Breaking bio on the Ketchum Sasquatch sequences

Interested in what scientists trained in evolutionary biology think of the Melba Ketchum DNA paper?

You’ll want to watch 25 minutes of this Google Hangout of biologists called Breaking Bio.

The guest is David Winter, a PhD in evolutionary biology currently in New Zealand, who looked a bit closer at the sequences provided in the study. Here is what he and the others think.

If you don’t have time to watch it, I’ll summarize (and will notify David that this is online in case he wishes to correct anything I get wrong). Just an observation, David did a fine job of explanation. If you know a little biology, you should be able to follow his descriptions, no problem. David mentioned that he did this analysis as an obvious first step that any geneticist would do in an analysis. It’s basic.

First he noted that the sequences were distributed via a PDF file. Unconventional, to say the least. Also, it’s clear that this whole genome sequencing project was expensive work.

dnaHe says the first thing you do is “BLAST” the sequences [1]. You may have heard Melba Ketchum mention “blasting” in some of her interviews. That means to take sequences and compare them to existing mapped sequences in a huge genetic database. GenBank® is where all DNA sequences should go to be shared with the scientific community. As was noted by Ketchum in the paper (see here: Update), that the results didn’t go there because of “lack of taxon” made little sense to the scientists.

The sequence did not match a hominin sequence but part of it did match very well with human chromosome 11. 60% didn’t match with anything on Earth (So called “Angel DNA“? Sorry, I went there…)  and the rest of it matched with various animals such as panda, dog and bear, etc. These bits that matched may be a sign of a mixed sample.

So, as Winter notes, he’s not sure if the researchers are inept or deliberate in their interpretation but some of the DNA is perfectly matched to humans and the rest is “crap”. Some of the sequences, he said, were far too short to be the result of hybridization, making Ketchums claim of hybridization from 15,000 years ago not plausible. Others have also questioned the hybridization idea.

Contamination remains the obvious question. It’s not that the samples were contaminated necessarily by the collector but that the sample itself was a mix. So, no matter how careful they were in the lab to prevent investigator contamination (as Ketchum insists), the damage was already done if it was junk to begin with.

Conclusion? Bad.

The folks on the show are not kind to the idea of Sasquatch so be forewarned of the snarkiness and many giggles (for the Ketchum apologists). But, you do have to sympathize with them. They have a hard time with this horrendous study. This is their field of study and this work is not of good quality. Therefore, this is further damning evidence that the paper was not shunned by science, it was simply rejected because it was not up to par.

I still suspect that other analyses will come forward to perhaps explain what might have happened with this samples. But, bottom line is, it is NOT being accepted as evidence of Sasquatch.

More:

What do geneticists think of the Bigfoot paper? | SciGuy | a Chron.com blog.

“The [phylogenetic] tree in Fig 16 is inconsistent with known primate phylogeny and generally makes no sense” – Leonid Kruglyak, Princeton U.

“I read as much of it as I could until the sheer weight of the BS became unbearable. Yes, I do have a PhD in genetics and do feel qualified to say that the manuscript is utter nonsense.” – Will in comments

Bigfoot genome paper “conclusively proves” that Sasquatch is real | Ars Technica.

Is Figure 13 (the Bigfoot “steak”) opossum skin? Is this a viral marketing campaign? When will it end?

Any further links to comments by actual geneticists and experts are welcome.

——-

1. The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

  29 comments for “Breaking bio on the Ketchum Sasquatch sequences

  1. Bob
    February 26, 2013 at 8:01 PM

    That was hilarious. Someone should gather a weekly panel to discuss things like that…..oh.

  2. February 26, 2013 at 8:07 PM

    I do believe that, in the field of science, Melba is fast approaching, if not breaking the record for the deepest hole one has dug for their self.

  3. February 26, 2013 at 8:09 PM

    This is an excellent summary. From one who is inside cryptozoology, I register my appreciation for adding this important overview critique to what we all must consider in thinking about these problematic “results.”

    I recall an early conversation with Matt Moneymaker, in which we openly wondered if the early “near human” findings were nothing more than human sampling contamination. No one wanted to hear it.

  4. terry the censor
    February 26, 2013 at 9:07 PM

    Mr. Coleman, good to see you commenting here. Good to see your leadership on this matter. Plenty of people in the various fringe sciences respect facts but they are vastly outnumbered by the partisans and the uncritical fandom. Thank you for not sitting this one out.

