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How do genetic patterns relate to archaeological evidence about Indian pasts?

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The story so far: Last Thursday, the journal Cell published a paper, ‘An Ancient Harappan Genome Lacks Ancestry from Steppe Pastoralists and Iranian Farmers’, which claimed that the inhabitants of the Indus Valley civilisation lacked the steppe-pastoralist ancestry which had brought Indo-European languages into South Asia. The findings of the paper, whose key authors are the archaeologist Vasant Shinde, and the geneticists Vagheesh M. Narasimhan and David Reich, et.al, are based on the DNA sequencing of the remains of a woman found at Rakhigarhi in present-day Haryana. Another paper, published in the journal Science by the same authors, established baselines for the DNA of South and Central Asian populations over the last 10,000 years.

What is ancient DNA (aDNA) and what has it been used to study?

Ancient DNA can be carefully extracted from archaeologically recovered bones, teeth or fossil plant remains. Small fragments are processed to sequence the genome of those ancient organisms. aDNA becomes degraded, on account of its age and the climatic and soil conditions it was buried in. Techniques developed over the past three decades have led to a revolution in how we understand the evolution and genetic history of a range of animals and plants, including species that are extinct today. Palaeogeneticists have been able to establish, for example, how genetic variation might relate to the independent evolution of species on different continents that were previously thought to be related, or, how populations that today appear distinct and in different geographical areas were once related and likely existed together in one region.

What can be done with aDNA from human samples?

Special challenges are attached to the study of ancient human DNA, especially as contamination from modern human DNA is a real hazard and requires special techniques at every stage of the recovery and extraction process.

Modern human DNA databases are built on samples from people like us, alive today. They have been used for several applications, prominently including attempts to understand the genetic predisposition towards certain diseases and responses to medicines in different social groups in South Asia. The comparison of aDNA samples with other aDNA and modern DNA databases can reveal otherwise unsuspected genetic histories. Scientists can trace the deep ancestry of ancient individuals and assess how their genetic makeup is distinct on account of specific variant genes (alleles), mutations and other markers (99% of all human DNA is common) and see how this compares with that of modern groups.

Thus the most common way of understanding the relatedness of DNA between groups and individuals is by their admixture percentages.

Importantly, genes may co-vary with a group’s ethnicity — understood as the combination of language and material practices — but they also may not. There is no necessary correlation between the genes of the author of these words or the reader and what language their ancestors must have spoken, nor what their ‘identity’ was. The social processes of history are not the same as those which can be observed through population genetics. While populations display aggregate trends of admixture and patterns of deep shared ancestry, there are no ‘Aryan’ or ‘Harappan’ or ‘Dravidian’ genes.

What are the recent results? What do they establish?

The two recent papers, (in Science and Cell), have provided complementary levels of insights into South Asian population history. For a detailed account of their findings and misunderstandings of their conclusions please see Tony Joseph’s article in this newspaper (Magazine, “We are all migrants”, September 15, 2019; https://bit.ly/2kJdrss).

The first paper, ‘The Formation of Human Populations in South and Central Asia’, establishes baselines for the genetic history of populations in these two linked regions. Based on an unprecedented 523 aDNA samples ranging over 8,000 years across Eurasia, the authors demonstrate clearly what was known before but is now shown in greater detail with clear evidence, that over the last 10,000 years, the present-day distinctive mix of South Asian genetic variability was formed through the admixture of populations then resident in the region with successive groups who moved into the region. This is a process that happened not just once but several times.

They make clear that these mixing of populations were far from “invasions”, and the trends in their data show slow long-term processes of migration, co-mingling and integration.

The best documented of these admixture events is the genetic interaction of populations then resident in Northern South Asia with groups associated with ‘steppe pastoralist’ ancestry and is unequivocally dated to 2000-1500 BCE. This period is well understood archaeologically as a complex era of post-Harappan deurbanisation, when different regions from Gujarat to Haryana show varying trends in crop patterns, settlement sizes and material culture at a time when rainfall and climate patterns underwent significant changes. Distributions of this ‘steppe pastoralist’ genetic ancestry broadly correlate with the distribution of Indo-European language speakers today, and the presumed areas where earlier Indo-European speaking groups lived. Since Sir William Jones’s Third Discourse in 1786, (https://bit.ly/2mg8dF9) every generation of scholars has tried to address how the philological links between Sanskrit, Persian and Latin, i.e. the Indo-European language family, can be linked and understood with reference to ancient migrations, material culture and ancient literatures. Ours is an era when DNA evidence, which intrinsically tells one nothing about language, ethnicity or religion, provides important but difficult to correlate new data to these debates. Contrary to what can only be called motivated misreadings: the aDNA studies make clear that the genetic makeup of South Asian populations changed between 2000-1500 BCE.

