The Ketchum Report

[Guest]

So, please correct me if I am wrong. If she simply used the primers she developed - before they passed any kind of peer review or a patent was applied for (and approved)-- could this spell problems for her paper? Would a Scientific Journal even consider publishing her work - if she had not yet passed through the process for her primers? I am going to assume she has not received a patent as of yet - I would think that would be big news.. "Scientist gets patent approval for Bigfoot DNA primer."

I could be wrong Melissa, but my understanding is it isn't really necessary to design primers since there are primers already in existence that will pull DNA sequence from any primate, including humans. There are protocols for designing your own primers for whatever it is you are specifically looking for but it is not the big deal it once used to be. If she did not follow the protocols for creating primers then, yes, peer review will question the science. I did find this and I don't think she can patent her primers:

What is not yet clear is whether a patent may claim a method of genetic analysis if specific chemical manipulations are required. Based on this decision, it appears that a patent may validly claim a method of analyzing DNA if the claim requires the use of specific isolated DNA molecules, such as an oligonucleotide probe or PCR primer. It is not at all clear whether a patent may validly claim analyzing DNA if it requires more generic approaches to analysis.

http://www.mondaq.co...ad Genetics Inc

Edited December 28, 2012 by CTfoot

[bipedalist]

....such as an oligonucleotide probe or PCR primer. It is not at all clear whether a patent may validly claim analyzing DNA if it requires more generic approaches to analysis.

My understanding is that there was some forms of patents or trademarks either she personally developed or a corporate entity associated with her developed (VeriSNP?). Maybe it was specific to domesticated animals. Maybe someone could refresh my memory.

[Guest]

I would have to go back and read it , but I believe it was a genetic test for a condition in cats. I would think that in identifying a species it would call for several different approaches as it refers to in the last statement, all speculation, since we have no idea what she did.

Edited December 28, 2012 by CTfoot

[Guest]

BP, if you read that link I posted up at #12367, there's some information about the experimenter needing to control temperatures according to the behavior of her primers. Controlled temperature variation is what drives the bonding of nucleotide strands to each other. But like controlling for contamination by collectors or lab techs, these are practical issues. I wonder how Ketchum selected target sites which would support her conclusions. In Ketchum's C2C interview she spoke about supercomputers being required for her study, and it may be she was referring to the simulations that assist the researcher in creating primers. From my link, we can read that making novel primers requires much more computing power since there aren't readily available reference sequences.I don't think the Trent lab work went far in Ketchum's direction, since they write in their report that they used off-the-shelf primers for Human and Black Bear.

she said in the past that many labs came up human or human contamination.

in the recent results,they said there were minor differences between the 2 labs they used, if they used the same sample, shouldn't the results be identical ?

Edited December 28, 2012 by zigoapex

[Guest]

^"One of her samples" that NO ONE can demonstrate she has EVER said that tested positive for her "unknown". Lots of claims that she said it, but not one person has linked to any proof that she did. As you point out, she steers clear of the issue in interviews.

First time poster, fascinating issue to me. I was listening to an interview conducted with Dr. Ketchum on December 10. The interviewer asked whether all of the samples which were tested resulted in consistent findings and Ketchum responded in the affirmative and said that, "We have 109 samples in the study. And they all gave us the human mito component." You can listen to the interview here: http://www.youtube.com/watch?v=VvISxByYxUg. The relevant exchange occurs at about the 4:00 minute mark.

It seems like everyone agrees that the Smeja Sierra Kills sample was submitted to Ketchum and the point of contention seems to be whether that sample resulted in the human hybrid determination. In that interview, Ketchum reveals that "all" of the samples (including the Smeja sample by definition) came back with the human hybrid finding. At least that is the way I interpret it. Perhaps I am incorrect.

[Guest gerrykleier]

It seems like everyone agrees that the Smeja Sierra Kills sample was submitted to Ketchum and the point of contention seems to be whether that sample resulted in the human hybrid determination. In that interview, Ketchum reveals that "all" of the samples (including the Smeja sample by definition) came back with the human hybrid finding. At least that is the way I interpret it. Perhaps I am incorrect.

'

I think she means all the samples that are presumptive for BF came back that way. As I recall, she did not include every sample that was sent to her in the study. Some were other animals, Bear etc. I don't remember where I got this-Lindsay maybe.

GK

[Guest slimwitless]

Right, their ---Trent's study techniques (to me) seem pretty dilute.

But they used a blender! Actually, I'm not going to pretend to be qualified to speak on the subject.

Here's a hypothetical. What if Ketchum's study comes out and the information (also by multiple labs) is at least as complete as the data provided here but with a different result? It seems to me the critics will go with bear regardless of whether they can prove all labs tested the same sample or were all equally qualified to deal with contamination or whatever else. Occam's Razor wins the day. I know Derek Randles still believes the sample Justin sent is from a bigfoot and maybe the science really is conclusive beyond all doubt BUT...maybe it's time to go with two genomes and drop this hot potato. Release the data specific to the Sierra Kills elsewhere. It actually pains me to say that.

[Guest]

'

I think she means all the samples that are presumptive for BF came back that way. As I recall, she did not include every sample that was sent to her in the study. Some were other animals, Bear etc. I don't remember where I got this-Lindsay maybe.

GK

I read in one of Mulder's posts the following:

Quote:

EVERY sample tested is "in the study". Doesn't mean that every sample is claimed to be diagnostic for the "unknown". Gonna keep pointing that out until it sinks in around here.

