Earth-logs

About 33.7 Ma ago, at the Eocene-Oligocene boundary marine invertebrates suffered their largest downturn in the Cainozoic.  Marine-core oxygen isotope records suggested that this coincided with a major cooling, when East and West Antarctica both possessed ice sheets.  Deep ocean water temperatures, recorded by the oxygen isotopes of benthonic forams, fell by 3-4°C, yet surface waters at low latitudes appear to show little detectable change in the isotopics of planktonic forams.  Data from cores become less well resolved in time, the older the sediments are, for a variety of reasons.  Tying down a climatic cause for the E/O extinction demands much better precision.

From an astonishing piece of ingenuity and technical skill, we are closer to an answer.  Lida Ivany and colleagues, from the Universities of Michigan and Syracuse, USA, collected the tiny ear bones or otoliths of fossil fish from a boundary section on the Gulf of Mexico.  Because these grow with the fish and contain growth layers, potentially they can give resolution to the level of a single season.  The trick is to get samples on a layer by layer basis and then analyse the tiny masses so extracted for oxygen isotopes.  That is what the team managed to do (Ivany, L.C. et al.  2000.  Cooler winters as a possible cause of mass extinctions at the Eocene/Oligocene boundary.  Nature,  407, 887-890).  Comparing the fine detail from Eocene and Oligocene fish ears shows that the local climate was much more seasonal in the early-Oligocene.  While summer temperatures stayed at much the same level as in the immediately preceding Eocene, early-Oligocene winters were much colder.  That would account for the inability of marine core data to detect any significant global cooling, and seasonal contrasts could have knocked out marine invertebrates evolved to more equable conditions.

News and Views in the same issue of Nature includes a fascinating look at these novel data in the context of wider knowledge of what was happening at the E/O boundary (Elderfield, H.  2000.  A world in transition…  Nature,  407, 851-852

Primordial slime

A timeless phrase from the film One-eyed Jacks is Marlon Brando’s, “You ain’t nothin’ but a ball o’ spit”, to the oppressive and corrupt lawman played by Slim Pickens.  Some molecular biologists would come close to agreeing, though not in anyway to mock that fine actor.  In Lyn Margulis’ theory of endosymbiotic origin for the Eucarya, of which we are a multicellular one, a candidate for the organism that played host to several others that went on to become eucaryan organelles is a slimy beast.  It is Thermoplasma acidophilum, a member of one of the three fundamental domains of living things, the Archaea.  Thermoplasma has no proper cell wall, contains DNA with proteins like those which bind nucleic acid in eucaryan cells, and it thrives in burning coal heaps.  It is pretty much slime that needs both highly acid and very hot conditions to metabolise, and both result from the spontaneous oxidation of sulphides in coal exposed to air.  Its very sliminess makes it worth considering as the original envelope for the baggage of the first Eucarya, so that they could get in.  It is also an anaerobic fermenter – a methanogen – on whose waste products aerobic Bacteria might live while protecting the host from oxygen that would be highly toxic to it and perhaps supplying it with useful chemical products.  Very roughly, that is how Margulis explained mitochondria, the organelles that are common to all eucaryan life.  For a symbiosis to become a cellular unit from which all animals, plants etc descended demands an exchange of genetic material between all the participants, so that they become incapable of independent reproduction.

A few months after gongs were beaten to announce the completion of the human genome sequencing, Andreas Ruepp and colleagues from Germany and the USA laid out the genome of the loathsome Thermoplasma (Ruepp, A. and 9 others  2000.  The genome sequence of the thermoacidophilic scavenger Thermoplasma acidiphilum.  Nature, 407, 508-513).  Thermoplasma, being an “extremophile” is also a candidate for having evolved in the hot environment of sea-floor, hydrothermal vents.  It comes equipped with so-called heat-shock proteins, that eucaryan cells have turned to a multiplicity of other uses in their later, cooler, oxygen-loving evolution.  The astonishing feature of its genome is that it is either a molecular thief or prone to being burgled.  Many of its genes are identical to those in the sequences of other bacteria species whose habitats overlap with that of Thermoplasma.  As well as offering little hindrance to large molecules entering it, the archaean seems not to generate enzymes that in many other cells detect and destroy alien DNA.  The fact that Thermoplasma shows less affinities with eucaryan genetics than with that of Bacteria, suggests that it probably was not our ultimate ancestor.  But that is hardly surprising, since such an organism would have had to share an environment with aerobic ancestors of organelles, one very different from the high temperatures and low pH of Thermoplasma and its fellows.  To me, the new information serves to show strongly that an endosymbiotic origin of the Eucarya was indeed possible, given this mixture of larcenous and tolerant metabolism.

