The Ketchum Report (Continued)

[Guest]

More for SLOWSTEPPER,

 

N50 is a data quality measure that would be useful but is not in the paper or attachments.  There are other data quality measures given in the supplementary data of the paper, some of which unfortunately did not appear online but was sent to me.  However, RR, HR, and ER are determined by comparison to a specific reference sequence.   These do not measure the quality of the raw data.  They measure how well the contigs match a larger reference sequence.  What would you have that reference sequence be, given that we have none for "Bigfoot."?  All four values can be computed from BLAST output by the sequencing software, but were not provided by the authors.  In principle, I could do the calculations myself from the Excel search output, but it would take some programming.  I will send your the missing data from the paper by em if you leave an address on my facebook page.  But please do not forward to anymore.  People should pay for the article, BUT it should have had all the referenced attachments(which it didn't).  This was an unresolved frustration for me.  

 

 

[Sunflower]

Thanks Mr Hart! 

 

Cotter,

 

Spit it out..........please?   

[Guest]

hvhart,

   

   I will try and keep this brief as I have pretty much said all I want to about this paper.   

 

1.  You are very late to this discussion - much of what you want interpreted has already been said - go back and read the posts.

 

2.  If you want us to look at something, post it here.  I am not going to go onto your facebook page or have you email it to me. I get a distinct feeling you are trying to fish for peoples ids here.  Post it here, and I will look at it.

 

3.  If you have "private" information, share it here if you wish.  Again, trying to get peoples emails to send it to them is not ok.  Use the PM if you want to keep something confidential.  Otherwise, I am not interested in hearing about it.

 

4.  Your comments about 100bps homology not being relevant is ludicrous.  The whole contig is base on 100bp sequences.  And it is assembled using Human CH11 as a reference.  As to context, again the contigs are a totally artificial creation (and wrong).  By deconvolving the data (first 5,000 bp of each contig), I was able to break down the regions of homology that were spliced together.  I then took these regions and blasted them as ~100bp segments.  The results have been previously stated, and I don't feel like reposting them.  I am very confident of my findings. I have blasted large pieces of the contigs, but they really have so little homology to any one sequence it comes back as meaningless - NOT a novel species.  

 

Overall, I would guess I have spent the better part to 100 hours analyzing the data and trying to make sense of it.  I have read the paper too many times.  It is just bad and the data very flawed and in NO WAY supports the conclusions.  Believe what you will.  I feel this study needs to be retracted.  There is really nothing more I have to say on this.

[Guest]

Yes. Those pendulous breasts were horrifying.

You mean Like the ones in your Avatar?

[Guest]

hvhart,

   

   I will try and keep this brief as I have pretty much said all I want to about this paper.   

 

1.  You are very late to this discussion - much of what you want interpreted has already been said - go back and read the posts.

 

2.  If you want us to look at something, post it here.  I am not going to go onto your facebook page or have you email it to me. I get a distinct feeling you are trying to fish for peoples ids here.  Post it here, and I will look at it.

 

3.  If you have "private" information, share it here if you wish.  Again, trying to get peoples emails to send it to them is not ok.  Use the PM if you want to keep something confidential.  Otherwise, I am not interested in hearing about it.

 

4.  Your comments about 100bps homology not being relevant is ludicrous.  The whole contig is base on 100bp sequences.  And it is assembled using Human CH11 as a reference.  As to context, again the contigs are a totally artificial creation (and wrong).  By deconvolving the data (first 5,000 bp of each contig), I was able to break down the regions of homology that were spliced together.  I then took these regions and blasted them as ~100bp segments.  The results have been previously stated, and I don't feel like reposting them.  I am very confident of my findings. I have blasted large pieces of the contigs, but they really have so little homology to any one sequence it comes back as meaningless - NOT a novel species.  

 

Overall, I would guess I have spent the better part to 100 hours analyzing the data and trying to make sense of it.  I have read the paper too many times.  It is just bad and the data very flawed and in NO WAY supports the conclusions.  Believe what you will.  I feel this study needs to be retracted.  There is really nothing more I have to say on this.

