Tag Archive: DNA


Bigfoot research over the decades has had its ups and downs. What I love most are the true scientists that come forward to assist us in the daily fight against pseudo-science and at the same time assist us in the fight against the mainstream science which out of many times, opinion discounts what thousands of witnesses have seen over the generations.

 

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(Left): Track found investigating a sighting report in Whitehall, NY 2003, (Right) Track found along the Poultney River, Vermont. (Photo Credit: Steve Kulls)

 

One other double standard was the discovery of the Bili Ape. It began to originate from footprint evidence that there was a different type of primate inhabiting the jungles of Africa. However since day one, science has discounted the numerous tracks found by people, citing hoax or misidentification from minute one.

 

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(Left) Print found in Chautauqua County, NY 2016, (Right) Track-way of the Fort Ann Cast 2006) (Photo Credit: Steve Kulls)

Also misleading are some of the statements made by the skeptical scientists interviewed on some documentaries. They generally state opinion. One skeptical scientist actually stated, “If these things were out here, people would be seeing them.”

WHAT????

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Squatchdetective Field Investigation Team camp shot 2013

 

The sad fact is though with the proliferation of social media, it has become easy for false news stories and junk science to be promoted as fact. And it allows people whom naively follow people without doing their homework.

We have seen this time and time again with some of the folks exposed in the Hall of Shame. They obtain a following and what they say is gospel to the people who blindly accept what they preach. That is usually until they do their own research.

I’ve always said here, “Don’t take my word for it. Do your own research and use what I say as a starting point.”

 

Deflating the Claims of the Ketchum Study

One such scientist that’s on our side, being that he is looking at things from an unbiased point of view is Dr. Haskell V. Hart, who breaks down the nitty-gritty of DNA results and puts them to the test. Particularly Dr. Melba Ketchum’s DNA Study.

The first thing that threw my BS Meter abuzz was the manner in which she released the information.

Many forget about a press release a day or two before the release of the study. This violated the normal standard for scientific studies being released into the public.  Dr. Ketchum was charging $30  for a download of the report the next day. Sounded to me like it was a promotional pitch to increase sales, much the way Apple releases their products.

Now one might say she was trying to recoup what she spent in the study, however she was charging the folks that submitted samples in the study for those costs. Not to mention a draconian non-disclosure agreement. Basically stating they had a right to get the results, but couldn’t talk about it, ever, at all unless Dr. Ketchum herself, gives permission.

All of this sounds highly irregular right? But it goes on.

Ketchum had published the study in a scientific journal called the Denovo Journal, which at the time of release was called the Journal of Advanced Multidisciplinary Exploration in Zoology.

Shortly thereafter, as all skeptical Bigfoot researchers do, dug up the fact she owned the very journal and was purchased very recently to the study being published.

Ketchum stated,

“After this journal agreed to publish the manuscript, their legal counsel advised them not to publish a manuscript on such a controversial subject as it would destroy the editors’ reputations (as it has already done to mine).  I have documentation on all of this drama.  So, rather than spend another five years just trying to find a journal to publish and hoping that decent, open minded reviewers would be chosen, we acquired the rights to this journal and renamed it so we would not lose the passing peer reviews that are expected by the public and the scientific community.  Denovo, the new journal is aimed at offering not only more choices and better service to scientists wanting to submit a manuscript, but also reviewers and editors that will be fair, unlike the treatment we have received.

It has been a long and tedious battle to prove that Sasquatch exists.  We have had the proof for nearly 5 years but building enough data to convince mainstream science has taken a lot of time.  Trying to publish has taken almost two years.  It seems mainstream science just can’t seem to tolerate something controversial, especially from a group of primarily forensic scientists and not “famous academians” aligned with large universities, even though most of our sequencing and analysis was performed at just such facilities.

We encountered the worst scientific bias in the peer review process in recent history.  I am calling it the “Galileo Effect”.  Several journals wouldn’t even read our manuscript when we sent them a pre-submission inquiry.  Another one leaked our peer reviews.  We were even mocked by one reviewer in his peer review.”

 

Did Ketchum realize that Albert Einstein formulated his theory of General Relativity in 1911 and didn’t get it published until 1919?

