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. 

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. 

Seeing things - A short story

 His watch beeped at him and told him he was stressed.  "Would you like to do a breathing exercise?" It asked.

"No" he thought.  "I would not."  The plane was close to arrival and the seatbelt light was on.  He needed to pee. His foot hurt and one side of his thumb ached for no reason at all. He did not look at the thing standing by the lavatory. 

No one else could see it, he assumed.  It was one of the things he didn't talk about.  Like the emails he should have answered that lay pulsing in his inbox, nagging at his guts and blinking behind a list of other undone things. Like his feelings about god or his father's death. You just didn't tell strangers you saw faeries on an airplane.  

Some of them looked like regular people. They sat in their seats and queued up with everyone else.  But there was something off about them.  Once he had sat across from one and was sure that everyone else saw that she had carried a large basket of earth complete with turf and wildflowers growing out of it.  It fit in the bin, but dribbled dirt and sweet pollen down the aisle.  She was pretty.  He couldn't look at her without staring so instead he looked ahead and imagined she was a college student in a hoodie and not an elven cloak. 

Today it looked like a furry tree was growing out of the back of the plane.  The flight attendants nudged the cart through the leaves and absently brushed the moss.  It moved out of the way when someone needed to use the lavatory.  

He needed to pee. 

But he sat and tried not to notice that the tree seemed to get closer.  Maybe it was going to sit in first class when we landed or it would squeeze through the pilots door and look out of the front windows looking for home, its leaves touching the pilot's shoulders and the controls.

A bird flew down the aisle and he lost sight of the tree.  It smelled like wet earth and soft wood.  He imagined pushing into a log to see what was inside.  How had it gotten on the plane? How did it move? Why no one else could see it was a question he stopped asking.  When you see trolls hiding as a rock along the road and faeries dancing on the sidewalk, the answer is easy. . . You're crazy.  

It was a manageable insanity, he told himself.  Once he talked to an online therapist about it.  It went about like you imagine. 

He set up the appointment after he tried to talk to the young man with hair like a house sparrow.  The youth was surprised he had been spotted and shyly chatted with him on the trail as they walked together.  The faerie had offered him a drink from his canteen as they rested together by the water.  It tasted like elderberry and burned a little like it was distilled mead.  His memory is a bit fuzzy after that.  There might have been dancing.  He could remember playing the fiddle while someone played a drum and pipes.  The song nagged at him when he was on the edge of sleep but couldn't remember how it went when he was all the way awake. 

He missed work the next day and woke up in his apartment, lying in a pile of leaves, in clothes that he didn't remember owning. 

He was nervous logging into the therapy session.  The woman that was on the screen wrote in a notebook he couldn't see. She seemed tired.  They started with the basics - name, age, what he did for a living, some of the kinds of therapy she was comfortable with, how she ran the sessions.  Then the real questions.

"Why did you set up this meeting." She asked

He shrugged and paused to find the words.  She assured him that this was "a judgement free zone," that whatever he said to her would be kept in secret, unless it was something that she was "legally obligated by law to disclose, if you have harmed yourself or others or plan to."

She waited.

He hoped she would talk again.  She waited.  It was not her first time with patients that were reticent to say what was wrong.  It was best to wait. 

He sighed and looked away from the screen.  Oddly this meant he looked directly at the camera by mistake.   She stared in his eyes while he tried to look away. "I see things." He finally said

"Like what?" she asked after another long pause.  Tapping her pen. 

He paused again and then without a breath jumped directly into his story at the end instead of the beginning. 

"There is a pile of oak and beech leaves in the corner of my kitchen." He said. " They are still green as if a wind blew them off of the trees or someone picked them off of the branches. The oak leaves have a dusty fuzz on them that rubs off.  Underneath they are shiny.  The beech leaves are veiny and stiff.  I don't recognize the species."

She blinked and waited, Assuming that there is more. 

"When I woke up the leaves covered my face and I didn't get up at first because I was afraid I had been buried alive."

"Why did you think that?" She asked.

"I didn't remember getting into a pile of leaves and waking felt like this was still a dream that could turn to a nightmare." He described the music and that he couldn't remember everything.  

