Biology for Writers: What Scientists Do All Day

Hello, everyone! It’s the second Monday of the month, which must mean I’m doing a biology-for-writers post. Okay, so I know “what scientists do all day” doesn’t have that much to do with scientific topics of interest to writers, but it’s finals week and I wanted a post that would be quick to write but still informative. And hey, some of you might have scientist characters and be wondering what research looks like, or what different stages of academic science look like. (Science also happens in industry–pharmaceuticals, anyone?–but I’m most familiar with academia, so I’m going to focus on that!)

Life Stages of Academic Scientists

(I’m going to talk a little bit about this first, so I can talk about how research looks for the different stages of scientist in my next section.)

People don’t become scientists overnight. Especially in academia, there’s really a hierarchy, and you can find every stage of scientist working alongside each other in a lab.

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The first step is to get your undergraduate degree in a science field (which is where I’m at right now). If you’re an undergrad scientist, you’re probably taking a fairly heavy course load to complete all your general education, major, and elective courses in four years. Undergrad costs a lot, too (at least in the U.S.), so you might be working on the side to help cover that. If you think you want to go to grad school, you’re probably working in a lab, helping a grad student with their research and/or assisting with lab maintenance things (yes, someone has to wash the flasks and beakers). If you’re extra motivated, you might have your own research project, but you get a lot of help from the professor who runs your lab since you’re still so young and inexperienced. And the project can’t be too big, because you really don’t have that much lab time when you’re also taking four classes and working. But you do what you can to get you into grad school.

The next step is to get one or more graduate degrees. If you want to work in industry, or you don’t have enough research experience yet to get directly into a PhD program, you get your master of science degree first. If you want to teach at the college level and run a lab (i.e. be an academic scientist like your faculty mentor), you need a PhD (short for Doctor of Philosophy). Master’s programs usually take two to three years, and PhD programs in the biological sciences average around five years. You take some courses, but not as many as you did when you were an undergrad, and once you’ve selected a faculty advisor, you get right to work in their lab on your thesis project. In order to graduate with your degree, you need to write a thesis (basically a book on your research) and defend it orally to your faculty committee, who will then decide if you get your degree or not. In a PhD program, you also have to pass a comprehensive exam somewhere around halfway through your degree, which will determine if you get to go on to “candidacy” (full-time dissertation research) or not. Now I’ve gone into a lot of details, but basically grad students do a lot more research than undergrads, because their degree depends on it.

Say now you’ve gotten your master’s and your PhD, and after eleven years you’re finally out of university schooling. Phew! What happens next? Well, if their research is outstanding, some lucky souls get hired straight to faculty positions. Most go on to postdoctoral fellowships (“postdocs” for short). The postdoc is the most senior member of the lab save the faculty member who runs it, unless it’s a really big lab and has a professional lab manager who reports to the professor. Postdoc fellowships usually last one to three years, and they work full-time, similar to grad students except no classes and no thesis defending. As I understand it, this serves as a time to build up one’s resume before applying to become a faculty member.

The highest tier is your PI (primary investigator), the faculty member who runs the lab. They determine what is studied in the lab and who works under them doing their projects. They also teach classes and, when they’re young, try to get tenure (which is basically where your university can’t fire you because you’ve proved the quality of your work). I’ve heard there’s a lot of pressure on young faculty to publish a lot of research in order to get tenure. Older professors (like my PI), who already have tenure, can be more relaxed since they are freer to study whatever they might be interested in–contingent, of course, on the availability of funding. PIs manage all aspects of the lab, mostly from their offices, although mine sometimes comes in and reorganizes things in the freezers or teaches students techniques. They usually teach classes for undergrads and grad students, and write up research articles for publication in scientific journals.

What Science Looks Like (In a Laboratory)

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With some understanding of the academic science hierarchy, we can now get a general idea of what scientists actually do all day. Naturally, this depends on the discipline, in that different scientists do different things. A neuroscientist, for instance, might do behavioral experiments or brain dissections on mice. I have less idea what ecologists do, but my guess is they go into the field to at least collect their samples. When I worked in a seaweed lab, I used to go to the shore and collect seaweed sometimes. Now, as a rice geneticist/biochemist, I split my time roughly 85% lab/15% greenhouse. Some of the things I’ve done in my lab are in bullet points below.

