The Ketchum Report (Continued)

[Guest]

I need some help here. Dr. Ketchum made this claim:

Whole Human Genome SNP analysis:

Twenty-four samples were tested on the whole human genome (2.5 million SNPs) Illumina® Bead Array69 platform using the Illumina® iSCAN instrument.

Of these, in a clear departure from the results obtained with normal human DNA, 100% of the 24 samples failed to meet the human threshold of 95% SNP

performance. The results ranged from 53% to 89% SNP performance. In the top 12 performing samples, only 45 SNPs out of the 2.5 million SNPs tested failed

across all 12 samples, while simultaneously the human controls all yielded above 95% results on those SNPs.

But she did not reference the 95% claim. Does anyone know where that information came from? When you make that big of a claim, it is typical that you reference where that information came from.

So I am hoping someone here knows where I can find that in a peer reviewed journal or book!

I am not certain about where the 95% came from, but I have a couple of comments on this portion of the study. If these are all the same species, why the large variation in the results (53-89%)? And which samples were the top performers?? There is no data associated with these claims. Did samples 26, 31, and 140 fall into the top 12 samples? Another example of serious scientific deficiency in this paper.

[Guest]

The big difference between standard sequencing and next-generation sequencing is the number of templates.

In standard sequencing, you are working on a single template, or piece of DNA, either a pcr product, purified DNA fragment, or plasmid containing a DNA fragment of interest. You typically use either a sequence specific primer (for a pcr product), or a generic primer for something cloned in a plasmid. By using sequential primers, you can in a few independent runs sequence moderate amounts of DNA (for example get 5000 bp from 10-15 sequential runs). Often you will get your first sequence, then make a new primer to begin sequencing from the farthest end, and repeat.

For next gen sequencing, you are looking at millions of templates at one time and determining their sequence in a massively parallel fashion. The methods and chemistries for doing so are varied and complex, but in short you synthesize a complementary strand and using color specific nucleotide analogs (colored bases) you can determine the order of the bases in the sequence.

In standard sequencing you typically can have "reads" of 300-500 bases, where as the next gen technology often gives only short (50-100bases) sequences which are then re-assembled using complex computer algorithms, potentially generating contigs of hundres of thousand of bases. For standard sequencing the data is technically raw or unprocessed with little interpretation other than it is good sequence or not (analogous to a good Q30 score). With the next gen sequencing, what is usually presented is the processed concatenated sequence that can have assembly errors. Often 500-5000 bp of standard sequence is more convincing than 100,000 bp of concatenated sequences as it is less prone to error. This is especially true for really novel sequences (ie a never before discovered bacteria from the Antarctic) where there is no good reference to gage it too. With the MK sequence, even though it was supposedly assembled using human Chromosome 11 as a reference, it "bears" little homology to its' own template. This is where I think the assembly went awry and standard sequencing may have been more reliable. Mixed or contaminated samples, especially if it had two separate hominids of very similar sequence, would come back clearly as one species (for one DNA fragment) with conventional sequencing - no franken DNA. BF and human may still come back very similar, and might not be clearly identified with too little sequence though.

Thanks for the explanation. Next question - when using next-gen sequencing, do you need to amplify the data, or is it similar to Pääbo et al's work with unamplified neanderthal DNA?

[Guest]

Is it possible that the nuDNA sequence that was provided was simply fabricated?

It is possible, but I don't think it is. MK or any scientist would know this would be quickly found out. If this study had been well received by the scientific community (as I am sure MK wanted), many qualified geneticists would be analyzing the data. Something this blatantly wrong would be quickly jumped upon (as it has been). My theory is that she sent this material out to a contract lab to be sequenced with the Illumina technology, either saying it was human or unknown, then the bioinformatics person attempted to assemble the data as best they could. At some point they must have been informed it was "human" to use Ch11 as a reference. With the mixed samples, the results are as shown (in the paper). I think MK wanted novel sequence to demonstrate a new species, so accepted the data presented.

Thanks for the explanation. Next question - when using next-gen sequencing, do you need to amplify the data, or is it similar to Pääbo et al's work with unamplified neanderthal DNA?

I would need to look at Paabo's methods more closely to compare for certain, but there is an in situ amplification step with primers specific to the linkers ligated onto the initial DNA fragment library. This is a required step for the Illumina technology, to provide enough template for detection during sequencing.

[Guest Tyler H]

Bart or Tyler, If your samples had tested differently, as almost certainly being from an unknown primate, would your labs have stood behind their work, or disavowed it because of the implications? I,m just wondering how hard it would be to actually get a professional with a lot to lose and maybe nothing to gain to publicly state they have definitive proof of BigFoot. I know your samples didnt indicate that, I was just wondering if you think they would have stood behind it if it did and enter the fray. Thanks PB

I truly have EVERY confidence that my lab would have stood behind a result of "unknown primate" 100%. And I don't speak in absolutes very often.

THey won't say "sasquatch" of course. It would be a huge feather in their cap to have worked on a novel primate... and my lab went above and beyond in everyway - including tolerating me and my challenges to their conclusions! lol. While I did not deal directly with Bart's lab, Dr. Cassidy has shown time and again that he is open to whatever the evidence shows.

[Guest]

I'm being polite and controlled, and keeping the conversation intelligent.

Open up his PDF and read who his author is. How can anyone take that seriously? Would you, or anyone for that matter, take any private medical results seriously if your doctor signed off the same way?

