Release Of Forensic Dna Results For Sierra Kills Sample

[bipedalist]

Nothing is impossible, but the amount estimated in your report would suggest that tissue was attached. I think maybe the point is that the tests are now sensitive enough that it is no longer required that a dermal papilla (bulb at root) be apparent to ensure good results. But, I'm not a forensics guy.

Last I looked a large amount of homogenized hair shafts could now produce even odds of success with nuDNA (not an expert though). But I guess even odds with the best of the best would result in slightly less among the mediocre labs. (maybe that was really mtDNA though, like I said not an expert).

lol

I think storing it with Kryptonite was the wrong way to go.

There's nothing worse than good green bear meat that has taken a turn toward the bad-side!

Edited January 4, 2013 by bipedalist

[Guest Tyler H]

Laboratories are quite often emotional hothouses full of pressure and tension with conflict sprouting all over the place. Nearly everyone has an ego and the boss may bruise a few along the way. It always feels good to make the point in return that the boss isn't all that smart or is a flaming unmentionable. Therefore, such assertions by insiders should be taken with a grain of salt.

point taken, but these were insiders that were singing her praises, and doing nothing but lauding her at the time. They had no axe to grind, and she was not "their boss." This was from investors and submitters and ... confidantes. NOt that I care. She can be as cooky as a cookie. If the science is sound, then the science is sound. History is rife with crazy characters who play a role in important discoveries.

I would like to add to this conversation a few things that need to be taken into consideration. I am NO DNA expert, nor do I play one on TV, but when this sample was first obtained it was handled by hand. I have picture proof of that. When Melba received the sample she extracted a "tube" of tissue from the inside of the sample, and yes there was enough to do that easily.

1. The sample first went to a very avid bear hunters house.

2. The sample was stored in a freezer with other bear meat.

3. I would guess that the sample was cut into pieces using the same knife and cutting board that had cut up many pieces of bear, and yes I Will try and confirm this with

Justin .

4. I can say beyond a shadow of doubt that there is bear DNA all over that particular environment.

5. When this sample was first obtained he had no idea how to handle it. I educated him, the best I could after the sample had already been collected.

When Justin went and found the flesh, that was the last thing he'd expected to find. He was up there looking for bodies.

Justins contamination is obviously all over the outside of the sample, and it's pretty safe to say that due to the bear rich environment that is Justins house, and the very real possibility that it was chewed on by a bear prior to recovery obviously makes clear where the bear contamination could have came from. I'm not saying this is fact, but I am saying that this is a very real possibility.

DR

I actually think the statement you gave is extremely accurate Derek.

As such, the single strand hair test attempted to minimize any contamination issues. (Can't guarantee it did, but that was the attempt). And again, only two mammalian contributors were ever identified. One of which is human, one of which is bear. The human is haplotype A which matches Justin, and according to the latest statements from Ketchum, does not match her "human" component. We seem to be left with Justin, and Bear. When Melba reveals her "third" contributor, then I guess we'll know what the other labs missed, and how and why.

Nah, no worries, I just thought if there were MULTIPLE PhDs weighing in on this, surely one of them would have recognized the magnitude of proving the existence of a huge undiscovered, unclassified, North American bipedal primate. And surely if they recognized the possible advancement to their career from this discovery and classification, they would have been on this like white on rice. There would have been something announced in a reputable journal, discussions amongst geneticists, biologists, zoologists, all sorts of '..ists' that specialize in this sort of thing, and mainstream science sitting up and very much paying attention. As this is not happening, it doesn't fill me with a whole lot of optimism.

RayG

Well, I do think that that is why the lab director got directly involved in these efforts, rather than just letting his techs run it. That being said, I don't think most Dr's want their name associated with it, as they already rule out the possibility.

Edited January 4, 2013 by Tyler H

[Guest BartloJays]

I would like to add to this conversation a few things that need to be taken into consideration. I am NO DNA expert, nor do I play one on TV, but when this sample was first obtained it was handled by hand. I have picture proof of that. When Melba received the sample she extracted a "tube" of tissue from the inside of the sample, and yes there was enough to do that easily.

