Parpola and the Indus script by Iravatham Mahadevan

June 20, 2010

Parpola and the Indus script by Iravatham Mahadevan

June 17, 2010

http://beta.thehindu.com/opinion/op-ed/article462079.ece

He richly deserves the honour of being the first recipient of the Classical Tamil Award instituted by the Tamil Nadu Chief Minister.

In the recent interview with Asko Parpola published in The Hindu (April 15, 2010), readers were made aware of the lasting contributions by Professor Parpola to Indological studies, especially in the field of the Indus Civilisation and its script. Having known him personally for four decades and having closely watched his great contribution to the study of the Indus script, I am in a position to amplify the information provided in the interview.

Professor Parpola’s contributions to Harappan studies are truly monumental, and these are not confined merely to the study of the Indus script. He has published a long series of brilliant papers to establish the fact of Aryan immigration into South Asia after the decline of the Indus Civilisation. As a Vedic scholar-turned-Dravidianist, he has the best academic credentials to prove that the Indus Civilisation was pre-Aryan and that its writing encoded a Dravidian language. In addition to his linguistic skills and deep scholarship of Vedic Sanskrit and the Dravidian languages, he has harnessed the computer in one of the earliest scientific attempts to study the structure of the Indus texts through computational linguistic procedures. Professor Parpola has produced the first truly scientific concordance to the Indus inscriptions. His concordance is accurate and exhaustive and has become an indispensable tool for researchers in the field.

Equally impressive, and again truly monumental, are the publications inspired and co-authored by Professor Parpola, of two volumes of the Corpus of Indus Seals and Inscriptions. These volumes reproduce in amazing clarity and detail all the Indus seals (and their newly-made impressions) and other inscriptions. I happen to know personally the enormous difficulties Professor Parpola faced in publishing these volumes, nudging and goading the slow-moving bureaucracy in India and Pakistan to make available the originals, most of which were photographed again by the expert whom Professor Parpola sent from Finland for the purpose.

He published his magnum opus in 1994, Deciphering the Indus Script. The book contains the best exposition of the Dravidian hypothesis relating to the Indus Civilisation and its writing. Even though the Indus script remains undeciphered, as Professor Parpola readily admits, his theoretical groundwork on the Dravidian character of the Indus Civilisation and the script, and the fact of Aryan immigration into India after the decline of the Indus Civilisation, have been accepted by most scholars in the world.

Most of the Early Dravidian speakers of North and Central India switched over to the dominant Indo-Aryan languages in Post-Harappan times. Speakers of Aryan languages have indistinguishably merged with speakers of Dravidian and Munda languages millennia ago, creating a composite Indian society containing elements inherited from every source. It is thus likely that the Indus art, religious motifs and craft editions survived and can be traced in Sanskrit literature from the days of the Rigveda, and also in Old Tamil traditions recorded in the Sangam poems. Professor Parpola is aware of the Harappan heritage of both Indo-Aryan and Dravidian languages, the former culturally and the latter linguistically. His profound scholarship in both families of languages enables him to mine the Indian cultural heritage holistically in his search for clues to solve the mysteries of the Indus script.

It may be asked: What has Tamil to do with the Indus script that Professor Parpola should be honoured with the inaugural Classical Tamil Award? Tamil happens to be the oldest and the best-documented Dravidian language. It is mainly for this reason that the Dravidian Etymological Dictionary of Burrow and Emeneau accords the head position to Tamil entries in the dictionary. That this distinction is well-deserved is also proved by the fact that Old Tamil contains the most archaic features of Dravidian phonology and morphology, like for example, the retention of the character aytam and the sound zh. Dravidian linguists have also established that most proto-Dravidian reconstructions are in close accord with words in Old Tamil. The earliest Tamil inscriptions date from the Mauryan Era. The earliest Tamil literature, the Sangam works, are from the early centuries of the Common Era, but record oral traditions from a much earlier time. It is for this reason that Professor Parpola and other Dravidian researchers consider Old Tamil to be a possible route to get at the language of the Indus inscriptions.

Professor Parpola speaks for himself in the following excerpt from his message of acceptance of the Classical Tamil Award. He says: “When the Chief Minister of Tamil Nadu’s award is given to me for a Dravidian solution of the Indus enigma, this award will inevitably be interpreted by many people as politically motivated. Nevertheless, I am ready to fight for the truth, and in my opinion, the Tamils are entitled to some pride for having preserved so well the linguistic heritage of the Indus Civilisation. At the same time, it must not be forgotten that though their language has shifted in the course of millennia, people of North India too are to a large extent descended from the Harappan people, and have also preserved cultural heritage of the same civilisation.”

Professor Parpola’s work on the Indus script will prove to be as important and as long-lasting as U.Ve. Swaminathaiyar’s resurrection of the Tamil Classics from decaying palm leaves. He richly deserves the honour of being the first recipient of the Classical Tamil Award instituted by the Tamil Nadu Chief Minister.

(Iravatham Mahadevan is a noted epigraphist and Tamil scholar.)

Iravatham Mahadevan and Asko Parpola have to answer many questions without mincing words, which are pointed out as follows:

1. The expression, “Vedic scholar-turned-Dravidianist” proves the change in ideology that is not good for any scholar of his stature. IM has already brought Michael Witzel, the Rig Vedic Pundit last year here in Chennai and he talked differently. Of course, IM prevented native Pundits to question nand test his Sanskrit capabilities. He was struggling to repeat few words mentioned by one of the audience.

2. That he has academic credentials “to prove that the Indus Civilisation was pre-Aryan and that its writing encoded a Dravidian language”, makes no credentials, as researchers have such qualifications and acumen in their steadfast work carried on for years. Scholars respect scholars till they are biased with other motives.

3. Even though the Indus script remains undeciphered, as Professor Parpola readily admits, his theoretical groundwork on the Dravidian character of the Indus Civilisation and the script, and the fact of Aryan immigration into India after the decline of the Indus Civilisation, have been accepted by most scholars in the world. Acceptance or non-acceptance of any hypothesis, theory etc., cannot be a criteria for coming to any final conclusion in a research plan, particularly, where the script remains undeciphered.

4.  “When the Chief Minister of Tamil Nadu’s award is given to me for a Dravidian solution of the Indus enigma, this award will inevitably be interpreted by many people as politically motivated”. Definitely, because, he has been known for his extremist views, racist bias and linguistic fanaficism and all couched with anti-Hindu, anti-Sanskrit, anti-Hindi, anti-north, anti-Brahmin and so on. Moreover, award for Dravidian solution of the Indus enigma, reminds the the world war period, where the racists scholars used to be honoured in the same way by the racisr regimes, because any other solution means no award!

5. Nevertheless, I am ready to fight for the truth, and in my opinion, the Tamils are entitled to some pride for having preserved so well the linguistic heritage of the Indus Civilisation”. Why some pride, they have “full / more” pride, whether they preserve or not the linguistic heritage of the Indus civilization. In fact, the queation is whether the Indus cicilization had any preserved linguistic heritage f the Tamils conclusively, instead of taking few seals and giving convenient interpretation.

6. At the same time, it must not be forgotten that though their language has shifted in the course of millennia, people of North India too are to a large extent descended from the Harappan people, and have also preserved cultural heritage of the same civilisation.” Had both people descended from the same lineage, where is the question of linguistic heritage preserved by one group of people and cukltural heritage by other group? His theory that “Aryan immigration into India after the decline of the Indus Civilisation” shows after the decline of the Indus civilization, the Dravidians moved to north and then canme down to south. Aryans came thereafter and moved in the same way.

7. When Aryans immigrated after the decline of Indus-Dravidian civilization, there was no “Aryan invasion”. Karunanidhi would not accept such academic exercise.

8 . The time gap between the two historical processes has to be specified and explained. The peak period of IVC has been c.2250-1950 BCE. The Sangam period starts from c.300 BCE.  Why then, the “Dravidian speaking people” took nearly two millinea to shift from IVC to north and north to South?

9. Why they should have taken such a long period to compose Sangam literature only at Tamizhagam insyead of IVC or north India? It is also surprising that they could not develop any script during those 2000 years!

10.  The earliest Tamil inscriptions date from the Mauryan Era. That Asoka should copy from the Persians and start indscribing on the stones so that Indians could read at different paerts of India in the same language or in their languages! And the intelligent Dravidian speaking people / immigrant Tamils from the IVC should wait for Asoka and start cpying his script to write in Tamil only from that particular period!

11.  As the IV Dravidian speakers had been the expert makrers of the seals, why they should wait for 2000 years to copy script from Asoka?  Does it make sound?

12.  Asoka and even Kharavela, whose territories were threatened with the “confederation of Dravidian kings” could write many lines, how is that the Dravidian speaking people could leave only few-line inscriptions, broken ones etc?

Vedaprakash

20-06-2010

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War of words in the cradle of south Asian civilisation!

May 14, 2010

War of words in the cradle of south Asian civilisation

In the heart of Pakistan, the ruins of a 4,000-year-old city have spawned a cross-continental row about language, culture – and racism in academia, By Andrew Buncombe, Thursday, 25 March 2010

http://www.independent.co.uk/news/world/asia/war-of-words-in-the-cradle-of-south-asian-civilisation-1927005.html

Curator Mohammed Hassan
ANDREW BUNCOMBECurator Mohammed Hassan

At the quiet ruins of Harappa, one of the two main centres of an ancient civilisation that once spread from the Himalayas to Mumbai, Naveed Ahmed took in the arid hills dotted with thorn-bush. “I think the people who lived here were very different from us,” said the part-time guide. “The stones and the beads [they made]; it was as if they were more sophisticated.”

However peaceful this ruined city of the Indus civilisation may appear, the former residents of Harappa and the remnants of their society are today at the centre of one of the most acrimonious disputes in academia, a controversy that has allegedly led to death threats and claims of racism and cultural chauvinism.

Many experts in south Asia and elsewhere believe that symbols and marks inscribed on seals and other artefacts found here represent an as yet undeciphered language. Arguing it may be the predecessor of one of several contemporary south Asian argots, these experts say it is proof of a literate Indian society that existed more than 4,000 years ago.

But other experts based in the West say although the symbols may contain information, they are not a true language. They claim the judgement of their counterparts in south Asia may be swayed by regional nationalism.

Mohammed Hassan is curator of the museum beside the dust-blown ruins. Before leading a tour, the government official served tea and biscuits in his office and insisted the people of Harappa must have possessed a written language to store information. “If they were not literate, then how could they do so many things?” he said. “They had well-made pottery, big cities that were well-planned. They had a lot of knowledge about these things. They grew cotton, wheat, rice and barley. They traded with other cities.”

The Indus civilisation covered more than 500,000 square miles and lasted, during what experts term its “mature phase”, from 2,600 till 1900 BCE. The ruins, 100 miles south-west of the Pakistani city Lahore, the ruins were rediscovered in the early part of the 19th century.

The skills of its residents – at least in terms of making bricks that could endure centuries – were revealed by two British engineers, John and William Brunton, who were building the East Indian Railway Company line to connect Lahore and Karachi and needed ballast for their track. The engineers later wrote that locals told them of well-made bricks from an ancient ruined city that the villagers had made use of. With little concern for preserving the ruins, huge numbers of the Indus-era bricks were reduced to rubble and used to support the tracks heading west.

In the early 20th century, excavation of Harappa proceeded along with that of the other Indus city at Mohenjo-daro, in the south of Pakistan, and it was at that time many of the seals now on display in Mr Hassan’s museum containing symbols and images of animals were discovered. And they have continued to beguile, fascinate and frustrate scientists, causing a running controversy that has played out on internet message boards, scientific papers and at academic conferences.

Like Mr Hassan, Iravatham Mahadevan, an expert in epigraphy from southern India who has been awarded the country’s highest civilian award for his work, has no doubts the symbols on the Indus seals represent a genuine language. “Archaeological evidence makes it inconceivable that such a large, well-administered, and sophisticated trading society could have functioned without effective long-distance communication, which could have been provided only by writing,” he wrote last year in a magazine.

“And there is absolutely no reason to presume otherwise,considering that thousands of objects, including seals, copper tablets, and pottery bear inscriptions in the same script throughout the Indus region. The script may not have been deciphered but that is no valid reason to deny its very existence.”

Mr Mahadevan believes the Indus script may have been a forerunner of so-called Dravidian languages, such as Tamil, spoken today in southern India and Sri Lanka. In addition to technical clues, he says the continued existence of a Dravidian language in modern Pakistan – Brahvi, which is spoken by people in parts of Balochistan – supports his idea.

Over the years, there have been plenty of other theories both from established experts and enthusiastic amateurs. Some, with the backing of Hindu nationalists, have claimed the script may be an early Indo-European language and that remnants of it may even exist in Sanskrit, an ancient language that is the root of many present languages in north India, including Hindi. It has even been claimed the Indus script belonged to metalsmiths, and others believe it died out with the city of Harappa itself and gave rise to no successor.

Part of the problem for the experts is that, unlike for those who cracked the hieroglyphics of Egypt, there is no equivalent of the Rosetta stone, the slab of granite-like rock discovered in 1799 that contained Egyptian and Greek text. In the 1950s, academic interest in Mayan hieroglyphics intensified when experts began to study modern spoken Mayan, but for the Indus scholars there is no agreement on which, if any, modern language is the successor to their script.

In 2004, the debate was jolted into a war of words after three American scholars claimed the Indus symbols were not a language at all. In a paper provocatively subtitled The Myth of a Literate Harappan Civilisation, they said there was insufficient evidence that the symbols constituted a proper language. They pointed to various factors: that there was no single long piece of text; that there was disagreement over the number of actual symbols and that other well-organised societies had been illiterate. The symbols, they argued, may well contain information in the same way that an image of a knife and fork together might represent a roadside eatery but they were not a language that could record speech.

The ensuing uproar came mainly from south Asians. One of the American scholars, Steve Farmer claimed people would approach him in tears after he gave talks and that he had even had death threats. Comments on internet discussion boards accuse him and his colleagues of trying to prove that “non-Western cultures were less advanced”. Mr Farmer, who lives in California, said he believed much of the anger was driven by those wishing to promote pet theories about Dravidians, indigenous Aryan Hindus or “the general man in the street who wants to think ancient India was of the same order as Egypt or Mesopotamia. It’s total rubbish”. He added: “I have never seen anything like the passion that there is in India. There is not that sort of passion in the Middle East about ancient things.”

More recently, the Indus controversy has been joined by a team of Indian scientists who ran computer programmes which led them to conclude the symbols almost certainly constitute a language. Central to their claims, published last year in Science, was the theory of “conditional entropy”, or the measure of randomness in any sequence. Because of linguistic rules – such as in English the letter Q is almost always followed by a U – in natural languages the degree of randomness is less than in artificial languages.

One of the authors, Rajesh Rao, who was born in Hyderabad but is now based at the University of Washington, became fascinated by the Indus culture after studying it at school. His team measured the randomness with which the individual Indus symbols appeared on seals and compared that to the randomness of several natural and artificial languages. Mr Rao said it was closest to a natural language. “The Indus civilisation was larger than the ancient Egyptian, Chinese, and Mesopotamian civilisations and the most advanced in terms of urban planning and trade,” he said. “Yet we know little about their leaders, their beliefs, their way of life, and the way their society was organised. Many of us hope that decoding the script will provide a new voice to the Indus people.”

Yet as soon as Mr Rao’s team published its findings, Mr Farmer and his colleagues hit back, denouncing their conclusions and methodology. Mr Rao, whose team has since issued a detailed defence of their theory, said he was surprised at the level of contention, within south Asia and beyond, but also at some of the comments he claims Mr Farmer’s group levelled at him.

So whether the Indus is a script with hidden meanings may never be deciphered. Naveed Ahmed, a 24-year-old part-time guide, whose family has lived “forever” in a village on the edge of the ruins speaks Punjabi, an Indo-Aryan language from the same family as Sanskrit. Was it possible a linguistic thread connected the language he used with what had been spoken – and possibly written – by the people who once occupied the ruined city? “I don’t know if it is the same,” he said. “But it’s a possibility that our language came from them. It is always a possibility.”

Why Michael Witzels, Steve Farmers, Karunanidhis are so worried about IVC?

April 20, 2010

Why Michael Witzels, Steve Farmers, Karunanidhis are so worried about IVC?

If the scholars are genuinely interested in researching and presenting facts without any bias, such type of presentation could be understood by even common man by going through.

But when a certain pattern with bias, prejudice, pre-determined attack on one particular linguistic or religious group counched under the so-called not following racism, racialism etc., then there is a reason to doubt their credentials whether they are Indian, Indian born or non-Indan, European or American categories.

