Guest Steve Byrne Posted March 24, 2013 Share Posted March 24, 2013 The restraint from "Man-Bear-Pig" references is impressive. Kudos to all, except me. Link to comment Share on other sites More sharing options...
Guest Posted March 25, 2013 Share Posted March 25, 2013 (edited) Another Facebook post from Dr. Ketchum, DVM: Dr. Melba Ketchum about an hour ago What people don't understand if they are not in the field of genomics/bioinformatics, when you have a genome that is novel, new and never sequenced, there is nothing to compare it to (in this case only small amounts of human sequence scattered about). Without anything to compare it to, it is extremely difficult to assemble. The contigs (sequences) we used in the manuscript took literally months to assemble and BLAST. Emphasis added. Also, in the comments section from her A. John Marsh Post. All emphasis mine. Please note that Ketchum's spokesperson is now admitting that Marsh is not a trained geneticist, but continues to claim that he is running a DNA lab. Archived here in case anything disappears: Dr. Melba Ketchum shared a link. Friday The following was a unsolicited commentary by A. John Marsh on a genealogy DNA page which scientists use to discuss mtDNA origin. This is not the complete discussion . However, it sums up the analysis. T2 BIGFOOTS FOUND IN 5 DIFFERENT STAT...MtDNA analysis of global populations support that major population expansions began before Neolithic www.nature.com Agriculture resulted in extensive population growths and human activities. However, whether major human expansions started after Neolithic Time still remained controversial. With the benefit of 1000 Genome Project, we were able to analyze a total of 910 samples from 11 populations in Africa, Europe… 1Like · · Share 22 people like this. Mark Fillman Let's see a bigfoot male with T2b Female, wouldn't that suggest that there were Bars around 13,000 years ago Friday at 7:41pm · Like · 4 Gary Stouffer What's all this mean for those of us with 60.1's IQ ? Friday at 7:56pm · Like Bill Connelly Federal grant dollars at work people. Friday at 9:14pm · Like Paula M. Brown I suppose it was just a matter of time, once they stopped snickering amongst themselves!, Friday at 10:45pm via mobile · Like Jim DiBattista So exciting Doctor, It's so good to read about REAL stuff, and not have to read about a faked dead sasquatch from a lying dirtbag. Thank you Friday at 10:52pm · Like · 2 Bigfoot Seekers Bigfoot is real. Yesterday at 2:43am · Like Chris Dorsey Gary, it means this is a human group that developed different mutations than you and I. When the hybrid pairing happened, the human female didn't have the mutations that we do today therefore zeroing in on the time when the hybridization occurred. It tells us that it is part human but didn't interact with us. Secondly it means this is real. You can't fake this science. It's consistent and repeatable. Great news. Keep it coming. Yesterday at 3:04pm via mobile · Like · 2 Pat H Meister Now, This is Very interesting ! And, further proof to back you up, Melba . Good bye to American Ape thoughts. 9 hours ago · Like · 1 Steve Alcorn John Marsh is an Architect, not a geneticist. 3 hours ago · Like · 1 Cathiee McMillan Steve, So what if he is a Archetict He is very organized with his DNA and I believe he has more experience with it and reading the results than some of the others in the BFF forums. Like Tyler and Bart who keep pushing a DNA report from a Person who loaded his Microsoft word program as Superme ruler of the universe. 3 hours ago · Like · 1 Cathiee McMillan He also seems to have figured out something by the Report and Paper that the others have failed to see. 3 hours ago · Like · 1 Robin Lynne Forestpeople Cathie you are so very right. Also Mr. Marsh runs Marsh Families Y-DNA Project, which , is a World wide project for anyone of the surname Marsh, or variants of Marsh, he also has web site at http://www.kin.marshdna.com/index.htm .He has been using Y-DNA to reconstruct the relatedness tree of all Marshes. It might be that in rapidly developing field of genetic genealogy, the amateurs pick up on things which the mainstream scientists have not noticed. 3 hours ago · Like Steve Alcorn I'm sure that Mr. Marsh is a very intelligent man. I'm sure the project that he heads is a great project. I am also sure that none of that matters because he is not a geneticist. 