See also: Cowan, D.  2000.  Use your neighbour’s genes. Nature, 407, 466-467

Eve never met Adam

A bit of molecular biology never did Earth scientists any harm, and new research on connectedness in DNA between people now living in different parts of the world sheds new light on the origin of fully modern humans.

All humans are, at most, one tenth of a percent different in their genetic make up; we are ten times more closely related than are chimps from different bands in the forests of West Africa.  This low variance almost certainly results from the origin of fully modern humans in very recent times.  The well-known comparison between DNA in mitochondria (mtDNA) of people across the world points to a divergence in our “bush” of descent about 140 000 years ago.  Because mtDNA passes through the female line, this aspect of modern human origins has been said to stem from a mitochondrial “Eve” living in Africa at the time.  This does not mean that only one fully-modern woman was alive at the time, but that lines of descent from others died out subsequently.

The other side of the evolutionary coin is descent worked out through the male line.  Molecular biologists have focussed on DNA in Y-chromosomes that only men possess and pass on to their sons.  A team at Stanford University in California used cell material from over a thousand men from 24 widely separated regions to investigate relatedness and divergence with the highest precision yet.  Their results point to a time of divergence between 50 and 70 000 years ago; half that for female inheritance.  While the mismatch certainly knocks creationism and its literal reading of the Old Testament still further out of the park, how the mismatch arose is hard to fathom.  One possibility is that a mutation affecting Y-chromosome DNA only imparted such an advantage to the males who carried it that their descendants survived, while those not so favoured had their lines snuffed out.  Alternatively, it may simply have been that some important technological discovery, or maybe even a cultural change, such as art that seems to first appear in Africa around 70 000 years ago, gave a very small family group the potential for only their descendants to survive through 3 to 4 000 generations.  Whatever, the “bottleneck” through which all our genes passed at the time was in Africa.

Source:  Cohen, P.  2000, Eve came first.  New Scientist, 4 November 2000, p. 16.

The undead

The notion of bringing to life ancient organisms carries overtones of Jurassic Park, and more scientifically those of contamination by modern organisms.  But has it been done?   Russell Vreeland and colleagues from West Chester University, USA, claim to have cultured bacteria preserved in fluid inclusions from a Permian salt deposit (Vreeland, R.H. et al.  2000.  Isolation of a 250 million-year-old halotolerant bacterium from a primary salt crystal.  Nature, 407, 897-900).  The stringent conditions of sampling suggest that indeed this is an old bug, as does the fact that it seems to be a salt-tolerant bacterium.  However, it is hard to believe that living organic material can survive without apparent damage for so long.

In the accompanying News and Views pages, John Parkes, of the University of Bristol, UK, discusses the ramifications, and that surrounding claimed revival of bee-dwelling bacteria from Miocene amber.  Some are worrying. Bacterial spores might survive indefinitely, to be released on an ill prepared world that has lost any shred of resistance to pathogens.  Others bring a spark to some dormant ideas, particularly that of life spreading galactically by meteorite transportation.

