A problem with the "Eddowes Shawl" DNA match

[mickreed]

Lynn is right krinoid. As infallible as science is purported to be my modern society, this case is a perfect example of how misleading science can be.

Science as such is an abstraction. It's no more misleading than history is, or geography, or any other discipline.

People mislead, intentionally or otherwise, by making mistakes, by misusing evidence, generally by stuffing up, and yes, very occasionally, by fraud. No discipline is free from these risks, and no practitioner hasn't fallen foul of them from time to time.

All we can do, is to do our best not to make mistakes, and, when we do, to 'fess up and move on.

What is wrong is people assuming that 'eminent' people can't make mistakes or when people dismiss something because it doesn't fit their preconceptions.

At the moment JL is one of five geneticists who have expounded on this. He is the only one who thinks he's right. That is, 80% disagree with him. And the 80% comprise some of the top names in the business. Some of them even developed and oversee the information he used.

So JL has a responsibility to check the science if he is to have a valid opinion. At the moment he's just shooting the messenger by suggesting the Independent has an agenda.

Unbecoming and silly.

[Chris]

Think of how often bad evidence is misrepresented as good evidence. Surely this isn't the first "error of nomenclature" to condemn an innocent man guilty. I think the point is how easy it is to mis-use "cutting edge" technology which isn't fully understood by the public. Thankfully there are people like you guys who are willing to analyze scientific results, break them down for everyone to understand and point out where they are inaccurate.

Well, I agree that weak scientific evidence can be a lot less accessible to scrutiny than weak documentary evidence, which does make it dangerous.

The disturbing thing about this case is that if the "rare mutation" hadn't actually been named in the book, we'd have been powerless to question it directly. The only possibility would have been to arrange our own DNA analysis by contacting other descendants of Catherine Eddowes, which might not have been possible.

[RockySullivan]

Well, I agree that weak scientific evidence can be a lot less accessible to scrutiny than weak documentary evidence, which does make it dangerous.

The disturbing thing about this case is that if the "rare mutation" hadn't actually been named in the book, we'd have been powerless to question it directly. The only possibility would have been to arrange our own DNA analysis by contacting other descendants of Catherine Eddowes, which might not have been possible.

Which is why I assume there's no indepth info about the Koz " match". Although as I'm sure you know...I haven't read my copy of the book yet

[Caligo Umbrator]

Yes. Some of us (naively, with the benefit of hindsight) helped Russell Edwards. So we can confirm that he was given the details of a descendant (one we hadn't previously been in contact with) in October 2013.



As I read it, the epithelial cell that was used for the comparison was one of the ones that had been obtained from the shawl by December 2012 (Chapter 9). At a later stage they thought all the material had been lost and took new samples, but were able to recover some of the original epithelial cells from microscope slides instead.

Hi Chris,

Yes, my mistake. I re-read the relevant sections and it does indeed seem that the 'AK' cells were recovered from the shawl before the sample from 'M' was taken.
It was the amplification of the information on these 'AK' cells that was done after the 'M' sample was given and that's, I think, the point that caused me to get the timeline muddled.
Apologies to richardh for handing him somewhat incorrect information.

Yours, Caligo

[mickreed]

Which is why I assume there's no indepth info about the Koz " match". Although as I'm sure you know...I haven't read my copy of the book yet

The real info about the Kosminski 'match' is in the final chapter or Conclusion of the book, Rocky. To my mind it's very, very weak. There is no data to get your teeth into, other than a reference to mtDNA haplogroup T1a1, which is said to be 'very typical' of Russian/Polish Jews. In fact it's not, but still.

There is a reference to a database at the National Center for Biotechnology Information (NCBI), based in Bethesda, USA which was used to check frequency. Allegedly one perfect match was found. With a Russian (but not necessarily a Jew).

There is also a mention of an unnamed article from Annals of Human Genetics which I think is this:

Mitochondrial DNA variability in Poles and Russians
by MALYARCHUK, B. A; GRZYBOWSKI, T; DERENKO, M. V; CZARNY, J; WOZNIAK, M; MISCICKA-SLIWKA, D

And that's about it. If Caligo is right that he has found the sequence on the database, then we may have the data we need.

[mickreed]

Did I post this earlier. It's hilarious?

http://www.mhpbooks.com/spoilsport-scientists-ruin-recent-jack-the-ripper-book-revelation-with-their-stupid-bummer-science/

[RockySullivan]

The real info about the Kosminski 'match' is in the final chapter or Conclusion of the book, Rocky. To my mind it's very, very weak. There is no data to get your teeth into, other than a reference to mtDNA haplogroup T1a1, which is said to be 'very typical' of Russian/Polish Jews. In fact it's not, but still.

