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Saturday, August 30, 2014

Hart on Carpenter on Sykes

Read Scott Carpenter's blog on the Sykes paper first:

http://bf-field-journal.blogspot.com/

No, Scott, once again, you got it wrong.  The Ketchum paper is THE ”JOKE,” as proven by CORRECT analysis of HER OWN DATA.  See my papers.  Nothing Sykes wrote even begins to overshadow that “inconvenient truth.”  If you find that my analysis is wrong, then the scientifically responsible thing to do is to refute it publically, not continue to defend the indefensible.  This you have not done, and I believe you cannot do.   PROVE ME WRONG!  I do agree that Sykes should have recognized Ketchum and not have claimed that his was the “first ever systematic genetic survey….”  Maybe he thought her study wasn’t “systematic.”  Regardless of their experimental protocols, the Ketchum team did not correctly interpret their results to identify other (bear, dog) species, where they claimed “unknown sequence.”  They were also TOO QUICK to attribute anomalous results to a new species, when more probable explanations were readily available (See my papers).  Know also that NONE OF THE AUTHORS of the Ketchum paper are experts in what they attempted to do.  They are not any of them geneticists or anthropologists.  They’re a collection of mostly unknown or little known “forensic scientists,” a microscopist, a computer jockey with degrees in mechanical and aeronautical engineering (who did the interpretations with Melba), and a vet.  Not that people cannot extend their expertise to new areas (which is laudable), but at the same time they should not be considered “experts” in new ventures until so judged by peers, who are the proven experts.  I also fall into the category of an unproven nonexpert in genetics/anthropology, but I so stated in the Preface to my first paper.  If Ketchum’s “experts” are so expert, why have they all remained so silent throughout the debate, while their paper is being hacked to pieces?  Until they speak up, my hypothesis will be that they realize that they made mistakes, are embarrassed, and are fearful for their reputations.  OR, they allowed their names to be put on a paper that they hadn’t fully vetted - a real scientific “NO-NO.”  I myself would certainly not want to be accused of a crime in a jurisdiction where potentially testifying “DNA experts” can’t tell the difference between a bear, a human, and a dog.  I wouldn’t want to be falsely convicted of stealing a bone, breaking into a cabin, or digging up somebody’s garden or something.  (PS Have you heard from David Swenson lately?  He’s moved to Peoria, Arizona).  

You have to believe that Sykes would be delighted to have proven the existence of a cryptid primate, rather than just have analyzed a bunch of extant mammals’ DNA.  People with his reputation do not need to publish negative results.  In this case, however, I do believe there is some value in doing so for high profile samples which are the basis of previous remarkable claims of existence of yeti or bigfoot.  AND, to show that a relatively simple technique, requiring minimal sample, can be relevant to future “bigfoot” samples and claims.  AND, to challenge and counter the whining of some bigfooters that “mainstream science ignores us…”  Get some better documented samples, people.   

Numbering of points below corresponds to your numbers. 

1.   The reference [10] is to a technique described in a paper authored by Mitotyping Technologies, not to a collaborator or a laboratory.  This in no way implies that the sequencing in Sykes’ paper was done by Mitotyping Technologies, any more than any reference implies the authors of that reference did the work of the present paper in which it is cited.   I noticed, however, that Dr. Terry Melton, a coauthor with Sykes, is director of the lab at Mitotyping Technologies, and that Charity Holland, a coauthor of the reference [10], is acknowledged for her “technical assistance,” as were Bonnie Higgins, Gloria Dimick and Michele Yon, all of whom are on the staff of Mitotyping Technologies.  So I asked Dr. Melton about this, and she replied, "All the sequencing was done here at my lab, as well as all the DNA extraction and amplification."  So, Scott, your instinct was correct this time. That being said, what would be your point, Scott?  (You might try direct questioning sometime instead of open-ended insinuation and innuendo).  Many academics collaborate with industry to the benefit of both.  I've done it from both sides myself.  Everybody was properly credited and acknowledged here.
     I do agree that the paper should have been clearer that Mitotyping Technologies did the sequencing, not because this is morally required, but because it is useful information for any potential new customers (like me!)

