Month: June 2001

Climate and heavy breathing

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The kingdom of the eukaryotes rests on a very simple environmental economy.  Plants are producers of carbohydrate through photosynthesis, thereby generating excess oxygen from the photo- and molecular chemistry involved.  Animal consumers use up oxygen in their metabolism and return carbon dioxide, the ultimate source of carbohydrate, to the air.  A simple view is that animals contribute to global warming, whereas plants help cool the world.  Perhaps because of that “common sense” view, most environmental scientists take a very different line, linking it with volcanic exhalation of CO2, “capture of carbon through rock weathering and the burial of dead organic matter  in the global carbon cycle.  Greg Retallack of the University of Oregon is about to publish a reappraisal of the animal versus plant part of the C-cycle (in press, Journal of Geology) that is based on observed imbalances between the two opposed kinds of respiration.  Specialists in the C-cycle hold that there is a an overall balance, taking all components into account, whose inevitable result is the build up of oxygen in the atmosphere of an inhabited world.  Yet oxygen is extremely reactive and should quickly combine in mineral oxides and hydroxides – after all, the iron in an untended car reverts to its oxide ore in the space of a few decades at most.

Partly following James Lovelock’s Gaia hypothesis, Retallack focuses on the major fluctuations in atmospheric chemistry evidenced in the geochemical record, the most immediate being the see-saw fluctuation of modern levels of CO2 in the atmosphere – a 2% annual variation controlled by the waxing and waning of vegetation in the northern hemisphere (where plant cover is greatest) according to season.  One of the largest shifts in atmospheric CO2 concentration followed the evolution of land plants from about 450 Ma ago.  To thrive, they had to develop hard cellular material (lignin) that formed stems and trunks, which animals of the Palaeozoic were unable to oxidise efficiently.  Both living biomass and burial of undigested lignin drew down CO2 and boosted oxygen levels.  Animal evolution eventually exploited this “free lunch” through the humble termite and reptilian and then mammalian megafauns.  Retallack believes that heavy breathing that resulted from lignin digestion reversed the declining CO2 trend for the 200 Ma following the Carboniferous to Permian glacial epoch in Gondwana.  Though displaying some ups and downs, the Mesozoic saw a “greenhouse” world.  Removal of the mighty and extremely abundant herbivorous dinosaurs by the K-T mass extinction provided and opportunity for plant diversification.  Many Mesozoic plants evolved armour against browsing dinosaurs, exemplified by the surviving Andean “monkey puzzle” tree Araucaria.  Their demise removed the need, and the plant Kingdom’s evolutionary response was the appearance of grasses.  Reatallack points out that grass itself is not as good as lignin-rich plants in holding CO2, but grasslands encourage the development of thick carbon-rich soils that hold more than the soils of the forest floor.  It is this development that Retallack believes lay at the base of the decline in average global temperature through the Cainozoic, to culminate in the present Ice Age.  Unsurprisingly, proponents of the complexity and diversity of the C-cycle, particularly in the oceans, are disinclined to have truck with the hypothesis.

Source:  Pearce, F.  The Kingdoms of Gaia.  New Scientist, 16 June 2001, p. 30-33.

Carbonates and biofilms

Above the low level that is essential for their role in molecular “information” transfer, calcium ions pose a fatal threat to cell processes.  That is simply because excess calcium combines with carbonate ions to form minute calcium carbonate crystals within the cell when the solubility product of calcite is exceeded.  The solubility product is the concentration of calcium ions multiplied by that of carbonate ions, so that increase in one or the other can lead to supersaturation of calcium carbonate and imminent precipitation.  Because CO2 is an essential need for photosynthesis and a product of animal metabolism, this risk is always present.  In the most common photosynthesising bacteria, the cyanobacteria that have been around for at least 3.6 billion years, the drawing in of CO2 in the form of carbonate (CO32-) or bicarbonate (HCO3–) ions in water can result in supersaturation immediately around the cell.  When it occurs, the “blue-green” bacterial biofilms induce precipitation of calcium carbonate.  That is why such micro-organisms can act as reef builders, as they did to great effect during the early Precambrian (stromatolites), and also from Cambrian to Cretaceous times.