  • Lab Maintenance
    • Washing dishes
    • Making tissue culture medium (think Petri dishes)
    • Disposing of biohazardous waste (seriously not a big deal–I’m only in a Biosafety Level 1 lab)
    • Cleaning up ethanol spills (also not a big deal–it’s basically handcleaner)
    • Preparing/organizing work surfaces (we put this paper on our prep room bench to absorb any spills)
  • Experimental Things
    • Collecting samples (read: cutting up rice leaves and putting them in tubes)
    • Subculturing tissue cultures (the medium dries out every so often)
    • Checking tissue cultures for bacterial contamination (things have to be sterile)
    • Extracting and quantifying biomolecules
    • Data analysis (Microsoft Excel, anyone?)
    • Checking raw data files for quality control (on lab computer)
    • Pouring salt water on plants (so I’m a little sadistic once in a while)
    • Planting seeds
  • Common Genetics/Biochemistry Lab Equipment
    • Petri dishes
    • Pipettes (used for EVERYTHING)
    • Disposable pipette tips
    • Microcentrifuge tubes
    • Boxes with little dividers for freezing things in tubes, and tube racks
    • Freezers (4, -20, and -80 Celsius)
    • Autoclave (a kind of steam sterilizer; usually common to multiple labs)
    • Heat/stir plate and stir bar magnets
    • Small spatulas, forceps, scalpels, razor blades, “scoopulas” (cross between spoon and spatula)
    • Beakers, flasks, graduated cylinders, other glassware
    • Test tubes (although I use these less than the microfuge tubes mentioned above)
    • Centrifuges, spectrophotometers, and other larger equipment
A pipette and Petri dish with medium (Image source)
A lady with some cool lab glassware. (Image source)

 

So that post was a little bit longer than I meant it to be, and it didn’t even include anything about specific techniques that are often used in biology. If there’s interest in a post about techniques, let me know in the comments and I’ll drum up something for next month!

That’s it for me this week! Did you find the day-to-day of science interesting? Do you think it will be helpful to you? Would you like to hear about techniques? Isn’t lab glassware awesome? (I’m going to be that person with chemistry-themed dishes someday!) Are you interested in becoming a scientist? Let me know in the comments!

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Story Starters #10: A Wizard of Earthsea

The island of Gont, a single mountain that lifts its peak a mile above the storm-racked Northeast Sea, is a land famous for wizards.  From the towns in its high valleys and the ports on its dark narrow bays many a Gontishman has gone forth to serve the Lords of the Archipelago in their cities as wizard or mage, or, looking for adventure, to wander working magic from isle to isle of all Earthsea. Of these some say the greatest, and surely the greatest voyager, was the man called Sparrowhawk, who in his day became both dragonlord and Archmage. His life is told of in the Deed of Ged and in many songs, but this is a tale of the time before his fame, before the songs were made.

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Good morning, everyone! Happy Monday and welcome to December! For this first Monday of the month, I am as usual analyzing the first paragraph of a novel. A Wizard of Earthsea is an excellent classic young adult fantasy by Ursula K. Le Guin (see my review for more!), which I highly recommend. Having been originally released in 1968, however, its opening isn’t quite as gripping as other’s we’ve looked at. Let’s break this down sentence-by-sentence.

