Earth-Pages Archive News, Geobiology

Coming up with a theory for the origin of something so complex and ancient as life on Earth might seem to be at the pinnacle of hubris, yet such ideas are not uncommon. A novel slant on the 'Big Question' centres on how cells get their energy, rather than on trying to put together all manner of chemical prerequisites (Lane, N. 2009. The cradle of life. New Scientist v. 204 (17 October 2009) p. 38-42). Mike Russell began his career as a geochemist looking at hydrothermal mineral deposits and the intricacies of their formation, while at the University of Strathclyde, Scotland. He now works at NASA-JPL in Pasadena, California inspired by the views of a self-funded eccentric Cornish farmer, Peter Mitchell. Cell energetics, according to Mitchell, are about pumping protons through cell membranes to effect the oxidation and reduction fundamentals of metabolism; in short electrochemical gradients. That is now recognised by every cell biologist, though once it was considered absurd. Russell's take on that novel truism is that the environment of life's origin must have involved similar processes taking place in the absence of living cells, which inherited proton pumping. His choice is mineralised pinnacles full of foam-like voids that can act as minute chemical factories: not the famous sulfidic black smokers of ocean ridge systems, but cooler features formed of carbonates precipitated from alkaline sea-floor hydrothermal vents. The carbonate foam in ancient examples, well-known to Russell from their mineralisation, contains bubbles lined with iron sulfides. Sulfides are known to have catalytic properties; proteins in living cells that convert CO₂ to sugars have Fe-S bonds at the core of their structure; alkaline hydrothermal vents emit hydrogen released by alteration of olivine in ocean-floor basalt to serpentine minerals; bubbles in carbonate foam look very like potential precursors to cells. To produce the first living cells, these features together in one enclosed space need 10 steps of quite simple chemistry. Except, that is, for nucleic acid production...

End-Permian crisis not so bad for ammonites

The greatest known mass extinction at the end of the Permian Period snuffed out 85% of fossil marine species. It is widely understood to have taken at least five million years for ecosystems to begin recovering, and some animal groups remained depressed for longer still, especially those living at or near the sea floor. Yet one group of cephalopods, the ceratidid ammonites, almost immediately began to thrive, despite the ammonoid sub-Class having been among the hardest hit groups (Brayard, A. et al. 2009. Good genes and good luck: ammonoid diversity and the end-Permian mass extinction. Science, v. 325, p. 1118-1121). Only three genera of ceratidids survived the cataclysm, but within 1-2 Ma there were almost 100 representatives. A similar swift recovery is shown by the completely unrelated conodont animals (now-extinct eel-like vertebrates whose teeth are generally the only parts to be fossilised). For such a success story to emerge by pure chance seems intuitively unlikely: for cephalopod equivalents of Lazarus to go forth and multiply so nicely requires genes well-suited to the conditions that followed the mass extinction.

What’s green and above sea level?

Most geologists would answer, ‘The continents after the start of the Silurian Period’, and from now on they could be wrong. Evidence for an earlier ‘greening’ of the land comes from a detailed analysis of thousands of oxygen- and carbon-isotope measurements in Neoproterozoic carbonate rocks (Knauth, L.P. & Kennedy, M.J. 2009. The Neoproterozoic greening of the Earth. Nature, v. 460, p. 728-732). An important consideration in understanding the geochemistry of limestones is that however they originally formed as wet sediments at some later stage their constituents were largely transformed into crystalline aggregates by lithification through the intermediary of pore fluids. During lithification chemistry is equilibrated between crystals and the pore fluids, so if pore fluids are chemically (in this case isotopically) different from the sediment the resulting rock will have been changed isotopically. Studies of Cenozoic carbonates strongly suggest that the place where carbonate sediments are lithified most quickly is in coastal areas where terrestrial groundwater mixes with marine formation water in sediments. Since colonisation of the land by photosynthesising organisms groundwater C- and O-isotopes evolves in equilibrium with those organisms. The terrestrial biomass fixes ¹²C preferentially thereby depleting their proportion of ¹³C by up to 20‰. Groundwater, having originated as water vapour evaporated from the oceans that acts preferentially on ¹²O is also depleted in ¹⁸O. Consequently, low õ¹³C and õ¹⁸O signatures are passed on to groundwater and thence to carbonate rocks when groundwater participates in lithification.

Neoproterozoic carbonates plot in the same õ¹³C vs õ¹⁸O fields as those from the Phanerozoic. Earlier Precambrian carbonate data plotted in the same way show depletion in d18O but not in õ¹³C, which signifies no terrestrial life, but normal preferential evaporation of ¹⁶O from the ocean surface to form rain and then groundwater. Knauth and Kennedy’s results suggest a strong likelihood that carbonates of the late Precambrian were lithified by groundwater from a land surface where photosynthetic organisms were well-established and abundant. There is likely to be a sceptical backlash to this remarkable conclusion, largely because it seems that the terrestrial biomass in the Neoproterozoic would have needed to be of the same order as that in later times. Yet molecular evidence from modern fungi, lichens, liverworts and mosses suggests that they evolved in the Neoproterozoic and Chinese scientists have found traces of what look remarkably like lichens in the 600 Ma Doushantuo lagerstätte - fungus-like hyphae and cells that resemble those of cyanobacteria (see The earliest lichens in May 2005 issue of EPN). In an earlier paper, Martin Kennedy had noted that around 700 Ma, the record of marine limestones show increasing ⁸⁷Sr/⁸⁶Sr ratios, suggesting an increase in the chemical weathering of ancient continental rocks. That may have coincided with biological agencies helping break down bare rock chemically to swelling clays that show a surge in Neoproterozoic sedimentary sequences (see Clays and the rise of an oxygenated atmosphere in March 2006 issue of EPN). The same paper pointed out that such clays increase the chances of preservation of buried organic matter, thereby boosting build-up of atmospheric and dissolved oxygen, as would terrestrial photosynthesisers. The feedback of increased oxygen to other eukaryotes that had evolved as heterotrophic animals would have enabled them to increase in size. Interestingly the earliest fossil animals occur in the same Chinese lagerstätte as the putative terrestrial photosynthesisers.

See also:: Arthur, M.A. 2009. Carbonate rocks deconstructed. Nature, v. 460, p.698-699; Hand, E. 2009. When Earth greened over. Nature, v. 460, p.161.

Mantle link with biosphere

It is pretty clear that events in the deep Earth, which give rise to surface changes, such as topographic uplift and increases or decreases in the pace of continental drift, feed into changes in the biosphere. A convincing example of that is the manner in which uplift of the flanks of the East African Rift System led to climate change that favoured bipedal apes. But is there a more direct link involving chemical influences?

It is likely that the earliest autotrophic organisms performed a variety of chemical tricks in order to create energy and chemical conditions that moved matter back and forth through their cell walls. As well as photoautotrophs of different kinds, including those that release oxygen as waste there would have been chemautotrophs, such as sulfate-sulfide reducers, methanogens and considerably more. Oxygenic photosynthesis apparently was functioning almost 3500 Ma ago, long before the Great Oxidation Event (see Early signs of oxygen…but in the wrong place in this issue) yet it was slow to make any impact on the atmosphere. In the Archaean oceans free oxygen would have been consumed by oxidation of soluble iron-II, probably creating banded iron formations. But photosynthesis has to take place in shallow sunlit water, so it would have been easy for oxygen to enter the atmosphere. Since carbon dioxide in the atmosphere is unable to react with oxygen, oxygen build up in the air might be expected to have built far faster than it did. That is, unless there was a reducing gas present in sufficient amounts to consume oxidation. The most likely buffering agent holding back an oxygen-bearing atmosphere is methane produced by methanogen autotrophs, and it has been suggested that falling methane levels towards the end of the Archaean and start of the Proterozoic Aeons eventually permitted atmospheric oxygen to remain unreacted. Since very little methane is produced by inorganic processes, that hypothesis has a corollary; that there was a decline in methanogen Bacteria and Archaea. So, how might that be tested?

A cunning piece of lateral thinking presents a test, and suggests a mechanism linked to processes in the Late Archaean – Palaeoproterozoic mantle (Konhhauser, K.O. and eight others 2009. Oceanic nickel depletion and a methanogen famine before the Great Oxidation Event. Nature, v. 458, p. 750-753). The first cunning bit comes from the biochemistry of modern methanogens: Methyl-coenzyme M reductase (MCR) catalyses the formation of methane from methyl-coenzyme M and coenzyme B in methanogenic Archaea. This enzyme contains the nickel-centred porphinoid F430 tightly bound in its structure. Needless to say, the olivine-rich mantle contains abundant nickel, so the greater the percentage of mantle partial melting, the more nickel enters the surface environment. Archaean stratigraphy, especially its earlier parts, contains abundant ultramafic lavas known as komatiites, associated with some of the world’s big nickel mines. From the Late Archaean onwards, komatiites are rare rocks. The second master stroke by the authors is to find a means of charting the varying abundance in Archaean and Proterozoic seawater: they analysed the Ni content relative to that of Fe in banded iron formations. To as late as 2700 Ma the Ni/Fe ratio remains high in BIFs, but thereafter it falls sharply. That seems to support the hypothesis that a decline in the mass of methanogens did allow oxygen to build up in the atmosphere, and that decline reflected a fall in the supply of mantle nickel to the oceans. The next step would be to exploit the recently demonstrated ability of methanogen Archaea to fractionate nickel isotopes during their metabolism of dead organic matter. That would ideally be done using Ni-rich BIFs, as in this study.

