My Life This January: In Which There are Holidays and Deadlines and Another Semester Begins

Hi, everyone! It’s the last Friday of January (seriously, what happened to the month?), so I’m here to tell you what happened this month. This will actually cover a longer period than usual, since I didn’t post on Christmas last month. In rough chronological order, here we go!

Christmas and New Year’s

Ah, I love those end-of-year holidays! On Christmas Day, it snowed here in the Northeast, so we went down to Connecticut to visit my aunt and uncle and grandparents on Christmas Eve day. It was a really nice visit with lots of good food and family socializing, and really, at the holidays, what more do you want?

Then, of course, came Christmas itself. (Merry Christmas, belatedly!) I did pick up a few books, including DNA by James Watson and The Battles of Tolkien and The Heroes of Tolkien by David Day. The former is a history of modern genetics and biotechnology, and the latter talk about the inspiration behind Tolkien’s works and include some nice illustrations.

I also bought a few books after Christmas: a one-volume edition of C.S. Lewis’s Space Trilogy, my own copy of Ender’s Game by Orson Scott Card, and (finally) King’s Blood by Jill Williamson. I have not cracked open the first two yet, except to look at the Tolkien-letter foreword in the Space Trilogy, but I did devour the 600-page King’s Blood in two days. It was SO good! If you like epic fantasy with a Christian bent, and you haven’t read Williamson’s Kinsman Chronicles, you need to. I’m so excited for the third book to come out in June!

Winter Break

So thankfully, this was also a thing. The University of New Hampshire happens to have a nice long winter break, five weeks to be exact, but even that felt too short. I pretty much worked full-time in the lab so I could get some research done; I’m still catching up on summer and fall work. In the last week of break, I managed to get into some more explicitly genetic-engineering type stuff, working with bacteria preliminary to transforming plants, so that’s been fun! I’m looking forward to where my research will go next.

Spring Semester

It’s only been a week so far, but spring semester still merits inclusion in this post. This semester, I’m taking Genetics of Prokaryotic Microbes (so, bacteria), Plant Systematics, and Principles of Biochemistry II. I was also going to take a biostatistics class, but I dropped that in favor of not overwhelming myself, since I’m also an undergrad teaching assistant for a genetics class, an undergrad researcher, and a biology tutor. So far, all my classes look to be enjoyable, and I like being a TA since I get to help out with the class without doing any homework!

I am also trying to write more this year; as I talked about in last week’s goals post, I have a goal to write/outline/revise/worldbuild at least 3 days a week this year. This month, I think I’ve averaged a little over 2 days a week, but that’s still better than normal! I am keeping track with little check marks on my calendar. I initially set out to do more work on Circle of Fire, my NaNoWriMo project from 2016 that really needs to be rewritten, but my mind wound up wandering to Windsong instead. So far, I drew a map (again, see last week’s post) and found out more about one of my key villains. I’m starting to like where this is going, and plan to do more with it in the next couple months!

Well, that was my month in a nutshell! How was yours? Have you done much writing? How were your holidays? Did you get any books? If you’re in school, what classes are you taking this semester? What did you do over winter break? Tell me in the comments!

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My (Obligatory) 2018 Goals Post

Hey everyone! So it’s 2018, and it seems (at least to me) as though everyone out there in the blogosphere is putting together posts about their goals for the new year. I figured I’d hop on the bandwagon, just for fun! Plus, it’s a nice quick post to put together for the first week of the spring semester. So, in no particular order, here are some of my goals!

1. Read the books of the Bible I’ve never read.

Yes, it’s true: I’m 20-and-a-half, and I haven’t read the whole Bible. Last year, I started going backwards through the Old Testament to finish up the books I’ve never read, and I want to finish this year. I’m currently a good way through Jeremiah, then I only have 1 and 2 Maccabees (Catholic here) to go!