1. The sample first went to a very avid bear hunters house.

2. The sample was stored in a freezer with other bear meat.

3. I would guess that the sample was cut into pieces using the same knife and cutting board that had cut up many pieces of bear, and yes I Will try and confirm this with

Justin .

4. I can say beyond a shadow of doubt that there is bear DNA all over that particular environment.

5. When this sample was first obtained he had no idea how to handle it. I educated him, the best I could after the sample had already been collected.

When Justin went and found the flesh, that was the last thing he'd expected to find. He was up there looking for bodies.

Justins contamination is obviously all over the outside of the sample, and it's pretty safe to say that due to the bear rich environment that is Justins house, and the very real possibility that it was chewed on by a bear prior to recovery obviously makes clear where the bear contamination could have came from. I'm not saying this is fact, but I am saying that this is a very real possibility.

DR

I'm at Justin's house right now in Sac (actually we're en route to my aunt's) and I can confirm Derek is correct on every point. Everything mentioned from a contamination standpoint was my hope but as CTfoot mentioned how do you get around what should the predominant contributor, noticeably absent?

Edited January 4, 2013 by BartloJays

[Guest]

I will never understand why not even a phone pic was taken. Incredible.

[masterbarber]

^^ I haven't seen a good answer for that query either......

[Guest]

Everything mentioned from a contamination standpoint was my hope but as CTfoot mentioned how do you get around what should the predominant contributor, noticeably absent?

My sentiments 100%...I have maintained that the most significant result of testing the Smejia samples was that there was NO CONFIRMATION of this sample comming from a *BF*..ie, unknown hominid.

[Guest]

Now it really all depends on what MK can put forth when her much anticipated study is released. She has insinuated that the JS sample is a big part of her study and I'm assuming that she means it tested positive for Bigfoot DNA.

No she hasn't. Others have insinuated (or outright claimed) this, but no one has documented ANYwhere that Ketchum has made that claim.

3) She has Modern human not in genbank.

That is not possible. GenBank has a HSS (modern human) sample. ALL HSS will match to the HSS diagnostic sample in GenBank for all important markers.

Further, her claim is very specific that there are significant parts of the nuDNA that are NOT HSS, which also rules out a misdiagnosis as a possibility.

Mulder - could you provide evidence where Melba denied this? The closest I heard her say is "well, some people have said that" and "some people may have believed that" But I have never heard her say she never said that. I DID hear assertions directly from people involved in her study, that Melba used those terms - that she felt it was 'something not of this world'.

You're the one claiming that she in fact said it...not me.

Who are these "people directly involved with the study" claiming this? Lindsay? Stubsted (now deceased)? Others? What is their proof?

Links to any place where these people are named and links provided where we can examine their statements?

Here are all the conceivable possibilities in no particular order. Feel free to add your own.

1. Smeja sent a different sample to the independent labs (accidentally or on purpose).
   
2. Ketchum tested a different sample (accidentally or on purpose).
   
3. Someone did the old swithcharoo on Smeja's sample (in-transit or otherwise).
   
4. Ketchum is being deceitful about the result.
   
5. Ketchum has wrongly interpreted Smeja's maternal eve as the mother of all bigfoots.
   
6. Both Bart and Tyler's labs somehow made an error (bear contamination unified field theory).
   
7. Smeja's sample was contaminated by sasquatch in Ketchum's lab.
   

Any others? I left out the Bigfoot Knights Of Templar. Anyway, don't cut yourself with Occam's Razor.

8. Ketchum's sample did not test out for BF at all and those claiming she said it did are either a) misinformed, or are themselves being deceitful

Edited January 4, 2013 by Mulder

[Guest]

8. Ketchum's sample did not test out for BF at all and those claiming she said it did are either a) misinformed, or are themselves being deceitful

"Ketchum's sample did not test out for BF at all"

How do you know this?

