I know this is not a question and answer session, but I have questions. Thought I might as well ask them. Maybe someone here has time to answer or correct anything I've misunderstood in the following posted by Ramana:
<!--QuoteBegin-->QUOTE<!--QuoteEBegin-->Germ in belly proves Aryan theory
Hyderabad, Feb. 5: India got its genes through Indo-Aryans and the Neolithic practices and languages from the Fertile Crescent that makes up the ancient Egypt and the Mediterranean region. A joint study by Ms S. Manjulatha Devi, Irshad Ahmad and a few others of the city-based Centre for Liver Research and Diagnostics, Deccan College of Medical Sciences and Allied Hospitals, and the Centre for DNA Fingerprinting and Diagnostics, supported the hypotheses related to the gene flow in India through Indo-Aryans.
The scientists conducted the study on Helicobacter pylori, a pathogen that lives in human stomach. The species of H. pylori that is found in present day Indian population is similar to that of the European strain inhabiting the stomachs of people who live in the West. "This perhaps conveys the message that H. pylori was most probably introduced to the Indian subcontinent by ancient Indo-European nomadic people and our findings are, therefore, consistent with the idea of a possible gene flow into India with the arrival of Indo-Aryans," the scientists pointed out.
According to the study, H. pylori might have arrived in India at the same time when Indo-European language speaking people crossed into India around 4,000 or 10,000 years ago. The city scientists arrived at the conclusion that as H. pylori co-evolves with its host, the multiple population and sub-population of the pathogen speak about ancient human migrations. Since it was not clear how different waves of human migrations in South Asia shaped the population structure of H. pylori, the city scientists went for mapping genetic origins of the present day H. pylori in India and its genomic comparison with hundreds of isolates from different geographic regions.
"All the isolates analysed revealed European ancestry and belonged to H. pylori sub-population named hpEurope," they said. This simple looking organism has now emerged as a reliable biological marker for host-pathogen co-evolution and ancient human migration. It could even provide an insight into human origins and migration. The study is consistent with the hypothesis of co-evolution of H. pylori with human and could form a reliable foundation to test and reconstruct gene flow into India with the arrival of Indo-Aryans or otherwise, they added.<!--QuoteEnd--><!--QuoteEEnd-->I've been looking this over and it only produces more questions instead of answering things concretely. Part of this has to do with the way things are formulated in the news report (and may be made clearer in the published article of this research - if and when such a thing comes out), but some other questions are rather basic.
Basic questions first:
(1)
<!--QuoteBegin-->QUOTE<!--QuoteEBegin-->According to the study, H. pylori might have arrived in India at the same time when Indo-European language speaking people crossed into India around 4,000 or 10,000 years ago.<!--QuoteEnd--><!--QuoteEEnd-->No pro-AIT/AMT person has contended that IE speaking peoples came to India in that time-frame. So there is a fundamental mistake they've made here. It doesn't add up with anything else proclaimed about the AIT/AMT by its supporters. If the H pylori dates any event to that timeframe it still is meaningless as evidence for the pro-AIT/AMT side because the timing is sadly all wrong for WitSSel and his buddies. Herr WitSSel orders it to be 1800 bce (3800 bp) or later, no earlier - "Linguistically impossible do you hear." "Ja, wir horen es, Herr Kommandant!" replied the stroedels.
(2) Why is it that the Indian H. pylori strain(s)'s evolution as per the above research does not align with other genetics data coming in from Kivisild, Oppenheimer et al? Do the researchers not need to take that into account before they start turning data into a story of "what probably happened"? Because there are conflicting stories now.
<!--QuoteBegin-->QUOTE<!--QuoteEBegin-->"This perhaps conveys the message that H. pylori was most probably introduced to the Indian subcontinent by ancient Indo-European nomadic people and our findings are, therefore, consistent with the idea of a possible gene flow into India with the arrival of Indo-Aryans," the scientists pointed out.<!--QuoteEnd--><!--QuoteEEnd-->So no. This message that it "perhaps conveys" is rather inconsistent with other data. Why ignore that? Or are they saying only one research area's data is right and should be used to reconstruct the history of human migrations with? In that case, why do they choose H pylori DNA data over human DNA data? Do they not figure human DNA data might explain things more directly? (Personally, I think they should take everything into account and - if there must be stories - adjust stories accordingly.)
