The difficulty of replicating scientific methods - a personal story

                                                      

 Reposting from LinkedIn.  Someone I followed posted a paper about how hard it is to replicate biology experiments. 

I am immensely proud of my quinoa project that I help restart at BYU that has continued for the last 25 years. Academically, my part of the project wasn't a huge success, but it was a catalyst that has resulted in a continuous effort at BYU that has included the sequencing of the quinoa genome, work at KAUST, Bolivia, Chile, Peru, Morocco, Netherlands, and Poland on quinoa breeding and genomics. Alejandro Bonifacio, the quinoa breeder I worked with in Bolivia, is really the reason we all have eaten quinoa due to his work with PROINPA to promote quinoa and improved varieties and he saved the quinoa germplasm collection when it would have been lost.

For my master's thesis, I needed to make SSR markers for quinoa and then use them for measuring diversity in the germplasm and breeding populations and for building a genetic map. I used a method from a paper for making my library that used blunt-end cuts and ligation with enzymes, but I didn't know that the temperature needed to be higher or else you get chimaeric sequences in the plasmids.

This was found after I graduated by a reviewer that thought some of the markers were behaving oddly. We retracted the paper and my professors did additional sequencing and found a high percentage of chaemeric sequences, which I couldn't have seen since when I did the work there were no quinoa sequences to compare with. One of my professors was upset that we had to retract two papers and redo my microsatellite markers, in part because he was up for tenure and was not approved. He accused me of covering up the mistake in my thesis and academic dishonesty. I had to return to BYU on my own time and money to redo a significant amount of work and to defend myself. I replicated all of the key experiments in a short time and showed where the mistake came from and the department chair and other professors were on my side. I returned to TAMU and finished my PhD with overall a good relationship with my previous professors. Such a stressful situation that come from a very simple mistake.

It was a huge deal at a tough time in my life, all because I didn't know what temperature to set the water bath. After this I always contact authors for methods I want to replicate from their paper and recommend students to travel and work temporarily in other PI's labs to learn the nuances in techniques.

Biology experiments are not always replicate-able for lots of reasons, but it is tough to squeeze all of the details of experiments that take years into the few hundred words of a materials and methods section of a publication.