The Ketchum Report (Continued)

[HOLDMYBEER]

From the comments from hvhart and ridgerunner, any future DNA tests are going to require full documentation. Sykes needs to make sure he doesn't just put things in a table and expect people to take his word. ........... And without all the submitters DNA reports that show their haplotypes, and the broken chains of custody there's no way to verify that each sample doesn't simply match the haplotype of the submitters or testers. I remember hearing from sources that samples were mixed up, so it becomes impossible to verify the table isn't just wrong without the full documentation. ...................

 

Honestly, if I've learned anything from this, it's that when you're collecting evidence, always come at it from a skeptical point of view. Don't jump to conclusions and rule everything out first. Make sure you know everything about the nature and wildlife in your area. Take a trapping course, even if you never trap in your life. You'll learn and be able to observe things you've never seen before while you're out in the woods. If you can follow the food sources of every predator in the forests, finding what feeds on them won't be much harder. Dot your I's and cross your T's and I don't think anyone will have any issues with taking you seriously. It's better to be sure than to "be right." 

Which is the same as vetting the evidence to at least a standard of probability before submission. The few vetting documents made available for review came nowhere near that standard. I suppose there was always the chance that genuine sasquatch DNA could  have selected and submitted, but it seemed doubtful. Stubstad said the samples were vetted for being 'biologically viable' and didn't give a hoot what they came from and said 'science would sort it all out'. Guess not.

 

Edited May 9, 2013 by HOLDMYBEER

[Guest ewashguy56]

 

 

See the next to last paragraph about a long-standing ordinance

in Skamania county, WA, which makes it a felony to shoot/kill

a sasquatch. 

http://www.loweringthebar.net/2012/05/bigfoot-fair-game.html

 

I guess cart may go before horse depending upon locale. 

 

This combined with a 1975 Army Corps of Engineers manual

which states that BF is local fauna in parts of the state . . . well,

maybe in Washington, the acceptance of Bigfoot is greater

than the reflexive denial of him we see elsewhere.

 

One thing is sure, discussion of Bigfoot's legal rights belongs 

in it's own thread, and I believe such thread(s) already exist on

this forum. 

 

Lived in Washington State for most of my life and thats' the first time I became aware of this. Learn something new each day!

[Cotter]

Well, from the report, I doesn't appear that 'science' was applied fully or properly.

Maybe someone else will employ science to see what the heck is going on.

[Guest]

ewashguy56- you may want to look up the Wathcom county regulation #92-043 outlwing the shooting of Sasquatch. Also the Sasquatch is listed as a wetlands protected species inKings county, 1965.

[Guest]

And if they don't do something fast Scaleburgers is going to be to renamed Squatchburgers.

[Guest njjohn]

 

You can't put the cart before the horse. Regardless of what experiences people have had, there is zero tangible proof of their existence that would be evidence enough for any political body to pass any laws at all. IF/When proof is established that is acceptable to the scientific community in the way of a proven theory that is testable and re-testable then and only then will elected officials put themselves out there to pass laws. 

 

From the comments from hvhart and ridgerunner, any future DNA tests are going to require full documentation. Sykes needs to make sure he doesn't just put things in a table and expect people to take his word. Even the 16 haplotypes don't prove relation to human because when you throw out samples that don't fit the time period of the hypothesis, it looks like you're forcing the science. And without all the submitters DNA reports that show their haplotypes, and the broken chains of custody there's no way to verify that each sample doesn't simply match the haplotype of the submitters or testers. I remember hearing from sources that samples were mixed up, so it becomes impossible to verify the table isn't just wrong without the full documentation. 

 

I think it's pretty telling that she refuses to talk to the BF community and has moved onto the larger alien theory community. I very much doubt we'll ever hear anything new about this study or the "experts" that were supposed to be looking into things. 

 

Honestly, if I've learned anything from this, it's that when you're collecting evidence, always come at it from a skeptical point of view. Don't jump to conclusions and rule everything out first. Make sure you know everything about the nature and wildlife in your area. Take a trapping course, even if you never trap in your life. You'll learn and be able to observe things you've never seen before while you're out in the woods. If you can follow the food sources of every predator in the forests, finding what feeds on them won't be much harder. Dot your I's and cross your T's and I don't think anyone will have any issues with taking you seriously. It's better to be sure than to "be right." 

 

 

Um, nijohn, if you have DNA that splits human haplotypes, it's human, okay? There is no evidence she obtained anything else from the mtDNA, except by her admission that some were identified as known animals other than human. No nonhuman apes showed up. What else could you do with that data set but look at the male lineage?

 

 

SY - I agree she got human. But that doesn't prove they were human samples from bigfoot. Is your haplotype anywhere on the table? All I'm saying is this is another area of the study that there is a lack of information. There should be full DNA reports from each submitter to be able to eliminate each from consideration. Not just a table of what the haplotypes of the samples are. A table isn't scientific evidence. Coupled with the fact that every sample that fell out of the timetable of her hypothesis was automatically discarded, just looks fishy. SY, I'm not discarding the mtDNA completely, not at all. I just think it needs to be backed up, not just taken as fact without any proof to back it up. Especially with all the contradictions elsewhere. 

