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Orwell
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PostPosted: Tue Mar 06, 2012 12:09 am    Post subject: Reply with quote

Meretseger wrote:
You will also learn that professionals like Neseret NEVER express one hundred percent certainty about anything. Sort of like medical doctors.


That can only be prudent, Meretseger, when ultimately everyone is still 'guessing' rather than 'proving'. Laughing
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PostPosted: Tue Mar 06, 2012 1:36 am    Post subject: Reply with quote

Orwell wrote:
Meretseger wrote:
You will also learn that professionals like Neseret NEVER express one hundred percent certainty about anything. Sort of like medical doctors.


That can only be prudent, Meretseger, when ultimately everyone is still 'guessing' rather than 'proving'. Laughing


Especially when it comes to the Armana tar pits. When there are so few actual undisputed facts, a cast of really exciting characters, a religious movement that was short lived but at least for a time altered an entire civilization so that the usual rules may not have applied to this set of characters, plus the fact that later generations pretty much tried to erase them all from history--well pretty much everything's on the table.

Each new discovery, while it might settle a few points, seems to open up new areas of controversy and of course everyone has passionate opinions about the whole period and isn't budging from their opinions unless pried from them with a crowbar.

Fun isn't it!
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Orwell
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PostPosted: Tue Mar 06, 2012 2:53 am    Post subject: Reply with quote

Naunacht wrote:
Each new discovery, while it might settle a few points, seems to open up new areas of controversy and of course everyone has passionate opinions about the whole period and isn't budging from their opinions unless pried from them with a crowbar.

Fun isn't it!



I'm hanging on like a jellyfish to a few 'ideas' at the moment, Naunacht - or as grimly as my tentacles are able! Very Happy


I really should get some of my personal focus back on nailing down a few more 'Fatcs' on the KV55 thread - but it's just too easy to get distracted by other perplexing things on this Forum. Laughing
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Meretseger
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PostPosted: Tue Mar 06, 2012 5:22 pm    Post subject: Reply with quote

Orwell wrote:
Meretseger wrote:
You will also learn that professionals like Neseret NEVER express one hundred percent certainty about anything. Sort of like medical doctors.


That can only be prudent, Meretseger, when ultimately everyone is still 'guessing' rather than 'proving'. Laughing


Well that's the fun of it of course! Very Happy But one must be ready to go with the flow. For example my beloved theory that Kiya owed her high favor to being the mother of both Smenkhkara and Tutankhamun by Akhenaten has been very thoroughly exploded by the DNA evidence. Darn it!
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PostPosted: Tue Mar 06, 2012 5:35 pm    Post subject: Reply with quote

Meretseger wrote:
But one must be ready to go with the flow. For example my beloved theory that Kiya owed her high favor to being the mother of both Smenkhkara and Tutankhamun by Akhenaten has been very thoroughly exploded by the DNA evidence. Darn it!

Ah yes, but I was just reading a letter to the editor of JAMA from some geneticists who raise serious questions regarding the validity of the data. Very Happy


Quote:
To the Editor: In their study, Dr Hawass and colleagues reported ancient DNA data from 11 royal Egyptian mummies and used microsatellites to ascertain kinship among specimens. We question the reliability of the genetic data presented in this study and therefore the validity of the authors' conclusions. Furthermore, we urge a more critical assessment of the ancient DNA data in the context of DNA degradation and contamination.

The long-term survival of DNA is determined by the environmental history of the samples, and Gilbert et al argued in reference to mitochondrial DNA that “in most, if not all, ancient Egyptian remains, [ancient DNA] does not survive to a level that is currently retrievable.” <..> Long-term survival of nuclear DNA sequences, as accessed by Hawass et al, is even less likely than mitochondrial DNA, given lower copy numbers per cell. Success in the retrieval of putative nuclear DNA sequences is also surprising given the use of traditional polymerase chain reaction techniques rather than newly developed capture approaches coupled with second-generation sequencing that allow for successful capture of degraded (shorter) DNA sequences.​

Contamination is a major obstacle in human ancient DNA research. Although laboratory members involved in the study were genotyped, no persons handling the specimens prior to the study were included, raising a question of the reliability of the microsatellite profiles. Precautions such as genotyping of associated nonhuman remains and including information on the microsatellite allele frequencies in present-day Egypt would have clarified the issue of modern contamination.

Another cause for concern is the lack of reported quality control measures in the genotyping of microsatellites. Potential genotyping errors include allelic stutters, allelic dropout, short allele dominance, and null alleles, all of which can result in the incorrect identification of alleles. Even small error rates (0.01 per allele) can lead to high error rates in downstream applications, such as false paternity exclusion in kinship testing.


