A problem with the "Eddowes Shawl" DNA match

[Lechmere]

Maybe it was felt your presence would adorn the proceedings?

[Nick Spring]

Why is it that none of the awkward question wallahs are attending the conference?
The £130 isn't to listen to Russell Edwards or Dr Jari. This is the delegate fee that was set before anyone even knew about the book.
I believe a certain P Begg is on the schedule along with Sarah Wise and many more speakers with interesting talks. I believe there is a musical (!) and also a mock trial of Maybrick. And of course meals are inclusive... and there is the opportunity to socialise and discuss matters with like minded people.
Who could possibly want more!
Questions can be put to Russell Edwards and Dr Jari - and they will be there for the whole weekend so far as I know - and not hiding. So over an all inclusive cup of coffee with, who knows, maybe a digestive or custard cream thrown in as well for good measure, you may be able to pin Dr Jari down over the 314.1c haplogrep and the EMPOP database.
All this 'will they or won't they answer questions' is quite academic as those members of the awkward squad and who ponder this dilemma are steadfast in not attending.

Hi,

Well said. The conference isn't just about the shawl.

I'm going and it will great just to be there and meet people.

Best wishes

Nick

[MrBarnett]

To paraphrase Mrs Merton:

So, Dr Loopylou, what was it that first attracted you to multimillionaire Russell Edwards?

[mickreed]

To paraphrase Mrs Merton:

So, Dr Loopylou, what was it that first attracted you to multimillionaire Russell Edwards?

I think there are two issues here. There's the book overall, and my views on that are clear. I don't think it stacks up. I also think that the author takes liberties with the available information and that his conclusions don't follow from his 'facts' most of the time and his arguments are very weak. In fact, as I've said, I don't think the book is at all good.

And then there's the science conducted by JL. Some harsh things have been said about him, and I don't think they are fair. There is no evidence that he has done anything except to try and help RE, and Robin Napper before him. All we have to go on regarding that help, and the results obtained, are the book and various interviews in the media. From these sources we are entitled to try and clarify our understanding of what the science means. Chris Phillips, in particular, has produced what seems to me to be a plausible critique of the work as published in the book and those questions should be resolved. We are absolutely entitled to question and to wonder how to get answers.

I'm not sure that shooting JL is going to achieve such a resolution. It would be ironic if we lost our chances of such a clarification by spouting off willy-nilly.

The nature of these forums is to be informal. We all express ourselves a bit loosely at times, and that's fine, but really we ought to play the ball and not the bloke.

When I've been guilty of playing the bloke rather than the ball, then I shouldn't have done. We might get better information if we all strive to do better.

[Peter Griffith aka gryff]

I think there are two issues here. There's the book overall, and my views on that are clear. I don't think it stacks up. I also think that the author takes liberties with the available information and that his conclusions don't follow from his 'facts' most of the time and his arguments are very weak. In fact, as I've said, I don't think the book is at all good.

And then there's the science conducted by JL. Some harsh things have been said about him, and I don't think they are fair. There is no evidence that he has done anything except to try and help RE, and Robin Napper before him. All we have to go on regarding that help, and the results obtained, are the book and various interviews in the media. From these sources we are entitled to try and clarify our understanding of what the science means. Chris Phillips, in particular, has produced what seems to me to be a plausible critique of the work as published in the book and those questions should be resolved. We are absolutely entitled to question and to wonder how to get answers.

I'm not sure that shooting JL is going to achieve such a resolution. It would be ironic if we lost our chances of such a clarification by spouting off willy-nilly.

The nature of these forums is to be informal. We all express ourselves a bit loosely at times, and that's fine, but really we ought to play the ball and not the bloke.

When I've been guilty of playing the bloke rather than the ball, then I shouldn't have done. We might get better information if we all strive to do better.

Totally agree Mick

cheers gryff

[MrBarnett]

OK, let's play the ball. Why would a respected scientist be keen to help a wheeler dealer businessman construct a case for Kosminski being JTR when the science could never support such a claim?

