Month: May 2020

Arsenic hazard on a global scale

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I have been following the harrowing story of how arsenic gets into domestic water supplies for 20 years (see: Earth-logs Geohazards for 2002; 2003; 2004; 2005; 2006; 2008; 2009; 2011; 2013; 2017). In my opinion, it is the greatest natural hazard in terms of the numbers at risk of poisoning. In 2006 I wrote about the emergence in Bangladesh of arsenic poisoning on a huge scale during the mid 1990s for a now defunct Open University course. If people depend for drinking water on groundwater from tube wells driven into alluvium they would not know of the risk, unless the water is rigorously analysed for levels of As greater than 10 micrograms per litre (μg l-1), the WHO recommended maximum. The sad fact is that the affected population were advised to switch from surface water supplies, which carry a high risk of biological infection, to well water. That is because during downward percolation from the surface oxidation destroys bacteria and viruses as well as parasites. Opportunities provided by a massive UN-funded drilling programme and local well digging made the choice seemingly obvious. Most people came to prefer well water as gastro-intestinal infections and child mortality fell rapidly.

Arsenic adds no taste, which is why it was once the ‘poison of choice’. How it gets into groundwater is difficult to judge, unless wells are downflow of areas riddled with metal mines. Years of research uncovered an unsuspected mechanism. The most common colorant of mineral grains, and thus sedimentary rocks, is brownish iron hydroxide (goethite), and that is able to adsorb a range of dissolved elements, including arsenic. One would think, therefore, that groundwater should be made safe by such a natural ‘filtering’ process: indeed goethite can be used in decontamination. The problem is that iron hydroxide, which contains Fe-3, is only stable in water with a high capacity for oxidation. Under reducing conditions it breaks down to soluble Fe-2 and water, thereby releasing to solution any other element that it has adsorbed. In alluvium, beds containing organic matter are prone to this ‘reductive dissolution’ of goethite. If weathering upstream has released even seemingly insignificant amounts of arsenic during the build up of alluvium, there is a potential life-threatening problem as arsenic builds up in the goethite coating of sedimentary grains to become ‘locked in’, with the potential to be released in high concentrations if subsurface chemical conditions change. The colour of the alluvial sediments penetrated by wells is a clue. If they are reddish brown, groundwater is safe, if they are greyish and goethite-free then, ‘beware’. But it is rare to examine ‘cuttings’ from a drill site aimed at groundwater, unlike those aimed at ores or oil

Since the tragedy of Bangladesh, which resulted after 5 years or so in obvious signs of arsenicosis – dark wart-line keratoses on hands and feet or black blotches on facial and torso skin – several alluvial basins in large river systems have had their well water tested. But by no means all such basins have been screened in this way, and there are many less-obvious signs of arsenic poisoning. After long exposure to the lower range of dangerous arsenic levels a variety of cancers develop in known areas of arsenic risk. There are also high levels of endemic respiratory problems, cardiovascular disease, reduced intellectual development in children and even diabetes. Geochemical monitoring of all populated and farmed river systems is a huge task that is far beyond the resources of many countries through which they run. One approach to ‘screening’ for hazard or safety is to use geological, hydrological, soil, climate and topographic data. Those from known arsenic-prone basins and those where its levels are shown to be consistently below the 10 μg l-1 danger threshold help to develop a predictive model (Podgorski, J. & Berg, M. 2020. Global threat of arsenic in groundwater. Science, v. 368, p. 845-850; DOI: 10.1126/science.aba1510).

Modelled global probability of arsenic concentration in groundwater exceeding 10 μg l-1. Click to display a larger map in a separate browser tab. (credit: Podgorski & Berg; Fig 2A, with enhanced colour)

Rather than trying to model the full range of arsenic concentrations, Joel Podgorski and Michael Berg of the Swiss Federal Institute of Aquatic Science and Technology focussed on assessing probabilities that arsenic in well water exceeds the WHO recommended maximum safe level of 10 μg l-1. Their global map highlights areas of concern for environmental health. Thankfully, huge (blue) areas are suggested to present low risk, the pale, yellow, orange and red patches signifying areas of increasing concern. No populated continent is hazard-free. What is very clear is that Asia presents the greatest worries. Most of the Asian ‘hot zones’ are spatially close to large mountain ranges and plateaus. In the case of the Indus and Ganges-Brahmaputra plains the sources for excessive arsenic in groundwater implicated by previous geochemical investigations lie in the Himalaya. The factor common to all major hot spots seems to be rapid transport of huge amounts of sediment released by weathering from areas of high topographic relief, rather than local large-scale mining operations. There are hazardous areas related to historic and active mining, such as the Andes of Bolivia, Peru and Chile and the western USA, but they are tiny by comparison with the dominance of natural arsenic mobilisation.