2. Read 24 (non-Bible) books.

A little history of my Goodreads yearly goals…. In 2016, when I joined Goodreads (in March), I thought 24 books would be a feasible goal for the year. I failed miserably with only 17 books finished by the end of the year, so last year, 2017, I set a goal of 20. I reached that goal, and even read two books extra–yay! So this year, I figured I’d go back to 24 and see if I can do it. So far, I’m already on my third book, re-reading To Darkness Fled by Jill Williamson.

3. Apply to graduate school.

My initial reaction upon thinking of this goal: Oh, shoot, is that this year already?!?

Seriously, though. I’m going into my senior year of college this coming fall (!) and it’ll be time to start applying to PhD programs. I am currently working toward this goal by making very many spreadsheets (thank you, Microsoft Excel) of potential schools I’d like to apply to and faculty I’d like to work with. It’s so crazy to think that in about a year’s time, I’ll start hearing back…. Let’s move on, shall we?

4. Make time for writing and other creativity.

This is SO important this year. I think in previous years, I’ve gotten so caught up in college that I haven’t been able to make time to do the other things I really want to do, specifically writing. So I have resolved to write, outline, edit, or worldbuild–anything that contributes directly to one of my books–at least five minutes three days a week, just to keep in practice. So far I’ve already failed on that, with only two days last week (don’t look at me like that; I took the GRE on Saturday), but I think I made up for it with the map I drew Saturday night. I think it’s my best version yet!

DSC_0004 (2)
My latest map for my fantasy book Windsong.

Well, those are some of my goals for the year! What are some of yours? How are they coming so far? Tell me in the comments!

Biology for Writers: Some Awesome Genetics Techniques I Use in the Lab

Good morning, everyone! Welcome to the first Biology for Writers post of the new year! Today, I wanted to talk about some common techniques used in genetics and molecular biology, particularly those I use in the lab, since those are what I’m most familiar with. As a result, the list will probably be skewed toward plant biology, but I will include other techniques I’m somewhat familiar with too. If you’re interested in a specific discipline or something you don’t see listed here, let me know in the comments, and I’ll be happy to tell you what I know or help you find some resources! Let’s get started!

DNA/RNA Extraction

Why? If you’re working in genetics or molecular biology, you often need to isolate a nucleic acid, be it DNA or RNA. These molecules are useful for learning about genes and the various proteins, including enzymes, they produce (more on this another time).

Why DNA vs. RNA? Well, the DNA contains a gene’s complete sequence, including introns (which are removed in the messenger RNA that determines the protein’s amino acid sequence) and regulatory sequences that control when the gene is turned on or off. So if you’re interested in the pure molecular genetics of an enzyme, you might extract DNA. DNA is also useful if you’re trying to sequence a new genome (the complete DNA of an organism); genomes are often useful for future research.

DNA
Image source

RNA, on the other hand, might be useful if you want to, say, produce a human protein in bacteria. To do this requires gene cloning, which is much easier with only the coding sequence (the part that actually codes for the protein–i.e. messenger RNA) rather than all the extra introns and “junk DNA” that comes along with a complete gene. So for things like genetic engineering, it’s better to extract RNA and back-convert it into DNA (more on this in a minute).

How? Extracting DNA/RNA is, in a nutshell, getting it out of the cells of your plant or bacteria or whatever organism you’re starting with, and separating it from the proteins, fatty acids, and other stuff that also belongs in a cell. (If extracting DNA, you also want to separate it from RNA, and vice versa.) The first thing to do, then, is to break open your cells. In plants, you usually start this by freezing your leaves in liquid nitrogen, which helps minimize molecular degradation, and grinding them up in a mortar and pestle. Then, a lysis (cell-opening) buffer is added to fully lyse the cells. (Buffers are solutions with a specific pH that “buffer” against big changes in acidity.) During this process, nucleases, which degrade DNA, are inhibited by the cold temperature from the liquid nitrogen. Other chemical inhibitors may be added as well.

