The Ketchum Report (Continued)

[southernyahoo]

I thought Ketchum or a representative of hers qualified the chain of custody as well as the sampling of dna from participants to help sequester or identify any potential contamination? Am I wrong in that assumption SY? Or were we just fed that as best practices?

My group sent her three different bucal swabs with our sample at Dr. Ketchum's request, and can't answer for the rest of the samples on that. I think there is a table in the paper representing these. So the chain of custody on my sample was from the tree, to the bag with tweezers, then from the bag to the envelope wrapped with paper and mailed to Ketchum. She sent them to an examiner then back to her lab or the lab that sequenced the entire mitochondria.

[bipedalist]

Thanks SY that is more consistent with procedures I heard were in the protocol thru the grapevine.

[southernyahoo]

Ignoring for a moment the fact that Family Tree completely contradicts Ketchum's claim chain of custody is crucial in any kind scientific testing, even if it is only a portion of a much larger batch of tests. There's simply no excuse to not maintain a proper chain of custody.

You seem to be saying the sample wasn't labeled in any way, is this true or are you saying they didn't tell Family tree who the sample was supposedly from? There is too much that can be lost in translation from what you are saying so far.

[Guest]

My group sent her three different bucal swabs with our sample at Dr. Ketchum's request, and can't answer for the rest of the samples on that. I think there is a table in the paper representing these. So the chain of custody on my sample was from the tree, to the bag with tweezers, then from the bag to the envelope wrapped with paper and mailed to Ketchum. She sent them to an examiner then back to her lab or the lab that sequenced the entire mitochondria.

Did Ketchum arrange for your own DNA to be submitted so that contamination issues could be addressed?

[bipedalist]

I assume the buccal swabs weren't from the cheek of the Bigfoot, PP, LOL!

[Sasfooty]

She asked me to send a swab, and told me that my DNA was not on the sample that I sent. So she obviously checked.

[Guest ajciani]

I have seen some of the rejection letters, and the singular grounds of rejection was that the samples must have been contaminated. The paper grew to a considerable size, just to address contamination, and yet many of the reviewers still ignored those sections.

Ketchum did a lot of work to address contamination, including testing the submitters, people at her lab, and people at the other labs. Also, even if there was contamination, the sequencing would have produced a result for each contributor. If the sample was contaminated by two handlers, then there would have been three sequences. Because of the careful in-lab handling and preparation, no sample ever showed more than one genetic contributor. So either bigfoots do not have mtDNA, and all of the mtDNA hits came from a single contaminator on each sample (which is so unlikely that it is ridiculous), or none of the samples were contaminated. Also, the nuDNA showed a unique sequence. Where would the contamination have come from to produce that? You would have us believe that three samples were contaminated by three different people with non-human nuDNA? That is a major discovery right there.

[Guest]

I have seen some of the rejection letters, and the singular grounds of rejection was that the samples must have been contaminated. The paper grew to a considerable size, just to address contamination, and yet many of the reviewers still ignored those sections.

Ketchum did a lot of work to address contamination, including testing the submitters, people at her lab, and people at the other labs. Also, even if there was contamination, the sequencing would have produced a result for each contributor. If the sample was contaminated by two handlers, then there would have been three sequences. Because of the careful in-lab handling and preparation, no sample ever showed more than one genetic contributor. So either bigfoots do not have mtDNA, and all of the mtDNA hits came from a single contaminator on each sample (which is so unlikely that it is ridiculous), or none of the samples were contaminated. Also, the nuDNA showed a unique sequence. Where would the contamination have come from to produce that? You would have us believe that three samples were contaminated by three different people with non-human nuDNA? That is a major discovery right there.

Thanks for filling us in on this. I tend to agree that it is not human contamination here. Did the reviewers specifically say the samples were contaminated with human dna or just contaminated?

The new nuDNA is so unique that it is not showing up in the genbanks databases. This is odd. I have been spending a good portion of my free time blasting the sequences provided with the manuscript, and the homology to human is rather minor over the whole sequences. I believe it is well less than say 10% (perhaps as low as 2%). Furthermore, the three samples do not appear to be related to each other - they are not highly homologous. So they are not the same species - perhaps 3 different species though. Do you know which of these three samples MK clames as HSC? It is not clear what samples in the study did not pass the test of being BF. I have this evening picked ups some homology to Streptococcus sanguinis (a bacteria), and Acremonium sp (mold) from sample 31. Given where these samples have been retrieved from, this is not surprising. You can call the non-human nuDNA a discovery, but I don't know where it came from! But I doubt it was from a mammal and hence BF. Imo, of course!