[Guest]

Um... Mulder... I get the impression that you consider yourself a logical thinker.

Do you realize that we CAN'T (not in an NDA type "can't" sort of way) say anything about her claims, because she has not tried to provide any proof of her claims?

I'm not talking about her claims. I'm talking about all the claims her detractors are making alleging that she said (among other things): that "Smeja's sample tested positive for her "unknown" DNA, or that her paper mentions "angel DNA", or that the BBB report shows that her laboratory work is sloppy and unprofessional generating wrong results.

That's not our fault that we have none of her data. What we HAVE done is release hard data that seems (notice I say "seems") to invalidate or at least call in to question many of her claims.

No, that invalidate what YOU claim she claimed.

Prove that she claimed it in the first place. Obviously for you to claim that Smeja's sample tested positive by Ketchum for her unknown then you must be privy to her data...no? Then YOU have no basis to claim that your results in any way say anything about Ketchum's study.

It's that simple.

Regarding our data, or Disotell's speculation. Our data and his speculation do not need to be held to the same standard.

Yes they do. It's called "requiring evidence to support a claim".

Neither he, nor I, nor Bart are making "extraordinary claims" which, as you know, "require etraordinary proof".

You haven't even provided ordinary evidence as far as your claims about Ketchum go, let alone "extraordinary".

We are releasing reports with very pedestrian conclusions. I have yet to find a single PhD biologist or geneticist who has contentions with my report.

Again, it isn't your report that I have a problem with. It's your use of that report to improperly attempt to impeach Ketchum's study that I have very real problems with.

"Ketchum's sample did not test out for BF at all"

How do you know this?

Slim asked for possibilities. That is as likely as any on his list.

[Guest]

Photo? Bones? Carcass? Anything? 50+ yes of searching and what do we have? 0 nada zilch

[Guest Tyler H]

No she hasn't. Others have insinuated (or outright claimed) this, but no one has documented ANYwhere that Ketchum has made that claim.

You're the one claiming that she in fact said it...not me.

Who are these "people directly involved with the study" claiming this? Lindsay? Stubsted (now deceased)? Others? What is their proof?

Links to any place where these people are named and links provided where we can examine their statements?

No Mulder, YOU claimed she DENIED saying it - those are your words. So it's up to you to provide proof that she denied it. I never asserted that she DID say it, I only asked you to prove that she denied it. I heard her choose her words very carefully on a radio interview, when asked. She said 'some people think that' but she never DENIED having made claims about extraterrestrial sources, or angel DNA, etc. I'm just asking you to provide proof of your claim that she has categorically denied saying that. If I had ever claimed that she said it, then I should provide proof of my claim. I only claim heresay on that one, and admit it. But it was heresay from prominent players in this story. A major benefactor, a major sample provider, and a major research contributor as well as Stubstad and a more recent advisor and contributor. They all claimed it, but I admit I can't prove it. You however claim she denied it - please provide the denial.

[Guest tomafoot]

point taken, but these were insiders that were singing her praises, and doing nothing but lauding her at the time. They had no axe to grind, and she was not "their boss." This was from investors and submitters and ... confidantes. NOt that I care. She can be as cooky as a cookie. If the science is sound, then the science is sound. History is rife with crazy characters who play a role in important discoveries.

Tyler,

I think we can agree that so long as the belief system does not inhibit the presentation of facts, nor overly bog down the interpretation of the data, that we should be tolerant, if not respectful. We won't really know the situation until we see what she puts in her paper and her presentations.

Anyway, I thought I'd come back to what I mentioned earlier: the idea that all three parties could in good faith report information that they know to be true, but can't possibly all be 100% true. So, for the sake of this discussion, let's accept that the following are true:

1. JS gave portions of the same sample to MK and to Tyler/Bart who in turn provided to service labs.
   
2. MK generated data that upon extensive analysis is indicative of an uncharacterized animal in the primate lineage.
   
3. Service labs return results and interpretations indicating presence of material from known animals (includes human) only.
   