What does the woman from Rakhigarhi teach us?

The second paper presents the results of the first successful aDNA extraction from prehistoric South Asia. Individual 6113 was an elite woman buried between 2300 and 2800 BCE (estimated) in a cemetery on the outskirts of the Harappan town of Rakhigarhi, located near the present-day city of Hissar in Haryana. This is a scientific achievement, especially as efforts to extract archaeological DNA have hitherto been few in South Asia and several attempts resulted in DNA that was too degraded or was contaminated.

The DNA of this person from Rakhigarhi, it turns out, is a mixture with contributions coming from very ancient ancestry shared with Iranian populations and that from what the authors term Andamanese or South-East Asians in the deep past of her ancestry. Of all the ancient samples, contemporary to her that we can compare her to, she turns out to be genetically closest to another group who were buried in Khorasan (principally at the site of Shahr-i-Sokhta in Iran). These individuals — some of whose graves had objects that were previously known to have connections to the Indus Valley Civilisation — share a similar mixture of ancestry and are also outliers in the larger comparative database.

Much media coverage has stressed her ‘indigeneity’ and not the fact that her genetic admixture makes one rethink the social geographies which the data groups her with, which are significantly more westerly than the limits of present day India. The result makes sense when we remember that the Indus Valley Civilisation, famed for its celebrated technical virtuosity, wonderful ornaments and cosmopolitan urbanisms were not one “people” let alone presumably those of one genetic signature. Rakhigarhi is one Harappan settlement out of thousands, in one of several cultural domains known within the larger civilisation and we know that only the elite were buried in these cemeteries. This is only the first aDNA result from the Indus Valley Civilisation, and, as the authors of these studies note, we need hundreds of samples from the South Asian archaeological past to begin to understand the complexity of South Asian population genetic history. Even so, what we can assert from these results is that our ancestor from Rakhigarhi was so different from us that no one alive today has her particular suite of admixed DNA ancestry.

What does all this mean? What happened in Indian history?

It is key that we use genetics to answer questions it can answer; and not use its evidence for answers we might want for other questions. Population genetic history does open new lines of evidence into pasts, but these do not correlate easily or well with what we have long known in South Asia to be complicated, messy pasts where lines of difference and assertions of similarity were historically contested and braided time and again.

Most people today would readily accept information about their susceptibility to diabetes or cancer from their genetic data. But no matter what our political sympathies, we would hesitate to accept that genetic cleavages that happened a 100 generations ago define our actions, choices and identity today. The aDNA results reflect what we already knew in greater detail from archaeological research conducted over the last 50 years. A host of Chalcolithic (Copper-Bronze using) and Iron Age cultures prosper between 2000 and 1000 BCE in almost all regions of the subcontinent.

No single larger story of genetics, or of language families (Indo-European/Dravidian), nor of the movement of people hypothesised from either can explain the manifest geographic, technological and cultural complexities of this millennium.

We must remember genetic population history is only one line of evidence and often a very reluctant one. Linking genetics and linguistics is difficult at best, and joining either to archaeology additionally so.

Similarly, what possible pride can there be in claiming an indigenous unbroken past, when even the newest of evidence, in this case genetic, reaffirms what history and archaeology have consistently shown: that the South Asian subcontinent has never been “one people”?

Genetics can only offer slim and contestable claims about how this history moved, and the authors make a series of conjectures about differences in present day caste group genetics and their relevance for understanding Indian history.

These conjectures cannot however speak for our history, where ideologies of one-ness and high-ness have always been resisted and contested. It is indeed, these contestations of one-ness that truly define Indian history.

Mudit Trivedi is a PhD student in Archaeology and Anthropology at the University of Chicago

Has India’s moon mission been affected by the setback to the ‘Vikram’ lander?