Hadean not so hellish for life

Although the Earth’s history before 4 Ga is not the mystery that it was, following the discovery of 4.3 Ga-old metasedimentary rocks in NE Canada (see At last, 4.0 Ga barrier broken in November 2008 issue of EPN), the early history of the Moon suggests that it was hectic and plagued by very large asteroid and comet impacts. The mightiest events occurred around 3.9 Ga, forming the huge mare basins on the Moon. Scaling up for the Earth’s greater gravitational pull even larger catastrophes would have pounded our planet, although its turbulent tectonics has removed all tangible traces of them. From detailed studies of rocks and impact melts from the Moon – much of the lunar regolith comprises glass spherules produced by cratering over its entire history – the late heavy bombardment (LHB) was not prolonged in geological terms, lasting 20 to 200 Ma. Yet it involved the most extreme delivery of kinetic energy since the giant Moon-forming event around 2.45 Ga, which generated stupendous power – the rate of energy delivery by impactors moving at a minimum of 15 km s-1 is about a second. This has encouraged speculation that the Earth was effectively sterilised for a second time in its history. The 500-600 Ma of Hadean history may have witnessed emerging life forms of the most basic kind, only to see them wiped out, perhaps more than once. It has been assumed, therefore, that the earliest living things which left descendants, including us, had a universal ancestor that appeared only after 3.9 Ga. Now it seems a serious rethink is needed (Abramov, O. & Mojzis, S.J. 2009. Microbial habitability of the Hadean Earth during the late heavy bombardment. Nature, v. 459, p. 419-422).

Feeding the impact data from the Moon and terrestrial planets into new modelling software run on a super-fast computer, Oleg Abramov and Stephen Mojzis of the University of Colorado have been able to model the degree of thermal metamorphism that the Earth’s crust may have undergone during the LHB. Interestingly, they reveal that less than 10% of the surface would have been heated above 500ºC, and only 37% would have been sterilised, even if all the huge impacts predicted for Earth landed at the same time. Assuming that any basic life forms that had arisen in the Hadean were randomly distributed at the surface and in the subsurface – a variety of extremophile bacteria still live at depths down to 4 km – populations would survive to leave descendants. If they could survive temperatures up to 110ºC, which modern hyperthermophiles do, then so much the better for life as a whole. Although based on modelling, the work by Abramov and Mozjis, gives palaeobiologists another half billion years in which inorganic processes could have assembled the immensely complex molecules the living processes demand. The earliest possible signs of life, based on carbon isotopes locked in stable minerals of a Greenland metasediment, date to 3.8 Ga. Previous assumptions about life’s slate being wiped clean by the LHB therefore left only a few tens of million years for that assembly by some kind of thermodynamic miracle. The new vista will please Mike Russell of the University of Strathclyde in Glasgow. Russell is an economic geochemist turned palaeo-biochemist set on testing the Oparin-Haldane hypothesis of the origin of life using apparatus and approaches that are much more sophisticated than those used by Miller and Urey who created amino acids in vitro during the early 50s. The 21 May 2009 issue of Nature includes an account of Russell’s plans and the views of those with a more cautious outlook (Whitfield, J. 2009. Nascence man. Nature, v. 459, p. 316-319).

See also: Rothschild, L.J. 2009. Life battered but unbowed. Nature, v. 459, p. 335-336.

Irresistible brevia

Surprisingly, the most abundant crustacean fossils are those of ostracodes, which have two carapace shells. They reach back as far as the Ordovician. Although modern ostracodes are an ecologically very diverse group, much used in assessing changing environmental conditions, they are not the most prepossessing creatures being small and externally smooth. Ostracode bodies and appendages are rarely found as fossils, but a German, Japanese, Czech, British and French team has set out to find soft parts using X-ray synchrotron tomography on a Brazilian ostracode of Cretaceous age (Matzke-Karasz, R et al. 2009. Sexual intercourse involving giant sperm in Cretaceous ostracode. Science, v. 324, p. 1535). A third of the ostracode’s body is devoted to reproduction, males having large Zenker organs or sperm pumps. This is unsurprising, when one is informed that the ostracode sperm are sometimes longer than an individual creature. Indeed, Matzke-Karasz et al. assign some significance to them; ‘persistence of reproduction with giant sperm through geological time may add a criterion to test for the pressure of sexual selection’...

Gas source for flood basalts

Although there are several coincidences between flood basalt eruptions from large igneous provinces and mass extinction, not all basalt flood events made an impact on the biosphere and not all mass extinctions link to a LIP. Where there is a connection, two mechanisms dominate discussion: dust and noxious gas such as SO2, stratospheric aerosols from which can also induce global cooling, or global warming stemming from CO2 emissions. The odd thing is that most flood eruptions in LIPs are of tholeiitic basalt magma, which is generally low in gas content. Of sizeable flood basalt provinces, the Ethiopian (30 Ma), Karoo (~180 Ma), Parana (130 Ma) and North Atlantic (55-60 Ma) had no truly significant impact on life. Those that certainly did were the Siberian Traps implicated in the end-Permian devastation, those of Emeishan in China at the time of35 % of all genera went extinct around 260 Ma, the Central Atlantic Province the main suspect for the end-Triassic extinctions and the Deccan Traps that coincided with the Chicxulub impact at the K-T boundary. Two of these massive tholeiitic magma events have been assessed in terms of how they might have emitted gases.

The Emeishan LIP emerged through crust that contains large volumes of carbonates of Proterozoic to Silurian age. Conceivably the magma might have released carbon dioxide by inducing thermal metamorphism (Ganino, C. & Arndt, N.T. 2009. Climate change caused by degassing of sediments during the emplacement of large igneous provinces. Geology, v. 37, p. 323-326). Clément Ganino and Nick Arndt of the University of Grenoble, France investigated a monstrous sill almost 2 km thick in the deeply eroded Emeishan province. It proved to have a 300 m contact aureole dominated by brucite (Mg(OH)2) marble, evidence of melting of carbonates and calc-silicate marbles, production of which by metamorphism would have yielded huge amounts of CO2. They go on to discuss other possibilities for gas generation by magmatism, involving thermal metamorphism of coals, oil shales and evaporites. The last is a distinct possibility in the case of the Siberian Traps (Li, C. et al. 2009. Magmatic anhydrite-sulfide assemblages in the plumbing system of the Siberian Traps. Geology, v. 37, p. 259-262). A large stratiform intrusion associated with the end-Permian flood basalts contains around 7% sulfides; truly huge for mafic magma and making it a major exploration target for platinum-group metals, yet unusual for a tholeiite. It also contains abundant anhydrite, calcium sulfate that is more usually found in sedimentary evaporites. The isotopic composition of sulfur in the intrusion is enriched in ³⁴S, suggesting that at least 50 % was derived from a sedimentary rather than a mantle source. The sedimentary sequence through which the Siberian flood basalt magmas passed contains evaporites around 5 km thick. That would be a suitable source for the sulfur in the intrusion, but would also yield stupendous amounts of SO₂ if carried to the surface by erupting magma. An example of a LIP that had little if any effect on the biosphere is that which mantled both side of the North Atlantic with flood basalts in the Palaeocene. The magma that was involved moved through almost entirely crystalline ancient continental crust. The same set-up characterised the Ethiopian, Parana and Karoo provinces.

Social behaviour among giant trilobites

There’s something about a trilobite that causes outbreaks of hyperbole: as far as I know they are the only class of animals to warrant an expletive in serious literature (Fortey, R. 2001. Trilobite! Flamingo). The title conjures a vision of a three-lobed, segmented alien hurtling for one’s nether regions, hideous malice in its compound eye. Well, most trilobites were little, albeit with anorak-rending diversity in form and habit: they ranged from burrowing bottom feeders to inhabitants of the ocean meniscus, rather like early water boatmen. If you want to use an exclamation mark for an invertebrate, then it might be better to reserve it for the fearsome Eurypterids or sea scorpions. At up to 2 m, with mighty pincers and capable of galloping across a beach, they certainly would have best been avoided in the Ordovician to Permian. Yet, from time to time big trilobites do turn up, such as Paradoxides, Ogyginus and Hunioides that break the metre barrier. Rather a lot of them have been found in a Portuguese lagerstätte of Middle Ordovician age (Gutiérrez-Marco, J.C. et al. 2009. Giant trilobites and trilobite clusters from the Ordovician of Portugal. Geology, v. 37, p. 443-446). They were up to something, as the locality described by Gutiérrez-Marco et al. contains huge numbers that were apparently having been overwhelmed by a sudden turbidity flow once they had gathered together. Some of them are in single file… It could be some sexual frenzy; fearfulness when moulting synchronously or something at which we cannot even guess. Whatever, it seems likely that the gigantism in the deposit is something to do with these being high-latitude animals.