1.A dodge of my questions, which you have not previously answered.   I read your relevant post.  "Late"?  Really? The paper is only two months old.  Science takes a while, man. 

 

2.  I have no use for anyone's e-mail address except to answer their questions.  Limiting your knowledge to this discussion group greatly limits your INFORMATION.  Most of the people here are just sharing OPINIONS, without much basis. The smarter ones at least ask questions. 

 

3.  I never called anything "private."  Tables of data do not copy well to this word processor.  The author will provide them to you if you ask. 

 

4.  You confuse sequencing relatively short segments and stitching them together with searching, which is best done with the longest possible sequence.  Find me an expert who thinks that breaking apart a 1-2 million bp sequence into 100 bp segments to search a database is a good idea.  You get what you got: matches to many distantly related mammals, such as your bear, human, and sheep.(your sample 26 analysis).  Nothing can be concluded from this.  Your 100 bp arbitrary segments have little relationship to the original raw sequencing segments. Even if they did, so what?  They're too short to be useful by themselves.  Also, how do you know that the first 5000 bp of a couple million is the most relevant(species unique) part of the sequence?  It really doesn't matter anyway if you're going to break it up in 100bp segments.  You haven't "deconvolved" anything; you've lost information.  My full sequence search of sample 26 vs the human G + T database showed up to 35% query cover, mostly on chromosome 11(see below), but it wasn't a complete match.  Hence the sequence is not entirely human.

 

You haven't proven the data is "bad,"(neither have I that it's good),  just that it makes no sense to you.  Some of the conclusions in the paper are supported; some are not.  Read on.

 

So you won't have to go anywhere to learn something, here's my review.  Sorry for the relative lack of good formatting.

 

 

Revised April 16, 2013.

Review of “Novel North American Hominins….â€

by Haskell V. Hart, PhD

Introduction and Disclaimer

This is not an “expert review†or a “peer review,†as I am not a geneticist or hair analyst. My education and professional experience are in the fields of physical and analytical chemistry, not biochemistry.  Therefore, I am not prepared to comment on the experimental protocol, the integrity of the raw data, or the broader implications for primate phylogeny.  However, I have learned to interpret DNA mutations results, make sequence comparisons through BLAST, and I have well practiced general scientific, logical, database, and proofreading skills.  I have been keenly interested in the subject of unknown hominins for a number of years and welcome the scientific results in the paper.  I have no competing interests.  This unsolicited review is presented in the interest of open discovery and discussion and in the accuracy and completeness in reporting, nothing else.

Hair Analysis

Suggestions:1) Obtain the mean and variance of the diameter of human hair from the literature.  This may vary with the demographics.  Calculate the mean and variance for your hair samples.  Use the standard statistical test (http://en.wikipedia.org/wiki/T-distribution)to determine the probability that the difference in sample means is statistically significant at some level.  The hair size comparisons in the paper could be made much more precise by the above.2) Release/Publish all your photomicrographs(as in figure 5) of all the hair samples for independent analysis.  Unlike the measurements in 1) above, appearances can be subjective.  These important results should be reviewed by a panel of experts.

 

Electron Microscopy

The unusual finding of single-stranded DNA sections deserves much more discussion.  What does it suggest? Degradation(If so, what  possible mechanism, e.g. a viral or fungal attack), genetic disease, gene-splicing, or other?  How would it affect the DNA sequencing results?

