Guest Posted December 28, 2012 Share Posted December 28, 2012 (edited) bipedalist said: http://seqcore.brcf....eq/primers.html http://seqcore.brcf....eq/primers.html Read them both and you will be as informed as most BF researchers I'd imagine. The headaches for free, and gee doesn't look like there is any way such a process could ever go wrong?! Remember Ketchum was looking at three or four specific regions that had to do with MC1R, etc etc When in doubt: http://www.genome.gov/19016904 Thank you Bipedalist. I will read those links over the next few days.. Without opening either one, something tells me I should put an internet dictionary on standby.. LOL Apehuman said: If the primers are new, and untested by others, it would need to be peer-reviewed as a method to gain "approval." One could just apply for a patent, then produce a product w/o peer-review of course. But, to gain wide acceptance in the scientific community someone somewhere must replicate those results...for that primer, or whatever.... So, please correct me if I am wrong. If she simply used the primers she developed - before they passed any kind of peer review or a patent was applied for (and approved)-- could this spell problems for her paper? Would a Scientific Journal even consider publishing her work - if she had not yet passed through the process for her primers? I am going to assume she has not received a patent as of yet - I would think that would be big news.. "Scientist gets patent approval for Bigfoot DNA primer." My whole BF thing was supposed to be a few trips, one summer, for fun and relaxation..a Mythical being as backdrop for some me time in the forest...LOL....I am way past my intent on this one. That's how it starts for many.. I have never seen a Bigfoot - and I have been around for 7 years - I think you still have a few years left in ya Edited December 28, 2012 by Melissa Link to comment Share on other sites More sharing options...
Guest Posted December 28, 2012 Share Posted December 28, 2012 (edited) So, please correct me if I am wrong. If she simply used the primers she developed - before they passed any kind of peer review or a patent was applied for (and approved)-- could this spell problems for her paper? Would a Scientific Journal even consider publishing her work - if she had not yet passed through the process for her primers? I am going to assume she has not received a patent as of yet - I would think that would be big news.. "Scientist gets patent approval for Bigfoot DNA primer." I can't speak for a Journal's choice to publish, my perspective is when science is challenged in the courts. If she is using, and relying, on a novel method and/or analysis for her conclusions relative to her chosen hypothesis, then it is critical the underlying novel method be reliable or proven. If that underlying method isn't demonstrated as reliable through peer-review (or in some cases maybe authoritative texts, or even expert witnesses....but with novel methods experts are a plenty both sides) her work might be rejected as potential evidence on the existence of BF in a court...(it may get in too, but with little hope of winning the judgment - and I am assuming some type of case that is addressing "what Bigfoots are" .just talking ) . The legal standard of proof is a much tougher standard than we talk lightly here about proof or science....it is in most jurisdictions called the Daubert Standard for Scientific Evidence (at the Fed level, and most States, although it can vary at the state level) .I am sure Wikipedia has a great explanation, and all BFers so interested in proof via Government might want to read it. So, such a situation is not necessarily a death knell for her to publish (and science is about advancement through novel thinking so one hopes scientific Journals are eager), but ultimately proof, must be proven! Okay.. adios, I promised I wouldn't linger here too much, and I already blew it! Edited December 28, 2012 by apehuman Link to comment Share on other sites More sharing options...
Guest Posted December 28, 2012 Share Posted December 28, 2012 Apehuman said: The legal standard of proof is a much tougher standard than we talk lightly here about proof or science... Oh, on that we completely agree. In fact I have no problem with anything you said in that post. I can see from which direction you are coming from and your right, the standard is much higher. But - can she publish a paper if her science and methods are unproven? I would think without peer review of her primer and/or a patent on her primer this is still muddy waters for her... Could this be part of the reason why she is having trouble with publications? Just asking, cause I have no idea.. Link to comment Share on other sites More sharing options...
Guest slimwitless Posted December 28, 2012 Share Posted December 28, 2012 Did he? Link? Here's one from this morning. LINK The upshot is that he still feels the sample Melba tested is from a sasquatch. Link to comment Share on other sites More sharing options...
Guest mitchw Posted December 28, 2012 Share Posted December 28, 2012 (edited) Here is a delightful link to the world of designing primers. There goes the weekend, but at least I may have a better grip on what may or not be happening, subject to Journal disclosure policies, NDAs, sleepy time needs, and selective handholding. (I'm drinking Tito's vodka from Austin, Melba, in case you want to 'keep up') http://www.cybertory...sign/index.html Edited December 28, 2012 by mitchw Link to comment Share on other sites More sharing options...
Guest Posted December 28, 2012 Share Posted December 28, 2012 Does anyone else see the "out" the scientific community will possibly use to keep us in limbo for another year? Their problem will be with Ketchum having too develop a new primer... Can it possibly be the reason other alleged samples of BF came back as some other species? Does anyone else detect the smugness in Melba's interviews? There's a reason for that smugness and this subject gives me a possible reason. I also believe this is what the wait and big stink is about: Patenting the primers used. Are the other labs mad/jealous that she isn't sharing this discovery of hers if they are even aware? Will her work be dismissed because her primers haven't been peer-reviewed yet? Link to comment Share on other sites More sharing options...
Guest mitchw Posted December 28, 2012 Share Posted December 28, 2012 Primers are not oracles. They are short nucleotides that initiate the process of DNA copying. If you want to target a specific region of a chromosome, you need a primer suited to the task. We speculate here that Ketchum developed her own primers, but there's nothing extraordinary about custom primers. Link to comment Share on other sites More sharing options...
