Release Of Forensic Dna Results For Sierra Kills Sample

[southernyahoo]

Let’s say hypothetically Dr. Ketchum’s study is successful and validated with next generation sequencing being the game-changer for example. In that case, I think the email communications back and forth with both labs (especially Trent) may contain significant clues with respect to some of their “difficulties†through processing which could ultimately help substantiate Dr. Ketchum’s study even more, particularly if she circumvented those same issues. Just something to think about and one of many reasons why I’d contend it was better this information was shared now as opposed to later.

Can someone explain to me how this would even be a possibility if we are to be sure the Sierra sample contains only female black bear and Justins DNA mito and nuclear confirmed by the midwest lab?

[Guest FootDude]

Can someone explain to me how this would even be a possibility if we are to be sure the Sierra sample contains only female black bear and Justins DNA mito and nuclear confirmed by the midwest lab?

Tomafoot has written several posts about some possible scenarios:

Two possibilities that I can think of: 1) the "special" primers may be the short primers that are used in the Next Generation Sequencing approach - they are short and will latch onto target DNA somewhat indescriminately so that just about everything in the mix gets amplified and then sorted out by genetic sequence information - and 2) she may have generated sequence information and then designed very specific primers that would allow her to do quick and easy assessments of incoming samples. I thought she has said that her sequences are different from known hominid (e.g. neanderthal and denisovan) sequences.

And it isn't necessarily a matter of "extracting DNA where others fail," but actually amplifying the DNA where others were unable to because her primers are different.

I think the key information that has come from MK is that she has a lot of sequence. Once you have the sequence sorted out and you begin comparing it to other sequences, things begin to fall into place.

Tyler,

Your report is not flawed. The results are consistent with the design of the tests used. These tests would have been designed, developed, and validated using known sources. Therefore, one can expect them to perform well against known sources especially the more common and anticipated ones. However, this may have little relevance with regard to unknown or unanticipated sources, because they would be omitted from the process of design, development and validation.

[southernyahoo]

My point was that Tyler and Bart have taken issue with Ketchum's claims and alluded to something prophetic stated behind the scenes, stated the sample is likely from a bear and that Justin's DNA is on it and confirmed by another lab. Then it is also stated that the technical difficulties experienced by Trent might corroborate her study in some way. What gives? This flip flopping around is hardly transparent and seemingly deliberatly confusing.

[bipedalist]

Good point, why as clear as mud?

[Guest FootDude]

My point was that Tyler and Bart have taken issue with Ketchum's claims and alluded to something prophetic stated behind the scenes, stated the sample is likely from a bear and that Justin's DNA is on it and confirmed by another lab. Then it is also stated that the technical difficulties experienced by Trent might corroborate her study in some way. What gives? This flip flopping around is hardly transparent and seemingly deliberatly confusing.

Which is why I posted the above:

Based on some of the things Tomafoot has discussed that scenario seems reasonable.

Though in my opinion it still would have been better to wait and not have these debates especially since Derek is your good friend and has had much more access to Ketchums's report and has shared his perspective on the soundness of the report and data.

The posts you and Tyler have made with regards to whether or not Ketchum indeed 'has a viable report' directly contradict what Derek has publicly posted about it which when considering your close relationship to Derek make me logically question yours and Tyler's motives here.

[Guest BartloJays]

My point was that Tyler and Bart have taken issue with Ketchum's claims and alluded to something prophetic stated behind the scenes, stated the sample is likely from a bear and that Justin's DNA is on it and confirmed by another lab. Then it is also stated that the technical difficulties experienced by Trent might corroborate her study in some way. What gives? This flip flopping around is hardly transparent and seemingly deliberatly confusing.

What don't you understand? Tyler and I feel strongly the two lab reports are correct as they are good labs we deferred to. Absolutely nothing has changed.

My point was, and which was deliberately taken out of context (big surprise as is many things I say) was "if" this next generation sequencing caught something our labs didn't (will believe it when I see it), "maybe" there's clues from some of the difficulties (that've been repeatedly brought up btw) our labs had through the process and documented in our emails. For instance, no genomic DNA through microsatellite testing with decent amount of mtDNA on human side.

We haven't ruled out every possibility, as we certainly made an effort to explore every possibility.

