Saturday, March 23, 2013

Bigfoot DNA or Garden Gnomes?

As I pointed out at the end of my last article, I made a mistake in my notes. Instead of simply deleting my mistake when I realized it, I did a strike-through and left it up so that others would see that I am accountable for my mistakes. I will never claim to be perfect and if I do make a mistake I expect to be called out on them. She has since edited the paper and removed Sarah Bollinger from the co-author list. 

And as I also pointed out, there have been mistakes and contradictions in Dr. Melba Ketchum’s Bigfoot DNA study. I don’t point them out as a personal attack, I point them out because finding the truth is the most important thing in my job as part of this community. When I felt I was being spun after some rather simple and softball questions that I was allowed to ask, I felt the whole truth wasn’t being told.

The following will be a list of some of those mistakes and contradictions only since the paper was released. Dr. Ketchum is more than free to respond and explain to us why these took place. 

The Journal. 
  • It begins with her signing up on Zoobank on Oct. 25, 2012. 
  • The name of her paper and the species name is registered on Zoobank on Nov. 18, 2012. 
  • The Journal of Advanced Multidisciplinary Exploration in Zoology is registered on Zoobank on Jan. 9, 2013. 
  • A Scholastica page for this journal is created on Jan. 11, 2013. 
  • Denova Scientific Journal is registered on on Feb. 4, 2013. 
  • Denova Scientific Journal publishes Novel North American Hominins after she obtains journal and renames it. 

The editor of the journal is unknown. The editor of the paper is Dr. Rayford Wallace. He’s not a medical or scientific doctor though. His doctorate is in Ministry. 

I won’t even get into Casey Mullins and the blogger site that showed up weeks after the paper had been released. The timeline above is troubling. The sudden rush not only seems like a mistake, if was going to raise enough eyebrows to actually look into the rush. 

The Peer Review.

Dr. Ketchum has repeatedly claimed that there was obscene scientific bias against her paper. That was the entire reason for having to purchase the journal.

Darren Naish was actually one of those reviewers that rejected the paper. Around the 72nd minute, they start discussing the paper and Darren makes the reveal. He claims there was no bias and reveals the real reason the paper was denied. He would have been thrilled to spread the news that Bigfoot was real. But he said the paper simply did not prove the claims it was setting forth. 

The Paper. 

As I laid out in my last article, Dr. Ketchum claims there’s no more data, while the paper says otherwise. She supplied 2.7Mbp, 2.1Mbp, and 0.53??Mbp for her 3 genomes. A single genome should be approximately 3Gbp or even 135Mbp for just the chromosome 11 section. That’s a substantial chunk of missing data. 

When I contacted co-authors and contributors I was met with the similar response from all of them that bothered to answer. Here is one of those emails: 
Dear Mr. Weeast, Thank you for your email concerning the sequencing that we provided to Dr. Ketchum and co-workers. This work was performed as a fee for service. We have not been involved in the analysis of the results. Further, we are not at liberty and have no intention of discussing the laboratory results that we obtained with anyone but Dr. Ketchum or her colleagues. I would suggest that you direct your questions to her. Our core has only provided sequencing service for this study and we are not involved beyond that.All the best,Ward WakelandEdward K. Wakeland, Ph.D Edwin L. Cox Distinguished Chair in Immunology and Genetics Director, Walter M. and Helen D. Bader Center for Research on Arthritis and Autoimmune Diseases Director, IIMT Genomics Core Professor and Chairman, Department of Immunology
Notice he says there was no analysis done at their labs. None. Her paper claims otherwise: 
In depth analysis of all three genomic sequences (samples 26, 31 and 140) was performed at the University of Texas, Southwestern and alignment confirmed by the University of North Texas Health Science Center. Using CLC Bio Genomic Workbench version 5.1, a subsample of extracted reads were assembled to create a consensus sequence using the human chromosome 11 ….
So if they didn’t do the analysis, who did? 

And finally on Friday, Mar. 22, 2013, Dr. Ketchum posted the following on facebook:

The following was a unsolicited commentary by A. John Marsh on a genealogy DNA page which scientists use to discuss mtDNA origin. This is not the complete discussion . However, it sums up the analysis.
Along with the fact that all Bigfoots seem to have several different mtDNA mutations from each other, they also are found in 5 different states. It suggests that if a single T2b human female mated with a Bigfoot male 13,000 years ago, that the descendants of the T2b ancestor have spread widely in USA since then.
Web site
If T2b is 12-10kya, and T1/ T2 coalesced about 19kya, T2b might very roughly originate about 10,000 to 15,000 years ago.
One thing I noted was that all the 52 number diverse T2b haplogroup listed humans in the T2 project had a mutation 146T, but none of the Bigfoot had that mutation. It seems in fact that all T haplogroup have 146T. I am guessing that the earliest common ancestor of all Bigfoots had a back mutation on that marker to the CRS value.
Another thing I noticed was that all Bigfoots which appear to have been tested on the lower number markers, have mutation 73G. Yet not one of the
52 human mtDNA T2b persons had the mutation 73G. Why not? Was 73G a very early mutation in the Bigfoot line?
All the fully tested 4 Bigfoots had the 263G mutation, but not one single one of the 52 humans had 263G. Why not?
It seems all human T2bs have have 16187C and 16189T, but no bigfoots have either. In fact, all human haplgroup T are postive for both these mutations, so presumably in the common ancestor of all Bigfoots there was a mutation reverting to CRS.
According to the Ketchum knockers, all the mtDNA Haplotypes in her project are modern contamination. All of these Bigfoot haplotypes are different.
Isn't it a bit puzzling that all of these humans mistaken as Bigfoot have different T2 mtDNA haplotypes, all have 73G and 263G mutations not found in humans, and all seem to have had back mutations on 146T, 16187C and 16189T, where these back mutations are apparently not found in any human T2b s?

That sounds interesting. Dr. Ketchum was very excited. An hour earlier she posted:
"We just received permission to post. There will most likely be a new paper come from this so we will not post the new findings but you will see enough of the proof to validate the paper. I am SO excited!!!!!"
I apologize for tempering your excitement, but the thread is from, not a genealogy DNA page. And A. John Marsh isn’t a scientist. He is an architect. A landscape architect to be precise, so according to Dr. Ketchum’s analysis of doctors, would that make him a lawn-chair scientist? But he built the excitement to write another paper... Did she see what he said about Q30 scores? 
Does the Q30 quality scores of above 88 mean 30 times average coverage, and 88 percent of the genome reconstructed? Just my guess, I don't know what it means. But on the face of it, does the scores obtained hint at a reliable coverage? 

The Foundations.

All of her foundations have one thing in common. They are businesses. All of the payment methods point to her paypal address at DNA Diagnostics. Claiming to run a non-profit while actually operating as a for-profit business is a serious matter. Even the newest foundation the Melba Ketchum Global Sasquatch Foundation announces itself as a non-profit, but is only registered in Texas as a business. It is not listed as a non-profit, nor is it listed in the pending applications for non-profit license. 
You can do the texas look up here: and enter Global Sasquatch Foundation as the name 
You can search the IRS non-profit list here: and enter the same name with Garland, Texas as City and State. You can search both existing and those that have applied from that page. 

This entire project may have started with a noble goal, but it’s obviously steered in an unknown direction. Perhaps the missing data also holds a key to the direction it’s going. 

As before, I call on Dr. Ketchum to answer the questions. There are plenty of qualified scientists that can validate your data if it really says what you claim it does. What you released doesn't. I'm sure Mr. Marsh is a great guy and it looks like he's done a decent job with his family's history, but for Sasquatch it's going to take someone a little more experienced. 

Tuesday, March 19, 2013

Based on a True Lab Report

The great tragedy of science - the slaying of a beautiful hypothesis by an ugly fact - Thomas Huxley 

The hypothesis of Dr. Melba Ketchum dared to answer one of the great questions of our age -- if there is a missing link, another hominid, a distant relative of humans and where this fits in within the evolutionary tree, all in one fell swoop. 

Instead focusing on the task of proving if they were real or not, she skipped ahead and declared  they are an extant species that arrived after the hybridization of modern females and an unknown novel hominin approximately 13,000 - 15,000 years ago. 

Many scientists have stepped forward to question the results presented in this paper, and while a few have raised questions about the number of haplotypes found in the near 100% homology to human mitochondrial DNA sequences, the real issue has been the nuclear DNA. 
Nuclear DNA holds the information inherited by both parents, unlike the mitochondrial DNA which only holds information inherited by the mother.  

Ridgerunner is a member of the BFF and a Molecular Biologist with 30 years experience in functional genetics. He is not what I could call an "armchair scientist." He had he following to say:

During fertilization, the genomes from the two parents recombine, having cross-over events along the chromosomes at regions of homology, creating a novel hybrid chromosome. Given that mammals have similar size genomes, and primates even more so, the resulting hybrid chromosome should be of similar size to human if that is the maternal side. So the whole genome should be 3Gbp and the chromosome 11 135Mbp, give or take say 10%.  The size of the contigs (Dr. Ketchum) has provided (2.7Mbp, 2.1Mbp, and 0.53??Mbp) ,while appearing to expand the whole of human Ch11, are simply way, way too short if they are meant to represent the whole chromosome.”