"Tell me what you can"

"I never dance." He said.  I don't remember how.  I am not sure that I ever learned and it isn't something that we did when I was a kid." 

"Was this the dream?" she asked. 

"Maybe, but when I dared sit up the leaves fell off and I was alone in my apartment.  They are still there." He pointed behind him.  "Can you see them?"

She couldn't.  The angle was bad so he turned his laptop and pointed to the corner where the leaves touched the cabinets and the kitchen table.  It was a big pile. He said.  She still couldn't see them. 

"I didn't think so" He said.  She asked him why he wasn't more surprised.  He shrugged again.  "I see things." He said again as if that was an answer.  She wrote in her notebook. 

He waited. 

She asked to hear more.  He tried to explain.  They only had an hour and he was frustrated.  He wasted 20 minutes on what seemed like procrastination now that they had only 15 minutes left and he seemed unable to explain why ordinary things sometimes shifted and walked away or why some people seemed to leak magic in their wake like they were part in this world and part in another where it was perfectly normal to have antlers or be invisible. The more he talked the faster the time flew.  She wrote and didn't interrupt. He didn't make much sense.  He didn't tell her about the elven youth and his flowery drink or his lost time. 

She wanted to meet again.  Next week.  As soon as possible.  Recommended an appointment with a psychiatrist for a prescription.  He was embarrassed remembering because he closed the screen and never came back. 

Did it get worse after that? He didn't think so, but avoiding thinking about officially being diagnosed as schizophrenic broke a wall inside maybe. 

It seemed like the magic was pushing into his life everywhere he went. When they landed everyone shuffled out of the plane past the tree.  The leaves touched the shoulders of the flight attendants as they said goodbye over and over again. 

When it was his turn he absent-mindedly reached over and picked an acorn and handed it to the flight attendant. She thanked him and then shivered as a wind rustled the leaves behind her.  She furrowed her brow and pulled a leaf out of her hair as she wished him "good day". 

He smiled, turned and walked away on the jet bridge, humming a tune that felt light and new. 

Tanzania and Kenya

 

Spoiled dog

 

Chapter 1. Awake

 He awoke to alarms and bright lights that made no sense. For a moment the astronaut remembered the edges of a dream where the stars were so bright and cold. He felt the warmth of a woman's hand brush his face and felt sad to leave her behind for the claustrophobic and overwhelming present. A memory of music threatened to pull him back into the dark, but he swam towards the discordant and insistent call of the alarms that started to make some sense. He was awake and something was very wrong.

The computer was supposed to wake him slowly feeding him the drugs to wake his mind, nutrients and stimulants for his body, and then information he needed to get out of his sleepcoffin ready to take over his mission. He had trained half his life for this planned moment when he would climb out and see a hopefully habitable, but alien planet with his own eyes.  The computer would have seen it for years as he travelled and built an approach and mission plan.  The astronaut would then review the plan, adjust as needed, report back to earth and get to work.  That was the plan. That is what he had rehearsed till it was second nature. 

The alarms were wrong.  The dreams were wrong.  He was confused and weak.  Blinking was hard. Staying awake was a fight. The lights . . faded . . . and came back like a nightmare.  

He had trained for this kind of contingency plan of course.  Days of simulations for what to do if he had to wake suddenly and make quick decisions or repairs.  Many simulations had no winning solution, no way that he could fix the problem, but they all required him to start by deciding to fight through the fogginess of artificial sleep, disconnect himself from the machines, and choose to act, to do what he could, even if it was impossible and all he could do was try to send a message home.  Communication was a success, even if death was inevitable. 

So he decided to act. Step one in his emergency checklist complete.  Next figure out what kind of mess he was in so he could build the next steps to check off.

Finally writing the book I wish I could find

How do you find a book that isn’t lost, but half forgotten? I remember reading it. I swear I found it in the Boise Library where they had a shelf of popular books on the first floor near the check out desks. I can see the cover in my mind. It had an old computer terminal with letters in green and an old computer terminal font. In my memory, it said “Press enter. . .” But that can’t be the title, or else I could have found it. I don’t remember the author’s name. I don’t remember the character’s names.