Therefore, the changing stands of the scholars also worry common men, as their views are picked up by the ideologically biased journalists and politicians to interprete and propagate according to their viewpoint. Here only Karunanidhi comes. He never bothered when Asko Parpola visited Madras / Chennai about 100 times. It is not known as to whether he has ever met him and discussed. In 1990s, he said that the whole affairs of fighting with each other etc., were Aryan issues! Rama and Krishna were black and Kshtriyas……………and so on! Or his friend Iravatham Mahadevan used his good offices to make him meet.

However, now he has been chosen for the award!

In deed, it should have been given to Michael wizel or Steve Farmer appropriately, as they have done excellent work. not only that, Michael could come right inside the so-called “Aryan-bastion”, the much hated “Parppaniya den” – Sanskrit College and declared that he had developed some skills to read and understand Rifvedic verses. However, he could not pronouce “Indrasul, Mitrasil,Nasatya…….”, as his tingue was not co-operating!

However, his humour has been phenomenal and epigenetic!

Kindly have more fun, dear friends cheers!

With due acknowledgments to Sanskrit Professor!

Steve wrote:

>>It is tedious to keep going over these materials, but if it’s one
thing
we’ve learned over the years, it is that these people *only* win if you
don’t stand up to them. When you do, ignoring the smears and just
giving the facts, their plans crumble.

>> Michael will have more on Rajaram’s Hindutva Love Fest at U. Mass
Dartmouth later today or tomorrow, I believe.

Indeed, I went down to Dartmouth, MA, to take a look at the
“Symposium on Aryan/Non-Aryan Origin of Indian Civilization.”

The Aryan invasion of India is a 19th c. theory that no serious
scholar today takes seriously, but that plays a great role in current
Indian and NRI (Indian immigrant) politics in the US (as we have seen
in California recently).

Scholarly speaking, what is to be explained is the introduction into
South Asia of an Indo-European language (Vedic Sanskrit), of
Indo-Iranian poetry, poetics and religion, as well as some of the Vedic
material culture (horses, chariots, etc.) This is fervently denied by
Hindutvavadins as the cannot allow that a central part of their culture
that continues until today has come from the outside. In their eyes,
this would threaten the supposedly indigenous character of the (North)
Indian Vedic civilization, and thus, much of the roots of later
Hinduism.

I went to Dartmouth as to take a stand in what promised to be a
Hindutva-centered meeting that was to propound the victory against the
so-called “Aryan invasion theory”.
Also, as not to leave our archeologist and geneticist colleagues alone,
exposed to severe doses of Hindutva and being unwittingly co-opted, as
has happened before (such as in the Long Beach conference some 3 years
ago).

People were flown in from as far as Europe and India to attend the
“symposium”. Clearly, some major funding is behind this effort “to
settle the theory of an Aryan Invasion” at c. 1500 BCE.

This so-called symposium was fun, if you can savor the nutty “theories”
these people propound. There were just a few exceptions among the
speakers from the Hindutva mindset (see list below):

* P. Eltsov, a young archeologist (PhD Harvard, now at Berlin) who gave
a grand view of indian civilization based on indigenous ideas of the
development of culture, from texts such as the Puranas (that have never
been used for that purpose).

* P. Underhill, well known Stanford geneticist, gave an overview of Y
chromosome studies relating to India (see below for details).

* V. K. Kashyap, of the National Institute of Biologicals at New Delhi,
gave a serious genetic paper (overview of recent mtDNA and NRY
studies related to India), but unfortunately his conclusions were again
quite Hindutva-like (see below)

* Makarand Paranjpe, (JL Nehru U., Delhi) gave a macro-civilizational,
post-colonialist speech, clearly inspired by measured nationalism . It
was a plea for the decolonizing of the Indian mind (now 50 years after
independence!), but he is not of a Hindutva mindset.

* Dr. Asiananda, Intercultural Open University, Netherlands, gave a
Blavatsky-inspired talk, free from Hindutva. Instead, he actually
quoted Parpola and Witzel with approval (what a combination!). He
proposed a grand scheme of ‘megacycles’ in history: the pre-vedic,
postvedic and transvedic civilization, into which we enter now,
supposedly: the beginning of a new Axial Age: a great Asian peace zone
expanding world wide. Sure. Just ask the emerging new powers in Asia
and South America.

As the last few cases show, the meeting was as nutty as expected. A few
characterizations about the hard core Hindutva characters and their
camp followers.

N. S. RAJARAM
was stuck, as is usual with him, in the 19th century (Max Mueller),
though now (after having posed a historian Indologist for the past 15
years) he wants to be a scientist again, using modern science to
explain the Vedic age.

He gave his usual erroneous overview of the word aarya in the Rigveda,
underlining that aarya does not mean a ‘race’ but just is cultural term
(as long explained, unbeknownst to him, by Kuiper, 1955), that and
means ‘noble’ (which is wrong as Thieme has shown long ago). He also
denies that the Aarya distinguished themselves from others in the RV
(again untrue) and maintained that seeing Arya a “race” was a product
of European thought and was necessary for German nationalism in the
19th c. and unification in 1870/71. (Well, ask Bismarck whether he ever
read the Vedas or studied comparative linguistics).

Of course, Dr. R. is unaware of the fact that arya, aarya – he
mentions only aarya– in the RV means something else, (probably
‘hospitable’, i.e. “us’) and he is unaware of the seminal study of the
term by Thieme ( Der Fremdling im Rigveda. Leipzig 1938; Mitra and
Aryaman. New Haven 1957; JAOS 80, 1960, 301-17 the latter two in
English).

Once again, he expressed his nonacceptance of comparative historical
linguistics, which “would not exist without Sanskrit”. A typical
Indo-centric view, that neglects that other language families were
discovered earlier than the Indo-European one, and that the
establishment of IE ling. could have proceeded without the knowledge
of Sanskrit: it merely was facilitated by Skt as the constituent
elements of words (root, stem suffix, endings) are a little clearer
their than, say in Greek or Latin.

In short, historical and technical ignorance, which characterized all
of his writings of the past 15 years. (He cannot even get the
intellectual history of the 19th c., right as he depends on secondary
and tertiary sources).

Then, he cherry-picked from other sciences, such as genetics (“which
shows that there was no recent immigration into India!” — see below),
archaeology, etc. Again, without clear understanding of the procedure
of these sciences and the way some of their “results’ are arrived at,
by speculation. Thus, when he talks about the connection between the
Harappan civilization and the Veda (“by one group of people”), he
cherry-picks some similarities and neglects the fundamental differences
between the city civilization of the Harappans and the (largely)
pastoral, semi-nomadic Rgvedic culture.

All of this as to show that a “paradigm change” in understanding early
Indian history is underway. Well, just in his own mind and that of his
camp followers. (I will not go into details here. I have discussed all
of this madness of alleged paradigm change in along and tedious
fashion in EJVS 2001)

Instead, as he has now noticed that the Rigveda represents a maritime
civilization (see below, BB Lal’s talk), he wants to move on and study
the connections between Harappan and Rgvedic civilization on the one
hand, and the S.E. Asian (such as Cambodia) ones on the other. He is
clearly inspired by the popular books of S. Oppenheimer, and his failed
“paradise in the east”, based on the Toba explosion of c. 75,000 BCE
(ironically when Homo Sap., sap. had not yet left Africa).

Focusing, like Oppenheimer, on SE Asia Rajaram attributes, against
recent botanical data, the origin of rice agriculture to the Cambodian
Tonle Sap area some 12 kya ago, thus at 10,000 BCE. But we know that
domesticated oryza japonica originated in S. China and oryza indica in
the eastern parts of N. Indian plains, all quite a few millennia later
than 12 Kya.

Obviously I opposed these points in the discussion period (as mentioned
above) and ironically encouraged him to get all departments of
linguistics abolished world wide….

(By the way, no words by Rajaram about his proposed 2nd vol. of
“translations” of the Indus signs. Unfortunately, I forgot to ask him
about it. What a pity!)

S. BAJPAI

This former, rather unproductive Prof. of history at the CA State
University (Northridge) was very active in the long ranging CA
schoolbook debate that he “won” — of course, only in his mind. He
wanted to show that the theory of an “Aryan” invasion or even influx
into India was just a myth, and that the Vedic and Harappan (Indus)
civilizations were connected: by identifying the area of the Seven
Rivers (Sapta Sindhavah), the Sarasvati River, and the epicenter of
Rgvedic culture.

In doing so, he did not repeat what specialists have known for long,
that the 7 rivers define the greater Panjab area, but he propounded the
strange idea that the western Panjab rivers (Jhelum, Indus etc.) were
excluded… Note that this “result” excludes much of Pakistan and E.
Afghanistan (whose rivers are of course clearly mentioned in the text)

As for the Sarasvati, he tried to show that this is a “mighty” river in
Haryana State (northwest of Delhi), again something well known to
specialists. He propounded the typical Hindutva theory that this river
flowed from the mountains (Himalaya) to the ocean (samudra), neglecting
the studies of K. Klaus (in the Eighties) that showed that samudra
means many things in the Veda, including lakes. Thus, he overlooked the
point that the Sarasvati (Sarsuti)-Ghaggar-Hakra river ended in a delta
and in terminal lakes in the Cholistan/Ft.Derawar area in Pakistan,
well east of the Indus. He also overlooked the recent studies by two
Indian and two German geologists who have pointed out (Current science
2004) that the “great river” of the Harappan and Vedic period could
not have been so large anymore as its area does not show mineral
deposits of Himalayan glaciers. This renders a perennial glacier-fed
river into a smaller, monsoon fed one that could not fill the 10 km
wide river bed of former times.

Hindutvavadins need the big river, that they say dried up in c. 2000
BCE, as they want to make it the center of the Harappan Civilization,
that they call the Sindhu (Indus) –Sarasvati civilization. (But, it
has been shown by R. Mughal in 1977 that this drying up happened in
stages, with several reversals. Not mentioned of course).

Bajpai had the great idea (not substantiated by historical leveling of
the RV) that the original Sapta Sindhu region was in the Sarasvati
area, (called “the best place on earth” in RV 3 ) and that the concept
was later expanded to include areas west and east of it. Strange that
the Avesta also has it (Videvdad), but Avestan was never mentioned by
this Indocentric person (who told me during a CA meeting that he is not
interested in materials from outside India). Nor was any attention
paid to the fact that RV 3 is a book that deals with the victorious
Bharata tribe, who settled in the Sarasvati area and naturally praised
this river to the skies… Such is the lack of background and scholarly
sense of this great historian.

His conclusion was that the Rigvedic civilization and the Harappan one
overlapped in one geographical area and also in time, as the RV “must
be older than 2000 BCE” since it still mentions the great Sarasvati
flowing to the ocean.

In sum, he now wants to reconstitute the history of the Harappan and
Vedic times: “the myth and baggage” of the Aryans as coming from the
outside must be given up. In the question period, BB. Lal (see below)
honed in on this erroneous idea that must be discarded, and Rajaram
added that scholars now need to take one more step: join archeological
and literary evidence (as if we and others had not done that, for
example at Toronto 1990 (Erdosy 1995) and in the yearly Harvard Round
Tables (since 1999).

Again, it became clear how narrow, Indocentric and uniformed the
Hindutva proponents are and how much they lack proper information on
past studies. P. Eltsov and I criticized some of the points mentioned
above. Time however always was too short during the meeting to go into
any detailed discussion of the many points mentioned, so I had to pick
and choose among some obviously inane proposals and the lack of
information and vision.

B.B. Lal

Lal is the former Dir. Gen. of the Indian archaeological service. At
that time, he has done some very good work, though he has published
little of it and is doing so only now, after severe public criticism in
India some 2 years ago.

However, after his retirement he became religious and Hindutva-like. I
still must make a streaming video of interviews he gave in 1985 to a
Japanese TV crew about his digs that were meant to follow the footsteps
of the (god!) Rama , from Ayodhya southwards across the Ganges and
beyond… Maybe I can do so this summer.
Lal too propounds the identity of the Vedic and Harappan civilizations.

Anyhow, he also billed himself as a Sanskritist this time — but he
has never heard that Vedic Sanskrit is as different from the commonly
taught Classical one as Homeric Greek is different from Classical
Greek. Consequently, he made serious mistakes in his long discussion
of Rgvedic culture.

After blaming Max Mueller and M. Wheeler as originators of the Aryan
theory, and rejecting the old explanation that the invading Aryans had
driven the Dravidians southwards, he stressed the continuity of the
Harappan and Vedic cultures, and went on a textual spree:

If the Aryan Invasion theory was right, then how come that among
Rigvedic place names there are no Dravidian ones? (He never mentioned
the fact that many words have a third language origin, loans from a
prefixing, Austro-Asiatic like language). He then talked about plants
and animals as typical Indian (forgetting about temperate climate IE
words such as those for the wolf, otter, beaver, willow, oak, etc.),
and merely mentioned that the birch tree (another IE word) is not
found in the RV (it of course occurs prominently in post-RV texts, with
derivates to this day…)

Next came M. Witzel’s “abortive attempt” to find the immigration in a
Sutra text. The passage in question (BS’S 18) has found various
interpretations, and Lal, as a non-specialist, was of course not aware
of the fact that the Brahmana-like texts play with popular etymologies:
in case that of “going, moving” (I, ay) and staying at home (amaa vas),
which is found in the tribal names involved (Ayu, Amavasu), which I
had to point out to him. His summary, predicable again, was: no Aryan
invasion.

Next a discussion some terracotta “spoked wheels” in Harappan layers:
remember we need horses and chariots in pre-RV times! (An Indian
archaeologist had described them to me recently as spindle whirls,
confirming my own interpretation).

As expected he also found horses in archeology (figurines and the
Surkotada skeleton). I had to point out to him that the horse is a
steppe animal that was introduced into the near East and S. Asia only
around 2000 BCE, and that only by finding the phalanges of equids one
can decide whether we deal with a donkey, a horse or a half-ass
(onager, hemione) skeleton. Onagers still are found in the Rann of
Cutch.

Further a discussion of pur ”fort”, and sea trade with 100-oared boats.
As an archeologist, he had never heard that 100, 1000 are commonly used
as ‘many’ in Vedic texts and anyhow, the boat in question is a
mythological one, not one of human traders.

He also saw great rulers in the RV, just because samraat means
‘emperor’, in post-Vedic texts., Again philological failure. And so on
and so forth.

Finally, the Sarasvati again, drying up at 2000 BCE. Thus the RV must
be dated before that event. Indeed, Haryana settlements (the center of
RV culture, see above) go back to excavations showing a date of 6431
BCE (!) And genetics were thrown in for good measure (Sahoo 2006)

In sum, though the RV occupied only the northwest of the subcontinent,
it “overlaps in time and area with the Harappan civilianization”.

It is surprising how an established archaeologist can be so naïve, in
his old age, about facts from outside his field (palaeontology,
genetics, texts, linguistics) and still loudly proclaim his
‘revolutionary’ result (also in his latest book “The Sarasvati flows
on”.) I felt sorry for him that I had to point this out, but since he
is a well respected authority, it had to be done.

N. KAZANAS

Kazanas is the head of a new age-like institution in Athens (Greece).
He has studied some Sanskrit way back in Britain, and has joined the
anti-Migration bandwagon in recent years.

Interestingly, his talk put the RV not at 2000 BCE but at 3000 BCE and
earlier, but he still made the same assertion of a link between the
Harappan and Vedic civilization.

No problem: he has spoked wheels in an Indus sign where a man stands
above to ‘spoked’ circles; he has “plenty” horses in India, since
17,000 BCE (but, the Sivalik horse disappeared, like its American
relatives, in the megafaunal extinction around 10,000 BCE), all of
which fits the RV evidence of horses and chariots.

However, as indicated, he has the RV well before the Indus civ. : thus,
istaka ‘brick” is not found in the RV (never mind that it also is found
in Avestan and Tocharian, an old BMAC loan); pur does not mean fort or
town (W. Rau has shown in the Seventies that it means exactly that:
‘fort’); Rgvedic people were oceangoing; the RV has no fixed, built up
altars like the (supposed) Harappan ones at Kalibangan (well, what
about, e.g., RV 2.3.7 with 3 ‘ backs/hills’ for the 3 sacred fires?);
and echoing Sethna, the word for cotton is found only in the late Vedic
Sutra, while it has been found in the Indus civ.

His simpl(istic) summary: the RV must be older than the Harappan civ.

He also believes that many ideas and myths of the RV have been
forgotten after 3000 BCE, that the genealogies (which ALWAYS are
subject to expansion and contraction) found in the Brhadaranyaka
Upanishad add up to a Vedic period of some 900 years; that Achar’s
calculation of the date of the Mahabharata at 3067 (see below) shows
the age of Indian civ..

