The Ketchum Report

[Guest Theagenes]

10-4 Theagenes.

I wasn't sure what he was basing his comment on (had he seen the data an intrepreted it that way and what have you).

Thx.

The more I think about, it would probably have to human DNA contaminated by bear because the mtDNA is human (and not Justin's haplotype interestingly; so maybe his wife?)

[southernyahoo]

If she destroyed any remaining samples then that pretty well cements it in my mind. That displays a desire to hide one's tracks so to say. In other words just take my word for it... not good, not good at all.

common sense says the samples sequenced get destroyed in the process of sequencing because they get "digested" by the chemicals, isn't that what she means?

[Guest]

Theagenes,

I spoke with Bart last night. He told me when Justin was asked to send off that sample - it was already packaged. Justin called his wife and told her where it was. All she did was go to where Justin told her - grabbed the sample in the package and mailed it.

BUT ----- There were so many people around the day that sample was collected - and humans being what they are, I know they were all over it checking it out.. So, lord only knows who the DNA could be from.

[Guest Theagenes]

Theagenes said:

First of all --- In her last "information leak" I thought she said 15,000 for the hybridization- anyone know what happened to that number?

We can go down this rabbit hole but I can tell you it isn't pretty. Give me a few minutes.

Edited February 15, 2013 by Theagenes

[southernyahoo]

Theagenes, wouldn't it be a reasonable deduction that if all the samples had human mtDNA that originated 13 to 15kya this species "if new" could be no older than the date the hybridization event occured? Only the paternal line would be older?

[Guest]

We can go down this rabbit hole but I can tell you it isn't pretty. Give me a few minutes.

I will patiently wait..

[Guest Llawgoch]

If she destroyed any remaining samples then that pretty well cements it in my mind. That displays a desire to hide one's tracks so to say. In other words just take my word for it... not good, not good at all.

As someone has said, I'm not implying she destroyed them deliberately but that they were destroyed in the process. What we don't know is whether any of the 3 "interesting" samples are remaining to be retested by anybody else. We know of course that one of the three was from a source that was submitted separately to two labs who said it was a bear/human contaminated sample. What the other two were, I don't know. But there isn't much remaining on the table, it seems, metaphorically or literally.

[MIB]

I am not a scientist - but I have to be honest and say I am pretty upset that she did not disclose the information about the Trent results. Full Disclosure is always a good thing - and causes fewer problems down the road. I fear if those looking at this paper find out about the Trent results on their own - it will kill any hope that this paper might survive. That is very important information for these reviewers to have, I would think.

Melissa -

It's a good point, but perhaps its a matter of timeline. We don't know the actual dates the peer review, such as it was, whatever it was, was completed. It's possible that was some time back with a long delay while the journal "changed hands." It is possible Dr Ketchum chose to publish the paper as-reviewed even though newer information, like the bear results, were known, rather than "doctor" the paper with post-review editing or delay it further by sending it back for re-review to address the bear questions.

Dunno. Just speculation.

MIB

[Guest]

Could be MIB. Honestly, I find it next to impossible to believe Trent came up with results that all of her "experts" did not. I would have preferred she go back and make the corrections - if for nothing else but the fact that her paper would address this glaring problem.. Now, if this information is discovered - I am afraid she will be accused of deliberately trying to mislead the scientific community...

Full disclosure is always better - even if it means the work might take a little longer. Melba is trying to prove the existence of something - all boxes should be checked..

Just my opinion.

[Guest poignant]

If you claim to have a winning hand, the least you could do is show all the cards...

[Guest Theagenes]

As near as I can tell here is where this whole 15kya thing came from. A few years ago Stubstad came out with his reports on the early stages of Ketchum's project. Here is the link to those:

http://www.sciencealivenews.com/#stay.

Here is what he said about the eariest mtDNA results that came back:

Most likely, these two specimens—widely separated within North America—share the same "mitochondrial Eve" who probably existed somewhere between 10,000 and 30,000 years ago based on the number of mutations or polymorphisms present in their mtDNA genomes.

- This mitochondrial Eve was most likely European in origin, belonging to some version of Haplogroup H*. This haplogroup occupied the so-called "Franco-Cantabrian glacial refuge," covering the late Wisconsin glacial period when most of northern Europe was covered by glaciers. This is around the middle of the same epoch when the continent of Beringia existed, creating a 1,000 mile wide Asian-North American land bridge.