In the United States’ legal system I believe there is a statute of limitations.  It doesn’t apply to the Cretaceous Period.  More precisely, the most complete and fierce-looking specimen of a Tyrannosaurus rex skeleton has been the subject of legal wrangles from the moment she – a female named Sue after Sue Hendrickson of the Black Hills Institute of Geological Research (BHIGR), South Dakota who found her – was excavated.  The legal saga is the subject of a new book by a lawyer, Steve Fiffer (Tyrannosaurus Sue, Freeman, New York, ISBN 0-7167-4017-6).  The trouble started when the owner of the land on which Sue was discovered in 1990 was paid a paltry US$5000 for the privilege of seeing the awful fossil removed.  The rancher’s subsequent claim on her was matched by another from the Cheyenne River Sioux, because the owner had placed his land in trust with the US Department of the Interior, and that conveys certain advantages to Native Americans….  The plot indeed thickened.  The FBI and the local sheriff pounced on the hapless saurischian in 1992, and the National Guard supervised her impoundment, pending due process of law.  Five years of hearings and criminal proceedings later –  a raft of 148 felonies and 6 misdemeanours fell on the owners of BHIGR and one was jailed for 18 months – Sue became probably the oddest lot at Sotheby’s auction rooms.  To add further insult, the auction price of US$8.36 million was partly raised by Disney and McDonald’s, and the landowner made US$7.6 million after commission.  Sue now entertains in Chicago’s Field Museum of Natural History.

Source: Pojeta, J., 2000.  Fossils, G-men, money and museums.  Science, v. 289 8 September 2000, p. 1695-1696.

The most familiar photosynthesis is that associated with green plants, members of the Eucarya, in which organelles known as chloroplasts play a crucial role.  Lyn Margulis’ theory of endosymbiotic incorporation of various bacteria in the origin of the eukaryote cell, sees cyanobacteria as the most likely progenitors of chloroplasts in plants.  Aspects of the genetic material in chloroplasts are sufficiently similar to that of blue-green bacteria to make this a robust view.  Tracking down when that melding of bacterial ancestors took place is a difficult task, both for molecular biologists and palaeontologists, partly because the record of cell material similar to that of cyanobacteria goes cold about 2.5 billion years ago.

Stromatolites, which today grow through the action of cyanobacteria excluding calcium from their cells in hypersaline environments, go back into the Archaean 3.46 billion years ago, but there is no guarantee that stromatolite forms were always confined to oxygenic photosynthesisers.  However, the manner in which photosynthesis by blue-greens fractionates carbon isotopes possibly gives a signal in the d¹³C record of ancient hydrocarbons.  Sadly, the overlaps between carbon-isotope fractionation oxygenic photosynthesisers, chemoautotrophs and anoxygenic photoautotrophs are too broad for this kind of study to give a definitive answer.  Nonetheless, some researchers have claimed an Archaean origin for the cyanobacteria using this approach.

The advance of molecular biology, which compares gene sequences among living organisms to seek degrees of relatedness (phylogenies), steadily moves towards widely accepted molecular “clocks” that might resolve the timing of emergent life processes.  A joint US-Japan team of molecular biologists have compared the photosynthetic genes of two modern photoautotrophs – green sulphur and green nonsulphur bacteria, neither of which are oxygen producing – with those of other photosynthetic bacteria (Xiong, J. et al., 2000.  Molecular evidence for the early evolution of photosynthesis.  Science, v.  289 8 September 2000, p. 1724-1730).  Their results firmly place oxygenic photosynthesis, as in cyanobacteria, as descendent from earlier anoxygenic photoautotrophy, purple bacteria likely being the first to emerge by developing pigments capable of using solar energy to fuel proton pumping across cell walls.  Jin Xiong and co. do not derive any timing for this phylogeny, but palaeobiologists are suggesting from their evidence that the six major photosynthetic bacterial lineages were around in the mid-Archaean (2.8 to 3.0 billion years ago) and maybe earlier.  This comes nowhere close to the greater antiquity of stromatolites, but tagging purple bacteria as the first photosynthetic organisms, albeit not producing oxygen, gives a helping hand.  Organic molecules originating in them are sufficiently distinct to already have shown up in kerogen from ancient shales, and such precursors to petroleum are present in Archaean sediments.