Despite the WHO recommended maximum of 10 μg l-1 of arsenic, many countries base their policy on levels that are five times higher, largely because of the difficulty of analysing for the lower concentration without expensive analytical facilities. Field analyses are often done using simple semi-quantitative tests based on paper impregnated with reagents that show a colour range for different concentrations, which are unreliable for those lower than 100 μg l-1. Thankfully, despite the many risky areas, most of them have population densities less than 1 per km2.

If you are interested in the geological details of the arsenic problems of Bangladesh, the course text that I produced for the Open University (Drury, S. 2006. Water and well-being: arsenic in Bangladesh. The Open University: Milton Keynes, UK. ISBN 0-7492-1435-X), the course itself (S250 Science in Context) was withdrawn some years ago.  It may be possible to arrange a PDF for private use.

See also: Zheng, Y. 2020. Global solutions to a silent poison. Science, v. 368, p. 818-819; DOI: 10.1126/science.abb9746

Update on climate and sea-level change during the Cenozoic

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The Cenozoic Era was a period of fundamental change in the outer part of the Earth system. It culminated in the greatest climatic cooling since the Permian Period, during which upright apes emerged between 6 to 10 Ma ago.  The most decisive part of hominin evolution – the appearance of our own genus Homo – took place in the last 2.5 Ma that saw icecaps plastered over both polar regions and repeated pulses of major climate upheaval that dramatically affected all parts of the continents. Whereas the Mesozoic was dominated by reptiles, most famously the dinosaurs, the Cenozoic is rightly known as the age of mammals and of birds. The flowering plants, especially grasses, also transformed terrestrial ecosystems. The background to what has become ‘our time’ is not only climate change, but massive shifts in sea level and the outlines of the continents. For more than two decades many palaeoclimatologists have focused on the Cenozoic, gathering data using a variety of rapidly advancing technologies from a growing number of sites, in sediments from the continents and the ocean floor. One problem has been correlating all this global data precisely, coming as it does from many incomplete sedimentary sequences dotted around the planet. A great deal of basic information has come from the petroleum industry, which, of course, has continually eyed sedimentary rocks as the source of hydrocarbons through the 20th century. It was seismic reflection surveying that first gave clues to global ups and downs of sea level from onlaps and offlaps of strata that are visible on seismic sections, amplified by sequence stratigraphy. Six geoscientists from Rutgers University in New Jersey, USA have blended oil-industry archives with academic research to produce the first fully calibrated, comprehensive record of the Cenozoic (Miller, K.G. et al. 2020. Cenozoic sea-level and cryospheric evolution from deep-sea geochemical and continental margin records. Science Advances, v. 6, article eaaz1346; DOI: 10.1126/sciadv.aaz1346).

Latest palaeoclimate data for the Cenozoic Era. A oxygen-isotope data from benthic foraminifera (pale blue = polar icecaps, green = ice-free, pink – hothouse); B estimated mean sea-surface temperature from the calcium/magnesium ratio in Pacific Ocean cores; C variation in global mean sea level estimated from A and corrected for changes in the density of seawater due to water temperature (B); D atmospheric CO2 variations estimated using various proxies – see top right box. Click on the image to show a full-size version in a new browser tab. (Credit: Miller et al. 2020; Fig. 1)

Fluctuations in the proportion of 18O (δ18O) in the tests of foraminifera that lived in deep water are the key to global changes in sea level  and point to the influence of glacial ice accumulating on land (see Cooling sets in: Stepping Stones, Chapter 17). This is because glaciers are made from water that has evaporated from the oceans. When this happens, water that incorporates the lighter 16O isotope evaporates more easily and becomes enriched in atmospheric water vapour. When this water falls as snow that accumulates on land to form ice, the oceans are slightly enriched in the heavier 18O: δ18O incorporated into the shelly material of organism dwelling in the deep ocean increases at levels of a few parts per thousand. Conversely, their δ18O decreases when huge ice caps melt (A on the figure). The oxygen isotope records from fossils in ocean floor sediments give a far more precise impression of fluctuating sea level than do seismic sections and sequence stratigraphy of sedimentary rocks that interest the oil industry. But it is an ‘impression’, because other factors affect sea level.