So the first two samples they got back were haplogroup H* ---Note that's H with an asterisk. So Stubstad googled "Haplogroup H*" but of course Google ignores the asterisk and the first hit he gets is the Wikipedia entry for "Haplogroup H." Here's the link:

http://en.wikipedia....ogroup_H_(mtDNA)

Note the 13kya date for Haplogroup subclades H1 and H3 in the first main paragraph. Stubstad then apparently clicked on the first citation for that passage which took him here:

http://www.ncbi.nlm....les/PMC1182122/

It doesn't look like he read much more than the abstract (which he copied as an appendix to one of his reports), but this where he got the idea that the mtDNA Eve for the hybridization had to date back to 15kya and this Eve that mated with an unknown hominin was a Solutrean Cro-Magnon woman from southwest France. That was when he hit on the idea that the dubious Solutrean hypothesis might explain it. This would have Cro-Magnon people crossing the Atlantic in boats to North America where they encountered BF and there was crossbreeding.

But he was misunderstanding how haplogroups work. 15,000 years ago is when Haplogroups H1 and H3 began---they are both still very common haplogroups in people of European descent. Having a BF sample with H1 mtDNA does necessarily mean that the BF is descended from a hybridization event 15kya---it could have been a hybrid child from a BF and human (white) women one generation ago or hundred years ago. Had he read the whole paper he might have understood that but he fixated on those couple of sentences in the Wikipedia page and the article abstract about Cro-magnons 15,000 years ago.

BUT WAIT! There's more. Remember the H with the asterisk? The article that started this whole thing was about Haplogroup subclades H1 and H3. But their samples were H*. The asterisk means that this is a "paragroup" of Haplogroup H. There are thought to be about two dozen subclades of Haplogroup H, of which only eleven have been mapped fully: H1 through H11. The H* means that their samples are from one of the other unmapped, unnamed H subclades, but definitely not from H1 or H3, which this article was discussing!

When I discovered that this was where Stubstad was getting his info from I figured that he was just misunderstanding or misconstruing what MK had told him, because there is no way she would not recognize the problems here since she's supposedly a specialist at this. But here we are four years later and even though she now has a multitude of haplogroups that don't have anything to do with this original idea, she's still sticking to this 13 or 15kya Solutrean hypothesis that is based on a false premise to begin with. It is so amateurish that I don't even know where to begin.

People please understand, when I said earlier in this thread that this portion of her paper was "superficial Wikipedied garbage" I wasn't just being a jerk. It meant it literally. Can you guys now understand why I'm treating this with such disdain?

Edited February 15, 2013 by Theagenes

[southernyahoo]

Could be MIB. Honestly, I find it next to impossible to believe Trent came up with results that all of her "experts" did not. I would have preferred she go back and make the corrections - if for nothing else but the fact that her paper would address this glaring problem.. Now, if this information is discovered - I am afraid she will be accused of deliberately trying to mislead the scientific community...

Full disclosure is always better - even if it means the work might take a little longer. Melba is trying to prove the existence of something - all boxes should be checked..

Just my opinion.

Maybe she didn't have Trent's data. What we have is a report from B&T the says low divergence from bear and significant similarity to bear with no actual numbers and based on a low percentage of template. Funny how full disclosure can be interpreted.

[Guest Scout1959]

As someone has said, I'm not implying she destroyed them deliberately but that they were destroyed in the process. What we don't know is whether any of the 3 "interesting" samples are remaining to be retested by anybody else. We know of course that one of the three was from a source that was submitted separately to two labs who said it was a bear/human contaminated sample. What the other two were, I don't know. But there isn't much remaining on the table, it seems, metaphorically or literally.

common sense says the samples sequenced get destroyed in the process of sequencing because they get "digested" by the chemicals, isn't that what she means?

common sense says the samples sequenced get destroyed in the process of sequencing because they get "digested" by the chemicals, isn't that what she means?

If you don't hold back some material as a control then you can never go back and double check. Certainly some of the samples had enough material to hold some back as a control. If any was left over and it was then destroyed this is obviously a farce.

[Guest slimwitless]

Theagenes,

I spoke with Bart last night. He told me when Justin was asked to send off that sample - it was already packaged. Justin called his wife and told her where it was. All she did was go to where Justin told her - grabbed the sample in the package and mailed it.

BUT ----- There were so many people around the day that sample was collected - and humans being what they are, I know they were all over it checking it out.. So, lord only knows who the DNA could be from.

So many people?

The sample was collected by the Justin Smeja, Jack Evans and a dog.

[Guest Theagenes]

To summarize my wall of text above for those who don't want to read it.

Ketchum's theory of a hybridization event 15,000 years ago comes from her misunderstanding Stubstad's misinterpretation four years ago of a Wikipedia article on a haplogroup that has nothing to do with any of the haplogroups in her study!

(with a pseudo-archaeology hypothesis thrown in unnecessarily just for fun)