I really don't understand the problem here. In ecotoxicology there are piles of standardized methods published in ASTM, AWWA, EPA. All you do is quote the standard and then tell how you modified it; if you did. So, with PCR you just cite the methodology and follow that with a sentence/paragraph or two of how you modified the former methods.
OLAY! its done and its concise. Malcolm On Mon, Jun 8, 2009 at 10:24 AM, Cara Lin Bridgman<[email protected]> wrote: > That's the problem with PCR. My students can't just write "We followed the > methods of Author (year)." because everyone does PCR slightly differently. > Times and temperatures and number of cycles vary--sometimes by miniscule > amounts--but they vary. > > PCR really is about following a cookbook, but the recipe constantly gets > tinkered with to improve results for the particular species, primers, > whatever. So, standardizing times and temperatures in my examples below > have probably confused things. Those temperatures and times and number of > cycles vary. Well, 94*C and 72*C are used in many studies, as are 35 > cycles. > > CL > > malcolm McCallum wrote: >> >> Just write "We Followed the PCR methods of AUTHOR (year)." >> >> Malcolm >> >> On Fri, Jun 5, 2009 at 9:28 AM, Cara Lin Bridgman<[email protected]> >> wrote: >>> >>> One of my students did a quick survey of 18 papers from 9 journals and >>> found >>> a total of four ways of describing conditions for PCR reactions. I’ve >>> tried >>> to standardize these examples for temperatures and times. >>> >>> Ten papers used this formula: “All PCR reactions included an initial >>> denaturation of 94*C for 30 s, 35 cycles of 94*C for 30 s, >>> 58*C for 45 s, and 72*C for 2 min, followed by a final elongation step at >>> 72*C for 7.” >>> >>> Five papers used this formula: “30 s denaturation at 95*C, 45 s annealing >>> at >>> 58*C and 2 min extension at 72*C, a final extension step of 7 min at >>> 72*C.” >>> >>> Two papers used this formula: “PCR cycling conditions of an initial >>> denaturation step (94*C, 30 s), followed by 35 cycles at 94*C (30 s), >>> 58*C >>> (45 s), 72*C (2 min) and a final extension step of 7 min at 72*C.” >>> >>> One paper used this formula: “The reaction was cycled 35 times with 94*C >>> (30 >>> s), 58*C (45 s) and 72*C (2 min).” >>> >>> The question is this: When writing your own paper, does using (or >>> copying) >>> one of these four ways constitute plagiarism? >>> >>> If it does constitute plagiarism, then are these papers plagiarizing each >>> other? Also, how does one go about describing methods for PCR reactions >>> without commiting plagiarism? My students and I agree that the ways are >>> rather limited--especially since there is not much diversity in these 18 >>> published papers. This is a real dilemma, because these conditions have >>> to >>> be described in each paper that uses PCR--the details in terms of times, >>> temperatures, and cycle number change with every study and every >>> experiment. >>> >>> If it does not constitute plagiarism, then how much of the descriptions >>> for >>> other methods (statistical analysis, definitions for formula, figure >>> legends, table titles, etc.) can be copied before it constitutes >>> plagiarism? >>> (My students and I can see a slippery slope here...) >>> >>> When writing her own PCR methods, my student tried going around this >>> problem >>> by finding a paper that came close to doing the same things she did, >>> citing >>> that paper, and adding a sentence to explain the changes in times or >>> temperatures to describe what she actually did. We do not find this a >>> very >>> satisfactory solution because my student did not use the cited paper when >>> actually deciding how to do her PCR reactions or in any other part of her >>> thesis. In other words, citing that paper gives it undue credit for >>> helping >>> her with her methods. >>> >>> Finding ourselves in an impasse, I told my students I'd ask you here at >>> Ecolog what you think and how you cope with these sorts of dilemmas. >>> >>> Thanks, >>> >>> CL >>> >>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >>> Cara Lin Bridgman [email protected] >>> >>> P.O. Box 013 Shinjhuang http://megaview.com.tw/~caralin >>> Longjing Township http://www.BugDorm.com >>> Taichung County 43499 >>> Taiwan Phone: 886-4-2632-5484 >>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >>> >> >> >> > > -- > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Cara Lin Bridgman [email protected] > > P.O. Box 013 Shinjhuang http://megaview.com.tw/~caralin > Longjing Township http://www.BugDorm.com > Taichung County 43499 > Taiwan Phone: 886-4-2632-5484 > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > -- Malcolm L. McCallum Associate Professor of Biology Texas A&M University-Texarkana Editor, Herpetological Conservation and Biology http://www.herpconbio.org http://www.twitter.com/herpconbio Fall Teaching Schedule & Office Hours: Landscape Ecology: T,R 10-11:40 pm Environmental Physiology: MW 1-2:40 pm Seminar: T 2:30-3:30pm Genetics: M 6-10pm Office Hours: M 3-6, T: 12-2, W: 3-4 1880's: "There's lots of good fish in the sea" W.S. Gilbert 1990's: Many fish stocks depleted due to overfishing, habitat loss, and pollution. 2000: Marine reserves, ecosystem restoration, and pollution reduction MAY help restore populations. 2022: Soylent Green is People! 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