[Guest]

I have seen some of the rejection letters, and the singular grounds of rejection was that the samples must have been contaminated. The paper grew to a considerable size, just to address contamination, and yet many of the reviewers still ignored those sections.

Ketchum did a lot of work to address contamination, including testing the submitters, people at her lab, and people at the other labs. Also, even if there was contamination, the sequencing would have produced a result for each contributor. If the sample was contaminated by two handlers, then there would have been three sequences. Because of the careful in-lab handling and preparation, no sample ever showed more than one genetic contributor. So either bigfoots do not have mtDNA, and all of the mtDNA hits came from a single contaminator on each sample (which is so unlikely that it is ridiculous), or none of the samples were contaminated. Also, the nuDNA showed a unique sequence. Where would the contamination have come from to produce that? You would have us believe that three samples were contaminated by three different people with non-human nuDNA? That is a major discovery right there.

I'm not much up on DNA stuff, but do understand the change of custody, and contamination issues (my dad was a sheriff at one time, a lawyer too)....but your post should shut the critics down and hard. Is that what I think I see in the air....arrows of flames being extinguished.

[bipedalist]

So ajciani is saying there were no substantive qualms with reviewers about the paper's conclusions and findings..... only the methodology? I assume that is what singular means?

If that is the case, then why are there no previous publications prior to Ketchum's available for perusal from the Journal of Multidisciplinary Explorations in Zoology? Can you find reviewer comments for another paper in that same journal ajc?

Edited February 23, 2013 by bipedalist

[Guest BartloJays]

ajciani-

Can you explain how she was able to definitively determine that the Sierras sample was a bigfoot in just 4 days of receiving it and well before a genome and or next gen sequencing was even "purportedly" utilized? How about why Justin's DNA was not requested after she was supposedly shaking her head about the photo she saw with the sample in his hand? How did she rule out Justin as the human source from that sample to confidently make that determination?

How do you explain our labs results from independent testing (where they got a sample of Justin's DNA) at two highly reputable labs where the only contributors present were bear and Justin?

Why are no lab reports attached to her paper when with respect to her hypothesis and subject matter, it's logical to suspect that you would need as much ammunition as possible absent a physical specimen? Why do you think there's not one independent third party voice being heard on her behalf who actually participated in any of the processes, rather through any testing or even that an actual "successful" peer review took place?

Just curious what you think of all these issues as it's not even 1% of the questions that could be objectively asked with consideration of where we're at right now?

Thanks in advance

Edited February 23, 2013 by BartloJays

[Guest]

I am just going to keep putting data out there to hammer down the point. One blog challenged the "critics" to blast the data. I only wish the supporters would do likewise.

Ok, so I just did an alignment of sample 26 vs 31. Again there is alignment over the length of the full contigs (one being 2.7Mbp the other being 0.53Mbp). Again, if they were the same species (and the contigs legitimate) they should not be broken up into so many pieces and the two contigs should be the same length. This demonstrates they are not related - or the contigs were not assembled correctly, or had contaminating (NOT HUMAN) dna integrated into the contig.

[Guest]

one last piece of analysis from me for tonight. just did an alignment between sample 26 and 140 over the entire length of the contig, and there is a fair bit of homology - 47%. Left panel. Still low homology, but when you look at the plot, it looks a lot smoother. With the recent discussion of the origin of sample 26, I don't know what to make of this, but I put it out there.

Ok, this is the last bit to round out the set. Alignment of 31 and 140 looks quite low (7%) and again broken up. Right panel.

Take home is that 26 and 140 appear more similar to each other than to 31.

Edited February 23, 2013 by ridgerunner

[Guest Tyler H]

Did you speak with him on the phone? I always thought he sounded a bit like Jimmy Stewart, actor and Yeti enthusiast.

Yes, we spoke a few times. In the end, he wanted me to take custody of samples that seemed to be under his oversight. I hadn't realized that he was asking because he knew his time was running out. Had I known that, I might have obliged, but I felt his samples were sketchy, and my plate was quite full with my own research.

I think from an early stage, many viewed the sheer quantity of samples as being insurance that there was no need for dependence on a so-called "centerpiece" sample. Such sentiment has been reiterated for years in this thread. I think if the study is valid then there should be plenty of sequencing done to uncover a result without the Smeja sample.

I thought Ketchum or a representative of hers qualified the chain of custody as well as the sampling of dna from participants to help sequester or identify any potential contamination? Am I wrong in that assumption SY? Or were we just fed that as best practices?

I have tried to shout this from the rooftops at least 10 times on this forum, but I guess it keeps getting missed. Melba did not collect Justin's DNA. She keeps trying to phrase things so as to leave the impression that she got DNA from all submitters, but it is patently false. Perhaps she got some, but she did not get all. I find it shocking that of three fully mapped genomes which she claims "match human", at least one of them was never compared to the DNA of the submitter.