  5. Kitty Lapin Agile
    February 26, 2013 at 9:21 PM

    I will say, Ketchum should be glad other scientists are talking about her work. This is how science is. If she or her followers think the scientists here are being especially mean.. well scientists are mean about each others work. Science requires a tough skin. Their work is not at first supported by others until it has been scrutinized, mocked, studied and restudied, and re created. The more scientists look and study, the more science should agree with a result. Instead, the more the Ketchum paper is studied and looked at, the more problems other scientists find with it. I think science is at least paying attention to Ketchum, which she should be grateful for considering the quality of her work. Simple attention to detail and checking references alone would have saved her a lot of the grief she’s getting now. But this is how science works.

    My hope, the other Bigfoot DNA studies out there won’t make the same mistakes. I still may not agree with the results or I may be doubtful. But this paper so far has not been the quality the subject of Bigfoot deserves.

  6. February 26, 2013 at 9:32 PM

    Hi all, and thanks Sharon for linking to our discussion.

    I wanted to take a quick moment to talk about the “snarkiness” in what we were saying. I realise Sharon wasn’t complaining about it, but, in general I think skeptical-types should carefully explain why we don’t give outre ideas the repsect some people think they deserve, rather than just make fun of folks that hold them.

    Everyone on the panel (I’m just a guest by the way) is a scientist, and most of us are young scientists for whom new good publications are the only way we’ll ever get to the next step of academic career. We have probably all dealt with amazing-looking results that faded to nothing when we went hunting for alternative explanations, or have had papers we really liked rejected from journals (this happened to me yesterday!).

    Many of us would like to see some parts of the publishing system change, but, equally, we understand that the standards for reporting evidence that journals and scientists have developed exist so that bogus results are less likely to be published. So, when you see a paper taking all these short cuts, blaming the closed-minded establishment for rejecting the paper rather than failing of their own data, it’s just so far from the world we work in that it’s a little hard to take the whole thing seriously.

    That being said, peer review doesn’t stop when you publish a paper. If Ketchum an colleagues want to make a case that their results are not the result of contamination they are welcome to. One step might be to clone individual DNA molecules – sequencing the results and determining which species that arise from ,

  7. Stuart Robbins
    February 26, 2013 at 10:13 PM

    Ketchum already went back on Coast to Coast to defend herself and kept making references to extra material (as in, mainly referee reports) that she sent to the host (George Knapp) to “prove” that they were being mean to her and not being fair. So one non-academic showing stuff to a news guy. I’d love to see what those referees actually said.

  8. RDW
    February 26, 2013 at 10:26 PM

    Man that must have been one kinky animal orgy !!! I don’t even like having to think about something like that.

  9. drwfishesman
    February 27, 2013 at 7:59 AM

    Peer review definitely has it’s flaws, but it has a self-correcting mechanism in place that eventually sorts out the good from the bad research. The derision and “snark” heaped on this terrible paper is justified. Most people with some science background see it instantly, the general public seems overall unimpressed by it, and even many who would love for the paper to be true are rightly skeptical of it’s findings and methods.

  10. Graham
    February 27, 2013 at 8:24 AM

    I’m not a scientist, but surely common sense would have told Melba that she should have obtained DNA samples from the people supplying the so-called Bigfoot DNA samples to guard against possible from that source.

    My own common sense view also leads me to believe that she would have got a better result if she had insisted that people supplying samples:

    1. Photograph the sample in situ.
    2. Wear gloves when collecting.
    3. Put the sample into a clean (Sterile?) container that has not been used for anything else.
    4. Write the time/location of the sample on the container.
    5. Store in a cool location until given to the lab.
    6. As noted above supply a copy of their own DNA to guard against contamination.

    What I think she analysed were worse case samples collected using the following procedure.

    1. Pick up sample with bare hands.
    2. Put in lunchbox.

    • Randy
      May 27, 2014 at 12:50 PM

      Ketchum has said that many of the samples had a chain of custody that was completely intact. (Don’t know if true, obviously). And regarding human contamination of samples creating results that inferred hybrid species. Ketchum describes in detail how a contaminated sample would appear to have overlapping characteristics–as if the samples were one on top of the other. She said that her results were not that at all–they were singular samples with clear (well, sort of) results. Something that was partially human (but less so than an ape) and part something else. Also, she has said that some of the samples came from traps where they supposedly had Sasquatch activity and they set out traps to collect blood and hair specifically for this purpose. they didn’t find “possum skin” on the side of the road and yammer “Squatch!” Is it all bunk? No idea. But let’s be fair with what her claims are and what is being said about her.