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The story so far: Chandrayaan-2 took off from Sriharikota on July 22 to safe land the ‘Vikram’, carrying its ‘Pragyan’ rover, in a suitable high plain on the lunar surface, at a latitude of about 70º South. But soon after 1.50 a.m. on September 7, in the final minutes of the lander’s descent on its own, the Indian Space Research Organisation (ISRO) team in Bengaluru lost contact with the module.

What went wrong with the mission?

Chandrayaan-2, comprising an orbiter, a lander and a rover, journeyed from earth for eight days and reached the moon’s vicinity on August 20. On September 2, the lander riding on the orbiter was separated and got into a closer orbit around the moon, moving pole-to-pole at a distance of 35 km x 100 km.

Mission planners at ISRO had divided the last critical 15-minute parabolic descent into four smaller phases. At 1.38 a.m. IST on September 7, the lander perfectly cleared the ‘rough braking phase’, swooping down from 30 km to 7.4 km of the lunar surface in 10 minutes. Its velocity had dropped as required from 1,640 metres a second to about 400 metres a second.

It had now entered the second part, the ‘fine braking phase’ of 3 minutes, with the four throttleable motors switching off to further lower the velocity. It had to re-orient itself, take pictures of the landing site to look for hazards like slopes and rocks. The moon was just over 2 minutes and 2.1 km away. But by then, at the command headquarters in Bengaluru, the green lines on the screens showed that it had strayed from its path; mission managers said they were not receiving any signal from the lander.

Vikram had developed a problem, gone silent and had crashed at the fag end of a perfect journey, along with the stillborn rover. Some 20 minutes later, ISRO Chairman K. Sivan announced that contact had been lost with Vikram and that ISRO was piecing together its last set of data.

While the failure analysis committee reconstructs and simulates the last moments to infer the causes, theories abound about what may have caused the crash: did the thruster/s overperform? Did Vikram lose altitude and not recover, losing the earth link? Or was it some other anomaly?

However, since then, ISRO has spoken only once in the last seven days: just to say it had located the crashed Vikram and would try to reconnect with it. It must do so before the lunar night sets in around September 21, cutting off any solar power supply to the spacecraft.

Why was this mission important?

For ISRO this was the second moon mission after Chandrayaan-1 of 2008. The project, approved in 2007 and planned for 2012, had undergone a few twists, turns, delays and redesigns over the last few years. Finally in June, Dr. Sivan formally announced that it would be launched in mid-July.

Chandrayaan-1 was an orbiting mission and died just after eight months in orbit, but not before confirming the exciting presence of water molecules on the lunar surface. Chandrayaan-2 planned to take off from where its precursor left off and look intensively for water deposits from up close. It was a formidable combination of an orbiter, a lander and a robotic rover which aimed to look at the moon’s exterior, surface and interior in that order.

What were the challenges?

Dr. Sivan had repeatedly spoken of the challenges of soft landing on moon — the spacecraft had to land unharmed and intact, remain in touch with earth and do its assigned job. Of nearly 80 missions sent to moon since the early 1960s, less than 40% have succeeded. This year alone, China’s Chang’e 4 mission made the first ever landing on the far side of the moon in January and also deployed a rover. But in April, Israel’s Beresheet craft crashed on the moon.

The lunar terrain is rocky and uneven. The moon’s gravity is about 17% of the earth and the moon dust that slowly rises and falls on landing can disable sensitive instruments of a lander. Many technologies of Vikram are new: the lander and its legs, the autonomous rover, and the four throttleable motors.

What happens after this?

In the end, India did not arrive on the moon. The country had the aim of becoming the fourth member of the lunar club, after the Soviet Union, the U.S. and China. As for Chandrayaan-2, we may have heard the last of the lander and the rover. But the orbiter gliding 100 km above continues to bear the Chandrayaan-2 torch, beaming back pictures of the moon. The information it will send as it revisits the spot where Vikram lies may offer precious lessons for future planetary missions by India and other countries.

Why has the debate on its functioning, especially on the issue of transfers in the judiciary, been revived?

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The story so far: The recent controversy over the transfer of the Chief Justice of the Madras High Court, Justice Vijaya Kamlesh Tahilramani, to the Meghalaya High Court has once again brought to the fore a long-standing debate on the functioning of the ‘collegium’ of judges that makes appointments and transfers in the higher judiciary. Justice Tahilramani has submitted her resignation after her request for reconsideration of the transfer was rejected by the collegium headed by the Chief Justice of India (CJI), Ranjan Gogoi, and four senior-most judges of the Supreme Court. While sections of the Bar have questioned the transfer as well as the lack of transparency about the exact reason, the Supreme Court (SC) has issued an official statement that the collegium indeed had cogent reasons and that these could be revealed, if necessary.

