Posted by Kate Phizackerley on Tuesday, June 01, 2010

Marianne Luban has bought the Discovery video about the DNA testing of King Tut and family and, with some pausing and reversing of the film, has managed to copied down what Carsten Pusch handed to Hawass to look at comparing the DNA of Tutankhamun and the larger foetus.

This is what Marianne sent me:

Tut:9/101210(11)15+1727293391318206122323
F2:9/10--61418/19262530813102011(12)12(13)2623


I've not seen this segment of the documenary yet so I've not copied this down myself and cannot vouch for the accuracy.  I'll try to do it after the show this week.  (Saturday's repeat of the second part also started earlier than expected so I also missed a lot of it but I did record the comparison between the Elder and Younger Ladies so I'll work on that at some point.

What is clear is that the DNA table in the documentary does include some data which was dropped from the JAMA paper.  This may be because some data is not considered reliable; however as a general point I believe that papers should include all data in an appendix and give reasons why it has been excluded.  It also looks as if some of the data might have been "sharpened" before publication (possibly by comparing the results from the second lab).

My thanks to Marianne.  As copying from screen can be hard, if anybody else manages to copy DNA down then I'd appreciate an email so that I can verify my own jottings.

15 comments:

Marianne Luban said...

What I think is also quite interesting is that Yuya and Thuya, Amenhotep III, Tutankhamun and the KV55 individual all share the rare blood group of A2. Many years ago, before anyone ever heard of DNA an Egyptian national, Dr. Daoud Matta did a serological study of some people in both Upper and Lower Egypt. It was shown that less than 1% of this population bore the subgroup of A2.
A2 is a rare type, in general. Most people, who carry blood type A have A1--about 95%. The greatest incidence of A2 is in the Scandinavian lands.

The Elder Lady does not have A2 but O. That is also the group that was determined, with difficulty, from the larger foetus.

Anonymous said...

My apologies if this is a stupid question, but shouldn`t the Elder Lady have A2 as both of her parents have it? Could she have inherited a different blood group from a grandparent which "skipped" both Yuya and Thuya?
And how could the blood group 0 have come down to the foetus? I suppose this would be another indication that Nefertiti must have been related to Queen Tiye in order for this blood type to be passed down assuming the babies really were Tut`s and Ankhesenamun`s kids.
Have they found out the bloodtypes of the KV21 ladies yet?
Sorry this is more a bulk of questions than a comment. I`m very grateful for any answers.

Anonymous said...

I`ve just quickly compared the data provided by Marianne Luban with the data from the JAMA paper and I am quite confused. The data from the show does not only contain more numbers but many of the numbers from the paper do not show up here (e.g.29,34,23 etc.).
Isn`t it possible that in the show not the real data but some sort of control data was displayed as it obviously was the case with the Y-DNA?

Kate Phizackerley said...

Blood Group
I had not looked at blood group and am endebted to Marianne for pointing it out.

It is possible though for two parents with blood group A to give birth to a child with blood group O so it is not a barrier to regarding the Elder Lady as the child of Thuya and Yuya.

DNA
I certainly want to compare the data myself when the show is broadcast but I did compare the data Marianne sent me with that in the JAMA paper and I believe they did show the real data. I'll try to write it up neatly in the same format. There are some discrepancies in the last digit in a number of alleles - I want to check those very carefully. There are others were there is a substantial difference.

I don't think this would be surprising. I suspect the TV documentary shows the results from just one lab (the one managed by Carsten Pusch) whereas the JAMA paper probably shows the combined results. If that is the case we might be able to deduce where data has lower confidence. I repeat again we shouldn't need to do that as the confidence for each data point should be clearly set out in the published paper. The more time I spend on this the more I feel that while the DNA gathering and analysis might have been top-notch, the paper iteself displays some significant weaknesses.

Kate Phizackerley said...

I watched the show (but put it on disk as well). The shots in the meeting where the DNA is displayed look to me to have been shot contemporaneously (although that is obviously just my personal opinion). The difficulty Marianne had is that there are no headings for the alleles. That makes it hard to tie back to the JAMA paper. However, since much of the DNA matches the JAMA paper I think that can give us columns (and it is probably sorted in the same order anyway). On that basis, I think the show does offer a window. I won't have chance to look until next week as I've just volunteered to draft a briefing paper for a charity and that's going to take most of my time over the next couple of days.

Anonymous said...

Kate, why don't you just stop all this speculation and leave it to the experts - whatever you think you might discover is hardly going to be accepted by JAMA and the SCA anyway........

Anonymous said...

Why leave it all to the experts? I think we are right to look at their work and their results with interest and a critical eye. Experts are still humans and as such they can make mistakes, draw wrong conclusions or fail to recognize implications. Therefore scientific work is usually not only reviewed by peers but also repeated by independent institutions, something that Hawass does not want to happen for whatever reason.
So regardless of any attention of "real" scientists we should go on discussing points we think might yield additional or different information to that being presented to us. Keep it up, Kate!

Kate Phizackerley said...

When I did A Levels it was considered unaccptable to present the results of any experiment without publishing all of the raw data. Anybody who reads the UK press of magazines like New Scientist will also be aware of the controversy surrounding climate change with the allegations that scientists selected the data that supported their case and suppressed (or in some case deleted) raw data which could allow other scientists to form a different opionin. While not suggesting this has happened in this case, it highlights why everybody should be rightly sceptical of *any* science paper which presents only selected data.

My view is that if scientists fail to publish the raw data their findings should be questioned and their professional credibility abd standing should be legitmately on the on the line. That is especially true if their findings are in any way controverisal or disputed.