[georgerm]

Really nice work Haskell. The part the in bold below could use more explanation.

 

So do you find any DNA that could be BF?

 

 

 

 

Summary

Except for the problems described above, the paper is very readable and extremely interesting and intelligible, even to a “nonexpert†with some common scientific background.  Some of the Figures, Tables, and Supplementary Data and Figures need more explanation, in the form of text comments, better headings, or footnotes.  Some of the figures and data referred to in the text are entirely missing in the on-line version, or have been incorrectly referenced there.I find the Haplogroup assignments in Table 2 and Supplementary Table 2 to be correct for 28 of the 29 samples, based on the reported mutations only.  The conclusion that the mtDNA of all 29 samples(plus the control) is essentially human is supported by the sequence data.  I make no assessment of the validity of the raw data from which the mutations were determined.My above searches support the conclusions in the paper that:1) Samples 26, 31, and 140 contain nDNA that is not entirely human, but has similarities to human chromosome 11 and other primate sequences.2) The nDNA in Samples 26, 31, 140 shows no significant similarity to a raccoon, a black bear, or an opossum.

 

The following conclusion, is not supported by results in the paper and needs to be revised: “All known ape and relic hominin species such as Neanderthal and Denisovan were excluded as being contributors to both the nuclear and mitochondrial sequences.â€In addition, the apes portion of this conclusion conflicts with the conclusion discussed below.Nothing can be said about Neanderthal and Denisovan nuclear DNAs, since virtually none of the former and none of the latter can be found in the NCBI nucleotide database, which contains only five short “environmentalâ€(hence uncontrolled) Neanderthal nDNA sequences of 89 bp or less.Because of the high degree of homology between human and Neanderthal and Denisovan mtDNA and the paper’s finding that the 29 samples in Table 2 and Supplementary Data 2 all showed essentially human mtDNA, excluding Neaderthal and Denisovan as mtDNA contributors would need support from 1:1 complete genome mtDNA comparisons, as recommended above in the mtDNA section, and supporting comments on the significance of the differences.  Sample 26 mtDNA searches above, marked with a “@â€, were “constructed†by adding the reported Sample 26 mtDNA mutations to the rCRS sequence. There is a slight preference for Homo sapiens over Neanderthal and Denisovan, but the differences should be carefully compared and analyzed, before excluding Neanderthal and Denisovan mtDNA.   

 

The following conclusion is not supported by results in the paper and needs to be revised:“Analysis of whole genome sequence and analysis of preliminary phylogeny trees from the Sasquatch indicated that the species possesses a novel mosaic pattern of nuclear DNA comprising novel sequences that are related to primates interspersed with sequences that are closely homologous to humans.â€In addition, this conclusion conflicts with the conclusion discussed above.The two types of sequences mentioned above, i.e. the mosaic of human and other primates, are in fact one and the same in Samples 26, 31, and 140. For example, the homologous sequence on Sample 26, from position 189026 through position 191141, matched sequences on Homo sapiens and the primates: Pan troglodytes, Pan paniscus, Gorilla gorilla gorilla, Pongo albeii, Nomascus leucogenys, macaca  mulatta, Saimiri boliviensis boliviensis, Papio anubis, Callithrix jacchus, Saguinus labiatus, Lagothrix lagotricha,  and Otolemur garnettii. There is no interspersion of sequences. Also, Samples 31 and 140 showed no other primate homology(except Homo sapiens) in Supplementary Figures 5 and 6, respectively.  Supplementary Figure 5 shows mouse, chicken and fish homologies, Supplementary Figure 6, a mouse. 

 

However, my BLAST searches, above, do show some primate homology for these two samples, significantly more for 140 than 31, but again, there is no interspersion of sequences.  The other primate sequences are also Homo sapiens sequences.I sincerely believe that “peer reviewers†would/should have noticed the matters described in this review and possibly more that were not obvious to me.  They would/should have facilitated a better presentation of this important study.I strongly recommend that an addendum be published, clarifying the matters addressed above and offering new data for others to analyze, e.g. hair photomicrographs and mtDNA sequences as you did with the nDNA in Supplementary Data 4, 5, and 6, for example. Complete mtDNA sequences would be particularly useful in addressing the independent find that Sample 26 contains both black bear and human mtDNA of a different haplogroup from that listed in Table 2 and Supplementary Data 2 and black bear nuclear DNA, with only a trace of human nuclear DNA, which was probably from the submitter.  The lab report is attached.

 

 

Haskell V. Hart, PhD

Canyon Lake, Texas

April 16, 2013

References

D. M. Behar, et al, "The Genographic Project Public Participation Mitochondrial DNA Database,"  PLoS Genet 3(6): e104 (2007),   http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030104

D. M. Behar, et al, “A  ’Copernican’ Reassessment of the Human Mitochondrial DNA Tree from Its Root, Am. J. Hum. Gen, 90(5),  936 (2012).