My memory is not trustworthy though. I recently retold a story from that time to a friend that I remembered about his father losing his job and not telling anyone in the family. In my memory he went to the park or the library while he was looking for work, while spending down his savings and pretending that all was well. He was caught in the lie in my retelling of the story and the loss of their savings precipitated their move to Denver. My friend laughed and said that sounds like something his father would do, but that didn’t remember anything like that happening to them. Which of us is remembering wrong? I am assuming me. My own memory is full of holes and stories that have taken on a life independent of the truth.

The internet seems to have all of the information you could ever want. Wikipedia is a better encyclopedia than the World Book Encyclopedia that my mom bought from a travelling salesman. With Google I can find which restaurant has banh mi near Pikes Place Market and Amazon will send me the cord I have lost to charge my headphones in a day. But, I can’t find the book. I wrote about it once on my blog. I asked Reddit and Twitter and Facebook. No one seems to remember it like I do. Maybe in some forgotten database there is my library history from 1992 with the true title and author hidden in the list of sci fi books that I checked out. Maybe I just read it while I procrastinated doing my homework or waited for the bus? I don’t remember having the book at home or other places. Just there in the library.

I think of the book and its story at the most random times. There are moments that seem as real as my own memories, embedded in the times I have tried to find the book or debated making up my own. I remember the book being good enough that I would think other people would have read and remembered it.

The story is a fantastical one, not a profound book or a great one. If one day this finds its way to the original author, don’t take my description as criticism, only that it wasn’t something inspirational or intending to be the great American novel. It was just a fun story. It assumes the reader accepts the sci fi and fantastical elements of the story without too much of a skeptical eye.

It had an astronaut that comes back from a long and lonely trip to find Earth empty and abandoned. The people appear to have disappeared in an instance but without obvious violence. There are no bodies, just a mystery. He walks through the empty cities to find a broadcasted radio signal. The source of the signal is a library or an office. Inside the power is on, the transmitter on repeat with a simple message - Press Enter. The computer screen is waiting for someone to push the button.

Nothing happens when he pushes the button, except the story within the book. It is a flashback to the beginnings of the story to the protagonist - a young boy that has bad dreams. He dreams of a beautiful woman floating in space outside a broken colony ship. The stars are bright and too close to be real. Space feels cold and she talks to him in his dreams. He writes about his dreams on a 1990’s imagined version of an internet message board and obsesses about her being cold and alone in space. His obsession starts to interfere with his life and all he talks about is his beautiful girl floating alive in vacuum of space.

His worried mother seeks treatment for his obsession as it becomes a mental illness. The treatment is an experimental drug that was used to help soldiers with PTSD forget and recover. He seems to forget and goes back to his normal life, but he is wounded and sad.

This starts him on a path that ends with him becoming the reason why the Earth is empty and the astronaut is reading this story with us. The astronaut has a choice and a job to do that requires him to believe and act on the fantastical story to bring everyone back. It is a New Agey magic mixed with sci fi elements.

I remember moments from this story with great detail, but large chunks are missing. I would love to read this book again. Maybe I would be disappointed, that it required too much suspension of disbelief or that the characters weren’t likable. Maybe the story has leaps of logic or tedious bits that I skimmed over. But, since I can’t find it and I have the framework of the plot in my mind still after 30 years, I plan to write what I remember of the book instead of randomly searching Google for it.

Is this fan fiction? Kind of, but a fan fiction for a story that only I remember. A book for a fan base of one - me. It is more of a retelling I guess.

Is this plagiarism? I hope not. I doubt it could be proven to be since I don’t have the book in front of me and if I did I wouldn’t be trying to write it myself. The names and details are all my own. The arc of the story might not even match the book, if it exists. It is the best that I can do to write the book that I think I might have read on a day at the library when my friend’s father probably wasn’t there pretending to go to work at a job that he didn’t have because that memory doesn’t check out. It didn’t happen and since I can’t trust my life to be real, I guess that means that maybe this book is one that I invented all by myself.

If as I write or if this is published and you are reading this thinking - this sounds awfully familiar and you know the book - please send me the actual author and title. If you are the author, my apologies for butchering your book as I remember it. I hope you see this as the praise I mean it to be.