The interest in the emergence of photosynthesis is understandable, because of the huge increase in opportunities that it presented, by comparison with chemoautotrophic metabolism that seems likely to have been the first life strategy.  The latter depends on chemical tricks with reduced materials, such as S, Fe²⁺ and methane delivered by sea-floor hydrothermal vents.  Assuming appropriate rates for Archaean magmatism, that could sustain about 10¹² moles of carbon fixing in cells per year.  The anoxygenic photosynthetic pathway would have multiplied that by ten times.  However, it is oxygenic photosynthesis that exploded life’s potential for interaction with the inorganic world, and that stemmed from the chemical-physical process at the root of what blue-greens did.  The essence of oxygenic photosynthesis is that the pigments (like chlorophyll in plants) involved in transforming photon energies into electron flows, which are essential in the reduction of CO₂ and water to carbohydrates, actually break the very strong bond between hydrogen and oxygen in water; that is why it releases free oxygen as a by-product.  That feat involves a combination of the processes used by green sulphur and purple bacteria, which in itself implies the later emergence of cyanobacteria as confirmed by Xiong et al’s work.  By using water molecules in this way, however, oxygenic photosynthesis opened up the whole near-surface of the hydrosphere, increasing potential bioproductivity by a further two or three orders of magnitude at least.  It can be said that such a development truly brought life onto the front stage from hiding in obscure nooks and crannies.  But we still have little precise idea of when that happened.

See also:  Des Marais, D., 2000.  When did photosynthesis emerge on Earth? Science, v.  289 8 September 2000, p. 1703-1705.

The mass extinction that marks the boundary between the Palaeozoic and Mesozoic Eras snuffed out more than 90% of marine animal species and about 70% of terrestrial vertebrates.  The most complete record of the Permian-Triassic boundary is in marine sediments atop an obducted ophiolite in Japan (Isozaki, Y., 1997.  Permo-Triassic boundary superanoxia and stratified superocean: records from lost deep sea.  Science, v. 276, p. 235-238).  These record a 20 million-year period when deep ocean water was lacking in oxygen, and the anoxia reached extreme conditions for about 4 million years across the boundary.  All the palaeontological signs are that shallow marine faunas dwindled slowly in the 10 million years before the P-T event.  Carbon isotopes from hydrocarbon-rich boundary strata in Canada suggest that over a period of  only 1000 years the oceans were almost devoid of life.  The open oceans had become dead from top to bottom; a scenario graphically expressed by Ken Hsu as a “Strangelove” ocean.  Whatever the pace of preceding extinctions the boundary event was a catastrophe, and the Japanese and Canadian sections suggest that maybe a half-million years passed before surviving organisms began to recover and diverge.

The much-studied K-T boundary’s association with abundant evidence for an associated giant impact, prompted geologists to look for a similar story for the near end of Earth’s life 190 million years earlier.  Supporting evidence has yet to emerge, although the boundary includes the period when huge volumes of continental flood basalts poured over what is now Siberia.

Terrestrial records are far less easy to divide into fine time divisions, partly because they record both deposition and erosion, and partly because fossils are less well-preserved than in marine sediments.  Continental sediments spanning the P-T boundary are particularly frustrating, because of the wide extent of arid to semi-arid conditions then.  The Karoo Basin of South Africa does record wonderfully the fate of vertebrates (only 6 out of 44 genera survived the  boundary event), but less so that of plants.  Abrupt changes in plant-life are equally as important as those of animals, simply because they are at the base of the terrestrial food chain.  One way of addressing vegetation shifts of the most general kind is to look for evidence of how river systems changed their patterns of deposition, and this is what a team from the University of Washington (Seattle) and the South African Museum have done in the Karoo Basin (Ward et al., 2000.  Altered river morphology in South Africa related to the Permian-Triassic extinction.  Science, v. 289 8 September 2000, p. 1740-1743).

Peter Ward, David Montgomery and Roger Smith examined sedimentary structures produced by river channels in the sandstone members of the Karoo sedimentary pile.  Permian rivers seem to have flowed in distinct, meandering channels, whereas those of Triassic age laid down sands that show consistent evidence for intricately braided  channel systems.  The shift from one to the other type falls right at the P-T boundary.  Meanders of large river channels typify land surfaces with abundant vegetation that binds alluvium.  Where vegetation cover is sparse, there is little to constrain river flow and alluvial erosion, and wide braided river courses develop.  The authors conclusion is that vegetation suffered a catastrophic die off at the P-T boundary, leaving formerly lush plains as sandy wastes.  Such a loss of plants that would previously have contributed to balancing the atmosphere’s CO₂ levels and the proportions of light and heavy carbon isotopes in the global environment would have helped produce the “Strangelove” signal in the ocean sediments.  The land was seared, and evidence from similar sediments in Australia and Antarctica suggests a global loss of plant life.  Incidentally, the boundary in many places shows a leap in the abundance of fungal spores, so the Mesozoic began with decay on a grand scale.