The ancestral animal

The Cambrian Explosion of shell-bearing animals and the preceding, diverse and very odd Ediacaran fauna that left imprints and moulds in the Late Neoproterozoic both posed two puzzles for early palaeontologists. What organisms evolved so that unmistakable traces of animal life were able to leave fossils after about 600 Ma, and what pace did evolution take to present us with virtually all the animal phyla, including some not around nowadays, ‘fully separated’? Molecular genetic studies of living animals are beginning to throw up some answers (Holmes, R. 2009. The mother of us all. New Scientist, v. 202 (2 May Issue), p. 38-41). It is a complex and growing field, so Bob Holmes’ review of current ideas on the last common ancestor of the animals is welcome for non-specialists. It does look as though the radiation was long before the Ediacaran, but may well have been very rapid. The genetically closest single-celled organism to metazoan animals are the rare choanoflagellates; filter feeders with a collar-like structure and a tail. They bear some resemblance to the feeding cells of sponges, but sponges in their current form seem highly unlikely as the Ur-creature, totally lacking any organs and really just a coexistence of clone-like cells. Gene sequencing from 42 animal groups puts sponges at the bottom of a relatedness tree, yet at the bottom of two of the main branches. So the sponges do indeed seem to have it as our ultimate ancestors. Yet the flurry of ever-more detailed sequencing, for more and more groups using increasingly sophisticated statistical analysis has fired up controversy. Jellyfish-like ctenophores now have a look-in too, as do mysterious placozoans, according to one or other researcher. This field is throwing up an object lesson for hubristic scientists used to counting their chickens… No, the votes are never all in, and surprises always lie ahead for both the unwary and the patient.

Luckily, Holmes closes by looking at a careful proposal for the ‘How’. Claus Nielson of the University of Copenhagen, a major ‘player’ in this field, has suggested how starting with a slab-like choanoflagellate, with all its function cells on the outside, might have evolved be curling to enclose a tube of inward facing cells; a precursor of a gut. One next step from there could be specialisation of some cells as nerves, then the development of a ‘mouth’ and ‘anus’ – the basis for the bilateral symmetry of all higher animals including ourselves. As for the ‘When’, there are sufficient leads from a molecular clock approach to settle on the oddest climatic events of the last 1.5 Ga of the Proterozoic, the near global glaciations or ‘Snowball Earth’ events that began around 750 Ma ago.

Photosynthesis from way back when: the hunt for RuBisCO

Charles Darwin had an abiding fascination with plants, though one that was essentially practical through observation and breeding. That is sufficient excuse in his bicentenary for reviews, but a good way to honour his legacy is again to push essays to the leading edge of present understanding (Leslie, M. 2009. On the origin of photosynthesis. Science, v. 323, p. 1286-1287). Being able to convert sunlight, water and carbon dioxide to the basis of their own life and that of the rest of the planet, plants and other photosynthesising organisms are the fundamental essence of the living world. Land plants are recent developments, emerging in the Silurian around 425 Ma ago with presumed terrestrial spores some 50 Ma earlier. Their forbears were almost certainly marine algae. Yet they are highly evolved, and it is not to separate precursors that palaeobotanists can look for origins, but to the internal chloroplasts that look remarkable like cells in their own right with separate DNA and RNA. They perform the astonishing trick of breaking the extremely strong OH-H bonds that form the water molecule otherwise achieved either by extremely high temperatures or by electrolysis. The trick is for an organism to grab an electron thereby releasing the bond and both hydrogen and oxygen. The hydrogen links to carbon and oxygen from CO₂, and the other oxygen is freed. Similar to a magician’s trick with smoke and mirrors, photosynthesis uses pigments. Colour in any object or material results from photons of one wavelength range in sunlight being absorbed so that those reflected make up the colour. The most familiar is chlorophyll which absorbs two wavelength ranges: the red and the blue regions to leave green to be reflected for us to see. It is actually a bit of quantum mechanics, as the absorbed photons carry the energy needed to stoke up that of electrons so that they can break free of the OH-H bond in water and split the molecule. The chain of organic chemistry which follows this trick is hugely complex, and it seems to have taken several forms reflected in specific genes in a growing array of photosynthesising bacteria of various genetic antiquities. There are green ones, blue ones, the reds, yellows and oranges.

Luckily the chemical remnants of photosynthesising bacteria are pretty robust, and also distinctive. The central one for most photosynthesising organisms is an enzyme that is complicated, called Ribulose-1,5-bisphosphate carboxylase/oxygenase, or RuBisCO for short. Euan Nisbet of Royal Holloway, University of London has been hunting RuBisCO for most of the latter part of his career as a Precambrian geologist. he and colleagues found relics of it in 2.7 Ga Archaean sediments from Zimbabwe and Canada (Nisbet, E.G. et al. 2007. The age of Rubisco: the evolution of oxygenic photosynthesis. Geobiology, v. 5, p. 311-335) and claim there are signs far older. Needless to say.

A fluffy grazing dinosaur

The Cretaceous of NE China is becoming a favoured destination for palaeobiologists interested in well-preserved vertebrates, little dinosaurs, especially. An increasing number turned up by fossil hunters have skin relics covered in feathers, although they are rarely if at all equipped for flight, are. Recently, something even more bizarre was unearthed (Zheng, X.-T. et al. 2009. An Early Cretaceous heterodontosaurid dinosaur with filamentous integumentary structures. Nature, v. 458, p. 333-336). In plain-speak, Tianyulong confuciusi was fluffy. And as readers really ought to know, the heterodontosaurs were largely Jurassic herbivorous creatures, 70 Ma older than T. confuciusi; a good example of a ‘living fossil’ in its own time. They evolved to large Cretaceous herbivores, such as the famous duck-billed hadrosaurs, Triceratops and Stegosaurus, members of the Ornithischia as opposed to the more commonly carnivorous Saurischia. It was the latter that were widely believed to have been evolutionary branch from which birds sprang. There is a complex argument surrounding T. Confucius, based on which is a proposal that the ancestral dinosaurs were themselves fluffy. First, thoughts of brightly coloured ‘monsters’ and now the possibility that some may even have looked cuddly.
See also: Witmer, L.M. 2009. Fuzzy origins for feathers. Nature, v. 458, p. 293-295.

Nitrogen isotopes and a change in the Archaean biosphere

All life forms require nitrogen fixation; pretty obvious since they are largely made of C, H, O, N and P. It happens through two main processes in the nitrogen cycle: anaerobic reduction of dinitrogen (N₂) to ammonium ions (NH₄⁺) and the degradation of that by oxidation to nitrite (NO₂-) or nitrate (NO₃-) ions (nitrification). Both kinds of process allow nitrogen to enter cells today, but before the Earth’s biota evolved oxygen production through photosynthesis only the first, anaerobic process was possible. As with many elements that have several stable isotopes – nitrogen has two: ¹⁴N and ¹⁵N – such chemical processes favour one isotope over the others leading to fractionation in the overall environment. A measure of the relative proportions of nitrogen isotopes is d¹⁵N, and its mean value in modern seawater is +5‰ due mainly to the reduction of nitrite and nitrate ions by denitrification. In an oxygen-free ocean d¹⁵N would be significantly lower. Nitrogen-isotope studies of the organic matter in ancient sediments should therefore be a test for the presence of free oxygen in the environment.

In Archaean shales that have not been much metamorphosed d¹⁵N is generally low, as expected. However, there have been hints of higher values from the youngest Archaean strata that do indicate oxygen. The Hamersley Group of Western Australia, famous for its vast reserves of banded ironstone formations (BIFs), includes a 50 m thick carbonaceous shale deposited at the very end of the Archaean around 2.5 Ga (Garvin, J. et al. 2009. Isotopic evidence for an aerobic nitrogen cycle in the latest Archaean. Science, v. 323, p. 1045-1048). Detailed geochemical analyses through the shales and enveloping BIFs, including nitrogen isotopes, show considerable variations ascribed to environmental changes. Aerobic denitrification is marked by a shift from 1 to 7.5‰ in d¹⁵N within the shales, which correlates with shifts in molybdenum and the proportions of sulfur isotope. The real significance of the paper is not that the study detected evidence of free oxygen in the Archaean – the BIFs formed by combination of iron-2 ions with oxygen. It shows that before 2.5 Ga prokaryote organisms had already to perform aerobic nitrification as well as denitrification, of which there are only three groups nowadays, two of Bacteria the other of Archaea.

The Palaeocene Snake of Death and torrid times

As a reader of anything connected with exploration of the Amazon as a kid, I developed a perfectly rational fear of snakes, especially anacondas that ate pigs. To my horror I awoke one snowy February morning to an item on the BBC Radio 4 Today programme about the biggest snake that ever lived (Head, J.J. and 7 others 2009. Giant boid snake from the Palaeocene neotropics reveals hotter past equatorial temperatures. Nature, v. 457, p. 715-717). At 13 m long and weighing in at over a ton, Titanoboa could have eaten an entire family at one sitting, and gone next door for seconds: and it would probably get in the house with the booid’s celebrated stealth. Becoming calmer, I saw how interesting this gigantic people crusher must have seemed to its discovers. Seemingly the maximum size of snakes is governed by ambient temperature. The anaconda that gave me bad dreams gets to a maximum length of around seven metres in present equatorial South America (mean annual temperature in the upper 20s). Modelling based on a range of snakes now living at different latitudes suggests that Titanoboa grew Topsy-like at hotter Palaeocene tropical latitudes (a mean around 33ºC at least). We can all be thankful that such tropical temperatures would require atmospheric CO₂ levels around 2000 parts per million, but this century’s possible global warming will probably mean bigger anacondas and boas for the Amazonian explorer to grapple with.

