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Monday, September 1, 2014

Dr. David Swenson, Where Are You Now?

Do you remember that shortly after the Ketchum paper was released, a professor of biochemistry at Saginaw Valley State University (MI), Dr. David Swenson, came out in support of the Ketchum study and went so far as to be interviewed on radio shows in her support?  Here’s what he said on Melba Ketchum’s FB page, repeated on Scott Carpenter’s blog page (link on right):

“Brien Foerster, Jeff Kart, and other interested parties. I went over the manuscript by Melba Ketchum on Bigfoot genomics. My desktop had difficulty with a blast analysis of the consensus sequences. It helped me understand more about the project. This collaborative venture has done a huge project that taxes me to fully grasp. I see interesting homology with a standard human sequence with 99% match for mitochondria. From my abbreviated study, the nuclear genome seems to have human and nonhuman sequences.

“My opinion of the creature is that it is a hybrid of a human mother and an unknown hominid male, Just as reported. For all practical purposes, it should be treated as human and protected under law.

“Brien, selection of Melba's lab for your studies is a very good call.

“Sasquatch is real, as proven by genetic analysis.”

You’ll also notice another quotation from an unknown “Hascall” Hart on Scott’s page, lifted from Melba Ketchum’s FB page:

"1. The mtDNA of 29 samples is essentially human.

2.  The nDNA of three samples (26, 31, and 140) has homology to human nDNA on chromosome 11, but is not entirely human. 

3.  The nDNA of three samples (26, 31, and 14"0) is not related to black bear, raccoon or opossum."
OK, I confess, “Hascall” is Haskell is me.  The spelling mistake was made by Robin “Forestpeople” Pfeiffer, Melba Ketchum’s blissfully overeager publicist.
Now let’s review the events of the past year and a half. While still believing in Melba’s conclusions, I contacted Dr. Swenson and told him that the “difficulty” with his desktop was not with the desktop at all but was probably due to a too short word size for searches of long sequences, like Ketchum S26, S31, and S140.  I suggested changing it from the default 28 to 64 bits on the BLAST™ input page.  I never heard back from him, and soon thereafter his FB page went down and the radio appearances stopped.

To be perfectly honest, I encountered the very same “difficulty” when I first began my investigation of the Ketchum DNA sequences.  The online help quickly pointed out the fix that I mentioned above, and I moved on.  Where did Dr. Swenson move to?  To Peoria, Arizona, where he hopefully enjoys his retirement.

Using the BLAST™ software (see link on right “BLAST™”) can be tricky, and it took some time before I understood it well enough to be confident of my results and what they represented.  For example my initial conclusions, above are mostly wrong.  Absolutely wrong, with no chance to cover up, crawfish, or crabwalk.  Here’s where I went wrong (numbering as above):

1.  Of  the 29 mtDNA samples (plus one control) listed in Ketchum et al. Supplementary Data 2, actually only 18 were completely sequenced; the other 11 samples were analyzed for Hypervariable Region I (about 600 bases) only.  The Ketchum paper never mentions this, and, in fact, this table is poorly constructed and not adequately explained in caption, footnotes or text.  In my second paper (see links on right) I point out that eight of the 18 fully sequenced samples have TOO MANY EXTRA MUTATIONS.  I pointed this out to Melba initially, but did not yet know the statistical significance.  Matching them to the closest haplotype (see “Family Tree DNA” link on the right), leaves up to 17 unaccounted for mutations. Probabilities of these eight samples being from the normal human population ranged from 1 in 128 to 1 in 1,606,186,760.   These are outliers that were never recognized as such by Ketchum et al.  They are improbably human (but not impossibly – which is not in the statistics vocabulary).  See my second paper.

2.  This statement is subjective and not precise.  All mammals have some homology to humans.  Both Dr. Swenson and I were surprised by how much.  The critical question is just precisely how much, 75%, 85%, 95%, or 99%?  It makes a big difference, when attempting to match an unknown sequence to a known species.  Only after experience with many searches did I realize that S26, S31, and S140 were not from the same animal, and that, in fact they were from a bear, a human (completely), and a dog, respectively.  See my first paper.

3.  This statement is 1/3 wrong for S26 only, which is a bear.  No raccoon or opossum DNA was found in any of the samples, however.  “SciGuy,” Eric Berger, the science writer for the Houston Chronicle, said it’s “a mix of opossum and other species,” based on his consultant’s searches.  NO WAY, NO HOW.  The consultant made the same “rookie errors” that Melba did.   See my first paper.  I’d like to see his BLAST™ results.  The many conflicting analyses of the Ketchum nuDNA sequences convinced me that “something had to be done” about this scientifically untenable situation.  Hence, I wrote my first paper on the subject.  And people are being convicted or let free on the testimonies of “experts” like this who can’t tell the difference between an opossum, a bear, a human, and a dog? attributes the following quotation to David Swenson, via the Ketchum FB page, so maybe there is some hope for him, too.

“I did more blast analyses and came up with the same confusion the independent labs had. The genome has some good human matches and some unknowns.

“The sequences are not contaminated, near as I can tell. I have not searched for open reading frames, but that is beyond the scope of my tools. The close matches are gapped with sequences that match nothing. AMEL and MY genes match humans in some cases, in others, not. If I am wrong, I would like to be shown with data, not uninformed opinion from ‘experts.’”

David, I concur, generally, with your findings on AMEL and MY genes (MY showed all human, AMEL was mixed); see my third paper and “data.”  I disagree that you have any basis for saying that the sequences are not contaminated.  Don’t you mean “the samples?”  Sequences are what they are.  Samples that show different species for different genes are surely “contaminated,” e.g. Sample 26.  The only question is what minor component is contaminating what major component?

Details of my findings are found in my first and second papers (links on right), and are too lengthy to repeat here.  Both Melba and I are amused by the number of different species which people find (and blindly accept) in their BLAST™ output.  The difference is that Melba thinks this is evidence for an unknown new species.  I say the searches were not conducted according to the 12 rules in my first paper.   That’s two more than the Ten Commandments, so searchers, please pay attention.

Melba Ketchum said on her webpage that I am not qualified to review her work because my degrees (chemistry, chemical engineering) are not in the right subject, presumably genetics or anthropology, (hers is in veterinary medicine and her coanalyst Fan Zhang’s are in aeronautical and mechanical engineering), I don’t have the right software (we both used the same BLAST™ program), and because I have changed my mind.  You be the judge.  I think you’re smart enough to see through this.  I’ve never caught one, but “red herrings” come to mind.

In spite of locating some of Melba’s coauthors, sharing my findings with them, and asking for their comments, none have responded in any way.  Coauthors are authors, with all the rights and responsibilities of the principle investigator, which do not include answering my e-mail. However, one would normally expect them to defend their paper SOMEWHERE as Melba has vigorously.  Not one of the nine shared the stage with Melba at her last big “news conference” on ABC in Dallas, although many of them live nearby and only one lives more than a state away.  They’ve all been dead silent.  So we ask…….

……..“wa...Wa…WA… why, Why, WHY?”  Answers to this question may be found in the link on the right under “Badly off Track.”  Thanks go to Sally Ramey for this reference.

The moral of this story is to admit your mistakes and learn from them, not to run from them or attempt to cover them up, especially not in science.  Reputations are easiest to repair sooner rather than later, because people will naturally wonder WHAT TOOK YOU SO LONG TO WAKE UP?  Rewards can be great when you get to the bottom of something and discover the truth, even after, or especially after, having to recant a public statement, as I have.

Try it sometime, Melba et al. You’ll feel much better afterward.  You, too, David Swenson.

Haskell Hart,  August 31, 2014.