The Ketchum Report (Continued)

[Guest]

@TM

Summarizing the paper, MK had more than 168 samples (perhaps 200, I don't know), of which she identified 111 that did not have obvious hair morphology of a known species (or were some other type of sample). She tested these 111 samples for cytochrome b, ALL 111 of 111 tested positive as human with no contamination or mixed bases.

From the paper:

"Since the amount of hair available in the samples was finite, we opted to begin this project by screening tissue samples that had larger quantities of DNA. Universal mitochondrial DNA cytochrome b primers for species determination as well as universal mammalian primers designed for species identification in the hypervariable region 1 were utilized. All 111 screened samples revealed 100% human cytochrome b and hypervariable region 1 sequences with no heteroplasmic bases that would indicate contamination or a mixture. "

Three samples, having more abundant amounts of DNA were subjected to the nuDNA Illumina sequencing - generating the three nuDNA genomes (well chromosome 11 contigs).

My reading of the paper, every one of these samples were assigned as BF - the 111 mtDNA sequences that were found to be human - but MK states not due to contamination, and for the hair samples, they were not consistent with them being human.

For the three samples that were subjected to Illumina sequencing, human and other sequences were found, which MK claims is due to a novel species, BF. From many statements, it has been stated that she had three BF genomes, so I would say that 3 of 3 nuDNA genomes scored positive for BF. I know of no negative samples from the Illumina part of the study. My analysis of the presented sequences show limited homology to each other, further suggesting they do not represent a single species. The fact that they are so divergent and of both inconsistent sizes (to each of the three samples or to the human CH11) strongly suggests that these sequences were incorrectly assembled.

[Guest thermalman]

If her terminology of hybridization was misquoted or in error, then the hypothesis is not incompatible. Some are not as eloquently gifted in verse as others.

[Guest njjohn]

TM - it's not verse when you say X mated with Y to create Z. That's completely different than saying Z is a combination of X and Y. Breeding was specifically mentioned in the paper, which is incompatible with it just being a weird combo of genes.

[Guest Silent Sam]

In regards to the misquoting of the hybridization claim, as well as the 111 samples testing modern human the following quotes are lifted directly from the Conclusion section of Ketchum's paper.

In summary, we have extracted, analyzed and sequenced DNA from over one hundred separate samples... DNA analysis showed two distinctly different types of results; the mitochondrial DNA was unambiguously human, while the nuclear DNA was shown to harbor novel structure and sequence.

The data further suggests that they are human hybrids originating from human females. This hybridization can be likened to humans with Denisovan admixture resulting from Denisovan males mating with human females103. The same type of mating potentially occurred with Sasquatch; however, in the case of Sasquatch, the admixture is human.

[Guest]

I don't understand the point of confusion here. She has ALWAYS maintained that they were a hybrid species (mDNA = human and nDNA = something else), and she brought up the "closer to lemur" factor during one of her interviews when discussing the nDNA.

[Guest thermalman]

In regards to the misquoting of the hybridization claim, as well as the 111 samples testing modern human the following quotes are lifted directly from the Conclusion section of Ketchum's paper.

In summary, we have extracted, analyzed and sequenced DNA from over one hundred separate samples... DNA analysis showed two distinctly different types of results; the mitochondrial DNA was unambiguously human, while the nuclear DNA was shown to harbor novel structure and sequence.

The data further suggests that they are human hybrids originating from human females. This hybridization can be likened to humans with Denisovan admixture resulting from Denisovan males mating with human females103. The same type of mating potentially occurred with Sasquatch; however, in the case of Sasquatch, the admixture is human.

Nice. And thank you.

TM - it's not verse when you say X mated with Y to create Z. That's completely different than saying Z is a combination of X and Y. Breeding was specifically mentioned in the paper, which is incompatible with it just being a weird combo of genes.

Explain the platypus genomes to me then John. Quotes are from my link in post # 2169.

"Our cross-species painting studies of the monotreme sex chromosome complements shows that the platypus and echidna translocation chains share homology over four of the five X chromosomes, but one in each species is entirely non-homologous. This means that the chains continued to evolve after the divergence of platypus and echidna.

Our comparative mapping studies show chicken Z homologous genes in the sex chromosome system with the main clusters on platypus X3 and X5 and echidna X3 and X4. Other Z homologous genes map to autosomes, indicating many rearrangements between the monotreme and avian lineages.

In combination with the mapping data available in current Ensembl release 44, our results also reveal homology of platypus X1 to chicken 3, 13, Z, 11, and 12, which are homologous to human autosomes. This suggests that the monotreme's XY chromosome system is unrelated to the therian XY system. This is further explored by F Veyrunes (personal communication) in comparative studies with therian X-linked genes, and it may mean that the therian XY system evolved after the prototherian and therian divergence, but before the divergence of marsupials, and is, therefore, younger than previously anticipated [31].

It is important to note that three monotreme X chromosomes have large differential regions. The differential region on platypus X5 (echidna X4) is homologous to chicken Z, that of X3 is homologous to chicken 2 and Z, and the large differential region on X1 seems mostly homologous to chicken 3 and 12. These differential regions are completely different from those of the therian X and Y chromosomes, indicating again that the monotreme and therian sex chromosome systems have different origins. We believe that the comparative mapping results reported here will be useful in the continuing search for the monotreme sex determining switch, and in future studies on sex chromosome evolution and dosage compensation mechanisms.

It will be instructive to extend the genome comparison between birds and monotremes to other amniotes, such as snakes and lizards. These comparisons will enable the construction of the ancestral karyotype of sauropsids and mammals and reveal the chromosome evolutionary events that occurred at the origin of the sauropsid and mammalian lineages."

