Wednesday, August 31, 2016

Life Began As Clay Crystals

There is a fine article on BBC Earth by Martha Henriques on the work of chemist Graham Cairns-Smith and his theory that life may have begun as clay crystals. Cairns-Smith reasoned that clay minerals are made up of sheets of atoms bonded in a regular lattice pattern that is stacked in layers.  Pieces of this latticework break off, forming offspring crystals often with minor dislocations to the latticework. These offspring crystals grow ..break off with more minor changes... grow.. and so on. Organic molecules like the precursors of DNA might have used such a "replicating entity" as a scaffolding to build an organic replicating system.

His idea stood at the intersection of geology, chemistry and biology and his wife Dorothy recalls the reaction he got from his peers:

"He could never get funding," Dorothy says. A major stumbling block to securing research grants was that his work straddled too many different disciplines.

One time we went to California, and Graham gave lectures to the Menlo Park Geology Survey," says Dorothy. "They all said, well, your geology's fine but I don't think your chemistry's right. Then he gave a lecture to NASA on the chemistry side and they said, well, your chemistry's fine but I'm not sure about your biology. And then he lectured to Berkeley and they said, well, your biology's fine but I'm not sure about your geology".

Nowadays such grand problems are tackled by multi-disciplinary teams of sub sub specialists. If a chemist is asked to talk on the geology aspects,  he just forwards the email of his teammate.

Thursday, August 25, 2016

Photomicrograph- Micro Fault Displacing Proterozoic Stromatolite Laminae

From the Paleoproterozoic Vempalle Dolomite near the village of Gani, Cuddapah Basin, South India,

This was my M.Sc dissertation area. Vempalle Dolomites got me fascinated with carbonate rock textures and diagenesis.

The image shows a micro fault displacing stromatolite laminae. Stromatolites are biosedimentary structures formed when sediment is either trapped within microbial sheets or when CaCO3 minerals like aragonite precipitate around the sheets that cover the sea floor. The microbial colonies grow in a variety of shapes and structures in response to the wave energy conditions. Flat sheet like structures like the one seen in outcrop from where I sampled this rock indicates a low energy regime.

Of interest here:

a) The presence of oolites associated with these lamellar stromatolites. Oolites form in high energy conditions where sediment grains are constantly rolled around and held in suspension for periods of time. This allows layers of calcium carbonate to precipitate around a nucleus resulting in a coated grain containing concentric rings of CaCO3. The presence of layers of oolites in a lamellar stromatolite rock suggests that oolites forming in high energy tidal channels and shoals were transported by storms onto adjacent lower energy settings such as these microbial covered tidal flats.

b) There is variation in the shape and size of dolomite crystals. This variation is not randomly distributed but is fabric selective. The fine grained stromatolite laminae has been replaced by fine grained dolomite. There is some patchy neomorphic (recrystallization) growth of this dolomitized mud into coarser irregular dolomite.  Pore spaces and sheet cracks and fractures are filled with coarser irregular shaped dolomite crystals.  Rhomb shaped dolomite crystals are associated with oolites. This suggests that the rock underwent multiple episodes of dolomitization. The fine grained stromatolite aragonite mud got replaced early by very fine grained dolomite crystals. Contemporaneously, sheet cracks and pores filled with a coarse irregular shaped dolomite crystals.  Both the saturation levels of the replacing fluid and the abundance of nucleation sites affect dolomite crystal shape and size. Finer grained substrates offer abundant nucleation sites resulting in finer grained dolomite. Crystals growing from supersaturated fluids form quickly and interfere with adjacent crystals resulting in irregular shaped interlocking textures.

Oolites made up of either aragonite or high Mg calcite crystals were replaced by rhomb shaped crystals. Rhombic shapes form when dolomite replaces coarser grained substrates or precipitates from fluids which are mildly saturated. In such instances there are fewer nucleation sites and individual crystals have a degree of freedom to grow crystal facets.

There is also chert (microcrystalline silica) in this rock. Its replaces oolites and is present in pores spaces and in fractures.