 

mtDNA

My findings along with the original mutation data are found in the attached Excel file, “Supplementary Data 2 Revised.† Supplementary Data 2 in the original paper reports two different kinds of sample data: nineteen samples (including a control) with mutations from whole mtDNA genome sequencing and eleven samples with mutations from HVS-1(HVR1) only.  These should have been clearly distinguished in the text or by footnotes.  Among the former, nine samples had all the required mutations for the assigned haplogroups.  Five samples had one missing mutation each, four had two missing mutations and one had five missing mutations(Sample 39b, for T2).  This result stands alone in being above the accepted maximum number of missing mutations (four) for a haplogroup assignment as judged by Family Tree DNA, guided by Behar, et al (2007).  Of the eleven samples in the HVS-1(HVR1) only category, only one seemed misidentified: Sample 33 fits haplogroup U5 better than haplogroup H according to Behar et al(2007), Table S2 –“Hg-Predicting Motifsâ€.  Additionally, Samples 117, 118, and 71 fit L3e4 equally well, a relatively minor difference from the reported L3d.  Though there were extra mutations in most cases, the other seven “HVS-1 only†samples were correctly haplogrouped according to Behar(2007).  The significance of numerous additional mutations (eight in Sample 24, 18 in Sample 26) not required by the respective haplogroups cannot be addressed by me, but should be by an expert.   Also in Supplementary Data 2 there are two additional sample entries in the far lower right of the online version that are not labeled or assigned a haplogroup.  These results don’t align with the columns and the other sample data.  What are these samples?  Controls?  Explain.Some of the mutation sequence locations in Supplementary Data 2 lack a base designation.  For example: Sample 81 has “16223â€, no A, G, T or C suffix.  These should be rechecked and restated with the correct base.  I put a “(?)†in my attached Excel file following these locations.If the complete genome mtDNA sequence was obtained for Sample 140(used to construct Supplementary Figure 3), why were only the mutations from HVR1 listed in Supplementary Data 2? In summary, The results of the mtDNA analyses support the conclusion in the paper that at least 28 of the 29 samples(only sample 39b might be questioned) in Table 2 and Supplementary Data 2 are from distinctly human matrilineal descendants.The following statement needs revision:“No mitochondrial DNA homology with apes, Neanderthal or Denisova cave sequences were found?.â€How was this concluded?  As shown by the search results below(marked with a *), human mtDNA is highly homologous to both Neanderthal and Denisovan DNA(99% and 98% identities, respectively).  Since the samples in the study proved to contain essentially human mtDNA, they must also prove highly homologous to Neanderthal and Denisovan DNA.  Direct 1:1 comparisons to Neanderthal and Denisovan mtDNA in BLAST should be made for all samples with complete genome mtDNA sequences.  Results will be very similar to what was found in the search results below(*). Perhaps the term % homology should be used, e.g. 99% for Neanderthal and 98% for Denisovan as found in the searches below. Even the apes showed significant homology(86-91%) to human mtDNA as shown in the searches below marked by #.  “No mitochondrial DNA homology†is much too strong a term as used above.   Supplementary Figures 7, 8, and 9 mentioned in paragraph 4 of the Discussion are nowhere to be found in the online version.  They were not sent to me separately, either.  In order to be consistent however, mention of Supplementary Figures 4,5,and 6 in paragraph 7 of Next Generation Whole Genome Sequencing, where they refer to mitochondrial DNA sequences, should read Supplementary Figures 7,8, and 9(all missing).  Supplementary Figures 4, 5, and 6 are based on nuclear DNA, as mentioned in paragraph 5 of Next Generation Whole Genome Sequencing, not mitochondrial DNA as implied in paragraph 7 of Next Generation Whole Genome Sequencing.Figure 19, mentioned in paragraph 6 of Next Generation Whole Genome Sequencing is nowhere to be found in the on-line paper(nor Figs. 17 or 18 either).  Could this be an error in which Figure 16 was intended? The remains of Zana(Discussion, paragraph 6) have never been found ( http://www.bigfootencounters.com/articles/zana.htm), yet you mentioned her haplotype(group) as H. Was this assumed based on her son Kwit’s haplogroup(which would be the same), or was it actually determined by sequencing?  Are there new developments concerning discovery of Zana’s remains that I am unaware of?  The female remains near Kwit’s are known not to be Zana’s.In paragraph 7 of Discussion you mention a haplotype (group) H12 for sample 37, but in Figure 2 and Supplementary Data 2 you list it as H3.  Explain, please.  Also Supplementary Data 8 mentioned there is a Sequence Analysis View (as are Supplementary Data 9, and 10), obviously not what you meant to refer to.  Supplementary Data 8 mentioned there should be Supplementary Data 11(the unpublished paper), which is not found in the online version but which you kindly sent me separately.Throughout, the term “haplotype†is incorrectly used where “haplogroup†should have been.

