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.

Airplane novels. Judging books by their covers

While I have been travelling, I have splurged on books.  Two reasons, simplest is that I am waiting for flights for too long and the best shop in any airport is the bookstore.  The other is I want to bring something home.  I used to buy wall hangings, but there are only so many wall hangings I can put up and I have too many sitting in closets already.  I usually get some chocolate or local treat to bring back to share, but that disappears very fast especially if it is fancy.  Books seem practical and easy to transport.  I want to have bookstores and decided that I needed to spend some money in them if I wanted them to flourish.  

I have been buying books, but I am biased by ones that look cool.  The better the cover, the more likely I am to buy it.  I also am biased by size, I don't want a 1000 page hardcover tome that I won't finish even on a 14 hour flight to Addis.  My usual genre is science fiction, and that dominates what I have on my kindle, but I have tried to branch outside of that genre. 

Bookstore: Near the Zocalo and museum in Mexico City

Title: Asesina Íntima 

Author: Bernardo Esquinca

Review: I bought both of the Spanish language books on this list when I was in Mexico City for a visit to CIMMYT purchased last year when I was doing a project review for Gates Foundation.  I asked the owner of the bookstore for some recommendations for something that wasn't a translation of an English language novel, but also wasn't like Borges or "literature".  I wanted something that was fun, or different.  Both of his recommendations were different, but I wouldn't say either was fun.  

I tried to like this book.  It is the story of a middle aged wrestler that was convicted of murdering 40 women.  This is based on a true story - Juana Barraza Samperio. It is not a linear narrative, but more like versions of this story told from different perspectives.  The first was my favorite, but I wasn't as interested in some of the other characters version of the events.  

Would I recommend? Yes, but you would have to like true crime more than I do.  This would be a great podcast.  The audiobook could be amazing if you had different voice actors when the narrative voice shifts.  

Bookstore:  Near the Zocalo and museum in Mexico City.  

Title: Trece Latas de Atún

Author: Bernardo Esquinca

Review: This was the shop owners second recommendation.  I think this is the "fun" pick.  It is short and also not a linear narrative.  This feels like someone's diary, but it also is a bit like poetry or short stories.  Some of it is true - biographical sketches from the life of Amandititita - Amanda Escalante Pimentel, daughter of Rockdrigo Gonzalez .  He was a famous rock guitarist that died in an earthquake in Mexico City.  Amandititita's music is a lot like this book - funny, punk, absurd, and angry.  

I have read this through a couple of times.  It is easy to fly through because each entry is short and the whole book is like 120 pages.  I am not sure how this got published or what it is trying to say/do.  Does it have a message? I don't know.  It is voyeuristic, like reading a found diary. But like her music, it is winking at you because she knows it is voyeurism and knowing and doing it on purpose make it something else.   

Would I recommend? Maybe not.  It is vulnerable, funny, emotional, and bizarre, but I am not sure it is something most people would like. 

Bookstore: Kenya International Airport

Title: Death of the Author

Author: Nnedi Okorafor

Review: Okorafor is one of my favorite science fiction authors.  She has won a pile of awards.  I highly recommend her Binti trilogy that is about an Himba girl that leaves Earth to attend an alien university.  During the spaceflight, they are boarded and attacked by almost jellyfish like aliens that kill everyone else on board.  She survives because the aliens react to her otjize - a clay and aromatic mixture that her culture wears on their skin and hair.  

This book is probably still science fiction, but also somewhat autobiographical, but also not, and so is more contemporary fiction than classic sci fi.  It isn't a book that could have been written before social media and the internet.  It seems to be very aware that the reader is there in the story and aware of how the life of the author and all that we know or could know about an author gets mixed up in the story in the book.  

Because the narrative is mixed up with current internet culture, it is a story of our time.  I don't know what readers of 50 or a hundred years will think of it.  It is about an author writing a book after her rise to fame.  It mirrors some of the events that I can imagine from Okorafor's own life.  Her struggles with her health, fame, internet backlash, family life in US and Nigeria.  I feel like it is a very personal novel, maybe something that an author would write while procrastinating writing a very different contracted book.  I am glad she published it and I look forward to whatever she has next. 

Bookstore: Edinburgh international terminal

Title: Companion Piece

Author: Ali Smith

Review: Like "Death of the Author", this novel's structure and story could not have existed without the contemporary internet.  I had not heard of the author before and it is not a genre I usually like. It seems at times more like poetry than prose and the narrative is not always reliable or linear. 

The editor must have struggled with this manuscript because it doesn't follow traditional writing conventions. Sometimes one sentence runs for an entire page. Punctuation is sometimes missing or seems like a poem with line breaks used instead of commas or periods.  

The story starts when the main character is staying at her father's house, taking care of his dog, while he is in the hospital during covid lockdown in the UK.  She gets a phone call from a college acquaintance that tells her about a strange experience while being held by customs in a locked room.  She hears a disembodied voice that asks her "Curlew or curfew . . . You choose." What does this mean and why the choice? Her friend called her because when they were in college the main character helped her understand and analyze an ee cummings' poem and this seemed like the kind of puzzle that the main character could solve.  It reminded me of "The Chosen" when Reuven analyzes a difficult section of Talmud in front of his class.  There are flashbacks to an imagined blacksmith girl with a pet curlew during medieval history, but the imagined character pays a "real life" visit to the main character, sleeping in the corner of her room and chastising her about how she is taking care of the dog.  

If I taught a writing class, I think I would include this book in the class.  I think it shows both how to address poetry and prose in a intellectual and emotional way.  The covid lockdown storyline feels more surreal, and probably more cringe, than the story within the story about the medieval blacksmith and it would be interesting to see how students relate to that. I bet students would hate me because I would assign books like this.