Many of the critical reviews of the paper that I have read, have said that we must wait for Dr. Ketchum to release more data. "Only 1% of the data is there." But they’re wrong. The contigs are homologous to human chromosome 11, but it’s still only 2% of what should be there. (solely based on total DNA content the contig size of 2.7Mbp and the Hu Ch11 size of 135Mbp). 

In conversations with Troy Hudson, a spokesperson for Dr. Ketchum who has been very patient and tried to explain things to the best of his abilities, reiterated that fact multiple times. 

All the answers to the questions people have are in the paper and data"
“The scientists and journal peer review passed it and understood it, why can't everyone else understand, but again that is why some of her scientist that worked on writing the paper said, not everyone will understand the results, because they do not work in genetics and DNA on a daily basis.”
Melba said everything is in the paper, except the physical samples.”
“No no, she told me and I told you everything is in the paper.”
The paper contradicts Troy and Dr. Ketchum's claims though. 

"The DNA from these three samples was sequenced using the next generation Illumina platform at the University of Texas, Southwestern in Dallas, TX, a laboratory that sequences human genomes75-77On average, there were 70-110 million total reads for each sample in each lane, which is well over 90 Gb of raw sequence for each sample comprising greater than 30X coverage"Next Generation Whole Genome Sequencing section of the "Novel North American Hominins." 

The illumina sequencing is not chromosome 11 specific, so there should be more data. Could this be the confusion with the 1%  number being thrown around? Melba asserts multiple times that everything is there and it is all that is needed to prove her hypothesis. Does she think the other data won't help that proof? Or did she only request the chromosome 11 specific data? 

So if what was thought to be 1% turned out to be 100%, what does that say about the data? Did they tell me that so that others would only focus on what's there, instead of what could be missing. That would be misleading, so I'll trust that it's all of the data, but based on what's there...

"The three samples can not be the same species, and are too far removed from any biological sample to fit in with any theory of evolution and are simply not human, period!" - Ridge Runner
Contamination has been brought up by both sides of the argument, especially when related to the Q30 scores. Dr. Ketchum's paper said this:

"Q30 can also be used to determine if there was any contamination (or mixture) found in the samples sequenced.  According to Illumina, a pure, single source sample would have an Q30 score of 80 or greater with an average of 85. However, if there was contamination present in the sample sequenced, the divergent sequences would compete against one another prior to sequencing causing a contaminated sample to have a Q30 score of 40 to 50."Next Generation Whole Genome Sequencing section of the "Novel North American Hominins."
She used this reference here, which doesn't once mention contamination. The technical notes are a complete and finished project, like the paper in question is supposed to be. Q30 scores show how consistent the readings are, not how contaminated.

I attempted to contact co-authors and contributors listed in the paper and either didn't get a reply or was told they only did sequencing and did zero analysis on the paper. Some had never read it or offered no comment on it if they did. 

For the record, I am not attacking Dr. Ketchum. I adhere strictly to the “attack the argument, not the arguer” mantra. I am a reporter and have a need to find the truth. If something doesn’t sit right with me, I will obsessively dig into it until I find the answers. It’s an admitted flaw, but one that helps in what I do. 

When I initially inquired about the questions with the data, I was contacted by Troy and after explaining my position, was invited to submit a few questions that would be forwarded to Dr. Ketchum. The answers stalled mainly because of the confusion related to the “1% data” that was finally explained above. There was a constant repeat of the reluctance to deal with anyone in the Bigfoot community. 

As a writer that didn’t sit right. As a reporter, I took it as a challenge. It made me want to dig deeper. And I have much more information than is listed here, but sources do not wish to come forward at this time. I have my own ethical standards to uphold as a journalist. 

To Dr. Melba Ketchum and anyone else involved, I welcome a response. The truth will always be accepted here. If anything I wrote is incorrect, please correct me. I will evaluate your comments and if warranted post an update immediately and apologize publicly.

I have no position on whether Bigfoot is ape or human, or if it's real or not real. I'm not trying to prove anything. I only care that what is put out as fact is accurate and truthful. If there's more data, release it and I'll make sure it gets into qualified hands that will give an unbiased analysis. 

**Edited out this section until I can find my initial copy of paper that shows the changes. I can't print something as fact without the proof to back it up. Until I find it,  I apologize for my mistake. **

(Note - this timetable has been edited out of the latest online version of Dr. Ketchum’s paper - “Novel North American Hominins.”)

Publication of a scientific research paper is supposed to be the final stage of that research project. What are the ethical implications of editing the paper without a change log? Does this fall on the journal or the author? Both?