Tuesday, August 15, 2017

Links: Human Evolution

Sharing links to interesting articles I have read in the past few months. Better understanding of human evolution is being driven by a) New fossil finds giving valuable insights into morphologic variation and geography, b) DNA analysis of both modern and extinct populations giving us an understanding of genealogical relationships and migration histories and c) better absolute dating of fossils that constraint evolutionary scenarios.

1) What Are Our Best Clues To The Evolution Of Fire-Making? Anthropologist Barbara J King examines the physical evidence of fire making by ancient hominins and presents speculations on how natural fires may have played a role in hominin cultural evolution.

2) A world map of Neanderthal and Denisovan ancestry in modern humans- Phys.Org. " There are certain classes of genes that modern humans inherited from the archaic humans with whom they interbred, which may have helped the modern humans to adapt to the new environments in which they arrived," says senior author David Reich, a geneticist at Harvard Medical School and the Broad Institute. "On the flip side, there was negative selection to systematically remove ancestry that may have been problematic from modern humans. We can document this removal over the 40,000 years since these admixtures occurred."

3) Three new discoveries in a month rock our African origins- Prof. John Hawks on new fossil dating of hominin fossils from Morocco and evidence from archaic DNA from S. Africa that complicates the African story of the origins of Homo sapiens. The scenario suggested here is that Homo sapiens did not evolve due to changes in a population which was genetically isolated from other Pleistocene African hominin groups. Rather there was a pan-African gene flow. This is multi-regionalism within Africa.

4) Out of North Africa- Dienekes argues the exact opposite.. that the Morocco fossils imply that Homo sapiens evolved in north Africa from a reproductively isolated population and that multi-regionalism is wrong.

5) Features of the Grecian ape raise questions about early hominins- Did the hominin clade evolve in Europe and not Africa? Prof. John Hawk's critique of a recent paper suggesting that view. He cautions that convergent evolution is common among different hominin lineages. A single feature, such as the mandible used in this paper, cannot indicate relationships.

6) Early modern humans in Sumatra before the Toba eruption- Steve Drury in Earth Pages summarizes new evidence that indicates early ( more than 70,000 years ago) migration of Homo sapiens into SE Asia. .." Together with the dating of the earliest Australians the Sumatran evidence is at odds with the view, widely held by palaeoanthropologists, that the ‘Out of Africa’ exodus began by crossing the Straits of Bab el Mandab between 74 and 58 ka when global sea-level fell markedly during marine oxygen-isotope Stage 4 (MIS4). A problem with that hypothesis has been that climatic and ecological conditions in southern Asia during MIS4 were unfavourable. But is seems that modern humans were already there and capable of adapting to both the climate shift and to the devastation undoubtedly caused by Toba."

Thursday, August 10, 2017

China Hydraulic Engineering - Yellow River And The Grand Canal

I am reading Philip Ball's excellent book The Water Kingdom: A Secret History Of China. It describes the epic problems of river flow management that China has grappled with over millennia. Enormous floods have always ravaged China. At the site of a large dam at Sanmenxia on the Yellow River is an inscription in honor of the Great Yu ( ~ 2200- 2100 B.C), who as the story goes,  conquered a flood. The inscription says " When the Yellow River is at Peace, the Nation is at Peace". Flood control required enormous civic resources and cooperation and the ability to tame river waters gave political and moral legitimacy to the ruling class.The taming of nature using cooperative people power and as a sign of a strong united society has deep roots in Chinese political thinking.

One particular vexing problem was the very high rates of silt load carried by the Yellow River. A vast area of the Yellow River watershed drains the Loess deposits of north central China. This is a plateau made up of loose friable sand and silt blown in from the Gobi desert of Mongolia. Erosion of Loess fills the river with sediment. There is 300 grams of sediment for every kilogram of Yellow River water giving the river a reddish golden color. Erosion has carved the Loess Plateau in to a landscape of ravines and gorges. The American journalist Edgar Snow in the 1930's described it thus:

" an infinite variety of queer, embattled shapes - hills, like great castles, like ranges torn by some giant hand, leaving  behind the imprint of angry fingers. Fantastic, incredible and sometimes frightening shapes, a world configurated by a mad God - and sometimes a world of strange surrealist beauty. "

High rates of sedimentation meant that the Yellow River bed could aggrade or rise, increasing the risk of the river breaking its banks and flooding the countryside. Dyke building to constraint the river channel began as early as the seventh century B.C. by the state of Qi.

