly the same orientation from the bulk to the repaired surface.

Interesting paper, I think, I thought I'd share it.

Have a great Friday.

Milk of ruminants in ceramic baby bottles from prehistoric child graves

The paper I'll discuss in this post is this one: Milk of ruminants in ceramic baby bottles from prehistoric child graves (J Dunne et al Nature 574, 246–248 (2019)).

It is, I think, a good thing that we found out that the most modern approach to infant nutrition is breast feeding. Chemical analysis of human breast milk has shown - aside from chemical toxins associated with our modern life style, for example the common presence of brominated diphenylether flame retardants in the women who recycle our electronic stuff in China - that it is unique among all animal species. One of the major differences concerns lipids; human breast milk contains for example certain polyunsaturated lipids such as EPA, eicosapentenoic acid, and the related DHA and aracadonic acid which is thought to offer certain developmental neurological advantages owing to their propensity to undergo cycloadditions to make important molecules such as prostaglandins and certain hydroxylated species. I'm not sure that I know the precise mechanisms of the neurological effects, but I do know they are real.

I used to joke with my wife that I hoped that my sons would wean before they went to college; I'm sure both of them breast fed at least past their third birthday, although they ate other foods before their first birthday. They're men now, and it's possible, I think, it all worked out for the better. They're pretty smart guys.

Anyway, it appears that the problem of feeding children nonhuman animal milk has a very long history according to this paper. From the abstract which is open sourced:

The study of childhood diet, including breastfeeding and weaning, has important implications for our understanding of infant mortality and fertility in past societies1. Stable isotope analyses of nitrogen from bone collagen and dentine samples of infants have provided information on the timing of weaning2; however, little is known about which foods were consumed by infants in prehistory. The earliest known clay vessels that were possibly used for feeding infants appear in Neolithic Europe, and become more common throughout the Bronze and Iron Ages. However, these vessels—which include a spout through which liquid could be poured—have also been suggested to be feeding vessels for the sick or infirm3,4. Here we report evidence for the foods that were contained in such vessels, based on analyses of the lipid ‘fingerprints’ and the compound-specific δ13C and Δ13C values of the major fatty acids of residues from three small, spouted vessels that were found in Bronze and Iron Age graves of infants in Bavaria. The results suggest that the vessels were used to feed infants with milk products derived from ruminants. This evidence of the foodstuffs that were used to either feed or wean prehistoric infants confirms the importance of milk from domesticated animals for these early communities, and provides information on the infant-feeding behaviours that were practised by prehistoric human groups.

From the introduction to the paper, which is probably not open sourced:

The study of past infancy—including infant care, breastfeeding and weaning practices—provides valuable information on population demographics and health, reproduction rates, mortality patterns and fertility of individuals of past societies. Today, feeding practices for babies can be attributed to various ecological and socioeconomic constraints and cultural factors, such as health beliefs and food taboos1,5,6. Prehistoric humans probably practised a range of infant-feeding behaviours2,3,4,6,7, which had profound consequences for the biological and social wellbeing of the infants. Ethnographic, historical and social studies have shown differences across the breastfeeding phase, the nature of the addition of supplementary foods (during weaning) and the timing of cessation of breastfeeding1,5,6,8.

Breastfeeding is integral to infant care in all human groups and fundamental to the mother–infant relationship4. Breast milk provides an infant with all of the macro- and micronutrients that are required to sustain growth for the first six months of life9, together with bioactive components, which protect the infant from pathogenic organisms and facilitate the development and maturation of the immune system10. The introduction of energy and nutrient-rich, easily digestible, supplementary foods in infant feeding (that is, during weaning) is unique to humans11,12. Supplementary foods are generally introduced at around six months of age, when the metabolic requirements of an infant exceed the energy yield that the mother can provide through milk, contributing to the infant diet as chewing, tasting and digestive competencies develop1,12,13.

