Saturday, December 23, 2017

Rakhigarhi news

Tony Joseph in the Hindu writes: (highlights added)
(PS: for a take on the non-news content of Tony Joseph's article, see this.)
The site was excavated and the skeletons were recovered in the beginning of 2014 by a team of archaeologists led by Vasant Shinde, Vice Chancellor of Deccan College, Pune. For the 61-year-old Shinde, this project is the culmination of a long and distinguished career in archaeology that has seen him lead excavations at important Harappan and other sites across the country. But Rakhigarhi is a project with a difference.

In the three-and-a-half years since its excavation, Professor Shinde has brought together scientists from Indian and international institutions like the Centre for Cellular and Molecular Biology, Hyderabad (CCMB), Harvard Medical School, Seoul National University, and the University of Cambridge to work on different parts of the project, including extracting and analysing DNA from these ancient people, reconstructing their faces, and studying the remains of their habitation to understand their daily habits and ways of life.

The last time Professor Shinde tried to take ancient DNA from an Indus Valley site was when he led an excavation at Farmana in 2007-2010. Farmana is also in Haryana, about 100 km away from Rakhigarhi, and the team excavated probably the largest Harappan burial site, with more than 70 burials. But that didn’t turn out well.

“One of our aims was to understand the Harappan population and we wanted to get DNA for that. So we excavated the burials and tried to extract the DNA but we failed miserably. We even got some scientists from Japan. They also failed, even though they had used some advanced techniques. Then we realised that our method was wrong, in the sense we had kept the burial site open for too long — one-and-a-half to two months, so that people could see that we were not there to dig out treasures. This is a different kind of treasure for us. A lot of people came, and contamination also happened. Then big rains came and everything got flooded. So we realised that we had done it wrongly.

What Professor Shinde and his team learned was that once the skeletons are excavated, they should be documented and packed for analysis immediately. So that is what they decided to do in Rakhigarhi, where they started excavating for skeletons. But the problems didn’t end there, as the box below {quoted below} explains. The efforts of geneticist Niraj Rai, now with the Birbal Sahni Institute of Paleosciences in Lucknow, and earlier with the CCMB, were critical to the attempt to decode the ancient DNA.
The research is expected to be published in a leading international journal in a month or so....
There is also this:

It has been known for long that the key to many puzzles of ancient human history lies in ancient DNA (aDNA). But it was only within the last eight years or so that technology advanced enough for geneticists to confidently sequence aDNA extracted out of human skeletons that are thousands or even tens of thousands of years old.

But one problem still remained: DNA preserves far better in cold climates than in warm climates and, therefore, all the early aDNA studies were done on fossils recovered from cold regions. Extracting and analysing aDNA in Africa, India or West Asia remained a formidable challenge. The science of genetics had to wait for one more leap before it could tackle this problem too. This happened sometime in 2014, when it was found that DNA taken from the inner ear region of the petrous bone could yield up to 100 times more DNA than other skeletal elements – a vital advantage, especially in poor DNA-preservation contexts. This discovery was followed by the development of new techniques to enrich the extracted DNA and filter out microbial and non-informative human DNA. These new methods were put to use first in a path-breaking study published in 2015 titled “Genomic insights into the origin of farming in the ancient Near East”, co-authored by geneticist David Reich of the Harvard Medical School.

Using these techniques required new tools and new skills, and scientist Niraj Rai, then with the CCMB and now with the Birbal Sahni Institute of Paleosciences in Lucknow, spent a few months in Harvard Medical School in 2016. Rai, who has done extensive work in population genetics, has been the leading Indian scientist directly involved in the ancient DNA analysis from Rakhigarhi and is now working on other ancient DNA samples from around the country. “The most difficult challenge was always ensuring the integrity of the DNA,” he says. “The petrous bone discovery was a turning point. Without it, this may not have been possible.”


1. The news-item from September that I posted, that the Birbal Sahni Institute is entering the aDNA game is, I suppose, explained by Dr Niraj Rai now working there.

2. The skeletons were excavated in 2014, it is now 2017; the promised publication has always been just around the corner, and has constantly receded.   I'm still dubious that they've found anything meaningful.

3. The Vasant Shinde-South Korean collaboration seems quiescent.  Previously, Tony Joseph tells us, the Vasant Shinde-Japan collaboration failed.  It seems it is now Vasant Shinde-Harvard.

4. AFAIK, Tony Joseph is no friend of the current government; if he's not pretending to know more than he does, he brings welcome news of an impending publication;  if there was anything of a suppression of results going on,  I'm sure it would have leaked to him, and I see no reason why he wouldn't write about it.  His home publication, The Hindu, is no friend of the current government either.  Further, I suppose there is no shutting up of Harvard or Cambridge possible from India (for that matter South Korea, too).  So all the conspiracy theories floating around the internet are likely bogus.

5. Cambridge University has long been conducting archaeological digs at Rakhigarhi. Their recent work I found out about weeks ago through a mention in the Hindi press; as far as Google news is a reliable reflection of India's English press, it hasn't appeared there.  The Cambridge University websites and blogs for the project mentions nothing about aDNA (as far as I could tell).  They do mention a new paleohydrography for the region (interesting stuff, with open source code made available too!)  So I suspect the mention of Cambridge University as part of the aDNA project is a bit of name-dropping.  We shall see, let the publication begin!

PS: we know that Seoul was involved in Rakhigarhi aDNA - they even had a blog; but at some point they started saying "refer all questions about Rakhigarhi aDNA to Dr. Shinde".   My uninformed  guess would be that little of value was found, and Dr. Shinde thus keeps changing the collaboration.