Thursday, July 30, 2015

Amazonia Before Columbus

This is an interesting article published in the Royal Society's Proceedings B.

During the twentieth century, Amazonia was widely regarded as relatively pristine nature, little impacted by human history. This view remains popular despite mounting evidence of substantial human influence over millennial scales across the region. Here, we review the evidence of an anthropogenic Amazonia in response to claims of sparse populations across broad portions of the region. Amazonia was a major centre of crop domestication, with at least 83 native species containing populations domesticated to some degree. Plant domestication occurs in domesticated landscapes, including highly modified Amazonian dark earths (ADEs) associated with large settled populations and that may cover greater than 0.1% of the region. Populations and food production expanded rapidly within land management systems in the mid-Holocene, and complex societies expanded in resource-rich areas creating domesticated landscapes with profound impacts on local and regional ecology. ADE food production projections support estimates of at least eight million people in 1492. By this time, highly diverse regional systems had developed across Amazonia where subsistence resources were created with plant and landscape domestication, including earthworks. This review argues that the Amazonian anthrome was no less socio-culturally diverse or populous than other tropical forested areas of the world prior to European conquest.

I had read 1491 by Charles Mann so none of this came  as a surprise  to me. I would recommend Mann's book  too.  It is a very well researched richly detailed book on the human landscape of the America's (south and north) before the European conquest. The Amazon basin is covered too and the two things that stuck with me are the "anthrosols" or soils produced or rather enriched in organic matter and nutrients by humans activity like mulching and composting. The map below shows the distribution of these anthropogenic soils.

 Source: Clement C. 2015

Their concentrations along the banks of rivers match early European descriptions of farming communities settled along river bluffs, with the interfluvial areas being occupied by semi-nomadic and nomadic hunter gatherers.

The other aspect that fascinated me was the observation of Europeans of the incredibly varied fruit trees from the Amazon jungles. Many true wild fruit are generally small, sour, bitter, thorny, spiky. The native people over millennia had transformed them by selective breeding into the edible fruit smorgasbord that one sees today. Imagine large areas of "virgin" Amazon forests were actually abandoned fruit orchards!

Read this article though.

Tuesday, July 28, 2015

Those Magnificent Vedic Men In Their Flying Machines

“Aeroplane is a vehicle which travels through the air from one country to another country, from one continent to another continent, and from one planet to another planet.”

...was the timely explanation given at the 2014 Indian  Science Congress as part of a paper titled “Ancient Indian Aviation Technology” by Anand Bodas and Ameya Jadhav.

Siddartha Deb writes about the curious story of how the supposedly ancient document "Vymanika Shastra" or “Science of Aeronautics" on which this presentation was based came to be written. Except that the document is not that ancient.. it is about a hundred years old and the flying machines that it describes are incapable of flying...

Deb also opines about the role of a resurgent Hindu nationalism and what all this tells us about India's place in the modern world. There are some very funny passages in the article, but ultimately you are left feeling sad... sad about a spineless science administration for letting this absurdity play out at a science conference. And sad at the delusions that drive people, at the resulting perversion of science, at the increasing intolerance for rational debate in this country and the damage it is doing to our society.

Tuesday, July 21, 2015

Simon Conway Morris On The Burgess Shale

Don't miss listening to Prof. Simon Conway Morris on the Burgess Shale fauna on Paleocast hosted by Dave Marshall. The Burgess Shale is an important Middle Cambrian deposit in the British Columbia Rocky Mountains. It is a Lagerstatte, i.e. it contains exceptionally well preserved fossils and therefore gives us rich details about the animal life and biodiversity of the early Paleozoic oceans and some insights into the geologically rapid diversification of early metazoans. (the Cambrian "explosion").

Why is preservation so exquisite in the Burgess Shale? Reconstructions of the sedimentary basin indicate that the mud that became the Burgess Shale was deposited at the base of a high relief limestone reef which essentially formed a sort of an underwater sea cliff.  Periodic turbidity currents swept in fauna living in shallower  areas and buried them rapidly in the deeper  water at the base of the cliff. These currents form deposits a few cm thick, encasing animal remains a few mm in dimensions. The waters were oxygen starved, thus there was less aerobic bacterial degradation of soft tissue. Add to that were some peculiar geochemical conditions of the Cambrian ocean. One was a paucity of sulphate which retarded degradation by sulphate reducing bacteria. The other, as some recent work by Robert Gaines and colleagues suggest, was the high calcium carbonate saturation levels of the ocean, which lead to rapid cementation of the sea floor in between episodes of turbidity flows.