"If" and "maybe." Why is everything I suggest as a "possibility," (repeatedly admitting and conceding I'm not an expert in this area), taken as literally as if we strongly believe that or saying something is definitive. Believe me, when I say something is "definitive," you'll know and can hold me to it as I won't state it unless I can provide evidence.

Once again, we didn't perform testing, we outsourced to experts who did and are sharing the results. You talk as if we did the testing ourselves.

In addition, you should depend on us for the transparency we promised, not depend on our opinion not being experts in diagnostics.

It's really not hard to make that obvious distinction on your own. It really isn't.

Edited January 9, 2013 by BartloJays

[southernyahoo]

What don't you understand? Tyler and I feel strongly the two lab reports are correct as they are good labs we deferred to. Absolutely nothing has changed.

My point was, and which was deliberately taken out of context (big surprise as is many things I say) was "if" this next generation sequencing caught something our labs didn't (will believe it when I see it), "maybe" there's clues from some of the difficulties (that've been repeatedly brought up btw) our labs had through the process and documented in our emails. For instance, no genomic DNA through microsatellite testing with decent amount of mtDNA on human side.

We haven't ruled out every possibility, as we certainly made an effort to explore every possibility.

"If" and "maybe." Why is everything I suggest as a "possibility," (repeatedly admitting and conceding I'm not an expert in this area), taken as literally as if we strongly believe that or saying something is definitive. Believe me, when I say something is "definitive," you'll know and can hold me to it as I won't state it unless I can provide evidence.

Once again, we didn't perform testing, we outsourced to experts who did and are sharing the results. You talk as if we did the testing ourselves.

In addition, you should depend on us for the transparency we promised, not depend on our opinion not being experts in diagnostics.

It's really not hard to make that obvious distinction on your own. It really isn't.

Actually it wasn't taken out of context, the whole context is there. The main sticking point here is that either Trent is sure there is a single contributor of human DNA or there was another. You paid them to get that right, even challenged them about it right? The mtDNA being human can be sequenced with human primers, (no next generation required) and should have been obvious if they were actually checking for it.

So if there is potential ambiguity in the results, including the midwest lab results, is there any reason to insinuate that someone other than the labs used needs to answer for it?

[Guest Tyler H]

The posts you and Tyler have made with regards to whether or not Ketchum indeed 'has a viable report' directly contradict what Derek has publicly posted about it which when considering your close relationship to Derek make me logically question yours and Tyler's motives here

Wouldn't the fact that Bart is risking this friendship with Derek (which Justin risked as well) actually make you LESS suspicious of motives? He seems to have more to lose than to win here. Crash his hopes of proof in something he's been waiting for for years, and risk friendships while doing so. To me, it seems abundantly clear that Bart, Derek, and myself all feel strongly about the positions we have taken. Now, for Derek - he has seen more evidence from Melba than we have - so, if he feels that it outweighs what Bart and I have provided - I get that. But for Bart and I, we ONLY have science from the labs we worked with - everything else is hearsay, and unsubstantiated claims. Neither Bart, Derek nor myself are scientists - we can only take a stance based on what the scientists we have worked with have told us. What would you do when faced with that choice?

How long do YOU feel we should have let Melba's claims (without substantiation, and with a fair amount of redflags), gone on without any vetting? After 5 more years, THEN would it have been appropriate for us to be "allowed" by folks like yourself, to test Justin's sample and make statements about our results which happen to appear to contradict Melba's claims?

I'm quite serious - what would you have done? When, How, and Why?

Edited January 9, 2013 by Tyler H

[Guest]

Bart and Tyler...your "transparency" is a measure of a good faith effort on your part to tell us all what you got. It's appreciated. Really.

Unfortunate how your transparency hasn't worked out quite how it was intended.

[Guest Tyler H]

Actually it wasn't taken out of context, the whole context is there. The main sticking point here is that either Trent is sure there is a single contributor of human DNA or there was another. You paid them to get that right, even challenged them about it right? The mtDNA being human can be sequenced with human primers, (no next generation required) and should have been obvious if they were actually checking for it.

So if there is potential ambiguity in the results, including the midwest lab results, is there any reason to insinuate that someone other than the labs used needs to answer for it?