2 hours ago · Like Steve Alcorn Please don't consider this an attack on any individual. I think that if this study were ever to be taken seriously, referring to an Architect is not the way to go. 2 hours ago · Like Robin Lynne Forestpeople He has knowledge of genomics and we value the opinon of people that take the time to read and understand it. Im not critising you at all steve. We also have other scientist that are going over the paper and giving opinons. Whe we get them all gathered we will let people know. 2 hours ago · Like Robin Lynne Forestpeople It also occurs to me that if he understands this why is it so many others dont? I personally think that its because they dont understand it enough when they read it, or dont read it at all. Also are so busy hating everything because they are keeping it on a personal level not a professional one. Again only my opinon. However how can one critize something that they are not capable of understanding . hm........ just something to think about. 2 hours ago · Edited · Like David H. Swenson Please look at the data and not the messenger. Appeal to authority bespeaks a failure of argument. Marsh's study seems valid based on the data. 2 hours ago · Like · 1 SiniÅ¡a Soćanin One thing I'm sure of - I'll be quiet for a while now. 2 hours ago · Like Robin Lynne Forestpeople SiniÅ¡a Soćanin all we ask is that you use a open mind. about an hour ago · Like David H. Swenson Avoid bowing to authority. You decide about an hour ago · Like Robin Lynne Forestpeople exactly! about an hour ago · Like Haskell Hart Marsh's comments are strange. 73G and 263G are REQUIRED mutations for T2b when referenced to rCRS, which is H2a2a1. Check the established human phylotree at phylotree.org, build 15. Everybody on this thread should do this exercise for themselves. Also 146T, 16187C, 16189T are NOT required mutations for T2b. Apparently the data in Supplementary Data 2 of the paper are more human than Marsh's samples, or the mentioned phylotree is in error, or Marsh has misidentified his sample haplogroups. EVERY human haplogroup has 263G when referenced to rCRS except a very few with the reverse 263A mutation which cancels. This is because 263G is the first mutation encountered going from H2a2a1 to H2a2a and then on to ANY other haplogroup. Most of the samples in the paper of many different haplogroups(not just T2b) had 263G. "Please look at the data and not the messenger."(thanks to David H. Swenson). This applies whether you like the message or do not like the message. Einstein was a postal clerk. about an hour ago · Like Cathiee McMillan Also everyone keeps missing this fact in the Persons thing. The Marsh Families DNA Project is being run on a voluntary, non profit basis, by enthusiastic amateur genealogists, with an interest in contributing something of benefit to the wider community of Marsh genealogists around the World. Apart from John Marsh, there is a group of Marsh genealogist around the World, from different Marsh families, who lend moral support, and help out in various ways. We would welcome involvement from any other Marsh genealogists, so if you feel you have something to offer the project, in any way, we would be pleased to hear from you. 40 minutes ago · Like Haskell Hart I have contacted Mr. Marsh concerning his comments and asking for some clarifications. Hopefully, he'll have more light to shed. I caution against taking comments of "amateur genealogists" on ancestry.com as the final word on anything so complicated as the findings in the paper. 15 minutes ago · Like Edited March 25, 2013 by leisureclass Link to comment Share on other sites More sharing options...
Guest Posted March 25, 2013 Share Posted March 25, 2013 Archived here in case anything disappears: Thanks, that was quite the read Cathiee McMillan ...... Apart from John Marsh, there is a group of Marsh genealogist around the World, from different Marsh families, who lend moral support, and help out in various ways. We would welcome involvement from any other Marsh genealogists, so if you feel you have something to offer the project, in any way, we would be pleased to hear from you. Welcoming involvement from other Marsh's if they have something they can offer the project? Like a bigfoot family tree? Holy moly. Link to comment Share on other sites More sharing options...
Oonjerah Posted March 25, 2013 Share Posted March 25, 2013 Cathiee McMillan "Apart from John Marsh, there is a group of Marsh genealogist around the World, from different Marsh families, who lend moral support, and help out in various ways. We would welcome involvement from any other Marsh genealogists, so if you feel you have something to offer the project, in any way, we would be pleased to hear from you." I don't see the significance. The same is true for every common and many uncommon surnames. This getting together, sharing family info is what sites like Rootsweb and Ancestry.com are for. It's one of the most popular hobbies in the USA for the last decade or two. However ... I never did search Rootsweb for Bigfoot or Sasquatch. -- My bad. Link to comment Share on other sites More sharing options...
