Fish ears at the Eocene-Oligocene boundary

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 acidiphilumNature, 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.


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