A lot has been said concerning 1 and 2, so let me cut to the chase and focus on 3. How could mammalian universal primers fail to pick up an unknown mammal, if it's DNA was present in the sample? There are a number of reasons, but I can think of two that could be consistent with the data in Tyler's report. First of all, those results look very clean and appear to be relatively unambiguous. The lab has designed their assays with known entities in mind - they've gone and found all "relevant" DNA sequences, lined them up and designed their PCR primers to ensure broad detection. Hell! The DNA sequence is unambiguous...about what has been amplified. As far as they are concerned, they have their positive. It totally fits with their reality and their test design. Case closed.

So, "how do you get around what should the predominant contributor, noticeably absent?"

There are 2 types of disruption that will kill the PCR amplification of a target nucleic acid: 1) nucleotide insertions and 2) nucleotide deletions. Oligonucleotide primers (or just "primers" are designed to associate with a complementary DNA sequence of determined length. So, typically a researcher will look at a stretch of defined DNA sequence and design 2 primers (one commonly called the "forward primer" and one called the "reverse primer") based on a number of criteria that the researcher feels confident will lead to good performance in the assay. Let's say the researcher decides on primers that are 20 nucleotides in length and sends in an order to have them synthesized to specification. The primers are tested against known targets and they work as expected, i.e. they match perfectly or nearly perfectly with all 20 nucleotides each in the targets (DNA) of interest and give the expected results. Hurray! Now, it is true that primers can tolerate some kinds of mismatches in the specified sequence and still work - that's generally how universal primers work across a broad specturm of species. But insertions and deletions are difficult because they create unique physical constraints in the pairing of primers and target DNA. It will only take one insertion or deletion in either forward or reverse primer to pretty much kill the amplification of that specific DNA. So, if you have a mix where predominant (unknown) DNA has a bad match due to insertion/deletion you get no amplification, whereas the known matching DNA targets will amplify preferentially.

The problem here is that insertions and deletions are also very disruptive to protein coding sequences, and there may be evolutionary pressures against such disruptions. However, disruptions in sequences outside of protein coding regions may be more forgiving (and therefore evolutionarily acceptable). I am not familiar with the design of these primers, so I can't assess the probability of this occuring here, but it is certainly possible.

So, how might MK have gotten around this? Well, in her press release and interviews she has identified "Next Generation Sequencing" as the technology platform that has generated her most convincing data. Next Generation Sequencing is a relatively new technology platform that couples generic nucleic acid (DNA) amplification with high-throughput sequencing. It uses much shorter oligonucleotide primers to pretty much amplify all DNA in a sample for sequencing. The sequence data is rapidly fed into very powerful computer software that sorts and aligns the information. The view of the sample would be much more comprehensive and pitfalls due to insertions/deletions would be avoided or rendered insignificant due to massive amounts of corroborative information. It is a tremendous investigative tool, but would also have technical pitfalls of its own. I believe that some have indicated that this work was actually contracted out to labs with expertise and the appropriate instruments and computer systems.

So, that is one possible explanation. However, there still seems to be a strong case for bear.

[Guest Tyler H]

Quote from Tyler

"That's not our fault that we have none of her data. What we HAVE done is release hard data that seems (notice I say "seems") to invalidate or at least call in to question many of her claims."

No, that invalidate what YOU claim she claimed.

Prove that she claimed it in the first place. Obviously for you to claim that Smeja's sample tested positive by Ketchum for her unknown then you must be privy to her data...no? Then YOU have no basis to claim that your results in any way say anything about Ketchum's study.

It's that simple.

Well, you are right about one thing... it IS that simple... she has claimed on radio that her results support an uncatalogued primate. And she claimed to me personally on the phone that Justin's sample was one of the three complete genomes that she had mapped. So I guess in that respect, I AM privy to that data (if you count that claim as data). Even Derekfoot will tell you that she has made the same claim to him, and Justin will tell you she made that claim to him, and her major financier will tell you he made that same claim to him. Many other people will tell you the same thing - some that are in her corner, and some that are not in her corner. She has not denied this, and it seems that she has no plans to deny this. So stop picking this particular battle - it's the wrong hill to die on, and Melba herself would not back you on this.