Then, that the mighty Sarasvati (see above) leads to a period of 3200
or 3800 BCE, his time of the RV (never mind the other Hindutva dates
given above). Additionally, saras in Saras-vati does not mean a lake
but the root sr means to ‘rush’. Well, Mayrhofer’s etymological
dictionary (which he quoted!) lists saras itself and links it with a
different root, as seen in Greek helos ‘swamp,’ which he –as a Greek–
did not mention. (See my discussion of his ideas in JIES 31, (2003),
107-185).

Finally, the “full agreement of “all archeologist’’ in not accepting an
Aryan invasion as there “never can be any peaceful immigration” Huh?
Which was “possible only thorough conquest by nomadic horse riding
barbarians.”

In sum, the usual omnium gatherum of disjointed elements that all can
be disputed (as I did of course), point by point.

Simply put: horses and chariots in South Asia at 3500 BCE (before they
actually appear, after 2000 BCE)?

N. ACHAR

N. Achar gave another version of his paper (already widely distributed
on the net) that dates the Mahabharata tale to 3067 BCE, based on
the description of the movement of some planets, some eclipses, etc.
If we were to take these descriptions (found in post-Vedic,
non-standard Epic Sanskrit) as a given, the (unanswered) question would
arise: how this knowledge would have been transmitted, from its form in
the Harappan language, to Vedic and post-Vedic Sanskrit, in an ever
changing medium like the epic.

Anyhow: what would the Mahabharata be without horses and chariots (at
3067 BCE??)

In discussion, he maintained his belief that the astronomical data are
based on actual observation and somehow made it into our present
version of the Mahabharata (compiled probably only around 100 BCE.!)

Y. “Rani” ROSSER

She was, in a certain way, the most amusing highlight of the meeting.
Talking at high volume, shouting at times, she complained about the
state of schoolbooks with regard to the ‘debunked Aryan Invasion
Theory’ and that the ‘paradigm shift’ away from it does not appear in
American schoolbooks or in Summer school-like meetings that inform US
high school teachers. She has started a project collecting statements
about various scholars about the theory.

More amusingly, she took pot shots at me three or four times, laced
with faulty memory and confabulation as well as plainly wrong
information, and including even personal items. As it turned out later
she was confusing my website (where she does not figure) with that of
a second generation India group on the web (IPAC). I had to tell her “
first read, then speak…” several times.

Not satisfied with this, she accosted me in the break period, loudly
calling me, quote, “an asshole” (twice) . So much spiritualism for this
sari-clad, self-professed Ganesha worshipper.

(Others had contended themselves with complaints that I had not
answered their email (Kazanas), etc., or that I had not taken up their
invitation to speak at the meeting. Why should I legitimize them in
doing so? — After all his slander & libeling, Rajaram did not say
anything about me, of course not about his role in CA, but I
confronted him, and told him what I think of his defamation and
libeling since December. And too bad that Harvard did not buy his
libeling. No answer.).

Some such amusement apart, Rani Rosser clearly is very angry that I
disturbed her nicely planned scheme to saffronize CA schoolbooks (she
was involved in the planning and writing of the edits), and that I had
shown her ignorance on another list some 5 years ago. Another
Rajaram-like “forget me not” case.

Finally coming to some actual science:

P. UNDERHILL

Is a geneticist at Stanford U., and participant in our yearly Round
Tables. He gave an overview of the genetic data presently known for
India. It was loaded with caveats about what genetics can say about
ancient populations and how limited our knowledge actually is at this
moment. (Interestingly, Rajaram often interrupted and asked follow up
questions, as he now fancies himself as budding population geneticist).

Underhill stressed the fact that we have little ancient DNA, and use
modern one as proxy material that is supposed to indicate actual
historical events. Second, that there is no direct connection between
genes, language and archaeology. Third, that different population
histories can create the same genetic landscape, that certain
demographic events may be hidden, and that late arrivals [such as the
Aryans] may not be easily detectable.
Fourth, that there always is the possibility that results of genetics
are cherry-picked to suit political desires (a clear hint of Hindutva
efforts), but that good science always is self-correcting.

He then proceeded to give some details of the Y chromosome landscape of
South Asia, pointing out some haplogroups that arose in India and
others that came for the outside.

Of special interest is R1a1-M17 (which he discovered in 1995) and that
has often been attributed to the spread of Indo-European (while
Hindutvavadins let it originate in India). That is a gross
simplification. According to him, it probably arose in the area around
the Hindukush around 10,000 BC (+/- 3000 years), and spread eastwards
and westwards. It has the largest impact on S. Asia (some 25%), but is
found from E. Europe to India.
However, its resolution, that means as subgroups of M17, still are too
inadequate, so that nothing specific can be said about a possible
(re-)introduction of a variety of M17 into S. Asia [along with the
Aryans].

He re-asserted this in the discussion, when BB Lal wanted to know more
about the chronology of this haplogroup. I also brought up the lack of
genetic resolution for any recent movements of people such as Aryans,
Turkic Muslims and British, as the error bar still is 3000 years for
events around 1000 BCE and later. He affirmed this, taking the wind
out of the sails of those who had used the Sengupta/Sahoo papers
(2005,2006) that dealt with events around 10,000 kya, as to refute an
Aryan invasion. I also brought up the Kivisild paper of 1999 that has
been used in the CA debate to show that “genetics had refuted an Aryan
migration” — well, at 60,000 BCE, not at the likely date of 1500 BCE.

One can only hope that this and other ridiculous statements will now
disappear. Not easily, though, see the following:

V. K. KASHYAP

Kashyap is a DNA specialist at a national institute in Delhi. He gave
an even more detailed, valuable overview of the Indian genetic
landscape based on his project of studying 415 Indian populations.
However, some strange features appeared in his talk:
Dravidian at 50,700 kya
Austroasiatic at “??”
Tibeto-Burmese at 8-10 kya
Aryan at 3.5 to 5,.5 kya.
Dravidian at 50, 000? At that time, not even the hypothetical Nostratic
ancestor language had developed, not to speak of its daughter families,
such as IE, Dravidian, etc,

He then quoted some genetic papers with pro and contra for an Aryan
migration from Central Asia, and proceeded to Sahoo (2006) and his own
study: with similar results as those in Underhill’s. So far so good.

However the local atmosphere must have shaped his actual interpretation
of the data. For, he used them to show that there are [currently, I
add] no data for an Aryan Immigration and that the Aryan gene pool is
a myth.

In the discussion, Underhill intervened and stressed again that his
agrees with Kashyap’s genetic data. But that he hesitated to put a
specific origin on some of them, such as M17-R1a1 [which Hindutvavadins
have used for an Out of India theory of IE – at 10 kya ! ]. M17
could just as easily have arisen on the Iranian plateau and then have
moved into India, just as other lineages did. The lack of informative
sub-haplogroups makes it impossible to say anything more.

In sum: genetics has nothing to say yet about the Aryan migration. Too
bad for the Rajaram’s of this world.

(Kak did not come; nor was our old favorite, Dr. K, present nor his
buddy, the budding self-appointed linguist Kelkar who lives close by in
the Boston area).

(I skipped the other sessions, such as the one on the Indian family
system — which, I hear, was just as nutty, apparently inspired by the
fear of loosing the joint family system and the Indian “racial”
identity when NRI children are intermarrying with Non-NRIs left and
right. And I skipped the “Workshop on Indian Civilization”, apparently
used for planning Hindutva style college text books,– which would have
been even a greater loss of time and energy).

In the summary session, I stressed again that the “Aryan Invasion
Theory” is dead and gone, it is a 19th c. theory. But, not to be
misquoted, that they still have to explain how a temperate climate
Indo-European language got into the subcontinent (and Iran), along with
its poetics, religion and rituals. That they finally must learn some
linguistics and philology, and explain their facts. Just to cherry-pick
and cut and paste the interpretations of the various sciences does not
do.

In sum, as expected, another event that brought out Hindutva goals and
methods. A loss of time, sure, but these guys had to be confronted…

Cheers, M.W.

PS:
Here the official list which does not quite reflect the actual list of
speakers, as give above.
————————————————————————
———-
Symposium on Aryan/Non-Aryan Origin of Indian Civilization

Session I Chair: Vanita Shastri

4:00 PM – Dr. Petr Eltsov, Deutches Archaeologische Institut, Germany-
From Harappa to Hastinapura: A study of the earliest South City and
civilization from the point of view of archaeology and ancient Indian
literature
4:45 PM – Dr. N. S. Rajaram, Indologist – The Aryan Myth In Perspective
-History, Science and Politics
5:30 PM – Dr. Asiananda, Intercultural Open University, Netherlands –
Situating Aryan/Non-Aryan Origins of Indian Civilization within a
Mega-cyclical View of Indian History
6:15 PM – Dr. Shiva Bajpai, California State University, Northridge –
Epicenter and Ecumene of the Rigvedic Aryans

Saturday June 24, 2006

Session II Chair: S. S. Chakravarti

7:30 AM – Registration and continental breakfast

8:30 AM – Dr. B. B. Lal, former Director General, Archeological Survey
of India – An Ostrich-Like Attitude Is Perpetuating -The ‘Aryan
Invasion’ Myth?
9:15 AM – Dr. Nicholas Kazanas, Omilos Meleton, Athens – Dating the
Rigveda and Indigenism
10:00 AM – Dr. Subhash Kak, Louisiana State University – Vedic
Astronomy and the Aryan Problem

10:45 AM – Break

Session III Chair: C. M. Bhandari

11: 00 AM – Dr. Yvette Rosser, UMass Dartmouth – Aryans and Ancestral
Angst.
11:45 AM – Dr. Peter Underhill, Stanford University – Patterns of
Y-chromosome diversity in the contemporary South Asian gene pool
12:30 PM – Dr. V. K. Kashyap, National Institute of Biologicals, New
Delhi, India – Aryan Gene Pool in India- Reality or Myth; Evidences
Revisited

1:15 PM – Lunch

2:15 PM – Dr. Makarand Paranjape, Jawaharlal Nehru University –
Symposium Roundup
3:00 PM – Break

==============

Michael Witzel
Department of Sanskrit and Indian Studies, Harvard University
1 Bow Street , 3rd floor, Cambridge MA 02138
1-617-495 3295 Fax: 496 8571
direct line: 496 2990
<http://www.fas.harvard.edu/~witzel/mwpage.htm>
<http://groups.yahoo.com/group/Indo-Eurasian_research/>
< http://users.primushost.com/~india/ejvs/>

Michael Witzel and Rajaram: Interesting encounters!

April 19, 2010

Michael Witzel and Rajaram: Interesting encounters!

As I am an Indian and poor man, I could not have gone there to watch fun, but our Sanskrit Professor at Harvard have done a nice coverage to that event and I thank Michael Wizel and present the details as follows:

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id=”message_view_subject”>[Indo-Eurasia] Rajaram, in Boston, requires withdrawal of Horseplay in HarappaSunday, 18 April, 2010 8:45 PM

From:
“Michael Witzel” <witzel@fas.harvard.edu>

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To:
Indo-Eurasian_research@yahoogroups.com
Cc:
“Michael Witzel” <witzel@fas.harvard.edu>

Dear List,

since it is the weekend, a few amusing details about our old friend,
NS Rajaram’s, talk at MIT last week (4/10) and his subsequent
interview in the local Indian immigrants’ (NRI) newspaper Lokavani
“Voice of the People’ — sponsored by a clueless US immigration lawyer.

Along with one or two of my students, I went to MIT to have some fun.
And fun it was. Some very emotional people (among the c. 40
listeners) objected to our snickering at his “ideas” (see below).

Rajaram indeed repeated all the fantasies and unscientific nonsense
that he has propagated since he abruptly turned, overnight (why?),
from a mathematician at some US colleges and a (very occasional, but
hyped) collaborator of NASA-Houston, into a “historian” back in his
home town of Bangalore in India.

No need to repeat all of this as we have discussed it on and off over
the past decade. (Just read his interview, below)

Only a few highlights.

I thought to challenge his many fantasies (see Lokavani), but as
there was little time and chance, I merely pointed out the obvious:
that his “scientific” dating of the Vedic civilization BEFORE the
Indus civilization (2600-1900 BCE) is impossible precisely on
*scientific* grounds: before 2000 BCE, there were no horses
(caballus) in India, nor had spoke-wheeled chariots been invented by
then. Both are of course prominent in the “preceding” Vedic texts.

Rajaram and friends (e.g., an *always present* loud associate of a
local temple) took up the usual secondary and tertiary ‘arguments’
and ways out: that there were “Indian” horses with seventeen ribs in
the Rgveda (of course *not* a genetic trait of horses [that have
16-18 ribs]),and the Narmadicus horses (well, dead for hundreds of
thousands of years, — along with their 3 toes (!) ). Fun.

Or quoting a Graham Hancock film (Kathy?) … No comment.

More funnily, one young women, objecting emotionally to the husband
of my student, showed him the finger and called him an asshole.
Remember the same from our Dartmouth, Mass. meeting of June 2006?
(Where Rajaram is now invited by the miniscule setup of a “Center of
Indian Studies”, at U. Mass., Darthmouth). See my detailed June 26,
2006 report:

<http://groups. yahoo.com/ group/Indo- Eurasian_ research/ message/4278>

She also wanted to ‘correct’ my Sanskrit pronunciation of shaanti and
told us the familiar Hindutva standby that we were not entitled, as
non-Indians, to talk about Indian culture. When I told her that, in
that case, she was not entitled to talk about American culture, we
only got blank, non-comprehending stares, even after explaining it
for a 2nd time. — Fun.

But back to Rajaram. More fun: He came up to me after his 2 hour (!)
talk to “greet” me, and I told him to stop lying about me (…
forgetting, by the way, about his monthly missives to my president
and provost to throw me out of the University.. .).

**He then required me to withdraw our 2000 paper “Horseplay in
Harrappa” in the Indian magazine Frontline**
that completely destroyed his credibility, even in the then Hindutva-
led (BJP) circles.

I told him: no way.

He also told the audience that his 2nd volume on the “decipherment’
of the Indus signs would come out now. Cannot wait for more
decipherments such as “mosquito”.. .

And, that he has now shifted to a maritime interpretation (along with
David Frawdley) of the Rgvedic texts. (Good luck with traveling in
the night time sky = samudra!) And to South East Asian maritime
input on Vedic civilization — a pet idea of their part-time fellow
traveller, Koenraad Elst, in Belgium.

And, even more remarkably, researching now a connection between the
late 1st millennium CE Vedanta philosophy and … physics. On that
point, he was challenged by MIT/Harvard students, of course…

For all of this (in Rajaram’s words) see the link and mssg. quoted
below.

At any rate, apart from the loss of our time, it was good weekend
entertainment.
Hope you, too, enjoy his pronouncements. …

Cheers, Michael

His interview in Lokavani: <http://www.lokvani. com/lokvani/ article.php? article_id= 6418>

For convenience, it is reproduced here:

In Conversation With Dr. Navaratna Rajaram
Ranjani Saigal 04/13/2010

(This article is sponsored by Attorney Rachel C. Tadmor)
Dr. Navaratna S. Rajaram is a mathematician and scientist who after more than twenty years as an academic and industrial researcher turned his attention to history and history of science. He has authored several acclaimed books on ancient history including Sarasvati River and the Vedic Civilization, Vedic Aryans and the Origins of Civilization (w/ David Frawley); and The Deciphered Indus Script (w/ Natwar Jha). He is best known for showing the connections between Vedic Mathematics and Indus archaeology and proposing a decipherment of the 5000 year old Indus script jointly with the late Natwar Jha. He is currently visiting faculty at the University of Massachusetts , Center for Indic Studies at Dartmouth.

He spoke to Lokvani about his work and the need for technically minded Indians to learn more about India and its history.

What motivated , a mathematician by profession to do research in Indian history and Indology?

I was always interested in history and history of science. My maternal grandfather Sri R. Vyasa Rao wrote Sri Krishna Caritra in Kannada (my mother tongue) based on Sri Bankima Chandra Chatterji’s Bengali masterpiece of the same name. My study of the work taught me that there advantages to looking at history from a scientific point of view. I had long planned to bring out an English version of that work, which finally happened a few years ago in my English Search for the Historical Krishna. It is not a translation though but a new work that uses a lot of data which was not available to Sri Bankima Chandra.

How did you learn the techniques required to do research in History? Do you consider your “non-training” in the colonial-Eurocentric approach to history an advantage?