Why? Of the over 100 samples, only ~20 tested + for the human mtDNA. Of those, only 3 had good enough nuDNA to fully sequence.

In the interview I posted earlier, Dr. Ketchum said something directly contradictory to this statement. I have always had the impression that the 109 samples were the entirety of what Ketchum tested and she indicated that they "all" tested postive for the human mtDNA. I suppose Mulder may have assumed incorrect information himself and that led to a faulty conclusion on my part.

[Guest BartloJays]

Couple points for you guys.

Hard to see people still speculate about if the Sierras piece is part of Ketchum's study or not as I can tell you right now, links or no links...if it wasn't claimed to be then what in the hell did we waste our time desperately trying to screen it for? Justin, Wally, Derek, Tyler etc... have all been told from day one (it's common knowledge) that a full genome has been performed and "paid" for and is the centerpiece of her study. It's not even a question and I don't even think she'd contend differently at this point other then she intentionally received a "different" piece. I refuse to share private emails without Dr. Ketchum's permission, though technically it's at our discretion (I have a thing about sharing private messages publicly when "intent" was privacy), but let's just say if I had you over for dinner tonight, I wouldn't have to even show you more then two sentences on my computer in a recent exchange with Tyler before you'd say "yep, ok, got it."

On another note, I think the email communications we'll be consolidating and releasing soon back and forth with Trent will shed a lot of light on the whole process and the frustrations Tyler and I went through. You'll see and probably ask us "****, you guys must've been excited that day?" ...or... "oh man, I can picture how frustrating that was to hear that after what you thought was good news." The die hards with a much better understanding of diagnostics then me will get a much better feel for what Trent did or didn't do and in what order.

I will tell you that my Midwest lab got a lot stronger report with ample bear, human (Justin) contamination (through genomic dna) and an absence of any third contributor unless something has changed since I last talked to the Doc......report due any time.

I also tested two samples to try and tie up any loose ends or questions as I sent in both the salted piece from the site during our body search in July 2011 informally examined by Jeff (Meld) & John (Mio), and a frozen piece of tissue (just like Trent) to determine if they are from same subject species. I tried to cover every basis I could to get preliminary determinations. We had a lot of concerns about this tissue.

I'm also looking forward to sharing all of these emails as some of these people questioning our motivations in the first place (many with an agenda themselves) will see the sincerity of our efforts..."if" they bother to read what we provide before commenting.

[Guest slimwitless]

I refuse to share private emails without Dr. Ketchum's permission, though technically it's at our discretion (I have a thing about sharing private messages publicly when "intent" was privacy), but let's just say if I had you over for dinner tonight, I wouldn't have to even show you more then two sentences on my computer in a recent exchange with Tyler before you'd say "yep, ok, got it."

Bart, I don't mean to sound snide so please don't take this the wrong way. Have you considered inviting Derek over for dinner?

[david75090]

I'm wondering why a person with NDAs, like Dr. Ketchum, is expected to share information from her study that is covered by these NDAs. She was given the chance to share her findings, ahead of the release of her paper, but refused to do so. Isn't she supposed to refuse to share her findings with just anyone? It seems like she's being blamed for not being transparent, when she's not allowed to be transparent. If she shares her information with these people who've had their samples tested independently, doesn't that blow her whole study before it's published?

[Ronnie Bass]

Why is Ketchum's company's website down?

[Guest mitchw]

Hacked, Christmas Eve.

[Ronnie Bass]

I just thought it was her email. That's pretty rotten.

[Guest BartloJays]

I'm wondering why a person with NDAs, like Dr. Ketchum, is expected to share information from her study that is covered by these NDAs. She was given the chance to share her findings, ahead of the release of her paper, but refused to do so. Isn't she supposed to refuse to share her findings with just anyone? It seems like she's being blamed for not being transparent, when she's not allowed to be transparent. If she shares her information with these people who've had their samples tested independently, doesn't that blow her whole study before it's published?

You bring up an excellent point and I'm happy to answer it:

Don't worry about what we do based on our results which are preliminary findings (screening, not a "study") as we have a responsibility and committment of transparency and the submitter has a right to test his sample wherever he chooses.

Us not doing so as promised and should be expected, is irresponsible in my opinion and if you're asking us to delay or abolish that committment then you better give good, tangible justification for that because you bet your butt we're going to be held to it and we should expect nothing less.

Dr. Ketchum was never cornered or bullied into sharing information with us as her propriatery methods and work on any other sample (outside of Sierras) in her possession is absolutely none of our business. She was given an opportunity (requested) because there was a "perception" concern of us sharing the results we received prior to hers. Had there not been a concern with what we were doing, we wouldn't be concerned with her justifying the deviations or providing third-party validation on Sierra's tissue only.

In my opinion, if her "in-depth" testing trumps the labs we contracted, " interim perception" doesn't matter as the science must stand on its own anyways. I hope she's got them trumped, believe me.

Let me state for the record as well if it hasn't been brought up prior, had our findings confirmed anything leaning towards an "unrecognized" species, we would not have run out and undercut Dr. Ketchum's study in any manner by publicly sharing it, we would've consolidated our information and supplied that corroboration when she released her study (in same transparent manner) and hopefully provide ammunition for her if she was contended. That was the original hope (putting my personal feelings towards Dr. Ketchum completely aside as they are not as important as the objective or ramifications of new species verification)

Edited December 29, 2012 by BartloJays