  • The island of Gont, a single mountain that lifts is peak a mile above the storm-racked Northeast Sea, is a land famous for wizards. So this might not be the most immediately engaging opening line ever written (personally, I prefer openings that start right off with character action or dialogue), but it still catches the interest, which, as K.M. Weiland writes, is required for a hook. Why? Well, I think the answer is in two things: genre and phrasing. Genre, because as a fantasy novel should, this describes an interesting setting far outside the average experience, which helps to catch interest. Phrasing, because of the short-long-short phrase structure within the sentence (look at where the commas are). There’s a graphic I’ve seen floating around the Internet about how varying sentence length and structure reduces boredom in the reader, and I think it applies here to phrases within the sentence as well. In fact, if you want to go really far, you could say it echoes the three-act structure typical of writing in general. No matter how far you go with it, the phrasing does keep reader interest, in a slightly intangible and intriguing way. And of course, the mention of wizards doesn’t hurt; it helps reinforce what we expect from the title.
  • From the towns in its high valleys and the ports on its dark narrow bays many a Gontishman has gone forth to serve the Lords of the Archipelago in their cities as wizard or mage, or, looking for adventure, to wander working magic from isle to isle of all Earthsea. Ah, back to my later point on the previous sentence, here’s a longer sentence to support that shorter hook. The hook can’t reveal everything at once, so this second sentence is here backing it up. By now we can gather that there’s going to be an omniscient narrator, not uncommon in older works, and that this narrator is currently setting the scene, giving us the historical context before we actually get to our character. Of course, it’s dangerous to do too much of this, which is called “infodumping;” we want to save tidbits for later reveals, both in the cases of backstory and worldbuilding. In this case, though, it’s appropriate; we have just learned a little about Gont, and now we learn a little more, and that there’s a whole Archipelago out there of which Gont is only a part. And the wizard theme is reinforced once again, which leads into our next sentence.
  • Of these some say the greatest, and surely the greatest voyager, was the man called Sparrowhawk, who in his day became both dragonlord and Archmage.
    Aha, our character makes an appearance (if only through the narrator talking about him)! And now that we have some background, we think, “Of course the greatest wizard came from Gont. Gont is known for wizards. Doesn’t everyone know that?” It makes sense with the information we’ve already been given. And the shorter sentence holds our attention better than if we’d been given another behemoth like the second sentence, which is good for introducing the main character. Oh, and dragons–don’t you want to keep reading now?
  • His life is told of in the Deed of Ged and in many songs, but this is a tale of the time before his fame, before the songs were made. Wow, this guy really is important–they made songs about him! Oh, but we realize now that this story is about something the songs don’t tell about, which heightens our interest, because even if said songs are fictional, we like having exclusive information. This sentence completes the hook started in the first sentence.

Overall, this paragraph led in very nicely from setting scene and historical context to the context of our character, which in the next paragraph, will become a sort of biography of his early life. Although not necessarily something used in today’s fiction, this “funneling in” technique works well for A Wizard of Earthsea.

That’s it for me today! Have you read A Wizard of Earthsea? If not, I’d love to know: did this post make you more interested in it? What do you think of setting the scene in your opening? Any further analysis that I may have missed? Tell me in the comments!

My Life This November: In Which College Life is Crazy and I Give Up on NaNoWriMo

Hi folks! It’s the last Monday of the month (already), which must mean I’m here telling you all about my life. It’s been a little crazy this month (isn’t it always? I can’t remember the last time I had a quiet month), so I shall try to organize my thoughts by putting them into semi-coherent sections, and hopefully thus not overwhelm you all. Here goes!

Student Life

Ah, the dominant section in the great dichotomy of my life. Well, by November, the fall semester is always in full swing. All my classes have ramped up considerably; we’re doing unknown labs in microbiology and the very complex topic of intermediary metabolism in biochemistry, and I have three exams on December 1st, lucky me! But at least I had Thanksgiving break this past weekend; happy Thanksgiving, everybody! I’m thankful that I got to sleep in for three days in a row (luxury!). And I’m also thankful for time spent with family this weekend, and creative time (more on that later), and that I registered for spring classes before Thanksgiving–yay! Next semester, I will officially be taking Genetics of Prokaryotic Microbes, Biochemistry II, Biostatistics, and Plant Systematics, which I’m the most excited about because I love plant classes.

Research-wise, I’ve been plugging right along. In two weeks, I should see the end of a long experiment involving rice leaf development that I’ve been working on since September. Then, over winter break, I plan to get cracking on all the work I haven’t been able to do by being busy with classes, as well as running another drought/salt experiment (I just love torturing rice plants, haha). But before then, we will of course have Christmas, and I’ve enjoyed watching decorations get put up this weekend, though I haven’t been able to participate because of studying. It’s so strange to think the year is almost over already. But more of that next month.

Writing and Creativity

Those couple paragraphs I wrote above do not convey how completely school has taken over my life. Yet I’ve had more creative time this month than I thought I would. I started the month on the whim of doing NaNoWriMo again, knowing how good it was for me last year, and I epically failed. I got almost to 2,000 words in two scenes, and that took five days. I have concluded from this (and other) experiences that you really can’t force creativity. Don’t get me wrong, writing every day and being super disciplined like that is amazing, and I admire all you who do it; but I’m at a stage right now where it’s more beneficial to the quality of my work (and my mental health) to go with the flow, write whatever comes into my head, create however I feel like it.