I don’t think you need any special training in history except a capacity to look at all claims with skepticism and never to accept anything on authority or reputation. The same is true of science also. In that sense my training in mathematics (and math physics) prepared me well for history.

Why is the Aryan Invasion theory which we now know is a myth important to Indian historians? Why are so many scholars afraid debunking the Aryan theories?

It was important because it was an attempt by outsiders, even those hostile to us, to tell us how we should see ourselves and our heritage. Now that the Aryan myth, not just the theory is dead, we need to move to a new phase– to understand what drove Europeans and even some Indians to hold on to it long after science and history had discredited it. European scholars like Leon Poliakov and Stefan Arvidson (in The Aryan Myth and Aryan Idols) have done it from a European perspective.

But Indian scholars seem to be still reluctant and even timid to face it and hesitant to call a spade a spade and expose these Aryan theories for what they are. It is residual inferiority complex.

Why is colonial-Eurocentric approach towards understanding Indigenous culture still strongly followed in intellectual history circles ?

Inferiority complex that is programmed into Indian humanities and social science programs. This is a colonial hangover or ‘dhimmitude’ towards their former masters. Colonialism may be dead but the mindset of the colonial subject is still there in the intelligentsia. This is by no means limited to India.

Why do western professors studying the history of an Indigenous culture place no value on the multiple sources of literature and  philosophies which guide the lives of the millions in the culture they study that have evolved through the ages some of which totally contradict their writings?

It is precisely because they contradict their long-held positions! It also strikes at the root of their presumption of superiority. But here the problem lies more with Indians than with the Western scholars. A clear message should be sent out that we judge everything on its merit regardless of whether source is indigenous (Indian) or Western, and no special consideration will be shown to anyone. After all this how we judge people and their work in other fields. A theorem in mathematics must be proved, no matter who states it. Why should it be any different in history or any other subject?

What is the danger in allowing  colonial-Eurocentric works go unchallenged?

We must reject all shoddy work, Western or Indian. But because West had a monopoly on such scholarship without competition, it generated a lot of shoddy scholarship. My objection is that it has given rise to shoddy scholarship and nationalistic responses that are also shoddy in scholarship. Now that the field is opening up, we must try to lift the standards of scholarship. But people with a stake in the status quo will fight it.

You have worked on  deciphering the Harappan Script and that claim has been vociferously opposed by professors following the Eurocentric approach. Are professors  closing the doors on Academic research and shutting the window to knowledge by closing their mind and not allowing their students to  look at rational thinking?

I don’t want to make too much of the vitriolic reactions of a handful of frustrated scholars — both Western and Indian — to the solution that Jha and I proposed. Several people, both in India and the West have received our work favorably and others have offered constructive criticisms. Actually the script doesn’t tell us much more than we already know– that the Harappan civilization was Vedic and also the Rig Veda came before Harappan archaeology (of the Indus Valley).

THIS IS THE REAL ISSUE– THE VEDIC-HARAPPAN IDENTITY. The rest is just diversion. Once this basic reality is accepted, it means the collapse of the academic discipline called Indo-European Studies.

As far as the script is concerned, it is just one piece of the puzzle, not the whole solution. Jha and I and David Frawley also have much more now that relate to the Vedic-Harappan equation. Jha and I had made progress towards a successor to our book The Deciphered Indus Script that would place greater emphasis on the Vedic symbolism and the identity of the Harappans. But we decided that in the prevailing climate a book would not get a reasonable hearing and be subjected to diversionary attacks and misinformation campaign. So we decided to wait until the climate turned more normal.

Unhappily, Jha died a few years ago but I and some of my colleagues are working on books on the subject. Now that these hostile academics and their followers have discredited themselves, we may bring out our books in the next few years. But for the desperate diversionary attacks by some scholars — both Western and Indian — worried about their positions and reputations, much of this work would have been available by now. So they succeeded in delaying progress by about a decade, that is all. My regret is that Jha, who made such a major contribution is no longer here to share it.

How do you hope to create a shift in the study of indigenous cultures which are currently being dominated by some powerful academics at prestigious universities?

Ignore their unsupported claims and demand that they give evidence and proof. Look at evidence without being swayed by prestige or reputation.  Above all, don’t give them  any support– financially or in terms of students. Their programs are dwindling, and it would be unwise for a young man or woman to try to make a career or gain fame following in their footsteps.

What advice do you have for our readers?

For young readers, first, study the past but don’t live in the past. See if we can bring ancient wisdom like Vadantic metaphysics to apply to problems of modern physics like quantum reality. Incidentally, this is my current area of interest. Next don’t waste time studying nineteenth century ideas like Aryan and Dravidian, etc. They are dead, no matter what their advocates may claim. (They will also be dead.) Except for details we have pretty much solved the problem of Vedic and Harappan origins and their mutual relationship. So start looking at proto-Vedic and pre-Vedic ages. This will call for a thorough understanding of natural history from the Ice Age to the present and of population genetics.

For everyone– don’t support these hostile programs just because they are at ‘prestigious’ universities or because some of these people have big reputations, at least according to themselves. Most of these are in decline and let them die a natural death. Don’t prolong the agony by giving them any life support.

On the other hand support and organize programs that stress an indigenous perspective like yoga, vedanta and science others that have a rational basis and are scientifically and intellectualy exciting.

Thank you for your time

Thank you

Asko Parpola gets award from the controversial Karunanidhi!

April 4, 2010

Asko Parpola gets award from the controversial Karunanidhi!

Karunanidhi has been modern day racist Dravidian leader, who runs government in the name of “Dravidian race superiority” against the imaginary “Aryans”.

Just like Hitler, he believes that “Aryans” were responsible for the “downfall” of “Dravidians” and therefore, he has been waging perpetual war against those “Aryans”.

Now, the racist Karunanidhi has recognized that asko Parola has been responsible for indetifying the undeichiphered IVC script as “DRavidian” and therefore, he is awarded by that Dravidian racist leader!

Let us see the response of the academicians.

Already, his controversial “Tamil conference” is infested with various problems. The original Tamil Body had refused to participate in the conference.

Classical Tamil Award for Asko Parpola

Asko Parpola. Photo : N. Sridharan
THE HINDU Asko Parpola. Photo : N. Sridharan

Kalaignar M. Karunanidhi Classical Tamil Award: For his work on Dravidian hypothesis in interpreting Indus script, Asko Parpola gets the award in the name of controversial racist leader. Asko Parpola, leading authority on the Indus script and Professor Emeritus of Indology in the University of Helsinki, Finland, has been chosen for the Kalaignar M. Karunanidhi Classical Tamil Award for 2009. He was selected for his work on the Dravidian hypothesis in interpreting the Indus script because the Dravidian, as described by him, was very close to Old Tamil, an official release issued on Saturday said. Professor Parpola will receive a cash prize of Rs. 10 lakh, a citation and a memento during the World Classical Tamil Conference to be held in Coimbatore in June.

Selection appears to be more political than academic: His selection was made at a meeting chaired by Chief Minister M. Karunanidhi, who is also chairman of the Central Institute of Classical Tamil. Two hundred and thirty nominations were received from different countries, including Australia, U.S., the United Kingdom, Sri Lanka and Finland besides India. Administered by the Institute, the award was established out of a donation of Rs.1 crore made by Mr. Karunanidhi in July 2008. The amount is being deposited in the name of Kalaignar M. Karunanidhi Classical Language Trust.

Asko Parpola: Born in July 1941, Professor Parpola has devoted his life to the task of solving the Indus script. Since 1968, he has been stressing that the Indus civilisation and its writing are Dravidian. His research and teaching interests include Indus Civilisation, Samaveda, Vedic rituals, South Asian religions and pre-historic archaeology of South and Central Asia. His magnum opus “Deciphering the Indus Script” proposing Dravidian as the language of the Indus script has been hailed a classic in the field. His ‘Concordance to the Indus Texts’ has been serving as a valuable source for researchers. The two volumes of ‘The Corpus of Indus Seals and Inscriptions,’ reproduced the original seals and their impressions.

Richard Meadow on Indus script!

February 20, 2010

Indus: The Unvoiced Civilization, Press Release , 02/02/2010

“Indus: The Unvoiced Civilization” – Video and Discussion at Harvard University, C. Gopinath and Thomas Burke

“Indus, The Unvoiced Civilization,” a video and following discussion, was presented in the Harvard Science Center on January 10. The lecture was sponsored by the Harvard Department of Sanskrit and Indian Studies in its ongoing Outreach lecture series on “Indian Society through the Ages.” The session was introduced by Dr. Bijoy Misra of the Outreach Committee, who outlined the progress of the series and summarized the lectures of the past months.

Ms. Nalini Gopinath, who presented the video, first offered an overview of facts that have hitherto come to light about the long-forgotten Indus civilization. For a 900-year span from about 2600 BCE to 1700 BCE a sophisticated urban civilization flourished in the region of the Rivers Indus and Gagghar-Hakra, extending to south to modern Gujarat and east nearly to Delhi. The territory was rich in many kinds of flora and fauna, which are now extinct there. Crops such as wheat, barley, millets, sesame and cotton were cultivated.  This sophisticated urban civilization had trading ties to Mesopotamia and the Arabian Peninsula. Seals bearing Indus characters have been found as far west as Abu Dhabi and Bahrain. These, together with a few Mesopotamian texts, point to a thriving trade between the Indus region and Western Asia.

The DVD Presentation titled “Indus:  The Unvoiced Civilization” lasted about one hour. It took the audience through the three most prominent sites – Harappa, Mohenja-Daro and Dholavira. It depicted the archeological finds, such as carnelian jewelry, pottery and seals. The urban centers of Harappa (Punjab), Mohenjo-Daro (Sindh), Dholavira (Gujarat), and Rakhigarhi (Haryana) as well as many smaller settlements reveal a concern for urban planning and sometimes include very sophisticated drainage and water storage systems. Mohenjo-daro, in particular, had many wells, while Dholavira was designed to channel rainwater into huge reservoirs. Harappa had both wells and tanks. It is speculated that as many as 40,000 people may lived in the city of Harappa and about 20,000 in Dholavira.

The presentation was followed by a lively question and answer session with Dr. Richard Meadow, who appeared in the film and participated in the excavations of Harappa. The questions pertained to the script and the extent of the civilization. Dr. Meadow explained that a total of 400-600 characters have been identified from the various Indus inscriptions. No single inscription contains more than 17 characters. We do not know which language or languages were spoken in the Indus region. None of the many attempts which have been made to decipher the script have gained general acceptance. Sites of the civilization have been found as far as  northern Afghanistan.  Gaps in the archeological record do not permit us to speak of cultural continuity from the Indus civilization to the modern day, but many undeniable similarities suggest possible survivals.

Question and Answers by Dr. Richard Meadow

Why is the script not deciphered as yet?
We do not know which language or languages were spoken in the Indus valley. We have no bilingual inscriptions, no known inscription of more than 17 characters, and no obvious successor script. There is a theory that the characters do not reflect spoken language but are non-linguistic symbols, although this is widely debated.

How many characters have been identified so far?
About 400-600, the larger number is arrived at by regarding some similar characters as being separate.

How come there is so much evidence of trade out of the Indus region but no evidence of imported goods?
It is speculated that imports were mainly perishable items like textiles, which have not survived.

Why is there little evidence of tombs like those found in Mesopotamia and Western Asia?
Although few tombs are known, there are some sites at which have been found a large number of burials, for example at Harappa and at Farmana (Haryana). There seems to be no evidence so far that the Indus people had very rich graves of the kind known in ancient Mesopotamia, Egypt, or China. One must also remember that the long-lived Indus civilization left extensive remains, still largely unexplored. So far, excavations have in general uncovered only the topmost third of the many sites. “We still have only a hazy picture of the earlier phases of the culture,” as represented by the lower levels at the archaeological sites.

Why do archaeologists speak of a gap between the end of Indus culture and the beginning of the Vedic period, even though many of the Indus artifacts shown in the DVD are still in use today?
It is true that many cultural traits and artifacts may survive from an earlier into a later period. But it is methodologically problematic to speak of archeological continuity without some evidence of survival of artifacts in the interval between the two periods.

How far did the civilization extend?
Sites of the Indus civilization are found almost to the border of Central Asia in the northwest, east almost to Delhi, south almost to Mumbai, and west nearly to the Iranian border as well as to coastal Arabia.

Is it possible that some Indus people are buried in Western Asia in one of the 80,000 tombs found in Bahrain?
Evidence is still lacking.

Is it true that the British built the Indian Railway system using bricks from the Harappa site?
The sites were always known to the local people. The British first became aware of Indus sites in the early 1800s. In the 1850s the Archeological Survey of India began to scout them. When the British built the Northwest Railway in the 1860s they used vast quantities of ancient bricks from Harappa to prepare the roadbed for the tracks. All have probably disintegrated by now. The ancient people of Harappa themselves recycled bricks, reusing old ones in new structures.

What do the names Harappa and Mohenja-Daro mean?
These are the names used by the local people and they may possibly be very old. There is no convincing explanation of their meaning. We do not know what the Indus people called themselves. Mesopotamian texts seem to refer to the Indus region as Meluhha.

Where can we find the DVD?
It’s a Japanese production and can be procured on the internet. Harvard affiliates can borrow it from Tozzer Library.

The next lecture in the series will be “The Indus Civilization: Myth and Reality.” It will be presented by Dr. Richard Meadow of the Peabody Museum, Harvard University. Dr. Meadow will note that while the Indus civilization has often been characterized as highly structured, uniform, and unchanging, in fact it was a highly diverse, varied, and dynamic cultural phenomenon with many different kinds of sites with strong local and region characteristics that changed over time.  The lecture is scheduled for Sunday, 14 February in Hall A, Harvard Science Center, 1 Oxford Street, Cambridge, at 3.00 pm. Admission is free and all are invited.

http://www.lokvani. com/lokvani/ article.php? article_id= 6272

‘Earliest writing’ found

http://news.bbc.co.uk/2/hi/science/nature/334517.stm

The fragments of pottery are about 5,500 years old

Exclusive by BBC News Online Science Editor Dr David Whitehouse

The first known examples of writing may have been unearthed at an archaeological dig in Pakistan.

So-called ‘plant-like’ and ‘trident-shaped’ markings have been found on fragments of pottery dating back 5500 years.

Dr Richard Meadow of Harvard University: “We may be able to follow the history of signs.”

They were found at a site called Harappa in the region where the great Harappan or Indus civilisation flourished four and a half thousand years ago.

Harappa was originally a small settlement in 3500 BC but by 2600 BC it had developed into a major urban centre.

[ image: Harappa was occupied until about 1900 BC]
Harappa was occupied until about 1900 BC

The earliest known writing was etched onto jars before and after firing. Experts believe they may have indicated the contents of the jar or be signs associated with a deity.

According to Dr Richard Meadow of Harvard University, the director of the Harappa Archaeological Research Project, these primitive inscriptions found on pottery may pre-date all other known writing.

Last year it was suggested that the oldest writing might have come from Egypt.

Clay tablets containing primitive words were uncovered in southern Egypt at the tomb of a king named Scorpion.

They were carbon-dated to 3300-3200 BC. This is about the same time, or slightly earlier, to the primitive writing developed by the Sumerians of the Mesopotamian civilisation around 3100 BC.

“It’s a big question as to if we can call what we have found true writing,” he told BBC News Online, “but we have found symbols that have similarities to what became Indus script.

[ image: Work at Harappa is likely to fuel the debate on early writing]
Work at Harappa is likely to fuel the debate on early writing

“One of our research aims is to find more examples of these ancient symbols and follow them as they changed and became a writing system,” he added.

One major problem in determining what the symbols mean is that no one understands the Indus language. It was unique and is now dead.

Dr Meadow points out that nothing similar to the ‘Rosetta Stone’ exists for the Harappan text.

The Rosetta Stone, housed in the British museum since 1802, is a large slab of black basalt uniquely inscribed with the same text in both Egyptian hieroglyphs and Greek.

Its discovery allowed researchers to decipher the ancient Egyptian script for the first time.

The Harappan language died out and did not form the basis of other languages.

Dr Meadow: “The earliest inscriptions date back to 3500 BC.”

“So probably we will never know what the symbols mean,” Dr Meadow told BBC News Online from Harappa.

What historians know of the Harappan civilisation makes them unique. Their society did not like great differences between social classes or the display of wealth by rulers. They did not leave behind large monuments or rich graves.

They appear to be a peaceful people who displayed their art in smaller works of stone.

Their society seems to have petered out. Around 1900 BC Harappa and other urban centres started to decline as people left them to move east to what is now India and the Ganges.

This discovery will add to the debate about the origins of the written word.

