A problem with the "Eddowes Shawl" DNA match

[Rosella]

A piece of red gauze silk (neckerchief) was reportedly around Eddowes' neck when she was undressed at the mortuary. It was among the clothing itemised.

Incidentally, isn't it strange the way red appears over again in this case?

A red glow in the sky due to a huge fire in the Docks the night Polly Nichols was killed.

Chapman had a neckerchief of white with a red border around her neck.

Eddowes was wearing a piece of red gauze silk around hers.

Stride had a red rose on her breast (perhaps bought by a client.)

Kelly wore a dark red shawl.

Jack was attracted to the colour or excited by it maybe?

[Mr Lucky]

314.1C isn't a location. The location is just 314. It just means the 314th letter in the sequence.

314.1C describes the mutation. It describes the way in which the sequence differs from the standard reference sequence. It's just shorthand for the insertion of one extra C after position 314. That's all there is to it.

Of course it's a location - what are you talking about ? And as for the rest of it that's not the case at all, you are making a false assumption that the inserted sequence is the same length as the replaced code, but this is not always the case. mtDNA can vary in length by hundreds of base pairs. How the sequence starting nomenclature is defined is clearly dependent on the length of the insertion and where the mutation finishes and the standard sequence continues - none of which we know in this case.

Just to be clear, all I am saying at present is that some kind of error has been made. It could be an error in the description of the sequence variation, or it could be an error in the estimation of its frequency, or it could be a combination of the two. To understand what's gone wrong, we need information from Dr Louhelainen.

No, nothing has "gone wrong" at all. What specifically leads you to believe something has "gone wrong"?

Similarly, you have created a thread claiming there is "a problem with the "Eddowes Shawl" DNA match". Yet you have so far failed to produce any evidence in support of this, whatsoever.

Are you still claiming there is a problem with the match or not ? Is this what you think has "gone wrong" ?

Can you produce any evidence at all to back up either of these claims?

And are you going to address any of the points raised previously that seriously damage your argument put forward so far?

1) What is the distinction between the kind of rare mutations known as a "global private mutation" and standard genome variance as found in a variety of databases.

2) Why the Eddowes family mutation is being specifically described as a "sequence variation" when the error you believe this refers to only actually alters the number of C's in the sequence, when this particular type of mutation is known as polymorphism and not a sequence variation at all.

3) Why does this issue only effects two of the many samples tested, yet the issue with the variance in the poly-cytosine region as describe by you would effect all the samples tested.

Perhaps it would be a good idea just to wait for that now. I hope it won't be too long in coming.

Perhaps it would have been a good idea if you had waited from the start, rather than publicly claiming that there is a problem with "the Eddowes shawl DNA match" without any evidence of this in the first place.

[Mr Lucky]

All this DNA talk goes right over the head of this small town midwestern boy. But I'm hoping my comparatively simple questions to Mr. Lucky don't go unanswered.

Mr. Lucky, you're on record as a hardcore Lechmerian, yet you seem to believe in the 'science' that puts Eddowes' and Koz's DNA on the shawl. Does this mean you think Eddowes was a one-off by Koz and thus not a Ripper victim?

Yours truly,

Tom Wescott

Hi Tom,

From what I know so far, whether the mtDNA matches or not, we cannot conclude anything from the evidence along those lines.

I still think Cross killed all the W10

[Natasha]

A piece of red gauze silk (neckerchief) was reportedly around Eddowes' neck when she was undressed at the mortuary. It was among the clothing itemised.

Incidentally, isn't it strange the way red appears over again in this case?

A red glow in the sky due to a huge fire in the Docks the night Polly Nichols was killed.

Chapman had a neckerchief of white with a red border around her neck.

Eddowes was wearing a piece of red gauze silk around hers.

Stride had a red rose on her breast (perhaps bought by a client.)

Kelly wore a dark red shawl.

Jack was attracted to the colour or excited by it maybe?

Hi Rosella

I think there is something important about the items the women had in their possession, for example the bonnet that Nichols had that no one had seen before.

Could it be possible that 2 people were involved in the killings? I think so. I think maybe one of them picked the women out, for what reason I don't know, by giving them an item that made them identifiable to the killer.

[Chris]

Mr Lucky

The problem is that you are misunderstanding so many of the basics, and when someone does try to explain them to you, you refuse to accept the explanation.

But I'll try again.

The positions in the reference sequence are just whole numbers, such as 314. So 314.1C is not a position. As I keep explaining, it is shorthand for a variation in the sequence - it means an extra C inserted after position 314.

I'm not making an assumption that there is no change in the length of the sequence. Obviously, if an extra C is inserted in the sequence, the length of the sequence increases by one!

"What has gone wrong" is that 314.1C results in an identical sequence to 315.1C, and 315.1C is not rare, but extremely common.

In answer to the final three questions:

(1) "Global Private Mutation" appears to be a term particular to the HaploGrep web application. It's defined as a "mutation never observed in Phylotree, probably due to inconsistent alignments, phantom mutations or point heteroplasmies".

http://haplogrep.uibk.ac.at/docs/UserManual-HaploGrep.pdf

(2) A polymorphism is a sequence variation.

(3) That's a good question (assuming you mean "if 314.1C is equivalent to 315.1C, and 315.1C is common, why wasn't it found in any of the control samples?"). But as I've said, it's not clear whether what's happened is an error in the description of the mutation, or an error in the estimation of its rarity. That's why we need more information from Dr Louhelainen.

And no - obviously it would not have been a good idea to keep quiet about this problem, because if I'd done that it might not have been spotted at all!

[Abby Normal]

A piece of red gauze silk (neckerchief) was reportedly around Eddowes' neck when she was undressed at the mortuary. It was among the clothing itemised.