Apparently vessels that are believed to have been ceramic "baby bottles" were placed in the graves of children buried in prehistoric Germany:

he widespread use of animal milk, either to feed babies or as a supplementary weaning food source, became possible with the domestication of dairy animals during the European Neolithic14, during which time generally improved nutrition contributed to an increased birth rate, with shorter inter-birth intervals, that resulted in considerable growth of the human population: the so-called Neolithic demographic transition15. Broad trends identified from the Neolithic to Iron Age in Central Europe suggest that supplementary foods were given to babies at around six months of age and weaning was complete by two to three years of age3.

Possible infant-feeding vessels that are made from clay first appear in Neolithic Europe. One of the earliest of such finds is a Linear Pottery Culture feeding vessel from Steigra, Germany, that has been dated16 to around 5500–4800 BC. These unique vessels, which have a small spout through which liquid could be poured or suckled, come in many forms and sizes and occasionally have a zoomorphic design (Extended Data Fig. 1). They become more common in Central Europe during the late Bronze and early Iron Age4 and are found in settlements, as stray finds, and in graves (particularly those of children), which strongly suggests that they were feeding or weaning vessels for infants.

The precious nature and often small openings of these vessels makes their sampling for organic residue analysis extremely challenging. However, infant-feeding vessels that have an open, bowl form, found in graves from cemeteries of Dietfurt-Tankstelle and Dietfurt-Tennisplatz in Germany, have recently become available for chemical analysis. The graves are part of a large early Iron Age cemetery complex (dating to approximately 800–450 BC) found in the lower Altmühl valley in Bavaria, Germany, with Dietfurt-Tankstelle encompassing 99 burials in 72 graves17 and Dietfurt-Tennisplatz containing 126 burials18. Child grave 80 at Dietfurt-Tennisplatz contained an east–west-oriented inhumation of a young child (0–6 years old), who had a bronze bracelet on the left arm, and in which feeding vessel 1 (Fig. 1a) was placed at the child’s feet18.

A graphic:

The caption:

a, b, Drawings of child graves from Dietfurt (left) and images of the feeding vessels found in each grave (right). Photographs of vessels were taken by A.F. (a) and K.R.-S. (b). Drawings of the graves were reproduced from a previously published plan17 (a) and drawing18 (b).

In the labs where I work, we analyze fatty acids by LC/MS/MS which is generally more sensitive than GC-MS single quads with derivatization to FAMES (fatty acid methyl esters), but the authors here have used the latter, and apparently it got the job done, utilizing the NIST databases. (I'd personally be reluctant to do this with samples this precious, but it worked out apparently; the paper is published in Nature.)

Their results:

The caption:

n = 3 vessels. a–c, Partial gas chromatograms of transmethylated trimethylsilylated extracts from infant-feeding vessels 1–3. Red circles, n-alkanoic acids (fatty acids); blue triangles, n-alkanes; IS, internal standard, C34 n-tetratriacontane. d, δ13C values for the C16:0 and C18:0 fatty acids for archaeological fats extracted from infant-feeding vessels 1–3. The three fields correspond to the P = 0.684 confidence ellipses for animals raised on a strict C3 diet in Britain20. Each data point represents an individual vessel. e, The Δ13C (δ13C18:0 – δ13C16:0) values are from the same vessels as in d. The ranges shown here represent the mean ± 1 s.d. of the Δ13C values from a global database comprising modern reference animal fats, which have been published previously24. f, Partial high-temperature gas chromatogram of trimethylsilylated total lipid extract of infant-feeding vessel 2, showing degraded animal fat. Red circles indicate short- and long-chain n-alkanoic acids with the indicated number of carbon atoms; monoacylglycerols (M) containing 16 and 18 acyl carbon atoms; diacylglycerols (D) containing 28, 30, 32 and 34 acyl carbon atoms; triacylglycerols (T), containing 40, 42, 44, 46, 48, 50, 52 and 54 acyl carbon atoms; the plasticizer is indicated by an asterisk. IS, internal standard n-tetratriacontane (n-C34). Replication was not possible owing to the unique and irreplaceable nature of the archaeological artefacts sampled, although the objects were analysed using two different extraction methods.

