The Ketchum Report (Continued)

[Guest]

This is a terrible question, but just to gauge the degree of difficulty in determining these questions about species dna recognition: If one submitted a sizable tissue sample, thick enough to take undisturbed tissue from within to test. And this tissue was taken from a horse. Would, or could there be questionable results that would indicate anything other than horse? If the tissue had been in contact with zebra tissue or donkey or burro tissue, could that contamination be identified exclusive of knowing of it beforehand? I understand the horse, zebra and donkey/burro are known species and have documented genomes. would the identifying of the actual tissue and the components of the contaminates be just a matter of plugging in the algorithms or running it through the BLAST protocol or program?

edited for spelling

Edited February 22, 2013 by people booger

[Guest]

This is a terrible question, but just to gauge the degree of difficulty in determining these questions about species dna recognition: If one submitted a sizable tissue sample, thick enough to take undisturbed tissue from within to test. And this tissue was taken from a horse. Would, or could there be questionable results that would indicate anything other than horse? If the tissue had been in contact with zebra tissue or donkey or burro tissue, could that contamination be identified exclusive of knowing of it beforehand? I understand the horse, zebra and donkey/burro are known species and have documented genomes. would the identifying of the actual tissue and the components of the contaminates be just a matter of plugging in the algorithms or running it through the BLAST protocol or program?

edited for spelling

A horse sample, uncontaminated, would come back as horse, 100% homologous to the reference sequence. It would also likely come back as 99.something homologous to zebra or donkey, but it would be lower than horse. Now if you had a mule sample, it would come back as both a horse and a donkey, with almost equal homology to the reference (as references are typically a single individual sequence there will be minor variations)

If this horse sample was contaminated with zebra, there would be horse sequences that are100% homologous to horse, sequences that are 99.something homologous to zebra, and zebra sequences that are 100% homologous to zebra (and 99.x homologous to horse). Looking at the original raw data, blasting these reads, you should be able to determine the degree of contamination - horse reads would be much more frequent if the zebra was a minor contaminant.

Now if we were to try and piece together these sequences to make long DNA sequences (using a de novo strategy that just looks for overlapping sequences), the resulting "contig" would likely be a mixture due to high degree of homology between the two species. The final contig when blasted against the data base would likely show high homology for horse and donkey. If you assembled with a horse reference I think you should be able to eliminate the less homologous donkey sequences.

What we have with the MK contigs is a mixture of human and unknown (really does not match to anything obvious). Given that they supposedly used the human chromosome 11 as a reference in assembly, I don't know how they could come up with this. Again, based on the below quote form the paper by Ketchum et al, on part states a use of a reference for assembly, one does not.

"For each sample, the subsets of genes were concatenated to produce a long, single sequence used to generate a supertree. The length of the concatenated sequences was 656,048 (26), 541,435 (140), and 74,589 (31)."

"Utilizing a human chromosome 11 reference sequence, preliminary Sasquatch concatenated sequences of 656,048, 541,435 and 74,589 base pairs, were derived from the full genomic sequence from samples 26, 140 and 31 respectively."

Given that these three samples were hopefully from the same species (ie BF) I don't know why their contigs ended up being such different sizes. If they had 30x coverage, they should all have complete genomes, and should all be, within a few bp, the same size. There must be some attempt at assembly though as samples 26 and 140 show some degree of homology (30 -38%) but much lower than two of the same species should be (human and gorilla are 98% homologous). As they line up on the diagonal (see earlier post), this means they are place in the same relative order.

Edited February 22, 2013 by ridgerunner

[Guest njjohn]

The three samples were from California(26), St. Louis(140)and Kentucky(31), so could the geographic variables in the species (the height and size of reports get smaller going south and east) be a possible explanation for the difference in size of the sequences? I know sample 31 is a drastic drop from the other two, but it does shrink in comparison to location.

[Guest]

PB, looking over your original set of questions after my rather verbose response, I don't think I addressed many points. I will think about this a bit more and get back to this.

[Guest]

The three samples were from California(26), St. Louis(140)and Kentucky(31), so could the geographic variables in the species (the height and size of reports get smaller going south and east) be a possible explanation for the difference in size of the sequences? I know sample 31 is a drastic drop from the other two, but it does shrink in comparison to location.

Even if they were each novel species (possible), they should still be highly homologous and their contigs of similar size. Again as human and gorilla are 98% homogous, something that is only 38% (the upper number), are likely highly unrelated. Humans and mouse are ~85% homologous (I only read this very quickly, and it may refer to genes rather than genomic sequence).

http://www.ornl.gov/sci/techresources/Human_Genome/faq/compgen.shtml

But species size (or location) should not influence genome size (inferred form the contig size).

[Guest]

PB,

I am going to try and answer succinctly point by point

This is a terrible question, but just to gauge the degree of difficulty in determining these questions about species dna recognition:

1. If one submitted a sizable tissue sample, thick enough to take undisturbed tissue from within to test. And this tissue was taken from a horse. Would, or could there be questionable results that would indicate anything other than horse?

see above

2. If the tissue had been in contact with zebra tissue or donkey or burro tissue, could that contamination be identified exclusive of knowing of it beforehand?