Suggestion:  Publish the raw mtDNA sequences (not just the mutations)in FASTA format for all the samples in Table 2 and Supplementary Data 2 for which a whole genome was sequenced, just as you did for the nDNA sequences from samples 26, 31, and 140.  People can then independently evaluate them vis a vis mutations.  Also, explicitly state on which reference sequence, rCRS or RSRS, the mutation data in Supplementary Data 2 are based.  My assumption in the above is that these are referenced to rCRS, the standard for Family Tree DNA until December, 2012, at which time the study was essentially complete.

 

nDNA

The following statement is not supported by results in the paper and needs revision: “As shown in Supplementary Figures 4, 5 and 6, the Sasquatch consensus that showed homology to human chromosome 11 reference sequence is related to primate lineages including Homo sapiens, Otolemur garnettii, Pan troglodytes (Chimpanzee), Macaca mulatta (Rhesus Monkey), Nomascus leukogenys (White cheeked Gibbon) and Callithrix jacchus (Common Marmoset) and other primate species.†Actually, only Supplementary Figure 4 contains primates other than Homo sapiens; Supplementary Figures 5 and 6 do not.Supplementary Figure 5, Sample 31, is also very strange.  You show nDNA homology to a chicken(Gallus gallus), a mouse (Mus musculus) and numerous species of FISH! This is in stark contrast to Supplementary Figure 4, which shows only primate homology. Can the results in Supplementary Figure 5(Sample 31, a paper plate from a food trap) be from the chicken and fish bait and a mouse which ate it?  You should explain better how Supplementary Figures 4, 5, and 6(Also Supplementary Figures 1, 2, and 3 on mtDNA) were generated from sequence data.  Presumably these were computed from the respective BLAST outputs, but there are some options in this.  Which ones did you choose to present this data? What are the numbers on the branches?  There are multiple ways to calculate “branch length†or “distance†in the literature.Similarly, Supplementary Figure 6, Sample 140, shows homology to the mouse(Mus musculus).Such unusual results deserve much more discussion in the paper.  What is one to think of chickens, mice, and fish in the context of primate phylogeny?  A modest question.

BLAST Searches

A summary of my BLAST search output follows.  Unless indicated, searches are based on the nDNA sequences in the paper, Supplementary Data 4, 5, and 6, for Samples 26, 31, and 140, respectively, against the NCBI nucleotide database.

Sample 26

S26 vs. Homo sapiens: 4 best matches all on chromosome 11, Query Cover 9-35%.

S26 vs Ursus americanus: No significant similarity not shared with primates.

S26 vs. American opossums: No significant similarity.

S26 vs. Neanderthals:  No significant matches.  But virtually no  nuclear DNA in database.

S26 vs. Denisovan: No significant matches.  But no nuclear DNA in database.

S26 vs. Primates: matches Homo sapiens chromosome 11 and with numerous other primate species.

S26 mtDNA(constructed) vs. Homo sapiens@: 100% Query Cover, 99% Identity, Max. Score 30504.  

S26 mtDNA(constructed) vs. Neanderthal@: 100% Query Cover, 99% Identity, Max. Score 29416.

S26 mtDNA (constructed) vs. Denisovan@: 100% Query Cover, 98% Identity, Max. Score 28373.

Sample 31

S31 vs. Homo sapiens: Top four matches on chromosome 11, Query Cover 23-27%. 9 best matches on Chromosome 11, Query Cover 9-27%

S31 vs. Opossum(Monodelphis domestica): No significant similarity.

S31 vs. Ursus americanus: No significant similarity.