The process of publishing a scientific paper is grueling and tedious. No doubt she had some push back given what I stated earlier, but patience and perseverance is what normally wins the day.

So this puts the entire publication in doubt, whether it be by misstep or otherwise.

I was waiting too for something incredible and instead was immediately disappointed.

Soon afterward Dr. Ketchum fell into the category of what some researchers call the “woo.” She began to claim Bigfoot was braiding her horses hair on her ranch, and a very bizarre to say the least Bigfoot encounter.

“She is the fairies’ midwife, and she comes

“In shape no bigger than an agate stone…

That plaits the manes of horses in the night

And bakes the elflocks in foul sluttish hairs,

Which once untangled, much misfortune bodes.”

(Shakespeare: Romeo and Juliet Act One Scene 4).

An article on Elf and Fairy Knots and lore can be read here. Now we can move those into the Bigfoot column.

Enter Dr. Haskell V. Hart…

image Dr. Haskell V. Hart holds a PhD in chemistry from Harvard University and has a physical, inorganic, and analytical chemistry research background. He was Associate Professor of Chemistry, University of North Carolina at Wilmington, after which he was Senior Staff Research Chemist and Research Manager at Shell Chemicals. At Shell he both conducted analytical research and managed various analytical departments. His research interests have included analytical applications of x-ray diffraction, electron diffraction (two database patents), and gas chromatography-mass spectrometry. Since his retirement, he has focused on long-range detectors and application of DNA sequencing to species identification, especially relict hominoid candidates. His blog, www.bigfootclaims.blogspot.com, contains over thirty articles on this subject and related issues.

Dr. Hart did a study of his own on the Ketchum Study and came up with some interesting take aways for those who want the science to debunk Ketchum’s rather incredible findings of a new Relic Hominid.

As suspected by this writer, and stated in the past, the problem was the Primer which is used to scan an area for like DNA. They used a Human primer, and not surprisingly we got mostly human results aside from contamination. They did not use a universal primer approach which would have been the appropriate primer to use for an unknown sample. (Hence could be the fitting of evidence to a story rather than fitting the story to the evidence.)

Dr. Hart breaks down the processes and how Ketchum was dealing with either contaminated or degraded DNA samples. And he breaks down some of the Study’s samples into a proper reading in the GenBank. Here’s just some of the highlights:


Further examination of the extra mutations in Table 2 here shows that in S2, S26, S36, S39b, S44 and S46, most of these extra mutations could be attributed to a second haplogroup, i.e. a contamination. However, Ketchum et al., in their paper and publicly, steadfastly deny any contamination in any of their samples…

Clearly, the Ketchum et al. study would have benefitted from this universal primer approach. Sequencing “whole” nDNA genomes of a black bear (S26) and a dog (S140) would have been avoided, and likely many other samples would have shown nonhuman matches by mtDNA sequencing with universal primers. It seems unlikely that all 111 of their study samples collected in the woods would turn out to have human mtDNA as reported, unless, of course, they were contaminated.

 Short Tandem Repeats at Microsatellite Loci… The method is used in criminal forensics and population genetics, and was used by Ketchum et al. (2013). Unfortunately, the method requires that you know what species you are dealing with and what the lagging and leading strand sequences are in order to pick the correct primers to sequence the intervening STRs (number of repeats). The method is not suitable for totally unknown samples.  

Specific Gene Sequencing…In a manner similar to mitochondrial methods, primers can be selected to target a specific portion of a nuclear gene, usually to detect SNPs related to a specific phenotype (gene expression). Ketchum et al. (2013) used this method with several genes, as discussed below. Again, the method requires detailed knowledge of the specific species’ gene sequence to select appropriate primers. The method is not suitable for totally unknown samples.  

 Bead Array Analysis for SNPs…The method is not suitable for totally unknown samples, except as a very expensive and complex way of matching an unknown sample to a very specific known species, with no indication of the species if there is no match.  This was the Ketchum et al. (2013) approach: attempting to match unknown samples to human.  

Use of a reference sequenceUnfortunately, their method used human chromosome 11 as a reference for the sequencing, thereby both greatly reducing the length of the resulting consensus sequences and biasing them toward only highly conserved human genes.