I would think that blasting the individual sequences would identify the contaminating species, as the majority of sequence would come back horse with a sprinkling of zebra (depending on level of contamination). No prior knowledge would be required.

3. I understand the horse, zebra and donkey/burro are known species and have documented genomes. would the identifying of the actual tissue and the components of the contaminates be just a matter of plugging in the algorithms or running it through the BLAST protocol or program?

The type of the tissue could not be determined by genomic sequencing but the species certainly. And the contaminants should be likewise identifiable. If you had some totally new contaminant, with no reference in the data base, it should still have some homology to something related. When you have millions of reads (sequences), you would process the data using a similar protocol.

I have never personally processed this sort of sequencing data, so this may not be possible with the shear volume generated. But theoretically, it should be possible.

[Guest]

Well, some critics (mostly) want answers about Ketchum's reasoning's. So without further ado....the following is a good read.

Bigfoot DNA Study Update - Dr. Ketchum Responds to Critics

1. Where are the passing peer reviews and why are they not available for the public?

They never are with published scientific journals. You can be sued for revealing them.

Comments: Some critics are ignorant and do not know that peer reviews are confidential while others critics in the scientific community do know! These critics are using the public's ignorance on the peer review process unethically and unfairly to tarnish Dr. Ketchum and the DNA Study.

Article

[Guest crabshack]

From the article above and I think he hit the nail on the head.

"What is this truth? A unknown, Veterinarian WOMAN from the SOUTH no less with the help of common everyday people have made one of the greatest scientific discoveries of our generation. This is a fact, a truth their belief system just can not tolerate. The religion of Darwinism demands this can not be true and not be allowed to stand."

Edited February 22, 2013 by crabshack

[Guest Tyler H]

Trust me Tyler, I have no illusions that it's simple lol. The other two samples were blood taken from a downspout which could be taken without human contamination and the food plate was also dealt with forensic methods to eliminate contamination. I never said there was no chance during the illumina setting, but if the contamination is at the illumina and all testers had their DNA on file, it's easy to remove those from contention.

All i'm saying is that it's too convenient to just write it off to contamination until they dig deeper on the full raw data. I haven't jumped in support of or against anyone with this ordeal.

I'm glad pics will be included this time. The only pictures of Justin's sample I've seen were the ones circulating here with it in his hand, until I saw the one in Melba's report. I have the utmost respect for you and Bart, so this hasn't been an attack on your work at all. I think those that have paid attention to me in my short time since officially joining the forum will see that I will question anyone and everyone in search of the truth. If things raise questions, I won't hesitate to question it.

Nope, no worries, not taking it as an attack at all - I rarely do, unless it is obvious.

But what I meant is that there is no such thing as employing methods at the site of the evidence that will "eliminate" contamination. Minimize? Sure. But even a forensic scientist has to breathe on the site. And they could lose an eyelash, or a skin cell could fall off their cheek, or what have you. I hear of boring into dinosaur bones and having the sample turn up human DNA. And this is done by highly specialized scientists who take every precaution to remove human contamination. But when you get a couple of contaminant skin cells in a sample, and then test it in an illumina system, those skin cells WILL likely show up. It seems that contamination can actually be dealt with a bit more easily in the traditional PCR testing methods, since they aren't quite as sensitive.

I remain a loyal bleever.

My son & I saw the bigfoot at the tree where we found the sample that I sent her, so I have no problem believing that her findings were factual. Hopefully, she will eventually get the recognition & credit that she deserves for a job well done.

You can say "for a job ... done" perhaps.. but it most CERTAINLY is not "WELL done." When science is "well-done" it is not as indecipherable as this report is.

I will remind everyone again though, that I can only speak with confidence about the results of Justin Smeja's sample. She got that wrong. (that's a period at the end of that sentence.)

But with as many trustworthy submitters as her study had, I think it is entirely likely that there is some Squatch DNA in there somewhere. It's just a shame that it took millions of dollars, and that it had to be through someone with such a shady past and who wanted so much control and riches out of this. If this had been handled by someone with better credentials this would have all been over much sooner, and with more clear-cut results.

Edited February 22, 2013 by Tyler H

[Guest]

Nope, not taking it as an attack at all - I rarely do.

But what I meant is that there is no such thing as employing methods at the site of the evidence that will "eliminate" contamination. Minimize? Sure. But even a forensic scientist has to breathe on the site. And they could lose an eyelash, or a skin cell could fall off their cheek, or what have you. I hear of boring into dinosaur bones and having the sample turn up human DNA. And this is done by highly specialized scientists who take every precaution to remove human contamination. But when you get a couple of contaminant skin cells in a sample, and then test it in an illumina system, those skin cells WILL likely show up. It seems that contamination can actually be dealt with a bit more easily in the traditional PCR testing methods, since they aren't quite as sensitive.