"Monotreme sex chromosomes are easiest to explain on the hypothesis that autosomes were added sequentially to the translocation chain, with the final additions after platypus and echidna divergence. Genome sequencing and contig anchoring show no homology yet between platypus and therian Xs; thus, monotremes have a unique XY sex chromosome system that shares some homology with the avian Z."

Edited April 1, 2013 by thermalman

[Guest njjohn]

I'm not a geneticist, so I can't explain the platypus to you. It is a unique creature. That's not at question here. Are you trying to say BF is a human/something combination? That would be an interesting find. But what does that have to do with what Ketchum's proposing? She's claimed multiple times that humans mated with the original creature which is completely opposite of what you're saying.

The human mtDNA traces back to a maximum of 15k years ago. To have the type of hybridization required to produce a platypus type combination would take in the millions of years I'm presuming. Again, it's an interesting idea, but more things that would further prove problematic for her paper.

[Guest thermalman]

I'm trying to point out a possible correlation between my link and MK' s proposed hypothesis, and your non geneticist x,y and z assumption. I'll let the knowledgable people answer the idea put forth.

Edited April 1, 2013 by thermalman

[Guest njjohn]

But what link? They're two completely different hypotheses. Humans only showed up a short time ago in comparison to what you're suggesting.

[southernyahoo]

How many sample were submitted for testing? How many were rejected before DNA testing? How many samples were tested for DNA? How high do the numbers assigned to samples go? Where did the 111 out of 111 number come from?

The highest sample number was 168 listed in table 1, so it was at least this many samples. The 111 comes straight from the paper...

"All 111 screened samples revealed 100% human cytochrome b and hypervariable region 1 sequences with no heteroplasmic bases that would indicate contamination or a mixture. "

RR , could Dr. Ketchum have meant "all genetically screened" samples? I've also read that any sample which had bacteria present was removed from the study. Using the tables given, which samples are suggested to have yielded DNA? Are any omitted?

[Guest thermalman]

But what link? They're two completely different hypotheses. Humans only showed up a short time ago in comparison to what you're suggesting.

Gonna wait for a proper analysis from a geneticist, if no one minds? Thanks for your journalistic views though.

[southernyahoo]

No, that would make her entire hypothesis false. That's not poor wording, that's just not understanding what you're looking at. All life shares some genes... that's not even a debate. But her hypothesis is that this male donor chose to mate with humans about 15k years ago, and the resulting offspring are what our current Bigfoot are. Not that it's some weird hybrid of two species.

If she would have stuck to just proving their real instead of trying to prove her theory of hybridization, then I would 100% agree with you that it's a possibility to look at. But because she linked the two together, and still keeps pushing the hybridization (that's what she was using A. John Marsh's statements for) it invalidates the possibility of a platypus type being, at least in her view. Her paper and the hypothesis you propose are incompatible.

niJohn, I really don't get why people don't understand that if you are going to prove something exists using DNA, it's relatedness to knowns will be self-evident and thus indicative of "what" it is. Proof and what it is, are inseperable.

The logic flow is...........

1. Samples are not 100% human by morphology

2. Samples are 100% human in the mitochondria.

3. Samples produce novel nuDNA in various loci and do not give a consistent read on the male lineage.

Novel morphology + human maternal line + novel male lineage = new hybrid hominin found by bigfooters.

[Guest njjohn]

Except the novel male lineage was only novel when compared to chromosome 11.

Also to the mitochondrial DNA, without the haplotypes of each and every submitter and tester, you can not rule out contamination. You can claim it's not, but word doesn't get you far in science. Remember, she's claiming 111 samples are BF, and "most" shared the non-human morphology on the hair, but only showed one photo. The results could come up 100% human and be the submitter's DNA. Why not show the results that eliminate that possibility? Just a table isn't sufficient for this forum, let alone science.

Go back and look at the Trent and OK lab reports. Ignore the results, but those are what lab reports look like. There should be one for every single sample, and then three more for nuDNA reports. What I don't understand is that if you are trying to prove something, the evidence is inseparable from the claim of proof. That would be the logical expectation right?

Could there be something in her data? Yes. Was her paper and data sufficient to prove anything? No. And her constant flip flopping on explanations as well as contradictions just don't sound kosher. Nothing should be accepted without proof and no matter how many times it's repeated over and over that it's proven, just saying it doesn't make it so.

[southernyahoo]

nijohn, I was addressing this only...

If she would have stuck to just proving their real instead of trying to prove her theory of hybridization, then I would 100% agree with you that it's a possibility to look at.

................not whether it was actually accomplished in the paper, I agree that the data "raw sequences" for the male lineage is insufficient along with showing why the mito can't be from a submitter, however 100% human DNA might always have that stigma no matter how many potential people you included to rule out. The message seems to be that this result repeats, regardless what you do to eliminate it in certain samples.

[Guest]

How many sample were submitted for testing? How many were rejected before DNA testing? How many samples were tested for DNA? How high do the numbers assigned to samples go? Where did the 111 out of 111 number come from?

The highest sample number was 168 listed in table 1, so it was at least this many samples. The 111 comes straight from the paper...

"All 111 screened samples revealed 100% human cytochrome b and hypervariable region 1 sequences with no heteroplasmic bases that would indicate contamination or a mixture. "

RR , could Dr. Ketchum have meant "all genetically screened" samples? I've also read that any sample which had bacteria present was removed from the study. Using the tables given, which samples are suggested to have yielded DNA? Are any omitted?

Yes, I have been reading this as genetically screened samples. I believe that samples that had bacteria (visibly - I am guessing they were doing some sort of Gram stain) present would be removed from further analysis. I have not gone through the tables to try and figure out exactly which yielded DNA and if any are omitted. But it is stated that the 111 samples submitted to the cytochrome b analysis all yielded DNA, and all tested as human. If there was data omitted, it was not stated to my knowledge.