by Naomi L. | April 8, 2016 | Flash Fiction, J.C. Wolfe's Writing |
Science never ceases to surprise me.
I’d have sworn my project was like any other of its kind: collect samples in the field, run DNA tests, analyze and discuss the data, write the paper. Simple as that. Ironically, evolutionary studies don’t usually qualify as groundbreaking, just substantiating at best. We’re all trying to support the same idea: that life is constantly changing.
I studied reef fish biogeography and evolution for half my years at college, so by the time I got into grad school, I knew their patterns pretty well. I didn’t expect anything different when I took on a project about yet another reef fish species. Evaluate its genetic connectivity along the coast, that’s all there was to it. My project was a simple matter of collecting specimens from different locations and comparing their DNA to get a picture of how it was evolving in a given biogeographic province.
Nothing out of the ordinary came up during the sampling and amplification periods. The surprise came when I analyzed the data.
I remember that moment distinctly. Exhausted from weeks of amplifying DNA, reading papers, and writing and rewriting the first parts of my thesis, I was finally sitting down at my computer to compare the sequences. I took a sip of coffee just as the program finally finished running the data… and almost spit it out at the sight of the phylogenetic tree that appeared on the screen. Where I had expected to see a single branch containing all my sequences, there were two separate clades dividing the samples collected from the northern and southern coastal regions. Two geographically close populations that should have been almost identical somehow had a 10% genetic divergence between them. Was that even possible?
An excitement like I hadn’t felt in years overcame me, but I still had to be sure. I ran the data again using three different parameters. All three trees produced the same result: North here, South there. I couldn’t believe my eyes. Yet there it was on my screen, plain as the nose on my face. The results were clear beyond a shadow of a doubt: I was dealing with…
“A new species?!”
I jumped up from my chair and ran next door to my professor’s office. Within the minute, I was showing him the trees on my computer and watching his expression change from puzzled to amazed. I knew exactly why we should be so excited by this result; it meant there were other evolutionary processes at play that we hadn’t expected. In anticipation of the stimulating discussions ahead, I knew the grin on my face wouldn’t disappear for at least a week. My project had just gotten way more interesting.
Science never ceases to surprise me. And I hope it never will.
by Naomi L. | April 1, 2016 | J.C. Wolfe's Writing, Poetry |
All the jokes you’ve been wanting to say,
Pranks you’ve always been dying to play,
Right and left, they begin.
If you’re smart, you’ll stay in,
Lest you fall for the tricks of today!
Friends outside have been beckoning you.
Out the door, you’re now covered in goo!
Oops, now what do you hear?
Laughs from far and from near?
Surprise! You’re an April Fool too!
by Naomi L. | March 25, 2016 | J.C. Wolfe's Writing, Poetry |
Holy day it is to
All people of good faith.
Praise be to the Lord, for whose
People He sacrificed His Son.
Your love is great, Father!
Evangelical teachings tell of the
Agony suffered for our sins by the
Son of God, yet on the
Third day, He lived again!
Everyone, rejoice!
Risen is the Lord!
Happy Easter to all my family, friends, and readers who are celebrating! May you all have a blessed weekend!
by Naomi L. | March 18, 2016 | J.C. Wolfe's Writing, Short Stories |
Welcome to the conclusion of “Dance of the Fairies”. If you haven’t yet, read Part 1 here. Otherwise, enjoy!
The music gradually died down as Cindy, Joey, Shea and Eldan moved toward the center circle. The next thing the children knew, the fairies were all staring at them in awestruck silence as they stood before the queen.
“Your Majesty”, said Shea, bowing deeply alongside Eldan while the children stood wide-eyed behind them, “we found these two humans watching from the outskirts of our sacred field. We beseech your judgment of their permission to stay.”
The queen fluttered down from her high throne, and Shea and Eldan moved aside to allow her passage to the children. Cindy and Joey gazed at her in wonder; though she was considerably smaller than them, they felt humbled in her presence. The great fairy studied them seriously for a minute, then broke into a smile.
“Welcome, children,” she said kindly. “I see you’ve discovered our secret festival. Please tell me your names.”