I feek that all believers in the independence of science should protest loudly if raw data has been withheld from publication and as a point of principle refuse to accept the findings until the lacunae are filled.

Anonymous said...

Anon, Kates reworking and "unpacking of the experts case strikes a chord with many readers including myself. I never cease to be amazed how often the so called experts miss something significant. However if you are happy with a world where you accept everything you are told then you are very, very welcome to it! DaveH

Anonymous said...

I find it striking that in the data presented in the show there are quite a lot dissimilarities between Tut`s and the foetus` data sets. There are no matching alleles on three loci (the second, third and fourth) which would to my knowledge not suggest a fathr-daughter relationship, yet Pusch announces to Hawass that they found half of Tut`s DNA in the foetus` DNA.
The JAMA paper presents different data which shows matching alleles where available. How does it come that the data has changed in a way that supports the theory that the foetus is Tut`s daughter? Has anyone any explanations?

Marianne Luban said...

All the loci don't have to match on a paternity test.

But I am curious about Yuya and Thuya. Since they are both A2 with antigen of N, what are the chances of two people with a blood type from a pool of less than 1% of the population marrying? Surely they have a common ancestor somewhere. Novelist Thomas Mann had them as brother and sister in his book about Akhenaten, but we now know this wasn't so,

Stephanie said...

To be honest I am still confused because what I heard up to now is that even one mismatching locus excludes paternity.
And IMO it is intruiging if not fishy that in one profile are several mismatching loci but in the other all loci match (as far as available).

Witlessd said...

I've checked the data that Marianne copied down and I can see how the figures relate to the columns that were published in JAMA. The final figures must've been averages of the 16 readings (if I understand this correctly) so that the sheet that was seen on the TV show was simply one of these.

As the paper stated it: "Sixteen Y-chromosomal short tandem repeats (DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385, DYS393, DYS391, DYS439, DYS635, DYS392, Y-GATA-H4, DYS437, DYS438, DYS448) were amplified according to the manufacturer's protocol using the AmpF\STR Yfiler PCR amplification kit (Applied Biosystems, Foster City, California). The Identifiler kit and the AmpF\STR Minifiler kit (Applied Biosystems) were used for amplification of 8 polymorphic microsatellites of the nuclear genome (D13S317, D7S820, D2S1338, D21S11, D16S539, D18S51, CSF1PO, FGA)."

In all the instances except one, the variation between the version Marianne copied and the one published is no more than one. Eg: for Tutankhamun, Marianne'snumbers for the 1st five microsites are as follows:
9/10, 12; 10(11), 15+; 17, 27; 29, 34; 9, 13 (for the first 5 microsites) become the published:
10, 12; 10, 15; 16, 26; 29, 34; 8, 13.

The one exception is the 30 for Foetus 2, which in the published paper becomes a signifcantly higher 35. That's important, of course, because that 35 matches with KV21A's 35. If they hadn't matched, then the latter couldn't possibly be the mother of the second foetus. I daresay this was a rogue low reading, excluded because a significant number of other readings gave the higher number.

As for the apparent additional numbers noted by Anonymous on 2 June, alleles for a full 8 microsatellites were published in the JAMA paper. I suspect that this reader was using Kate Phizackerley's table (http://2.bp.blogspot.com/_58zNbfB6CcM/S4yYQpcQXAI/AAAAAAAAAq8/EYSrnVxIC4E/s1600-h/Extended-Tut-Family-Alleles.png) which omits the final two sites (CSF1PO & FGA). The JAMA version cannot now be accessed free so I can't link to it, though at some point, I managed to save a copy.

Witlessd said...

I've checked the data that Marianne copied down and I can see how the figures relate to the columns that were published in JAMA. The final figures must've been averages of the 16 readings (if I understand this correctly) so that the sheet that was seen on the TV show was simply one of these.

As the paper stated it: "Sixteen Y-chromosomal short tandem repeats (DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385, DYS393, DYS391, DYS439, DYS635, DYS392, Y-GATA-H4, DYS437, DYS438, DYS448) were amplified according to the manufacturer's protocol using the AmpF\STR Yfiler PCR amplification kit (Applied Biosystems, Foster City, California). The Identifiler kit and the AmpF\STR Minifiler kit (Applied Biosystems) were used for amplification of 8 polymorphic microsatellites of the nuclear genome (D13S317, D7S820, D2S1338, D21S11, D16S539, D18S51, CSF1PO, FGA)."

In all the instances except one, the variation between the version Marianne copied and the one published is no more than one. Eg: for Tutankhamun, Marianne'snumbers for the 1st five microsites are as follows:
9/10, 12; 10(11), 15+; 17, 27; 29, 34; 9, 13 (for the first 5 microsites) become the published:
10, 12; 10, 15; 16, 26; 29, 34; 8, 13.

Witlessd said...

The one exception is the 30 for Foetus 2, which in the published paper becomes a signifcantly higher 35. That's important, of course, because that 35 matches with KV21A's 35. If they hadn't matched, then the latter couldn't possibly be the mother of the second foetus. I daresay this was a rogue low reading, excluded because a significant number of other readings gave the higher number.

As for the apparent additional numbers noted by Anonymous on 2 June, alleles for a full 8 microsatellites were published in the JAMA paper. I suspect that this reader was using Kate Phizackerley's table (http://2.bp.blogspot.com/_58zNbfB6CcM/S4yYQpcQXAI/AAAAAAAAAq8/EYSrnVxIC4E/s1600-h/Extended-Tut-Family-Alleles.png) which omits the final two sites (CSF1PO & FGA). The JAMA version cannot now be accessed free so I can't link to it, though at some point, I managed to save a copy.

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