Monday, August 22, 2016

Photomicrograph- Marine, Meteoric And Burial Carbonate Cements

JSR Paper Clips in their "A Look Back" series highlights an influential paper by J.A.D. Dickson on the use of staining of carbonate rocks to differentiate in a thin section the different mineral phases of calcium carbonate.

A staining procedure consisting of preliminary etching with dilute hydrochloric acid, treatment with a mixed solution of alizarin red-S and potassium ferricyanide, and a final treatment with alizarin red-S alone (Dickson, 1965) permits the distinction of orthorhombic carbonates and of calcite from other trigonal carbonates. The potassium ferricyanide stain reveals the distribution of iron in both calcite and dolomite. The use of the stains is illustrated by a discussion of the petrography of selected specimens and interpretations of the origin of various petrographic entities.

I am heartily thankful for this technique. I stained literally hundreds of thin sections of Ordovician carbonates for my PhD work. It helped me understand the changes in cement types and their chemical composition as the limestones passed from a marine setting to becoming a freshwater aquifer during sea level drops to their ultimate burial to depths of hundreds of feet where they encountered Mg rich brines from which precipitated the mineral dolomite.

Here is that sequence brought out so clearly by a mix of Alizarin Red S and Potassium Ferricyanide.

1) Bladed crystals of non ferroan marine calcite nucleated on a brachiopod shell (stained pink)
2) Equant crystals of ferroan calcite precipitated in a confined fresh water aquifer that formed during a late Ordovician sea level drop (stained purple)
3) Rhombic crystals of a non-ferroan dolomite precipitated during deep burial (not stained). This dolomite cuts across the early marine and later ferroan calcite cements.

... my series on photomicrographs of carbonates will continue...

Wednesday, August 17, 2016

Rhizome Structures Of Early Plants And Their Impact On Paleosols And Landscapes

From time to time it is instructive to move away from the subject of animal evolution that does tend to dominate media reports. From a sedimentology perspective, plant evolution too has played an extremely important role in shaping sediment composition and fabric, fluvial architecture and the structure of our landscape:

Belowground rhizomes in paleosols: The hidden half of an Early Devonian vascular plant- Jinzhuang Xue 2016

The colonization of terrestrial environments by rooted vascular plants had far-reaching impacts on the Earth system. However, the belowground structures of early vascular plants are rarely documented, and thus the plant−soil interactions in early terrestrial ecosystems are poorly understood. Here we report the earliest rooted paleosols (fossil soils) in Asia from Early Devonian deposits of Yunnan, China. Plant traces are extensive within the soil and occur as complex network-like structures, which are interpreted as representing long-lived, belowground rhizomes of the basal lycopsid Drepanophycus. The rhizomes produced large clones and helped the plant survive frequent sediment burial in well-drained soils within a seasonal wet−dry climate zone. Rhizome networks contributed to the accumulation and pedogenesis of floodplain sediments and increased the soil stabilizing effects of early plants. Predating the appearance of trees with deep roots in the Middle Devonian, plant rhizomes have long functioned in the belowground soil ecosystem. This study presents strong, direct evidence for plant−soil interactions at an early stage of vascular plant radiation. Soil stabilization by complex rhizome systems was apparently widespread, and contributed to landscape modification at an earlier time than had been appreciated.

My interest in this subject is a little tangential. It deals with how to recognize unconformities and disconformities in the field in carbonate sequences. During episodes of sea level falls, marine basins covered by layers of calcium carbonates shells and skeletons get exposed to atmospheric elements. Plants colonize this exposed surface and their root systems physically disrupt the layers of sediment. Rain water and organic acids released by plants dissolve sediments creating pore spaces. The disruption may be clearly visible as solution pits and collapse structures... a karst topography...

I have written a detailed post about this topic and so I won't repeat the lecture over here except to put up this image of a karst developing on Pleistocene limestones from South Florida. Notice how chemical dissolution and the action of roots have caused collapse pits on the limestone surface - 

Land Plants And Expression Of Disconformities in Limestone Sequences

Do read..