Calcite mineralization by biofilms is, however, a complicated process.  It is connected with highly reactive substances that cyanobacteria exude outside their cell walls.  Depending on their degree of ordering and the supply of calcium ions, these substances control the manner in which calcium carbonate precipitates.  The detailed biochemistry and the form of calcite biofilms obtained by study of modern cyanobacteria in different watery environments has allowed Gernot Arp and co-workers at the University of Göttingen to evaluate varying calcium and CO2 concentrations in ocean water since 540 Ma, and suggest differences in Precambrian oceans (Arp, G. et al. 2001.  Photosynthesis-induced biofilm calcification and calcium concentrations in Phanerozoic oceans.  Science, v. 292, p. 1701-1704).

Their studies suggest that up to the Cretaceous, the Phanerozoic oceans must have had higher calcium contents than they do today.  Microbial reefs formed in that period preserve details of the “blue-green’s” cell structure, suggesting that calcite was nucleated directly by the extracellular substances.   Vast burial of the calcite shells of planktonic metazoan organisms to form the Chalk deposits of Cretaceous age reduced very high levels to give the calcium-depleted oceans that prevailed during the Cainozoic.  Microbial carbonates of these younger ages show no structure.  The stromatolites that are so characteristic of Precambrian limestones are stuctureless too, although they show evidence of progressive build-up from myriads of thin layers.  Irrespective of the Precambrian oceans’ calcium content, this lack of structure can be explained by more dissolved CO2 that resulted from its higher concentration in the atmosphere.  About 700-750 Ma ago, stromatolites that contain calcified cyanobacterial cells appear, and that may signify the massive drawdown of CO2 from the atmosphere that is implicated in creating icehouse conditions on a global scale during the late Proterozoic Aeon.

Universal access to peer reviewed articles?

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Scientists without access to libraries that subscribe to scientific journals, or whose institutions are poorly funded, are cut off from the mainstream of research developments.  That is, unless they request offprints of papers from authors.  The growth of electronic versions of journals and increasing access to the Web, even in poor countries (Eritrea recently went “on-line”) seemed to promise wider availability of primary sources of research information.  That is an illusion.  Unless you are a subscriber to paper journals (for instance Nature and Science subscribers automatically get free access to on-line versions) or are registered with a library that has subscribed to all electronic journals made available by a publishing house, such as Elsevier’s Science Direct, then downloading more than an abstract is on a pay-per-view basis.  (Note:  even the Web of Science, that hosts the Science Citation Index database, requires a paid-for user id and password).  Being a university academic in a rich country, I have the luxury of free access to many electronic resources through the Open University Library’s subscriptions, and the same goes for any of our students.  However, the economic facts of academic life occasionally rear up.  A reference to an interesting paper in the Journal of Human Evolution came to my attention.  Using my id and password for the publisher’s web site, I was able to locate the entry for the paper.  However, we do not subscribe to that journal, and to download an Adobe Acrobat PDF file would have cost me about £35, charged to my credit card.  Instead I requested an offprint from the authors, and am still waiting for its arrival after 2 months.

Authors provide papers free of charge to publishers of journals, referees review submissions without payment, and many editors compile issues for little if any return, other than satisfaction and kudos.  Publishers of journals make enormous profits, and increase subscriptions at rates far above that of inflation (one veterinary science journal increased in price by 7 time between 1991 and this year).  The average total income received by publishers of the roughly 20 000 scientific journals for each one of the 2 million papers published each year is around US$2 000 – the trade has a US$4 billion annual income.  In the Earth sciences annual subscriptions are beyond the budgets of most 3rd World institutions (6 issues of Elsevier’s Journal of African Earth Sciences cost £1003), apart from a few (the University of Chicago’s Journal of Geology costs £79 per annum).

The Public Library of Science  – http://www.publiclibraryofscience.org -is campaigning for a way out of the increasing cost for freedom of access to scientific information.  One simple and foolproof strategy is for authors to “self-archive” their preprints and manuscripts of published papers in their institutions’ “e-print” archive in such a way that they can then all be harvested into a global virtual archive, its full contents freely searchable and accessible online by anyone.  Stevan Harnad of the University of Southampton is one of the driving forces for the self-archiving initiative, and provides full details of the possibilities at http://www.cogsci.soton.ac.uk/~harnad/Tp/nature4.htm

See also:  Harnad, S.  2001.  First Person: In the name of freedom.  New Scientist, 26 May 2001, p. 53.