Constant dredging of the Yellow River and the associated tributaries and canal systems ( the Grand Canal) was also required to maintain a channel deep enough for navigation to move armies and grains from south to north.  River channel and canal maintenance acquired a new urgency when Zhu Di known as the Yongle Emperor of the Ming dynasty moved the capital north from Nanjing in the eastern province of Jiansu to Beijing in the early 1400's. The rational was probably to keep the political center closer to the armies amassed on the northern frontier where the Ming faced a threat from the Mongol and Manchurian steppe people. Later in the 1600's, the Manchurians overthrew the Ming and established the Qing Dynasty. Although over time, the Qing assimilated into the larger Han cultural milieu, they felt more at home in the north of the country. That meant the Yellow River and the Grand Canal system had to kept in top navigable order.

Desperation to unclog  the river channel spurred technological innovation. 

An extract:

Removing silt from the Yellow River demanded some impressive technology, not to mention serious organization. The Song government set up a Yellow River Dredging Commission in 1073 which began to deploy boats equipped with dredging tools. The vividly named  "iron dragon-claw silt dispersing machine" was a great rake pulled along the riverbed to agitate the silt and return it to the flow. This principle was extended with the 'river-deepening harrow', a 2.5 metre-long rotating beam fitted with iron spikes, like a thresher for riverine mud. The Ming imperial censor Chen Bangke introduced new techniques in the late sixteenth century, such as wooden machines set rolling and vibrating by the current to constantly stir up the sediment. In the dry season Chen proposed simply digging out the silt manually.

The Ming official Pan Jixun in 1565 or so came up with a solution that has made him one of China's water heroes. He pointed out that if one confines the water flow to a narrow channel, it will have enough strength to scour the sediment off the river bed. There would be minimal need for laborious manual dredging. He may have borrowed the  idea from a Confucian text of the Han era (~200 B.C - 220 A.D) called Zhou li (Rites of Zhou) which stated "A good canal is scoured by its own water"

Chinese philosophical tradition impacted river management strategies. Daoists argued that the river be given room to spread and build wide floodplains in concert with the principle of wu wei which could be read to mean "do nothing" or "having a yielding attitude".  Confucians on the other hand wanted the river to be managed by human  engineering and recommended the construction of high dykes to keep the river channel narrow and constrained.

Joseph Needham, the noted historian of China writes that 'during twenty centuries the two schools contented'.. 'and neither proved wholly successful'.

Highly Recommended.

Friday, July 28, 2017

The Lost Rivers Of The Harappan Civilization- Remote Sensing Analysis

A lot of ink has been spent of this topic, both in the scientific literature as well as in popular books about the Harappan Civilization. The focus of many of these efforts has been on locating the "Vedic Saraswati", a river mentioned in the Rig -Ved. It is described as occupying the region between the Yamuna and the Sutlej and has been identified by many workers as the present day Ghaggar-Hakra.

Settlements of the Harappan Civilization were spread out over quite a large area in northwest India. Hence, it is necessary to map in detail the broader once existing hydrologic networks to assess the relationship between settlements and patterns of water availability and water use. This study uses remote sensing data and image processing techniques to unearth some of the buried paleo-river networks of this region of northwest India.

Twenty eight years of Landsat 5 imagery totaling 1711 multi-spectral images was bulk processed. This use of data covering multiple dates in a year allowed the investigators to reduce visibility issues related to shifting land use and cultivation, changing moisture patterns and variable cloud cover. 8000 km of paleo-river channels were mapped, some identified in previous studies, but many recognized anew.

The paper describes the various image processing techniques used to tease out the spectral signatures of the buried rivers. Don't be alarmed by words like Normalized Difference Vegetation Seasonality Index (NDVSI), Principal Component Analysis and the Tasselled Cap Transform.  One can understand the final interpretations without getting into the details of these techniques. Let me give a brief idea though.

These are techniques has increase the contrast between vegetation, soils with different moisture levels and bare terrain. For example, due to stronger water flow the river channel itself and the levees it builds contain coarser sediment as compared with the adjoining floodplains. These coarser sediment contain less organic matter and are less fertile. Less vegetation grows on the buried channels and levees than on the more fertile fine grained floodplain sediment. This contrast shows up well on data processed using NDVSI which essentially maps the vigor of vegetation. This technique was useful in delineating channels in the northern part of the study area.

