What If? Writing Prompts: Nature IV

It’s Earth Day this week, so let’s mark the occasion with some new “What If?” Writing Prompts! To spark your “natural” creativity, here’s a new set of prompts set to the theme of nature and environmentalism! What sorts of stories can you create from these ideas? Have fun!

What If - Parchment and QuillWhat if… all wildlife rose up in a revolution against humankind?

What if… one tree were planted for every person in the world?

What if… a global effort were made to end all pollution?

What if… the entire world population could be fed on sustainable food sources?

What if… only you had the power to save the natural world from total destruction?

Good luck writing more tales about nature and the environment!

If you have any “What If?” writing prompt suggestions (for any theme), please feel free to share them in the comments below. Ideas I like may be featured in future “What If?” posts, with full credit and a link to your blog (if you have one)! Also, if you’ve written a piece based on an idea you’ve found here, be sure to link back to the respective “What If?” post. I would love to see what you’ve done with the prompt! Thank you!

Surprising Science

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.

Off The Bookshelf: A Fish Caught in Time – The Search for the Coelacanth

How about a new book recommendation for this year’s reading list? This one’s a little different from my other Off The Bookshelf entries as it’s actually a nonfiction tale, and a marine biology-themed one at that! I read this book last year for school, and I was so enraptured by this incredible true “scientific epic” that I had to share it on my blog.

So if you’ve never heard of the coelacanth, or you have but want to learn the details of its history, you’re in for a treat! I hope you’ll enjoy my review of this must-read book: A Fish Caught in Time: The Search for the Coelacanth by Samantha Weinberg.

A Fish Caught in Time

A Fish Caught in Time: The Search for the Coelacanth, by Samantha Weinberg

Summary

A Fish Caught in Time tells the true story of the coelacanth (SEE-luh-kanth), one of the most mysterious and fascinating fishes (yes, “fishes) in scientific history, as written by English journalist Samantha Weinberg. Originally published in 1999 by HarperCollins, the book recounts the events surrounding this prehistoric fish, from the shocking discovery of a living specimen (Latimeria chalumnae) in 1938 to the discovery and study of a second species (Latimeria menadoensis) 60 years later. The narrative relates these events from the perspective of the researchers who dedicated much of their time and resources to studying this fish, all of whom played an important role in the amazing story of the elusive “King of the Sea”.

Review

I read this book last year in preparation for a Vertebrate Zoology class I had to help teach as part of my Master’s program. My lesson was about the Sarcopterygii class of fishes, so my professor lent me his copy of A Fish Caught in Time as supplementary material for telling the story of the coelacanth. By the time I was done, I was ready to teach an entire semester on this one fish. I never thought I would feel so strongly about any one fish, but then again, the coelacanth is no ordinary fish.

Marjorie Courtenay-Latimer with the first modern coelacanth discovered (Latimeria chalumnae), 1938

Marjorie Courtenay-Latimer with the modern coelacanth (Latimeria chalumnae) she discovered in 1938

To summarize, the coelacanth was long thought lost to history by the Cretaceous-Paleogene extinction event that wiped out three quarters of the plant and animal species living on Earth (most famously the dinosaurs). It was known only by its fossil record for (almost exactly) 100 years, until, to the world’s surprise and excitement, a living specimen was fished off the South African coast in 1938. Over the next six decades, the coelacanth would be the focus of global headlines, political plays, and scientific rivalries, all the while remaining an enigma to the world that it continues to captivate to this day.

A rare example of a nonfiction story told in a highly narrative form, A Fish Caught in Time does an excellent job of capturing the majesty and mystery of the coelacanth while staying true to the history of its discovery and study. Ms. Weinberg paints such a vivid picture of this 60-year-long story that I couldn’t help but be completely drawn in, as if I were living the story along with the real-life characters: the excitement of discovering the coelacanth wasn’t extinct after all, the rush to find out where it had been hiding for the past 65 million years, the desperation to not only capture a living specimen but keep it alive at the surface, the awe that only a lucky few in history have ever known of watching this deep-sea fish swim in its natural habitat. I’d even go as far as to say that it’s impossible to read this book and not fall in love with the coelacanth!

Arnaz Erdmann swimming with the Indonesian coelacanth

Arnaz Erdmann swimming with the Indonesian coelacanth (Latimeria menadoensis)

A fair note of warning: oftentimes the story focuses more on the researchers who dedicated their lives to studying the coelacanth than on the coelacanth itself. Readers who hope to gain an insight exclusively into the life of the fish may find this a bit off-putting, but then again, it hardly makes sense to attempt to recount the history around the animal without offering even a glimpse into the lives of the people who shaped that history. It’s much more than a story about a fish; it’s a lesson about what it means to be a researcher. It takes intelligence, curiosity, patience, an unquenchable thirst for knowledge, and an unrelenting passion for science, all of which shine through the pages of this brilliant narration of scientific truth.

Overall, A Fish Caught in Time is a captivating read that any science enthusiast will enjoy. I owe much of my appreciation for the coelacanth to this book, and I recommend it to anyone who wants to immerse themselves in a world of marine biology without being overwhelmed by the technicalities of it all. As quickly becomes evident from the first chapter, science doesn’t have to be fictional to blend well with creative writing!

Inspiration

I love science and I love a good story, but it’s rare that I get to enjoy both at the same time, or at least in the same book. A Fish Caught in Time offers an opportunity to glimpse the joy and passion that goes into conducting good science by presenting it in an enjoyable narrative format. Though much research has gone into understanding the coelacanth, A Fish Caught in Time never conveys that research in a manner too difficult for the layman to comprehend or appreciate, making it an unusual kind of literary gem: a scientific subject made accessible to the general public, that is, a community of non-scientific readers.

So if you appreciate science and a good story based on true events, A Fish Caught in Time may be just the inspiration you need for your creative writing! It certainly has been for me; in my opinion, there’s never too much writing inspiration to be found in science!

Too Many Variables

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.

The Science of Life

Beautiful Earth full of life,
I love to study your ecosystems, from your
Oceans teeming with fascinating creatures to your
Landscapes rich with lush vegetation.
Only your beautiful nature, rich with
Greens and blues, can pique such curiosity in me.
Your living world is my science, my knowledge, my life!

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