Dinosaur update

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BBC-2’s Live from Dinosaur Island (4-16 June 2001) brought palaeontology into Britain’s living rooms.  Centred on a frantically excavated series of Jurassic sites on the Isle of Wight, and fronted by the irrepressible Bill “Birdman” Oddie and genuinely excited (and sometime irascible) professional palaeontologists, the series used the now familiar approach of Channel 4’s Time Team, with the added frisson of being unedited and live.  The BBC was in debt to its viewers after the truly dreadful, if visually astonishing, Walking with Dinosaurs, and has repaid them handsomely by showing the bone-people working in their natural habitat.  It should help repopularize geology after a century of our being the brightly coloured anoraks seen dimly in the drizzle.

Dinosaurs are perhaps the main link between the popular imagination and the Earth’s past.  However, leaving them at the level of awesome animals that a comet strike snuffed out 65 Ma ago may enthuse, but does not really educate.  Live from Dinosaur Island began to break the T rex – My Little Pony connection, by also showing how we can recreate the environments that long-dead creatures inhabited, and how they changed.  Climate and life (above), hints that dinosaur breath may even have affected climate during the Mesozoic.

Barely a month passes without dinosaur news.  The latest concerns the rediscovery of the Egyptian site, from which Ernst Stromer von Reichenbach gathered  a rich collection of animal fossils between 1911 and 1936.  Stromer’s collection, housed in the Bayerische Staatssammlung museum in Munich, was destroyed by wartime bombing.  Because Stromer left no clues regarding the precise location of his site, except that it was near the Baharyia Oasis in the Western Desert, it seemed unlikely ever to be found again.  A team from the University of Pennsylvania, let by Josh Smith, more or less tripped over the site by luck, when combing the area for coastal Upper Cretaceous sedimentary outcrops, after Smith’s inspiration by Stromer’s monographs (Smith, J.B. and 7 others 2001.  A giant sauropod from an Upper Cretaceous mangrove deposit in Egypt.  Science, v. 292, p. 1704-1706).  The highlight of their excavations is Paralititan stromeri, a sauropod reckoned to be the second most massive animal that lived, after South America’s Argentinosaurus.  The tidal sediments also yielded a diversity of lesser animals that matches and will certainly transcend Stromer’s destroyed collection.

See also:  Stokstad, E.  2001.  New dig at old trove yields giant sauropod.  Science, v. 292, p. 1623-1624.

Doubts cast on the increase in diversity with time

The late John Sepkoski of the University of Harvard painstakingly spent 20 years trawling the palaeontological literature to build an archive of the duration of every marine fossil known.  Others did similar work for terrestrial fossils, but Sepkoski’s database stands out, head and shoulders, for its comprehensiveness.  It is largely from his work that the record of extinction events took on semi-quantitative form.  Plotted against Phanerozoic time, his counts of genera also seem to show patterns that chart the fluctuations of biodiversity; rapid rise from the Cambrian Explosion to plateau in the mid-Palaeozoic, a decline in the late Palaeozoic and early Mesozoic, and then a post-Jurassic explosion in diversity.  Much speculation has hung on Sepkoski’s empirical data, such as the influence of “modern” evolutionary designs on the number of ecological niches that life can exploit.

Enormously important as Sepkoski’s work was, inevitably it rested on the selective nature of fossil collecting, itself partly determined by the variable quality and quantity of preservation, but also by the limited numbers of active palaeontologists, the manner in which they worked and their selection of sites.  There are gross biases in fossil collections, but how can archivists possibly allow for their influence?  Without a superhuman effort to re-collect more intensively, to plunder every conceivable stratum wherever it crops out and perhaps standardise what is meant by a genus, the only available means is through statistics.  Palaeontologists at the universities of California (Santa Barbara) and Harvard, led by John Alroy and Charles Marshall respectively, are compiling information along more comprehensive lines than did Sepkoski, including the dimension of geographic occurrence as well as duration, in the Palaeobiology Database.  Their first attempts to allow statistically for the welter of biases, published in the 25 May 2001 issue of Proceedings of the National Academy of Sciences, all point in the same direction.  The Cretaceous to Tertiary genera show patterns of change that are little different those for the Silurian to Carboniferous, compared with Sepkoski’s suggestion of explosive diversification in the first and a plateau in the second.  The main problem remains; vast as they are, fossil collections are not truly representative of life in the past.