See also: Kerr, R.A., 2000.  Biggest extinction his land and sea.  Science, v. 289 8 September 2000, p. 1666-1667.

Organisms at the base of the food chain, autotrophs that synthesise biological compounds directly from carbon dioxide, water and other fundamental materials in their environment, favour incorporating the lighter of the two common isotopes of carbon, ¹²C, as opposed to ¹³C.  Consequently, one of the prime signatures of life in the carbon found in rock is a depletion in ¹³C, usually expressed as d¹³C with a negative value.  It is this signature that has allowed the origin of life to be pushed back almost to the age of the oldest rocks on Earth (around 3.9 billion years ago) from carbon isotope studies of carbonaceous compounds (kerogen) in ancient sediments.

Different organisms alive today, particularly among the ecologically diverse bacteria, use different biochemical reactions in synthesising living material.  Each of these have different effects on d¹³C.  Potentially these differences could be used to identify roughly the kinds of bacteria that lived in the distant past.  Up to now, however, isotopic studies of organic carbon have only been possible for bulk extracts from rock.  That enables some bold conclusions, such as the current suggestion that oxygen-producing blue-green bacteria were around 3.5 billion years ago, but whole-rock results are ambiguous because of mixing of carbon originating from different metabolic pathways. 

Being able to analyse carbon isotopes from individual fossil cells is a major breakthrough, and a team of palaeobiologists from the universities of California and Regensburg, Germany has done just that (House, C.H. et al., 2000.  Carbon isotope composition of individual Precambrian microfossils.  Geology, v. 28, p. 707-710).  They used an ion microprobe that allowed the discovery of biological carbon encapsulated in resistant materials from 3.8 billion-year old metamorphosed iron formations from West Greenland.  That involved probably mixed carbon of biological origin.  In the new work, the isotopic analyses are from individual bacterial cells preserved in 850 and 2100 Ma banded iron formations, and suspected to be blue-green bacteria.  The results clearly distinguish one metabolic pathway – the Calvin cycle used by blue-greens – from other possibilities.

Tangible bacterial fossils go back, albeit rarely, to more than 3 billion years ago.  It is the older life forms that are most intriguing, because by 2100 Ma ago the Earth’s atmosphere had become oxygen bearing, thereby allowing the rise of the Eucarya from which we stem.  Older material might give clues to the more primitive Bacteria and Archaea that were the exclusive rulers of the biosphere before about 2200 Ma, and controllers of the Earth’s atmospheric composition and thereby its climate, which remains a mystery.

Searching for sudden events that might explain the disappearance of sizeable proportions of fossil taxa is a growing cottage industry among geologists.  Until 1980, with Alvarez’ discovery of geochemical evidence for a comet or asteroid impact at the Cretaceous-Tertiary boundary, such tumbles in life’s diversity and volume were merely palaeontological markers which geologists chose to divide the stratigraphic column of the Phanerozoic into Periods and Stages.  Mass extinctions now take on a much greater importance through the hunt to explain them.  The popular vision of herds of dinosaurs writhing in the inferno following the Chixculub bolide strike at the K-T boundary dwarfs to a large degree the equally certain knowledge that at the same time vast basalt floods in what is now north-western India may have had an equally doleful outcome.

Super-large volcanic events, akin to the Deccan Traps, are a great deal simpler to spot than the subtle signs of impacts in the rock record.  Improved precision in dating such basalt piles shows that three of the “Big Five” mass extinctions occurred within the 1 to 2 million-year life spans of flood-basalt paroxysms: the Deccan Traps at the K-T; The Parana Basalts at the Triassic-Jurassic; and the Siberian Traps at the Permian-Triassic boundaries.  A similar correlation exists for the lesser Palaeocene-Eocene boundary event at 55 Ma, which implicates the North Atlantic large igneous province responsible for flood basalts in north-west Scotland and Greenland.