It probably suggests that writing developed independently in at least three places – Egypt, Mesopotamia and Harappa between 3500 BC and 3100 BC.

Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA

December 26, 2009

Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA

Adrian W. Briggs*, Udo Stenzel, Matthias Meyer, Johannes Krause, Martin Kircher and Svante Pääbo

Max-Planck-Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany

*To whom correspondence should be addressed. Tel: +49 (0) 341 3550 539; Fax: 49 (0) 341 3550 550; Email: briggs@eva.mpg.de// <![CDATA[// <![CDATA[
var u = “briggs”, d = “eva.mpg.de”; document.getElementById(“em0”).innerHTML = ‘‘ + u + ‘@’ + d + ”
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Received September 28, 2009. Revised October 30, 2009. Accepted November 24, 2009.

 ABSTRACT
Note: This is reproduced only for research purposes, discussoion and debatr with due axcknowledgments to the original researchers and other scholars connected in this regard

DNA sequences determined from ancient organisms have high error rates, primarily due to uracil bases created by cytosine deamination. We use synthetic oligonucleotides, as well as DNA extracted from mammoth and Neandertal remains, to show that treatment with uracil–DNA–glycosylase and endonuclease VIII removes uracil residues from ancient DNA and repairs most of the resulting abasic sites, leaving undamaged parts of the DNA fragments intact. Neandertal DNA sequences determined with this protocol have greatly increased accuracy. In addition, our results demonstrate that Neandertal DNA retains in vivo patterns of CpG methylation, potentially allowing future studies of gene inactivation and imprinting in ancient organisms.

 INTRODUCTION
Note

Under favourable conditions, DNA can survive in tissue remains for several millennia and in some cases over 100 000 years (1). Over such long time periods, DNA is invariably affected by degradation and modifications. A ubiquitous feature of ancient DNA is the presence of miscoding lesions that causes incorrect nucleotides to be incorporated during DNA amplification. The identities and underlying biochemical processes of nucleotide misincorporations in ancient DNA have been the subject of some debate (2–5). However, it has now been established (4,6,7) that the vast majority of damage-derived errors in ancient DNA sequences are caused by hydrolytic deamination of cytosine to uracil or possibly hydroxyuracil, which leads to apparent C->T or G->A substitutions in the DNA sequences determined.

Uracil–DNA glycosylase (UDG), which removes uracil residues from DNA to leave abasic sites (8), has been shown to reduce C/G->T/A misincorporations from ancient DNA (4). However, abasic sites prevent replication by Taq polymerase used in the polymerase chain reaction (PCR) (9). Consequently, the use of UDG has not been widely adopted in ancient DNA studies since template molecules in ancient DNA extracts are often limited in number such that UDG treatment may destroy all amplifiable templates available in an extract (4). This is particularly the case when direct PCR is used to retrieve DNA sequences since comparatively long templates are needed to accommodate two primers; furthermore, investigators often target the longest possible templates by PCR in order to reduce work and costs. UDG treatment is then particularly likely to be detrimental since longer template molecules are especially rare in ancient DNA (10) and are more likely than short molecules to contain at least one uracil residue.

High-throughput direct sequencing (11,12), which sequences DNA molecules of all lengths, has opened new possibilities to analyze ancient DNA (13–15). In this approach, the ends of ancient DNA fragments are made amenable to ligation by treatment with T4 DNA polymerase and T4 polynucleotide kinase (PNK). Subsequently, DNA adaptors are ligated to the fragment ends and then used to amplify individual molecules and initiate sequencing reactions on a highly parallelized platform. In theory, UDG treatment would be less harmful with this method than with direct PCR, since most ancient DNA molecules are very short and so are less likely to contain uracil than the few longer molecules accessible to direct PCR. However, direct sequencing of ancient DNA molecules generates many C/G->T/A errors at fragment ends (6). These misincorporations probably derive from single-stranded overhangs of a few bases in the ancient DNA (6,7), where cytosine deamination is much faster than in double-stranded DNA (16). Thus, in some extracts, up to ~60% of all endogenous DNA fragments are estimated to contain at least one uracil (Supplementary Table S1) and would be excluded from sequencing if the template was treated with UDG. It would therefore be valuable if DNA fragments could be repaired following the removal of uracils by UDG.

Here, we demonstrate that a simple modification to high-throughput sequencing library preparation removes uracil residues from ancient DNA and subsequently repairs the DNA fragments, greatly increasing the accuracy of the DNA sequences determined while maintaining DNA sequence yield from precious DNA sources. In addition, we show that remaining C/G->T/A misincorporations are due to in vivo methylation of cytosine in Neandertal DNA, demonstrating the survival of this epigenetic modification in DNA over 38 000 years old and thus potentially allowing its study in ancient organisms.

 MATERIALS AND METHODS
Note

Synthetic oligonucleotides
Oligonucleotide design
Oligonucleotides designed to simulate typical ancient DNA fragments were ordered from Sigma-Aldrich. Each ~60 bp double-stranded oligonucleotide (A–D, Figure 2) was created by mixing the constituent ssDNA oligonucleotides together to a concentration of 50 µM each, heating to 95°C for 10 s and ramp cooling at 0.5°C s–1 to 25°C. Oligonucleotides were diluted to 5 µM and purified with QIAGEN MinElute spin columns to remove salts left over from oligonucleotide synthesis.

Figure 1
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Figure 1. Predicted activity of UDG and endoVIII in 454 library preparation of ancient DNA. T4 PNK phosphorylates 5′-ends leaving 5′-phosphate groups. UDG removes uracils, which are concentrated in short 5′- and 3′-overhangs in ancient DNA, leaving abasic sites. EndoVIII then cleaves on both sides of the abasic sites, leaving 5′- and 3′-phosphate groups. T4 polymerase fills in remaining 5′-overhangs and chews back 3′-overhangs, possibly aided by the 3′-phosphatase activity of PNK. Blunt-end ligation and fill-in of sequencing adaptors can then take place.

Figure 2
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Figure 2. Demonstration of UDG/endoVIII repair on synthetic oligonucleotides. 1 µg of each of four synthetic double-stranded oligos A-D (top) was subjected to 454 adaptor ligation after enzymatic repair in four conditions: (1) Incubation with PNK followed by addition of T4 polymerase; (2) PNK and UDG followed by T4 polymerase; (3) PNK, UDG and endoVIII followed by T4 polymerase; (4) UDG and endoVIII followed by T4 polymerase (i.e. no PNK). Products were first visualized on agarose gels (middle). The first lane on each gel after the ladder is the untreated oligo. Major bands in the other lanes correspond to the unligated oligos (62–67 bp), the oligos plus one 44-base adaptor and the oligos plus two 44-base adaptors. For some products higher weight bands are visible that probably indicate end-to-end chimeras of the oligos and adaptors. The cause of the faint, diffuse bands seen between 150 and 200 bp in the untreated oligos are unknown but may be artifacts of oligo synthesis. Ligated products were also quantified by qPCR without (dark brown) or with (light brown) prior incubation with UDG. The products marked a and b were sequenced directly on the 454 platform (bottom).

Repair
Each oligo of 500 ng was added to a 50 µl repair reaction containing 1x NE Buffer 2, 0.1 mg ml–1 bovine serum albumen (BSA), 1 mM ATP, 300 µM each of dATP, dCTP, dGTP and dTTP, and one of the following four enzyme repair combinations: (i) 20 U T4 PNK (New England Biolabs); (ii) 20 U PNK, 5 U Escherichia coli UDG (New England Biolabs); (iii) 20 U PNK, 3 U USER enzyme (New England Biolabs). USER enzyme is a proprietary-ratio mixture of UDG and endonuclease VIII (endoVIII) produced by New England Biolabs. Five units of USER enzyme perform similarly in this protocol to a self-made mixture of 5 U UDG and 20 U endoVIII (Supplementary Figure S1). After an incubation period of 3 h at 37°C, 6 U T4 DNA polymerase were added to every tube followed by incubation at 25°C for 30 min. Products were purified with QIAGEN MinElute spin columns and eluted in 14 µl buffer EB (Qiagen).

Ligation
Each purified repair product of 12 µl was mixed with 1 µl 454 adaptors (20 µM each adaptor) (12). The mixture was added to 27 µl ligation mix, making a 40 µl reaction containing 1x Quick Ligation buffer (New England Biolabs) and 1 µl Quick ligase (New England Biolabs). The mixture was incubated at 25°C for 15 min, after which products were purified with QIAGEN MinElute columns and eluted in 14 µl buffer EB.

Adaptor fill-in
Each purified ligation product of 12 µl was added to a 40 µl adaptor fill-in reaction containing 1x Thermopol buffer (New England Biolabs), 300 µM each of dATP, dCTP, dGTP and dTTP, and 16 U Bst DNA polymerase (New England Biolabs). The reaction was incubated for 30 min at 37°C. Note that unlike previous studies (17) we performed fill-in in solution and did not use streptavidin beads, as they are unnecessary (18) and likely to cause some loss of material.

Product visualization, quantification and sequencing
Twenty microliters of products were visualized on a 2.5% agarose gel (Figure 2). In order to quantify ligation success and to measure the extent to which uracils had been successfully removed from the templates, all products were quantified by quantitative (q) PCR using 454 adaptor primers, in the presence or absence of 1 U UDG. Apart from the addition of UDG and a 30 min, 37°C incubation step at the start of the qPCR, conditions for the qPCR were exactly as described (19). Two of the products (Figure 2 and Supplementary Figure S2) were subjected to emulsion PCR and sequenced on a 16th lane of the 454/Roche FLX platform according to the manufacturer’s instructions.

Mammoth DNA
DNA was extracted from 280 mg of a ~43 000-year-old mammoth bone from Siberia (20) as described (21). The DNA extract was prepared for 454 adaptor ligation and sequencing under different conditions as follows.

Standard blunt end repair
To reproduce the currently published library preparation protocol, 1 µl mammoth DNA extract (out of the 100 µl total) was incubated in a 50 µl reaction containing 1x NEBuffer 2, 1 mM ATP, 0.1 mg ml–1 BSA, 300 uM each of dATP, dCTP, dGTP and dTTP, 20 U PNK and 6 U T4 DNA polymerase. Two replicate reactions were made up, and incubated for 30 min at 25°C. Products were purified with QIAGEN MinElute columns, eluting in 14 µl buffer EB.

Damage repair, no CIP treatment
To test the new damage repair protocol, 50 µl reactions were set up each containing: 1 µl of the mammoth DNA extract, 1x NE Buffer 2, 1 mM ATP, 0.1 mg ml–1 BSA, 300 uM each of dATP, dCTP, dGTP and dTTP, 20 U µl–1 PNK and one of the following three repair enzyme conditions: (i) no repair enzyme; (ii) 5 U UDG; (iii) 3 U USER enzyme (equivalent to 5 U UDG and 20 U endoVIII; see Supplementary Figure S1). Two replicates were performed for each condition. Samples were incubated for 3 h at 37°C, then 6 U T4 DNA polymerase were added to each tube, followed by 30 min incubation at 25°C. Products were purified with QIAGEN MinElute spin columns and eluted in 14 µl buffer EB.

Damage repair, CIP-treatment
Ten microliter of the mammoth DNA extract was included in a 100 µl reaction containing 1x NE Buffer 3, 0.1 mg ml–1 BSA and 20 U CIP(New England Biolabs), incubating for 30 minu at 37°C. The product was purified in one QIAGEN MinElute column and eluted in 30 µl EB. The dephosphorylated product was split equally into six 50 µl reactions, each containing 1x NE Buffer 2, 1 mM ATP, 0.1 mg ml–1 BSA, 300 uM each of dATP, dCTP, dGTP and dTTP, and one of the following three repair enzyme conditions: (i) no repair enzyme; (ii) 5 U UDG; (iii) 3 U USER enzyme. Two replicates were performed per condition. Samples were incubated for 3 h at 37°C, then 6 U T4 DNA polymerase were added to each tube, followed by 30-min incubation at 25°C. Products were purified with QIAGEN MinElute spin columns and eluted in 14 µl buffer EB.

Ligation
All purified products of the standard blunt end repair, no-CIP-treatment damage repair and CIP-treatment damage repair reactions were subjected to the same 454 adaptor ligation and fill-in procedure as follows: 12 µl of each purified repair product was mixed with 1 µl 454 A and B adaptor mix (12), diluted 1:10 relative to the manufacturer’s instructions due to the low amounts of template DNA in this experiment. The mixture was added to 27 µl ligation mix, making a 40 µl reaction containing 1x NEB Quick Ligation buffer and 1 µl NEB Quick ligase. The mixture was incubated at 25°C for 15 min, after which products were purified with QIAGEN MinElute columns and eluted in 15 µl buffer EB.

Adaptor fill-in
Each purified ligation product of 12 µl was added to a 40 µl adaptor fill-in reaction containing 1x NEB Thermopol buffer, 300 µM each of dATP, dCTP, dGTP and dTTP, and 16 U Bst DNA polymerase (New England Biolabs). The reaction was incubated for 30 min at 37°C followed by 20 min at 80°C to inactivate the Bst polymerase. As with the synthetic oligonucleotide experiment described above, streptavidin beads were not used in this step.

Quantification and sequencing
Each product of 1 µl was quantified directly using qPCR as described (19). Products were then subjected to emPCR at 2 copies per bead, and each sequenced on one 16th lane of the 454/Roche FLX platform. Sequences were aligned to the draft elephant genome (Loxafr2.0, AAGU00000000.2/GI:202071911) using a custom mapper, ANFO (22) (freely available for download at http://bioinf.eva.mpg.de/anfo/).

Neandertal DNA
DNA was extracted from 150 mg of a ~38 000-year-old Neandertal bone from Vindija cave, Croatia (23) as described (21). Thirty-two microliters of the 100 µl total extract was split equally into four 50 µl reactions containing 1x NE Buffer 2, 1 mM ATP, 0.1 mg ml–1 BSA, 250 uM each of dATP, dCTP, dGTP and dTTP, 20 U PNK, and either (1) no repair enzyme or (2) 5 U UDG and 20 U endoVIII. Reactions were incubated for 3 h at 37°C, before 6 U T4 DNA polymerase was added, followed by 30 min at 25°C. Products were purified with QIAGEN MinElute columns and eluted in 14 µl EB. Ligation and fill-in were performed as described in (17), including use of a modified 454 adaptor containing a Neandertal project-specific key (6). Note that in this experiment, streptavidin beads were used in the fill-in step unlike in the synthetic oligonucleotide and mammoth DNA experiments; this was because we had not switched at that point to the more efficient no-beads protocol (18). To make use of the greater parallel sequencing capacity of the Illumina Genome Analyzers (GA) platform relative to 454/Roche, the library was first universally amplified for 5 PCR cycles using the protocol described in (24). The amplified product was subsequently converted into an Illumina-amenable library by a 7 cycle re-amplification under similar conditions except that tailed PCR primers were used that attach the Illumina P5 and P7 grafting sequences outside the 454 adaptor sequences (sequences available on request). This allowed subsequent bridge amplification and 2 x 51 bp paired end sequencing runs to be performed on the GAII platform, following to the manufacturer’s instructions except that sequencing primers were used that anneal to the 454 adaptor sequences. The sequencing run was analyzed starting from raw images using the Illumina GA pipeline 1.3.2. To overcome issues introduced by identical key sequences at the beginning of the first read, for cluster identification the first five sequencing cycles were used. The Ibis basecalling program was used (25). Raw sequences for the two paired end reads of each sequencing cluster were merged by checking for a minimum 11nt overlap between the first and the second read. For bases in the overlapping sequence, a consensus was called by considering the base with the higher quality score or, in case of agreement, summing up the quality scores observed. For further analysis, only successfully merged sequences were considered and aligned to the human genome (NCBI 36.1/hg18), all CpG islands annotated by UCSC (http://genome.ucsc.edu/cgi-bin/hgTables; table: cpgIslandExt) and the mtDNA sequence of this individual (AM948965) using a custom mapper, ANFO (22). Custom scripts were used to count alignment mismatch frequencies.

 RESULTS
 Note

A UDG/endoVIII repair scheme
In library preparation protocols for high-throughput sequencing of ancient DNA, PNK and T4 DNA polymerase are used to generate ends amenable to DNA ligation (17). This is achieved by phosphorylation of non-phosphorylated 5′-ends by PNK, and removal of 3′-overhangs and fill-in of 5′-overhangs by T4 polymerase, producing blunt ended, 5′-phosphorylated molecules. A large proportion of nucleotide misincorporations generated from ancient DNA libraries are caused by uracils present in short 5′-overhangs in ancient DNA fragments, which are filled in during this end-repair reaction (6). We reasoned that if DNA is incubated with UDG and endoVIII prior to T4 DNA polymerase treatment, this would result in the removal of uracil residues from DNA by UDG, and cleavage on the 5′- and 3′-sides of the resulting abasic sites by endoVIII. PNK and T4 polymerase would then remove 3′-phosphate groups and generate blunt ends (Figure 1), thus avoiding the loss of these molecules from the library.