(3) I'm not sure what they are saying here. Or rather, they could not possibly be saying what it looks (to me) like they're saying:
<!--QuoteBegin-->QUOTE<!--QuoteEBegin-->The scientists conducted the study on Helicobacter pylori, a pathogen that lives in human stomach. The species of H. pylori that is found in present day Indian population is similar to that of the European strain inhabiting the stomachs of people who live in the West. [...] Since it was <b>not clear how different waves of human migrations in South Asia shaped the population structure of H. pylori</b>, the city scientists went for mapping genetic origins of the present day H. pylori in India and its genomic comparison with hundreds of isolates from different geographic regions.<!--QuoteEnd--><!--QuoteEEnd-->Here's what I'm reading: present Indian H pylori strains are similar to European strain (that is, what is present in Europeans). Next, they appear to be assuming different waves of human migrations into the Indian subcontinent (bold bit above), and saying they don't understand how that has influenced current H pylori in India. Therefore they "went for mapping genetic origins of the present day H. pylori in India and its genomic comparison with hundreds of isolates from different geographic regions". If I'm reading this right, then what does the same data tell them if they did NOT assume human migrations into the subcontinent?
Like I said, they could not be saying what I think they're saying. Otherwise it comes out looking like that dreary circular reasoning again. That couldn't be - imagine, scientists applying circular reasoning. Not that the article is devoid of that altogether: without proving Oryans they're talking about them. Grandiose. But can't hold it against them - other researchers have done the same. Problem is, the way it is now, it doesn't even speak of the same question-marked entities ("Indo-Oryans"), because the timeframe of 4,000 - 10,000 years ago is talking about a different thing.
(4) <!--QuoteBegin-->QUOTE<!--QuoteEBegin-->The city scientists arrived at the conclusion that as H. pylori co-evolves with its host, the multiple population and sub-population of the pathogen speak about ancient human migrations.<!--QuoteEnd--><!--QuoteEEnd-->Maybe the reporter has misconstrued what they said. Else, it's another case of how these city scientists are totally ignoring earlier research. If so, these guys will/should never get published, because it's been established for some years that H pylori can indeed be used as an indicator concerning human migrations:
http://www.sciencemag.org/cgi/content/ab.../5612/1582
<!--QuoteBegin-->QUOTE<!--QuoteEBegin-->Science 7 March 2003:
Vol. 299. no. 5612, pp. 1582 - 1585
DOI: 10.1126/science.1080857
Reports
<b>Traces of Human Migrations in Helicobacter pylori Populations</b>
Daniel Falush,1 Thierry Wirth,1 Bodo Linz,1 Jonathan K. Pritchard,2 Matthew Stephens,3 Mark Kidd,4 Martin J. Blaser,5 David Y. Graham,6 Sylvie Vacher,7 Guillermo I. Perez-Perez,5 Yoshio Yamaoka,6 Francis Mégraud,7 Kristina Otto,8 Ulrike Reichard,1 Elena Katzowitsch,8 Xiaoyan Wang,1 Mark Achtman,1* Sebastian Suerbaum8
Helicobacter pylori, a chronic gastric pathogen of human beings, can be divided into seven populations and subpopulations with distinct geographical distributions. These modern populations derive their gene pools from ancestral populations that arose in Africa, Central Asia, and East Asia. Subsequent spread can be attributed to human migratory fluxes such as the prehistoric colonization of Polynesia and the Americas, the neolithic introduction of farming to Europe, the Bantu expansion within Africa, and the slave trade.<!--QuoteEnd--><!--QuoteEEnd--> Come on, if I can find this article, so can they.