I think the "ambiguity" here is in the eye of the beholder. Trent made very strong assertions to me about the certainty of their results, and Bart's lab made the same to him. We don't feel there is ambiguity. Some may think there is, but as I say, I have yet to see a PhD in a related field state that they feel there is any ambiguity in these results. Tomafoot has thrown some razzle dazzle stuff out there, but I had it vetted by as neutral of a third party PhD biologist as I think I would be able to find (one who works extensively in genetic testing realms and has a CV of published work as long as your arm), and they said:

"Scientists discovered that ALL mammals share a common sequence for cyto b, and they tested the universal mammalian primers to make sure they worked on people, cows, horses, wildebeast, elephants, lions, lemurs, mountain lions, bears, raccoons, yaks, polar bears, llamas, kangaroos, pronghorn antelope, German shephards, etc, etc, etc.

So, if the universal mammalian primers fail to amplify BF DNA, you have to conclude that BF are the only mammals on planet Earth that have a unique cyto b sequence. Actually, it's more stringet than that. You have to assume that BF are the only mammals on Earth that have a unique sequence at the site to which the PCR primers anneal. I'm not going to calculate the probability of that event, but what's more reasonable (Occam's razor)?

1. The sample you analyzed was from a bear.

2. The sample you analyzed was from a mammal that was totally uniques among all mammals on planet Earth.

I'll choose 1.

I know you already know this, but let me phrase it my way. Just because something is possible doesn't make it probable. My favorite example is from the field of Statistical Mechanics, which says that all the air molecules in a room can suddenly condense in one corner of the room, sufficating and freezing anyone in the room. You can calculate a probability for this to occur; it's someting like 10 to the minus 80th. Is it possible? - yes. Has it ever happened in the history of the universe? - no. Is it possible that the universal primers don't work on BF DNA? - yes; Is it probable? - no!"

Edited January 9, 2013 by Tyler H

[bipedalist]

Or, maybe BF isn't a mammal?! LOL.

[Guest]

Oh my...BartloJays. NOT trolling. Merely making an observation that your intentions to be transparent have been met with quite an abundance of argument. Not looking for a fight...you guys are on the defense as it is. I'll leave this well enough alone. Good luck.

Well...I don't know what happened to my reply.

I will re-post (not verbatim): BartloJays, this is the problem with the written word. My post was not meant to antagonize in any way and I'm not "trolling". I merely stated your intent at transparancy has resulted in an abundance of argument here. Go back to the first post by Tyler. He says he won't spend alot of time here responding...more on BFRO. Here it is 30 pages later. Anyway, you two are severely on the defensive as is and I'm trying (nor was trying) to add to it. Won't be sticking around though...not looking for a fight so I'll leave this well enough alone. Good luck.

[Guest BartloJays]

Actually it wasn't taken out of context, the whole context is there. The main sticking point here is that either Trent is sure there is a single contributor of human DNA or there was another. You paid them to get that right, even challenged them about it right? The mtDNA being human can be sequenced with human primers, (no next generation required) and should have been obvious if they were actually checking for it.

So if there is potential ambiguity in the results, including the midwest lab results, is there any reason to insinuate that someone other than the labs used needs to answer for it?

Well Trent provided us a final report explaining their conclusion and appear to have come to it based off the single strand DNA test where ample bear was found and minute traces of human were present (consistent with contamination) and sharing the same hablotype with Justin. That's pretty definitive in our opinion, especially when you consider our Midwest lab got almost parallel results through regular testing, except that (it's my understanding through verbal with Doc...waiting for final report) the salted piece was ample bear with Justin's nDNA contamination. BTW, just so you know, according to Justin, the piece that was salted and examined by Meldrum at the killsite during the summer of 2011 is the other half of the piece taken off the main tissue and was given to Dr. Ketchum in which she purportedly performed a successful genome on. One reason Justin is adamant there's no possible tissue mix-up.

My point is these are the results we're accepting until or unless it's proven differently by Dr. Ketchum's results. Although we aren't holding our breath based on the results we have, no one is shutting the door 100% and I pray she has something the folks we contracted don't.

In addition, as we stated throughout this thread, the process was a rollercoaster for us and took almost 7 months. There were several days in that process where we had every reason to believe we were in the game and we've already touched on them in this thread, including.... decent amount of "human" mtDNA in first report from Mito testing only but no genomic from microsatellite testing they performed which made them suspect that the sample could've possibly been manipulated by "the hunters." This was a non-issue though after they tested for the bear's genomic dna and got it no problem and it's our understanding that should a "cleansing" of some sort took place, you can't discriminate what you destroy within the sample, so by getting bear genomic rather easily the question of someone cleaning the sample with a solution to hide the dna was a mute point. Trent does have to contend with this periodically though through black market items like foreign toys made say, with illegal animal parts, and the item is bleached to hide the dna. Usually they work through this problem as it just encompasses much more time and testing.