Repair of oligonucleotides
In order to test the ability of UDG and endoVIII to repair ancient DNA, we designed four double-stranded oligonucleotides that carry short overhanging ends (Figure 2). Whereas oligos A and B contain exclusively the four natural DNA bases, C and D carry uracil bases in their overhanging ends as predicted to frequently occur in ancient DNA (6). Oligos A and C carry 5′-overhangs whereas oligos B and D carry 3′-overhangs. Oligo C carries a uracil base in the second position of the 5′-overhangs and is therefore the type of fragment that the UDG/endoVIII protocol is designed to repair. Oligo D carries a uracil base in the second position of the 3′-overhangs. In 3′-overhangs, deaminated cytosine should not lead to nucleotide misincorporations in ancient DNA sequences because T4 polymerase removes 3′-overhangs before adaptor ligation. However, we wanted to investigate if T4 polymerase activity may be blocked by the abasic sites left after UDG treatment or the 3′-phosphates left by endoVIII treatment (26) (Figure 1).

The three oligonucleotides were treated in four different ways: (i) With PNK to phosphorylate 5′-ends, followed by T4 polymerase to generate blunt ends; (ii) as 1 with the addition of UDG together with PNK; (iii) as 2 with the addition of endoVIII with the UDG and PNK and (iv) as 3 except that PNK was not used. Subsequently, 454 sequencing adaptors were ligated to the oligos. The ligation reactions were visualized on ethidium-stained agarose gels, and analyzed by quantitative (q) PCR with primers specific for the 454 adaptors, either with or without prior treatment with UDG to gauge the amount of uracil residues in the ligation product (Figure 2).

For oligos A and B, which contain no uracils, gel and qPCR results show that adaptor ligation was similarly efficient for treatments 1–3 (Figure 2). This indicates that UDG and endoVIII do not interfere with the generation of blunt ends in non-damaged DNA. The observed level of between-treatment variation is expected given that two spin column purification steps were performed during the procedure.

Oligo C, which contains uracil residues in 5′-overhanging ends, showed high ligation efficiency following treatment 1. However, the ligated product showed greatly reduced copy number in qPCR if treated with UDG prior to amplification. This is expected given that the ligated product should contain one uracil on each strand. Ligation efficiency was very low after treatment 2, consistent with UDG creating abasic sites and preventing T4 polymerase fill-in of ends. After treatment 3, ligation efficiency was high, and in this case the product was insensitive to UDG treatment prior to qPCR. This indicates that the uracils had been removed prior to ligation, as predicted by the scheme in Figure 1.

Oligo D, which contains uracil residues in 3′-overhanging ends, showed a pattern similar to oligos A, B and C in that ligation efficiency was high after treatments 1–3. This indicates that uracil-containing 3′-overhangs can be successfully removed by T4 polymerase after UDG and endoVIII treatment. The products were largely insensitive to UDG treatment prior to qPCR, as expected since uracils in 3′-overhangs should be removed before ligation. The apparent ~40% sensitivity to UDG after treatment 1 is surprising, but may be due to uracil misincorporation during manufacture of this oligo. Since oligos are synthesized in the 3′- to 5′-direction, uracil was added in the first coupling step and carry over to later synthesis steps would lead to UDG sensitivity of the ligated product.

When PNK is omitted (treatment 4), only oligo C shows a full-length ligation product. This demonstrates that the UDG/endoVIII repair reaction generates ligatable phosphorylated 5′-ends after removal of the uracils and cleavage of phosphodiester bonds by endoVIII (Figure 1).

To confirm that UDG/endoVIII repair of oligo C removes uracil-derived errors from DNA sequences as predicted (Figure 1), we sequenced oligo C products of treatments 1 and 3. As expected, after treatment 1, the oligo C product is full length and carries nucleotide misincorporations where uracil residues have been replaced by thymine residues. In contrast, after treatment 3, the oligo C product has been shortened by two bases at both ends, removing the uracil positions from the sequence (Figure 2).

Repair of mammoth DNA
We next tested the UDG/endoVIII protocol on DNA extracted from a ~43 000-year-old woolly mammoth bone. The extract was subjected to various repair reactions in duplicate, followed by 454 adaptor ligation, qPCR quantification and determination of between 783 and 20 935 sequences per sample on the 454 platform. The results were analyzed with respect to numbers of molecules in the 454 libraries generated as well as the percent of sequences in the libraries that show similarity to the elephant genome and are thus assumed to be of mammoth origin. In most ancient remains, only a small proportion of sequences retrieved are from the organism under study. For this extract, it is ~3%, the rest presumably stemming from microorganisms that have colonized the sample after the death of the individual. If the endogenous mammoth DNA carried more DNA modifications than the environmental DNA, the relative amount of mammoth DNA might be changed by the repair reactions. Other relevant aspects such as the length of the mammoth sequences and the frequency and type of nucleotide misincorporations were also analyzed.

One issue that potentially complicates the application of the UDG/endoVIII protocol to ancient DNA extracts is that DNA modifications other than deaminated cytosines may be present (27,28). Therefore, we first tested if mammoth DNA retrieval was affected by the longer incubation (3 h) at a higher temperature (37°C) that differs from the standard library preparation (30 min at 25°C) and thus could conceivably cause DNA degradation by affecting some unknown modifications. Neither in terms of numbers of molecules in the resultant 454 library, the percent of mammoth sequences, the length of mammoth sequences or patterns of misincorporations did the incubation conditions strongly influence the results (Supplementary Figure S3).

We next tested the three treatments previously performed on the oligonucleotides, i.e. (i) PNK + T4 polymerase; (ii) PNK + T4 polymerase + UDG; (iii) PNK + T4 polymerase + UDG + endoVIII. In a second series of experiments, the mammoth DNA extract was dephosphorylated with CIP, purified, and then subjected to the same three treatments except that PNK was never used. Dephosphorylation should prevent the DNA from successful 454 adaptor ligation except in cases where UDG and endoVIII generates phosphorylated 5′-ends where uracil bases exist close to the 5′-ends (c.f. oligo B in Figure 2). Thus, these experiments tested if endoVIII is active on the mammoth DNA.

Total library yield, which includes mammoth and microbial sequences, is reduced by ~30% upon UDG treatment (Figure 3a), consistent with uracil removal from damaged DNA fragments and blockage of T4 polymerase fill-in or Taq polymerase amplification by the resulting abasic sites. When endoVIII is added, library copy numbers increase by ~40% relative to the standard condition. This is unexpected since endoVIII is expected to rescue molecules carrying abasic sites generated by UDG but not to increase copy numbers relative to the standard treatment. We repeated this experiment with more replicates per condition, and again observed a reduction in yield upon UDG treatment but an increase in yield after UDG/endoVIII treatment only to approximately the no repair condition (data not shown). We conclude that UDG reduces copy number of a mammoth DNA library relative to the no repair condition, while UDG together with endoVIII does not, suggesting the repair of uracil-containing DNA fragments. None of the treatments differed in the percent of mammoth DNA sequence, suggesting that uracil or any other unknown modifications that might be affected by the treatments did not differ substantially in frequency between the mammoth DNA and the environmental DNA.

Figure 3
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Figure 3. The UDG/endoVIII repair protocol applied to mammoth DNA. (a) A mammoth DNA extract was subjected to 454 adaptor ligation after enzymatic repair in replicates in three conditions: (1) Incubation with PNK followed by T4 polymerase; (2) PNK and UDG followed by T4 polymerase; (3) PNK, UDG and endoVIII followed by T4 polymerase. The resulting libraries were quantified by qPCR. The same reactions without PNK were applied to mammoth DNA that had first been dephosphorylated by CIP (treatments 4–6). (b) All libraries were sequenced on 454. The proportions of sequences that aligned to the elephant genome are shown. (c) For the sequences resulting from treatments 1–3 and 6 the base composition of aligned elephant sequences is shown for 10 bases either side of the 5′-start point of mammoth sequences.

When the DNA was dephosphorylated prior to the experiments, a small amount of amplifiable material was present after treatments 1 and 2, probably representing both incomplete dephosphorylation of naturally phosphorylated 5′-ends by CIP and 454 adaptor artifacts. This is supported by the observation that only a very small proportion of the sequences determined after this treatment are of mammoth origin (Figure 3b). In contrast, treatment 3 yielded ~3.5 times more amplifiable library molecules than treatments 1 and 2, consistent with direct selection of DNA fragments that had uracil near the 5′-ends of both strands. Notably, after treatment 3, the proportion of mammoth sequences was 10–12%, four times higher than in the libraries made from non-CIP treated mammoth DNA in the presence of PNK. This suggests that the mammoth DNA carried more uracil residues on average than the environmental DNA, although this is probably a modest difference because selecting for damage at both fragment ends will multiply the effect of any difference in damage between sequence populations. Thus, the observed ~4-fold enrichment of mammoth DNA suggests a maximum 2-fold difference between the fraction of mammoth DNA strands and environmental DNA strands that carry uracil residues close to their 5′-ends. This is a small enough effect to be compatible with the fact that no obvious differences in mammoth DNA percentage were observed among the non-CIP-treated libraries where PNK was used.

The 5′-start points of the mammoth sequences represent the terminal bases of the ancient DNA fragments at the point of adaptor ligation (6). We plotted the base composition of the elephant reference sequence aligned to the mammoth sequences for 10 bases on either side of the mammoth 5′-ends. UDG/endoVIII treatment should lead to an increase in cytosine frequency at the base position immediately preceding 5′-ends (i.e. the –1 position in Figure 3c), as DNA fragments containing deaminated cytosine will be truncated to the 3′-side of such positions (Figure 1). Consistent with this prediction, we observed in the non-CIP-treated libraries an increased frequency of cytosine at position –1 in the UDG/endoVIII condition relative to the no-repair and UDG-treated conditions. This effect was much stronger in the CIP-treated, UDG/endoVIII repaired sample, where 84% of 5′-ends are preceded by cytosines. This is predicted since this library should predominantly contain fragments where ligatable ends were generated by excision and repair at positions of deaminated cytosine.

The average length of mammoth sequences is around 70–80 nt (Supplementary Figure S4), as is typical of ancient DNA (29). After UDG treatment, fragments are ~10 nt shorter. This is expected since longer fragments are more likely to contain uracil and thus to be left with an abasic site after UDG treatment. When endoVIII is added, length seems to be intermediate, perhaps representing rescue of some longer fragments by endoVIII treatment. If the DNA is dephosphorylated before UDG and endoVIII treatment, length is ~10 nt shorter than after UDG and endoVIII treatment without CIP-treatment, as expected if all of the ligated fragments in this condition have been truncated at both ends due to UDG/endoVIII repair, as opposed to the non-CIP-treated libraries where only a fraction of the fragments will have been truncated.

We investigated the effect of the repair protocol on nucleotide misincorporations, by plotting for each library the frequency of each of the 12 possible mismatches observed in the mammoth-to-elephant alignments. Ancient DNA sequences generally show an excess of C->T and G->A substitutions due to uracil-derived nucleotide misincorporations (4,6,7). As expected, this pattern is seen when the sample is not subjected to UDG treatment (Supplementary Figure S4). By taking the excess of C/G->T/A substitutions relative to T/A->C/G substitutions as an estimate of the amount of uracil-derived misincorporations in each sample, we found that uracil-derived misincorporations were reduced 4- to 10-fold in samples where UDG was used (Supplementary Figure S4).

In summary, UDG–endoVIII treatment allows more mammoth DNA sequences to be retrieved than UDG treatment alone, while generating much lower rates of nucleotide misincorporations than if UDG is not used.

Repair of Neandertal DNA
Mammoth and African elephant DNA diverged from each other more than ~7 million years ago (30,31). Therefore genuine sequence differences will dominate in pairwise alignments, reducing the ability to study patterns of nucleotide misincorporations. In contrast, Neandertals and humans diverged much more recently. Furthermore, in contrast to the elephant genome the human genome is of finished quality allowing better resolution of nucleotide misincorporations. We therefore applied the UDG/endoVIII repair protocol to DNA extracted from a 38 000-year-old Neandertal bone from Croatia and performed deep sequencing of the libraries. An additional advantage of this specimen is that its complete mitochondrial (mt) sequence is known (23), allowing detailed analysis of sequence errors in mtDNA. This may be particularly interesting as mtDNA does not carry 5-methylcytosine (5′-m-C), a naturally occurring modification in vertebrate nuclear DNA which when deaminated is converted to thymine (32). Since UDG will not remove thymine from DNA, deamination-derived misincorporations may still occur at sites of cytosine methylation after UDG treatment of the ancient DNA.

Between 10 and 11 million raw DNA sequence reads were generated on the Illumina GAII platform from four Neandertal DNA libraries prepared in the standard condition or with the UDG/endoVIII protocol (each in two replicates). In order to improve sequencing accuracy, which decreases substantially toward the 3′-end of Illumina reads (25), we sequenced into both ends of each molecules and merged the paired reads, requiring overlaps of at least 11 bases, and discarded all sequences that could not be merged to their paired read. Since the single read length was 48 bases, this creates a maximum read length of 85 bp. However, previous work has shown that the majority of Neandertal fragments in this bone are shorter than this (33).

Sequences were aligned to the previously published complete mtDNA sequence of this Neandertal (23), and to the human nuclear genome (hg18) using a custom mapping program (ANFO) (22). In each library, 0.007–0.009% of sequences aligned well to the mtDNA and 2.0–2.2% to the nuclear genome. Variation in these proportions was as high within as between treatments. Data from replicates were then pooled for each treatment and patterns of nucleotide mismatches between the sequences and the references were analyzed.

When analyzing Neandertal DNA sequences, contamination of experiments with contemporary human DNA is a potential problem (10,34). However, the level of such contamination in a Neandertal DNA library can be assessed by counting the ratio of Neandertal versus contaminant fragments at nucleotide positions where Neandertals differ from all or almost all present-day humans (33). The mtDNA of this Neandertal carries 133 such diagnostic positions (23). The ‘no repair’ dataset yielded 139 mtDNA fragments that overlapped such positions; 138 carried the Neandertal base while one matched modern human mtDNA. The UDG/endoVIII treated dataset yielded 128 informative fragments, of which all were the Neandertal type. Thus, the mtDNA in all libraries was almost completely free of contamination by modern human mtDNA, even after treatment with UDG and endoVIII. Since the ratio of mitochondrial to nuclear DNA may differ between the contaminating and the Neandertal DNA, this estimate is strictly applicable only to the mtDNA (33). However, the estimate of mtDNA contamination in these libraries is low enough that within even a few-fold variation in mtDNA:nuclear DNA ratios between the Neandertal and contaminating DNA, sequences aligning to the human nuclear genome will be predominantly of Neandertal origin.

To analyze patterns of nucleotide misincorporations, we plotted the frequency of each of the 12 possible nucleotide differences in alignments as a function of distance from the ends of DNA fragments for each dataset (Figure 4, top panels). In the ‘no repair’ results, the transitions C->T and G->A are drastically elevated toward the 5′- and 3′-ends ends of fragments, respectively, with up to 40–50% error frequencies at the fragment ends. This occurs in both mtDNA and nuclear DNA fragments, as shown previously (6,23). The G->A substitutions at 3′-ends of fragments originate during the fill-in of 5′-overhangs containing deaminated cytosines (6,7). After UDG/endoVIII treatment C/G->T/A differences were drastically reduced, consistent with the removal of uracils by UDG. In mtDNA this removal seems to be almost complete, whereas a small amount remains in nuclear DNA (see below).

Figure 4
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Figure 4. Effect of UDG/endoVIII treatment on all nucleotide misincorporation rates and on C->T rates at CpN dinucleotides along Neandertal DNA sequences. DNA from a Neandertal bone was subjected to 454 adaptor ligation after enzymatic repair with PNK and T4 polymerase (‘no repair’) as well as those enzymes plus UDG and endoVIII. Approximately 12 million sequences were generated on the Illumina GAII platform for each condition, and sequences were identified that aligned best to the complete mtDNA sequence of this bone AM948969 [GenBank] (947 and 1084 sequences for the no repair and UDG/endoVIII conditions, respectively, left panels) and to the human nuclear genome sequence hg18 (242 070 and 286 737 sequences, right panels). (a) All 12-nt mismatch frequencies are plotted as a function of position along the aligned fragments for the no repair and UDG/endoVIII conditions. (b) The rate of C->T misincorporations along DNA fragments is shown separately for the four dinucleotides that contain cytosine in the 5′-position.