The southeast part of the study area is more arid and has less changes in vegetation across the landscape. Here, the Tasselled Cap Transform was more useful in identifying river channels. This techniques organizes the spectral information into several (usually three) main axis or bands of information. One axis contains data variability of reflectance of bare terrain (mineral mixtures). The second contains variability in greeness (vegetation), and the third contains variability of wetness (water and soil moisture). Again, to give an example, this southeast region is fed by rivers draining Aravalli limestones. The calcium carbonate leached away from the rock is precipitated along river channels as a chalky mineral deposit. Buried channels show up as ribbons of  bright reflectance in  the Tasseled Cap Transform brightness band. Imagery of the dry months shows these channels more clearly, since in the wet months, increased soil moisture reduces the contrast of calcium carbonate rich sediment.

A judicious use of such techniques thus enabled the researchers to identify buried networks with different vegetation, soil moisture and mineral brightness properties. 

A map of the interpreted buried rivers is posted below.

Source: Hector A. Orengo and Cameron A. Petrie 2017

Of importance is a critique of some previous studies which attempted to highlight the spatial relationship between river channels and archaeological sites (emphasis mine):

The data provided by these analyses are also important in contextualising previous studies in which palaeo-rivers have been dated using the distribution of known archaeological sites. Notwithstanding the positional accuracy of these locations (see [10,63,64]), which would severely hamper their use for validation purposes, the results for the northern sector of the study area (Figure 3) suggest that proximity to the river might not be a good indication of contemporaneity as the fields close to the river channel might not have been the most productive in agricultural terms. Sites with an agricultural orientation might have preferred to occupy elevations above flooding level in the finer sediment accumulation area. Flooding events and changing river courses could also have had an important effect in the preservation of archaeological sites eroding and burying those that were locatedin the path of new courses or in their sediment accumulation areas.

In addition to these factors, the scale at which these correlations between specific palaeo-channels and settlement locations have usually been published (e.g., [30] (pp. 359–387), [31] (Figure 4.2)]) do not allow the accurate correlation between the two elements. The use of large area (small scale in a geographic sense) site distribution maps for these correlations results in a visual association between the shape of the palaeo-river and the line formed by the grouping of sites, but at these scales the sites could be aligned to a number of palaeo-channels given the number of rivers and the parallel morphology of the drainage in the Sutlej-Yamuna interfluve revealed here. This analysis thus suggests that at these scales it is not possible to co-relate lineal distribution of archaeological sites to any particular palaeo-river that we have documented. The results from previous studies reconstructing the chronology of the hydrological system using the position of archaeological sites and vice versa(e.g., [24,25], [30] (pp. 359–384), and [31]) are, therefore, considered unreliable.


Given the complexity of the hydrological system, the variety in the climatic and weather system of this region, and the diversity of ways that ancient populations are likely to have obtained water, it is unwise to use the date of occupation at specific settlements to date when specific channels carried water. It is essential to date the different palaeo-courses independently to properly reconstruct the evolution of hydrological networks over long periods. The chronologically consistent reconstruction of this palaeo-river network would allow the testing of different hypothetical scenarios of water availability through the use of network analysis in combination to hydrological analysis.

Interesting work. Open Access.

Saturday, July 22, 2017

Tsunami History Preserved In Indonesian Cave Deposits

How would you know if a coastline had been inundated by a tsunami say 5000 years ago? Well, a tsunami carries sediment stripped from the ocean bed and deposits this material over the flooded coastline, beyond the range of what a regular storm would. The problem is that such deposits have poor preservation potential and over time get eroded away. There are however some environments where such tsunami deposits may get preserved inland. These are estuaries, coastal marshes and lakes. Here, interlayered with normal estuarine, marsh or lacustrine sediment, one may find layers of sand of a distinctly different composition and texture and containing remains of organisms which live in an open marine setting. This implies a sudden incursion of marine waters into these inland coastal settings. The other coastal setting with a good preservation potential are caves. These too get flooded by storm surges and tsunamis and may preserve a record of such events in the form of sand deposits. The picture to the left (Source: Rubin et.al. 2017)  shows sand layers deposited by the 2004 tsunami.