The image on the left shows CaCO3 cement rich layers in the Burgess shale (source: Gaines et al 2012). These cemented crusts on the sea floor formed an impermeable barrier and reduced the influx of sulphate and oxygen bearing sea water in to the sediment, further slowing down microbial activity. How do we know there was less activity of sulphate reducing bacteria? The researchers analyzed the patterns of sulphur isotopes in the fossil rich turbidity layers and the background sediment.  Sulphate reducing bacteria preferentially take up the lighter isotope of sulphur from sea water. Thus, background deposits with normal or enhanced microbial activity have a lighter isotope signature relative to the Cambrian sea water standard. On the other  hand, less microbial  activity means  less fractionation of the lighter isotope into bacteria and ultimately into the sediment matrix. In Burgess Shale type deposits the fossil rich turbidity layers capped by CaCO3 cements show an enriched or heavier sulphur isotope signal indicating less microbial activity. Finally, since the bottom  waters were anoxic, there was little benthic fauna living there. This meant that the cement crusts were not disturbed and broken by bioturbation and remained effective seals throughout the crucial first few weeks of burial when degradation is at its peak. Soft tissue does break down due to slowed microbial activity and fermentation and methanogenesis. The three dimensional carcass collapses into a nearly two dimensional carbon rich film. The final result is that recalcitrant extracellular organic material like cuticles, chaetae, and jaws are preserved as compressed thin carbonaceous films often just a few microns thick, the soft fine grained mud encasing the carcass helping preserve fine morphological details. This preservation style also meant that some animals lacking recalcitrant tissues like flatworms, mesozoans, nemerteans and unshelled molluscs are less well represented in the Burgess Shale style deposits ( Butterfield 2003). Peculiar preservational styles by their very exceptional and localized nature impose a bias on the fossil record that palaeontologists must recognize to understand true evolutionary patterns.

The examples on the left shows Burgess Shale style preservation of Arthropod (B), Polychaetae worm (C) and Arthropod (D) [source: Gaines 2014]. This style of preservation actually appears first in the early Neo-Proterozoic  and then disappears for about 150 million years until the earliest Cambrian. It again declines by late Cambrian with the earliest Ordovician being the last recorded example of this taphonomic style. A unique combination of geological conditions and early diagenesis of sediment prevailing in the latest Proteozoic and earliest Cambrian resulted in these fossil deposits. This time period also has other forms of detailed preservation of soft tissues, the two most important being the Edicaran style preservation wherein the remains of macroscopic plants and animals deposited in sandy and silty sediment were draped by microbial mats and compressed to form impressions (death masks) on the sediment surface. The other important style is the Doushantuo style preservation (named after the Doushantuo fossil beds of late NeoProterozoic age, China, containing preserved algae and putative embryos and larval stages of early animals ) where phosphate minerals are attracted to and precipitate around organic tissue preserving delicate cell outlines and internal organs. Very occasionally, the same fossil will show two different preservational styles, for example, the extracellular tissue preserved in the Burgess Shale style while  internal organs preserved in the Doushantuo style. These taphonomic "windows", as they are referred to, appear and disappear through the Neo-Proterozoic to Cambrian period. For example, the Edicaran style preservation first appears in the late NeoProterozic around 580 million years ago or so. Considering that microbial mats which play an important role in this style of  preservation are pervasive through the late Archaean and the Proterozoic, the first appearance of the Edicaran remains is then likely an evolutionary signal of the first appearance of  macroscopic multicellular  eucaryotes on earth. The disappearance of Edicaran style by the earliest Cambrian also suggests a biological feedback. The evolution of macroscopic benthic animals burrowing and grazing on bacterial mats may have destroyed the cover protecting the faunal remains. Preservational styles are controlled not just by geological conditions but due to contemporaneous evolutionary innovations too.

Coming back to the talk! Prof Simon Conway Morris describes the history of research on the Burgess Shale,  how he got into researching it, details of some of the animals found in it including the famous Pikaia. This has been interpreted as an early representative of  the chordates from which the vertebrates evolved. Overall, Conway Morris gives a masterly authoritative talk.

I would have loved to hear him talk a little more about the broader questions that arise from this deposit. Are the origins of the Burgess animals to be found in the earlier Edicaran fauna? Does the Cambrian have greater morphological disparity than later periods in earth history? Has life followed a contingent unique pathway or does examples of convergence tell us something deeper about the general principles of evolution? ..or an intelligence which frames the ultimate laws and guides evolutionary processes. Simon Conway Morris has indicated elsewhere his thoughts that the Universe is the product of a rational mind and that evolution is but a search engine and I wish Dave Marshall had pressed him on his theist beliefs. But I guess the topic was the fauna of the Burgess Shale and in particular that iconic quarry in British Colombia.

