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letters in JAMA
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Sothis
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PostPosted: Fri Jun 25, 2010 11:49 am    Post subject: letters in JAMA Reply with quote

I just stumbled over an exciting news here
http://egyptology.blogspot.com/

The blog gives a direct link to the JAMA site which contains a number of letters from different scientists on various topics all related to the latest DNA study of Tut`s family.
One can only read the first 150 words for free. From what I have read one letter concerns once more the age of KV55, one Tut`s clubfoot saying it is no clubfoot at all but a condition of supine posture of the foot due to pain in the forefoot ( a suggestion which has already been made by a member of this forum - I`m not sure, maybe Osiris II?).
Another letter targets the "feminine appearance" of Tut and KV55 which was refuted by Hawass et al`s. The letter does not go on long enough (for free) to show what the author suggests but obviously it is said that the problem cannot be ruled out.
There are a few more topics including a response letter from Hawass`s team defending their testing methods.

Another blog entry states that German scientists claim that not Malaria but sickle cell disease might have killed Tut. It is not clear how they come to suspect this disease but they would like to test the DNA themselves (which of course they can only dream of).

Now is there anybody out there who is fanatic enough to download the whole letters? Or maybe we could agree on sharing the letters (and the financial burden - I don`t know how much they want)./

It is definitely very interesting stuff!!
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stephaniep
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PostPosted: Fri Jun 25, 2010 12:24 pm    Post subject: Reply with quote

These would certainly be good to read.

I wonder what happened to Hawaiss coming clean with the DNA information.
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PostPosted: Fri Jun 25, 2010 12:30 pm    Post subject: Reply with quote

A quick addition: I got the hang to the suggestion of sickle cell disease (SCD). The scientists claim that Malaria is unlikely to have killed Tut at his age as most deaths of Malaria occur before the age of 10.
SCD is a pretty common disease in Malaria infested areas. They say that the bone necrosis seen in Tut`s left foot could well be related to SCD.
Yuya and Thuja could have been carriers of SCD as they both were infected with Malaria but survived for long. Having only one gene for SCD obviously gives a certain protection against the Malaria parasite. Having inherited SCD from both parents though means that one suffers from this disease itself.
They conclude that both Yuya and Thuya may have had one SCD gene and Tut may have inherited two.

Interesting thought IMO.
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Toth
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PostPosted: Fri Jun 25, 2010 4:23 pm    Post subject: Reply with quote

I went to the JAMA site, hit the subscribe link (https://subs.ama-assn.org/ama/exec/subscribe and found out that they want US$ 165 for an annual subscription
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PostPosted: Fri Jun 25, 2010 6:07 pm    Post subject: Reply with quote

You`re right, it`s really a rip off. I don`t understand how they can charge $30 for a single article now when at the time Hawass`s report was published it costed only $12 or so.
I think our only hope is that someone may already be a subscriber.
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Toth
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PostPosted: Fri Jun 25, 2010 6:21 pm    Post subject: Reply with quote

Sothis wrote:
You`re right, it`s really a rip off. I don`t understand how they can charge $30 for a single article now when at the time Hawass`s report was published it costed only $12 or so.
I think our only hope is that someone may already be a subscriber.


Sothis,

I agree with you and have the same hope of someone here already having subscription and willing to share the article with us; I think they are trying to apply the rules of the the free market mechanism: If there is demand, then he who has the merchandise makes the prices.

Richard,aka
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neseret
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PostPosted: Fri Jun 25, 2010 7:18 pm    Post subject: Reply with quote

Toth wrote:
Sothis wrote:
You`re right, it`s really a rip off. I don`t understand how they can charge $30 for a single article now when at the time Hawass`s report was published it costed only $12 or so.
I think our only hope is that someone may already be a subscriber.


Sothis,

I agree with you and have the same hope of someone here already having subscription and willing to share the article with us; I think they are trying to apply the rules of the the free market mechanism: If there is demand, then he who has the merchandise makes the prices.


If anyone is interested in the JAMA letters, you will need to e-mail (PM) me with your private e-mail address and I can send a copy onto you.

Someone sent it to me in PDF format.
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Toth
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PostPosted: Fri Jun 25, 2010 8:17 pm    Post subject: Reply with quote

neseret wrote:
Toth wrote:
Sothis wrote:
You`re right, it`s really a rip off. I don`t understand how they can charge $30 for a single article now when at the time Hawass`s report was published it costed only $12 or so.
I think our only hope is that someone may already be a subscriber.


Sothis,

I agree with you and have the same hope of someone here already having subscription and willing to share the article with us; I think they are trying to apply the rules of the the free market mechanism: If there is demand, then he who has the merchandise makes the prices.