      • May 27, 2014 at 6:46 PM

        Her study was not well done according to experts in genetics. She is also not a geneticist. There is a long list of huge red flags in her work. But the bottom line is the results would have to be reproduced or verified by other samples. Results, if true, do not exist in a vacuum. But that’s all that exists right now!

        I have been more than fair with Dr. Ketchum through my following of her work and was ready to give her any praise that she warranted. She deserved none. This was crappy science. And excuses about prejuduce and forest people and Nephelim are helping not at ALL.

  11. February 27, 2013 at 8:30 AM

    Thank you, terry the censor. Yep, I’ve not been sitting this one out, that’s for sure. Appearing early on C2C and writing in my blog, for example, I have called for caution, while critically giving thought to what these DNA results really are telling us. While I draw the line and do not condone others’ personal attacks on Dr. Ketchum, I totally support what Sharon Hill is communicating in sharing the deeper examination of the results here, and thus regularly link to her discussions at CryptoZooNews.

    “No data, no discovery,” to quote anthropologist John Hawks, is the only way to go.

    Plus we must extend a critical eye to how the results are standing up to peer critiques, while watching if Dr. Ketchum can hear the reviews without being defensive and taking everything so personally.

  12. Haskell Hart
    February 28, 2013 at 5:51 PM

    This video is misinformation. The nDNA sequences WERE given in standard FASTA format in the DeNOVA on-line paper at the very bottom. I used them to do my own blast searches. Even the mtDNA mutations in Supplementary Data 2, though in PDF format, can relatively easily be converted to a text file, then to an EXCEL spreadsheet which was convenient to compare to the mtDNA genetic tree. Most samples matched fairly well. Other human haplotype identification entries are in error and should have been recognized as such immediately. So I wonder…. Finally, EVERYBODY, $30 for access to an on-line journal article is not unusual. All journals charge in the range of $25-35$US. Let’s not be petty in our criticisms. Those who are reveal their lack of scientific background. The data ARE presented in the paper. If you don’t think so, you are not qualified to criticize the paper because you can’t recognize the data or use it. I’m a physical chemist and I was able to do the necessary BLAST searches and mitochrondrial mutations checks in short order. It was not even necessary to be a geneticist. The fur is not POSSUM fur. Its nDNA does not match the possum nDNA in the GenBank.

    [editor - deleted derogatory statement]

    Haskell Hart, PhD

    • February 28, 2013 at 6:47 PM

      Sorry, I trust PhD evolutionary biologists who are curious without bias over chemist who disparages graduate students.

      $30 for access to one paper in Science or Nature or other respected journal is fine because we know their standards. Once again, and this has been said over and over…

      This is the only paper in this one issue of a new journal. Since it is so earth-shatteringly important, why not release it open access?

      With misstep after misstep for FIVE years with this project, she has worn out her Get out of Jail Free card. We have every right to criticize the mistakes. THAT’S HOW SCIENCE WORKS.

  13. Phil
    February 28, 2013 at 9:00 PM

    You’ve shown great restraint in not mentioning the “Matilda” film since December, in spite of its close links to this paper, and the recent flare-up over the creature’s resemblance to an off-the-shelf Chewbacca mask. I recognize the suspect nature of my 2nd and 3rd links, but that’s kind of the point:

    http://doubtfulnews.com/2012/12/bigfoot-dna-results-will-be-accompanied-by-video-footage-of-creatures/

    http://www.cryptomundo.com/bigfoot-report/john-kirk-supports-bill-munns/

    http://www.cryptomundo.com/bigfoot-report/moneymaker-confirms-matilda/

    Here’s hoping that TV’s Matt Moneymaker is among those whose reputations do not survive this fiasco intact. Bigfoot is good fun, but the damage being done to science is real.

    • February 28, 2013 at 9:33 PM

      Phil: I totally agree on the damage to science. I’m going to talk about exactly that in an upcoming engagement.

      As for the Matilda/Chewbacca thing… well, the crazy just spins out of control sometimes, don’t it?

      Thanks for linking those, though. People can check it out if they are interested.