Neandertal CpG methylation
In vertebrates, DNA methylation occurs at the 5′-position of cytosine residues at ~80% of CpG dinucleotides in somatic tissues (35). When 5′-m-C is deaminated it becomes a thymine residue that is not recognized as an unnatural base by UDG in vertebrate cells. As a consequence, CpG dinucleotides are preferentially lost from vertebrate genomes with the result that the frequency with which CpG dinucleotides occur genome wide is ~1%, while 4–5% would be expected from the base composition of the genome (36). In some regions of the genome, CpG content is less reduced and can be 60% or more of the statistically expected frequency. Such ‘CpG islands’ represent areas where methylation is reduced or absent. About half of CpG islands overlap transcriptional start sites where their methylation in a tissue is positively correlated with suppression of transcription.

We noted that after UDG/endoVIII treatment ~5% of C/G->T/A substitutions remained at the first and last positions of Neandertal DNA fragments in nuclear DNA whereas this did not seem to be the case in the mtDNA (Figure 4). Since cytosine methylation does not occur in mtDNA we speculated that this might be due to cytosine methylation at CpG dinucleotides. We therefore analyzed the rates of C->T mismatches seen along the DNA molecules separately for the four dinucleotides that carry cytosine at their first position (Figure 4, lower panels). Without UDG/endoVIII treatment, C->T differences to the human nuclear genome are common in all four dinucleotide contexts, but slightly more common in CpG dinucleotides (e.g. 52.4% at position 1 of DNA fragments) than in the other dinucleotides (38%–40% at position 1). This is likely due to the higher deamination susceptibility of 5′-m-C relative to unmethylated cytosine (32). With UDG/endoVIII treatment, C->T substitutions in the three non-CpG dinucleotides are greatly reduced (to 2–5% at position 1 of DNA fragments), whereas they remain abundant in CpG dinucleotides (40.6% at position 1 of DNA fragments). Thus, at CpG sites, ~80% of C->T substitutions are resistant to UDG/endoVIII treatment, consistent with findings that ~80% of CpG sites are methylated (35). At CpG sites in mtDNA, no such resistance of substitutions to UDG/endoVIII treatment is seen. This is consistent with the absence of CpG methylation in mitochondria.

In order to further investigate if the UDG/endoVIII protocol can be used to detect CpG methylation present in the Neandertal individual when alive, we analyzed CpG->TpG mismatch rates in CpG islands, where methylation is reduced relative to the genome-wide average (37) (Figure 5). As described, across the genome 52.4% of CpGs at 5′-ends of fragments are read as TpG without UDG/endoVIII treatment, and this is reduced to 40.6% upon UDG/endoVIII treatment. At CpG islands, 51.7% of 5′-terminal CpGs are read as TpG without UDG/endoVIII treatment and this is reduced to 23.4% with UDG/endoVIII treatment. Thus, deaminated CpG sites in CpG islands are more susceptible to UDG/endoVIII treatment than deaminated CpG sites elsewhere in the genome. This is consistent with a reduced frequency of cytosine methylation in CpG islands. Together with the observation that no resistance to UDG treatment is observed at deaminated CpG sites in mtDNA, we conclude that in vivo Neandertal DNA methylation patterns have survived over 38 000 years in the bone, and can be detected by the UDG/endoVIII protocol.

Figure 5
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Figure 5. CpG->TpG misincorporation rate along Neandertal DNA molecules, genome-wide and inside CpG islands. DNA from a Neandertal bone was subjected to 454 adaptor ligation after enzymatic repair with PNK and T4 polymerase (‘no repair’) as well as those enzymes plus UDG and endoVIII. Approximately 12 million sequences were generated on the Illumina GAII platform for each condition, and sequences were identified that aligned best to the human nuclear genome sequence hg18 (left panels) or specifically to CpG islands in the human genome (right panels) (35). The rates of CpG->TpG mismatches are shown for the first 30 bases of DNA fragments.

Neandertal DNA sequence accuracy
Although UDG/endoVIII treatment of ancient DNA clearly reduces nucleotide misincorporations, a remaining limitation to obtaining maximal sequence accuracy from ancient DNA molecules is the high rate of machine sequencing errors of current high-throughput platforms. The ‘merged-paired-end’ sequencing approach used here helps to decrease machine errors by requiring that the 3′-ends of fragments, where errors are most common (25), are sequenced in two directions. However, near-elimination of machine sequencing errors should be possible if libraries are first amplified (24,29), as they were here, and sequenced deeply enough so that multiple copies of each original molecule are sequenced, allowing a consensus to be generated from such replicate sequences, which can be identified by their strand orientation, start and end points (6,13).

To investigate the accuracy, that can be achieved when combining a deep sequencing approach with UDG/endoVIII repair, we determined the overall rates of each Neandertal nucleotide misassignment in (i) all sequences from the ‘no-repair’ dataset; (ii) all sequences from the UDG/endoVIII dataset; and (iii) all ‘multi-pass’ sequences from the UDG/endoVIII dataset, which we generated by taking consensus sequences of all distinct fragments that were sequenced more than once. Figure 6 shows that for mitochondrial sequences, overall error rate per base (Figure 6) was 2.20% for ‘no repair’ sequences; 0.40% for UDG/endoVIII sequences and 0.09% for multi-pass UDG/endoVIII-treated sequences. Thus, UDG/endoVIII treatment alone results in a 5.5-fold reduction in error rates while deep sequencing results in an additional 4.4-fold reduction. In combination this results in a 22-fold reduction in errors. In nuclear DNA, for which we removed CpG sites from the analysis due to the effect of methylation described above, a similar pattern is observed (Figure 6) although the true error rate at these low levels cannot be accurately calculated due to genuine sequence differences between this Neandertal and the human reference.

Figure 6
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Figure 6. Effects of UDG/endoVIII treatment and multiple-pass sequencing on ancient DNA sequence error rate. DNA from a Neandertal bone was subjected to 454 adaptor ligation after enzymatic repair with PNK and T4 polymerase (no repair) as well as those enzymes plus UDG and endoVIII. Approximately 12 million sequences were generated on the Illumina GAII platform for each condition, and sequences were aligned to the complete mtDNA sequence of this bone and to the human nuclear genome (hg18). Overall rates of each alignment mismatch type, and total mismatch rates, are shown for sequences from each condition, plus the result achieved when only fragments that were sequenced more than once (‘multi-pass’) are considered. For nuclear DNA, positions of CpG in the reference were excluded from the analysis since misincorporations remain frequent at these sites even after UDG/endoVIII treatment (see Figure 4).

 DISCUSSION
 Note

The damaged state of DNA recovered from ancient remains causes two major problems for the determination of ancient DNA sequences. First, the DNA quantities recovered are often extremely low. Second, chemical modification of bases, in particular deamination of cytosine to uracil, leads to frequent sequence errors. Because even in highly damaged DNA, only a minority of cytosines are deaminated (4,6,7), and deaminated cytosines are largely randomly distributed in ancient DNA sequences (4), deamination-derived errors can usually be excluded at positions where three or more overlapping molecules are sequenced, and a consensus is used (4,38). However, in sequencing libraries made from ancient DNA, sequence coverage is often so low that deamination-derived errors represent a problem.

When nuclear DNA sequences in ancient diploid organisms are determined, a further problem is caused by the need to accurately determine both alleles at heterozygous positions, or to select one correctly determined allele in an unbiased way. When sequencing ancient nuclear DNA without removing uracil, it will be hard to distinguish true C/T or G/A heterozygote sites from sites of cytosine deamination. Since homozygote sites greatly outnumber heterozygote sites [~1000:1 in present-day humans (39)], events where multiple damaged and undamaged templates are sequenced at a true homozygote site may be more common than the occurrence of true heterozygote sites. This could create a high proportion of false-positive heterozygote calls. If just one allele is required to be accurately called, errors could in theory be avoided by always taking the C or G allele at apparently C/T- or G/A-heterozygote sites. However, this will introduce a severe bias in population genetic analyses by systematically calling only one possible allele at heterozygote sites. Thus, it would be very valuable to reduce error rates when ancient nuclear DNA sequences are determined.

The UDG/endoVIII protocol presented here removes the vast majority of errors caused by miscoding lesions. When combined with machine error removal by sequencing multiple copies of each original molecule, the overall per-base error rate is reduced over 20-fold relative to single-pass sequencing of unrepaired DNA, at least for Neandertal mtDNA. We are unable to measure this reduction accurately for nuclear DNA due to genuine sequence differences between the Neandertal and the human reference sequence. However, outside CpG sites the error rate in nuclear DNA is presumably similar to that in mtDNA, at roughly 1 error per 1000 bases in UDG/endoVIII treated, multi-pass sequences.

It has been previously reported (4) that UDG treatment removes C/G->T/A errors from ancient DNA sequences. However, since UDG treatment causes molecules to be lost, use of the enzyme has not been widely adopted, with some exceptions (40). UDG is particularly problematic for direct PCR studies, which usually target the longest possible template molecules; longer templates are more likely to contain at least one uracil and so be destroyed by UDG treatment. Fortunately, the introduction of direct high-throughput sequencing of ancient DNA has allowed very short (<100 bp) DNA fragments, which make up the vast majority of ancient DNA, to be efficiently sequenced in large quantities. Since uracil bases are concentrated close to the 5′- and 3′-ends in single-stranded overhangs (6,23,29), endoVIII will rescue many of the fragments that would have been excluded from sequencing after UDG treatment alone (Figure 1). The UDG/endoVIII protocol also repairs sites of uracil in double-stranded parts of molecules, although in our hands this repair is only ~20% efficient (data not shown). Further work exploring the effects of other repair enzymes on ancient DNA library yield and sequence accuracy may be useful. However, it will be desirable for future repair approaches to avoid any extra purification steps, as these inevitably cause loss of material.

The UDG/endoVIII protocol has the additional advantage that any remaining C/G->T/A misincorporations can be attributed to deamination of methylated cytosine residues (provided that UDG treatment is complete). The observation that C->T substitutions in CpG dinucleotides, but not in other dinucleotides, are resistant to repair by UDG and that this pattern does not occur in mtDNA but in nuclear DNA where it is reduced in CpG islands, strongly suggests that the signal stems from in vivo Neandertal methylation as opposed to postmortem DNA modifications. In order to determine the methylation status of any particular CpG site by this approach, very high sequence coverage would obviously be needed. However, the methylation status of a region such as a particular gene or CpG island will be measurable with more moderate sequence coverage. Furthermore, emerging techniques such as bisulphite treatment of small DNA quantities (e.g. Genetic Signatures’ MethylEasy Xceed kit) or single-molecule sequencing technologies that can distinguish 5′-m-C from C (41) may soon allow high-resolution analysis of methylation in ancient DNA. It might therefore become possible to investigate the activity of genes and phenomena such as X chromosomal inactivation and genetic imprinting in extinct species, provided that the signals are manifested in cells present in bones.

 SUPPLEMENTARY DATA
Note

Supplementary Data are available at NAR Online.

 FUNDING
Note

We thank the Presidential Innovation Fund of the Max Planck Society for funding. Funding for open access charge: Max Planck Society.

Conflict of interest statement. None declared.

 ACKNOWLEDGEMENTS

We thank Hernan Burbano, Paul Czechowski, Ed Green, Gregory Hannon, Emily Hodges, Tomislav Maricic, Philip Johnson, Pavao Rudan, Dejana Brajkovic, Zeljko Kucan and Ivan Gusic and the Croatian Academy of Sciences and Arts for collaboration and help.

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Asia populated through a single migration event from the south!

December 11, 2009
Genetic ‘map’ of Asia’s diversity

http://news.bbc.co.uk/2/hi/science/nature/8406506.stm

An international scientific effort has revealed the genetics behind Asia’s diversity.

The Human Genome Organisation’s (HUGO) Pan-Asian SNP Consortium carried out a study of almost 2,000 people across the continent.

Their findings support the hypothesis that Asia was populated primarily through a single migration event from the south.

The researchers described their findings in the journal Science.

They found genetic similarities between populations throughout Asia and an increase in genetic diversity from northern to southern latitudes.

The team screened genetic samples from 73 Asian populations for more than 50,000 single-nucleotide polymorphisms (SNPs).

These are variations in pieces of the DNA code, which can be compared to find out how closely related two individuals are genetically.

This is the first study to give a clear answer to the question on the origin of East Asian populations
Shuhua Xu Chinese Academy of Sciences

The study found that, as expected, individuals who were from the same region, or who shared a common language also had a great deal in common genetically.

But it also answered a question about the origin of Asia’s population. It showed that the continent was likely populated primarily through a single migration event from the south.

Previously, there has been some debate about whether Asia was populated in two waves – one to South East Asia, and a later one to central and north-east Asia, or whether only a single migration occurred.

Diversity explained

Edison Liu from the Genome Institute of Singapore was a leading member of the consortium.

He explained that the age of a population has a much bigger effect on genetic diversity than the population size.

“It seems likely from our data that they entered South East Asia first – making these populations older [and therefore more diverse],” he said.

“[It continued] later and probably more slowly to the north, with diversity being lost along the way in these ‘younger’ populations.

“So although the Chinese population is very large, it has less variation than the smaller number of individuals living in South East Asia, because the Chinese expansion occurred very recently, following the development of rice agriculture – within only the last 10,000 years.”

Dr Liu said that it was “good news” that populations throughout Asia are genetically similar.

This knowledge will aid future genetic studies in the continent and help in the design of medicines to treat diseases that Asian populations might be at a higher risk of.

And the discovery of this common genetic heritage, he added, was a “reassuring social message”, that “robbed racism of much biological support”.

This provides another important piece to the jigsaw puzzle of global human diversity
Peter Underhill, Stanford University

Shuhua Xu from the Chinese Academy of Sciences, who was a member of the consortium, said that this was “the first comprehensive study of genetic diversity and history of Asian populations”.

“This is the first study to ive a clear answer to the question on the origin of East Asian populations,” Dr Xu added.

Vincent Macaulay, a statistical geneticist at the University of Glasgow in the UK told Science magazine that the team had produced “a fabulous data set”.

The evidence for the southern coastal migration route, he said seemed “very strong”.

The consortium involved 90 scientists from 11 countries including China, India, Indonesia, Japan, Korea, Malaysia, Philippines, Singapore, Taiwan, Thailand and the US.

Peter Underhill, a geneticist from Stanford University who was not involved in this study said that it represented an investment of a “tremendous amount of time, work and inter-institution collaboration”.

He told BBC News: “This provides another important piece to the jigsaw puzzle of global human diversity.”

Story from BBC NEWS:
http://news.bbc.co.uk/go/pr/fr/-/2/hi/science/nature/8406506.stm

Published: 2009/12/11 15:38:27 GMT

Indus civilisation reveals its volumetric system!

November 15, 2009
Indus civilisation reveals its volumetric system byT. S. Subramanian

 

Appearing in “The Hindu” dated 15-11-2009

http://beta.thehindu.com/news/national/article48883.eceNote: This is posted here for critical discussion and further research, as the involved media and persons many times do not provide opportunity for the views of others.

Dr. Bryan Well (unseen), an expert on Indus Valley Civilisation, holding a tablet at The Institute of Mathematical Sciences, Taramani, Chennai. Photo: M. Karunakaran

The Hindu Dr. Bryan Well (unseen), an expert on Indus Valley Civilisation, holding a tablet at The Institute of Mathematical Sciences, Taramani, Chennai. Photo: M. Karunakaran

Combination of `V’ signs and linear strokes were used to indicate volumes

The Indus civilisation had a volumetric system with inscriptions on ceramic vessels (glazed pots from Harappa) indicating that the sign ‘V’ stood for a measure, a long linear stroke equalled 10, two long strokes stood for 20 and a short stroke represented one, according to Bryan Wells, who has been researching the Indus script for more than 20 years.

These markings on the pots are identical to those found on the incised tablets and bas-relief tablets also found in Harappa, said Dr. Wells, who earned his Ph.D. from Harvard University for his thesis on “The Epigraphic Approaches to Indus Writing.” It is to be published as a book in 2010.

Besides, a ceramic vessel from Mohenjo-Daro, which had fragments of blue-coloured bangles inside, had one long stroke and seven short strokes inscribed on it. When these broken pieces were reconstructed with a computer, they turned out to be 17 bangles. This again established that one long stroke equalled 10 and each short stroke one, Dr. Wells said. He described the findings as “an important discovery” and “very interesting.”