Source:  Kerr, R.A. 2001.  Putting limits on the diversity of life.  Science, v. 292, p. 1481.

Earth System Processes conference

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Geoscientists from all over the world attended and spoke at this seminal meeting.  Its theme was moving from isolated studies to those linking contributions from many branches of science, thereby attempting to match the complex web of interactions on every scale and at every pace that is the essence of the way the world works and has evolved.  Topics covered a huge range, from the “Snowball Earth” hypothesis to issues linking life and inorganic processes, deep mantle processes to sea-floor hydrothermal systems, molecular palaeobiology to the fossil record.  Indeed, the scope is too broad for me adequately to summarise here.  While it remains active, readers can read all the abstracts of papers presented at: http://www.geosociety.org/meetings/edinburgh/prog.htm

Late Pleistocene mass extinction

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The recent fossil records of the Americas and Oceania are littered with species that became extinct in the last 100 000 years.  The majority of them are large animals whose body weights were greater than 45 kg – part of the megafauna.  While controversy rages about the date of entry of the first humans into both vast regions, for a long time archaeologists have suspected that the appearance of sophisticated hunters was somehow connected with the rapid decline in what would have been prey species.  One theory is that having never encountered weapon-bearing bipeds, large mammals were “naïve” and thus easily slaughtered.  Most visitors to the Americas and Australia soon notice how unafraid many animals are of humans, compared with their behaviour in Europe and Africa.  The suddenness of  the selective extinctions (around 15 to 11 000 and 47 000 years ago in North America and Australia respectively) is astonishing, if the cause was small bands of hunters, and other workers have suggested that human entry brought diseases that wiped out species susceptible to them, but with no immunity. The third main theory is that a sudden shift in climate wrought havoc among large herbivores and predators, by producing a change in vegetation.  The last is difficult to support for the Americas as the extinctions were in a period of increasing warmth and humidity following the termination of the last glacial period.  As always, new information from research directed at the problem has narrowed the choices, but revealed complexities.

Modelling the influence of changing predation on prey stems from the mathematical simplification of reality by Lotka and Volterra, in which “boom and bust” events pop out of the simulations.  John Alroy of the University of California applied an advanced version of the basic model to the likely effects of advanced hunters appearing suddenly in North America (Alroy, J.  2001.  A multispecies overkill simulation of the end-Pleistocene megafaunal mass extinction.  Science, v. 292, p. 1893-1896).  His model assumes slow human population growth, random hunting and the least possible effort – a conservative approach.  The results closely parallel the record, if human population expanded from 100 first entrants about 14 000 years ago to almost 1 million 750 years later, and suggest that a steady state population of around half that co-existed with the surviving fauna until the appearance of Europeans and their culture.  It is an entirely mechanistic model, but mimics what happened without recourse to any other influence, such as climate change.  So far, no human site in the Americas has been convincingly dated before 14 000 years ago.

Dating is even more of a problem in Australia, particularly for human arrival.  The earliest dated fossil is 60 000 years old (see Out of Africa hypothesis confounded? EP Feb 2001), but claims have been made for artefacts at least twice that age.  Alroy’s model applied to Australia would demand extinction (24 out of 25 genera Pleistocene megafaunal species) shortly after earliest arrival.  A large team of Australian scientists (Roberts, R.G. and 10 others 2001.  New ages for the last Australian megafauna: continent-wide extinction about 46 000 years ago.  Science, v. 292, p. 1888-1892) have systematically dated the age of burial of extinct faunas at 27 sites in coastal areas and the more humid SE of the continent (none from the vast, arid “red centre”), and one in Papua New Guinea.  The most likely interval for the extinctions, between 39 800 and 51 200 years ago, bears no relation to extreme aridity during the last glacial maximum, so the data weigh against that climatic cause.  However, the last 100 000 years have seen lesser, but still extreme shifts in climate, so climate change cannot be ruled out.  Though the authors also do not rule out humans eating their way through Australias bizarre megafauna, the lag between evidence for first entry and the extinction seems far longer than that in the Americas.  Closer inspection of their data, however,  does show precise 230Th/234U ages (+ 600 to 2 200) from 33 600 to 60 000 from 3 sites, and less well-constrained luminescence ages (+ 200-21 000) from 16 000 to 171 000 years from all the sites.  Applying simple statistics to samples from such a wide spread of localities does not seem justified to me – normal practice is for ages at individual sites to be accepted as dates within the errors of the method used.  Australia’s megafaunal extinction seems to have been protracted.  Using fuzzier dating of the extinction, earlier workers correlated it with evidence for an increase in bush fires marked by ash in offshore sediments.  Much of Australia’s flora is fire resistant, and the seeds of some species require light burning before they will germinate.  The most popular theory for the extinctions there is through deliberate fire setting by hunters – a culturally induced decline unique to Australia’s peculiar climate and terrain.

