A problem with the "Eddowes Shawl" DNA match

[Chris]

The DNA that is alleged to be Kosminski is haplogroup T1a1 and therefore will have 315.1c ...

Unless it's based on Y-chromosome DNA after all. I'm starting to think that anything is possible.

[mickreed]

Thanks for this Chris. I must say much of this is now going completely over my head! The reason I asked the question is that I thought that haplogroup T1a1, although not particularly common, wasn't rare either. Maybe I'm just misinterpreting the statistics.

No, you're quite right John. Not at all rare, although it is not at all typical (well under 5%) of Ashkenzai Jews, contrary to what RE says.

[mickreed]

Unless it's based on Y-chromosome DNA after all. I'm starting to think that anything is possible.

The book Chris, and I'm repeating myself, is so sloppy that anything is indeed possible.

[Peter Griffith aka gryff]

That's sad, and I must say at the moment I am regretting my involvement in this research.

I agree with mickreed and Robert, not your fault. And as I said on the other thread, TY for your patient attitude. A shining example of careful analysis amongst some of the over-the-top responses I have seen on the two threads I am following on this issue.

cheers, gryff

[mickreed]

even though it's a long time ago there are still great-nephews and -nieces of Aaron Kozminski living. I think there is a real responsibility on those concerned to provide credible evidence to back up the claims that have been published, especially considering the help that was given in the first place by members of this community.

Yes. This did happen a long time ago but it can still hurt. Neil Shelden tells us of one of his interviewees:

The lady told me at first she was very upset to learn that her great-great grandmother was a Jack the Ripper victim…

Such upset may be even greater amongst relatives of the alleged killer.

It's time for the purveyors of these claims to put up with some real evidence. Perhaps Admin should open a book where we can bet on whether they ever do. Odds, anyone?

[Chris]

Debs kindly sent me a link to a recent scientific paper by Kazakos et al., which was published in 2012 in the Annals of Human Genetics. It's available here:

http://onlinelibrary.wiley.com/doi/10.1111/j.1469-1809.2012.00711.x/pdf

The reason it's interesting is that the authors seem to have made a mistake similar to the one that appears to have been made here over 314.1C. They seem to have misdescribed the 315.1C mutation as 313.1C. They were studying members of a Greek family suffering from a rare disease, and sequenced their mitochndrial DNA. This table lists the differences they found from the standard reference sequence:



(Note that "homoplasmic" indicates the sequence variation is found in every copy of the mitochondrial DNA in the cell, whereas "heteroplasmic" means it's found only in some copies.)

Interestingly, they were using HaploGrep - the same web application that originated the "Global Private Mutation" terminology referred to by Dr Louhelainen. Obviously this application - unlike some other software - is not clever enough to recognise that 313.1C (or 314.1C) is equivalent to the common sequence variation 315.1C.

In this case, we have an additional indication that we should have expected 315.1C to be found, because the mitochondrial DNA is identified as belonging to haplogroup T2b, in which 315.1C is usually present:

http://www.ianlogan.co.uk/sequences_by_group/t2b_genbank_sequences.htm

The image below shows, on the left, how the HaploGrep application classifies the variations shown in the table above, with 313.1C described as a "global private mutation". On the right is the same thing with 313.1C replaced by 315.1C, which is described as a "hotspot", that is a very common variation. In both cases, the application ignores this variation when it tries to determine the haplogroup:

[lynn cates]

infallible scientists

Hello Chris, Debs. Thanks for posting that.

But surely the experts cannot make such mistakes? (heh-heh)

Cheers.
LC

[Theagenes]

Debs kindly sent me a link to a recent scientific paper by Kazakos et al., which was published in 2012 in the Annals of Human Genetics. It's available here:

http://onlinelibrary.wiley.com/doi/10.1111/j.1469-1809.2012.00711.x/pdf

The reason it's interesting is that the authors seem to have made a mistake similar to the one that appears to have been made here over 314.1C. They seem to have misdescribed the 315.1C mutation as 313.1C. They were studying members of a Greek family suffering from a rare disease, and sequenced their mitochndrial DNA. This table lists the differences they found from the standard reference sequence:

[ATTACH]16332[/ATTACH]

(Note that "homoplasmic" indicates the sequence variation is found in every copy of the mitochondrial DNA in the cell, whereas "heteroplasmic" means it's found only in some copies.)

Interestingly, they were using HaploGrep - the same web application that originated the "Global Private Mutation" terminology referred to by Dr Louhelainen. Obviously this application - unlike some other software - is not clever enough to recognise that 313.1C (or 314.1C) is equivalent to the common sequence variation 315.1C.