2.   Never in any journal that I have published in or am familiar with do the formal professions of the authors determine eligibility for coauthorship.  They must sign that they did some part of the work however and a CV may be required.  If Mullins did the American legwork collecting and organizing samples, he could be a legitimate coauthor without having done any experiments. 

3.  Adequately referenced techniques do not need extensive repetitious descriptions in M&M sections.  Journals discourage these unnecessary extra words.  Also, it gives a false impression that the technique is original with the present author.

4.  See 3 above.  Scott, did you read the references and determine that they do not adequately describe the M&M for a third party to reproduce the experiments?  If so, please elaborate.  If not, please do so before you make a claim of “incomplete” references.  I did read the references and concluded that they adequately describe the techniques in sufficient detail for a third party to repeat the work.
5.  I agree.  See 1. above.

6.  Yes, a reference to subsequent proof of contamination should have been provided.  Except for my papers, not peer published and unavailable to him at the time, I’m not sure there is anything published.  However, it’s the most likely (not the only possible) cause of Ketchum’s VERY mixed results on many (not all) samples.  All her samples were UNCONTROLLED, “environmental” samples as were Sykes’ for that matter.  He, however, found only a single human sample in 30 and no anomalous data or multiple species in the same sample.  You cannot say for sure that Ketchum’s clean-up was 100% effective, or that a much lesser amount of human mtDNA would have shown up in a gel agarose separation of a mostly nonhuman sample.

7.  The Use of the “mitochondrial 12S rRNA” technique does not require a full sequence, because it’s based on a hypervariable region that distinguishes between species well, while having little intraspecies variation. Also, a full sequence requires more DNA, which may not have been available in all these samples.  Ketchum based 11 of her 29 mtDNA identifications  – (in her Supplemental Data 2 - Samples 33, 41, 42, 43, 71, 81, 95, 117, 118, 140, 168) on Hypervariable Region I (unfortunately, not labeled as such by her), which has only about 600 bases.  Furthermore, her Tables 4 through 7 involve techniques which only look at a few hundred bases as do all the results in her "Supplemental Raw Data" on the SGP website.  Actually, Scott, Sykes' technique only uses 104 bp, not 503 as you claimed (See Sykes' p. 2, para. 1:  positions 1093-1196 on the human mtDNA genome).      

8.  It takes MUCH more sample (about 1000 X more) to do nuDNA testing (such as her Sample 26 hide cut), more than a hair or even several hairs can contain.  This is not an argument against Sykes’ results or conclusions, which stand on their own merit for what they are.  More data is always desirable, but is not always possible and is not necessary to identify species in this case.

9.  The samples are what they are.  Many were claimed to be from yeti or bigfoot, and had to be tested and documented.  Hair examination by microscopy is not nearly as exact a science as DNA sequencing, and should never be taken as the only evidence to support an identification.

10.  The technique has been validated and used successfully in many other cases.(See references [9] and [10] as well as others on the website: http://www.mitotyping.com/page/37 . Ketchum sequenced 2.7 M, 0.53 M, and 2.1 M nuclear bases in Samples 26, 31, and 140, respectively, AND STILL GOT THE WRONG ANSWERS for S26 and S140 (They’re a Bear, and a Dog, respectively. BELIEVE IT, SCOTT).   Experts say over 90% of a genome is "junk DNA," with no known genes or function. 

11.  POPPYCOCK!  Ketchum proved no such thing about the mtDNA content of sasquatch hairs. It is possible to extract “useable” mtDNA from the medulla of SOME hairs (but not all).   In fact, she identified haplotypes of HAIR samples 1, 2, 11, 12, 24, 28, 29, 33, 38, 39, 41, 42, 43, 44, 46, 95, 117, 118, 138, and 168 in her Supplemental Data 2 from their mtDNA and implied these were from sasquatch.  Again, the Sykes samples are what they are, and some are high profile “musts.”  If they don’t meet your standards, GO FIND SOME BETTER ONES.   Oh, and please also find a better principle investigator next time, or your efforts are wasted.  

Revised September 26, 2014.