(5) Now comes more confusion. As the above ScienceMag abstract shows, current H pylori strains' origins have (thus far) been traced back into <b>Africa, Central Asia and E Asia.</b>
But the following article forgets H pylori has any origins in Central Asia, but brings in Europe instead (unless CA suddenly means "Europe" - that would be quite a nazi statement of them, since the nazis first started talking about expanding their European base into C Asia. When did people first start substituting Europe for C Asia anyway? And does this mean that CA's Turkmenistan is now in Europe? <!--emo&:blink:--><img src='style_emoticons/<#EMO_DIR#>/blink.gif' border='0' style='vertical-align:middle' alt='blink.gif' /><!--endemo--> I think it wants to enter the EU now....)
http://www.nytimes.com/2007/03/13/science/13para.html
<!--QuoteBegin-->QUOTE<!--QuoteEBegin-->Another faithful member of the human road show is Helicobacter pylori, a bacterium that inhabits half the stomachs in the world. It is a usually well-behaved guest, but gives its hosts ulcers when it acts up. Its pattern of geographic distribution matches that of its hostâs migrations, Dr. Mark Achtman of the Max Planck Institute in Berlin and colleagues reported in the journal Nature last month.
There are five ancestral populations of H. pylori â two in Africa, two in Europe and one in East Asia. But all had a common origin, Dr. Achtman said, in a bacterium that started to spread out from East Africa 58,000 years ago, give or take 3,000 years. This is the same time period in which modern humans are thought to have begun their migration out of Africa. The match in dates âimplies that H. pylori was present in Africa before the migrations, suggesting that Africa is the source of both H. pylori and humans,â Dr. Achtman and colleagues conclude evenhandedly.<!--QuoteEnd--><!--QuoteEEnd--> The same article also declares:
<!--QuoteBegin-->QUOTE<!--QuoteEBegin-->From samples collected around the world, Dr. Page W. Caufield and colleagues at New York University have found that the bacterium can be assigned by its DNA to several distinct lineages. One is found in Africans, one in Asians and a third in Caucasians (the people of Europe, the Near East and India), his team reported in last monthâs Journal of Bacteriology.<!--QuoteEnd--><!--QuoteEEnd-->So now Indians are not Dravidioids and Oryans but all are Caucasians instead. <!--emo&:blink:--><img src='style_emoticons/<#EMO_DIR#>/blink.gif' border='0' style='vertical-align:middle' alt='blink.gif' /><!--endemo--> Rather different from what the recent 'Indian study' on H. pylori has been saying.... Anyways, are they defining Causasians here with "the people of Europe, Near East and India", or are they talking about the spread of that third strain? :confused It actually looks like the former to me.
And what to make of this one:
http://www.medscape.com/viewarticle/457393_21
<!--QuoteBegin-->QUOTE<!--QuoteEBegin-->Molecular genetics has also been used to determine whether H. pylori is a recent colonizer of man or is an ancient infection. According to these studies, man has probably been colonized by H. pylori for eons. One-thousand-year-old pre-Colombian mummies had H. pylori present as fecal antigens. Similarly, some Venezuelan strains appear to resemble Asian strains, suggesting an origin from Asia. Maori strains from New Zealand are also sometimes of Asian type. So H. pylori molecular genetics mimic human migration patterns over the past 50,000 years.<!--QuoteEnd--><!--QuoteEEnd-->Hmmm, when they talk of the Asian type, do they mean the C Asian strain or the E Asian one.... (Unless we're still talking about C Asia as if it's the new Europe....)
(6) Final question for now. And it's a confusing one to explain.
Going by what I have understood of that news report about the work of "Ms S. Manjulatha Devi, Irshad Ahmad and a few others", India's H pylori is only being mapped now:
<!--QuoteBegin-->QUOTE<!--QuoteEBegin-->the city scientists went for mapping genetic origins of the present day H. pylori in India and its genomic comparison with hundreds of isolates from different geographic regions.<!--QuoteEnd--><!--QuoteEEnd-->I'm going to dump the flashy "Europe=Central Asia" and talk about these two regions as the distinct entities that they actually are.
The research paper in Question (4) above posits Central Asia as an origin for one or more H pylori strains. Is that the precursor for those in Europe?
How is/are our strain(s) related to those of Central Asia? And how is it related to the European one(s)? And where, how do we fit in with respect to other originating strains? If the Indian one is only being mapped now, why assume Oryans and therefore assume that the strain came from Europe (see Question (3))? Can't the current situation of H pylori in India be understood in the context of the bigger picture, rather than them having to fit it in in the present understanding of the spread and evolution of H.pylori - as if the current H pylori world mapping is frozen and all new data must fit in the existing pattern - by making comparisons to who it must have been inherited/transmitted from?