There is a reference to a database at the National Center for Biotechnology Information (NCBI), based in Bethesda, USA which was used to check frequency. Allegedly one perfect match was found. With a Russian (but not necessarily a Jew).

There is also a mention of an unnamed article from Annals of Human Genetics which I think is this:

Mitochondrial DNA variability in Poles and Russians
by MALYARCHUK, B. A; GRZYBOWSKI, T; DERENKO, M. V; CZARNY, J; WOZNIAK, M; MISCICKA-SLIWKA, D

And that's about it. If Caligo is right that he has found the sequence on the database, then we may have the data we need.

so exactly what is it that makes a match to Koz? If the T1a1 is common for Russian/Polish Jews, then almost anyone in Whitechapel in 1888 could be the dna match on the shawl. If not it could come from anywhere. I'm not understanding anything at all about the shawl or Kozminski's descendant that makes even a match.

[mickreed]

so exactly what is it that makes a match to Koz? If the T1a1 is common for Russian/Polish Jews, then almost anyone in Whitechapel in 1888 could be the dna match on the shawl. If not it could come from anywhere. I'm not understanding anything at all about the shawl or Kozminski's descendant that makes even a match.

Hey Rocky. The T1a1 is NOT typical for Russo-Polish Jews, so that's a wee bit analogous to the claims about 314.1C. It's simply wrong, although not quite so devastating.

It's a not a hugely rare haplogroup and is very widely distributed, but it does seem to be uncommon, but not absent, amongst Ashkenazi jews. It's possibly slightly more likely to have come from a gentile, than from a Jew. As you say it could have come from anywhere as the following indicates.

T1a represents ~90% of total T1, and our new data have prompted substantial revision of its tree structure and nomenclature. Alongside minor subclades T1a2, T1a3, and T1a4, as well as several (mainly European) paraphyletic T1a* lineages, 80% of samples in the T1 tree fall within the subclade T1a1 (dating to ~15.5 ka ago), and 70% of the samples in T1a1 fall within T1a1a1 (Table S2). The geographic distribution of T1 is extraordinary—lineages are distributed, albeit at varying frequencies, across its range throughout the tree, from northwestern Africa throughout Europe, the Caucasus, and the Near East, into western India, and across central Asia into Siberia. The South Asian lineages tend to cluster with or match Near Eastern ones in the HVS-I network, but common HVS-I types frequently match across an extremely wide range. Indeed, the root type of T1a1a1, dating to ~7 ka ago, is very unusual among whole-genome mtDNA types in that it is shared between multiple geographically distant individuals from Scandinavia, the Baltic, the North Caucasus, Anatolia, and Morocco. The distribution of T1a is both widespread and patchy, although at low frequencies overall, the values rise to ~5% in the South Caucasus, ~6% in northeastern Iran, ~8% in Tunisia, and almost 9% in Romania (Table S3). Curiously, despite the age of T1a1a1, it has not been seen in any Neolithic remains to date.33–35,47–49 T1b, by contrast, is much less common and is largely restricted to the Near East, where it reaches ~2% in eastern Anatolia and southern Iraq but is vanishingly infrequent elsewhere.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3376494/

[mickreed]

It's interesting that, while the Toowoomba Chronicle, and probably the Woop-woop Argus, carries the Independent's story, JL's home rag, the Liverpool Echo, doesn't seem to have anything since the report about wanting Johnny Depp to play JL in the film.

[mickreed]

RE's next book?

[RockySullivan]

Hey Rocky. The T1a1 is NOT typical for Russo-Polish Jews, so that's a wee bit analogous to the claims about 314.1C. It's simply wrong, although not quite so devastating.

It's a not a hugely rare haplogroup and is very widely distributed, but it does seem to be uncommon, but not absent, amongst Ashkenazi jews. It's possibly slightly more likely to have come from a gentile, than from a Jew. As you say it could have come from anywhere as the following indicates.

T1a represents ~90% of total T1, and our new data have prompted substantial revision of its tree structure and nomenclature. Alongside minor subclades T1a2, T1a3, and T1a4, as well as several (mainly European) paraphyletic T1a* lineages, 80% of samples in the T1 tree fall within the subclade T1a1 (dating to ~15.5 ka ago), and 70% of the samples in T1a1 fall within T1a1a1 (Table S2). The geographic distribution of T1 is extraordinary—lineages are distributed, albeit at varying frequencies, across its range throughout the tree, from northwestern Africa throughout Europe, the Caucasus, and the Near East, into western India, and across central Asia into Siberia. The South Asian lineages tend to cluster with or match Near Eastern ones in the HVS-I network, but common HVS-I types frequently match across an extremely wide range. Indeed, the root type of T1a1a1, dating to ~7 ka ago, is very unusual among whole-genome mtDNA types in that it is shared between multiple geographically distant individuals from Scandinavia, the Baltic, the North Caucasus, Anatolia, and Morocco. The distribution of T1a is both widespread and patchy, although at low frequencies overall, the values rise to ~5% in the South Caucasus, ~6% in northeastern Iran, ~8% in Tunisia, and almost 9% in Romania (Table S3). Curiously, despite the age of T1a1a1, it has not been seen in any Neolithic remains to date.33–35,47–49 T1b, by contrast, is much less common and is largely restricted to the Near East, where it reaches ~2% in eastern Anatolia and southern Iraq but is vanishingly infrequent elsewhere.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3376494/