S31 vs. Neanderthals: No significant similarity.  But virtually no nuclear DNA in database.

S31 vs. Denisovans: No matches. No nuclear DNA in database.

S31 vs. Vertibrates: Results similar to Supplementary Figure 5.

S31 vs. Primates: No match >494 bp.  Match on Homo sapiens Chromosome 11 and short, less than 200 bp, sequences of several primates.

Sample 140

S140 vs. Homo sapiens: Top 8 matches were all on chromosome 11, 20-34% Query Cover.  Top 5 matches ranged 30-34% Query Cover. 

S140 vs. raccoon: No good matches.

S140 vs. Ursus americanus(black bear): No significant similarity not shared with primates.

S140 vs. Opossum(Monodelphis domestica): No good matches.

S140 vs. Neanderthals: No good matches (short, mitochondrial).  But virtually no nuclear DNA in database.

S140 vs. Denisovans: No good matches (short, mitochondrial).  No nuclear DNA in database.

S140 vs. Primates:  Matches on Homo sapiens chromosome 11, and other primates.

Cross Sample Queries

S31 vs. S26: 8% Query Cover(of S31).

S140 vs. S26: Query Cover 62%(of S140).

S26 vs. S140: Query Cover 48%(of S26).

S31 vs. S140: Query Cover 8%(of S31).

Miscellaneous Searches

Neanderthal vs. Homo sapiens(rCRS)*: mtDNA 99% Identity, 100% Query Cover.

Denisovan vs. Homo sapiens(rCRS)*: mtDNA 98% Identity, 100% Query Cover.

Denisovan vs. Neanderthal: mtDNA 98% Identity, 100% Query Cover.

Homo sapiens vs. Otolemur garnettii:  mtDNA No similarity. 

Pan Troglodytes(Jenny) vs. Homo sapiens(rCRS)#: mtDNA complete genome 99% Query Coverage, 91% Identity.

Gorilla gorilla gorilla vs. Homo sapiens(rCRS)#: mtDNA complete genome 98% Query Coverage, 91% Identity.

Pongo abelii vs. Homo sapiens(rCRS)#: mtDNA complete genome 97% Query Coverage, 86% Identity.

Nomascus leucogenys (northern white-cheeked gibbon) vs. Homo sapiens (rCRS)#:  mtDNA complete genome 95% Query Coverage, 87% Identity.