Not only the global volume of ocean water is involved: the volume of the ocean basins changes too. This can occur because of changes in the rate of sea-floor spreading: when that is fast the hot new oceanic lithosphere is less dense and so buoys-up part of the ocean floor to drive sea level upwards. Slow spreading does the converse, as more lithosphere cools and sinks slightly. Another factor is the changing rate of marine sedimentation of material eroded from the continents. That fills ocean basins to some extent, again displacing the water upwards. When sediments are compacted as they become more deeply buried that has an effect too, to increase basin volume and result in sea-level fall. Oil industry geoscientists have attempted to allow for these long-term, slow mechanisms, to give a more accurate sea-level record.

Yet there is another important factor: the density and thus volume of ocean water changes with temperature. The warmer it is the greater the volume of ocean water and the higher is sea level. This is where academic work comes in handy. Two common elements that are dissolved in ocean water are magnesium and calcium. They also occur in the carbonate tests of the same deep-water forams that are used for oxygen-isotope measurements. It turns out that the warmer the water is the more magnesium enters the foram tests, and vice versa: their Mg/Ca ratio is a reliable proxy for mean ocean temperature and can be measured easily, centimetre-by-centimetre through cores. Kenneth Miller and colleagues have used this with the oxygen isotope proxy for land-ice volume to correct the sea-level record.

The Cenozoic ocean temperature record (B on the figure) is, in itself, interesting. It reveals far more large fluctuations than previously thought, especially in the Palaeocene and early Eocene. Yet, overall, the trend is one of steady cooling compared with the sudden shifts in δ18O that mark the onset of the Antarctic ice cap at the Eocene-Oligocene boundary around 34 Ma ago, and the apparent, temporary emergence from ‘ice-house conditions in the Middle Miocene. Also, sea level corrected for ocean temperature effects (C on the figure) suggests that for much of the Cenozoic sea level was lower than expected; i.e. it rarely exceeded 60 m above the current level, which is that expected when no substantial mass of  land ice exists.

The other important compilation made by Miller et al. is that of the CO2 content of the atmosphere estimated using six different proxies. It is a lot more fuzzy than the oceanic records because the proxies are not precise. Nevertheless, it is interesting. The current, partly anthropogenic level of around 400 parts per million (ppm) is not unique. In fact from 55 to 23 Ma it was consistently above this ‘Anthropocene’ level, peaking at twice that level at the end of the Eocene. That’s odd, because it doesn’t tally with the oxygen isotopes that indicate the onset of large scale Antarctic glaciation shortly afterwards. In fact most of the climatic highlights shown by A on the figure are not reflected in the Cenozoic history of the most influential greenhouse gas. In the short term of glacial-interglacial cycles during the late Pleistocene, atmospheric CO2 levels are very closely related to fluctuations of land-ice volume. In the 65 Ma of the Cenozoic such a link is hard to argue for. There are more puzzles than revelations in this otherwise major addition to palaeoclimatology.

More time for modern humans to have mingled with Neanderthals

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When anatomically modern humans (AMH) became established in Europe the days of the Neanderthals were numbered. Yet, genomic evidence is mounting for many instances of interbreeding between the two groups (see Human evolution links). The longer they were in contact the chances of meeting and having sex were likewise increased. So, for how long were the two groups able to make contact? Neanderthals declined and eventually disappeared between 41 and 39 ka, except for a possible refuge for a tiny number in southern Spain until 37 ka and maybe in the northern Urals where there are disputed Mousterian stone tools as young as 34 to 31 ka. Undoubtedly, the appearance of AMH somehow contributed to the demise of our close relatives, but there are many possible reasons why. Until recently, the earliest European entry of AMH had been placed at around 41 ka, based on dating of H. sapiens remains in Romania (but note: a single 210 ka possible AMH skull from Greece). This is now exceeded by data from a Bulgarian cave.

Bacho Kiro cave in Bulgaria (credit: Getty images)

The Bacho Kiro site was first excavated in the 1970s, and revealed stone tools that represent the earliest Upper Palaeolithic culture, known as the Bachokirian. Mitochondrial DNA from excavated bone fragments is clearly of AMH origin (Hublin, J.-J. and 31 others 2020. Initial Upper Palaeolithic Homo sapiens from Bacho Kiro Cave, Bulgaria. Nature, v. 581, online; DOI: 10.1038/s41586-020-2259-z). Dating the Bacho Kiro cave sediments has been difficult, but new analytical and statistical approaches using the radiocarbon (14C) method have yielded ages between 46 to 44 ka and perhaps as far back at 47ka (Fewlass, H. and 20 others 2020. A 14C chronology for the Middle to Upper Palaeolithic transition at Bacho Kiro Cave, Bulgaria. Nature Ecology and Evolution, v. 4, online; DOI: 10.1038/s41559-020-1136-3). This is the earliest unequivocal, direct evidence of our species in Europe and its association with the initial Upper Palaeolithic culture. Among the finds are perforated animal teeth and ivory beads that probably formed pendants, which resemble those found elsewhere in association with late Neanderthals: the Chatelperronian culture that seems to have been shared between AMH and Neanderthals.