This is by Dr Eline D. Lorenzen, PhD, and Dr. Eske Willerslev, DSc, Center for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark

Soooo, maybe too early to throw out other theories?
I think the Amarna tarpits managed to capture some geneticists Twisted Evil
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PostPosted: Tue Mar 06, 2012 5:51 pm    Post subject: Reply with quote

Typical! There are NO certainties here in the tarpits! Wahahahah! Laughing
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PostPosted: Tue Mar 06, 2012 9:32 pm    Post subject: Reply with quote

I chanced over something about DNA evidence being a bit dicey where incest is involved... Idea

And it seems clear incest was involved! Laughing

(Though I shouldn't laugh about incest, I guess! Shocked )
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PostPosted: Wed Mar 07, 2012 2:06 pm    Post subject: Reply with quote

anneke wrote:
Meretseger wrote:
But one must be ready to go with the flow. For example my beloved theory that Kiya owed her high favor to being the mother of both Smenkhkara and Tutankhamun by Akhenaten has been very thoroughly exploded by the DNA evidence. Darn it!

Ah yes, but I was just reading a letter to the editor of JAMA from some geneticists who raise serious questions regarding the validity of the data. Very Happy




:


These critical letters were written quite early in June 2010 and were even treated to an own thread here

http://forum.egyptiandreams.co.uk/viewtopic.php?t=5076&start=0

The environmental conditions in the VoK (hot and due to flashfloods damp tombs) are of a kind that usually does not allow long-term DNA survival, whereas bodies found in cold or frozen conditions such as mammoths or Neanderthal bones stand much better chances to yield viable DNA although they are much older.

What do we make of it? Either take the DNA results as a big fraud and ignore them (what is quite hard) or go on happily wrestling around with the data, what is considerably more fun Smile
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PostPosted: Wed Mar 07, 2012 2:12 pm    Post subject: Reply with quote

Sothis wrote:


What do we make of it? Either take the DNA results as a big fraud and ignore them (what is quite hard) or go on happily wrestling around with the data, what is considerably more fun Smile


I completely forgot about the earlier thread!

My inclination is to go forward with the DNA data but to keep in mind that there is a possibility that they are not completely reliable.

LOL Yes it is way more fun to keep wrestling with the data provided Very Happy
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PostPosted: Wed Mar 07, 2012 3:22 pm    Post subject: Reply with quote

anneke wrote:
Meretseger wrote:
But one must be ready to go with the flow. For example my beloved theory that Kiya owed her high favor to being the mother of both Smenkhkara and Tutankhamun by Akhenaten has been very thoroughly exploded by the DNA evidence. Darn it!

Ah yes, but I was just reading a letter to the editor of JAMA from some geneticists who raise serious questions regarding the validity of the data. Very Happy


Quote:
To the Editor: In their study, Dr Hawass and colleagues reported ancient DNA data from 11 royal Egyptian mummies and used microsatellites to ascertain kinship among specimens. We question the reliability of the genetic data presented in this study and therefore the validity of the authors' conclusions. Furthermore, we urge a more critical assessment of the ancient DNA data in the context of DNA degradation and contamination.

The long-term survival of DNA is determined by the environmental history of the samples, and Gilbert et al argued in reference to mitochondrial DNA that “in most, if not all, ancient Egyptian remains, [ancient DNA] does not survive to a level that is currently retrievable.” <..> Long-term survival of nuclear DNA sequences, as accessed by Hawass et al, is even less likely than mitochondrial DNA, given lower copy numbers per cell. Success in the retrieval of putative nuclear DNA sequences is also surprising given the use of traditional polymerase chain reaction techniques rather than newly developed capture approaches coupled with second-generation sequencing that allow for successful capture of degraded (shorter) DNA sequences.​

Contamination is a major obstacle in human ancient DNA research. Although laboratory members involved in the study were genotyped, no persons handling the specimens prior to the study were included, raising a question of the reliability of the microsatellite profiles. Precautions such as genotyping of associated nonhuman remains and including information on the microsatellite allele frequencies in present-day Egypt would have clarified the issue of modern contamination.

Another cause for concern is the lack of reported quality control measures in the genotyping of microsatellites. Potential genotyping errors include allelic stutters, allelic dropout, short allele dominance, and null alleles, all of which can result in the incorrect identification of alleles. Even small error rates (0.01 per allele) can lead to high error rates in downstream applications, such as false paternity exclusion in kinship testing.


