Guest mdhunter Posted October 19, 2012 Share Posted October 19, 2012 I wouldn't think anyone would submit for peer review if the results hadn't been reproduced by different labs. I believe that was discussed earlier in the thread( that they were tested by different labs). That would rule out contamination long before it got to peer review. Link to comment Share on other sites More sharing options...
southernyahoo Posted October 19, 2012 Share Posted October 19, 2012 With a number of labs testing and tests to replicate results, I am going out on a limb here and suggest that they will be able to rule out contamination. In the end I think so, there is a point where they must have confidence in a pure sequence, otherwise the sequences in genbank would not be considered reliable comparison data. How many samples of Native American DNA are in Genebank? If there is a low number of samples... That would explain the modern human DNA that doesn't quite fall in normal human range Genebank samples, no? What do you guys think? I don't know how many complete Native American mito's are in genbank, but science seems to be familiar with their haplogroups. Link to comment Share on other sites More sharing options...
Guest Posted October 20, 2012 Share Posted October 20, 2012 How many samples of Native American DNA are in Genebank? If there is a low number of samples... That would explain the modern human DNA that doesn't quite fall in normal human range Genebank samples, no? What do you guys think? No it doesn't. N Americans are a distinct race, yes, but they are 100% Homo Sapiens Sapiens (modern man). And modern man is well represented in Genebank and it's analogs. Maybe the samples had human DNA contamination from the collector/submitter. That could skew the Mitochondrial DNA results but not the nuclear as I understand it. No, it would skew BOTH results. The mtDNA is the human result yes? yes Link to comment Share on other sites More sharing options...
Guest Posted October 20, 2012 Share Posted October 20, 2012 Their DNA and its variances from the existing sequences would add to the Homo Sapien range. So there are several places left in the world we still need genetic profiles from the indigenous peoples to have a complete view of Homo Sapien and what variances in DNA are possible between homo sapiens. Without having all the information the picture has less resolution. Most contaminants would come from a source that would not contain much/any nuDNA material. Skin oil, hair, sweat and others. Link to comment Share on other sites More sharing options...
Guest crabshack Posted October 20, 2012 Share Posted October 20, 2012 Still doesn't explain that the nuDNA differs so vastly from the mtDNA. Because it may have been never meant to mix. Link to comment Share on other sites More sharing options...
Guest Posted October 21, 2012 Share Posted October 21, 2012 I wouldn't think anyone would submit for peer review if the results hadn't been reproduced by different labs. I believe that was discussed earlier in the thread( that they were tested by different labs). That would rule out contamination long before it got to peer review. i think that there is a widespread misunderstanding of what peer review actually accomplishes. Nature, possible the world's most respected scientific journal often publishes articles discussing the good, the bad , and the ugly of peer review. i'll list a few articles below. i ask only that you frame your view of what this alleged article by ms. ketchum will truly represent by taking to heart the following: Quality and value: The true purpose of peer review http://www.nature.com/nature/peerreview/debate/nature05032.html Demystifying peer review http://www.nature.com/ncb/journal/v12/n5/full/ncb0510-413a.html Perspective: Does peer review mean the same to the public as it does to scientists? http://www.nature.com/nature/peerreview/debate/nature05009.html and finally, what i think is the most inportant of this collection... Ethics: Increasing accountability In order to function well, the journal peer-review system relies on the the integrity and accountability of authors, editors and reviewers. Each may behave unethically in the competitive world of science. Although we do not know how often crimes occur, forms of misconduct could include stealing or suppressing ideas and information, favouritism, and misleading reviews. Financial or personal competing interests can provide the motivation for misconduct. Failure to disclose these has eroded the credibility of scientific research and public trust in the publication process. http://www.nature.com/nature/peerreview/debate/nature05007.html the most important thing that the reader must realize about a peer reviewed work is that the review DOES NOT validate the author's results, it only attempts to validate that the proper scientific rigor was followed in determining them. it does not uncover bad data, dishonest representations of data, or outright lies, it can only attempt to verify that the author went about determining the findings in the proper manner. one needs to look no further than the 1998 research paper published in The Lancet that connected vaccinations with autism (link below). that paper was entirey fraudulent and The Lancet was forced to retract it's publication. original paper http://www.lancet.com/journals/lancet/article/PIIS0140-6736%2805%2975696-8/fulltext an article chronicaling the fraud http://briandeer.com/mmr/lancet-summary.htm Link to comment Share on other sites More sharing options...