The new data add up to 6 thousand years to the period of AMH-Neanderthal co-occupation of Europe, or about 400 generations. Plenty of time to ‘get to know one another’, and perhaps to assimilate genetically

See also: Rincon, P. 2020. Longer overlap for modern humans and Neanderthals. (BBC News 11 May 2020); Metcalfe, T. 2020. A tooth offers evidence modern humans reached Europe earlier than previously thought. (NBC News 11 May 2020)

Changing conditions of metamorphism since the Archaean

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Metamorphic petrologists have known since their branch of geology emerged that the intensity or ‘grade’ of metamorphism varies with position in an orogenic belt. This is easily visualised by the sequence mudstone-shale-slate-phyllite-schist-gneiss that results from a clay-rich starting material as metamorphic grade increases. Very roughly speaking, the sequence reflects burial, heat and pressure, and must have been controlled by temperature increasing with depth and pressure: the geothermal gradient. In turn, that depends on internal heat production, geothermal heat flow and the way in which heat is transferred through the deep crust: by thermal conduction or mechanical convection. A particular rock composition gives rise to different metamorphic mineral assemblages under different temperature and pressure conditions.

George Barrow was the first to recognise this in the Southern Highlands of Scotland as a series of zones marked by different index minerals. For instance, in once clay-rich sediments he recognised a succession of new minerals in the sequence chlorite; biotite; garnet; staurolite; kyanite; sillimanite in rocks of progressively higher metamorphic grade. Barrow found that once basaltic lavas interleaved with the sediments displayed zones with different characteristic minerals. Other metamorphic terrains, however, revealed different index minerals. Experimental mineralogy eventually showed that Barrow’s zones and others reflected a wide range of chemical reactions between minerals that reach equilibrium over different combinations of pressure and temperature. This enabled geologists to distinguish between metamorphism that had occurred under conditions of high-pressure and low-temperature, low-P and high-T and intermediate conditions (see diagram). This suggested that metamorphic rocks can form in areas with different heat flow and geothermal gradients. Geochemical means of assessing the actual temperatures and pressures at which particular rocks had reached mineralogical equilibrium, known as ‘thermobarometry’, now enable such variations to be assessed quantitatively.

The latest division in pressure-temperature space of different styles of metamorphism (colours) and the main mineral equilibria (dashed lines) that define them

It has long been suspected that the average T/P conditions revealed by metamorphic rocks have varied over geological time, as well as from place to place at any one time. A recent paper has analysed thermobarometric data from the earliest Archaean to recent times (Brown, M. et al. 2020, Evolution of geodynamics since the Archean: Significant change at the dawn of the Phanerozoic: Geology, v. 48, p. 488–492; DOI: 10.1130/G47417.1) They conclude that from the Archaean to the start of the Neoproterozoic the average P/T ratio was more than twice as high as it was in the following billion years. At about 2 Ga they suggests a relatively sudden decrease that correlates with what they regard as the first major assembly of continental crust: the Columbia (Nuna) supercontinent. The Mesoproterozoic Era, occupied by the disassembly of Columbia and the eventual creation of the Rodinia supercontinent, retained a high mean T/P. That began to decline with the break-up of Rodinia and a succession of tectonic cycles of ocean opening and closing during the Neoproterozoic and the Phanerozoic. This phase of truly modern plate textonics saw first the assembly of Gondwana and then the all-encompassing Pangaea, followed by its break up as we witness today. There are other correlations with the T/P variations, but they need not detain us.

The raw metamorphic data (564 points spanning 3.5 Ga) are by no means evenly spaced in time, and four dense clusters of points show a very wide spread of T/P – up to 2 orders of magnitude. Yet the authors have used locally weighted scat­terplot smoothing (LOWESS) to reduce this to a smoothed curve with a zone of uncertainty that is a great deal narrower than the actual spread of data. Frankly, I do not believe the impression of systematic change that this approach has produced, though I am not a statistician. To a lesser extent than me, it seems that neither does Peter Cawood, who comments on the paper in the same issue of Geology: more clearly than do the authors themselves.

