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 et.al. 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.

#ThinSectionThursday

Saturday, July 30, 2016

New Ancestor Of Man And Other Rants About Media Reports

I am ashamed to admit this, but these days I just shrug away the various instances of poor science reporting I notice in the Indian media. But enough outrage has been building up over a couple of  particularly bad misrepresentations of scientific findings to prompt this rant.

 1) Indian Scientists Find New Ancestor Of Man

One shudders with embarrassment at this jingoistic hyperbole. The study is an international collaboration. Why the chest beating?

The article in Deccan Herald on July 26 by Kalyan Ray completely misrepresents the evolutionary story of Homo sapiens. Here are the sentences which go badly wrong -

"Andaman’s Jarawas and Onges are descendants of a completely new family of early men unknown to science so far"..

"The discovery has the potential to open up a new window in the history of human evolution by suggesting that Homo heidelbergensis—the first group of men who came out of Africa—had given rise to multiple lineages and not just the Neanderthal and the Denisovan—the two known branches from which all modern human beings have evolved".

The writer is suggesting the modern humans evolved entirely from Neanderthals and Denisovans outside Africa and that this new research is showing that the Andamanese are descendants of a yet third branch of humans based outside Africa.

This picture given by Kalyan Ray is false. Take a look at the hominin family tree presented in the research paper.


Source: Genomic analysis of Andamanese provides insights into ancient human migration into Asia and adaptation

It presents our current understanding of human evolution and migration and admixing events between different branches of hominins. Modern humans migrating out of Africa about 60 thousand years ago met and admixed with the Neanderthals and Denisovans who were branches of an earlier wave of human migration out of Africa. This earlier wave of migration may have taken place about half a million years ago. This admixture between archaic and modern humans resulted in all living non -Africans having  2%-4% Neanderthal ancestry with additional Denisovan ancestry more common in Melanesians.  Now, this study is proposing that another unknown extinct hominid, a possible third diverged population from those earlier migrations, contributed a small amount of ancestry to south Asians. The Andamanese may be taken as an approximate proxy of the original modern humans who entered the Indian subcontinent from Africa since after diverging from a common South Asian population they have admixed less with other modern humans.

Another quibble is the sentence "Hominids are ancestors of the great apes and humans". Well, hominids is a grouping that includes both extinct and living great apes and humans. So yes, some extinct hominid would have been our ancestor, but modern humans are hominids too. As an aside, to confuse matters further, Hominin are the group that includes the extinct and living members of only the human family, excluding the chimpanzee, gorilla and orang-utans.

2) Before The Pharoah: Fresh Evidence Should Make Us Question Earlier Views Of Indus Valley Civilization

This piece which appeared in the Times of India on June 6 is referring to a paper about the link between Holocene monsoon record and the evolution of Harappan civilization. The authors also suggest a revision of the chronology of the various Harappan cultural stages.  Here is their proposed chronology.This is based mainly on the chronology proposed earlier by G.L Possehl. The authors of this study augment  that with new dates from two samples.

"The successive cultural levels at Bhirrana, as deciphered from archeological artefacts along with these 14C ages, are Pre-Harappan Hakra phase (~9.5–8 ka BP), Early Harappan (~8–6.5 ka BP), Early mature Harappan (~6.5–5 ka BP) and mature Harappan (~5–2.8 ka BP)"

And here is the conventional chronology

"Conventionally the Harappan cultural levels have been classified into 1) an Early Ravi Phase (~5.7–4.8 ka BP), 2) Transitional Kot Diji phase (~4.8–4.6 ka BP), 3) Mature phase (~4.6–3.9 ka BP) and 4) Late declining (painted Grey Ware) phase (3.9–3.3 ka BP). This chronology is based on more than 100 14C dates from the site of Harappa and nearby localities".

Here is the chronology Mr. Mehta presents:


The first line in the introduction section of the research paper makes it clear that all dates are presented in BP (Before Present). Yet Nalin Mehta in his article bungles up and without applying the necessary correction presents the chronology as representing dates in BC. The difference is 2000 years! For example, 5000 BP is 3000 BC.

Another big error he makes is lumping all the Harappan cultural stages into one mature phase spanning 8000 -2000 BC ! This gives an erroneous view of the evolution of Harappan society. The mature phase represents urbanization. The earlier cultural stages were rural antecedents represented by farming and pastoral communities and even earlier human settlements in this area. By terming the entire time span of Harappan culture as belonging to the mature phase, Mr Mehta gives an impression that Harappan cities were as old as 8000 BC. This is certainly not the case. This new study revises the mature phase of the Harappan culture from the accepted ~2600 BC-2700 BC (4700 BP) to ~ 3000 BC (5000 BP). This proposed revision at one cultural site should not be taken to mean that dates for cities like Harappa, Mohenjodaro, Dholavira will suddenly be changed to 3000 BC. Their chronology needs to be ascertained independently. As of now, large number of C14 and thermoluminescence dates have secured the age of these cities to be around 2700 BC or so.

One has to be careful with terminology. Mr Mehta uses dates as old as 8000 BP (wrongly presenting them as 8000 BC) to imply that the Harappan civilization is older than the Paraoahs of Egypt. Such a comparison is meaningless. These earlier dates represent a rural society. No doubt there was population and cultural continuity of these earlier people with the later urban phase, but you can say the same thing about pre-urban Egyptian and Sumerian cultures evolving into a full fledged urban civilization. There was a long pre-urban phase from 5-6 millenium BC in Eygpt and Sumer (synchronous to the Indus region) with central political consolidation and urbanism by around 3100 BC in Egypt when the first dynastic kings known as the Pharaohs seized power. In Sumer, the transition from rural to urban took place even earlier with cities like Uruk gaining prominence well before 3500 BC.

The differently named cultural stages of the Indus valley carry a specific meaning  in terms of societal complexity and cultural changes. You can't just call everything mature Harappan and then claim that the finding requires some kind of a fundamental rethink of Harappan society. 

As it happens, the dates presented in the paper that Mehta is ga-ga about are not new. Archaeologists have been aware of the alternate chronology presented by G.L Possehl for about 15 years now! In that sense there is nothing revolutionary about the chronology presented in this paper.

..rant over.