S26… Ketchum et al. concluded that all three sequences were from an unknown male primate/human female hybrid, and that they contained a mosaic of both human and other primate segments.  Sample 26 is a black bear  Ursus americanus). From searches of Genbank with BLAST™, using the whole S26 nDNA sequence as query, it was found that S26  matched  human and other primates only 94-95%, but matched polar bear (Ursus maritimus) about 98-99%. Black bear sequences in GenBank were sparse and relatively short, but matched S26 100%.

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Will someone please feed S26?

S31… Ketchum et al. correctly concluded that S31 is human. Most database hits were 100% ID modern human (Hart, 2016a).

 

 

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That’s not quite what we expected!!! 100% Modern Human???

S140… Sample 140 is a dog (Canis lupus familiaris) or less likely a wolf or coyote, not a sasquatch. Since there is a wealth of dog DNA in GenBank, no other source was queried.  Hits averaged 99% ID match to dog compared to 94% for both human and other primates (Hart, 2016a).

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Here’s what S140 is… (I knew I would work a way to get Watson on the blog!!)

Source: Research Article:  DNA AS EVIDENCE FOR THE EXISTENCE OF RELICT HOMINOIDS  by Haskell V. Hart Ph.D

Dr. Haskell outlines the proper DNA sequencing of unknown subjects at the end of his report as well. A great guideline for future DNA studies.

Dr. Hart’s report can be found at:

 http://www2.isu.edu/rhi/pdf/HART-DNA-Evidence.pdf


So there we have it. It would appear that the Ketchum Study had a theory prior to testing, and went with it.

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Picture on Dr. Ketchum’s site… wow.

The results for them were either one pointing to what they wanted to believe, versus what it was actually.  Her bias, I cannot prove, but in my opinion it was there. And now, there seems to be some science behind that opinion. 

Well at least that’s how I see it.

 

Now onto some hope…

I always love when things are found. In one case the Sea Blob was finally photographed after not being seen for over 100 years. The Bathochordaeus charon, not seen in 100 years was photographed in Monterey Bay, California.

 

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The Bathochordaeus charon. (Credit: Monterey Bay Aquarium Research Institute.)

And in other exciting news scientists have found dinosaur feathers (that’s right feathers) embedded in amber.

 

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(Source: Current Biology)

The Scientist.com writes:

The feathered tail of a 99-million-year-old dinosaur, complete with eight vertebral segments as well as evidence of soft tissue and blood, has been found in Cretaceous amber, according to a December 8 study in Current Biology. The 1.4-inch segment likely came from a coelurosaur about the size of a sparrow, the authors wrote in their paper.

New discoveries and rediscovered animals, motivates me as we still know very little about what has inhabited, or continues to inhabit, this planet!

Till Next Time

Squatch-D

Remember the Sykes study? You know the one that was being billed as going to be the one that defines Sasquatch, Yeti, Bigfoot?

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Geneticist Bryan Sykes

The study that dashed our hopes claiming that the Yeti was actually the reemergence of a fossil polar bear?

Well silently and off the BIG radar, some things about the Sykes have been revealed and they are not minor.


The Fossil Polar Bear

The crux of the study, at least in the Himalayas, was that the DNA collected on some of the samples belonged to a long thought extinct Polar Bear. A cryptozoological breakthrough if not necessarily the one anticipated. 

Sykes Samples and Results

List of samples tested by Sykes and results. (Credit: Royal Society Publishing)

But as always; hold the phone.  It appears an error was made.

In a letter to the Royal Society Publishing Organization, Sykes admitted to a  mistake by stating their GenBank search was in error, but now alluding that their discvovery was to the modern polar bear.

 

“Sykes and Melton acknowledged that their GenBank search was in error and but suggested that the hairs were instead a match to a modern polar bear specimen "from the Diomede Islands in the Bering Sea reported in the same paper”. They maintained that they did not see any sign of damage in their sequences and commented that they had “no reason to doubt the accuracy of these two sequences any more than the other 28 presented in the paper.”

Published Dec. 17th, 2014 – http://rspb.royalsocietypublishing.org/content/282/1800/20142434

 

 

However while retesting the samples for replication done by Eliécer E. Gutiérrez, a researcher at the Smithsonian Institution and Ronald H. Pine, affiliated at the University of Kansas stated that the samples were genetic variants of brown bear near impossible to derive the difference between them.