He did mention in passing something which I think  is an important aspect of this story. Just as he had finished his Master's degree from Bristol University in 1972, a project headed by Prof. Harry Whittington on the Burgess Shale was starting at Cambridge. Simon Conway Morris saw this as a good opportunity. At around the same time, the Chicago school of palaeontologists lead by David Raup (who died last week), Jack Sepkoski and Tom Schopf had started a program to broaden the scope of palaeontology to include rigorous quantitative methods on large sample sets to understand biodiversity and patterns of evolution, bringing the field of palaeontology, as John Maynard Smith famously said, to the "high table of evolutionary theory". These events underscore the important point that for all your brilliance in something, circumstances and timing matter. Simon Conway Morris was present at the right time at the right place. And he did the Burgess Shale fauna justice.

Friday, July 10, 2015

Darwin: Ancestry In Lyell's Pebbles And Herschel's Words

A lovely passage from the 19th century astronomer John Herschel's  letter to geologist Charles Lyell quoted in Darwin: The Life Of A Tormented Evolutionist:

Words are to the Anthropologist what rolled pebbles are to the Geologist- Battered relics of past ages often containing within them indelible records capable of intelligible interpretation- and  when we see what amounts of change 2000 years has been able to produce  in the languages of Greece & Italy or 1000 in those of Germany, France & Spain we naturally begin to ask how long a period must have lapsed since the Chinese, the Hebrew, the Delaware & the Maleass [from Madagascar] had a point in common with the German & Italian & each other. - Time! Time! Time! - we must not impugn Scripture Chronology,but we must interpret it in accordance with whatever shall appear on fair enquiry to be the truth for there cannot be two truths. And really there  is scope enough: for the lives of the Patriarchs may as reasonably be  extended to 5000 or 50000 years apiece as the days of Creation to as many thousand millions of years.

Besides a great age for earth, a notion which was becoming more accepted as geological observations poured in from Britain and other parts of the world,  in the passage are ideas on ancestry and divergence from a common stock. Herschel's musings on language change influenced Darwin. Were these applicable to life too? Darwin on his return from the Beagle voyage in 1836 was engrossed in geological thinking,  hoping to write a book on South American geology. Charles Lyell encouraged him,  and unlike the cantankerous zoology community, he found the geology fraternity more  approachable and gentlemanly. His paper to the Geological Society on the uplift of the Chilean coast was very well received.

But his zoological samples too were being processed by a variety of experts. Richard Owen found out that the large animal bones Darwin had collected were ancient relatives of living South American sloths and armadillos and not related to European and African mammals. There was, Darwin realized, a genealogical succession of fauna which jarred with the commonly held ideas about separate creation of species.  The ornithologist John Gould pointed out that the seemingly disparate collecting of Galapagos Islands ground dwelling birds with distinctive beaks that Darwin had presented to him and thought of as distinct species of finches, wrens and warblers were in fact a closely related group of finches, with more distant relatives found on the South American mainland. And his collection of mockingbirds which unlike  the finches were correctly labelled according to the islands,  turned out to be 3 related species, each distinct to an island... Ancestry and divergence from a common stock..

John Herschel's "mystery of all mysteries" began tempting him. His long association with dissenting intellectuals and radical thinkers who claimed that life should be explainable by natural laws and his own observations of  nature's bounty and variability had made him  receptive to the idea of species transforming into new species. In this, he departed from his geology mentor Charles Lyell who was a scientist molded in the conservative Anglican tradition. Lyell believed that the dynamics of landscapes and the succession of fauna ultimately revealed the hand of a creator. That humans could have originated via transmutation from an ape was anathema to him. For Darwin, such thoughts held no terror.

Geology was to remain an important part of his work life, but in July 1837 he opened and began scribbling ideas in what is one of the most famous scratchpads in the history of science- Notebook B which he titled Zoonomia (after his grandfather Erasmus Darwin's book), marking a decisive shift in emphasis in his thinking from geology to evolution.

Monday, July 6, 2015

Monsoon Trekking Season Is Here

I hereby declare the Deccan Volcanics Western Ghat 2015 monsoon trekking season officially open!

That picture is of the steep slopes of Fort Rajgad about an hour's drive from Pune, taken a couple of years ago.

Last year the geology highlight of my treks into the Deccan Basalt countryside was this dyke with horizontal columnar joints near the summit of Fort Ghangad.

Columnar joints are cooling cracks which develop perpendicular to the cooling surface. In lava flows, the cooling surface is mostly horizontal and so the result is vertically oriented, often hexagonal shaped columnar  joints.  In this case, the cooling surface was the near vertical contact between the intruding hot magma and the colder older lava flow. The cooling cracks therefore are horizontal.

I will be posting more pictures from this year's trekking season. The Western Ghats in the monsoon and the winter are a sight to savor!