Next, a series of centrifuging steps separates the DNA (in various liquid buffers) from proteins, lipids, and other cellular detritus (often in the form of a pellet at the bottom of the little test tube). DNA in the top liquid, or “supernatant,” is removed into several different tubes, until ultimately it is collected without the liquid on a little pad within a special tube. The DNA is then resuspended, or “eluted,” in super-sterile water (a small amount, like 150 microliters–a microliter is a millionth of a liter). This serves to make the DNA more concentrated. You can then measure how much DNA you extracted with an instrument called a fluorometer, and if you got enough DNA, you’re all set to go on to the next step!

Polymerase Chain Reaction

Why? Once you’ve extracted DNA, what do you do with it? If the answer is “isolate a gene,” your next step is polymerase chain reaction (PCR). PCR is an “amplification” technique that takes advantage of DNA’s structure to make many copies of your gene of interest. Then, you can move on to DNA sequencing, genetic engineering, or something else.

How? Let me first make a small digression into the basics of DNA’s structure. DNA is made up of four kinds of nitrogenous bases (let’s just call them A, T, C, and G) that join together in two long strands. The bases pair in a complementary manner to form that familiar double helix shape; A only pairs with T and C with G. When I talk about “DNA sequence,” I’m talking about the order of bases; AATCG is different from ATACG, for example. “Complementary sequence” refers to the sequence of bases on the other strand of the DNA; each DNA strand is the opposite of the other. For example, TTAGC is complementary (opposite) to AATCG. Got it? Great! Let’s go on to the technique.

PCR exploits DNA’s structure to make many, many copies of a gene or other sequence of interest. You can find a great fact sheet about PCR, including a helpful figure, here. Basically, if you know the sequence of your gene of interest, you can order custom short DNA molecules, called oligonucleotide primers (or just primers), of 15-25 base pairs each which are complementary to the ends of your gene. In a tiny little test tube, you mix together DNA, water, primers, and free nucleotides, and stick it all in a machine called a thermocycler, which can be programmed to heat and cool the tube for certain times. The heating profile basically does the PCR.

There are three basic steps to PCR. First, denature the DNA (separate the strands) by heating to about 95 Celsius. Next, drop the temperature to about 60 Celsius for annealing (of primers to DNA). The last step is extension (addition of new nucleotides to make a new DNA molecule), which happens at around 70 Celsius. Together, these steps make one cycle. PCR is usually repeated in about 36 cycles, which because there are more templates with each cycle, makes thousands of copies of the gene of interest, hence “DNA amplification.” PCR is a very useful technique and is indispensable in most genetics laboratories.

In fact, a form of PCR called reverse transcription-PCR (RT-PCR) is used to back-convert extracted RNA into complementary DNA (cDNA). RT-PCR uses primers that are specific for messenger RNAs, enabling the isolation and amplification of only the coding sequence of an organism’s genes. This is the next step from RNA extraction (see above).

Gel Electrophoresis

Why? This is a sort of confirmation technique. Once you have your extracted DNA/RNA or your PCR products, you want to make sure you did your previous techniques right, so you run an agarose gel. This helps you determine the size of your DNA fragments (or genomic DNA in the case of an extraction), so you know you can proceed with the next step in your research.

How? Gels are made from agarose, a compound found in seaweed, and buffer. You pour molten agarose into a rectangular mold with a comb stuck in, so when it hardens and you pull the comb out, you have a flat, rectangular Jell-O like surface with a line of wells at one end. After pouring buffer over the gel so it’s under the surface of the liquid, you mix your DNA/PCR product with a blue loading dye and put one sample into each well (called a “lane” once you’ve run the gel). You should always load a size standard, called a “ladder,” into one lane, and it’s good to run a positive control (you know the result will be what you want) and negative control (you know the result will be the opposite of what you want), so that if something’s wrong with your samples but not the controls, you know it’s the samples themselves, not your PCR.