Yet we are supposed to take MK's report seriously even though it has 3 references to farcical studies in it ?

TMan... It does not matter that Ketchum referenced those footnotes. It has nothing to do with her data. Neither does it matter what the author name in that PDF is. The gaunlet has been thrown down with that data as a challenge to her study.

Will Gondor not answer?

[Guest thermalman]

@ bpc "Neither does it matter what the author name in that PDF is."

Explain to everyone why your point is relevant?

[Guest Tyler H]

I'm being polite and controlled, and keeping the conversation intelligent.

Data, science, data... science... supportable conclusions... standing up under examination. That is what matters. WOuld you have felt better if my PhD had authored the paper under some fictitious name that maintained his anonymity, but sounded more like someone you would trust? Like, if he had authored under "Dr. Fletchum" or something like that, would that make you feel better? You see, it's about the data, and the science, and whether it can be supported. No person with credentials (actually... wait... not even any of you WITHOUT claims of credentials) has been able to take issue with the data in that pdf. And that data, is Melba's data. No one refutes that. Why do you want to keep re-visting a debate that you lose at so badly each time?

I thought someone reported that Sykes was doing mito-only. Has that changed? If not ... nothing new is going to come from Sykes' results, only "confirmation" of the same ol' "human DNA contamination" that's been reported in the pre-Melba samples. A mtDNA-only study is essentially pre-destined to only preserve the status quo, not discover anything new.

MIB

"Definitive" may be a stretch, but I do have contact with Sykes, and people involved. It was a while back now, but it was related to me that yes, he is only looking at mtDNA - but I don't think that means that he will only preserve the status quo, as I don't think the mtDNA of this animal will turn out to be human. I think it is likely that some sample or other, in Melba's arsenal could be an unknown primate, and I think Syeks could turn up unidentified mtDNA. If not from her samples, then hopefully from others that he has.

Edited March 14, 2013 by Tyler H
To remove deleted objectionable content

[Guest]

The Melba Ketchum global sasquatch foundation website is now online.

http://www.melbaketchum.org/home/

I like this quote from the site:

" . Due to the efforts of our founder Dr. Melba Ketchum it has been proven that the Sasquatch are a human hybrid."

oh and that disclaimer at the bottom is nifty too.

[Guest Tyler H]

The Melba Ketchum global sasquatch foundation website is now online.

http://www.melbaketchum.org/home/

I like this quote from the site:

" . Due to the efforts of our founder Dr. Melba Ketchum it has been proven that the Sasquatch are a human hybrid."

oh and that disclaimer at the bottom is nifty too.

Wow - I recant.

this proves it all http://www.melbaketchum.org/data/imagegallery/0e14cb59-443e-a993-76b3-6013b96c61bd/34a87981-8f80-b98c-1d8a-f0ec154b7f5d.jpg

[Guest]

@ bpc "Neither does it matter what the author name in that PDF is."

Explain to everyone why your point is relevant?

Let's say you and I play chess in person. Yet we both wear masks and have no idea about each other's true identity. The game starts and you put me in checkmate in less than 10 moves and win the game.

I ask you.

Does the fact that I have no idea who you are have any relavence to the fact you won the game?

Wow - I recant.

this proves it all http://www.melbaketc...0ec154b7f5d.jpg

OMG it's the proof we have all been waiting for. Tangled hair !!!

[Guest thermalman]

The disclaimer is hilarious. Obviously a misprint "our" should be "your".... LOL

[Guest poignant]

Bad grammar, campy website, anybody smell FBFB ?

[Guest thermalman]

Let's say you and I play chess in person. Yet we both wear masks and have no idea about each other's true identity. The game starts and you put me in checkmate in less than 10 moves and win the game.

You're at least visible and tangible. But to put all your faith and trust in a supposed reputable scientific report signed off by an unknown Phd with a fictitious name,........ I mean........come on? You seem more intelligent than that.

If that report went to peer review....... you know exactly where it would end up.

[Guest Tyler H]

The Melba Ketchum global sasquatch foundation website is now online.

http://www.melbaketchum.org/home/

I like this quote from the site:

" . Due to the efforts of our founder Dr. Melba Ketchum it has been proven that the Sasquatch are a human hybrid."

oh and that disclaimer at the bottom is nifty too.

And I loved the "do to their unbelieveable ability to stay hidden from us..."

You're at least visible and tangible. But to put all your faith and trust in a supposed reputable scientific report signed off by an unknown Phd with a fictitious name,........ I mean........come on? You seem more intelligent than that.

If that report went to peer review....... you know exactly where it would end up.

Then stop 'trusting', and start 'blasting'!

The difference here, for the tenth time, is that that data is transparent, and the claims are replicable. ANYONE can do what he has done, and I have provided the links to do so for yourself. The fact that you refuse to do so speaks volumes.

Once you try that, and find that it fails, come back here, and we can talk about your doubts.

Again, I said nothing on this forum about my Melba doubts, until I had lab reports, and evidence. You keep faulting me for critiquing Melba with evidence that you don't find credible, yet you fault my source, with ZERO evidence. Stop the double-standards.

[Guest thermalman]

Bad grammar, campy website, anybody smell FBFB ?

Agreed on the first two points. Time will tell if FBFB is involved?

Edited March 13, 2013 by thermalman