So writing-wise, I haven’t gotten much done. I’ve picked at my Windsong reboot a little (I actually need to finish a scene), and it’s at about 18,000 words, which I’m proud of. I did decide, against the conclusion of my last paragraph, to do a disciplined rewrite of Circle of Fire, last year’s NaNo novel, but first, I’m writing a synopsis for it. So far, I’ve almost finished the rough draft of that. I meant to work on it more this past weekend, but I got caught up in the visual arts; I don’t usually think of myself as being inclined toward, or having any talent in, painting or drawing, but I started a watercolor a couple weeks ago, found it fun, and on Thanksgiving surprised myself with a decent pencil drawing of one of my characters. It’s always good to have creative outlets other than writing, and I think I’ll be doing more visual stuff in the future when things pop into my head.

That’s it for me this month! How was your month, and your Thanksgiving? Did you do NaNo this month? Did you win, or give up like I did, or something in between? Did you not do NaNo but still write? What are your creative outlets other than writing? If you’re also a college or high school student, how’s your semester going? And have you started decorating for Christmas yet? Share in the comments!

 

 

Thoughts on The Two Towers, Part I

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Good morning, everyone, and happy Monday! Normally today I would do the Beautiful People link-up, but since this month it’s about NaNoWriMo and I’m not participating (anymore *cough* I gave up), I wanted to share some thoughts about one of my favorite books with you.

Every year and a half or so, I get a gut feeling that it’s Lord of the Rings time again. I love The Lord of the Rings. It’s my absolute favorite book ever and probably the single greatest influence on my writing over my lifetime. And (you guessed it) it’s Lord of the Rings time right now! Right now, I’m almost finished with The Return of the King, the third part, so that means I’ve recently finished The Two Towers, the (I think) underappreciated filling in the Lord of the Rings sandwich. And I have some thoughts on it, which I’ll share below! (There are, of course, spoilers here for anyone who has not read The Lord of the Rings.)

The Two Towers: The Bridge of The Lord of the Rings

As it says in the header, it is my opinion that The Two Towers (which, for simplicity, I’ll refer to as TTT for the rest of the post) is really the bridge of The Lord of the Rings (LotR). In other words, without it, The Fellowship of the Ring (FotR) and The Return of the King (RotK) would be lost and alone and probably make no sense. TTT pulls it all together in many ways.

Probably the most important thing about TTT is that everything is interconnected, at least within each of the two major parts, Book III (which follows Aragorn, Gandalf, and the rest of the fellowship after its breaking) and Book IV (concerned with Frodo and Sam’s journey to Mordor). In writing this post, I found that when thinking about one element of either book, three or four elements it was connected to would pop up. I attribute this to J.R.R. Tolkien’s seamless weaving together of storylines into one vast epic, and indeed this is one of the qualities that make LotR as a whole so enduring. TTT is an excellent example of this beautiful interweaving.

So what are some of those elements I was talking about? In Book III, let’s take Saruman. Saruman was introduced, but always off-screen, in FotR when Gandalf told the Council of Elrond about his imprisonment in Isengard, Saruman’s stronghold. In TTT, he is a much more present menace; for instance, it is revealed that some of the Orcs who captured Merry and Pippin at the end of FotR are acting on Saruman’s orders, to bring back hobbits, alive. They fail, of course, when Eomer and the Riders of Rohan intercept and destroy them. This leads us into the role of Merry and Pippin (who coincidentally constitute one of my favorite literary pairings ever), who, after escaping from the Orcs, wander into Fangorn forest and bump into Treebeard and the other Ents. This seemingly minor movement of two small characters proves to be earth-shattering (literally), when the information Merry and Pippin bring galvanizes the Ents to break Isengard.

This is one of the instances in which TTT reinforces one of LotR’s key themes: even the smallest people can change the world, especially when they don’t intend to. Merry and Pippin didn’t set out with Frodo to become great in their own right, but only to support him in his journey. But because they refused to be left behind, in the Shire and again in Rivendell, they became two of the most important movers and shakers in the War of the Ring. And their combined influence in TTT set them up to go even further when separated during the events of RotK.