 

By means of mitochondrial 12S rRNA sequencing of putative “yeti”, “bigfoot”, and other “anomalous primate” hair samples, a recent study concluded that two samples, presented as from the Himalayas, do not belong to an “anomalous primate”, but to an unknown, anomalous type of ursid. That is, that they match 12S rRNA sequences of a fossil Polar Bear (Ursus maritimus), but neither of modern Polar Bears, nor of Brown Bears (Ursus arctos), the closest relative of Polar Bears, and one that occurs today in the Himalayas… We have concluded that there is no reason to believe that the two samples came from anything other than Brown Bears.” 

Published March 16th, 2015 –

http://zookeys.pensoft.net/articles.php?id=4885%20

640px-Ursus_arctos_isabellinus_(in_Perm_Zoo) (1)

Himalayan Brown Bear (Source: Wikipedia)

 

Meaning there was really  no breakthrough in Yeti research.

 


From Bad to Worse

Even more recent was an allegation made by colleagues of Dr. Sykes as reported in the U.K. Sunday Times by Science Editor Jonathan Leake.

“A GENETICIST at Oxford University whose new book claims to offer ‘the first scientific evidence on the survival’ of apemen such as the yeti and Bigfoot, has been attacked by colleagues who say the claims are nonsense and his research institute does not exist.”

March 29th, 2015 –

http://www.thesundaytimes.co.uk/sto/news/uk_news/Science/article1537430.ece

 

 

According to an article on Retraction Watch entitled, “Bigfoot paper corrected because it doesn’t exist — the author’s institution, that is” quoted Leake stating Sykes admitted to his “white lie.”

"The paper gave Skyke’s affiliation as the Institute of Human Genetics at Wolfson College, Oxford. Sykes is a fellow of Wolfson but he admitted the institute was mythical. “The journal required some sort of additional address in the college and, hey presto, I became an institute!”

Source:

http://retractionwatch.com/2015/04/14/bigfoot-paper-corrected-because-it-doesnt-exist-the-authors-institution-that-is/

 

 

If this is true, with the above information what type of credibility does it lead to this study?

While people would consider Sykes “controversial,” every scientist out to put forth hypotheses into areas such as Cryptozoology, Ufology and Para-Anthropology, unless you’re towing the company (main-stream science) line, has been labeled as controversial. And in all science missteps are made such as the GenBank error.

However what I cannot condone, nor should anyone, is the acceptance of any untruth of any sort, any “white lie” or any misrepresentation to get published in a journal.

Has a familiar overtone doesn’t it?

Till next time,

Squatch-D

Well here goes a blog, I’ve had to think out a while. Last week I highlighted an article in this blog where Houston Chronicle science reporter, Eric Berger, belittles Dr. Ketchum using an anonymous geneticist who wishes to remain out of the fray for the sake of ridicule. 

 

 

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Houston Chronicle science reporter Eric Berger.

 

Some have criticized the fact that the source was from an anonymous source. I won’t hold that against the scientist, because how many times have we kept a witness confidential?

Would it be fair to discount the encounter reports by witnesses wishing to remain anonymous?

Obviously no.

But on the other hand, was it fair for this reporter to just state the results were this without any factual basis to back it up to be verified by the public?

Absolutely not.

(Why am I maintaining my source’s anonymity? Because some of his peers would question his engagement on such a topic, believing it unworthy of valuable research time. But make no mistake, he is a top-notch scientist at the top of his field.)

                                                                                             -Eric Berger, 7/1/13

What the journalist is asking us is to trust him, rather than trust Melba. He said she said…

Sorry, I call shenanigans.

More matter of fact, we reached out to Berger for him to come on the radio show and explain how his test came about, how the samples were provided what types of testing were done, insuring the anonymity of his source, and answer other questions. Of course our inquiries were not answered at all.

What does Mr. Berger have to hide? Why the professional discourtesy? A week is enough time to at least answer the request.

In my opinion an ethical journalist would find a source that would go on record and test the sample data, and provide some documentation in the article that condemns another scientist’s work. Not a “trust me” demeanor.

Even as a “mere little blogger and podcaster,” my ethics would have only allowed information with that standard to be allowed on my media outlets.

Since Berger’s article lacks that, is mere here say.