I have seen some of the rejection letters, and the singular grounds of rejection was that the samples must have been contaminated. The paper grew to a considerable size, just to address contamination, and yet many of the reviewers still ignored those sections.

Ketchum did a lot of work to address contamination, including testing the submitters, people at her lab, and people at the other labs. Also, even if there was contamination, the sequencing would have produced a result for each contributor. If the sample was contaminated by two handlers, then there would have been three sequences. Because of the careful in-lab handling and preparation, no sample ever showed more than one genetic contributor. So either bigfoots do not have mtDNA, and all of the mtDNA hits came from a single contaminator on each sample (which is so unlikely that it is ridiculous), or none of the samples were contaminated. Also, the nuDNA showed a unique sequence. Where would the contamination have come from to produce that? You would have us believe that three samples were contaminated by three different people with non-human nuDNA? That is a major discovery right there.

If you are going to get dogmatic about your opinions, you need to make sure you have read all the facts from more than just sources that tickle your ears. Each section that I bolded above is false. I will address them in order below:

1. There is much more to the critique of this study than just allegations of contamination.
   
2. In fact, the ONLY sample that was independently tested DID produce results for two contributors - bear and human.
   
3. So, yes, the sample DID show contamination.
   
4. The nuDNA showed a sequence that is SO unique, that it has less in common with people than does corn... So either claim it is extraterrestrial, or realize that her contigs are highly suspect - most likely due to using human genetic information as the reference to assemble them, while doing so with genetic samples that originated from bear, or dog, or what have you.
   
5. "You would have us believe that three samples were contaminated by three different people with non-human nuDNA?" The samples are so distinct from eachother that the animals in question would be about as closely related to eachotehr as people and turtles. Do you really think that she happened to get samples from three so distinctly unique animals, and that each one had such unique DNA that each one was not related to anything else in Genbank? The clear answer is that she has created frankenstein DNA.
   

All this having been said, I will again state that just because one Rolex that she is trying to sell is clearly a fake, that doesn't necessarily mean they all are. But it DOES make all the rest of her efforts just that much more suspect.

My PhD contact that has been puzzling away on this for a while now, and working with the raw data, thinks that sample 140 is dog, just as sample 26 (justin's) was bear. But he thinks that if any sample shows promise, it is sample 34. It shows only human sequences, with no junk sequences from non-primate contributors. So, either it is a purely human sample, or it could be the real deal, if you believe that Squatch are that human. I have no idea how thoroughly the chan of custody was tested against this sample, or how you could rule out the possibility that the sample was something that originated directly from an unidentified human.

Edited February 23, 2013 by Tyler H

[Guest]

Ignoring for a moment the fact that Family Tree completely contradicts Ketchum's claim chain of custody is crucial in any kind scientific testing, even if it is only a portion of a much larger batch of tests. There's simply no excuse to not maintain a proper chain of custody.

I am simply speechless.

In her paper Ketchum states the samples were treated as forensic samples and cataloged to maintain a chain of custody. However when I spoke with Family Tree DNA (one of the "For Hire" labs listed in the paper) they informed me that the samples they received had no chain of custody.

Okay... Question - any mention of the collection methods and storage on the part of the submitters? Or does she not go into detail about that?

In this part you say:

Ketchum states the samples were treated as forensic samples and cataloged to maintain a chain of custody

This make me worried that she has little to no idea of the collection methods or storage used by the submitters and she was only concerned about the chain of evidence once these samples came into her possession.

Ridgerunner said:

I have been giving this some thought, and yes I thing there is human bias. I feel there is bias in the writing, but also in the design, with use of human primers and the use of human chromosome 11 for alignment. There was use of more degenerate primers, but none of the sequences were provided and even exactly what they were amplifying in some case was deemed proprietary.

The bolded text -- is that standard procedure? As for the not bolded text - I was afraid you might say that.

Earlier you mentioned the length of storage and storage conditions, and I think this is an interesting point. Any living tissues/hair/toenail etc will have bacteria and fungi on it at some level. The longer this is stored, the more likely this will add to the makeup of the final DNA pool. Things that are stored very cold or very dry, tend to prevent this growth. And while contaminants tend to grow on the surface, I am not sure they can not migrate into the tissue (sorry for the double negative).

I don't know for certain, but I think it depends on the type of biological evidence being stored and how it's stored (as you mention above). For example: I would think a hair or soft tissue samples would be more susceptible and bone being less for obvious reasons. But, I could be wrong - but that has always been my understanding.

Edited February 23, 2013 by Melissa