Here's some explanation of the different lipid profiles of cow's milk and human milk:

As the Δ13C values are found to be at the top of the range for dairy fats, the vessels were also analysed by solvent extraction20 using high-temperature gas chromatography and high-temperature gas chromatography–mass spectrometry for diagnostic intact acyl lipids22. Figure 2f shows that triacylglycerols (TAGs) and their degradation products, di- and monoacylglycerols, were present in vessel 2, with TAGs comprising C40–C54 acyl carbon atoms with C48 being the most abundant homologue. The latter TAGs were not detectable in vessels 1 and 3, indicating complete diagenetic hydrolysis of the acyl lipids in these vessels. Fresh adipose fats are characterized by TAGs that contain 48–54 acyl carbon atoms, whereas dairy fats are distinguished by TAGs that contain 24–54 acyl carbon atoms23. Whereas shorter-chain TAGs (24–38 acyl carbon atoms) are rarely seen in degraded archaeological fats, owing to diagenetic loss (which has been demonstrated experimentally20), C40–C46 TAGs are highly diagnostic of dairy fats20,22. In summary, our findings provide unequivocal evidence that all three vessels were predominantly used to process dairy fats.

Nutritional differences:

Milks are species-specific and there are key differences in the composition of human and ruminant milk. Animal milk could have been used as a supplementary food, but it would not have been a full replacement for human milk, which contains similar amounts of lipid but more carbohydrates (in the form of lactose) and considerably less protein. These differences might affect an infant in various ways. For instance, cow’s milk is more difficult for an infant to absorb as it contains higher quantities of saturated fatty acids and much larger fat globules than human milk25, causing a reduced energetic input for the infant. The processing of animal milk and the possible incorporation of meat-based gruel may have served to balance out nutritional deficiencies. However, the introduction of inappropriate supplementary foods would have provided an opportunity for infectious agents and pathogens, causing diarrhoea and other diseases, and putting the infant at greater risk of iron-deficiency anaemia14. These supplementary foods may also have been nutritionally inadequate, leading to malnutrition, which is detrimental to future development.

My sons were both with me this weekend, and we had this fascinating conversation on why European culture came to be so widely adopted across the world, which of course, is tied to imperialism, the latter being tied to a cultural propensity for violence that was not absent in other cultures, but seems to have been less intense, the Mongols, perhaps excepted. I mentioned Kurt Vonnegut's description of Europeans as "sea pirates" which other cultures refused to believe could possibly be as greedy and violent as they turned out to be. My younger son had an interesting theory related to geography to explain the warlike practices of Europeans. We were just kicking stuff around. I don't know that we were being cartoonish; I'm sure we were.

This may only be loosely tied to nutritional differences, but these nutritional differences have had an effect on culture.

It is well known for example, from genetic data, that Europeans as distinct from other ethic groups exhibit more tolerance for lactose than other ethic regions, which is why one never sees cheese sauce for example, in Chinese or Japanese food. It is also well known that, albeit, with many exceptions, that certain cancers are less prevalent in Asia, notably breast cancer.

Seemingly small things matter.

In any case, I found this interesting chemoarcheology to be very interesting, and I thought I'd share it.

Have a nice day tomorrow.

Joan Brennecke Returns in Triumph to her Alma Mater with a 2.5M Grant.

Whenever I see a paper from Joan Brennecke while growing through titles in a journal I just have to read it. (Confession: The Journal she edits, Journal of Chemical Engineering Data, is not on my regular reading list; I wish I had more time.)

Most recently I came across this paper of hers: Effect of Water on CO2 Capture by Aprotic Heterocyclic Anion (AHA) Ionic Liquids (Gabriela M. Avelar Bonilla, Oscar Morales-Collazo, and Joan F. Brennecke, ACS Sustainable Chem. Eng. 2019, 7, 16858−16869)

I usually don't notice institutions, but it caught my eye, that after a long career at Notre Dame, she is now at the University of Texas at Austin. So I googled to find out what happened and came across this article: Engineering a New Era

Joan Brennecke, the first female professor of chemical engineering at the University of Texas, has charted her own career course.