Snowball Earth and the major division among animals

There are two basic kind of animals: those whose embryos show bilateral symmetry – bilaterians like ourselves, sea urchins and lobsters, for instance – and those that don’t, such as corals and sponges. Evidence from genetic differences among living animals suggests that the evolutionary separation of the two fundamental groups was probably during the Proterozoic Eon. Calibrating molecular clocks based on DNA sequences of living organisms is possible to some extent for animal groups and the ancestral kinds preserved as fossils, for instance humans and domesticated chickens share a common ancestor that lived during the Carboniferous Period. (A propos of very little, mammals have uvulas dangling in their throats that have no other function than to make one throw up if they are tickled, and we share the uvula with birds who still use them to sing: food for the imagination there.) However, the separation of bilaterians from the others, and a great many living phyla, must have taken place in Precambrian times among ancestors with no hard parts and therefore no palpable trace of their existence. Thus, any evidence of when one or another was around is highly useful in phylogenic studies. Most such evidence is likely to come from resistant kerogen and bitumen hydrocarbons found in reduced facies sediments that occur as far back as the Archaean.

Biomarkers include organic molecules that can sometimes be linked to specific phyla, and distinctive ones are associated with either side of the bilaterian-‘others’ split (Love, G.D. and 12 others 2009. Fossil steroids record the appearance of Demospongiae during the Cryogenian period. Nature, v. 457, p. 718-721). The US-UK-Australia team sampled kerogen and bitumen from reduced carbonate sediments in the now famous Omani sequence that almost continuously spans times from the Cryogenian Period of Snowball Earth episodes, through the trace-fossil rich Ediacaran and across the Cambrian boundary. Incidentally, strata like these are source rocks for petroleum reserves in many parts of the Arabian Peninsula. Among the various kinds of molecule identified by chromatography are 24-isopropylcholestanes, degraded remnants of steroids based on 30 carbon atoms per molecule. These are characteristic of one group of sponges, i.e. non-bilaterians, and occur in the oldest samples (around 700 Ma). This shows clearly that the big evolutionary divergence predated that time and may have happened during the climatically dramatic Cryogenian.

Broody dinosaurs

The most likely ancestors of birds evolved in the Jurassic from a group of nimble and mainly carnivorous theropod dinosaurs known as Deinonychosaurs, which included the now famed Velociraptor. One of the oddest fossils ever found was the skeleton of one of these preserved together with eggs of what were originally thought to have been laid by Protoceratops. This Mongolian animal, seemingly caught in the act, was given the name Oviraptor or ‘egg seizer’. Specimens of Oviraptor and closely related dinosaurs found subsequently show them sitting on eggs; clear evidence of bird-like brooding. If this wasn’t a sufficient surprise, the clutches were enormous: 20 to 30 eggs. Detailed study of the skeletons shows that they are all males (Varricchio, D.J. et al. 2008. Avian parental care had dinosaur origin. Science, v. 322, p. 1826-1828). About 90% of all living bird species involve males in care of chicks, including sharing of incubation (5% of mammals share parental care). However, only among ratites (ostriches and the like) and tinamous do males brood eggs clutches continuously. This behaviour is generally associated with polygamy and large clutches. So the misnamed Oviraptor and its kin were not only progenitors of birds but may well have passed on the peculiarities of avian parenting.

Molecular evidence for the environment of the universal ancestor

If ever there were a ‘holy grail’ for palaeobiologists, it would be the nature and ecology of the original beings from which all life on Earth subsequently evolved. That is, the primitive organism – among perhaps many that were extinguished ‘intestate’ – whose genetic ‘footprint’ alone survived to be common to all three domains of modern life: Archaea, Bacteria and Eucarya. For some time, attention has focused on extant heat-tolerant Archaea and Bacteria species (hyperthermophiles; ? 80ºC)) found in hot springs, whose genetics seem primitive. This, together with other features such as the adaptation of heat-shock proteins to other functions and the abundance of metals at the cores of other widespread proteins, has led to notions that life originated under high-temperature conditions such as those around sea-floor hydrothermal vents. The ongoing explosion in nucleic acid analysis and software to sift through vast amounts of molecular data from many sources potentially may provide the key to more concrete ideas of the origin of Earth’s life. A recent comparative study of both ribosomal RNA and protein sequences among representatives of all three of life’s domains gives a clue to surprises ahead for palaeobiologists (Boussau, B. et al. 2008. Parallel adaptations to high temperatures in the Archaean eon. Nature, v. 456, p. 942-945). ‘Exobiologists’, who nurture great, but perhaps folorn, hopes of being alive and sentient when extraterrestrial life forms are ‘bagged’ may also find themselves perplexed; such is the fate of hubris without substance.

The team of francophone biochemists claims that their analyses show signs of a two-fold adaptation to changing environments during the earliest period of surviving life. Rather than having emerged from high-temperature conditions, the last common universal ancestor, or LUCA, probably adapted to more temperate conditions (? 50ºC), the hyperthermophile Bacteria, Archaea and Eucarya evolving from it. Heat tolerance then declined as the later mass of life forms developed. Sadly, the authors do not address the issue of deep ocean-floor origins in their discussion, preferring to speculate about Archaean climate change and rather odd notions about adaptation to high-temperature meteoritic ejection from extraterrestrial sources. It may be that they too are in for surprises when more mature investigations hit the press.

When bacteria became more sturdy

It’s easy for geologists to forget that most of the genetic diversity on Earth is and always has been in organisms that rarely if ever fossilise; those with only a single cell, among the Archaea, Bacteria and Eucarya. All that is known is from those still alive, and they occupy a vast range of environments, most of which are not ‘friendly’ to multi-celled eukaryotes. Unsurprisingly, they don’t look very different from one another; just tiny bags full of water and a tiny amount of complicated biochemistry. They become distinct from their molecular make-up and also from what they do and where they live, some tending to reproduce best within the bodies of eukaryotes, such as ourselves sometimes with no noticeable effect, sometimes beneficially, but most spectacularly when they make us ill. Bacteria and Archaea have long histories, so their genetic material and proteins are easily distinguishable from group to group. This makes them amenable to the use of a 'molecular clock' approach in seeking out when and how they evolved. Analysis of these differences among more than 250 species of bacteria in the context of their living in water or under terrestrial conditions has thrown up some surprises (Battistuzzi, F.U. & Hedges, S.B. 2008. A major clade of prokaryotes with ancient adaptations to life on land. Molecular Biology and Evolution, doi:10.1093/molbev/msn247). Two thirds seem to stem from a common ancestor that had colonised the land around 3.2 Ga ago, 800 Ma before preservation of the first undisputed fossils. To live on the continental surface, all have to have evolved or inherited resistance to environmental hazards such as drying out, UV radiation and high salinity. Many pathogenic bacteria belong to the Gram-positive group, whose cell walls are distinctly adapted to terrestrial life. Despite having to live in eukaryote-free world for a billion years or more, their ancestors were especially well-suited to infesting multi-celled life when it emerged, and to being notoriously adaptable when they are threatened with toxicity themselves.

Chemical conditions for the end-Permian mass extinction

From an empirical standpoint the mass extinction at the close of the Palaeozoic, 251 Ma ago, links closely with eruption of the largest known flood basalt pile in Siberia, and there is no known extraterrestrial impact that tallies. So it seems likely that the P-T event was generated by the influence of a mighty mantle plume on surface conditions. Careful statistical analysis of the marine faunas that preceded and followed the event give some clues to geochemical conditions associated with the extinctions and slow Triassic recovery of animal diversity (Bottjjer, D.J. et al. 2008. Understanding mechanisms for the end-Permian mass extinction and the protracted Early Triassic aftermath and recovery. GSA Today, v. 18, September 2008 issue, p.4-10). Brachiopods, bivalves and bryozoans, in terms of their respective diversities and abundance relative to one another, changed markedly. On the late Permian seafloor, brachiopods and bryozoa fell in both measures, whereas bivalves exploded in numbers but became dominated by just 4 genera. This ecological lop-sidedness continued in the early Triassic. Such an oddity in itself suggests that some kind of geochemical stress was present in marine environments for a protracted period of time. The most likely stressful agents are increased CO2 and H2S, and decreased oxygen. The faunal review goes on to discuss the need for experimental manipulation of oxygen, carbon dioxide and hydrogen sulfide concentrations to see the effects on modern organisms.

Another approach to the issue of the P-T event is to model the conditions that may have led to anoxia linked with increased CO2 and H2S (Meyer, K.M. et al. 2008. Biochemical controls on photic-zone euxinia during the end-Permian mass extinction. Geology, v. 36, p. 747-750). The authors use an Earth system model of ocean circulation coupled with one for the distribution of atmospheric moisture when the continents were assembled into the Pangaea supercontinent. Chemical constraints were 12 times the current carbon dioxide content for the atmosphere and about one fifth of its present oxygen content (see New twist for end-Permian extinctions in the May 2005 issue of EPN), roughly those accepted for the time. The supply of phosphate to the oceans was varied up to 10 times present values. Specifically, the model examined the likely effects of such conditions on the likelihood of hydrogen sulfide production in the oceans and its transfer to the uppermost ocean water. Increasing supply of phosphate inexorably drives global near-surface conditions towards anoxia and H2S – rich conditions. Even adding sulfide-oxidising bacteria to the surface waters doesn’t prevent runaway toxicity, including export of hydrogen sulfide to the atmosphere that would drive many land animals to extinction. It is hard to think of a more pervasive and effective ‘kill mechanism’, nor one that would have lingered for longer, thereby satisfying the evidence, including the extremely long biota recovery time during the Triassic. The two accounts taken together cast doubt on a determining role for the Siberian flood basalts, which were relatively short-lived, although volcanic emissions of CO2 and SO2 may have placed a chemical ‘last straw’ on already stressed organisms.