The scales have tilted further towards a terrestrial cause for mass death with the recent discovery that the Karoo and Ferrar flood-basalt provinces of South Africa and Antarctica formed at a time (183.6+ 1 Ma) that brackets a lesser extinction event in the early Jurassic Period.  Jósef Pálfy of the Hungarian Natural History Museum and Paul Smith of the University of British Columbia (Pálfy, J.  and Smith, P.L., 2000. Synchrony between Early Jurassic extinction, oceanic anoxic event, and the Karoo-Ferrar flood basalt volcanism. Geology; v. 28, p. 747–750) use U-Pb dating of thin volcanic ash layers in the Jurassic sedimentary pile of North America to calibrate the ages of individual ammonite Zones of the Pliensbachian and Toarcian Stages of the Jurassic.  At that time, about 25 % of organisms at the family level became extinct globally over a period of about 4 million years – the Pliensbachian-Toarcian event was not abrupt.  The record in the British Jurassic for extinction of marine animal species shows a marked change at around 183 Ma, within the time span of the Karoo-Ferrar eruptions.

This correlation ties in well with the Toarcian ocean-anoxia event, recorded in the British and Swedish Jurassic (see Earth Pages archives – Methane hydrate – more evidence for the ‘greenhouse’ time bomb) which seems to have coincided with a huge gush of methane into the atmosphere, released by methane hydrate layers in ocean-floor sediments.  Methane, a greenhouse gas in its own right, oxidizes to carbon dioxide.  What may have happened is that the Karoo-Ferrar volcanism injected massive amounts of CO₂, leading to global warming.  This, transmitted to deep ocean water, could have triggered breakdown of methane hydrate to give a massive positive feedback to global climate.  The heat itself might have driven species and families to extinction, or changed ocean circulation to induce stagnation and anoxia.

Important as Pálfy and Smith’s findings are, they by no means resolve the complexities of interwoven terrestrial events.  The 90 million-year old Cenomanian-Turonian ocean-anoxia and extinction event had an associated methane burst, but no flood basalts.  That at the Palaeocene-Eocene boundary has no associated anoxia.  The largest basalt flood known, beneath the Pacific to form the Ontong-Java Plateau about 120 Ma ago, induced methane release and anoxia, but has no associated extinction peak

Despite well-funded attempts to link mass extinctions, other than the K-T event, to impacts, there is little tangible sign of such a connection using precise radiometric dating.  Still, the focus of high-profile stratigraphic research is on boundaries rather than what lies between them.

Putting numbers on ecological effects

In the same issue of Geology a team of American palaeoecologists (Droser, M.L.. Bottjer, D.J., Sheehan, P.M. and McGhee, G.R., 2000. Decoupling of taxonomic and ecologic severity of Phanerozoic marine mass extinctions. Geology; v. 28, p. 675–678) assess the degree to which ecologies change after mass extinctions.  They focus on the Late Ordovician and Late Devonian events (two of the “Big Five”).  Although both involved similar levels of loss of taxonomic diversity (about 22% decline in marine families), marine ecosystems underwent no significant change after the Ordovician event.  Following that towards the end of the Devonian, however, marine ecology changed drastically.  One example is reefs colonized by tabulate corals.  The early corals were devastated by both extinctions, losing about 75% of taxa.  Coral-rich reefs continued after the Ordovician, but virtually disappear from marine ecosystems after the Devonian, until much later in geological time.  The most likely explanation for this is that Palaeozoic reefs formed mainly from organisms known as stromatoporoids, which gave the 3-D structure required for tabulate corals.  Stromatoporoids lost 50% of their diversity after the Devonian event, and did not recover as reef-formers.  The main implication of this study is that the effects of extinctions do not simply depend on the quantity of taxa that are snuffed out, but on specific components of the ecosystems involved.