As a chemical-engineering student at the University of Texas in the 1980s, Joan Brennecke learned more than formulas and chemical processes; she learned how to stick up for herself. Some professors supported Brennecke in her engineering ambitions, helping her become more assertive and self-assured. Meanwhile, others represented the challenges she would face throughout her career in a male-dominated field.

Brennecke remembers casually chatting with a UT chemical-engineering professor about her career ambitions at a party in 1984, when he surprised her with a mocking laugh.

“A female faculty member in chemical engineering at the University of Texas? Over my dead body!” he declared.

After a $2.5 million governor’s grant returned the world-class researcher to her alma mater three decades later, Brennecke can’t help but laugh at the story’s irony.

“I try never to whine about others’ behavior,” says Brennecke, now UT’s first female full professor in chemical engineering. “I tend to ignore it and do my thing.”

Engineered to Succeed
Brennecke knew chemical engineering was her thing since early high school. She recalls hours spent in the garage with her father, a chemical engineer with a Ph.D., taking apart anything the two could find. When she was 12, they disassembled a massive mechanical calculator he brought home from his job at Alcoa.

Engineering runs in the family: Brennecke’s uncle works as a mechanical engineer, her mother is a secretary for an engineering company and three cousins ended up in engineering-related positions. Brennecke entered the family hall of fame as its first female engineer.

Today, women earn about 20 percent of all engineering degrees. When Brennecke hit high school in the mid-1970s, women earned just 3.4 percent of those degrees...

...Gabriela Avelar Bonilla, one of Brennecke’s Ph.D. students at Notre Dame, says Brennecke serves as a valuable resource for women in engineering.

“In a field that [is]usually dominated by men, it’s important to have role models that you can relate to,” Avelar Bonilla says, “[especially]someone like her because her career is very impressive and she is a good mentor.”

When paired with a female mentor, female engineering undergrads feel more confident, motivated and less anxiety, according to a study published earlier this year.

The first piece of advice Brennecke offers female engineering students is to focus on doing their best.
“There’s no substitute for competence,” she says.

“And for goodness’ sakes, don’t ever be dissuaded or even irritated by somebody’s stupid comments or what somebody does. Don’t waste your brain cells on them. Spend your brain cells on doing what you’re doing well.”

Dr. Brennecke gave a wonderful lecture at Princeton University which I attended a few years back. I have posted the video in this space here:

On the Solubility of Carbon Dioxide in Ionic Liquids.

I was, at the time, a little depressed about the remarks on SO2, but the world has gone beyond that.

In any case, it's great to see powerful women in Chemical Engineering. Dr. Brennecke is a national asset.

Diagramming making bad coffee.

I was reading a paper today, this one, Development and Optimization of Liquid Chromatography Analytical Methods by Using AQbD Principles: Overview and Recent Advances and I came across a reference to a "Ishikawa Fishbone Diagram."

We are fortunate in these times that when we don't know what something is, we can google it, and often end up at Wikipedia, which is what happened to me, where I learned how to make a diagram of how I might make bad coffee:

Feel free to follow these steps to making bad coffee.

It turns out that I've seen these types of diagrams before, but never knew what they were called. Now when I'm in a meeting, I can say "Ishikawa Fishbone Diagram" and sound like I know something, even if I don't know shit from shinola.

I was mistaken about the timing and magnitude of the 2019 Mauna Loa CO2 minimum.

On September 22 I wrote the following in a post in this section:

Each year, the minimal value for carbon dioxide levels in the atmosphere for a particular year is observed in the Northern Hemisphere's early autumn, usually in September. The Mauna Loa Observatory reports weekly year to year increases for each week of the current year compared to the same week in the previous year.

This year, in 2019, as is pretty much the case for the entire 21st century, these minima are uniformly higher than the carbon dioxide minima going back to 1958, when the Mauna Loa carbon dioxide observatory first went into operation. Weekly data is available on line, however, only going back to the week of May 25, 1975, when the reading was 332.98 ppm.