Peter Cawood’s ‘take’ on the relationship between tectonic development and other important variables in the Earth-system with the estimate by Brown et al. of the mean metamorphic T/P (‘thermobaric’) variation through Earth history

Cawood’s view is that it was all due to a steady fall in mantle temperature and related broad changes in tectonic processes. But metamorphic rocks form in only the outermost 100 km of the Earth. The post-800 Ma examples include a much greater proportion of those formed under high- and ultrahigh pressures – blueschists and various kinds of eclogite – than do the earlier metamorphic belts. This weights the post-800 Ma record to lower mean T/P. Such rocks form in subduction zones and their high density might seem to doom them to complete resorption into the deep mantle. Yet large chunks now end up embedded in continents, interleaved with less extreme materials. Cawood suggests, as do others, that cooling of the mantle has enabled deeper break-off of subducted slabs to meet their end at the core-mantle boundary. The retained low T/P lithosphere since 800 Ma may have been sliced into the continents by increased underthrusting during continent-continent collisions that dominate the more modern orogenic-metamorphic belts.

See also:  Cawood, P.A. 2020 Earth Matters: A tempo to our planet’s evolution: Geology, v. 48, p. 525–526; DOI: 10.1130/focus052020.1

Genetic material from a baby dinosaur

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A clutch of Massospondylus carinatus eggs from the Jurassic of South Africa (credit: Brett Eloff)

Recently, a lot of publicity focussed on stunning CT scans of embryos preserved in fossilised eggs of a Jurassic sauropodomorph dinosaur, which were obtained using very high energy X-rays generated by a synchrotron in France (Chapelle, K.E.J. et al. 2020. Conserved in-ovo cranial ossification sequences of extant saurians allow estimation of embryonic dinosaur developmental stages. Nature Scientific Reports, v. 10, article 4224; doi: 10.1038/s41598-020-60292-z). The images suggest that the embryos’ skulls developed in much the same way as do those of living reptiles. Within a week there emerged an even more compelling dinosaurian scoop: a fossil nestling of a duck-billed dinosaur (hadrosaur) from the Upper Cretaceous of Montana is reported to have yielded evidence for a broad spectrum of cellular materials (Bailleul, A.M. et al. 2020. Evidence of proteins, chromosomes and chemical markers of DNA in exceptionally preserved dinosaur cartilage. National Science Review, v. 7, advance publication NWZ206; DOI: 10.1093/nsr/nwz206).

Alida Bailleul, who works at the Chinese Academy of Sciences in Beijing, and fellow molecular palaeontologists from Canada, the US and Sweden, examined material from the nestling’s skull that was suspected to contain traces of cartilage. Their methods involved microscopic studies of thin sections together with staining and fluorochemical analysis of cellular material extracted by dissolving away bone tissue in acid. The same methodologies were also applied to similar material from modern emu chicks as a means of validating the results from the fossil. Staining used the same chemical that previously had revealed blood proteins in a specimen of Tyrannosaurus rex (see: Blood of the dinosaurs  in Palaeobiology, January 2011). The fluorescence approach dosed the dinosaur cartilage with antibodies against bird collagen, and revealed an immune reaction (green fluorescence) in both fossil material and that from the baby emus.

The researchers also isolated cartilage cells (chondrocytes) from the dinosaur preparations. Two stains (PI and DAPI, for short) that show up DNA were applied, giving positive responses. The PI (propidium iodide) stain is useful as it does not respond to DNA in living material, bit only to that in dead cells, thereby helping to rule out contamination with modern material. Apparently, the double-staining experiments support the presence of double-stranded material that involves at least six base pairs (of ACTG amino acids). This does not prove the existence of dinosaur DNA, but does demonstrate that the hadrosaur’s cell nuclei are preserved.

Does that suggest that the hunt is on for a dinosaur genome, with all its connotations? OK, a complete genome has been extracted from a frozen Siberian mammoth a few tens of thousand years old, which encourages ‘re-wilding’ aficionados, but that animal preserved intact cells of many kinds. A 70 Ma old dinosaur fossil, however exquisitely preserved, is mostly ‘rock’, in that preservation is through mineralisation of bone and tissue, and even cells … Moreover, it is possible that what the team found may even be material from post-mortem bacterial colonisation of any age younger than 70 Ma.

See also: De Lazaro, E. 2020. Scientists Use X-rays to Peer inside Fossilized Dinosaur Eggs Sci News, 10 April 2020; Black, R. 2020. Possible dinosaur DNA has been found. Scientific American, 17 April 2020