Guest Posted March 25, 2013 Share Posted March 25, 2013 A new posting on Dr. Ketchum, DVM's facebook page: Dr. Melba Ketchum · 1,585 like this 26 minutes ago · To those that arent finding all the data in the paper: The data is with the paper. It is in the Supplemental data files that can be downloaded with the paper. It gives the sequences that we used in the paper. The entire 3 terabytes of whole genome data is impossible to put out with the paper but we gave all of the sequence data we used in the paper. GenBank wouldn't take it when first sent to them. So we just provided what we used in the paper. Dr. Melba Ketchum 11 minutes ago Furthermore, we do have the entire dataset farmed out for independent evaluation but that takes time. 3 terabytes is a huge amount of data and just scratching the surface can take months. Uh, no. She does not provide the complete mtDNA sequences - only a table. She does not provide many of her assembled sequences, only 3. She does no provide the complete sequences of all of the sequences she talks about. Not that I expect this information to validate her claims, it may allow for a better understanding of how she came to her results. And yet now, she is providing the entire dataset for the independent evaluations? If that is not a clear acknowledgment that she has not provided all of the data, I don't know what is. Link to comment Share on other sites More sharing options...
Guest Posted March 25, 2013 Share Posted March 25, 2013 The best part in all this....she claimed in the past to have field experience observing BF, even at one point claiming she'd heard them speak. Why not release a single photo to regain just a little bit of the cred she had within Bigfoot circles? Apparently there were photos and video as part of the data...at least that was the claim. I know why, because the evidence does not exist...because Bigfoot does not exist! There, that was easy! Bigfoot does not exist..only Bigfootery does! Link to comment Share on other sites More sharing options...
Guest Posted March 25, 2013 Share Posted March 25, 2013 (edited) Another Facebook post from Dr. Ketchum, DVM: Dr. Melba Ketchum about an hour ago What people don't understand if they are not in the field of genomics/bioinformatics, when you have a genome that is novel, new and never sequenced, there is nothing to compare it to (in this case only small amounts of human sequence scattered about). Without anything to compare it to, it is extremely difficult to assemble. The contigs (sequences) we used in the manuscript took literally months to assemble and BLAST. If this is the case, WHY did she use human CH11 as a reference for assembly? And why is MK calling this Homo sapiens cognatus? The sequence provided has nothing to do with biology. The three nuDNA sequences are not even related to eachother! The fact that she says there is nothing to compare it to just points to the fact the MK knows little of both genomics and bioinformatics. And yes the contigs took months to assemble because they are garbage - if you do not recognize contamination in your sample and then attempt to assemble, this is exactly what you get - garbage with just "small amounts of human sequences scattered about". Edited March 25, 2013 by ridgerunner Link to comment Share on other sites More sharing options...
Guest Posted March 25, 2013 Share Posted March 25, 2013 I would have plussed you Ridge, but I used mine earlier today. You have said it all. Melba's contradictions are beginning to contradict earlier contradictions Genes Link to comment Share on other sites More sharing options...
Oonjerah Posted March 25, 2013 Share Posted March 25, 2013 Plus 1, ridgerunner. Thanks for bringing the garbage out. Link to comment Share on other sites More sharing options...
Guest Posted March 25, 2013 Share Posted March 25, 2013 A new posting on Dr. Ketchum, DVM's facebook page: Dr. Melba Ketchum · 1,585 like this 26 minutes ago · To those that arent finding all the data in the paper: The data is with the paper. It is in the Supplemental data files that can be downloaded with the paper. It gives the sequences that we used in the paper. The entire 3 terabytes of whole genome data is impossible to put out with the paper but we gave all of the sequence data we used in the paper. GenBank wouldn't take it when first sent to them. So we just provided what we used in the paper. Dr. Melba Ketchum 11 minutes ago Furthermore, we do have the entire dataset farmed out for independent evaluation but that takes time. 3 terabytes is a huge amount of data and just scratching the surface can take months. Uh, no. She does not provide the complete mtDNA sequences - only a table. She does not provide many of her assembled sequences, only 3. She does no provide the complete sequences of all of the sequences she talks about. Not that I expect this information to validate her claims, it may allow for a better understanding of how she came to her results. And yet now, she is providing the entire dataset for the independent evaluations? If that is not a clear acknowledgment that she has not provided all of the data, I don't know what is. RR, is a genome really 3 terrabytes in size? I was under the impression it was much smaller. Link to comment Share on other sites More sharing options...