Right, where was I? Oh, yes, Saruman. Another key personage who is intimately connected with Saruman is, of course, Gandalf. The end of FotR saw Gandalf fallen in the Mines of Moria, supposedly never to return. In TTT, however, it is revealed that he has in fact survived (or died and risen–I’ve always found the distinction rather ambiguous), and has returned to continue supporting Frodo’s quest by orchestrating the War west of the River Anduin. He takes up this role most fully in RotK, but first, Gandalf must deal with Saruman. He first throws Saruman’s influence out of the land of Rohan (more on that later), then rides on to Isengard, where he proves his primacy by asserting power to cast Saruman down from his high horse, as it were.

So in TTT, Gandalf grows (debatably–I suppose he always had this in him) into his new role as the head wizard and war-orchestrator, which he takes on more fully in RotK. His new primacy makes the reader wonder, though: if Gandalf is greater than Saruman, isn’t he on a level with Sauron? He is so wise and powerful; shouldn’t he have taken the Ring and taken Sauron on one-to-one, rather than sending Frodo with the Ring to Mordor? But deep down, we know that Gandalf would ultimately have been corrupted by the Ring, and that he did the wisest thing possible in sending Frodo. This also gives more impact to the climax of LotR; when the Ring is cast into Mount Doom, and Sauron is overcome, it has that much more impact because we know that little Frodo and Sam did something that great, wise Gandalf could not have done. Again, TTT reinforces that overall theme of the influence of seemingly unimportant people.

Then there are the other pieces on the chessboard of TTT: Rohan with its king, Theoden, and the other members of the Fellowship, Aragorn, Legolas, and Gimli. Like Gandalf, Aragorn grows during TTT into the king he was meant to be, and will become in RotK. He is sure of himself; he makes executive decisions, like when he goes west after Merry and Pippin rather than east after Frodo and Sam at the beginning of TTT, and it is clear that Legolas and Gimli acknowledge him as their leader. But he is not overconfident or over-proud; once they meet Gandalf, he submits to his authority, which he will continue to do in RotK, because he knows Gandalf is wiser. And he always treats Legolas and Gimli as equals, and befriends Eomer, who is much younger than he is. This last move pays off in RotK when Eomer and Aragorn are both kings and become official allies.

Rohan is also an important piece of the puzzle. Without Theoden and his host, Gondor would have failed in RotK at the Pelennor Fields, and the quest of the Ring most likely would have failed as well. But without the events of TTT, Theoden and his host could never have come to Gondor’s aid. For starters, it was Eomer’s Riders who ambushed the Orc host, allowing Merry and Pippin to be freed and having a domino effect on the rest of the story as discussed above. And if Theoden King had continued to despair after Gandalf cast out Wormtongue, or had given in to Saruman’s voice at Isengard, Rohan would have been bereft of a leader and probably overwhelmed by Saruman’s forces. Instead, they won the battle at Helm’s Deep (with the help of the Huorns, another piece moved by the hobbits’ escape) and lived to help Gondor and ultimately stand before the Black Gate of Mordor at the climax of RotK, with the other peoples of the world.

Well, those are my thoughts on Book III of LotR, the first book of The Two Towers. I was going to put my thoughts on Book IV in here, too, but I think this is long enough for one blog post. Come back next month for my thoughts on Frodo’s journey to Mordor!

That’s all for me today! What do you think? Do you have anything to add to my thoughts on TTT? Which installment of LotR is your favorite? Who are your favorite members of the Fellowship? Tell me in the comments!

 

Biology for Writers: The Human Microbiome

Good morning, everyone! Happy Monday! It’s the second week of November (already!), so here I am with a quick post on a bioscience topic which may be of interest to some of the writers who read my blog (and don’t have that much background in science). Let’s get right to it!

The Overview

One of the biggest topics in science right now is the human microbiome. What is a microbiome, you ask? Well, it’s simply the entire set of microbes that inhabit the human body.

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Yes, that’s right–there are microbes in you, right now, and they’re even supposed to be there! As a matter of fact, there are more bacteria, archaea (basically extreme-environment microbes), and unicellular fungi in your body than there are human cells. Yes, you heard that right–we humans are more microbial than human. Blows your mind a little, doesn’t it?

So what do these microbes do for us? Are they good for anything, or do they just sit there? Well, my friends, I’m glad you asked. Let’s take a look at some of the parts of our bodies where our normal microbes are most influential.