_____________________________________________________________

Summary

Except for the problems described above, the paper is very readable and extremely interesting and intelligible, even to a “nonexpert†with some common scientific background.  Some of the Figures, Tables, and Supplementary Data and Figures need more explanation, in the form of text comments, better headings, or footnotes.  Some of the figures and data referred to in the text are entirely missing in the on-line version, or have been incorrectly referenced there.I find the Haplogroup assignments in Table 2 and Supplementary Table 2 to be correct for 28 of the 29 samples, based on the reported mutations only.  The conclusion that the mtDNA of all 29 samples(plus the control) is essentially human is supported by the sequence data.  I make no assessment of the validity of the raw data from which the mutations were determined.My above searches support the conclusions in the paper that:1) Samples 26, 31, and 140 contain nDNA that is not entirely human, but has similarities to human chromosome 11 and other primate sequences.2) The nDNA in Samples 26, 31, 140 shows no significant similarity to a raccoon, a black bear, or an opossum.The following conclusion, is not supported by results in the paper and needs to be revised: “All known ape and relic hominin species such as Neanderthal and Denisovan were excluded as being contributors to both the nuclear and mitochondrial sequences.â€In addition, the apes portion of this conclusion conflicts with the conclusion discussed below.Nothing can be said about Neanderthal and Denisovan nuclear DNAs, since virtually none of the former and none of the latter can be found in the NCBI nucleotide database, which contains only five short “environmentalâ€(hence uncontrolled) Neanderthal nDNA sequences of 89 bp or less.Because of the high degree of homology between human and Neanderthal and Denisovan mtDNA and the paper’s finding that the 29 samples in Table 2 and Supplementary Data 2 all showed essentially human mtDNA, excluding Neaderthal and Denisovan as mtDNA contributors would need support from 1:1 complete genome mtDNA comparisons, as recommended above in the mtDNA section, and supporting comments on the significance of the differences.  Sample 26 mtDNA searches above, marked with a “@â€, were “constructed†by adding the reported Sample 26 mtDNA mutations to the rCRS sequence. There is a slight preference for Homo sapiens over Neanderthal and Denisovan, but the differences should be carefully compared and analyzed, before excluding Neanderthal and Denisovan mtDNA.    The following conclusion is not supported by results in the paper and needs to be revised:“Analysis of whole genome sequence and analysis of preliminary phylogeny trees from the Sasquatch indicated that the species possesses a novel mosaic pattern of nuclear DNA comprising novel sequences that are related to primates interspersed with sequences that are closely homologous to humans.â€In addition, this conclusion conflicts with the conclusion discussed above.The two types of sequences mentioned above, i.e. the mosaic of human and other primates, are in fact one and the same in Samples 26, 31, and 140. For example, the homologous sequence on Sample 26, from position 189026 through position 191141, matched sequences on Homo sapiens and the primates: Pan troglodytes, Pan paniscus, Gorilla gorilla gorilla, Pongo albeii, Nomascus leucogenys, macaca  mulatta, Saimiri boliviensis boliviensis, Papio anubis, Callithrix jacchus, Saguinus labiatus, Lagothrix lagotricha,  and Otolemur garnettii. There is no interspersion of sequences. Also, Samples 31 and 140 showed no other primate homology(except Homo sapiens) in Supplementary Figures 5 and 6, respectively.  Supplementary Figure 5 shows mouse, chicken and fish homologies, Supplementary Figure 6, a mouse.  However, my BLAST searches, above, do show some primate homology for these two samples, significantly more for 140 than 31, but again, there is no interspersion of sequences.  The other primate sequences are also Homo sapiens sequences.I sincerely believe that “peer reviewers†would/should have noticed the matters described in this review and possibly more that were not obvious to me.  They would/should have facilitated a better presentation of this important study.I strongly recommend that an addendum be published, clarifying the matters addressed above and offering new data for others to analyze, e.g. hair photomicrographs and mtDNA sequences as you did with the nDNA in Supplementary Data 4, 5, and 6, for example. Complete mtDNA sequences would be particularly useful in addressing the independent find that Sample 26 contains both black bear and human mtDNA of a different haplogroup from that listed in Table 2 and Supplementary Data 2 and black bear nuclear DNA, with only a trace of human nuclear DNA, which was probably from the submitter.  The lab report is attached.

Haskell V. Hart, PhD

Canyon Lake, Texas

April 16, 2013

References

D. M. Behar, et al, "The Genographic Project Public Participation Mitochondrial DNA Database,"  PLoS Genet 3(6): e104 (2007),   http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030104

D. M. Behar, et al, “A  ’Copernican’ Reassessment of the Human Mitochondrial DNA Tree from Its Root, Am. J. Hum. Gen, 90(5),  936 (2012).

M. van Oven & M. Kayser, Hum Mutat 30(2), E386-E394(2009), http://www.phylotree.org/.

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Edited May 8, 2013 by hvhart

[Guest]

They aren't just in my Avatar.

Let us get back to the DNA now shall we?

[Cotter]

@hvhart & leaftalker - sorry for the confusion.

 

The preceeding post prior to my 'uff da' statement was a bit hard to read, it appeared that there was an issue with the quoting function.

 

Hence, I posted 'uff da' - which is a Norwegian slang term for "wow" or "whew" or "ugh" or the like, depending on context.  I then provided a link to the quote/post browser fix gigantor provided in a separate thread to help hvhart out if he was experiencing issues.

 

Sorry for the derail, it appears that posts are looking good.

[1980squatch]

^^ Torpedoes away!

 

dmaker - tell me we are on target, for the love of god!