Guest thermalman Posted March 25, 2013 Share Posted March 25, 2013 The best part in all this....she claimed in the past to have field experience observing BF, even at one point claiming she'd heard them speak. Why not release a single photo to regain just a little bit of the cred she had within Bigfoot circles? Apparently there were photos and video as part of the data...at least that was the claim. I know why, because the evidence does not exist...because Bigfoot does not exist! There, that was easy! Bigfoot does not exist..only Bigfootery does! Explain your theory to all those who have seen a real living BF up close. Are they all liars? Link to comment Share on other sites More sharing options...
Guest maelsquatch Posted March 25, 2013 Share Posted March 25, 2013 For my inaugural on-topic post here on BFF, I figured I'd wade into this brier patch and give my 2 cents. There have been many arguments for and against the validity of the study in this thread alone, but two of the things that trouble me the most about Ketchum's report I haven't seen mentioned (and I read the whole 99 pages of posts but may have missed it if these points have been brought up.). The first thing is the report states that: ...electron micrographs of the DNA isolated from these samples show patches of double- and single-stranded DNA intermixed. This is extremely troubling to me as no known organism that I could find has DNA structure like this. The only thing I could find that had any single-stranded DNA were viruses. The best explanation for this odd occurrence I found was on the Ars Technica page. This is what you might expect if two distantly related species had their DNA mixed—the protein-coding sequences would hybridize, and the intervening sections wouldn’t. All of this suggests modern human DNA intermingled with some other contaminant. So in this case we either have contamination or an organism with a novel DNA structure. I found nothing in the report that would explain why this odd DNA structure is occurring, and for something as big as this (and I believe it is HUGE if accurate), there should be more than just an "Oh, by the way, the DNA looked funky." Crap, finding an organism with DNA that has both double- and single- stranded DNA intermixed is a whole paper in itself! The other thing that bothers me is that all of the mtDNA tested in the study is identified as modern human. All of it. From the paper: After extensive forensic controls to prevent contamination, mtDNA testing of the Sasquatch samples yielded fully modern human profiles. Sixteen haplotypes indicating 100% homology with modern human mtDNA sequences were observed from 20 completed whole and 10 partial mitochondrial genomes. What troubles me is the number of different haplotypes identified. In order for all the halpotypes identified to be present in the BF population, then either multiple hybridization events had to occur or the mtDNA in the BF population underwent the exact same mutations as it did in the human population. I think the probability of the latter is extremely unlikely so I will not discuss that here. We are left with multiple hybridizations. So now not only was there the initial hybridization event occuring ~15,000 years ago, but there were at least 15 other events since then. And some of these haplotypes could only have arrived with the European colonization of the Americas (most of the haplotypes are "European or Middle Eastern in origin"), then most these hybridization events have happened within the last 1000 years or so. Under this scenario, I would have expected to see one, maybe two, haplotypes represented significantly more than the others. As far as I can tell, this was not the case. Also, there was no non-human mtDNA reported. This would mean that every mtDNA donor was a direct descendant of one of these hybridization events. I would expect to see at least one sample whose maternal line was not a direct descendant of a human. Perhaps a larger sample size would reveal non-human mtDNA. I really wanted this paper to provide compelling evidence that there is something undocumented roaming the woods in North America, but I don't think it did. My conclusion is that the paper as presented is flawed and does not support the conclusions it makes. Perhaps the full data set generated by Dr. Ketchum's work will provide evidence of a new hominin. Please understand that I am NOT a gentisist by any means, but I do have a basic grasp of how DNA is inherited. I do expect some of y'all to poke holes in my conclusions and if you can make me understand what's going on better, I welcome it. maelbearpig 2 Link to comment Share on other sites More sharing options...
AaronD Posted March 25, 2013 Share Posted March 25, 2013 ^ Wow maelsquatch, very impressive initiation to the forums--welcome!!! Link to comment Share on other sites More sharing options...