That's something I would really like to know. I can think of only two possibilities: naivety or venality (the latter might not involve cash changing hands, the opportunity to self publicise would be just as attractive and potentially just as financially rewarding in the long run).


MrB

[robhouse]

post deleted.......

[Archaic]

"Global Private Mutation"

Hi everybody.

Does anyone have a reliable source within the field of DNA research for the definition of "Global Private Mutation"?

It strikes me as oxymoronic.

I've heard the phrase "Local Private Mutation" used in genetic research, which makes much more sense to me.

Medicine.net defines 'Private Mutation' as follows:

Private mutation: A rare gene mutation that is usually found only in a single family or a small population. A private mutation occurs and is passed to a few family members, but not to future generations.

So how does a 'Private Mutation' occurring in a single family or small definition go 'Global'? By mass emigration? By definition a 'Private Mutation' is NOT passed down to future generations.

- Wouldn't the fact of being passed to "future generations" by definition render the Genetic Mutation no longer 'Private'?

- Wouldn't becoming 'Global' by definition render the Genetic Mutation no longer 'Local'?

Thanks everybody,
Archaic

[Caligo Umbrator]

OK, let's play the ball. Why would a respected scientist be keen to help a wheeler dealer businessman construct a case for Kosminski being JTR when the science could never support such a claim?

That's something I would really like to know. I can think of only two possibilities: naivety or venality (the latter might not involve cash changing hands, the opportunity to self publicise would be just as attractive and potentially just as financially rewarding in the long run).


MrB

Hi MrBarnett,
" Why would a respected scientist be keen to help a wheeler dealer businessman construct a case for Kosminski being JTR when the science could never support such a claim?"
Firstly, being that JL is a scientist specifically engaged in DNA research I should imagine that he, along with many other scientists working in the same field, would be very interested in the proposition of extracting DNA and mDNA samples from such a reputedly antique artifact, particularly given its potential historical significance.
It would present an interesting and valuable research opportunity and allow for the use, development and demonstration of new DNA/mDNA extraction techniques. The benefits to the scientific community would be that such an undertaking would advance knowledge and understanding in regards to general forensic work that might be encountered in the future and specifically might also reveal valuable information that could be used to further the study of other historical artifacts.
Secondly, how can you assert that the science would never support such a claim? Its a bold statement. Until the science has been finalized; that is it has been investigated, reported in full and reviewed by others in the field, there is no way to determine whether a new technique, such as that used in the investigation, would have benefits or not.

I don't think it is any way helpful to describe JL as being venal. He is, I am sure, like most scientists, interested in seeking out the truth of the matter, whatever he is engaged in. To imply that he has engaged himself upon this project because he is open to some form of bribery, as the phrase you used does suggest, steers awfully close to libelous defamation.

Yours, Caligo

[mickreed]

Hi everybody.

Does anyone have a reliable source within the field of DNA research for the definition of "Global Private Mutation"?


Thanks everybody,
Archaic

Hi Archaic

It seems as though the answer is a local' one in that it is specific to the people behind Haplogrep rather than a definition used 'globally' within the field. They define it thus:

c. global private mutation: mutation never observed in Phylotree, probably due to inconsistent alignments, phantom mutations or point heteroplasmies (R, Y, K...)

See page 2.

It would be my contention, I think, that the issue of 314.1C is a case of an 'inconsistent alignment' or a 'phantom mutation'. Given that one of the most authorative books on the subject says this and seems to make clear that 314.1C should be expressed as 315.1C, I don't think that's unreasonable

[mickreed]

I don't think it is any way helpful to describe JL as being venal. He is, I am sure, like most scientists, interested in seeking out the truth of the matter, whatever he is engaged in. To imply that he has engaged himself upon this project because he is open to some form of bribery, as the phrase you used does suggest, steers awfully close to libelous defamation.

Yours, Caligo

Absolutely agree, Caligo. It's just simply wrong, in a human sense, to make claims like this based on nothing.

In addition, if we are to get to the truth of this matter, it won't help to antagonise those who can help us get there.

