What should I do in front of a McGill University Professor who does not care abo - (Apr/29/2015 )

I learned about these mistakes and "mistakes" as one of the very first thing at all in my scientific life.

 

On a masters program (that is basically the only college one there was at a time, Bc. programs were very rare on our universities then, you just got all 5 years at once and then masters), my first individual task on the diploma project. My supervisor gave me a paper about qPCR for a virus and asked me, what would I do first, when I want to use them. I finally guessed I should probably check them on some sample even if they are published to work and he said, "check them before ordering.. do you know what tools to use?" He told me and after some hours and rechecks I get back to him and I told him, surprised, that the published primers have a single bp mismatch that only aligns with one of the two virus strains. I was so shocked that they didn't mentioned it in the paper. My supervisor told me to design my own, correct then. Those were the first primers I ever designed :)

Trof on Wed Apr 29 21:08:42 2015 said:

I'm not sure if you are supposed to find fake papers or what, but true is many times there, the primers are wrong or have a mismatch not mentioned (mismatch can be tolerated in old papers, but not in new).

 

I think truth is, people just plainly don't care much about correct sequence and use primers that "their grandma used " (haha) and never check them later cause they "work", or they mistakenly switch the sequences for other primers, or for a reason of keeping them secret they intentionally don't publish the right ones, because this is so common that you can always say it was a mistake.

 

This of course is not true in "methodic" paper, since everyone will try it and find it doesn't work.. but in common papers.. primes, who cares..

 

My boss says, the better impact the less they care about what details of PCR you state, if you are putting it into lesser impact they will want to know exactly the sequences and conditions, if you were to publish in Nature? No one cares..

So mistakes are common and even if it's sometimes intentional probably, it doesn't mean the data are fake. But it is wrong to do so. Without primer sequence you cannot check for potential problems thay the study may not have addressed (like... later will be found, that these primers bind nonspecifically... it is important to include this right).
But I suppose it is considered a minor problem, faka data on the other hand is a serious scientific misconduct.

 

That is interesting, Trof. I would've thought the higher impact the journal, the MORE scrutiny you'd get about details like primers, since the readership is higher.

Michael Starr on Mon Mar 28 23:45:21 2016 said:

That is interesting, Trof. I would've thought the higher impact the journal, the MORE scrutiny you'd get about details like primers, since the readership is higher.

Yes and no. The high tier journals you can't just publish in like in any others. You need to have a name (or know someone to have a name or optionaly promise something so cool that the editors will be eager to push it). So, while you publish there, you are a well known leader in the filed, or rising star (or the paper has both) so noone bothers that much about the little details. They go for the cool story, many higher IF journals will reject saying the topic is not interesting enough or doesn't have a novel clear messaage, in other words, not cool. It's not that the data are bad, they just not that sexy to be in their journal.

I repetedly hate people publishing in Nature for using non-HGVS nomenclature for mutations for example. If you want to publish a devilishly difficult gene insertion in Human Mutation, you need to spend week in email correspondence with one of the curators to get even the notation right, because it is such a complicated mess. The journal would refuse to publish without a correct mutation name.
Now Nature? Who cares, it's sexy! (it is, though)

Then I sit with clinical diagnosticians and they ask me, which one is right.. the one by HGVS or the one everyone is using, even that famous paper in Nature.. what can you say?

You would think that top journals need to have a more rigorous control of the data, but they likely more rely on the people-basis than the data itself and more important is how cool the story is. Mostly they are right and the data are correct and cool at the same time. But sometimes, as with the case of the famous arsenic eating bacteria in Science.. it was soo cool and so anticipated, that it blinded them so much to miss the major flaws in the paper, and many objections were found within the second day the paper was out. Those would be caught by some sceptical-style reiewer, but for some reason they were not. Coolness won.

In Canada, educated people have low knowledge, especially authorities.

And the problem is they do not care too.

 

This is why the Canadian are successful in two jobs in US, because these jobs need low knowledge and talkative persons:

1) Comedian 2) Singer

 

Those who think Canada is the best and the Canada Health checks every thing, should see this:

 

Toxic jewelry: What’s in the cheap jewelry you buy (some had 100% cadmium even in Sears)

http://www.cbc.ca/marketplace/episodes/2015-2016/toxic-jewelry

https://www.youtube.com/watch?v=208-irQ1Yus

 

 

Canada does not do anything. They just sit and wait for US authority's decisions.

These two happened during past 3 years:

If US warns for a contaminated beef, 3 days after that, Canada warns for it.

If US warns for Tsunami, 3 days after, Canada warns for it.