If anyone is interested in the JAMA letters, you will need to e-mail (PM) me with your private e-mail address and I can send a copy onto you.

Someone sent it to me in PDF format.


Neseret, Katherine,

The [email] button below each of my posts will give you my private email-address, and I would like to receive the JAMA-letters from you.


(Rich)ard, aka
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Sothis
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PostPosted: Sat Jun 26, 2010 7:20 am    Post subject: Reply with quote

Yesterday I passed my email address on to you via pm, neseret.
Can you please send a copy of the letters over when you have the time?
Thanks a lot!
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Aromagician
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PostPosted: Mon Jun 28, 2010 4:30 am    Post subject: Reply with quote

Okay, so those of you have seen it now could let us know the juicy bits please Very Happy
Especially in this letter
http://jama.ama-assn.org/cgi/content/short/303/24/2471?rss=1
I quote from the excerpt

To the Editor: In their study, Dr Hawass and colleagues1 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 al2 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." The age of the mummies (more than 3300 years before the present) coupled with their preservation history suggests that DNA survival is highly unlikely. Long-term survival of nuclear DNA sequences, as accessed by Hawass et al, is even . . . [Full Text of this Article]

Eline D. Lorenzen, PhD
edlorenzen@snm.ku.dk

Eske Willerslev, DSc
Center for GeoGenetics
Natural History Museum of Denmark
Copenhagen, Denmark
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Toth
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PostPosted: Mon Jun 28, 2010 9:44 pm    Post subject: Reply with quote

Sorry, its took a while

Quote:
... 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 polymerase chain reaction techniques rather than newly developed capture approaches coupled with second-generation sequencing techniques that allow for successful capture of degraded (shorter) DNA sequences.
Contamination is a major obstacle in human ancient DNA research. Although laboratory members 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 allele frequencies in present-day Egypt would have clarified the issue of modern contamination.
Another cause for concern is the lack of reported control measures in the genotyping of microsatellites.Potential genotyping errors include Allelic stutter, allelic dropouts, 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

Eline D. Lorenzen, PhD
email address held back by editor
Eske Willerslev DSc
Center for GeoGenetics
Natural History Museumof Denmark
Copenhagfen Denmark



Aromagician I hope it brings you what you were looking for my post continues were yours stops Very Happy
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PostPosted: Mon Jun 28, 2010 9:49 pm    Post subject: Reply with quote

Thanks.
But wasnt really. She is just disputing that they could get any correct dna. Which seems a bit futile really.

I was hoping for more juicier disputes over the analysis of the dna. As per our discussions on here Smile
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PostPosted: Mon Jun 28, 2010 10:05 pm    Post subject: Reply with quote

Aromagician wrote:
Thanks.
But wasnt really. She is just disputing that they could get any correct dna. Which seems a bit futile really.

I was hoping for more juicier disputes over the analysis of the dna. As per our discussions on here Smile


Hmm, I see; well you also could read from it that she is disputing the way Hawass et all handle the specimens AND the fact that the present day researchers from Egypt weren't genotyped (which I understand as recording someone's DNA, just in case it contaminates a sample, a technique commonly used in criminal DNA research)

Although things gradually start to become clearer, most of you discuss is way over my head, coming from a whole different discipline (Computers), doesn' really help me, so please be patient with me; I'm trying Laughing
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PostPosted: Mon Jun 28, 2010 10:24 pm    Post subject: Reply with quote

There isn`t that much juice in these letters but I still try to filter out the "juicy bits".
Thanks to neseret I got them for free so I do not have to regret having spent money on the letters. That`s because they aren`t actually much longer than the first bit which could be seen free of charge.

Anyway, I`d better start with the letter quoted by Aromagician.
The main points besides contamination are that as even mtDNA is nearly impossible to recover from ancient mummies it must be even harder (virtually impossible) to recover nuclear DNA which was the base of the kinship analysis.
They criticize that traditional polymerase chain reaction techiques were used instead of newly developed capture approaches with second-generation sequencing.

The response of Hawass et al`s (thereafter only called "the response"):
nuclear DNA was recovered and it was highly informative when processed with next generation sequencing (did they mention in the JAMA report that they used 2nd-generation sequencing? I think not).

Of course there is detailed response denying all reproaches of contamination.

Age of KV55:
All the previous examinations with their results are given together with what is a new estimate I believe by Baker giving an age range fron 18-23 at death. Besides the various pathological findings such as partial cleft palette, scoliosis etc. are doubted.

The response states that the examination made by Hawass`s team was more accurate and thorugh because it used CT-scan techniques whereas the previous examiners relied on X-ray images and the naked eye.
In short, they now know better than anyone before and could also discover the various previously unknown disorders.
Interestingly they do not point so much to the alleged signs of degeneration of the spine but say that generally the whole examination of all the bones indicate a much higher age than previously thought.