In addition, as both Tyler and I stated in this thread, prior to performing the single strand dna test on the hair, they outsourced the tissue to the Ministry of Natural Resources and a well-known Ontario bear expert claimed the scaling matches ursus americanus, but this expert did question the lack of present underfur as at an elevation of 7000 ft in the Sierras in October, you'd expect dormancy is rightfully imminent at any time (this still puzzles me a bit). We also didn't like how he was asked "is this bear?" as the appropriate question should've been, "what is this?" I'm not too bothered by that however as if Trent is outsourcing to a bear expert, he obviously knows what they suspect may be the candidate.

Oh my...BartloJays. NOT trolling. Merely making an observation that your intentions to be transparent have been met with quite an abundance of argument. Not looking for a fight...you guys are on the defense as it is. I'll leave this well enough alone. Good luck.

Well...I don't know what happened to my reply.

I will re-post (not verbatim): BartloJays, this is the problem with the written word. My post was not meant to antagonize in any way and I'm not "trolling". I merely stated your intent at transparancy has resulted in an abundance of argument here. Go back to the first post by Tyler. He says he won't spend alot of time here responding...more on BFRO. Here it is 30 pages later. Anyway, you two are severely on the defensive as is and I'm trying (nor was trying) to add to it. Won't be sticking around though...not looking for a fight so I'll leave this well enough alone. Good luck.

Well if that wasn't your intent I sincerely apologize to you as I misunderstood your intent through your choice of words. I'm sorry and if it makes you feel any better, I already reported myself LOL.

I'm not surprised, nor intimidated in the slightest by any contentions and I don't think Tyler is either as it's expected. We know what our intentions are and there are many others on this forum who happen to be people I trust that I kept in the loop all through this process over the last year that took the ups and downs of information with us, so to them there's no question what our intentions are and those people matter most to me because if god forbid something terrible happened to me tomorrow away from bigfooting, they're the people who would be by my side and vice versa.

I think people questioning us in some manner is healthy because it also gives us a platform to bring out more information to the table, info we may've forgotten about or missed. There isn't one thing I'd do differently at this point and I sleep like a baby at night as I would challenge anybody to provide evidence of ulterior motives. What I don't appreciate is people spreading misinformation and making accusations without evidence or rationale like those who believe there's some BFRO agenda to take down Dr. Ketchum for instance. It's crap and perpetuated by a few with their own agenda.

Once again I apologize to you if that wasn't your intent as I honestly read it that way.

Edited January 9, 2013 by BartloJays

[southernyahoo]

I think the "ambiguity" here is in the eye of the beholder. Trent made very strong assertions to me about the certainty of their results, and Bart's lab made the same to him. We don't feel there is ambiguity. Some may think there is, but as I say, I have yet to see a PhD in a related field state that they feel there is any ambiguity in these results. Tomafoot has thrown some razzle dazzle stuff out there, but I had it vetted by as neutral of a third party PhD biologist as I think I would be able to find (one who works extensively in genetic testing realms and has a CV of published work as long as your arm), and they said:

Tyler , your PHD did not address hybrids, The cyto B locus is in the mitochondria, the mitochondria is human in bigfoot according to Ketchum,. therefore the universal primers will find human in every prospective bigfoot sample if she's right. This is her prediction, and so there is no resolution in the mitochondria unless she's wrong and there is a pure bred BF out there. Dr. Ketchum found resolution in the nuDNA.

You have to decide whether you are going to take your labs word for it, or make them show you there was a single human source in the sample and that it was Justin. Arguing about how adamant they were is no better than taking Ketchum's word for it right? Stick to the "believe it when you see it" mentality with your labs if this is a standard you really want to uphold.It looks hypocritical when you don't. The Trent report did not illustrate with electophergrams there was a single human contributor, and given your understanding of Dr. Ketchums claims, you let them slight you..

[TimB]

What "cards"? They're trying to claim the pot with empty hands.

It took me all night to figure this quote was a poker reference- I couldn't figure out how you could cook in a pot with empty hands...

Carry on.

Tim B.