M. van Oven & M. Kayser, Hum Mutat 30(2), E386-E394(2009), http://www.phylotree.org/.

_____________________________________________________________

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[southernyahoo]

Coupled with the fact that every sample that fell out of the timetable of her hypothesis was automatically discarded, just looks fishy. SY,

 

I'm really not getting this. Are you saying she got human DNA that was older than 15,000 years and discarded it? Or, are you saying that since you have no information on what samples or how many were negative, they might have been positive samples that were discarded?

[Guest njjohn]

Look at the haplotypes in the table. Those that were within a reasonable range of the timetable were continued on, and those that were outside that range weren't tested beyond the initial screening. All 111 samples returned human. Only the 30 that were looked into deeper were the ones that fit the timetable range. I think you said yours fit around the 20k years? So it was within a reasonable range. Again, this doesn't eliminate that any of the samples could have been BF samples, but it looks fishy when the only ones that went beyond initial screening fit the timetable. 

 

It's the questions about things like that, that show how important even the basic documentation is to a scientific study. This wasn't something to be explained by partial sequences, it's something you're supposed to show the full reports to support. With this many samples sent in, it's very possible there could be something there. I don't think anyone's said otherwise, but without the proper documentation, it gives the perception that samples were cherry picked to fit her hypothesis. And that's the major issue. I think most said A) Prove it exists and then Figure out where they came from, etc.. And this paper reads like A is a given and is only trying to prove B. 

[southernyahoo]

nijohn, not every sample produced the same amount of DNA. Certain samples were selected for whole mito or nuDNA because there were more intact hair roots than others. This information can be found in the materials and methods attachment.  I sent in about seven hairs, all with intact roots, one of which had a collar of tissue around the shaft just above the root as if it was a piece of surface skin. Clear evidence it had been pulled forcefully from the skin and not one that had simply fallen out.

[southernyahoo]

 

Those that were within a reasonable range of the timetable were continued on, and those that were outside that range weren't tested beyond the initial screening.

 

 I don't think anyone's said otherwise, but without the proper documentation, it gives the perception that samples were cherry picked to fit her hypothesis.

 

 

 

 

 

I'd appreciate it if you didn't state your perceptions as fact nijohn. You do realize how much that is frowned upon around here right? Hell I could sure stir up a hornets nest around here if I just let loose with my perceptions stated as fact.

[Guest njjohn]

They had enough to find the haplotype... 

 

And I'm not stating perception as fact. Here's the table. 

 

 

Table 2—List of Mitochondrial DNA Haplotypes

Sample Number

Haplotype

26

H1a, one novel SNP

1, 2, 12, 36,

T2b

28

H1

35

H10

29, 44, 46, 138

H2a2

39b,41, 42, 43

T2

37

H12

11

A6L2c

31

LOd2a

38

V2

24

H1s

4,37

H3

33. 95

H

140,168

D

81

C

71,117,118

L3d

8, 139, 18*

HV2 (human specific) only

46-137

Partial HV1 (human specific) screened only

 

HV2 and HV1 originated around 230,000 years ago from the end of Neanderthal until they broke off to H haplogroup at about 23,000 years ago which fits the timeline. All the HV1 and HV2 samples were just not included in the other supplementals, except the master list of who submitted what. Besides the obvious error on the HV1 that the range 46-137 would include samples of other haplotypes, you don't think it's fishy that all those samples just vanished from the rest of the paper? And if that's not an error, but a statement that all of those samples included some HV1 sequences, that would show contamination with two haplotypes, wouldn't it? 

 

There was enough DNA to get the haplotype that is listed in this table and then the other supplementals that are linked along with the hypothesis doesn't include any of those that contained HV1 and HV2. That's what I was pointing out. And I clearly said it was perception that it looks cherry picked for the hypothesis, that part wasn't stated as fact. I'm pretty clear when I state my opinion. If someone can give an explanation, I'm all ears.   I'm reading right out of the supplementals that anyone can look at. 

 

But to me (opinion coming), it looks like you've got every sample that fits the timeline expanded on, and every sample that goes back much further than the hypothesis is just screened. What if the older samples proved the timeline went back further? I completely understand what you're saying about different amounts of DNA, but are you understanding that these were all samples that they were able to test and obtain the haplogroups and haplotypes. If the table had said *these samples didn't return a haplotype due to amount of DNA* then I'd agree 100%. 

[southernyahoo]

nijohn, HV1 and HV2 refers to the hyper variable regions of the mitochondria. They would be more appropriately referred to as HVR1 and HVR2.

 

This is common to sequence those regions to identify the haplotypes or haplogroups.

 

http://www.familytreedna.com/products.aspx

[Guest njjohn]

If that's the case than why is it in the table of haplotypes? HV1 and HV2 are actual haplotypes, where HVR1 and HVR2 are those hyper variable regions. Or are you assuming it's the HVR1 & 2? See why complete and correct documentation is required? 

[Bonehead74]

It's sad how the so-called "Ketchum Report" went from promised (and much touted and anticipated) conclusive proof of the existence of sasquatch to this:

 

http://youtu.be/JkzjBfTDH20

 

I'm more convinced now than ever that only a body will be sufficient to prove the creature's existence, and I have doubts about even that.