How did the collegium system come into being?

The collegium of judges is the Supreme Court’s invention. It does not figure in the Constitution, which says judges of the Supreme Court and High Courts are appointed by the President and speaks of a process of consultation. In effect, it is a system under which judges are appointed by an institution comprising judges. After some judges were superseded in the appointment of the Chief Justice of India in the 1970s, and attempts made subsequently to effect a mass transfer of High Court judges across the country, there was a perception that the independence of the judiciary was under threat. This resulted in a series of cases over the years. The ‘First Judges Case’ (1981) ruled that the “consultation” with the CJI in the matter of appointments must be full and effective. However, it rejected the idea that the CJI’s opinion, albeit carrying great weight, should have primacy.

The Second Judges Case (1993) introduced the Collegium system, holding that “consultation” really meant “concurrence”. It added that it was not the CJI’s individual opinion, but an institutional opinion formed in consultation with the two senior-most judges in the Supreme Court. On a Presidential Reference for its opinion, the Supreme Court, in the Third Judges Case (1998) expanded the collegium to a five-member body, comprising the CJI and four of his senior-most colleagues.

What is the procedure followed by the collegium?

The President of India appoints the CJI and the other SC judges. As far as the CJI is concerned, the outgoing CJI recommends his successor. In practice, it has been strictly by seniority ever since the supersession controversy of the 1970s. The Union Law Minister forwards the recommendation to the Prime Minister who, in turn, advises the President. For other judges of the top court, the proposal is initiated by the CJI. The CJI consults the rest of the collegium members, as well as the senior-most judge of the court hailing from the High Court to which the recommended person belongs. The consultees must record their opinions in writing and it should form part of the file. The collegium sends the recommendation to the Law Minister, who forwards it to the Prime Minister to advise the President.

The Chief Justice of High Courts is appointed as per the policy of having Chief Justices from outside the respective States. The collegium takes the call on the elevation.

High Court judges are recommended by a collegium comprising the CJI and two senior-most judges. The proposal, however, is initiated by the Chief Justice of the High Court concerned in consultation with two senior-most colleagues. The recommendation is sent to the Chief Minister, who advises the Governor to send the proposal to the Union Law Minister.

Does the collegium recommend transfers too?

Yes, the collegium also recommends the transfer of Chief Justices and other judges. Article 222 of the Constitution provides for the transfer of a judge from one High Court to another. When a CJ is transferred, a replacement must also be simultaneously found for the High Court concerned. There can be an acting CJ in a High Court for not more than a month. In matters of transfers, the opinion of the CJI “is determinative”, and the consent of the judge concerned is not required. However, the CJI should take into account the views of the CJ of the High Court concerned and the views of one or more SC judges who are in a position to do so. All transfers must be made in the public interest, that is, “for the betterment of the administration of justice”.

What is the common criticism made against the collegium system?

Many have faulted the system, not only for its being seen as something unforeseen by the Constitution makers, but also for the way it functions. Opaqueness and a lack of transparency, and the scope for nepotism are cited often. Retired SC judge Justice Ruma Pal once said: “The mystique of the process, the small base from which the selections were made and the secrecy and confidentiality ensured that the process may on occasions, make wrong appointments and, worse still, lend itself to nepotism.” The attempt made to replace it by a ‘National Judicial Appointments Commission’ was struck down by the court in 2015 on the ground that it posed a threat to the independence of the judiciary. Dissenting judge, Justice J. Chelameswar, termed it “inherently illegal”. Even the majority opinions admitted the need for transparency. In an effort to boost transparency, the collegium’s resolutions are now posted online, but reasons are not given.

Some do not believe in full disclosure of reasons for transfers, as it may make lawyers in the destination court chary of the transferred judge. Embroilment in public controversies and having relatives practising in the same High Court could be common reasons for transfers.

In respect of appointments, there has been an acknowledgement that the “zone of consideration” must be expanded to avoid criticism that many appointees hail from families of retired judges. The status of a proposed new memorandum of procedure, to infuse greater accountability, is also unclear.

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