Thursday, August 11, 2016

A World Made Of Coccolithophores And Foraminifera

A tweet by Andrew Alden sent me to this paper:

Factors regulating the Great Calcite Belt in the Southern Ocean and its biogeochemical significance- William Balch et al 2016

The Great Calcite Belt (GCB) is a region of elevated surface reflectance in the Southern Ocean (SO) covering ~16% of the global ocean and is thought to result from elevated, seasonal concentrations of coccolithophores. Here we describe field observations and experiments from two cruises that crossed the GCB in the Atlantic and Indian sectors of the SO. We confirm the presence of coccolithophores, their coccoliths, and associated optical scattering, located primarily in the region of the subtropical, Agulhas, and Subantarctic frontal regions.

Great Calcite Belt, Coccolithophores - tiny unicellular phytoplankton covering 16% of the global ocean...

how can one not go back to that wonderful essay by Stephen Jay Gould on Crazy Old Randolph Kirkpatrick

Kirkpatrick was an eccentric natural historian who in the early 1900's  proposed an outlandish theory that the earth was made up of Nummulites, a group of the protist organism Foraminifera. He saw nummulites everywhere he looked, in the global ocean, the entire crust, even in igneous rocks. He concluded that the earth's shell must have been made up of nummulites., Heat from the earth's interior fusing them together and fluids injecting them with silica to form the hard rock we recognize as the igneous variety..

Rocks are sometimes classified as fossiliferous and unfossiliferous, but all are fossiliferous... Really, then, there is, broadly speaking, one rock..... The lithosphere is veritably a silicated nummulosphere.

He thought that nummulites were one of earth's earliest creatures and gave them the name Eozoon and with a flourish wrote:

"After the discovery of the nummulitic nature of nearly the whole island of Porto Santo, of the buildings. wine presses, soil, etc., the name Eozoon portosantum seemed fitting one for the fossils. When the igneous rocks of Madeira were likewise found to be nummulitic, Eozoon atlanticum seemed a more fitting name."

"If Eozoon, after taking in the world, had sighed for more worlds to conquer, its fortunes would have surpassed those of Alexander, for its desires would have been realized. When the empire of the nummulites was found to extend to space a final alteration of name to Eozoon universum apparently became necessary."

We remain trapped in perceiving our world as one teeming with large multicellular animals. But the world is much more. It is a world full of microbes and unicellular eukaryotes too. These creatures occurs in numbers that dwarf our metazoan presence. They are ubiquitous in the surface ocean layers, in the sunlight plankton zone, and their skeletons blanket the depths, creating a layer of ooze covering the sea bed. Their life and evolutionary cycles modulate in large part the global carbon cycle.

Randolph Kirpatrick in his feverish imagination saw an empire of Nummulites.. not too far fetched from the Great Calcite Belt of Coccolithophores covering 16% of the global ocean.

Thursday, August 4, 2016

Photomicrograph- Late Ordovician Calcite Cement Stratigraphy In Cathodoluminescence

Cathodoluminescence (CL) brings out beautifully the hidden growth history of calcite crystals. This photomicrograph is of a Late Ordovician pore space from the Fernvale Limestone, Georgia, Southern Appalachians. It is showing calcite cement grown syntaxially over echinoid fragments. Echinoid skeletons are monocrystalline. A syntaxial overgrowth means that pore filling precipitated calcite has maintained the same crystallographic orientation over this monocrystalline substrate. As a result, successive crystal masses even if precipitated at different times under different conditions appear to be one continuous block under polarized light and under crossed nicols. It takes CL to reveal these different growth phases.

The black growth zones were precipitated in oxidizing conditions by fresh water in the vadose zone (above the groundwater table). The black zones are pendant, hanging on the underside of skeletal grains. They are in essence micro-stalactites.

This was followed by another growth phase in suboxic conditions with the incorporation of divalent Mn(+2) in the calcite lattice. Divalent Mn is an activator of CL, hence the bright yellow growth bands interspersed with a thin black bands indicating periodic return to Mn poor oxidizing conditions.

The last phase is a pore filling phreatic ferroan calcite cement precipitated by reducing meteoric fluids in deeper burial conditions. Fe+2 is a quencher of CL. The cement appears dull brown.

The pore space is a couple of millimeters across.