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?


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