However…

Does the Ketchum Study reveal all the scientists and labs that worked on the samples? Could there be some equal ethical consideration on that side as well?

If not, it’s shenanigans as well. What’s good for the goose IS good for the gander as well. And I say to the proponents of the study, you can’t have it both ways.

There was one scientist more recently, who took to task the Ketchum study, not testing a sample from the project but rather reading the report itself and finding flaw with it.

Perhaps if Dr. Ketchum feels this scientist is in error she can send him a sample.

Thanks to Matt Knapp over at Bigfoot Crossroads, in this blog he highlights the Ars Technica website and a scientist who has written a rather lengthy article, technical, yet enough in layman’s terms to be understood, as he breaks down everything for us.

To me it is the best breakdown to date, why myself and many of my colleagues feel the study went askew.

The scientist, is Ph.D in Molecular and Cell Biology, Dr. John Timmer, not just a science reporter like Berger.

His bio is rather quite impressive, from his online bio:

John-TimmerJohn (Timmer) is Ars Technica’s science editor. He has a Bachelor of Arts in Biochemistry from Columbia University, and a Ph.D. in Molecular and Cell Biology from the University of California, Berkeley. John has done over a decade’s worth of research in genetics and developmental biology at places like Cornell Medical College and the Memorial Sloan-Kettering Cancer Center. He’s been a speaker at the annual meeting of the National Association of Science Writers and the Science Online meetings, and he’s one of the organizers of the Science Online NYC discussion series. In addition to being Ars’ science content wrangler, John still teaches at Cornell and does freelance writing, editing, and programming.

What we have is a breakdown by a science writer. who is credentialed, perhaps even more so in genetics than Dr. Ketchum, who’s doctorate is in veterinarian medicine. 

Here is one such sample from the article condemning the study to turning a blind eye to the truth, for a more romantic idea, which is the summation (not that we’ve seen that in the Bigfoot community over the years..ha..ha) :

If the DNA was human and had not degraded much during its time in the environment, then most of these reactions should produce a clear, human-like signal. The same would be true if, as Ketchum concluded, the samples contained DNA from a close relative of humans (remember, chimps’ DNA is over 95 percent identical to ours). If the animal were more distantly related, you might expect some reactions to work and some to fail, with the percentage of failures going up as the degree of relatedness fell. In some cases, you might expect the reactions to produce a PCR product that was the wrong size due to changes in DNA content that occur during evolution.

But you can’t necessarily expect the DNA to sit outdoors and remain intact. DNA tends to break into fragments, with the size of the fragments shrinking over time. Depending on how degraded the sample is, you might see more or fewer reactions failing.

What they saw was a chaotic mix of things. As Ketchum herself put it, "We would get these crazy different variants of sequence. We would get these things that were novel in genbank. We would get a lot of failure, and we’d get some that would have regular human sequence," Ketchum said. "We could not account for this, and it was repeatable."

All of which suggested that there was likely to be DNA present that was only distantly related to humans; anything that was from a human or close relative was probably seriously degraded…

…So all the initial data suggested that the DNA was badly preserved and probably contaminated. Which in turn suggests that whatever techniques they used to get DNA from a single, uncontaminated source just wasn’t sufficient for the samples they were working with. But instead of reaching that conclusion, the bigfoot team had an alternative: their technique worked perfectly fine. It was the sample that was unusual.

                                                                                                      Ars Technica, 7/7/13

Too often, as we’ve seen in the field, people get romantic about the existence of the Sasquatch and alleged evidence they have found. And they get dead set on it without stepping out of the area and looking at it without bias.

Bottom line, nobody except a few of you here even care about the truth. Most would rather perpetuate that BF is a myth or an ape.”

                                                                                        – Dr. Melba Ketchum statement

And that is the usual blanket excuse (as well as untrue) of those committed to an opinion rather than to the science and review of such.

Coming from a scientist, who needs to look at their own results without bias, I find the statement disappointing and typical of the same type of witness who insists there blobsquatch is a Bigfoot no matter what inconsistencies you point out.

Usually when the conversation devolves to a statement as such, any debate and constructivism is lost upon the statement maker.

Read Dr. Timmer’s article.

I will let the audience and time to be the judge.

Till next time,

Squatch-D

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