This is assuming I have read the news report right. As I said, I found it increasingly confusing.
<!--QuoteBegin-->QUOTE<!--QuoteEBegin-->Germ in belly proves Aryan theory
Hyderabad, Feb. 5: India got its genes through Indo-Aryans and the Neolithic practices and languages from the Fertile Crescent that makes up the ancient Egypt and the Mediterranean region. A joint study by Ms S. Manjulatha Devi, Irshad Ahmad and a few others of the city-based Centre for Liver Research and Diagnostics, Deccan College of Medical Sciences and Allied Hospitals, and the Centre for DNA Fingerprinting and Diagnostics, supported the hypotheses related to the gene flow in India through Indo-Aryans.
The scientists conducted the study on Helicobacter pylori, a pathogen that lives in human stomach. The species of H. pylori that is found in present day Indian population is similar to that of the European strain inhabiting the stomachs of people who live in the West. "This perhaps conveys the message that H. pylori was most probably introduced to the Indian subcontinent by ancient Indo-European nomadic people and our findings are, therefore, consistent with the idea of a possible gene flow into India with the arrival of Indo-Aryans," the scientists pointed out.
According to the study, H. pylori might have arrived in India at the same time when Indo-European language speaking people crossed into India around 4,000 or 10,000 years ago. The city scientists arrived at the conclusion that as H. pylori co-evolves with its host, the multiple population and sub-population of the pathogen speak about ancient human migrations. Since it was not clear how different waves of human migrations in South Asia shaped the population structure of H. pylori, the city scientists went for mapping genetic origins of the present day H. pylori in India and its genomic comparison with hundreds of isolates from different geographic regions.
"All the isolates analysed revealed European ancestry and belonged to H. pylori sub-population named hpEurope," they said. This simple looking organism has now emerged as a reliable biological marker for host-pathogen co-evolution and ancient human migration. It could even provide an insight into human origins and migration. The study is consistent with the hypothesis of co-evolution of H. pylori with human and could form a reliable foundation to test and reconstruct gene flow into India with the arrival of Indo-Aryans or otherwise, they added.<!--QuoteEnd--><!--QuoteEEnd-->I've been looking this over and it only produces more questions instead of answering things concretely. Part of this has to do with the way things are formulated in the news report (and may be made clearer in the published article of this research - if and when such a thing comes out), but some other questions are rather basic.
Basic questions first:
(1)
<!--QuoteBegin-->QUOTE<!--QuoteEBegin-->According to the study, H. pylori might have arrived in India at the same time when Indo-European language speaking people crossed into India around 4,000 or 10,000 years ago.<!--QuoteEnd--><!--QuoteEEnd-->No pro-AIT/AMT person has contended that IE speaking peoples came to India in that time-frame. So there is a fundamental mistake they've made here. It doesn't add up with anything else proclaimed about the AIT/AMT by its supporters. If the H pylori dates any event to that timeframe it still is meaningless as evidence for the pro-AIT/AMT side because the timing is sadly all wrong for WitSSel and his buddies. Herr WitSSel orders it to be 1800 bce (3800 bp) or later, no earlier - "Linguistically impossible do you hear." "Ja, wir horen es, Herr Kommandant!" replied the stroedels.
(2) Why is it that the Indian H. pylori strain(s)'s evolution as per the above research does not align with other genetics data coming in from Kivisild, Oppenheimer et al? Do the researchers not need to take that into account before they start turning data into a story of "what probably happened"? Because there are conflicting stories now.
<!--QuoteBegin-->QUOTE<!--QuoteEBegin-->"This perhaps conveys the message that H. pylori was most probably introduced to the Indian subcontinent by ancient Indo-European nomadic people and our findings are, therefore, consistent with the idea of a possible gene flow into India with the arrival of Indo-Aryans," the scientists pointed out.<!--QuoteEnd--><!--QuoteEEnd-->So no. This message that it "perhaps conveys" is rather inconsistent with other data. Why ignore that? Or are they saying only one research area's data is right and should be used to reconstruct the history of human migrations with? In that case, why do they choose H pylori DNA data over human DNA data? Do they not figure human DNA data might explain things more directly? (Personally, I think they should take everything into account and - if there must be stories - adjust stories accordingly.)