Plant evolution summarised

Papers on palaeobotany, especially the evolution of plants are a lot less frequent than those on many other broad geoscience topics. So to see a review is welcome (O’Donoghue, J. 2008. Petal Power. New Scientist, v. 200 1 November 2008 issue, p. 36-39). O’Donoghue summarises recent publications on the rise of the angiosperms – Darwin’s “abominable mystery” – since the Jurassic. Accepted wisdom has long been that the earliest flowering plants were akin to modern magnolias that seem anatomically primitive. That assumption has much to answer for, because palaeobotanists sought evidence for big, simple flowers. It was a piece of pure luck that resolved the issue, in the form of fossilised debris from an 83 Ma wildfire found in Sweden. The carbon-rich clay contained masses of flowers only a few mm across, which resemble those of walnuts, plane trees and saxifrages. A shift in focus to minute blooms enabled Chinese geologists working on evidence for the habitat of the famous feathered dinosaurs to find the earliest flowers yet in an early Cretaceous (125 Ma) lagerstätte. They are humble indeed, resembling duckweed. Pushing back further the time of separation of the angiosperms from a presumed gymnosperm (cycads, ginkgoes and conifers) has depended on molecular evidence from living primitive flowering plants, and came up with a humble shrub from New Caledonia (Amborella), the srat anise plant (a member of the Austrobaileyales group) and water lilies. A molecular-clock approach suggests an evolutionary jump from gymnosperms took place as far back as the early Jurassic. The peculiar means of sexual reproduction evolved by angiosperms – giving animals a ‘free lunch’ with the perk to plants of their carrying pollen – cut the amount of energy involved in reproduction by massive pollen release for wind fertilisation and production of seeds without guaranteed fertility used by gymnosperms. In turn is resulted in a massive adaptive radiation by insects in particular, seeing the bees evolve from predatory wasps in early Cretaceous times. Now, to a very large extent, angiosperms are dependent on the humble bee. An alarming fact since bee diseases and parasites are currently getting the upper hand, while we become ever dependent on food sources from a dominantly angiosperm crops.

The strange case of the line-dancing arthropods

Lagerstätten – sites of extraordinarily good fossil preservation – generally throw up surprises and oddities, and those of Cambrian age in China are no exception. Cambrian arthropods, notably the trilobites but also shrimp-like creatures, are not uncommon in them. But any animals that appear to have been engaged in communal activities are cause for both a double-take and a short communication (Hou, X-G. et al. 2008. Collective behaviour in an Early Cambrian arthropod. Science, v. 322, p. 224). About 22 groupings of shrimp-like fossils show individuals linked in ‘nose-to-tail’ chains, the tail (telson) of one in front being lodged in the carapace of that behind. Not only that, but the chains are meandering. ‘Follow-my-leader’ behaviour is seen in modern lobsters bent on migration; perhaps the inspiration for Lewis Carroll’s Lobster Quadrille in Alice in Wonderland. Since no modern arthropods link in such chains for reproductive purposes, and mouth-clenching a partner’s tail is not good evidence for feeding behaviour, the authors’ conclusion is that indeed the diminutive and very ancient creatures were probably hooked-up to go somewhere more conducive to their habits.

Evidence for earliest photosynthesisers takes a knock The first tangible and isotopic evidence for the permanent presence of oxygen in the Earth’s atmosphere appears in sedimentary rocks dated at about 2.4 Ga. From that we can surmise that some organisms had previously evolved the photosynthetic trick of breaking the hydrogen-oxygen bonds in water: nothing else is known in nature to produce free oxygen on a planetary scale. Frustratingly, the earliest undisputed fossils of such organisms – blue-green bacteria – are a lot younger; around 2 Ga. Structures in sedimentary rocks back to 3.5 Ga, such as stromatolites, which do look a lot like products of living cyanobacteria and may have a biogenic origin, do not contain cellular structures that would constitute proof. So a report in the late 1990s of organic-chemical evidence for cyanobacteria from 2.7 Ga old sediments was greeted with some relief. These oldest biomarkers also included compounds characteristic of eukaryotes; an even more astonishing outcome, given that the oldest undoubted eukaryote fossils are from 1.5 Ga sediments. The ancient biomarkers have been much celebrated, but there is a problem: if cyanobacteria were around at 2.7 Ga in sufficient amounts for their biomarkers to be preserved, how come it took 300 Ma for oxygen to build up in the atmosphere? A novel technology for geochemists has been applied to resolve the issue of the Archaean biomarkers (Rassmussen, B. et al. 2008. Reassessing the first appearance of eukaryotes and cyanobacteria. Nature, v. 455, p. 1101-1104). One of the co-authors, Jochen Brocks of the Australian National University, was an originator of the study on biomarkers, so clearly the new technology has thrown matters into considerable disarray. The oily biomarkers accompany solid kerogen in the late Archaean sediments, in microscopic amounts. Ion-probe mass spectrometry with a 50 nm resolution has provided carbon-isotope measurements of minute samples of several kinds of hydrocarbon in thin sections. These show, with little room for doubt, that the organic compounds thought to have been biomarkers for cyanobacteria and eukaryotes formed by ‘cracking’ of kerogen during thermal metamorphism at about 2.2 Ga. Any other claims based on supposedly specific biomarkers are likely to be ‘tarred with the same brush’. How annoying: complex life clearly was around before 2.4 Ga, some of capable of photosynthesis, but that conjecture cannot be proven!

Much ingenuity has been harnessed to design robotic geochemistry that will be aimed at the popular topic of ‘Life on Mars’ in the coming decades. It would be no surprise if biomarkers are targeted. Yet it is entirely possible that hydrocarbons of inorganic origin can yield such compounds, given some geothermal heating…

See also: Fischer, W.W. 2008. Life before the rise of oxygen. Nature, v. 455, p. 1051-2.

Ocean chemistry at the time of the earliest animals

The Ediacaran fauna of the late Neoproterozoic (occurring between 575-543 Ma) marks the first clear sign of animal life, although the affinities of many of the taxa are obscure. ‘Molecular clocks’ based on differences between the DNA of living organisms seems to suggest a last common ancestor of all animals somewhat earlier than the Ediacaran period, perhaps as early as 1000 Ma. Whatever that first animal was, its emergence and that of the Ediacarans took place in climatically and chemically peculiar times. The Neoproterozoic was marked by at least three glacial epochs that left traces at palaeolatitudes as low as the tropics: so-called ‘Snowball Earth’ events. It also contains the most erratic swings in carbon isotopes that are known from the geological record, which have something to do with ups and downs of life at the time, probably variations in global biomass and/or the rate at which organic carbon was buried in seafloor sediments. Among Neoproterozoic sediments two are outstanding: graphitic and sulfidic mudrocks; banded iron formations (BIFs) which are sulfur-poor. BIFs of that age have been an enigma, the most massive and long-lived being those in the Palaeoproterozoic (before 1.8 Ga) and the Archaean. Neoproterozoic BIFs seem to mark the return after a billion years of most peculiar ocean chemistry, when soluble iron(II) ions were abundant at all depths in the ocean yet were oxidised to insoluble iron(III) at the sites where Fe2O3 was deposited in huge amounts. In the earlier BIF period that had to have been where oxygen was being locally emitted by primitive blue-green bacterial photosynthesisers, i.e. in shallow water. We must surmise that occurred again in the Neoproterozoic, although the source of oxygen would then have included more advanced oxygenic photosynthesisers. But that is not the puzzle. How did ocean-wide conditions return to allow the abundance of dissolved iron(II) ions and why did those conditions not prevail in the BIF-less billion years?

Donald Canfield of the University of Southern Denmark has long been immersed in issues of ocean-chemistry evolution in relation to atmospheric oxygen levels, and offered an answer to the second question that has largely replaced the once accepted wisdom that ocean water became oxygenated throughout after 1.8 Ga thereby allowing iron to enter oxidised minerals immediately it emerged in ocean-floor basalts magmas. Instead, he suggested that the deep ocean, at least, contained abundant hydrogen sulfide as witnessed by sulfur isotope patterns in marine sediments. In other words, oceanic Fe(II) was efficiently precipitated through the Mesoproterozoic in the form of sulfides. The H2S was probably generated by bacterial reduction of sulfate ions, themselves derived by oxidation of on-land exposures of sulfidic rocks because of low but increasing atmospheric oxygen. Canfield and a rich variety of international colleagues once again has an authoritative say, this time as regards the Neoproterozoic iron formations (Canfield, D.E. et al. 2008. Ferruginous conditions dominated later Neoproterozoic deep-water chemistry. Science, v. 321, p. 949-952).