Guest Posted October 21, 2012 Share Posted October 21, 2012 Well, well, well, That's interesting. I have feeling that the Sykes report and Ketchums are going to be on the opposite sides of the scale. Link to comment Share on other sites More sharing options...
Guest icicle Posted October 21, 2012 Share Posted October 21, 2012 Hajibabaei used a broad primer that targets a very small segment of DNA (100bp) (Barcode method.) He wouldn't have known he was looking at squatch DNA even if he did get primate DNA. This paper outlines the problems with it. http://spectrum.libr..._Genome2006.pdf I was wondering why Ketchum was making her own primers. I still don't quite understand what primers are. Filters? So you don't have to look at all the code? Are there really so many base pairs that a whole genome cannot be looked at, all at once, and compared with sapiens, chimps and gorillas? Sorry for the noob questions. New to DNA. Link to comment Share on other sites More sharing options...
Guest mdhunter Posted October 21, 2012 Share Posted October 21, 2012 @ Slappy Please make no mistake or assumption. I fully comprehend every link you posted. I also fully comprehend bad science makes it through. I have just never posted my full thoughts on the scientific community and won't(it would be a boring book). The peer review process is still the best available at this date and time. I also fully understand "bucking the system" and "putting egg on the wrong face". Ethics and integrity seem to not be at the forefront of many arenas anymore. Even though I am not familiar with all the journals, I am familiar with hierarchy and reputable. That does not mean I believe everything I read. That also does not mean I would trust any layman's version either. As to your most important quote. I agree. And that can be interpreted several ways to the results of this study and others. It can also be applied to almost anything of competitive nature where money and/or prestige are involved. Prestige alone is enough to make some people lie,cheat and steal. I won't even speculate on whether any party involved in these DNA studies is involved in favoritism, suppression,cheating, or any corruption. That is for after the reports are out and subject to scrutiny from the rest of the scientific community. Then it is still "pick the side you trust" @ Icicle, somebody earlier in this thread or the Sykes thread gave a pretty good layman's description of primers, how they are used and how they work. Link to comment Share on other sites More sharing options...
Guest icicle Posted October 21, 2012 Share Posted October 21, 2012 Ah, still only on about page 40. By the time I get to the end of this thread, I'll maybe understand enough so that I can start again at page 1 and understand it. Link to comment Share on other sites More sharing options...
Guest Posted October 21, 2012 Share Posted October 21, 2012 i think that there is a widespread misunderstanding of what peer review actually accomplishes. Nature, possible the world's most respected scientific journal often publishes articles discussing the good, the bad , and the ugly of peer review. i'll list a few articles below. i ask only that you frame your view of what this alleged article by ms. ketchum will truly represent by taking to heart the following: Quality and value: The true purpose of peer review http://www.nature.co...ature05032.html Demystifying peer review http://www.nature.co...b0510-413a.html Perspective: Does peer review mean the same to the public as it does to scientists? http://www.nature.co...ature05009.html and finally, what i think is the most inportant of this collection... Ethics: Increasing accountability http://www.nature.co...ature05007.html the most important thing that the reader must realize about a peer reviewed work is that the review DOES NOT validate the author's results, it only attempts to validate that the proper scientific rigor was followed in determining them. it does not uncover bad data, dishonest representations of data, or outright lies, it can only attempt to verify that the author went about determining the findings in the proper manner. one needs to look no further than the 1998 research paper published in The Lancet that connected vaccinations with autism (link below). that paper was entirey fraudulent and The Lancet was forced to retract it's publication. original paper http://www.lancet.co...5696-8/fulltext an article chronicaling the fraud http://briandeer.com...cet-summary.htm Thanks for conclusively demonstrating that when Skeptics hold up "peer-reviewed papers" as the Gold standard for truth and accuracy they're talking out their hoo-has! Link to comment Share on other sites More sharing options...