  14. Graham
    February 28, 2013 at 9:50 PM

    Sharon: It’s not just the damage to science. Ketchum is claiming that she and her contributors (Havey they been contacted?) are forensics specialists. I have no doubt that there are defence attourneys out there who would happily pay $30 for that paper, simply for the opportunity to use it in a new appeal for their client.

  15. Jim
    February 28, 2013 at 9:52 PM

    Ketchum has released a statement on her Facebook page mentioning “armchair scientists.” (https://www.facebook.com/permalink.php?story_fbid=553297048024030&id=359075637446173) I can only imagine that she is referring to the biologists in the video. Just in case the link doesn’t work for whatever reason, here is a screenshot (http://img28.imageshack.us/img28/7899/sarmchairscientistquote.png).

    • February 28, 2013 at 10:19 PM

      She has an ego the size of Texas.

  16. Haskell Hart
    February 28, 2013 at 10:56 PM

    “Curious without bias?”. Not entirely. We’re all “curious” or we wouldn’t be on this page. Bias is another matter. They haven’t reported their independent evaluations of her results yet. She used independent established labatoratories. Either the samples are suspect, or the analyses are. But before that can be decided, at least critically evaluate whether the results: FASTA nDNA files for samples 26,31, and 140 and the mtDNA mutations in Supplementary Data 2 support her conclusions. I have and they do to some degree, but not entirely. More later.

    idoubtit, and what are your scientific credentials? My deleted comment was directed to the particular graduate students in the video, who spoke and acted unprofessionally and without knowledge in some cases.

  17. Jim
    February 28, 2013 at 11:42 PM

    The Breaking Bio group linked to a radio interview of Ketchum. She claims the DNA of this unknown primate is closer to a lemur, and then she refers to the extinct giant lemur that weighed nearly 400 lbs. But yet she refers to it as a Hominin in her paper. That’s like confusing a crap apple with a red delicious. You can listen to the interview here:

  18. Jim
    March 1, 2013 at 12:00 AM

    * crab

  19. ProGrocker
    March 1, 2013 at 1:22 PM

    For all those posters who cannot afford the $30 fee for the paper, let me know and I’ll email you a copy. I hate to think that a price equivalent to a couple of pizzas is so prohibitive, but such may be the state of the economy today.

  20. onyongnyong
    March 1, 2013 at 6:59 PM

    It is not so much that $30 is expensive, just that the paper is apparently not worth it. A manuscript with as many problems and mistakes as are being reported is not something that you could charge money for.

    I am not a specialist in vertebrate evolution but even so I can recognize the problems that the biologist in the video discuss as elementary mistakes that every postgraduate student in the field should be able to identify and correct. When the authors not only fail to correct this huge problems but make them the basis for their conclusions become clear not only that reviewers would reject the paper but that people with some understanding of biology would not be happy expending money to read it.

  21. March 4, 2013 at 1:25 PM

    I asked Dr. Ketchum on her FB page what the name of the old journal was and then she banned me. It would appear she has issues when people ostensibly censor her but she’s pretty free with the ban hammer.

  22. PJR
    March 5, 2013 at 9:35 PM

    Ketchums paper may well have flaws and she may be defensive, but I still really cant make heads or tails from watching this. The panel came across to me as a smug, self congratulating clique intent on gaining some social retribution by ridiculing an easy target. Critical objectivity is obsolete here, which is a shame, because as a casual Internet observer of this it would be interesting to see this evaluated as such. This biased treatment doesn’t contribute anything towards painting a clearer picture here… Not for me anyway.

  23. March 6, 2013 at 9:21 AM

    PJR the panel explains the snarkiness in the comment at February 26, 2013. See above. As Dr. Crislip is fond of saying on Quackcast “Ridicule is the only weapon which can be used against unintelligible propositions. Ideas must be distinct before reason can act upon them.” Ketchum herself seems to bring down the ban hammer when you ask honest, polite questions that challenge her propositions. What’s left but ridicule?

  24. terry the censor
    March 6, 2013 at 2:11 PM

    @PJR

    As Karl suggests, ridicule can be earned.

    This is an important point. Fringe believers pretend ridicule can never be earned — ever — so when ridicule is applied, they cite this as evidence of bias. It is an easy out that fringers think excuses them from engaging whatever valid criticism informed the ridicule. And as Karl pointed out, Ketchum is not the least interested in engaging criticism. Ketchem has earned whatever ridicule comes her way,

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