If the supply of sulfate from the continents waned, then bacterial production of sulfides would follow suit in sulfur-poor oceans. Provided deep-ocean oxygen levels remained very low, iron(II) derived from continually generated ocean-floor basalts and their hydrothermal alteration could once again pervade the oceans. Oxygen in shallow water would again encourage precipitation of hematite and BIFs. This hypothesis does not need a special explanation for fully oxygenated Precambrian oceans reverting back to anoxia in the Neoproterozoic and then back and forth in their oxygen concentrations to explain short BIF episodes, merely variations in the supply of sulfate from weathered continental surfaces. Canfield et al. tested this hypothesis by examining the proportions of total iron in 800-530Ma sediments contained by minerals able to react easily with their environment, such as sulfides and carbonates, and the proportions of such reactive iron in sulfide minerals. In modern oxygenated waters the proportion of such reactive iron in sediments does not rise above about 40%, and is often lower. In the Neoproterozoic samples, shallow marine rocks obeyed the modern <40% rule, but those from intermediate to deep-water settings (below storm-wave base) sometimes show far higher values. That is a clear signature of anoxic waters, and it persists into the Cambrian. Interestingly, many deep-water sediments from the Ediacaran Period do show signs of oxygenation, while others were anoxic. Among the sediments deposited under anoxic conditions none have iron sulfide proportions as high as those produced in modern euxinic basins such as the Black Sea, thereby signalling a dearth of bacterially generated H2S and low sulfate supply to the oceans as predicted. But why did the supply dry up? One possibility is that chemical weathering on the continents plummeted during ‘Snowball Earth’ episodes. Yet the evidence for anoxic, high iron(II) conditions in the oceans persisted well beyond the times of the known glacial epochs. Another plausible explanation is pyrite burial, analogous to that of carbon, and subduction of sulfide-rich sediments that progressively completely stripped the oceans of sulfate. What of the effect on early animal life? Iron is an essential micronutrient, much touted today as a means of encouraging phytoplankton blooms in ocean surface water. Together with rising shallow-water oxygen levels, perhaps an explosion in food supply enabled large early animals, such as the Ediacarans, to develop and thrive, instead of much smaller precursors whose survival as fossils would be less likely.

The next big step was also one of geochemistry, when animals became able to secrete calcium-rich skeletons by extracting that element from seawater. It took place around 543 Ma at the start of the Cambrian, while iron-rich deep waters were also common. Was there somehow a connection between the two chemical highlights of the late Precambrian? Calcium is very interesting metabolically: too little and cells do not function properly; too much and they die. The ‘window’ of metabolically tolerable calcium concentrations is narrow. One possible means whereby calcium-rich hard parts may have developed among animals is that their outer cells were harnessed by evolution to rid the body of excess calcium in an organised way, creating the opportunity for both armour and armaments. Would elevated iron enhance the solubility of calcium in ocean water?
See also: Lyons, T.W 2008. Ironing out ocean chemistry at the dawn of animal life. Science, v. 321, p.923-924.

The Great Ordovician Diversification

Geologists in general learn that the tangible fossils first appeared at the start of the Cambrian Period. So they did, but we refer to that event as the Cambrian Explosion, but it was hardly explosive as there were very few fossil taxa of Lower Cambrian age. Indeed, by the end of the Cambrian only 500 or so genera are known. Fossils truly exploded in the later Ordovician, reaching 1600 genera, which number wasn’t exceeded until the start of the Cretaceous, 300 Ma later. Sudden rises in diversity, like mass extinctions, demand an explanation, but few have been offered for the late Ordovician explosive diversification, unlike the mass extinction at its close, which halved the number of genera living at the time. That has been attributed to the widespread glaciation of Gondwanaland, the fall in sea levels drastically reducing ecological niches (a wilder scenario is that the extinction was caused instantaneously by a gamma-ray burst from a nearby supernova, but there is little evidence for such an event).

The Ordovician has been assumed to have been a period that experienced ‘supergreenhouse’ conditions because of a far greater proportion of CO2 in the atmosphere in the early Palaeozoic. Advances in stable-isotope analyses of small samples allow that idea to be tested (Trotter, J.A. et al. 2008. Did cooling oceans trigger Ordovician biodiversification? Evidence from conodont thermometry. Science, v. 321, p. 550-554). Julie Trotter of the Australian National University and her French and Canadian colleagues show that oxygen isotopes in conodonts that range in age from Lower Ordovician to Lower Silurian changed steadily with time. Assuming the conodont animals were planktonic, the increase in the proportion of 18O represents decreasing sea-surface temperatures, from around 40ºC (truly supergreenhouse) to levels very similar to those that prevail in today’s tropical ocean, around 30ºC, to even more temperate levels (24ºC) by the close of the Ordovician. So it seems as if cooling encouraged rapid evolution of new organisms at that time.

Stress and the Cambrian Explosion

The opening of the Phanerozoic Eon at the base of the Cambrian is, ‘as everyone knows’, characterised by the appearance of organisms’ body fossils that were preserved because they had calcium-rich hard parts. Thereafter biological diversity grew and grew, despite episodic sets back. Why calcium carbonate and phosphate skeletal parts evolved quickly is still a mystery, although it may have had something to do with an increase in the calcium-ion concentration of seawater. Earth had not long emerged from the last of several truly deep freezes, associated with evidence for which are carbon isotope signals that may indicate repeated mass extinctions of life forms that left few tangible traces. Whatever the truth, it must have lain in some major change in global environmental conditions. Evidence for one such widespread chemical stress has emerged from black shales at the Precambrian-Cambrian boundary in the Oman and China (Wille, M. et al. 2008. Hydrogen sulphide release to surface waters at the Precambrian/Cambrian boundary. Nature, v. 453, p. 767-769).

Molybdenum, like many transition metals, has several valence states, some soluble in oxidising conditions, others when conditions are reducing. Solution or precipitation when redox conditions change may cause fractionation among stable isotopes, and isotopes of Mo are a case in point. The Swiss-German-US team found that close to the base of the Cambrian the 98Mo/95Mo ratio underwent rapid changes in black shales of Oman and China. They ascribe this to a major upwelling of hydrogen sulfide-rich deep seawater, indeed it would be difficult to suggest any other mechanism that could have caused the shift. Molybdenum is soluble in oxidising waters, and the increase in Mo concentrations in the shales at the time of the isotopic anomaly must mark a shift to reducing conditions in 542 Ma surface seas, hence the link to such an upwelling. Such rises in highly toxic ‘sour gas’-rich water have been suggested as a possible cause for the mass extinctions at the ends of the Permian and Triassic (see Global warming, sour gas and mass extinctions in the January 2007 issue of EPN).

The globally abundant Ediacaran fauna of soft, bag-like and quilted organisms that lived in the late Neoproterozoic has no counterpart in the Cambrian record, even in lagerstätten. Moreover, the Cambrian shelly fauna does not simply spring into place fully formed: it developed over a protracted period and did not simply succeed or evolve from the Ediacaran. It looks like there was the last of a succession of Neoproterozoic mass extinctions at the outset of the Phanerozoic. Indeed the Mo anomalies coincide with abnormally ‘light’ carbon isotopes in the black shales, due the accumulation of massive amounts of dead organisms, and formation of large phosphatic deposits globally.

Yet another blow for creationism

The Devonian transition from fish to four-legged animals is represent by one of the best time sequences showing the development of physical features from one use to another, in this case from fins to legs. Lobe-finned fishes and the earliest amphibians show this nicely, with the missing link of Tiktaalik, found in 2006 (see A fish-quadruped missing link in EPN for June 2006), seeming to gild the lily. Now, yet another member of the sequence neatly connects the limb form and function of lobe-fins to the peculiar Tiktaalik (Ahlberg, P.E. et al. 2008. Ventastega curonica and the origin of tetrapod morphology. Nature, v. 453, p. 1199-1204). But perhaps the ID school will consider it a case of the designer continually changing his or her objective.

What, pray, is the platypus?

In a mood of solemn gaiety the world greeted the publication in May 2008 of the duck-billed platypus (Ornithorhynchus anatinus) genome (Warren, W.C. and a very large number of other authors 2008. Genome analysis of the platypus reveals unique signatures of evolution. Nature, v. 453, p. 175-183). My reaction to the title of the paper was, ‘So it blooming well should’. The eponymous platypus has few rivals for oddness: it has a beak for a start; detects its prey using electrosounding; has venom-injecting spurs; females lay eggs but suckle little platypuses, despite having no nipples (the milk is exuded by belly skin when sucked); has fur like an otter; no teeth and the male ejaculates sperm that hunt in packs. It lives in Australia and has kindly eyes. The vast authorship needed considerable space to fully document this strange package of characteristics, leaving little room to expand on the novelty of its genome. In a nutshell, the platypus combines features both reptilian and mammalian: no surprise there. But it is dissimilar from ducks.

Vivipary in armoured fishes

The extinct placoderms were formidable predators of Silurian to Devonian seas and brackish waterways; in fact they were the vertebrates of those Periods. Being covered by articulated platy armour, their heads are well represented in the fossil record, but their aft parts are not, having been naked of protection. They were anatomically advanced creatures, but succumbed to the late-Devonian mass extinction, unlike other fishes, including those that figure in the ancestry of all terrestrial vertebrates. Placoderms provide the first example of the evolution of live birthing, not to recur until the appearance of the higher mammals in the last 100 Ma. Evidence for placoderm vivipary comes from an astonishing Australian fossil that contain embryos a few centimetres long (Long, J.A. et al. 2008, Live birth in the Devonian period. Nature, v. 453, p. 650-652).