[dmaker]

^^ I wish I could, 1980..but it looks like the behemoth is rising again...

[Guest]

hvhart,

 

   Thank you for posting your report.  Very thorough, and I really don't have much to say on it.  Most of these conclusions I also reached.  

 

I disagree with you on the statement "he paper is very readable and extremely interesting and intelligible" for all of the points you mentioned.  

 

I also disagree with you statement "I strongly recommend that an addendum be published" again for all of the points you mentioned - way too much for an addendum, and the conclusion is not supported by the data, as you so clearly point out.  A retraction of this manuscript is the only way.  MK can re-evaluate her data and publish again.

 

It sounds like if you were a referee on this paper, you too would have rejected it in its current form.  

 

So do you feel that MK has three whole genomes from BF?  If so, why so little homology between them?  Did she prove BF's existence?  I don't think your report suggests you support these conclusions.  MK took a leap of faith in proclaiming these results as BF.  

 

I attempted to try to explain how she came up with her "novel" sequence.  You may offer up other plausible explanations as to how she came up with her sequences - but you will never convince me that they are a natural, real biological representation of a genome, and definitely not BF.  Plus to you post, all the same!

 

 

[Guest]

ridgerunner,

 

Thank you for your very honest and gracious post.  I totally agree that most of our conclusions are the same.  AND THESE WERE INDEPENDENTLY ARRIVED AT.  I had never read your posts until my review was complete. 

 

It's probably semantics, but yes, for all the points I mentioned some would say the paper is unreadable or unintelligible.  I chose to emphasize the positive in that, disagreements aside, I personally was captivated. 

 

Addendum/erratum/retraction or whatever, something needs to be done, I agree.  There are just too many obvious mistakes and omissions, not to mention the grander matters of conclusions.

 

You are correct, If I were a referee, I would have asked for a revision along the lines of my review comments-minimum.  Others would likely have asked for even more.

 

MK definitely does not have "three whole genomes of BF." The sequences(samples 26,31,140) are much too short to claim that.  When I Blasted the sequences against one another(see my review) I got relatively good homology between S26 and S140 (48% and 62% query coverages respectively against each other).  S31 had only 8% query coverage against both S26 and S140.  Agreed, this doesn't look too good for a single species, but someone with a better background in this should explore this.  These sequences are very short compared to the complete human genome, so maybe this is acceptable homology.  I don't know or even have an opinion.   

 

MK did not prove the existence of BF in my limited opinion.  I was careful not to conclude this in my review.  The results are very puzzling, which means MORE DATA is needed.  Someone else will have to decide if alternate interpretations of her results are plausible, and if the results were obtained by acceptable methodology.

 

I understand and, to a degree, share your skepticism about whether the published sequences are from a single real organism.  Much more research is needed.

 

I appreciate your good thoughts.  You're a "stand up" guy.  Keep in touch on this matter.  By the way, which ridges do you run?  I have loved walking on some of the beautiful ones in Canada.

 

Haskell   

[georgerm]

Hey, let's all take on step back and realize we all are very passionate about BF, or we wouldn't be spending hours and hours on the mystery. We are not going to achieve our goals by over heated arguments............let's cool down the rhetoric.

 

We have two obvious DNA experts dueling and two kill-no kill proponents. It seems as we all want the same goal, and that's to prove BF. We then want strict laws about shooting the creature. As we speak, one BF gets shot every month is my guess, and half go off and die. That's six dead BFs per year.

 

Once BF is proved, how do we stop the search and kill BF effort that could follow as Bipedal pointed out? Someone should be working on federal laws so when BF is proved, we are ready with a federal legislative bill. This needs to happen quickly or the taxidermist could be really busy. Guess how much a stuffed BF will bring? Even after DNA proof, it will take the political force months or even years to acknowledge BF.

[Guest njjohn]

You can't put the cart before the horse. Regardless of what experiences people have had, there is zero tangible proof of their existence that would be evidence enough for any political body to pass any laws at all. IF/When proof is established that is acceptable to the scientific community in the way of a proven theory that is testable and re-testable then and only then will elected officials put themselves out there to pass laws. 