I agree that these systems can be more sensitive than desired. I would actually like to see some "old school" cloning of BF DNA to confirm the findings. 100kbp of non-pcr based sequencing data would be a nice addition to the mega bp from the illumina. If it all holds consistent - great!

[Guest Tyler H]

This article : http://bf-field-journal.blogspot.ca/2013/02/bigfoot-is-real-dr-ketchum-has-3.html

is full of mistakes.

Perhaps the most glaring is this: "4. The SAME results were returned on 3 different samples from 3 different individuals, collected from 3 different locations, and at 3 different times."

That is patently false.

They were NOT the SAME results. The study points to three genomes that are NOT closely related to each other. How do you explain that?

Edited February 22, 2013 by Tyler H

[Guest Tyler H]

What we have with the MK contigs is a mixture of human and unknown (really does not match to anything obvious). Given that they supposedly used the human chromosome 11 as a reference in assembly, I don't know how they could come up with this. Again, based on the below quote form the paper by Ketchum et al, on part states a use of a reference for assembly, one does not.

"Utilizing a human chromosome 11 reference sequence, preliminary Sasquatch concatenated sequences of 656,048, 541,435 and 74,589 base pairs, were derived from the full genomic sequence from samples 26, 140 and 31 respectively."

Given that these three samples were hopefully from the same species (ie BF) I don't know why their contigs ended up being such different sizes. If they had 30x coverage, they should all have complete genomes, and should all be, within a few bp, the same size. There must be some attempt at assembly though as samples 26 and 140 show some degree of homology (30 -38%) but much lower than two of the same species should be (human and gorilla are 98% homologous).

Yes, the degree of homology is very low. Likely similar to the degree of homology our DNA has with corn... I'm quite sure we share more DNA with bananas and slugs. (Admittedly citing these from "urban myth" type memories from back in highschool biology courses, and I may be mis-applying that understanding). It seems there is almost no way the animals that were sequenced in this study can be primate. And even I can get that. I don't see how the people involved in the study set this point aside, and proclaimed this genome represents a close human relative.

Thanks for some great posts RR. I have some info from another scientist that I will be posting soon - just clarifying a couple points with him.

In the meantime - I'm curious. What basis would they have for using the human chromosome 11 as their reference to build their contigs, and how might this affect the results if the source tissue was say, bear, but the contigs were assembled with a human reference?

[Guest]

Yes, the degree of homology is very low. Likely similar to the degree of homology our DNA has with corn... I'm quite sure we share more DNA with bananas and slugs.

Could bacteria cause the results?

Edited February 22, 2013 by Scales

[Guest TwilightZone]

I am just happy that Sykes will be looking at the DNA data.  It is hard to believe any chicken salad will come from this... um, mess... but if there is anything to salvage I am sure somebody with those credentials can wring it out.

Should he pronounce the findings as baseless, I am wondering what that bodes for his own study. I get the impression that many honest people sent in what they really believed was physical evidence from Sasquatch, the best of the best, so is there any reason to think the evidence sent to him will be better?

[Guest]

From this article: http://bf-field-jour...tchum.html#more

We do not release reviewers' identities to authors or to other reviewers, except when reviewers specifically ask to be identified. Unless they feel strongly, however, we prefer that reviewers should remain anonymous throughout the review process and beyond.

This may be true, I don't know, if it is true - then why the need to buy the journal she now has her paper published in? Melba said she had to buy the journal so she could keep the peer reviews she already had. Well, according to the above quote - she can't ever release those peer reviews - less she be hauled into court and have the snot sued out of her. So, I don't understand why she needed to buy that journal so bad.

crabshack quoted:

"What is this truth? A unknown, Veterinarian WOMAN from the SOUTH no less with the help of common everyday people have made one of the greatest scientific discoveries of our generation. This is a fact, a truth their belief system just can not tolerate. The religion of Darwinism demands this can not be true and not be allowed to stand."

I really wish Melba and those close to her would stop saying things like this, especially since her paper is now being reviewed by "big name scientists" (per Melba)... I agree there is still a certain amount of "sexism" out there in the world - but I haven't seen an article yet saying she needs to get back in the kitchen and bake up some biscuits... Near as I can tell the criticism has been about the information contained within a paper she published - and not about Melba being a woman - or from the south. These allegations lose their sting, if said too often, and no substantial proof of it can be found. I would also hate to see a scientist looking to help Melba, turn away from helping her, for fear he may be labeled the same way if he does not see the "beauty" of her science. Just an observation.

Tyler said:

But what I meant is that there is no such thing as employing methods at the site of the evidence that will "eliminate" contamination. Minimize? Sure. But even a forensic scientist has to breathe on the site. And they could lose an eyelash, or a skin cell could fall off their cheek, or what have you. I hear of boring into dinosaur bones and having the sample turn up human DNA. And this is done by highly specialized scientists who take every precaution to remove human contamination.

This brings up something I have been wondering about for a long time. Some of these "samples" have been around a while... Sitting in someones home. How could they NOT be contaminated? Does Melba's paper say anything about when the samples were collected? How or does she address collection methods, preservation techniques and chain of evidence employed by each of the sample providers in her paper?