This is by Dr Eline D. Lorenzen, PhD, and Dr. Eske Willerslev, DSc, Center for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark

Soooo, maybe too early to throw out other theories?
I think the Amarna tarpits managed to capture some geneticists Twisted Evil


While the geneticists you mentioned may have doubts about the conclusions from the JAMA report, doubts alone won't invalidate those conclusions. If there is sufficient doubt about those conclusions then the testing should be redone with the latest methods and equipment available. This should also, if possible, include showing what mtDNA and Y Chromosome DNA lines Tutankhamun and family belong to.

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PostPosted: Wed Mar 07, 2012 4:32 pm    Post subject: Reply with quote

anneke wrote:

...

Quote:
To the Editor: In their study, Dr Hawass and colleagues reported ancient DNA data from 11 royal Egyptian mummies and used microsatellites to ascertain kinship among specimens. We question the reliability of the genetic data presented in this study and therefore the validity of the authors' conclusions. Furthermore, we urge a more critical assessment of the ancient DNA data in the context of DNA degradation and contamination.

The long-term survival of DNA is determined by the environmental history of the samples, and Gilbert et al argued in reference to mitochondrial DNA that “in most, if not all, ancient Egyptian remains, [ancient DNA] does not survive to a level that is currently retrievable.” <..> Long-term survival of nuclear DNA sequences, as accessed by Hawass et al, is even less likely than mitochondrial DNA, given lower copy numbers per cell. Success in the retrieval of putative nuclear DNA sequences is also surprising given the use of traditional polymerase chain reaction techniques rather than newly developed capture approaches coupled with second-generation sequencing that allow for successful capture of degraded (shorter) DNA sequences.​

Contamination is a major obstacle in human ancient DNA research. Although laboratory members involved in the study were genotyped, no persons handling the specimens prior to the study were included, raising a question of the reliability of the microsatellite profiles. Precautions such as genotyping of associated nonhuman remains and including information on the microsatellite allele frequencies in present-day Egypt would have clarified the issue of modern contamination.

Another cause for concern is the lack of reported quality control measures in the genotyping of microsatellites. Potential genotyping errors include allelic stutters, allelic dropout, short allele dominance, and null alleles, all of which can result in the incorrect identification of alleles. Even small error rates (0.01 per allele) can lead to high error rates in downstream applications, such as false paternity exclusion in kinship testing.


This is by Dr Eline D. Lorenzen, PhD, and Dr. Eske Willerslev, DSc, Center for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark

Soooo, maybe too early to throw out other theories?
I think the Amarna tarpits managed to capture some geneticists Twisted Evil


Isn't it amazing how many people get sucked into Amarna? I love your analogy of the "Amarna tarpits." Laughing

I was under the impression that wherever possible, genetic material in the Amarna mummies was extracted through the interiors of bones, in the marrow canals. While degradation is always a potential issue, contamination through this method should not be a concern.

Am I mistaken in this?

Cormac, thoughts?

However, I'm not saying the results should never be examined again. Nor should outside agencies be barred from studying the samples. That would be the ideal, but good luck getting the Egyptians to surrender any of the samples.
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cormac mac airt
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PostPosted: Wed Mar 07, 2012 5:13 pm    Post subject: Reply with quote

kmt_sesh wrote:
anneke wrote:

...

Quote:
To the Editor: In their study, Dr Hawass and colleagues reported ancient DNA data from 11 royal Egyptian mummies and used microsatellites to ascertain kinship among specimens. We question the reliability of the genetic data presented in this study and therefore the validity of the authors' conclusions. Furthermore, we urge a more critical assessment of the ancient DNA data in the context of DNA degradation and contamination.

The long-term survival of DNA is determined by the environmental history of the samples, and Gilbert et al argued in reference to mitochondrial DNA that “in most, if not all, ancient Egyptian remains, [ancient DNA] does not survive to a level that is currently retrievable.” <..> Long-term survival of nuclear DNA sequences, as accessed by Hawass et al, is even less likely than mitochondrial DNA, given lower copy numbers per cell. Success in the retrieval of putative nuclear DNA sequences is also surprising given the use of traditional polymerase chain reaction techniques rather than newly developed capture approaches coupled with second-generation sequencing that allow for successful capture of degraded (shorter) DNA sequences.​

Contamination is a major obstacle in human ancient DNA research. Although laboratory members involved in the study were genotyped, no persons handling the specimens prior to the study were included, raising a question of the reliability of the microsatellite profiles. Precautions such as genotyping of associated nonhuman remains and including information on the microsatellite allele frequencies in present-day Egypt would have clarified the issue of modern contamination.