Guest BFSleuth Posted October 21, 2012 Share Posted October 21, 2012 Ah, still only on about page 40. By the time I get to the end of this thread, I'll maybe understand enough so that I can start again at page 1 and understand it. Arrrrggghhhh! Anyone with the fortitude to read through this entire thread in order to find snippets of important content has my greatest sympathy.... .... there's an easier way. When you are in this thread type the word "primer" in the search function at the top right of the web page. Note that while you are in this thread the search function says "This Topic", so you will be searching only the Ketchum thread for any post that includes the word "primer". The result will yield 2 pages of posts that discuss primers and will be a quick and valuable way for anyone to get a quick bit of knowledge from our members, with particular discussion about possible challenges and potential methods of Dr. Ketchum. You can search particular threads (topics) or certain forums in this manner. Another example is if you are interested in only reading the posts of a particular member in a thread or forum you can use detailed search function. Happy abbreviated reading.... Link to comment Share on other sites More sharing options...
BobZenor Posted October 21, 2012 Share Posted October 21, 2012 I was wondering why Ketchum was making her own primers. I still don't quite understand what primers are. Filters? So you don't have to look at all the code? Are there really so many base pairs that a whole genome cannot be looked at, all at once, and compared with sapiens, chimps and gorillas? Sorry for the noob questions. New to DNA. I have heard they did sequence the entire genome. The primers should still be useful if you want to sequence genes from a suspected sasquatch. IF they sequenced the entire genome those tests of specific genes or parts of genes obviously wouldn't be as definitive since all genes are sequenced. The primers are more for screening and sequencing parts of specific genes I would think. If the whole genome were sequenced they could easily target regions and select what primer to use so I would imagine that making the primers was done before the sequencing of the entire genome. It seems a bit superfluous now as far proving sasquatch if they have entire genomes. She might have other uses for them planned. The machines that do the entire genome apparently automate some of that like what primer to use. They do entire genomes for a few thousand dollars now. I don't recall for sure since I have a difficult time forming new memories but I believe it was something like a couple of weeks and $5,000.00 to do an entire genome. It seems like the technology to sequence a whole genome has made leaps and bound even since her bigfoot project came out. It is hard to keep up with. I am guessing that sequencing the entire genome might have complicated the study by adding much more data and opportunities. Some of the peers might have wanted greater verification. This is good explanation of what primers are. Apparently the main enzyme that makes DNA can only add to an existing chain and primers are long enough sequences to select end and starting points to replicate. 2 Link to comment Share on other sites More sharing options...
Guest gershake Posted October 21, 2012 Share Posted October 21, 2012 BobZenor, you're still one of my favourite posters. You explain complex matters in a way that laymen like me can understand and appreciate. Thanks. Link to comment Share on other sites More sharing options...
Guest icicle Posted October 21, 2012 Share Posted October 21, 2012 (edited) Thank you BFSleuth and BobZenor! BF I shall take up your suggestion immediately, and Bob - when youtube starts working for me again (soon) I'll watch that too. I've been watching the Illumina instructional videos, and more or less understand the process, but there are bits and pieces they just assume you know. I'm trying to work out exactly why the paper did not get published a year ago. I'm pretty sure it wasn't for 'no testable hypothesis' or the subject matter, and whatever it was wasn't glaringly obvious, therefore it was the central premise, or the evidence for it, or an extraordinary burden of proof. At any rate it comes down to the DNA. And it was after that she started making her own primers, wasn't it? If primers increase the accuracy of reading specific sequences, then how on earth do you know where to look when human primers aren't enough? Anywhere not highly conserved? Conserved since when? We left the trees? It must be hard to design a primer when you don't even have a skeleton to look at - or perhaps the mtDNA established the divergence point? - Still I don't think SNPs come with date stamps, exactly, so its going to be a long job. And why publish a paper without the required mathematical certainty? I am beginning to see why this paper is taking so long. Its waiting for Moores Law to provide the computational power Edited October 21, 2012 by icicle Link to comment Share on other sites More sharing options...
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