The children glanced at each other awkwardly before turning back to the fairy. The girl was the first to find her voice.
“C-Cindy.”
“…Joey.”
The queen considered them both for a moment before nodding, never breaking her smile for an instant. “It’s a pleasure to meet you, Cindy and Joey. I’m Queen Tianna. Welcome to our magical field!”
“The pleasure is all ours!” Cindy replied. The queen’s kind smile had melted away all her fear.
“Forgive me, Your Majesty,” Eldan spoke up, “but what should we do with these…visitors? You have only to say the word, and Shea and I will readily escort them out.”
Queen Tianna grew serious again. Without taking her eyes off the humans, she fluttered down to lift each of their hands as Shea had done. She held onto their forefingers for a full minute, the silence deafening around them… until at last she smiled once more.
“There’s no need for that, Eldan,” she said sweetly, still gazing intently at Cindy and Joey. “These children are pure of heart. They will be our honored guests tonight!” The queen announced this to the entire field, then lowered her voice again as she addressed the visitors directly. “What do you say, children? Would you like to dance with us?”
“Would we ever!” Cindy exclaimed, then suddenly catching herself, she added with a polite bow, “I mean, it would be an honor, Your Majesty.”
Joey bowed as well, and the entire field of fairies cheered as the music started up again. Immediately, two pairs of fairies carrying a crown of flowers each came forth and placed them lightly on the children’s heads. The two were then escorted toward the center circle, Cindy giggling as she caught sight of Shea triumphantly sticking her tongue out at Eldan.
The rest of the night passed by like a dream. Cindy and Joey twirled together in the light circle to the cheering of the fairies around them. They gleefully lead lines of dancers around the field, clapped and chanted along to the music, and joined hands with the fairies to spin around the great center circle. They even had the honor of joining the final dance with Queen Tianna herself. It was a night they would never forget for as long as they lived.
At last, the night passed away and the morning sun began to glow on the horizon. As the music and dancing finally stopped, the queen fluttered before her guests to share a few final words with them.
“Thank you for joining us tonight, children! You have made this a most magical evening indeed! Know you are always welcome to our full moon festivals. May the Mother Earth always bless you both!”
“Thank you, Your Majesty!” Cindy and Joey exclaimed in unison, grinning and bowing deeply.
The other fairies had already begun to disappear, one by one in little fading balls of light. Shea waved her new friends goodbye, and even Eldan smiled as he disappeared with her. Queen Tianna was the last to vanish, leaving the warmth of her kind smile hanging in the air. The light circle faded away, and before they knew it, Cindy and Joey were standing in the middle of what appeared to be nothing more than an ordinary field at dawn, with no sign that anything magical had ever happened there.
Joey reached up to take the flower crown off his head, and stood staring at it as if in a daze while Cindy started walking back toward the rocks. Timidly, he turned his head up and called to her.
“Cindy?”
Cindy stopped and turned around to face her friend. Joey shuffled his feet awkwardly for a moment, gathering courage as he glanced at his crown, before looking her in the eyes again and speaking up.
“…Do you think we could come back here, at the next full moon?”
A smile spread across Cindy’s face. She walked up to Joey and took his hand in hers.
“It’s a date!”
Joey grinned and squeezed Cindy’s fingers as she replaced the flower crown on his head. Holding hands, the children left the field together, laughing and skipping all the way home. It had been more than a magical evening, a night they knew even then that they would remember for the rest of their lives together. Every full moon from then on would bring about the same cheerful thought: the next dance of the fairies could never come soon enough.
The End
Hope you enjoyed the story! Thanks for reading!
by Naomi L. | March 11, 2016 | J.C. Wolfe's Writing, Short Stories |
“What are we looking at?”
“Shh!“
“But there’s nothing here!”
“There will be! Now be quiet!”
Cindy covered Joey’s mouth with her hand. He brushed it off, but did as she told him nonetheless. The two children huddled closer as they stared over the rocks at the empty field ahead.
“I still don’t get why you brought me here,” Joey whispered after five uneventful minutes.