In this case, we have an additional indication that we should have expected 315.1C to be found, because the mitochondrial DNA is identified as belonging to haplogroup T2b, in which 315.1C is usually present:

http://www.ianlogan.co.uk/sequences_by_group/t2b_genbank_sequences.htm

The image below shows, on the left, how the HaploGrep application classifies the variations shown in the table above, with 313.1C described as a "global private mutation". On the right is the same thing with 313.1C replaced by 315.1C, which is described as a "hotspot", that is a very common variation. In both cases, the application ignores this variation when it tries to determine the haplogroup:

[ATTACH]16333[/ATTACH]

Well, that's probably the nail in the coffin. Thanks Chris.

The one issue that kept making me think that Edwards might have garbled something was the fact that he was calling 314.1c a global private mutation when it clearly wasn't. In other words it seemed like he was misusing the terminology. But this explains it -- it's a software problem, which was suggested as a possibility earlier in this thread.

I actually feel really bad for JL right now, as he's probably trying to figure out how to admit this publicly without destroying his career. If this were just a typical DNA identification gig it wouldn't be a big deal, but this has brought huge media attention to him and his university.

[Chris]

The one issue that kept making me think that Edwards might have garbled something was the fact that he was calling 314.1c a global private mutation when it clearly wasn't. In other words it seemed like he was misusing the terminology. But this explains it -- it's a software problem, which was suggested as a possibility earlier in this thread.

Just in case there's any remaining doubt about how HaploGrep would react to 314.1C, here's the result:

[Theagenes]

Just in case there's any remaining doubt about how HaploGrep would react to 314.1C, here's the result:

[ATTACH]16334[/ATTACH]

Yep, that pretty much takes care of it. It really is unfortunate, because this was pretty much the only worthwhile thing about this whole ordeal -- the possibility that there was a solid connection between a piece of physical evidence and one of the victims would have been a big deal, even without the dubious Kos connection.

Of course it's still important to remember that this does not disprove that the shawl could have been connected to Eddowes -- there's just no evidence to support it. It goes back to being a odd curiosity with an interesting but unverifiable backstory.

[mickreed]

Just in case there's any remaining doubt about how HaploGrep would react to 314.1C, here's the result:

[ATTACH]16334[/ATTACH]

Well done Chris and Debs. Superb work.

As Theagenes says, it's tough on JL. As one of my contacts said:

It is possible that he realized his mistakes (after they were pointed out to him) and he just does not know how to admit to them.

I think that could be right.

[mickreed]

Just in case there's any remaining doubt about how HaploGrep would react to 314.1C, here's the result:

Hi Chris

I just looked at the EDNAP/EMPOP page which has the following:

The EDNAP group chose to address these topics. The question to be answered was whether analyses performed in different laboratories using different strategies and technical equipment would have the same results. In order to find a standard procedure as a common ground for harmonised mtDNA analysis and sequence data interpretation, a collaborative exercise was performed according to existing principles of forensic quality control. A set of samples was sent to participating laboratories. The results were compared and employed to identify potential sources of errors in mtDNA analysis [Parson 2004]. Four major classes of mtDNA sequencing errors were identified in the collaborative exercise [Parson 2004, Bandelt 2004]:

clerical errors – mistakes in manual data transfer causing wrong sequence results (while raw data are correct)
sample mix-up or artificial recombination – wrong assembly of sequence data for samples analysed in separate reactions (while raw data are correct)
contamination
nomenclature inconsistencies – a sequence string can be aligned in varying ways to a reference sequence, leading to differing motifs while the mere nucleotide string is the same. If more than one approach of alignment is applied to a dataset, matches can be missed and haplotypes may appear rarer than they are. The phylogenetic approach [Parson 2007a, Bandelt 2008] respects the origin of a sequence and its signature mutations. It points out the similarity of closely related samples, as subsequently harboured (younger) mutations will not affect the alignment motif of the common (older) background. This approach is favoured by EDNAP. Difficulties in nomenclature also appear when length or point heteroplasmies in a sample are detected and called to varying extents.

http://gerichtsmedizin.at/empop_database.html

[mickreed]

As Theagenes says, it's tough on JL.

Paradoxically, I'm even finding myself slightly sorry for RE - at least on this point. Although he beat up the DNA unacceptably, he was entitled to - at least re Eddowes - to believe the science as expressed by JL. Of course a more self-critical writer would have got a second opinion at the very least.

However, on every other point, I feel no sympathy for him at all, so on balance my sorrow is limited.

[Chris]

Of course a more self-critical writer would have got a second opinion at the very least.

I think one problem with all of this is that the publisher seems to have placed such stringent limitations on the results being discussed with anyone else before publication.

Having said that, we're nearly a month on from publication now, and there is still no willingness to discuss the results.

[GUT]

I think one problem with all of this is that the publisher seems to have placed such stringent limitations on the results being discussed with anyone else before publication.

Having said that, we're nearly a month on from publication now, and there is still no willingness to discuss the results.

In my opinion the silence has been deafening.