Dr. Wells has proposed that “these sign sequences [sign ‘V’ plus numerals] are various values in the Indus volumetric system. The bas-relief tablets might have been used as ration chits or a form of pseudo-money with the repetitive use of ‘V’ paired with ||, |||, |||| relating to various values in the Indus volumetric system. The larger the ceramic vessel, the more strokes it has. This postulation can be tested by detailed measurements of whole ceramic vessels with clear inscriptions.”

For instance, he recently measured the volume of the three pots from Harappa, which are now with the Archaeological Survey of India (ASI) at Purana Quila in New Delhi. While the smallest of them had three long strokes and a ‘V’ sign, the bigger one had six long strokes and a ‘V’ sign and the biggest seven long strokes and a scale inscribed below it. When he measured their volumes, Dr. Wells found that the pot with three long strokes had an estimated volume of 27.30 litres, the vessel with six long strokes 55.56 litres and the one with seven 65.89 litres. Thus, the calculated value of one long stroke was 9.24 or approximately 10 litres.

Dr. Wells (58), who is now a Senior Researcher in the Institute of Mathematical Sciences, Taramani here, has also focussed on creating an adequate sign list and corpus for the Indus script and the structural analysis of the Indus texts.

He said he first saw the pictures of these pots with markings in the “Corpus of Indus Seals and Inscriptions,” edited by Asko Parpola and his colleagues. When he learnt that the pots were with the ASI at Purana Quila, Dr. Wells travelled there to measure their volumes.

No coincidence

It was Michael Jansen, another researcher on Indus civilisation, who discovered the pot with broken bangles at Mohenjo-Daro in 1987. What intrigued Dr. Wells was the text of one long stroke and seven short strokes inscribed on it. When he reconstructed these broken pieces, using their internal circumferences, with a computer, he found that 17 bangles must have remained intact inside. Besides, the rake sign in the Indus script had a value of hundred and the double rake sign, 200. “This is completely regular” and “not a result of coincidence,” he said. When the ‘V’ sign with linear strokes that occurred on the Harappan tablets were found repeated on a number of ceramic vessels, “it gave me the idea that the ‘V’ sign is probably a measure,” Dr. Wells explained.

It was possible that wages were paid in grain (from these vessels) dispersed from a centralised storage facility, or in the case of incised tablets, material for construction projects and other short-term projects was distributed. He asserted that “there is archaeological evidence bearing on this issue in the form of standardised ceramics with texts describing their contents.”

“Fish” for weights

Dr. Wells agreed with another Indus scholar Steve Bonta’s (Pennsylvania State University) theory that the “fish” sign in the script stood for weights. According to Dr. Bonta, the fish sign occurred frequently with numbers in the script and in clusters too. He later found that the Akkadian Sargonic texts referred to the weight systems of Dilmun (Bahrain) as “minus.” The system of weights from Dilmun was exactly the same as that of the Indus system. Dr. Bonta, who speaks Tamil, realised that “min” in Tamil meant fish. “So our theory is that the term “minus” is derived from the Indus and that the fish are weights,” Dr. Wells said. There were fish signs with one long stroke, two long strokes, a single rake or a double rake. “So the sign graph is doubling and the value is doubling. I think this is too much of a coincidence. But I am aware that a lot of people will disagree with me on the fish sign,” he added.

Indus civilisation reveals its volumetric system T.S. Subramanian

http://www.hindu.com/2009/11/15/stories/2009111556932200.htm

Combination of ‘V’ signs and linear strokes were used to indicate volumes

— Photo credits: Bryan Wells

(Above) The three pots from Harappa with volumetric inscriptions on them. Calculations indicate that the Indus volumetric system is based on multiples of 9.24 litres. (Below) A reconstruction of broken bangles from the Moneer area of Mohenjo-Daro. The number of reconstructed bangles (17) matches the number from the sealing text on the pot that had the broken bangles inside. The other photo shows Indus fish signs.

CHENNAI: The Indus civilisation had a volumetric system with inscriptions on ceramic vessels (glazed pots from Harappa) indicating that the sign ‘V’ stood for a measure, a long linear stroke equalled 10, two long strokes stood for 20 and a short stroke represented one, according to Bryan Wells, who has been researching the Indus script for more than 20 years.

These markings on the pots are identical to those found on the incised tablets and bas-relief tablets also found in Harappa, said Dr. Wells, who earned his Ph.D. from Harvard University for his thesis on “The Epigraphic Approaches to Indus Writing.” It is to be published as a book in 2010.

Besides, a ceramic vessel from Mohenjo-Daro, which had fragments of blue-coloured bangles inside, had one long stroke and seven short strokes inscribed on it. When these broken pieces were reconstructed with a computer, they turned out to be 17 bangles. This again established that one long stroke equalled 10 and each short stroke one, Dr. Wells said. He described the findings as “an important discovery” and “very interesting.”

Dr. Wells has proposed that “these sign sequences [sign ‘V’ plus numerals] are various values in the Indus volumetric system. The bas-relief tablets might have been used as ration chits or a form of pseudo-money with the repetitive use of ‘V’ paired with ||, |||, |||| relating to various values in the Indus volumetric system. The larger the ceramic vessel, the more strokes it has. This postulation can be tested by detailed measurements of whole ceramic vessels with clear inscriptions.”

For instance, he recently measured the volume of the three pots from Harappa, which are now with the Archaeological Survey of India (ASI) at Purana Quila in New Delhi. While the smallest of them had three long strokes and a ‘V’ sign, the bigger one had six long strokes and a ‘V’ sign and the biggest seven long strokes and a scale inscribed below it. When he measured their volumes, Dr. Wells found that the pot with three long strokes had an estimated volume of 27.30 litres, the vessel with six long strokes 55.56 litres and the one with seven 65.89 litres. Thus, the calculated value of one long stroke was 9.24 or approximately 10 litres.


Dr. Wells (58), who is now a Senior Researcher in the Institute of Mathematical Sciences, Taramani here, has also focussed on creating an adequate sign list and corpus for the Indus script and the structural analysis of the Indus texts.

He said he first saw the pictures of these pots with markings in the “Corpus of Indus Seals and Inscriptions,” edited by Asko Parpola and his colleagues. When he learnt that the pots were with the ASI at Purana Quila, Dr. Wells travelled there to measure their volumes.

No coincidence

It was Michael Jansen, another researcher on Indus civilisation, who discovered the pot with broken bangles at Mohenjo-Daro in 1987. What intrigued Dr. Wells was the text of one long stroke and seven short strokes inscribed on it. When he reconstructed these broken pieces, using their internal circumferences, with a computer, he found that 17 bangles must have remained intact inside. Besides, the rake sign in the Indus script had a value of hundred and the double rake sign, 200. “This is completely regular” and “not a result of coincidence,” he said. When the ‘V’ sign with linear strokes that occurred on the Harappan tablets were found repeated on a number of ceramic vessels, “it gave me the idea that the ‘V’ sign is probably a measure,” Dr. Wells explained.

It was possible that wages were paid in grain (from these vessels) dispersed from a centralised storage facility, or in the case of incised tablets, material for construction projects and other short-term projects was distributed. He asserted that “there is archaeological evidence bearing on this issue in the form of standardised ceramics with texts describing their contents.”

“Fish” for weights

Dr. Wells agreed with another Indus scholar Steve Bonta’s (Pennsylvania State University) theory that the “fish” sign in the script stood for weights. According to Dr. Bonta, the fish sign occurred frequently with numbers in the script and in clusters too. He later found that the Akkadian Sargonic texts referred to the weight systems of Dilmun (Bahrain) as “minus.” The system of weights from Dilmun was exactly the same as that of the Indus system. Dr. Bonta, who speaks Tamil, realised that “min” in Tamil meant fish. “So our theory is that the term “minus” is derived from the Indus and that the fish are weights,” Dr. Wells said. There were fish signs with one long stroke, two long strokes, a single rake or a double rake. “So the sign graph is doubling and the value is doubling. I think this is too much of a coincidence. But I am aware that a lot of people will disagree with me on the fish sign,” he added.

 

Naming the god and the theological fight, but is linguistic!

July 22, 2009

Naming the god and the theological fight, but it is only linguistic!

Vedaprakash

In the “Year of Darwin”[1], as scientists have started discussing about the evolution of man, language etc., ordinary man has also started thinking in the same lines about the connected factors, as they are more concerned about them than the professors, experts and others, who conduct “conferences” inside air-conditioned halls with all facilities[2], whereas, they have to worry about Dhal selling at Rs. 100/ kg, rice Rs.100 / kg and so on. The Dhal and rice families never fool man, but the man fool man by his skill of economics, statistics, inflation, negative-inflation[3], but still prices going up!  So also, our Sanskrit imported Professors[4] start talking about “phylogeny vs epigenesist”, “origin of language” etc. in India!

The evolution and / or creation of man are connected with the concept of god and naming the god. Evolution might oppose god, but still “god” is denied there, however, without naming. Naming god as per the existing literature or the so-called “revealed books” of the “chosen” people[5] with such “books” (al-kithabiya) has been semantics coupled with theological syntax.

Man started pronouncing or rather naming the god as follows, according to his “sound” producing capabilities:

  • El-eli-ela-elah-elahi-elohim-
  • El-elah-elohim-elahi-allah
  • l-la-lah-lahi-laha [when this is combined with al-lah, it becomes allaha]
  • ha-aha-aya-hayah-yhwh [here, “l” sound is avoided]
  • m-am-um-iam [without opening mouth]-om-ohm [opening mouth][6]

YHWH and ALM: Scholars, theologians and other experts confess that they do not know how these two words or expressions have come, how to pronounce or what is the meaning. As for as ALM is concerned, Quranic experts claim that many ayats start with ALM implying Alif-lam-mim[7], but none knows its meaning. Thus, many claims are made by the biblical and quaranic scholars and pundits. The first name that God told Moses about was Hayah and it is a Hebrew word meaning I AM. The second name that God told Moses about was YHWH and it is also a Hebrew word for which only four consonants are used without any vowels. Thus, god only knows what YHWH means, or how is has to be pronounced.

Lord, LORD, God, GOD, LORD-GOD: However, the King James Version translates YHWH as “LORD” — all in capital letters and the practice of representing YHWH by “LORD” is done in many translations, including but not limited to the KJV, NKJV, NIV, and NAS[8]. Thus, LORD represents God’s name, YHWH, whereas “Lord” represents God’s, adonay. As they have difficulty or do not know how to translate, they may still translate “adonay YHWH” as “the Lord LORD,” Elohim is translated as God / god which means “mighty ones.” They know El (God in Hebrew), Eli (Singular), Elohim (Plural), Eloi (Aramic), Ilahi, elahi etc., denote only GOD, but mentioned as differently in the context.

The word used

Meaning

How many times appears

example

“EL” Mighty One

225

Gen. 14:20, “Blessed be the Most High EL”.
“YHVH” GOD’s Personal Name, not to be pronounced or not known

248

Is. 40:10,   “The Lord YHVH will come with a strong hand.”
“Tzur” A Rock

1

lsa. 44:8, “Yes, there is no Tzur,   I know not any.”.
“Elah” An object of Worship[9]

88

Ezra 5:11, “We are the servants of Elah of heaven”.
“Elohim” Object of Worship

2222

Plural used  in Hebrew to denote plenitude of might
.  “EL” Mighty One

225

. Gen. 14:20, “Blessed be the Most High EL”. Gen. 1:1,   “In the beginning Elohim created.”
“Eloah” An object of Worship

55

Deut. 32:17,  “They sacrificed unto devils, not to Eloah”.
“Theos” Object of Worship (in Greek)

1274

Matt. 1:23,  “They will call Him (the Messiah)  Emmanuel,  a Name which means ‘Theos is with us’ “.

God, existence of God, God knowing other God: In Bible, the following are quoted as the word of God (Exodus: 20:2-5):

  • I am the Lord your God, who brought you out of the land of Egypt, out of the house of slavery;
  • Do not have any other gods before me.
  • You shall not make for yourself an idol, whether in the form of anything that is in heaven above, or that is on the earth beneath, or that is in the water under the earth.
  • You shall not bow down to them or worship them; for I the Lord your God am a jealous God, punishing children for the iniquity of parents, to the third and the fourth generation of those who reject me,

Thus, the doubt of God thinking about, warning about other God is intriguing and interesting to note [Ontogeny]. If one God is the God, then, that God cannot think of another God existing on the earth and that earth too, in fact creation of that God only. Therefore, where is the question of anything existing below the earth or above in the heaven? Thus, one God talking about the exigencies of existence of other Gods proves that that God knew the existence of other Gods and therefore, he was “jealous God” as declared himself!

Ontogenesis, phylogenesis and epigenesis of God: Thus, it is quite evident that the scriptures mentioned or the literature of the people mentioned talk about the existence of more than one God in the sense, that the “jealous God” is so jealous about other God. Thus, the evolution or creation of the concept of God is closely related to the speech or language of the people evolved or created. If the sounds came out represented words and words formed into meaningful sentences and such sentences with all semantics and linguistic laws made them into identifiable language, and that language related to one particular people, as they spoke and thus, the language speaking people with that particular literature could be identified easily. As now, evolution requires male and female, necessarily, there has to be a family for god. As there have been “Son of God” [generally understood as Jesus, the son of Mary], “daughters of Allah” [al-Manat, al-Uzza and al-Lat] etc, it is evident that progeny of god is also implied.

Man, sex, language and mixing of races and languages[10]: Monogenetic or autogenetic creation of humanity has been divine and thus such things cannot take place. Only one Man can create woman[11] and only one Woman can create Man[12] and none can do such things thereafter. Thus, “the babel of tower” confronts the theologians, who make the deployment of linguists, psychologists, genetic experts and others come to rescue to come out with the concepts of ontogeny, phylogeny and epigeny in the creation of languages. Heterogenetics and variety of species, different languages etc., question the monogeny, autogeny, immaculate conception etc[13]. Thus, homosexuality confronts such theologians and scientific experts. However, in flora and fauna, there have been species that produce on their own. Believing in one makes to bewilder at times about the existence of more than one. Accepting more than one has no problem in considering one or the only one also without any difficulty. But, knowingly the existence of more than one, if one claims that it is only one and there is no one other than it etc., makes not only mathematics but also theology complicated. However, monists, monotheists and such other “only one” / “The One” hypothesists and theorists confront with others.

Vedaprakash

21-07-2009


[1] The year 2009 is the bicentennial of Darwin’s birthday, and sesquicentennial of publication of his book “The Origin of Species”.  http://darwin-year-2009.org/

However, the Indians never bother about Indian literature, where thousands of books have been written and available since c.3500 BCE etc., but, they are not worried about such 35 century year, 30 century year…….celebrations of the poet, astronomer etc.

[2] As in Chennai, we used to attend such conferences held in Five-star Hotels, where the elite and rich would come in BMWs and lecture about “Anatomy of poverty” and so on!

[3] The moment Chidambaram was made HM instead of FM, all have changed upside down or going reverse etc. in India. Note, now Kasab has started confessing differently.

[4] Note the irony, our Sanskrit Pundits and others have to listen to such “species” (with all due respects to Darwin), who descended here from heavens!

[5] In that way, other then the “chosen people”, the heathen / kafirs etc., have no redemption without the acceptance of Christ or Allah. The Afganisthanis have already started demanding Jizya from Kafirs.

[6] Of course, our Christian friends of expertise would give different interpretation about such “sounds”!

[7] Refer to Hussian Mohammed Pikthall’s translation of Quran for more details.

[8] Now, remember about Iravatham Mahadevan’s assertion about Authorized Version etc. Anyway, our Wales Professor of Sanksrit at Harvard University, USA has not still sent his papers and his friend IM has ben keeping quite!

Dr. Michael Witzel, Wales Professor of Sanskrit at Harvard University (USA), will deliver a set of three conferences in India. A very proper event in the year of the commemoration of Charles Darwin (1809-1882), the famous scientist who was opposed by the Christian church for so long time.

http://asiatica.org/news/2009/06/26/conferences-in-india/

[9] Here, also there would be debate about “worship” and “veneration” of Mary, Joseph, Jesus, Christ, Allah, Mohammed etc., as the respective believers would give different interpretation.

[10] Vedaprakash, Honing Celina, Yogic Ramdev, Worrying Christians and Gleeful Gays, dated 19-07-2009 posted in different forums.

[11] As Adam created Eve [autogenetic].

[12] As Mary begot Jesus [autogenetic ignoring Joseph or epigenetic with the impregnation of the Holy Spirit].

[13] So in the year of Darwin, the battalion of Holy Warriors has started trotting global countries taking about such things and educates the believers properly.