Guest Posted December 28, 2012 Share Posted December 28, 2012 Primers are not oracles. They are short nucleotides that initiate the process of DNA copying. If you want to target a specific region of a chromosome, you need a primer suited to the task. We speculate here that Ketchum developed her own primers, but there's nothing extraordinary about custom primers. But is it possible she found the right combination which enable her to detect BF? Link to comment Share on other sites More sharing options...
Guest Posted December 28, 2012 Share Posted December 28, 2012 (edited) Apehuman said: Oh, on that we completely agree. In fact I have no problem with anything you said in that post. I can see from which direction you are coming from and your right, the standard is much higher. But - can she publish a paper if her science and methods are unproven? I would think without peer review of her primer and/or a patent on her primer this is still muddy waters for her... Could this be part of the reason why she is having trouble with publications? Just asking, cause I have no idea.. Well, in theory publication through peer-review is supposed to take such novel claims (or methods) and put them to a test of sorts via the reviewers and if it passes, then on to the scientific community (or public).. What manner they test such a paper is not cut and dried, although most appear to be paper reviews. A nested novel method in a larger paper could be handled within that review it would seem to me. Yes, they can so publish, assuming whatever it is they are reviewing rises to the standard of that Journal, or ability of those reviewers...hence the long arguments, here and everywhere, on anything of import published by Journals, but as yet not widely accepted/replicated. If the work is valid it will survive that lengthy process, if not it becomes something on the heap...that might still hold value for some...there is no cut and dried way it seems...but in the end, if you have a paper and 400 or so of your peers cite to it in their own research, you won. Edited December 28, 2012 by apehuman Link to comment Share on other sites More sharing options...
Guest mitchw Posted December 28, 2012 Share Posted December 28, 2012 (edited) Delta Zu #12370 I gather that Ketchum had three hurdles. First, to get enough nuclear DNA from which to do any PCR polymerase work at all(the PCR multiplies the copies of your target DNA). Second, she needs to select sites on the DNA that she wants to investigate. Third, she needs primers that will bond to the DNA well enough for the PCR to proceed. Of course she also needs to make sure there was no contamination from the people collecting samples or doing the testing. (I'm not talking here about mitochondrial DNA workup. Only nuclear) Edited December 28, 2012 by mitchw Link to comment Share on other sites More sharing options...
Guest Posted December 28, 2012 Share Posted December 28, 2012 ^When you guys do get if figured out, please highlight the posts! I don't mind studying what counts, it just hard to choose now what that is! Link to comment Share on other sites More sharing options...
Guest Posted December 28, 2012 Share Posted December 28, 2012 Seeing as there are now patents on 1/4 of the human genome, seems there is a long way to go with Sasquatch! Which is a whole other issue...no one should be able to patent a naturally occuring genome. "Bioprospecting" is the biggest "land grab" in modern history. But is it possible she found the right combination which enable her to detect BF? IIRC, back when Monsterquest was having the Snelgrove Lake sample tested, they had to build an original primer to get past issues with the sample being contaminated by the metal in the screws reacting with the blood. Link to comment Share on other sites More sharing options...
bipedalist Posted December 28, 2012 BFF Patron Share Posted December 28, 2012 Delta Zu #12370 I gather that Ketchum had three hurdles. First, to get enough nuclear DNA from which to do any PCR polymerase work at all(the PCR multiplies the copies of your target DNA). Second, she needs to select sites on the DNA that she wants to investigate. Third, she needs primers that will bond to the DNA well enough for the PCR to proceed. Of course she also needs to make sure there was no contamination from the people collecting samples or doing the testing. (I'm not talking here about mitochondrial DNA workup. Only nuclear) Not to mention there needed to be a program of error-checking throughout the process. My understanding is that the problem is prob. not the primers if she did that. Paulides early on stated that she developed novel primers at his blog site. That was the huge hurdle that released the floodgates apparently. Link to comment Share on other sites More sharing options...
Guest mitchw Posted December 28, 2012 Share Posted December 28, 2012 (edited) BP, if you read that link I posted up at #12367, there's some information about the experimenter needing to control temperatures according to the behavior of her primers. Controlled temperature variation is what drives the bonding of nucleotide strands to each other. But like controlling for contamination by collectors or lab techs, these are practical issues. I wonder how Ketchum selected target sites which would support her conclusions. In Ketchum's C2C interview she spoke about supercomputers being required for her study, and it may be she was referring to the simulations that assist the researcher in creating primers. From my link, we can read that making novel primers requires much more computing power since there aren't readily available reference sequences.I don't think the Trent lab work went far in Ketchum's direction, since they write in their report that they used off-the-shelf primers for Human and Black Bear. Edited December 28, 2012 by mitchw Link to comment Share on other sites More sharing options...
bipedalist Posted December 28, 2012 BFF Patron Share Posted December 28, 2012 (edited) Right, their ---Trent's study techniques (to me) seem pretty dilute. Unless somebody can tell me why it appears short-cuts were taken (unless they just didn't comprehensively report what they did), I am less impressed by the minute. The chances that bear spit could have entered into the mix and knocked the study for a loop isn't gonna happen though. More likely the government beat them to the "bear". Yah, I linked to primers on primers earlier in the afternoon, seems like every thread has a link now. Hah! Edited December 28, 2012 by bipedalist Link to comment Share on other sites More sharing options...
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