For many years now, I have kept spreadsheets of the data for annual, monthly, and weekly Mauna Loa observatory data with which I can do calculations.

In the weekly case, the week ending May 12, 2019 set the all time record for such readings: 415.39 ppm.

These readings, as I often remark vary in a sinusoidal fashion, where the sine wave is imposed on a monotonically increasing more or less linear axis, not exactly linear in the sense that the slope of the line is actually rising slowly while we all wait with unwarranted patience for the bourgeois wind/solar/electric car nirvana that has not come, is not here and will not come.

This graphic from the Mauna Loa website shows this behavior:

Here is the data for the week beginning on September 15, 2019

Up-to-date weekly average CO2 at Mauna Loa

Week beginning on September 15, 2019: 408.50 ppm
Weekly value from 1 year ago: 405.67 ppm
Weekly value from 10 years ago: 384.59 ppm...

...The operative point is that this reading is only 0.09 ppm lower than last week's reading, which was, 408.59 ppm. This suggests, if one is experienced with working with such data, that this is most likely the annual September minimum reading. For the rest of this year, and through May of 2020 the readings will be rising. We will surely see next May readings around 418 ppm, if not higher.

However, I was wrong, because the next two weeks at Mauna Loa showed values lower than 408.50 ppm. It actually took place this year during the week ending 09/29/19, when the reading was: 407.97

The most recent data point is the week ending October 6, 2019 is a follows:

Up-to-date weekly average CO2 at Mauna Loa
Week beginning on October 6, 2019: 408.39 ppm
Weekly value from 1 year ago: 405.50 ppm
Weekly value from 10 years ago: 384.06 ppm
Last updated: October 13, 2019

From here on out, until May, 2020, the values for each week will exceed the number reported on September 29 of this year.

Previous weekly data annual lows took place as follows over the last 5 years:

9/9/18: 405.39 ppm

9/24/17: 402.77ppm

9/25/16: 400.72ppm

9/27/2015: 397.2 ppm

9/14/2014: 394.79 ppm

No one alive today will ever see a measurement at Mauna Loa lower than 400 ppm again.

In 2000, the weekly data annual low took place on September 10, 2000: 367.08 ppm.

In 1980, the weekly data annual low took place on September 4, 1980, 339.87 ppm.

In 1975, the first year the weekly data was reported, the weekly data annual low took place on August 31, 1975 when it was 329.24 ppm.

The movement to late September is most probably a function of a warmer and longer summer in the Northern Hemisphere, during which the annual minimums take place.

The annual maxima show up in early May. We may expect that the 2020 maximum should approach or exceed 418 ppm.

I apologize for jumping the gun. It's possible that next year we'll see, for the first time ever, the minimum appearing in October.

Have a nice afternoon.

The amplitude and origin of sea-level variability during the Pliocene epoch

The paper I'll discuss in this post is this one: The amplitude and origin of sea-level variability during the Pliocene epoch (Grant et al, Nature volume 574, page s237–241 (2019).

This past Thursday I posted a similar paper about this epoch, which was also published in Nature, in the same issue, just above this one.

During the Pliocene Epoch, which was from 3 to 5 million years ago, the concentration of carbon dioxide in the atmosphere apparently surged (for a few hundred thousand years) to around 450 ppm, which, since we are doing nothing meaningful about climate change, we will hit in about 15 to 20 years.

The authors here use a different approach than the approach I discussed on Thursday.

From the abstract:

Earth is heading towards a climate that last existed more than three million years ago (Ma) during the ‘mid-Pliocene warm period’1, when atmospheric carbon dioxide concentrations were about 400 parts per million, global sea level oscillated in response to orbital forcing2,3 and peak global-mean sea level (GMSL) may have reached about 20 metres above the present-day value4,5. For sea-level rise of this magnitude, extensive retreat or collapse of the Greenland, West Antarctic and marine-based sectors of the East Antarctic ice sheets is required. Yet the relative amplitude of sea-level variations within glacial–interglacial cycles remains poorly constrained. To address this, we calibrate a theoretical relationship between modern sediment transport by waves and water depth, and then apply the technique to grain size in a continuous 800-metre-thick Pliocene sequence of shallow-marine sediments from Whanganui Basin, New Zealand. Water-depth variations obtained in this way, after corrections for tectonic subsidence, yield cyclic relative sea-level (RSL) variations. Here we show that sea level varied on average by 13 ± 5 metres over glacial–interglacial cycles during the middle-to-late Pliocene (about 3.3–2.5 Ma). The resulting record is independent of the global ice volume proxy3 (as derived from the deep-ocean oxygen isotope record) and sea-level cycles are in phase with 20-thousand-year (kyr) periodic changes in insolation over Antarctica, paced by eccentricity-modulated orbital precession6 between 3.3 and 2.7 Ma. Thereafter, sea-level fluctuations are paced by the 41-kyr period of cycles in Earth’s axial tilt as ice sheets stabilize on Antarctica and intensify in the Northern Hemisphere3,6.

The authors review, as the authors described in my previous post, the techniques for evaluating the sea level in the geological past:

Pliocene sea-level changes have been reconstructed using a variety of geological techniques including: (i) marine benthic oxygen-isotope (δ18O) records paired with Mg/Ca palaeothermometry (a proxy for global ice volume)4, (ii) an algorithm incorporating sill-depth, salinity and the δ18O record from the Mediterranean and Red seas8, (iii) uplifted palaeo-shorelines4,9, and (iv) backstripped continental margins2,4.

...and describe some significant limitations, for example with the δ18O method...

Although the global benthic δ18O stack provides one of the most detailed proxies for orbital-scale (glacial–interglacial) climate variability during the Pliocene3, the signal comprises both ocean-temperature and ice-volume effects that are not easily deconvolved2,4,11. Moreover, calibrations of δ18O to sea level do not account for the nonlinear relationship between marine-based ice-volume change and the δ18O of sea water12.

They then describe their approach:

Our record, which we term PlioSeaNZ, is constructed from sedimentary cycles that represent fluctuations between middle- to outer-shelf water depths that were recovered in sediment cores (3.3–3.0 Ma) and outcrop sections exposed in the Rangitikei River valley (2.9–2.5 Ma). Sediments accumulated continuously at rates of >1 m kyr−1 (see Methods). Erosion during lowstands did not occur on the middle to outer shelf, because the changes in the amplitude of Pliocene RSL were accommodated in these environments without experiencing wave base erosion or subaerial exposure. The palaeo-environmental interpretation of the cores and outcrops is described in detail in ref. 6 and summarized in Supplementary Figs. 1 and 2.

Reference 6 is this one, from the same group:

Mid- to late Pliocene (3.3–2.6 Ma) global sea-level fluctuations recorded on a continental shelf transect, Whanganui Basin, New Zealand (Grant et al Quaternary Science Reviews Volume 201, 1 December 2018, Pages 241-260) I have not personally accessed this paper.

A few more details on their approach:

We have developed a novel approach that utilizes the well-established relationship between sediment grain size and water depth14 to calculate palaeo-water-depth changes. Wave energy produces a decreasing near-bed velocity at increasing water depths across the shelf, resulting in a seaward-fining sediment profile14. Modern observations support theoretical calculations that show that maximum water depth for a given grain size corresponds to the depth at which wave-induced near-bed velocity exceeds the critical velocity required for sediment transport14 (see Methods; Extended Data Fig. 1a). Thus, the percentage of sand (grains of size 63–2,000 µm) in closely spaced geological samples can be used to estimate changes in palaeo-water depth provided that the sediment is wave-graded6 and that Pliocene wave climate can be broadly estimated.

Some pictures from the text:

The caption:

a, Overview of North Island. Whanganui Basin (grey shaded region) formed behind the Hikurangi subduction zone as part of a southward-migrating pattern of lithospheric flexure associated with southwestward propagation of the subducting Pacific Plate beneath the Indo-Australian Plate2. b, Magnified view of boxed area in a. Subsequent uplift in central North Island during the last 1 Ma, in response to redistribution of lithosphere over the mantle2, has exposed Plio-Pleistocene, shallow-marine sediments onshore where they tilt southwestward at 5°. Locations of Siberia-1 drill site (white ‘x’ marker) and Rangitikei River outcrop (bold dashed white line) are shown. Geological data in b adapted from GNS Science.