“You will.” Cindy glanced up at the full moon just beginning to poke through the clouds. “It’s almost time.”
They sat quietly for another several minutes, waiting. Joey opened his mouth, about to complain that it was cold and this was boring and he wanted to go home, but the words never left his throat. Just then, a circle of light appeared in the middle of the field, in the very spot Cindy had pointed out when they arrived.
“C-Cindy?” Joey stammered, suddenly afraid. “W-What’s happening?”
But Cindy didn’t seem to notice her friend cowering beside her. She was too busy grinning as she leaned over the rock for a better view.
“Here they come!”
She quivered with excitement as little balls of light began to appear across the field. One by one, the floating lights materialized into tiny glowing figures with wings. Joey’s eyes grew wide as he stared into the field, unable to believe what he was seeing.
“Are those…?” he gasped. Cindy nodded without taking her eyes off the scene ahead.
“Fairies!”
The fairies all gathered around the circle of light in the middle of the field. One of them, who was slightly brighter than the rest and wore a crown on her head, raised her hands to call for silence, a request immediately respected by all the others. Cindy turned to Joey, who was now leaning over the rock beside her.
“That’s the fairy queen!” she whispered. The two of them watched quietly as the leader of the fairies began to speak.
“My children!” she said in a kind yet authoritative voice. “Tonight, let us give thanks to our Mother Earth for her bounty. Let us praise her, that we may never find ourselves wanting of her generosity. Let her know that we are eternally grateful for her kindness. So sing and be merry, my children! Tonight, we dance!”
The queen raised her hands again and all the fairies cheered. A small group beside her began to bang and strum on tiny instruments, and soon the air was filled with music. Cindy and Joey watched, enthralled, as some of the little glowing figures joined hands and danced around the center circle while others twirled through the air in pairs. It was a sight to take the breath away.
“Aren’t they beautiful?” Cindy sighed dreamily, her head in her hands. Joey nodded without even realizing.
“They really are.”
The children giggled as they watched the fairies dance and sing. Before long, they too found themselves getting caught up in the spirit of the music.
“May I have this dance?” Joey said in a mock grown-up voice as he stepped back and bowed to his friend. Cindy curtsied and waved an imaginary fan.
“I thought you’d never ask!”
The two friends laughed as they imitated the fairies, twirling around in circles until they were dizzy. Then…
“Hey!”
Cindy and Joey froze, their smiles vanishing instantly. They turned around slowly to see two glowing figures floating before them, watching them with wide, pale blue eyes.
“What are you doing here?” one of the fairies asked, his brow raised in suspicion. While Cindy and Joey exchanged awkward looks, the other fairy turned to her companion.
“Don’t frighten them, Eldan!” she said in a much softer tone, taking him by the arm. “They’re not hurting anyone. They’re just children!”
“Human children, Shea,” said the first fairy as he turned to his friend. “You know we don’t allow humans here. What would the queen have to say about this?”
“Why don’t we ask her?”
“You want to take them to the queen?”
“Why not?” Shea smiled. “They clearly like to dance too! I’m sure she wouldn’t mind. She might even be delighted to have them join us!”
Eldan glanced at the nervous children, then turned back to his companion and sighed in defeat. “Fine, if you say so. But if we get in trouble for this…”
“We won’t.” Beaming, Shea fluttered over to Cindy and Joey and extended her hand to them. “It’s okay, don’t be afraid. Come with us! We don’t bite!”
“Speak for yourself,” said Eldan, sparing a piercing look at Joey. The boy drew back at those words, but Shea calmed him with a gentle laugh.
“He’s joking, sweetie. This guy couldn’t hurt a fly if he wanted to!”
The fairy fluttered down between the children and reached out to touch their hands. Dazed, Cindy and Joey stepped forward as Shea led them by their forefingers out from behind the rocks and into the field, Eldan following close behind. They didn’t know what to expect, but of one thing they were certain: the night was about to get far more interesting.
To be concluded next Friday
by Naomi L. | March 4, 2016 | J.C. Wolfe's Writing, Short Stories |
I really thought amplifying DNA would be easy. Molecular biology seemed simple enough in theory: extract, amplify, sequence, analyze. But I had no idea how difficult it would be to work with so many variables.