The Mouth

We all know about dental plaque, and brushing our teeth so we don’t get it. (Seriously, I hope you all brush your teeth, ’cause plaque is disgusting.) But your mouth also contains 50-100 billion normal bacteria of at least 500 different species, mostly anaerobes, or bacteria that don’t require oxygen to live. (In fact, some anaerobes die when exposed to oxygen.) Streptococcus mutans and S. sanguinis, the organisms that cause plaque when they build up into a biofilm, are both “facultative anaerobes,” which means that they can either use oxygen or not depending on conditions in their environment (the mouth). Many other normal mouth bacteria can cause problems for the human host if there is bleeding in the mouth, or some other abnormal condition, bringing up an important point for the microbiome in general: Microbes that are normal inhabitants of our bodies (“normal flora” or “microbiota”) can be pathogenic if they are moved to a different spot or if something abnormal happens. These are called “opportunistic pathogens,” and we’ll see more of them as we move through the body.

The Gastrointestinal Tract

This is one of the places where the human microbiome is most important and best characterized; a lot of work has been done linking the gut microbiome composition to everything from diet to Parkinson’s disease. And gut microbes do a lot for us. For instance, we can’t digest vegetables without our gut microbes, and other microbes make vitamin K for us. That’s pretty darn helpful of them, don’t you think?

But when I say “gut microbiome,” what am I talking about? It turns out that not every part of the human body is colonized by microbes; accessory organs such as the liver and pancreas are sterile, and the stomach has a very low level of microbes due to the high acid content there (the stomach’s pH, a measure of its acidic content, is about 2–so very acidic). Not many things can survive the acidic environment of the stomach, which is why it’s great for digestion. One Helicobacter species, however, survives by burrowing into the stomach lining and secreting basic compounds, which neutralize the surrounding acid to create a neutral pH (good for life). This species can also cause stomach ulcers when it has lived in the stomach lining for a long time.

So if the stomach doesn’t have very many microbes, where is this gut microbiome I’ve been telling you about? Most of the gut microbiota live in the ileum (the last part of the small intestine) and in the colon (also known as the large intestine), where, as I mentioned, they help us digest our food, give us nutrients, and take up space so invaders can’t enter. This is known as a “mutualism,” in which both symbiotic partners benefit from their relationship. How do the bacteria benefit from us? Well, most parts of the body are at a neutral pH, which as I’ve already said is good for life, and they remain at a constant warm temperature, which allows microbes to grow.

I also just want to point out quickly that taking too many antibiotics can interrupt your gut microbes, and thus actually make you susceptible to sickness, since with space freed up by antibiotic treatment, pathogens can easily colonize your gut. Since this post is mainly about the microbiome, that’s all the space I can give to this extensive topic, but if you’re interested in learning more, feel free to comment below!

The Skin

The skin is one of our first defenses against microbes, since we are constantly sloughing off dead skin cells, but it is also colonized by many microbes. Similar to the gut microbiome, these take up space on your skin, preventing infection by pathogens. The skin microbiome also includes Staphylococcus aureus, an opportunistic pathogen which normally lives on the skin surface, but can cause problems when it penetrates deeper into the body. For instance, if you have a deep puncture wound, your normal S. aureus may get under your skin (literally) and cause nasty carbuncles and things when it infects you. So if you’re writing a novel and your character gets wounded, this is one thing that could follow that up if you want to give them extra torture be realistic about the consequences of wounding.

Find out More!

Here are some resources if you’d like to find out more about the human microbiome!

Human Microbiome Project–This would be a great resource if you want to find out some of the specific microbes that exist in each place on the human body (there are many, many more microbes than the ones I talked about today).

The Gut Microbiome in Health and Disease–A scientific paper about the gut microbiome. (Please note this is intended for a scientific audience, so it may be a bit dense.)

When Gut Bacteria Change Brain Function–An interesting general-audience article about how gut bacteria impact the brain.

I will continue to add more resources here as I find them! If you find interesting resources, feel free to let me know in the comments and I will consider adding them to this page.

That’s it for my first Biology for Writers post! Are you thinking of using the microbiome in your story? If so, how? Is there anything else you’d like to know about the microbiome? (I’m definitely not an expert, but I can point you to more resources if you’d like!) Are there other biology topics you’d like to see addressed in this monthly post series? Let me know in the comments!