One letter concerns the clubfoot which isn`t a clubfoot after all as the authors say. The condition is consistent with a habitually supinated foot.

The response insists on the condition being not an acquired one but a congenital Grade1 clubfoot.


Interesting the letter on gynecomastia and craniosynostosis:
The author states that the absent to poorly developed interdigitated cranial sagittal sutures (of KV55 and Tut) are consistent with premature fusion seen in craniosynostosis.
The classic case of Antley-Bixler-syndrome manifests itself in deformed underdeveloped genitalia in both sexes due to insufficient estrogen production.
As Hawass speaks of Tut`s penis being well developed they suggest
another form of the disease:
They propose an as yet undescribed variant of the syndrome associated with excess estrogen production. That means they suggest a brand new disease for Tut and co.!
The response is not very enthusiastic saying in brief that the search for a novel disease gene would be inappropriate and impractical.

Finally the letter about malaria and SCD (sickle-cell disease):
The authors reason that death of malaria at Tut`s age is very unlikely as most of the victims are much younger (under 10).
The SCD can lead to death due to serious complications around the age of a young adult and can account for the alterations to the bone seen in Tut`s left foot. It interrelates with malaria infection ( to explain it all in detail I lack the patience but see my previous post, I believe the second one in this thread, for a bit more info) and can be determined by genetic testing for certain genes.

At least this time the response is more positive:
SCD is an interesting and plausible addition to the palette of potential disease diagnosis.

Apparently from now on they will have an eye on this disease as well.

That`s it as far as it concerns me, I hope my brief summary is a little bit helpful!
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Sothis
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PostPosted: Mon Jun 28, 2010 10:24 pm    Post subject: Reply with quote

There isn`t that much juice in these letters but I still try to filter out the "juicy bits".
Thanks to neseret I got them for free so I do not have to regret having spent money on the letters. That`s because they aren`t actually much longer than the first bit which could be seen free of charge.

Anyway, I`d better start with the letter quoted by Aromagician.
The main points besides contamination are that as even mtDNA is nearly impossible to recover from ancient mummies it must be even harder (virtually impossible) to recover nuclear DNA which was the base of the kinship analysis.
They criticize that traditional polymerase chain reaction techiques were used instead of newly developed capture approaches with second-generation sequencing.

The response of Hawass et al`s (thereafter only called "the response"):
nuclear DNA was recovered and it was highly informative when processed with next generation sequencing (did they mention in the JAMA report that they used 2nd-generation sequencing? I think not).

Of course there is detailed response denying all reproaches of contamination.

Age of KV55:
All the previous examinations with their results are given together with what is a new estimate I believe by Baker giving an age range fron 18-23 at death. Besides the various pathological findings such as partial cleft palette, scoliosis etc. are doubted.

The response states that the examination made by Hawass`s team was more accurate and thorugh because it used CT-scan techniques whereas the previous examiners relied on X-ray images and the naked eye.
In short, they now know better than anyone before and could also discover the various previously unknown disorders.
Interestingly they do not point so much to the alleged signs of degeneration of the spine but say that generally the whole examination of all the bones indicate a much higher age than previously thought.

One letter concerns the clubfoot which isn`t a clubfoot after all as the authors say. The condition is consistent with a habitually supinated foot.

The response insists on the condition being not an acquired one but a congenital Grade1 clubfoot.


Interesting the letter on gynecomastia and craniosynostosis:
The author states that the absent to poorly developed interdigitated cranial sagittal sutures (of KV55 and Tut) are consistent with premature fusion seen in craniosynostosis.
The classic case of Antley-Bixler-syndrome manifests itself in deformed underdeveloped genitalia in both sexes due to insufficient estrogen production.
As Hawass speaks of Tut`s penis being well developed they suggest
another form of the disease:
They propose an as yet undescribed variant of the syndrome associated with excess estrogen production. That means they suggest a brand new disease for Tut and co.!
The response is not very enthusiastic saying in brief that the search for a novel disease gene would be inappropriate and impractical.

Finally the letter about malaria and SCD (sickle-cell disease):
The authors reason that death of malaria at Tut`s age is very unlikely as most of the victims are much younger (under 10).
The SCD can lead to death due to serious complications around the age of a young adult and can account for the alterations to the bone seen in Tut`s left foot. It interrelates with malaria infection ( to explain it all in detail I lack the patience but see my previous post, I believe the second one in this thread, for a bit more info) and can be determined by genetic testing for certain genes.

At least this time the response is more positive:
SCD is an interesting and plausible addition to the palette of potential disease diagnosis.

Apparently from now on they will have an eye on this disease as well.

That`s it as far as it concerns me, I hope my brief summary is a little bit helpful!
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