A volcanic nursery for life

Aside from Darwin’s ‘warm, little pond’, all sorts of environments have been suggested for the origin and early nurturing of life. One possibility is in the nutrient-rich cavities between pillows in ocean-floor lavas. The evocative black smokers marking hydrothermal springs on the ocean floor have long been known to host abundant live, from the microbial to the large. Yet the entire volcanic pat of the oceanic lithosphere interacts with water to source hydrothermal vents. The hydration and oxidising reactions that take place in basalts are exothermic, and so yield plenty of energy, both thermal and chemical. This retrogression has offered potential for biological chemoautotrophy since mantle-derived magmas first met liquid water; arguably since 4.5 Ga ago. A study of organic infestation of glassy pillowed basalts reveals that today there are up to ten thousand times more prokaryotic cells in exposed seafloor basalts than there are in the overlying seawater (Santelli, C. M. and 7 others 2008. Abundance and diversity of microbial life in ocean crust. Nature, v. 453, p. 653-656). The study relied on RNA sequencing of organic material in the glasses, rather than microscopic examination. Using thin sections and high-powered microscopes shows up tell-tale signs of the effects of colonisation of surfaces on fractures in oceanic basalt, backed up evidence for the cells themselves. The effects are distinctive and potentially offer a means of judging microbial colonisation of ancient crust, especially that of early Archaean age.

New hope for very old molecular phylogeny …

Although DNA has been obtained from a number of fossils, including Neanderthals, its complexity more or less rules out any being preserved in a useful state beyond a few hundred thousand years ago. However, information about molecular relatedness also emerges from protein sequences, albeit with less chance of detailed comparisons. Collagen from bone is a potential resource for palaeobiologists, and fossils as old as the Jurassic Period have provided useable sequences. Prime targets are large extinct animals, as the greater the mass of a bone, the better the chance that it preserves some. Two irresistible beasts are the American mastodon (Mammut americanum) and T. rex (Organ, C.L. et al. 2008. Molecular phylogenetics of mastodon and Tyrannosaurus rex. Science, v. 320, p. 499). Unsurprisingly, the research group from Harvard, Boston and North Carolina, found that a Pleistocene mastodon contains proteins closely similar to those of African elephants. The T. rex, however, has a passably close relationship to the ancestral chicken, the South Asian Red Junglefowl (Gallus gallus) and the ostrich (Struthio camelus).

In fact, both connections were expected by the team, for their research set out to show that it is possible to extract intact parts of protein sequences from fossil bones. The matches confirm their hopes, and seem set to launch attempts at resolving evolutionary relationships among vertebrates that hitherto have depended on morphology alone.

Life perked up by repeated impacts

Following the blazes of publicity since the early 1980s about the demise of the dinosaurs at the K/T boundary it is easy to regard objects the size of mountains that fall out of the sky as bad news for life. That is despite the fact that, bar the Chicxulub impact structure that exactly matches the timing of the end-Cretaceous mass extinction, no other significant and rapid drop in the diversity of life has been found to be associated with an extraterrestrial impact. Whatever their cause, mass extinction events sometimes seem to be followed by bursts in biodiversity, presumably as the survivors eventually find lots of new opportunities and diversity to occupy them. One exception is the end-Ordovician mass extinction that was also preceded by a tripling in the number of families, which the extinction rudely interrupted. This has often been seen as a somewhat delayed exploitation of all the advantages and competitive opportunities conferred by the appearance of hard parts at the start of the Cambrian. But remarkable finds in the limestone-rich Ordovician of Scandinavia suggest an unexpected connection with meteorite bombardment (Schmitz, B. and 8 others 2008. Asteroid breakup linked to the Great Ordovician Biodiversification Event. Nature Geoscience, v. 1, p. 49-53).

The most usual measure of diversity used by stratigraphic palaeontologists is the number of families at a particular time, and the overall tripling in the Middle to Upper Ordovician is notable. However, if specimens of individual groups, such as brachiopods, are collected from the Scandinavian limestones on a bed by bed basis, increased diversity at the species level is even more dramatic. There are sudden doublings or triplings over periods of what can be no more than a few hundreds of ka, especially around 470 Ma ago. In the 1960s potassium-argon dating of chondritic meteorite collections revealed a cluster of reheating ages between 500 and 450 Ma (Upper Cambrian to Upper Ordovician); about 20% of all meteorites fall into this age-cluster, and most show evidence of having been shocked as well as heated up. This seems to signify a major collision or series of collisions in the Asteroid Belt around the early Palaeozoic. More reliable and precise 40Ar-39Ar dating narrows this event to a period between 463 and 477 Ma in the Middle Ordovician. In 2001, Birger Schmitz of the University of Lund reported, with others, more than 50 sizeable chondritic meteorites in the Middle Ordovician limestones of Sweden. Schmitz and his Damnish, US and Chinese colleagues in the new paper give plots of brachiopod species and also the abundance of chromite grains of meteoritic origin in Middle Ordovician limestones from Sweden and China. Two sharp jumps in brachiopod species numbers are preceded and accompanied by ‘spikes’ in the number of extraterrestrial chromite grains, so the link seems to be real. Yet what can have produced such a counter-intuitive result? One possibility is that the undoubted disturbance may have killed off species of one group, maybe trilobites, so that the resources used by them became available to more sturdy groups, whose speciation filled the newly available niches. Such a scenario would make sense, as mobile predators/scavengers (e.g. trilobites) may have been less able to survive disruption, thereby favouring the rise of less metabolically energetic filter feeders (e.g. brachiopods).

An old bat from Wyoming

The Lower Eocene Green River Formation of Wyoming is dominated by fine-grained lake sediments, mainly made of laminated limy mudstones. Many layers constitute superb lagerstätten teeming with remains of delicate organisms. As well as much else, The Green River Formation is noted for its early bats, which suddenly appear in the fossil record with all the prerequisites for flight. The cover of the 14 February 2008 issue of Nature depicts a perfect specimen showing the four elongated ‘fingers’ that supported its wing membrane, and a long tail, which few modern bats have, except in atrophied form to support the rear part of the wing. In many respects it has a transitional structure between non-flying mammals and later bats, but would definitely have been a good flyer or rather flutterer-glider.

Not only is the fossil spectacularly well-preserved, detail of its head morphology helps resolve the issue of whether echolocation preceded flight (Simmons, .B. et al. 2008. Primitive Early Eocene at from Wyoming and the evolution of flight and echolocation. Nature, v. 451, p. 818-821). Other, slightly later fossil bats from the Green River Formation probably did echolocate, as evidenced by their stomach contents, and enlarged larynx and cochlea for transmitting and receiving the now typical high pitched squeaks of many bats. Onychonychteris doesn’t have such characteristics, so it seems as if echolocation did not evolve before flight, thereby resolving one of Darwin’s vexations about the universality of natural selection. Prior to the discovery by Simmons et al. many bat-oriented evolutionists speculated that echolocation evolved among small arboreal mammals so that they could detect passing insects. A habit of leaping to grab the prey in turn selected for an ability to glide from a strategic perch, for quite obvious reasons. Success further encouraged the evolution of powered flight. Yet no other living mammals have echolocation, probably because it is a highly energy-intensive habit. However, the muscles used by a flying mammal serve also to make squeaking a ‘cost-free’ bonus. So, the findings in Onychonychteris seem to resolve the matter nicely.
See also: Speakman, J. 2008. A first for bats. Nature, v. 451, p. 774-775.

Last common ancestor of all the primates was a flying lemur

Vertebrate palaeontologists sometimes become precious after a career peering at old bones, especially when they are as remarkably tiny as those of most Mesozoic mammals – and most of those fossils are teeth. Some defend to death the notion that primates descend from tree-shrews, while others foam at the mouth at the mere suggestion of the ur-shrew. ‘A key feature in primate evolution is reduction of the snout’, is axiomatic to yet others. Again, geneticists have provided extreme selection pressures that will either cause vertebrate palaeontologists rapidly to evolve or to become extinct.

Analysis of living primate genomes produces a phylogeny that links all primates with a group that has been said to be ‘the sort of animals that defy taxonomic categorization, confuse one’s sense of aesthetics, and seem to largely fall under the umbrella of “weird.” ‘ (Janecka, J.E and 7 others 2007. Molecular and genomic data identify the closest living relatives of primates. Science, v. 318, p. 792-794). These are the colugos, or flying lemurs that include the wonderfully named sugar glider.

Planet of the beetles

More than 20% of the known diversity of life on Earth is made up by the order Coleoptera, which includes several hundred thousand species. Although that huge number is largely thanks to beetle collectors, Charles Darwin having been a particularly voracious one, it is difficult believe that any other order or even class of multicelled organisms will prove to be as diverse. Yet there is only a sparse fossil record of these ubiquitous creepy-crawlies. The earliest known beetle fossils date back to the Lower Permian, and the Triassic saw their radiation into wood-eating, predatory and fungus-eating clades – from morphological similarities with living beetles. Their modern diversity depends on the vast range of ecological niches that beetles can fill, many of which are environmentally so subtle that only the beetles exploiting them show that the niches exist at all. Like all organisms the evolution of the beetles has been within the interconnectedness of the whole Earth system, and it through the linkages that such subtlety has emerged and evolved. One of the best known is the sensitivity of different beetle species to small climatic changes, which has allowed their growing use for charting climate change on land: they are far better proxies for temperature than are the foraminifera of the oceans.