[Chris]

It would be my contention, I think, that the issue of 314.1C is a case of an 'inconsistent alignment' or a 'phantom mutation'.

I suppose it's a question of semantics how exactly it should be described. In a sense I think it's subtly different from either of those, in that the sequence has been correctly obtained, but has been described in a way that HaploGrep doesn't understand properly (though other software and search algorithms do).

[mickreed]

Hi Archaic

c. global private mutation: mutation never observed in Phylotree, probably due to inconsistent alignments, phantom mutations or point heteroplasmies (R, Y, K...)

And, moreover, if 314.1C would normally be expressed as 315.1C as I think it should have been, then it is extremely unlikely to appear in Phylotree, so would immediately show as a 'global private mutation'.

As Chris made clear earlier, most software seems to correct for these 'errors of nomenclature' but Haplogrep seems not to.

I did ask them about this - no response as yet.

[mickreed]

And, moreover, if 314.1C would normally be expressed as 315.1C as I think it should have been, then it is extremely unlikely to appear in Phylotree, so would immediately show as a 'global private mutation'.

As Chris made clear earlier, most software seems to correct for these 'errors of nomenclature' but Haplogrep seems not to.

Additional support for Chris's findings:

In the Batista,1995 study of HVR2, for example, additional cytosines were labeled 303.1, 303.2, and 313.1. In our nomenclature, these same sites are numbered 309.1, 309.2, and 315.1.

http://www.bioanth.cam.ac.uk/mtDNA/errata.html

Page 12 of this http://www.haplosite.com/static/reso...aplosearch.pdf

FBI site http://www.fbi.gov/about-us/lab/fore...002/wilson.htm Example 19 and associated alignments

[0070] When typing the HV2CS, the order in which the alignment algorithm computer programming instructions for the Standard Rules are applied is different. This change preserves the statistically-likely placement of the sixth C after the 310T as 315.1C in the event that there is a second indel in the sample in the 310 to 315 subregion of the HV2CS.

http://www.google.com.au/patents/WO2009143212A1?cl=en

There are countless other pieces like this. There seems to be no doubt that, where there are 6 cytosines between 311 and 315 (inclusive) rather than the 5 in the rCRS - which is what 314.1C is saying - then it should always be expressed as 315.1C and this is found in most people. Not rare at all.

[MrBarnett]

Hi MrBarnett,
" Why would a respected scientist be keen to help a wheeler dealer businessman construct a case for Kosminski being JTR when the science could never support such a claim?"
Firstly, being that JL is a scientist specifically engaged in DNA research I should imagine that he, along with many other scientists working in the same field, would be very interested in the proposition of extracting DNA and mDNA samples from such a reputedly antique artifact, particularly given its potential historical significance.
It would present an interesting and valuable research opportunity and allow for the use, development and demonstration of new DNA/mDNA extraction techniques. The benefits to the scientific community would be that such an undertaking would advance knowledge and understanding in regards to general forensic work that might be encountered in the future and specifically might also reveal valuable information that could be used to further the study of other historical artifacts.
Secondly, how can you assert that the science would never support such a claim? Its a bold statement. Until the science has been finalized; that is it has been investigated, reported in full and reviewed by others in the field, there is no way to determine whether a new technique, such as that used in the investigation, would have benefits or not.

I don't think it is any way helpful to describe JL as being venal. He is, I am sure, like most scientists, interested in seeking out the truth of the matter, whatever he is engaged in. To imply that he has engaged himself upon this project because he is open to some form of bribery, as the phrase you used does suggest, steers awfully close to libelous defamation.

Yours, Caligo

Hi Caligo,

Do you suppose that the first opportunity JL had of investigating DNA from an 'antique artifact' was when RE knocked on his door?

Perhaps it was. Poor old JL was sitting there drumming his fingers on his expensive Zeiss kit waiting for someone to turn up with a tabloid conundrum such as JTR, Nessie or the Turin shroud and, guess what, it was his lucky day.

MrB