See also:  Dayton, L.  2001.  Mass extinction pinned on Ice Age hunters.  Science, v. 292, p. 1819.

Where do subducted slabs go?

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Geophysicists and geochemists are generally opposed on what happens to subducted lithosphere.  Seismic tomography of the deep mantle shows convincing evidence for slab-like cold bodies down to the core-mantle boundary, yet differences in trace-element and isotopic signatures of volcanic rocks formed at ridges from shallow mantle and ocean islands that relate to deep plumes persuades geochemists that restriction of convection within the upper mantle, at the 660 km deep discontinuity, best explains the differences.  There are other models that might account for geochemical differences, such as heterogeneities throughout a poorly stirred mantle or because material in slabs subducted to the bottom of the mantle rarely rises again, but displaces more pristine materials upwards.

The more earthquakes that seismographs detect and locate, the better geophysicists are able to map in 3-D the zones on which they take place.  One destructive margin long known to have aberrant seismicity is the northern part of the Tonga system in the Pacific Ocean.  This is where the fastest subduction anywhere consumes lithosphere that has little time to warm up while it descends – surely a site for slabs to fall steeply into the deep mantle.  Much of the Tonga system shows the expected zone of steeply plunging Earthquakes, yet west and north-west of Fiji there are earthquakes that do not fit the regional pattern.  They are far too shallow to result from motion on the main subduction zone.  By detailed analysis of seismic data Wang-Ping Chen and Michael Brudzinski have revealed a strong possibility that a piece of old subducted slab has slid to the 660 km discontinuity since it parted company with the now rapid and steep motion at the Tonga trench (Chen, W-P. and Brudzinski, M.R. 2001.  Evidence for a large-scale remnant of subducted lithosphere beneath Fiji.  Science, v. 292, p. 2475-2478).  If such behaviour turns out to be more widespread, large volumes of old lithosphere may indeed sit at the discontinuity, satisfying many geochemists as a means to maintain very old differences in composition of the mantle.  The problem is, increasingly good resolution in seismic tomography has so far failed to detect the tell-tale high seismic velocity signature of such cold slabs.  Chen and Brudzinski suggest that they may be “invisible” to this method, because of their mineralogy – perhaps the crustal lithosphere has not equilibrated to eclogitic materials, or is given neutral buoyancy by being heavily hydrated.

Between a rock and a hard place

Plate theory stems from the notion that the lithosphere is overwhelmingly rigid and deforms only at the boundaries between plates, particularly at destructive margins.  The Earth’s seismicity is overwhelmed by earthquakes at discrete boundaries, and the mapping of seismic events along narrow lines by the world-wide network of seismographs (set up as a means of pinpointing nuclear weapon tests) formed on of the main planks in developing the theory of plate tectonics.  The plate whose evolution drove India into Asia bucks this definition.  It has long been known to host seismicity well inside its boundaries.  Oceanographic work has slowly built up a means of relating Indian Ocean seismicity to plate structure, whereas analysis of earthquake first motions from seismographs reveals that the deformation differs between various block of the ocean floor.  The plate suffers folding and thrusting, and transcurrent motions along ancient transform faults, such as the Ninety East Ridge.  The most likely explanation for the Indian plate’s aberrance is that sea-floor spreading from the ridge separating the Indian Plate from that carrying Antarctica can no longer be accommodated by subduction of the subcontinent beneath Asia, whereas it can be taken up by subduction beneath the Java-Sumatra island arc.  The Central Indian basin is being compressed, and must deform in some way, perhaps eventually to become a new subduction zone.

Source:  Deplus, C.  2001.  Indian Ocean actively deforms.  Science, v. 292, p. 1850-1851.