Guest J Sasq Doe Posted March 25, 2013 Share Posted March 25, 2013 Pure comedy! I love the logic behind their confirmation bias. A bunch of people who can't spell who constantly attack people versed in genetics is insane beyond comprehension, but it is hilarious! I guess that's just the nature of the anti-Ketchum camp. More fun than a barrel of lemurs as they trip over each other trying to arrive at a conclusion that cannot be arrived at until all of the data is released. Link to comment Share on other sites More sharing options...
Guest Posted March 25, 2013 Share Posted March 25, 2013 For my inaugural on-topic post here on BFF, I figured I'd wade into this brier patch and give my 2 cents. There have been many arguments for and against the validity of the study in this thread alone, but two of the things that trouble me the most about Ketchum's report I haven't seen mentioned (and I read the whole 99 pages of posts but may have missed it if these points have been brought up.). The first thing is the report states that: ...electron micrographs of the DNA isolated from these samples show patches of double- and single-stranded DNA intermixed. This is extremely troubling to me as no known organism that I could find has DNA structure like this. The only thing I could find that had any single-stranded DNA were viruses. The best explanation for this odd occurrence I found was on the Ars Technica page. This is what you might expect if two distantly related species had their DNA mixed—the protein-coding sequences would hybridize, and the intervening sections wouldn’t. All of this suggests modern human DNA intermingled with some other contaminant. So in this case we either have contamination or an organism with a novel DNA structure. I found nothing in the report that would explain why this odd DNA structure is occurring, and for something as big as this (and I believe it is HUGE if accurate), there should be more than just an "Oh, by the way, the DNA looked funky." Crap, finding an organism with DNA that has both double- and single- stranded DNA intermixed is a whole paper in itself! The other thing that bothers me is that all of the mtDNA tested in the study is identified as modern human. All of it. From the paper: After extensive forensic controls to prevent contamination, mtDNA testing of the Sasquatch samples yielded fully modern human profiles. Sixteen haplotypes indicating 100% homology with modern human mtDNA sequences were observed from 20 completed whole and 10 partial mitochondrial genomes. What troubles me is the number of different haplotypes identified. In order for all the halpotypes identified to be present in the BF population, then either multiple hybridization events had to occur or the mtDNA in the BF population underwent the exact same mutations as it did in the human population. I think the probability of the latter is extremely unlikely so I will not discuss that here. We are left with multiple hybridizations. So now not only was there the initial hybridization event occuring ~15,000 years ago, but there were at least 15 other events since then. And some of these haplotypes could only have arrived with the European colonization of the Americas (most of the haplotypes are "European or Middle Eastern in origin"), then most these hybridization events have happened within the last 1000 years or so. Under this scenario, I would have expected to see one, maybe two, haplotypes represented significantly more than the others. As far as I can tell, this was not the case. Also, there was no non-human mtDNA reported. This would mean that every mtDNA donor was a direct descendant of one of these hybridization events. I would expect to see at least one sample whose maternal line was not a direct descendant of a human. Perhaps a larger sample size would reveal non-human mtDNA. I really wanted this paper to provide compelling evidence that there is something undocumented roaming the woods in North America, but I don't think it did. My conclusion is that the paper as presented is flawed and does not support the conclusions it makes. Perhaps the full data set generated by Dr. Ketchum's work will provide evidence of a new hominin. Please understand that I am NOT a gentisist by any means, but I do have a basic grasp of how DNA is inherited. I do expect some of y'all to poke holes in my conclusions and if you can make me understand what's going on better, I welcome it. maelbearpig Welcome maelsquatch, Nice post, and I totally agree. I had been following this study for just over one year before it was published and truly thought it had promise. Until information came out that lead me to ask a few of the same questions you have here. I just cannot see how contamination can be ruled out and the ONLY explanation that is EVER offered is "After extensive forensic controls to prevent contamination." But, for a finding of this magnitude that "explanation" just isn't enough. I then saw how this entire thing was going to play out, and called it, and was beat down rather hard for that - and you guys know who you are. This is where it started to fall apart for me. There are far, far too many questions raised with no real answers. Commence the beat down... Link to comment Share on other sites More sharing options...
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