Being only sparingly preserved in rocks, how beetles evolved has long been a mystery, considering their overwhelming presence on the planet. Yet again, the rapid rise of molecular phylogeny, including means of timing when mutations took place, is starting to supplant the skills of the traditional palaeontologist (Hunt, T. and 15 others 2007. A comprehensive phylogeny of beetles reveals the evolutionary origins of a superradiation. Science, v. 318, p. 1913-1916). Toby Hunt of London’s Natural History Museum and colleagues from the UK, Czech Republic, USA, Germany and Spain have combined their own RNA sequencing with existing databases of 1880 species from all the beetle suborders, series and superfamilies, 80% of families and 60% of subfamilies, to represent more than 95% of all described species. This establishes a phylogenetic tree for the lineages that they analysed, details of which will excite the coleopterist sororities and fraternities. The general picture, however, presents a more a broadly fascinating surprise. Because a vast number of beetles are associated with plants and fungi, it might seem inevitable that their evolution has parallels with that of plants, especially their explosive diversification once the angiosperms (flowering plants) appeared. The molecular dating clearly shows that is not the case. While the angiosperms emerged in the Cretaceous Period, more than 100 living beetle lineages appeared earlier in the geological record. Unlike the Vertebrata, which diversified after mass extinctions (including the primates), the fundamental beetle lineages were clearly good survivors that were capable of their own diversification whenever opportunities arose. I think we might grow to worry about that…

Mammal evolution makeover

The Cenozoic has been the Era of mammals, and their diversification is the largest recorded adaptive radiation. However, the Linnean names of many mammal clades from the Mesozoic end in ..dont, i.e. they have been defined in terms of their teeth and not much else. Most fossil mammals from the Mesozoic are small and fragile and only survive as teeth and jaw fragments. As a result most of the course of early mammal evolution has been a bit uncertain, to say the least. The view until recently has been that early mammalian evolution was a step-by-step affair in which key innovations accumulated in an orderly manner. However, even on the basis of teeth, developing taxonomic approaches have proved able to reveal that considerably more complicated things happened (Luo, Z-X. 2007. Transformation and diversification in early mammal evolution. Nature, v. 450, p. 1011-1019). For a start, it turns out that mammals, despite their scanty remains, were almost as diverse during the Mesozoic as the dinosaurs that are often said to have driven early mammals underground or into the night (310 mammal to about 550 dinosaur genera). The potential for analysis stems from an explosive growth in fossil discoveries: from 116 genera in 1979 to the present 310, and a 200-fold increase in well-preserved specimens. Clearly, mammal-oriented palaeobiologists have been hard at work.

Zhe-Xi Luo of the Carnegie Museum of Natural History in Pittsburgh crams most of the developments into a 6-page review, from which it is possible to learn a great deal, albeit needing quite a firm grasp of cladistic terminology. One of the highlights is how evolution of the mammals before 65 Ma involved repeated evolutionary convergence, i.e. the end products of evolutionary bursts often looked superficially similar. That tendency carried over into the Cenozoic on a grander scale. One example is that of adaptations for burrowing to produce mole-like end products, even some with semi-aquatic habits. Many of the rapid diversifications ended in extinction of the lineage, but all seem to indicate a great deal of ‘experimentation’ with a range of original forms that channelled towards similar functions. The outcome was a vigorous occupation of potential ecological niches in which mammals clearly had the advantage over reptiles, possibly because of their physiologically greater adaptability, partly stemming from warm-bloodedness.

Permian shark bites fish-biting amphibian

It is worth queuing to await the appearance of the 22 January 2008 issue of the Proceedings of the Royal Society B: Biological Sciences. It contains unique evidence of predator-prey relations and the food chain in the Lower Permian Zechstein Sea (Kriwet, J. et al. 2008. First direct evidence of a vertebrate three-level trophic chain in the fossil record. Proceedings of the Royal Society B: Biological Sciences, v. 275, p. 181-186). The object for your amazement is a shark whose gut contains two amphibians. The last meal of one of the amphibians was a small fish.

The paper promises to be reminiscent of the final part of the Monty Python Fish Slap Dance sketch, which can be viewed at http://www.youtube.com/watch?v=d1xfp6Xeu0c&feature=related

Feared dinosaur probably feathered

The really scary dinosaurs in Jurassic Park were the velociraptors; they were smart and speedy. But it turns out that they were probably also well covered with feathers (Turner, A.H. et al. 2007. Feather quill knobs in the dinosaur Velociraptor. Science, v. 317, p. 1721). A specimen of V. mongolensis from Mongolia has well preserved forelimb bones that show traces of regularly spaced knobs. They look very like quill knobs on the wing bone of a living turkey vulture. On the velociraptor they were clearly not for flying, but may have been for thermal insulation, perhaps sexual display or to serve some aerodynamic purpose while the beast was running.

Robot shows how fishes walked out of water

Now and again palaeontologists relax with toys; they build models. Perhaps the most famous were flying pterodactyl gliders that featured in a BBC natural history programme. The presenter, David Attenborough, was most impressed. At a society dinner shortly after filming them, ‘Whispering Dave’ was asked by a formidable old lady what he had been doing lately. ‘Well, I was flying pterodactyls last week’, he replied, hoping to impress. ‘Yes’, said the dowager, in an instant, ‘They’re so graceful, aren’t they’. The same could not be said about the amphibians of the late Devonian and early Carboniferous, and the earlier lobe-finned fishes that managed to struggle onto land to give rise to all terrestrial vertebrates. While it is demonstrably easy for any land vertebrate to swim if needs be, the opposite would seem to be a problem. To explore the locomotive transition Swiss and French engineers and fossil aficionados built a robot, not entirely unlike a lobe-finned fish but almost so. It has a simple spinal-chord neural circuit designed to swim. Then they let the beast loose near a beach (Ijspeert, A. J. et al. 2007. From swimming to walking with a salamander robot driven by a spinal chord model. Science, v. 315, p. 1416-1420), and it did walk off. So, invasion of the land by vertebrates was not necessarily too difficult. It is almost as if they were predestined to clamber out and eventually reach for the stars…

Geobiology, Palaeontology and Evolution

Life originated as an oddity

End-Permian crisis not so bad for ammonites

What’s green and above sea level?

Mantle link with biosphere

Hadean not so hellish for life

Irresistible brevia

Gas source for flood basalts

Social behaviour among giant trilobites

The ancestral animal

Photosynthesis from way back when: the hunt for RuBisCO

A fluffy grazing dinosaur

Nitrogen isotopes and a change in the Archaean biosphere

The Palaeocene Snake of Death and torrid times

Snowball Earth and the major division among animals

Broody dinosaurs

Molecular evidence for the environment of the universal ancestor

When bacteria became more sturdy

Chemical conditions for the end-Permian mass extinction

Plant evolution summarised

The strange case of the line-dancing arthropods

Ocean chemistry at the time of the earliest animals

The Great Ordovician Diversification

Stress and the Cambrian Explosion

Yet another blow for creationism

What, pray, is the platypus?

Vivipary in armoured fishes

A volcanic nursery for life

New hope for very old molecular phylogeny …

Life perked up by repeated impacts

An old bat from Wyoming

Last common ancestor of all the primates was a flying lemur

Planet of the beetles

Mammal evolution makeover

Permian shark bites fish-biting amphibian

Feared dinosaur probably feathered

Robot shows how fishes walked out of water

Ancient protein

Ediacaran fauna reviewed

Fossil embryos debunked?

Microbial carbonate secretion

Our relationship with sea urchins

Oxygen and the explosion of large, soft animals

Global warming, sour gas and mass extinctions

Gliding mammal of the Jurassic

Fossil bee: the right place and the right time

Near-pristine traces of life before Earth’s surface became oxidising

Precambrian bonanza for palaeoembryologists

Pocket sauropods

A fish-quadruped missing link

Methane, methanogens and early climate control

Gaia: the ultimate frontier

Faster recovery after mass extinctions

Is the Cambrian Explosion real evidence for an evolutionary burst?

Yet more on the end-Permian extinction

Fig leaves over Palaeocene-Eocene boundary

Dinosaur dung, the Deccan Trap and grass

Clay minerals and the origin of life

Photosynthesis during a `Snowball' epoch

New twist for end-Permian extinctions

Evolutionary rhythms

Ancient baby penis worm hits the news

Fossil hamster's food cache

The selectivity of mass extinctions

Another K-T row

Gamma-ray bursts and mass extinctions

Source

Fossil oddities – a golfing trilobite and the ox-sized rodent

Setting the fossil record to rights

Origins of the vertebrates

Iron and nickel in life's origins

Extinction at the Precambrian-Cambrian boundary

"Snowball Earth" and evolutionary diversification: Australians speak out

Homing in on the great end-Permian extinction

Microbes showed no sign of change following a "Snowball Earth"

Flying feathers

Squirrels and tectonics

The Early Cretaceous lagerstätten of NE China

Did terrestrial life emerge later than geochemists think?

The chemical conditions for life