 

From the comments from hvhart and ridgerunner, any future DNA tests are going to require full documentation. Sykes needs to make sure he doesn't just put things in a table and expect people to take his word. Even the 16 haplotypes don't prove relation to human because when you throw out samples that don't fit the time period of the hypothesis, it looks like you're forcing the science. And without all the submitters DNA reports that show their haplotypes, and the broken chains of custody there's no way to verify that each sample doesn't simply match the haplotype of the submitters or testers. I remember hearing from sources that samples were mixed up, so it becomes impossible to verify the table isn't just wrong without the full documentation. 

 

I think it's pretty telling that she refuses to talk to the BF community and has moved onto the larger alien theory community. I very much doubt we'll ever hear anything new about this study or the "experts" that were supposed to be looking into things. 

 

Honestly, if I've learned anything from this, it's that when you're collecting evidence, always come at it from a skeptical point of view. Don't jump to conclusions and rule everything out first. Make sure you know everything about the nature and wildlife in your area. Take a trapping course, even if you never trap in your life. You'll learn and be able to observe things you've never seen before while you're out in the woods. If you can follow the food sources of every predator in the forests, finding what feeds on them won't be much harder. Dot your I's and cross your T's and I don't think anyone will have any issues with taking you seriously. It's better to be sure than to "be right." 

[Oonjerah]

 

See the next to last paragraph about a long-standing ordinance

in Skamania county, WA, which makes it a felony to shoot/kill

a sasquatch. 

http://www.loweringthebar.net/2012/05/bigfoot-fair-game.html

 

I guess cart may go before horse depending upon locale. 

 

This combined with a 1975 Army Corps of Engineers manual

which states that BF is local fauna in parts of the state . . . well,

maybe in Washington, the acceptance of Bigfoot is greater

than the reflexive denial of him we see elsewhere.

 

One thing is sure, discussion of Bigfoot's legal rights belongs 

in it's own thread, and I believe such thread(s) already exist on

this forum. 

[southernyahoo]

You can't put the cart before the horse. Regardless of what experiences people have had, there is zero tangible proof of their existence that would be evidence enough for any political body to pass any laws at all. IF/When proof is established that is acceptable to the scientific community in the way of a proven theory that is testable and re-testable then and only then will elected officials put themselves out there to pass laws. 

 

From the comments from hvhart and ridgerunner, any future DNA tests are going to require full documentation. Sykes needs to make sure he doesn't just put things in a table and expect people to take his word. Even the 16 haplotypes don't prove relation to human because when you throw out samples that don't fit the time period of the hypothesis, it looks like you're forcing the science. And without all the submitters DNA reports that show their haplotypes, and the broken chains of custody there's no way to verify that each sample doesn't simply match the haplotype of the submitters or testers. I remember hearing from sources that samples were mixed up, so it becomes impossible to verify the table isn't just wrong without the full documentation. 

 

I think it's pretty telling that she refuses to talk to the BF community and has moved onto the larger alien theory community. I very much doubt we'll ever hear anything new about this study or the "experts" that were supposed to be looking into things. 

 

Honestly, if I've learned anything from this, it's that when you're collecting evidence, always come at it from a skeptical point of view. Don't jump to conclusions and rule everything out first. Make sure you know everything about the nature and wildlife in your area. Take a trapping course, even if you never trap in your life. You'll learn and be able to observe things you've never seen before while you're out in the woods. If you can follow the food sources of every predator in the forests, finding what feeds on them won't be much harder. Dot your I's and cross your T's and I don't think anyone will have any issues with taking you seriously. It's better to be sure than to "be right." 

 

 

Um, nijohn, if you have DNA that splits human haplotypes, it's human, okay? There is no evidence she obtained anything else from the mtDNA, except by her admission that some were identified as known animals other than human. No nonhuman apes showed up. What else could you do with that data set but look at the male lineage?