(3) I'm not sure what they are saying here. Or rather, they could not possibly be saying what it looks (to me) like they're saying:
<!--QuoteBegin-->QUOTE<!--QuoteEBegin-->The scientists conducted the study on Helicobacter pylori, a pathogen that lives in human stomach. The species of H. pylori that is found in present day Indian population is similar to that of the European strain inhabiting the stomachs of people who live in the West. [...] Since it was <b>not clear how different waves of human migrations in South Asia shaped the population structure of H. pylori</b>, the city scientists went for mapping genetic origins of the present day H. pylori in India and its genomic comparison with hundreds of isolates from different geographic regions.<!--QuoteEnd--><!--QuoteEEnd-->Here's what I'm reading: present Indian H pylori strains are similar to European strain (that is, what is present in Europeans). Next, they appear to be assuming different waves of human migrations into the Indian subcontinent (bold bit above), and saying they don't understand how that has influenced current H pylori in India. Therefore they "went for mapping genetic origins of the present day H. pylori in India and its genomic comparison with hundreds of isolates from different geographic regions". If I'm reading this right, then what does the same data tell them if they did NOT assume human migrations into the subcontinent?
Like I said, they could not be saying what I think they're saying. Otherwise it comes out looking like that dreary circular reasoning again. That couldn't be - imagine, scientists applying circular reasoning. Not that the article is devoid of that altogether: without proving Oryans they're talking about them. Grandiose. But can't hold it against them - other researchers have done the same. Problem is, the way it is now, it doesn't even speak of the same question-marked entities ("Indo-Oryans"), because the timeframe of 4,000 - 10,000 years ago is talking about a different thing.
(4) <!--QuoteBegin-->QUOTE<!--QuoteEBegin-->The city scientists arrived at the conclusion that as H. pylori co-evolves with its host, the multiple population and sub-population of the pathogen speak about ancient human migrations.<!--QuoteEnd--><!--QuoteEEnd-->Maybe the reporter has misconstrued what they said. Else, it's another case of how these city scientists are totally ignoring earlier research. If so, these guys will/should never get published, because it's been established for some years that H pylori can indeed be used as an indicator concerning human migrations:
http://www.sciencemag.org/cgi/content/ab.../5612/1582
<!--QuoteBegin-->QUOTE<!--QuoteEBegin-->Science 7 March 2003:
Vol. 299. no. 5612, pp. 1582 - 1585
DOI: 10.1126/science.1080857
Reports
<b>Traces of Human Migrations in Helicobacter pylori Populations</b>
Daniel Falush,1 Thierry Wirth,1 Bodo Linz,1 Jonathan K. Pritchard,2 Matthew Stephens,3 Mark Kidd,4 Martin J. Blaser,5 David Y. Graham,6 Sylvie Vacher,7 Guillermo I. Perez-Perez,5 Yoshio Yamaoka,6 Francis Mégraud,7 Kristina Otto,8 Ulrike Reichard,1 Elena Katzowitsch,8 Xiaoyan Wang,1 Mark Achtman,1* Sebastian Suerbaum8
Helicobacter pylori, a chronic gastric pathogen of human beings, can be divided into seven populations and subpopulations with distinct geographical distributions. These modern populations derive their gene pools from ancestral populations that arose in Africa, Central Asia, and East Asia. Subsequent spread can be attributed to human migratory fluxes such as the prehistoric colonization of Polynesia and the Americas, the neolithic introduction of farming to Europe, the Bantu expansion within Africa, and the slave trade.<!--QuoteEnd--><!--QuoteEEnd--> Come on, if I can find this article, so can they.
