Hi Malcolm,
You know, some of the problem may be a case of bad habits among those
using PCR techniques (and other research tools, since it isn't just a
PCR problem). Published papers are not citing the original paper that
came up with the whole idea. They are not citing a standard lab manual.
I've requested my students to do one or the other and then explain the
changes. My students, looking at the papers in their field, seem to
think that's not the way to go. Instead, everyone (published papers, my
students) is 'reinventing the wheel' and redefining the wheel--all
without citation.
In fact, in summarizing Ecolog responses to my class last night, that's
what I told them. I suggested that they should find the original PCR
paper. One reason I gave is that since everyone is citing more recent
papers, maybe some errors have crept into the entire protocol. It's all
part of doing the library research of your research project--you have to
check and confirm and the best way is by digging out the original papers.
So, I agree with you. I guess the bottom line of all this (talk about
an idiom-filled email) is for me to be more confident in insisting my
students try it the right way: cite and explain any changes.
CL
malcolm McCallum wrote:
> 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:
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)."
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Taichung County 43499
Taiwan Phone: 886-4-2632-5484
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