The caption:

a, PlioSeaNZ RSL record (right-hand vertical axis), unregistered to the present day, for the middle to late Pliocene, with uncertainty represented by the shaded blue band, which does not exceed ±5.6 m (see Methods). Glacial–interglacial (G–IG) transitions are marked by the shaded grey bands. The age model is untuned and derived from linear sedimentation rates between magnetic reversals (orange-pink lines) with an uncertainty of ±5 kyr. Summer insolation (1 January) at 65° S (black curve) and the eccentricity parameters (dashed curve) are shown for ref. 18 (left-hand vertical axes). b–e, Multi-taper method time–frequency analyses (see Methods) displaying normalized power (colour scale) for eccentricity, obliquity and precession insolation parameter18 (b), the global benthic foraminifera δ18O stack3 (c), EAIS IBRD mass accumulation rate21 (d) and our RSL record (e; PlioSeaNZ Whanganui Basin). Periods are denoted for eccentricity (100 kyr), obliquity (41 kyr) and precession (23 and 19 kyr).

The caption:

Amplitudes of deglacial (glacial–interglacial; pink squares; n = 28) and glacial (interglacial–glacial; blue squares; n = 26) RSL changes are shown with error bars representing ±1 s.d. (after equation (10)) with an average of 5.1 m, and age uncertainty is ±5 kyr (as discussed in the text, and shown in the figure key). The grey shaded band (about 23 ± 5 m) shows the possible contribution from the marine-based sectors of the AIS (about 23 m)28 and the GIS estimated as19 ±5 m depending on the interhemispheric phase relationship. Glacial–interglacial amplitudes higher than approximately 28 m exceed the ice inventory of the marine-based AIS sectors (22.7 m; ref. 28) and the GIS (5 m; ref. 19) based on present-day volumes.


The caption:

Modelled result of 10 kyr linear melting between glacial and interglacial states required for 20 m of equivalent ESL, and according to the reference mantle viscosity profile30. a, 20 m ESL released from AIS only. b, AIS and GIS synchronously release 15 m and 5 m ESL, respectively. c, AIS releases 25 m ESL while GIS accumulates 5 m ESL (that is, in anti-phase). d, AIS and NHIS synchronously release 10 m ESL. The white band represents ±0.05 of the eustatic mean (bold black line), which equates to ±1 m. The Whanganui site is highlighted by the red and white bullseye on New Zealand.

AIS is the antarctic ice sheet, GIS, greenland ice sheet.

They speak on the effect of rotational precession changes the insolation patterns drive this historical warming, and that this in turn, they argue, means that the Antarctic Ice Sheet is more prominent in driving sea level rises.

This does not mean that they exclude carbon dioxide, far from it.

From their conclusion:

In conclusion, our results provide new constraints on polar ice-sheet and global sea-level variability during the middle and late Pliocene, that are: (i) independent of estimates from the global benthic δ18O stack3 and other geochemical proxies4, and (ii) broadly consistent with AIS models7,19,20 that simulate a contribution of 13–17 m to global sea-level rise above present. Because our record cannot be registered to present-day sea level, we cannot directly constrain the magnitude of peak Pliocene GMSL above present. Regardless, our results provide key insights into AIS sensitivity when Earth’s climate equilibrates at a CO2 partial pressure of about 400 ppm. Furthermore, if all the variability in the PlioSeaNZ record was above present-day sea level, then GMSL during the warmest mid-Pliocene interglacial was no more than +25 m. Although ice-sheet, ocean and continental geometries were subtly different during the mid-Pliocene, our results suggest that major loss of Antarctica’s marine-based ice sheets, and an associated GMSL rise of up to 23 m, is likely if CO2 partial pressures remain above 400 ppm.

Have a pleasant Sunday afternoon.

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