(5) Now comes more confusion. As the above ScienceMag abstract shows, current H pylori strains' origins have (thus far) been traced back into <b>Africa, Central Asia and E Asia.</b>
But the following article forgets H pylori has any origins in Central Asia, but brings in Europe instead (unless CA suddenly means "Europe" - that would be quite a nazi statement of them, since the nazis first started talking about expanding their European base into C Asia. When did people first start substituting Europe for C Asia anyway? And does this mean that CA's Turkmenistan is now in Europe? <!--emo&:blink:--><img src='style_emoticons/<#EMO_DIR#>/blink.gif' border='0' style='vertical-align:middle' alt='blink.gif' /><!--endemo--> I think it wants to enter the EU now....)
http://www.nytimes.com/2007/03/13/science/13para.html
<!--QuoteBegin-->QUOTE<!--QuoteEBegin-->Another faithful member of the human road show is Helicobacter pylori, a bacterium that inhabits half the stomachs in the world. It is a usually well-behaved guest, but gives its hosts ulcers when it acts up. Its pattern of geographic distribution matches that of its hostâs migrations, Dr. Mark Achtman of the Max Planck Institute in Berlin and colleagues reported in the journal Nature last month.
There are five ancestral populations of H. pylori â two in Africa, two in Europe and one in East Asia. But all had a common origin, Dr. Achtman said, in a bacterium that started to spread out from East Africa 58,000 years ago, give or take 3,000 years. This is the same time period in which modern humans are thought to have begun their migration out of Africa. The match in dates âimplies that H. pylori was present in Africa before the migrations, suggesting that Africa is the source of both H. pylori and humans,â Dr. Achtman and colleagues conclude evenhandedly.<!--QuoteEnd--><!--QuoteEEnd--> The same article also declares:
<!--QuoteBegin-->QUOTE<!--QuoteEBegin-->From samples collected around the world, Dr. Page W. Caufield and colleagues at New York University have found that the bacterium can be assigned by its DNA to several distinct lineages. One is found in Africans, one in Asians and a third in Caucasians (the people of Europe, the Near East and India), his team reported in last monthâs Journal of Bacteriology.<!--QuoteEnd--><!--QuoteEEnd-->So now Indians are not Dravidioids and Oryans but all are Caucasians instead. <!--emo&:blink:--><img src='style_emoticons/<#EMO_DIR#>/blink.gif' border='0' style='vertical-align:middle' alt='blink.gif' /><!--endemo--> Rather different from what the recent 'Indian study' on H. pylori has been saying.... Anyways, are they defining Causasians here with "the people of Europe, Near East and India", or are they talking about the spread of that third strain? :confused It actually looks like the former to me.
And what to make of this one:
http://www.medscape.com/viewarticle/457393_21
<!--QuoteBegin-->QUOTE<!--QuoteEBegin-->Molecular genetics has also been used to determine whether H. pylori is a recent colonizer of man or is an ancient infection. According to these studies, man has probably been colonized by H. pylori for eons. One-thousand-year-old pre-Colombian mummies had H. pylori present as fecal antigens. Similarly, some Venezuelan strains appear to resemble Asian strains, suggesting an origin from Asia. Maori strains from New Zealand are also sometimes of Asian type. So H. pylori molecular genetics mimic human migration patterns over the past 50,000 years.<!--QuoteEnd--><!--QuoteEEnd-->Hmmm, when they talk of the Asian type, do they mean the C Asian strain or the E Asian one.... (Unless we're still talking about C Asia as if it's the new Europe....)
(6) Final question for now. And it's a confusing one to explain.
Going by what I have understood of that news report about the work of "Ms S. Manjulatha Devi, Irshad Ahmad and a few others", India's H pylori is only being mapped now:
<!--QuoteBegin-->QUOTE<!--QuoteEBegin-->the city scientists went for mapping genetic origins of the present day H. pylori in India and its genomic comparison with hundreds of isolates from different geographic regions.<!--QuoteEnd--><!--QuoteEEnd-->I'm going to dump the flashy "Europe=Central Asia" and talk about these two regions as the distinct entities that they actually are.
The research paper in Question (4) above posits Central Asia as an origin for one or more H pylori strains. Is that the precursor for those in Europe?
How is/are our strain(s) related to those of Central Asia? And how is it related to the European one(s)? And where, how do we fit in with respect to other originating strains? If the Indian one is only being mapped now, why assume Oryans and therefore assume that the strain came from Europe (see Question (3))? Can't the current situation of H pylori in India be understood in the context of the bigger picture, rather than them having to fit it in in the present understanding of the spread and evolution of H.pylori - as if the current H pylori world mapping is frozen and all new data must fit in the existing pattern - by making comparisons to who it must have been inherited/transmitted from?
This is assuming I have read the news report right. As I said, I found it increasingly confusing.