After my third failed polymerase chain reaction attempt, I started to wonder what I could be doing wrong.
Was I using the right concentrations of each reagent? Buffer at 1X, MgCl2 at 1.5mM, dNTPs at 200µM each?
Were the primers optimized for my DNA template? Had they been designed for the correct gene? Did they have the right length, melting temperatures, GC content?
Were the PCR cycles optimized? Was I using an annealing temperature within a few degrees of the primers’ melting temperatures? Were the denaturation and extension times long enough to assure proper replication of the DNA fragments?
Was the electrophoresis gel being prepared and run correctly? 1% agarose gel with GelRed in TAE buffer, run for about 10V per centimeter between the electrodes?
Or what if – shudder – the problem was in the DNA itself? What if the extraction had failed, and I’d have to start the entire project over from Square One?
No, no, calm down, I told myself. One step at a time. First, eliminate the variables you know aren’t the problem. There’s no reason the extraction should have failed; the quantification returned optimal concentrations of DNA. These are the same universal primers used in countless other studies, specifically designed for the cytochrome-b gene. The thermocycler and the electrophoresis apparatus have already worked before. There’s nothing wrong with the gel because the ladder and primers appear in the UV photos. That’s already five ticks off the checklist.
Now start with a positive control, a sample you know has worked with these primers before. PCR #4: did it fail to amplify along with the others? Yes. Good, then the problem isn’t the DNA.
Next step: new aliquots. Replace the water, the buffer, the MgCl2, the dNTPs, even the primers. Everything must be fresh to minimize contamination. Double-check the concentrations before preparing the mix. PCR #5: still no bands in the gel. No problem; just move on to the next step.
Try altering the reagent concentrations. Use more DNA template, double the primers, increase the amount of MgCl2. PCRs #6-8: nothing. Don’t panic, it’s all part of the process. You’re zeroing in on the problem now.
Adjust the PCR procedure. Increase the number of cycles, raise the annealing temperature in increments of 2ºC, lengthen the initial denaturation and final elongation steps. PCRs #9-12: still nothing. It’s okay, every failure is just another step closer to success. These tears are totally normal; nothing to be ashamed of.
For weeks, I tried everything I could think of. I replaced the reagent aliquots three times. I used half a dozen standard PCR procedures from various troubleshooting references. I ran gradient tests and touchdown tests and hot-start tests. Zero, nothing, zip.
Finally, after over a month of PCR attempts and no results to show for it, I was at my wit’s end. One morning, when I was alone in the lab, I broke down into a sobbing mess. I couldn’t look at the thermocycler anymore, that beast of a machine that I had to work with every day. I felt like a knight facing off against the same dragon over and over, knowing that hours of battling would only get me burnt every single time.
So I resolved to take a break from it all. No more PCRs for a while, not until I could work up the energy to start trying again. Today, I would just sit at the desk and read papers while indulging in a bag of cookies. Stale cookies. Really stale cookies. Seriously, how old were these?
I turned the bag over to check the date on the back…and that was when it hit me. Could it be? Immediately I dropped the bag and ran to the freezer. The stock solutions were stored in the back of the bottom shelf; I searched through them one by one until at last I found what I was looking for, printed clear as day inside the lid of the Taq DNA polymerase box. “Expiration date: Oct 2010.” Of course! No wonder none of my reactions were working: the enzyme was over five years old!
My first grin in weeks spread across my face, and I was suddenly overcome with an urge to shout “Eureka!” I hurried to my professor’s office and told him about the expired reagent. He quickly ordered a new stock and it arrived within two weeks. Sure enough, the next PCR I ran yielded the most beautiful set of bright DNA bands I had ever seen in a gel. I wanted to kiss that UV photo. My very first successful DNA amplification! And it only took two months longer than expected.
Never again will I underestimate the work of a scientist. Molecular biology may seem simple in theory, but having learned my lesson the hard way, next time I’ll be prepared for the challenge of working with too many variables.
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