In one such cave on the coast of Aceh, Indonesia a record of the 2004 tsunami along with sand layers deposited by 11 older tsunamis going back to 7400 years ago have been preserved.

Highly variable recurrence of tsunamis in the 7,400 years before the 2004 Indian Ocean tsunami-
Charles M. Rubin, Benjamin P. Horton, Kerry Sieh, Jessica E. Pilarczyk, Patrick Daly, Nazli Ismail & Andrew C. Parnell


 We identify coastal caves as a new depositional environment for reconstructing tsunami records and present a 5,000 year record of continuous tsunami deposits from a coastal cave in Sumatra, Indonesia (Fig. 1), which shows the irregular recurrence of 11 tsunamis between 7,400 and 2,900 years BP. The sedimentary record in the cave shows that ruptures of the Sunda megathrust vary between large (which generated the 2004 Indian Ocean tsunami) and smaller slip failures. The chronology of events suggests the recurrence of multiple smaller tsunamis within relatively short time periods, interrupted by long periods of strain accumulation followed by giant tsunamis. The data demonstrates that the 2004 tsunami was just the latest in a sequence of devastating tsunamis stretching back to at least the early Holocene and suggests a high likelihood for future tsunamis in the Indian Ocean. The sediments preserved in the costal cave provide a unique opportunity to refine our understanding of the behaviour of the Sunda megathrust, as well as study in detail the sedimentology and hydrological characteristics of tsunami deposits.

There is one point that cannot be over stressed. The average recurrence time for earthquakes and tsunamis has been estimated to be on the order of several hundred years. However, there is a great variation in the actual occurrence, with several smaller tsunamis occurring just decades apart. While our understanding of earthquake mechanisms and tsunami generation will go on improving, ultimately what will save lives is better preparedness. This includes adherence to structurally appropriate building codes, functioning tsunami warning systems and well drilled and practiced disaster management plans. South East Asia has long neglected these issues and there needs to be a renewed focus on them.

Sunday, July 16, 2017

Olivia Judson On Energy Expansions Of Evolution

Nature Ecology and Evolution has published a fine perspective by evolutionary biologist Olivia Judson on energy availability and evolutionary transitions on earth -

" The history of the life–Earth system can be divided into five ‘energetic’ epochs, each featuring the evolution of life forms that can exploit a new source of energy. These sources are: geochemical energy, sunlight, oxygen, flesh and fire. The first two were present at the start, but oxygen, flesh and fire are all consequences of evolutionary events. Since no category of energy source has disappeared, this has, over time, resulted in an expanding realm of the sources of energy available to living organisms and a concomitant increase in the diversity and complexity of ecosystems. These energy expansions have also mediated the transformation of key aspects of the planetary environment, which have in turn mediated the future course of evolutionary change.Using energy as a lens thus illuminates patterns in the entwined histories of life and Earth, and may also provide a framework for considering the potential trajectories of life–planet systems elsewhere."

Coincidentally, I just finished reading Nick Lane's book The Vital Question, which covers the first three sources of energy discussed in this article. Nick Lane writes about energy currencies of the cell and the constraints it places on the early evolution of life on earth. Why don't bacteria become morphologically larger and more complex?... because there are intrinsic constraints on the energy available for ATP synthesis.  You'll have to read Nick Lane's book for a detailed account but Olivia Judson's essay mentions this and more. The other two, animals and fire, encompass the evolution of complex multicellular life and their impact on evolutionary arms races and ecosystem changes.

..and what about life on other planets?..

"As this is the only life–planet system we currently know of, it is impossible to know how representative it is of life–planet systems in general. But if the development of other life–planet systems requires a similar series of energy expansions, the framework presented here suggests a way to anticipate the paths that such systems might take. For instance, if a planet has only geochemical energy— perhaps because it is far from its star, or because it is a nomad and has no star at all—any life present may have “a limited future in terms of the heights it could achieve”. Or suppose a planet is unable to accumulate oxygen. This could happen if living organisms never evolve a way of splitting water to produce the gas in the first place, but even if they do, the planet itself may have characteristics that prevent oxygen from ever building up. Without oxygen, the geological, ecological and evolutionary potential of a life–planet system is likely to be constrained, even if life forms analogous to eukaryotes in their energy-harnessing power (Box 2) were to evolve. Conversely, some planets might be able to accumulate new forms of energy, and life forms able to take advantage of them, much fasterthan Earth has."

Open Access.