So, "how do you get around what should the predominant contributor, noticeably absent?"

There are 2 types of disruption that will kill the PCR amplification of a target nucleic acid: 1) nucleotide insertions and 2) nucleotide deletions. Oligonucleotide primers (or just "primers" are designed to associate with a complementary DNA sequence of determined length. So, typically a researcher will look at a stretch of defined DNA sequence and design 2 primers (one commonly called the "forward primer" and one called the "reverse primer") based on a number of criteria that the researcher feels confident will lead to good performance in the assay. Let's say the researcher decides on primers that are 20 nucleotides in length and sends in an order to have them synthesized to specification. The primers are tested against known targets and they work as expected, i.e. they match perfectly or nearly perfectly with all 20 nucleotides each in the targets (DNA) of interest and give the expected results. Hurray! Now, it is true that primers can tolerate some kinds of mismatches in the specified sequence and still work - that's generally how universal primers work across a broad specturm of species. But insertions and deletions are difficult because they create unique physical constraints in the pairing of primers and target DNA. It will only take one insertion or deletion in either forward or reverse primer to pretty much kill the amplification of that specific DNA. So, if you have a mix where predominant (unknown) DNA has a bad match due to insertion/deletion you get no amplification, whereas the known matching DNA targets will amplify preferentially.

The problem here is that insertions and deletions are also very disruptive to protein coding sequences, and there may be evolutionary pressures against such disruptions. However, disruptions in sequences outside of protein coding regions may be more forgiving (and therefore evolutionarily acceptable). I am not familiar with the design of these primers, so I can't assess the probability of this occuring here, but it is certainly possible.

So, how might MK have gotten around this? Well, in her press release and interviews she has identified "Next Generation Sequencing" as the technology platform that has generated her most convincing data. Next Generation Sequencing is a relatively new technology platform that couples generic nucleic acid (DNA) amplification with high-throughput sequencing. It uses much shorter oligonucleotide primers to pretty much amplify all DNA in a sample for sequencing. The sequence data is rapidly fed into very powerful computer software that sorts and aligns the information. The view of the sample would be much more comprehensive and pitfalls due to insertions/deletions would be avoided or rendered insignificant due to massive amounts of corroborative information. It is a tremendous investigative tool, but would also have technical pitfalls of its own. I believe that some have indicated that this work was actually contracted out to labs with expertise and the appropriate instruments and computer systems.

So, that is one possible explanation. However, there still seems to be a strong case for bear.

I'm open for scenarios that may have caused our two labs to miss. Hell, I fought hard for something like that when I was receiving their results. I should have had you handy then.

What would be the mechanism for this "insertion or deletion"?

And I'm not sure if I caught what exactly would be inserted or deleted. Like, what would the insertion of a nucleotide look like? I'll have to give it a second read.

Edited January 4, 2013 by Tyler H

[Guest tomafoot]

As I understand it, you should be able to get mtDNA from the hair alone, but you will need the follicle also to have a chance of getting nuDNA.

Happy to be corrected by the experts, e.g. genesrus.

I found a review from 2007 on the use of hair in forensic analysis and your statement is true, but the shaft would not be the source of choice - sort of a desparation move. Still, it's always a good day when you learn something new. So, thanks for the pointer.

[Guest slimwitless]

I will never understand why not even a phone pic was taken. Incredible.

Because it's not wise to have evidence on your person if you think may have committed murder? Just speculating.

8. Ketchum's sample did not test out for BF at all and those claiming she said it did are either a) misinformed, or are themselves being deceitful

I did ask for possibilities and that's a good one. There are also variations. For example, the sample did not test as BF but she wanted someone to believe otherwise.

Please note that although I believe the Smeja sample is a central part of the study, I never claimed she said it publicly. From my perspective, all evidence is either circumstantial or based on hearsay.

Edited January 4, 2013 by slimwitless