Thanks mick you've been very helpful in explaining the Technical aspects of this thread cheers

[Peter Griffith aka gryff]

It's interesting that, while the Toowoomba Chronicle, and probably the Woop-woop Argus, carries the Independent's story, JL's home rag, the Liverpool Echo, doesn't seem to have anything since the report about wanting Johnny Depp to play JL in the film.

Mick, it could also be considered RE's local rag too. RE comes from Birkenhead which is just across the Mersey River. When I lived in N. Wales, The Liverpool Echo was sold in the Wirral and all along the N.Wales coast.

So we have two "local" boys "making good".

As for the Van Gogh "theory", I did watch part of a video of some guy trying to show where bits of Mary Kelly's body were hidden in a painting. Desperate stuff.

cheers, gryff

[Peter Griffith aka gryff]

What is wrong is people assuming that 'eminent' people can't make mistakes

Mick, I spent 20+ years behind a lab bench and ran into science "mistakes" twice. Science that had come from published, peer-reviewed papers.

The first time was trying to use a published method of DNA extraction from a micro-organism. Spent over a month trying to get the method to work - nothing. My boss was beginning to grumble, until he got a letter from a friend at University of Manchester telling not to waste time as they could not get it to work either.

A few years later, I hit the same situation when I started using Nuclear Magnetic Resonance (NMR). I was trying to look at the effect of pH on a biological compound - and I could not duplicate published results. Then one day, I made up a bunch of samples, but because of a car problem was unable to run the samples that day - so I ran them the next day and got the published results. Further investigation showed that in fact the samples were breaking down at certain pH's

I have wondered many times how often this kind of thing happens. But usually, it is not the sort of thing that makes newspaper headlines.

What, at the moment, is driving Dr. JL and his current stance on 314.1c/315.1c, I do not know.

I still hope that he will eventually answer his critics in a meaningful way.

cheers, gryff

[alkuluku]

Hi alkuluku.

I meant to respond to your post earlier.

I can see that some publishers might want to publish a book they consider "easily readable" by the general public.

But when the entire premise of the book's conclusion rests upon Science, why not include a separate chapter on the nitty gritty details of the science that "non-scientific" types can skip over, insert it at the back of the book, or failing all that, simply provide a live web-link to the detailed scientific analysis?

If JL's DNA analysis was completed some time ago -apparently a few years ago? - at any rate well before RE began writing his book, wouldn't that have given JL adequate time to produce a paper explaining his results and submit it for peer-review?

Even if the publishers wanted JL to hold back on the release of the scientific paper until the book was out, wouldn't the paper at least be completed by now, and couldn't he state this to be the case and name a date for the scientific paper's official release date?

Did they not realize that other scientists and a sizable number of readers would ask for and expect to be able to examine the completed paper? That's what baffles me.

Best regards,
Archaic

Obviously logical would've been to publish all (or most) results in the book.

At the moment my guess is that JL is under a contract and can't publish/say anything against the published conclusions without a permission. It's quite possible that he/they all knew the results don't mean anything before the book came out.

He has said that he worked for free if he can publish the scientific paper(s) he wanted. The way he's been avoiding the tough questions it really looks like he's getting a share from the book sales. Or got a lump sum to keep his mouth shut as long as the book sells.

Also I find it extremely funny that I guy who claimed to have used £750k on the investigation is now offering JtR tours for 6 quid per person.

[Peter Griffith aka gryff]

At the moment my guess is that JL is under a contract and can't publish/say anything against the published conclusions without a permission.

That has been my thinking too alkuluku. Although he worked for free, Dr. JL stated that he had a budget from RE. As RE is a businessman, I'm sure there must have been some kind of contract to protect his cash. It may have been between JL & RE or it may have gone through an office LJMU has for dealing with private research funding.

Add to that, if RE is paying for services - who owns the data from those services? (Dr. JL may not have received cash, but it may have paid for a graduate student, post doc fellow, a technician to do the actual work, or to buy equipment.)

If RE owns the data Dr. JL may be stuck with some kind of NDA

As an aside, I'm not sure where you got the "JtR tours for 6 quid per person" from as the upcoming "Halloween Jack the Ripper Experience with Russell Edwards" is 25 quid a person - though it does include a meal.

cheers, gryff