Incidentally, isn't it strange the way red appears over again in this case?

A red glow in the sky due to a huge fire in the Docks the night Polly Nichols was killed.

Chapman had a neckerchief of white with a red border around her neck.

Eddowes was wearing a piece of red gauze silk around hers.

Stride had a red rose on her breast (perhaps bought by a client.)

Kelly wore a dark red shawl.

Jack was attracted to the colour or excited by it maybe?

the red hanky of sailor man and A man

[Mr Lucky]

The problem is that you are misunderstanding so many of the basics, and when someone does try to explain them to you, you refuse to accept the explanation.

I think we both know the problem is that I know enough about the subject to realise your 'explanations' are intrinsically unreliable.

But I'll try again.

The positions in the reference sequence are just whole numbers, such as 314. So 314.1C is not a position. As I keep explaining, it is shorthand for a variation in the sequence - it means an extra C inserted after position 314.

I'm not making an assumption that there is no change in the length of the sequence. Obviously, if an extra C is inserted in the sequence, the length of the sequence increases by one!

"What has gone wrong" is that 314.1C results in an identical sequence to 315.1C, and 315.1C is not rare, but extremely common.

Oh dear, yes, once again - that effects ALL the samples tested so by definition it isn't a "global private mutation". Therefore it isn't the "global private mutation" that ONLY effect the Eddowes family mtDNA. Is this simple chain of reasoning really too much for you to follow?

(1) "Global Private Mutation" appears to be a term particular to the HaploGrep web application. It's defined as a "mutation never observed in Phylotree, probably due to inconsistent alignments, phantom mutations or point heteroplasmies".

http://haplogrep.uibk.ac.at/docs/UserManual-HaploGrep.pdf

Well done. That's right a "global private mutation" is a mutation that doesn't appear in the databases, unlike the well known problem with poly-cytosine region you've described above.

(2) A polymorphism is a sequence variation.

No it's not, the mutation you are describing is called a 'single nucleotide polymorphism' and it is definitely not a sequence variation - I suspect what has confused you this particular time is that a sequence variation is made up of multiple single nucleotide polymorphisms.

(3) That's a good question (assuming you mean "if 314.1C is equivalent to 315.1C, and 315.1C is common, why wasn't it found in any of the control samples?"). But as I've said, it's not clear whether what's happened is an error in the description of the mutation, or an error in the estimation of its rarity. That's why we need more information from Dr Louhelainen.

No that's not what I asked at all, and no we don't need more information, I think even more information would simply confuse you further as you're still struggling to understand the stuff we have already, as you demonstrated again dealing with the above 3 questions

And no - obviously it would not have been a good idea to keep quiet about this problem, because if I'd done that it might not have been spotted at all!

What "problem" is this? how many problem(s) do you now believe there are in total ?

And once again;-

Have you got any evidence at all to back up your claims that there is a problem with "the Eddowes Shawl DNA match" or are you going to do the decent thing and publicly retract that claim.

[Chris]

Mr Lucky

OK - I give up at this point. Some people are simply ineducable.

[mickreed]

Have you got any evidence at all to back up your claims that there is a problem with "the Eddowes Shawl DNA match" or are you going to do the decent thing and publicly retract that claim.

I really can't be bothered with this. I must be potty.

But Lucky, all we have, so far, is the description of the science in the book, which admittedly includes an extract from an email by JL. The latter is written for a layman, Edwards, and - I'd lay good dosh on this - does not express JL's findings the way he would express them in a scientific paper.

If memory serves, Chris did, at some point, say there is a problem with the description of the science. Until we see the actual science, then we don't know whether there's a problem with that. Chris's work has enabled him to contact JL who, I hope, will be able to allay Chris's anxieties, or else correct the description of the science.

After all, you in an earlier post, said that you hadn't seen the actual sequence, so you don't know either.

[Mr Lucky]

Mr Lucky

OK - I give up at this point. Some people are simply ineducable.

Are you admitting there isn't a problem with the DNA match?

[Chris]

Are you admitting there isn't a problem with the DNA match?

No - I'm saying I've been very patient and explained it to you several times, and apparently you still can't understand it. So I am now giving up trying to explain it to you. Life's too short.

And frankly, comments like the one you've just made only go to confirm that that's the right decision.

[Mr Lucky]

Are you still sticking by notion of typing the wrong mtDNA sequence into the wrong data base, and then citing the production of the wrong answer as "evidence" that there is a problem with the DNA match?

[Chris]

Mr Lucky

You're now just misrepresenting the facts. Please stop doing that.

[Mr Lucky]

You're now just misrepresenting the facts. Please stop doing that.

No I'm not. Here it is

Incidentally, if you put 315.1C 315.2C into the EMPOP database, you'll see that while it is rare - about 0.18% - it's not remotely as rare as 1 in 290,000.

You have put the wrong information into the wrong database then got the wrong answer out, and finally you drew the wrong conclusion! ( I hope you have cited this in the correspondence you have had with the 'experts' btw.)

So is this the evidence that you believe shows there is a problem with the match between the Eddowes family DNA and the shawl sample?

[Chris]

Mr Lucky

I see what you mean.

Well, admittedly it was indeed the "wrong information", because it derived from your mistaken suggestion that "314.1C" meant "314.1C 315.1C", or in the correct nomenclature "315.1C 315.2C". I put it into the EMPOP database - the same one Dr Louhelainen is quoted as saying he used - simply in order to demonstrate that it was nowhere near as rare as 1 in 290,000, the figure quoted in the book.

But in any case, it was only an incidental remark, because it was obvious from the start that your suggestion was incorrect - because 314.1C means the insertion of a single C after 314, not two Cs.

The more of this stuff you come out with, the clearer you make it that you don't understand the first thing about the topic of discussion.