Another cause for concern is the lack of reported quality control measures in the genotyping of microsatellites. Potential genotyping errors include allelic stutters, allelic dropout, short allele dominance, and null alleles, all of which can result in the incorrect identification of alleles. Even small error rates (0.01 per allele) can lead to high error rates in downstream applications, such as false paternity exclusion in kinship testing.


This is by Dr Eline D. Lorenzen, PhD, and Dr. Eske Willerslev, DSc, Center for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark

Soooo, maybe too early to throw out other theories?
I think the Amarna tarpits managed to capture some geneticists Twisted Evil


Isn't it amazing how many people get sucked into Amarna? I love your analogy of the "Amarna tarpits." Laughing

I was under the impression that wherever possible, genetic material in the Amarna mummies was extracted through the interiors of bones, in the marrow canals. While degradation is always a potential issue, contamination through this method should not be a concern.

Am I mistaken in this?

Cormac, thoughts?

However, I'm not saying the results should never be examined again. Nor should outside agencies be barred from studying the samples. That would be the ideal, but good luck getting the Egyptians to surrender any of the samples.


Samples taken from bone marrow would be one place. Another place would be the interior of teeth (pulp) also.

The article Anneke quotes does bring up some valid concerns when doing DNA testing, but in and of itself it doesn't disprove the results. It's easy to say such and such is wrong, but it's kind of meaningless unless one can show HOW it's wrong. If the scientific community, or parts thereof, really feel the results are inaccurate then it behooves them to retest the mummies and prove it. Until then the results will have to stand.

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PostPosted: Wed Mar 07, 2012 8:02 pm    Post subject: Reply with quote

cormac mac airt wrote:

The article Anneke quotes does bring up some valid concerns when doing DNA testing, but in and of itself it doesn't disprove the results. It's easy to say such and such is wrong, but it's kind of meaningless unless one can show HOW it's wrong.

That is scientifically speaking not meaningless at all. If there are major questions about the methodology, then it is reasonable to raise these. And they have indicated what they think the problems are: unreliable results from the gene sequencing and likelihood of contamination. There are articles that show the degradation of DNA over time and definitely under influence of higher temperatures.

If the methodology is not sound, then neither are the results/conclusions.

cormac mac airt wrote:
If the scientific community, or parts thereof, really feel the results are inaccurate then it behooves them to retest the mummies and prove it. Until then the results will have to stand.

cormac

I respectfully but completely disagree with that statement. The burden of proof is on those who claim to have made the scientific breakthrough by which they claim to now be able to extract DNA from mummies where it was by many not believed to be possible.

The issue is that these results are under some question. I do not see them as "standing" at this point. I think we need to consider these results as preliminary until further tested. If they cannot reproduce the results, then we cannot argue much of anything.

I think the results are enough of a surprise with KV 55 and KV 35 YL being siblings where there is no evidence whatsoever of such a sibling marriage and the overlap in DNA between Amenhotep III and Yuya which is very surprising, that the specter of contamination or error propagated through gene sequencing should be considered.

I think further tests are necessary, but one of the problems is that Hawass always refused to let other labs test the mummies. Maybe now he is gone the DNA results can be duplicated by an independent lab and we can figure out if there are real results here or if it's a mirage.
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PostPosted: Wed Mar 07, 2012 9:43 pm    Post subject: Reply with quote

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That is scientifically speaking not meaningless at all. If there are major questions about the methodology, then it is reasonable to raise these. And they have indicated what they think the problems are: unreliable results from the gene sequencing and likelihood of contamination.


And what I’m saying is that raising questions doesn’t invalidate the given conclusions. Perhaps “meaningless” was the wrong word, but thinking something is wrong doesn’t make it wrong. And my understanding from the JAMA report is that they used two separately staffed labs to verify their results. So any results given weren’t just a one-off.

Quote:
If the methodology is not sound, then neither are the results/conclusions.


Which is the problem, as so far the methodology hasn’t been proven to be unsound. It’s only been questioned. Further tests are going to be the only way to prove it beyond a reasonable doubt, one way or the other.

Quote:
I think we need to consider these results as preliminary until further tested. If they cannot reproduce the results, then we cannot argue much of anything.


Whether called preliminary or final they stand as the best information we currently have, until further testing proves otherwise. Which I do think ought to be done. I myself would like to see the ‘Western European” claim for Tutankhamun put to rest once and for all.

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PostPosted: Thu Mar 08, 2012 4:36 am    Post subject: Reply with quote

didn't some guy 10 years ago claim he did DNA testing on the royal mummies?
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