Once you’ve loaded all your samples, the next step is to turn on the electric current and let the gel run. Because DNA has a slight negative charge, it will migrate toward the positive end of the gel (away from the wells in which you loaded it). As it moves, it will bump into all sorts of molecules within the gel, i.e., the gel itself will get in the way of the DNA’s movement. This allows for size separation of DNA fragments; smaller fragments will bump into the gel less and therefore move a greater distance in the same time. When you look at the gel under ultraviolet light, you see bright “bands” that indicate where the DNA is; the closer to the wells, the longer the DNA fragment. Comparing these bands to the ladder size standard (which shows up as many bands of known sizes) allows you to identify the size of your PCR product, so you can tell whether you got the right gene. This makes gel electrophoresis an immensely useful technique.

 

Story Starters #11: King’s Folly

Aldair Livina sat at the table in the great cabin of his privately owned ship, the Half Moon, looking over his most recent chart of the Eversea. After an eleven-night voyage north-northwest from the Port of Everton, he had discovered a new island. He had named the isle Bakurah in honor of the first ripe fruit of the season. Aldair hoped that this island would be the first of many.

King's Folly
Image source

Happy New Year, everybody, and welcome to my first post of 2018! In case you don’t know, Story Starters is a series of posts, on the first Monday of every month, where I analyze the first paragraph of a book. Sometimes that’s just a line, sometimes it’s a great big block of text, but today we have one in the middle.

King’s Folly is the first in the Kinsman Chronicles, a trilogy from Jill Williamson which is currently awaiting its third installment. I recently read the second book, King’s Blood, and it reminded me how much I love this series, so I thought today I’d feature the first. Let’s break down this opening sentence by sentence!

  • Aldair Livina sat at the table in the great cabin of his privately owned ship, the Half Moon, looking over his most recent chart of the Eversea. All right, so this is not the best opening line ever written. It does start with a character (although not a major one) and set the scene, though, which are good things. But because this first sentence is actually from a prologue, the character and setting we’re starting with are not things we’re going to return to as we read on. I have seen prologues discouraged for this very reason: they often block the reader from getting into the book right away. But in the case of this 544-page epic fantasy, the prologue exists to set the tone for the whole story in an immediate way you couldn’t get from any of the more major characters’ points of view. Read on for more about this.
  • After an eleven-night voyage north-northwest from the Port of Everton, he had discovered a new island. Here we have some action, or some narration of past action. But still, we’re left wondering: so a new island has been discovered. Why should we care? This turns out to be setup for the next paragraph, in which the immediate conflict of the entire story, the Five Woes that will destroy the continent, are first brought up. If you think about it, a lot of openings contain at least some setup, like the contextual zooming-in technique used a lot in classic literature. So this sentence is perfectly at home in the opening paragraph.
  • He had named the isle Bakurah in honor of the first ripe fruit of the season. This sentence is more or less filler, although it does actually plant some seeds of a goal for the end of this book and the beginning of book 2, which is impressive foreshadowing when you think about it.
  • Aldair hoped that this island would be the first of many. Again we wonder: Why? Why does he hope that and why should we care? And this leads us to the whole purpose of this opening paragraph: raising questions. We, as writers, must raise questions in our openings in order to get the reader to read on–as I’ve talked about before, this is the essence of a good hook. Of course, answering the questions is just as important; you want to give enough information to keep readers appeased and interested, while holding back enough that you can continue to have reveals throughout the book. That’s more of a second-paragraph thing, but still relevant to this first paragraph.

So there you have it, everyone! Before I go, I should note that most of the analysis in this post springs from my extensive reading of Helping Writers Become Authors, which is an excellent blog for all things writing! For more on hooks and so forth, check out the “How to Structure Your Story” series linked to on the left sidebar. I highly recommend it!

That’s all for me today! Happy New Year! Have you read King’s Folly or its sequel, King’s Blood? If so, what did you think? I’d love to discuss it with you! Did you have any further thoughts on this opening that I may have missed? Tell me in the comments!