Story Starters #9: The Two Towers

*Spoiler alert for anyone who hasn’t read this far in The Lord of the Rings*

Aragorn sped on up the hill. Every now and again he bent to the ground. Hobbits go light, and their footprints are not easy even for a Ranger to read, but not far from the top a spring crossed his path, and in the wet earth he saw what he was seeking.

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Good morning, everyone! It’s the first Monday of the month, and that must mean I’m here analyzing the first paragraph of a book. I currently have the joy of re-reading The Lord of the Rings, for what must be the fifth or sixth time, and recently finished The Two Towers, the underrated middle of the epic. So naturally I thought I’d analyze the beginning of that book today! Let’s break it down line by line.

  • Aragorn sped on up the hill. This starts with a character, and it’s also an action, which is great for getting the reader interested in what will happen next. In addition, since this is a sequel, it picks right back up where The Fellowship of the Ring left off.
  • Every now and again he bent to the ground. Another action. We get the hint that Aragorn is looking for something, without needing to be told.
  • Hobbits go light, and their footprints are not easy even for a Ranger to read, but not far from the top a spring crossed his path, and in the wet earth he saw what he was seeking. This sentence makes up most of the opening paragraph, and the two shorter sentences before it lead nicely into the longer phrasing. It also reintroduces some things from the previous book: the involvement of hobbits in this story, the worldbuilding fact that they’re hard to track, and the fact that Aragorn is a Ranger, a Numenorean of the North, which will become important later on. Aragorn’s searching for hobbit footprints here also nicely foreshadows his spending most of the book searching for the two captured young hobbits, Merry and Pippin.

Overall, this first paragraph starts with a character doing an action, picks up where the previous book left off, and reminds the reader of things that have been and will be important to the story, particularly regarding our opening character. It also foreshadows events important to how this book will play out. A good beginning, all in all!

That’s all for me today! Have you read The Lord of the Rings? Did you like The Two Towers? What do you think of its opening? Anything to add to my thoughts? Tell me in the comments!

I’m Back! Or, My Life This Summer and New Plans for The Story Scientist

Hello, followers! I’ve returned from my long hiatus! Yay! I’m so happy to be back with you all.

Now of course your question is, “But Anna, where have you been for the last six months?” Yes, I know. Six months is a long time. As such, this will be kind of a long post. I have a lot of exciting things to report, including new plans for this blog, as advertised in the title. So let’s begin!

Life

So I left you six months ago at the end of April, and a lot has happened since then. (No, I’m totally not being redundant. Why do you ask?)

In school: I finished my sophomore year. Yay! And now I’ve started my junior year. Small yay. I’m very busy and it’ll be a much bigger yay when I finish junior year. Anyway, I am currently taking General Microbiology, Applied Plant Genetics (which has no exams–!), Genomics and Bioinformatics (in which computers and I have a love-hate relationship), and Principles of Biochemistry I. That last is my major source of the dreaded College Nightmare this semester–for instance, before the first exam I dreamed that my professor spent 35 minutes of the exam period talking about what a hard grader he is, and didn’t hand out the exam until there were 15 minutes left . . . but I digress. Bottom line is, I’m doing well in all my classes so far, and more importantly, enjoying them (most of the time).

This summer, I also participated in a great full-time research program, in which I spent 35 hours a week doing my rice drought-and-salt-tolerance research. I’m still working on the preliminary work for that project now, actually. I’ve learned that research is incredibly slow and complex, and if you want to do anything big at all, it takes a lot of work and a lot of time. And yet I love it. I’m passionate about it. (I actually realized this because I was agonizing about it the same way I do about my writing, funnily enough, so that must mean I’m on the right track!)

I also did a lot of traveling this summer. In late May, I visited Pennsylvania for the first time with my family! We went to Pittsburgh, Fallingwater (a beautiful Frank Lloyd Wright house–look it up if you’ve never heard of it before!), and Punxsutawney, the home of Groundhog Day. Pennsylvania’s hills are massive; they really make New Hampshire look flat. Pittsburgh was surprisingly a great city; I think it’s really underrated. The Carnegie Museums of Art and Natural History were a real highlight, as was Point State Park.

In June, I went to a conference in Atlanta, Georgia with my summer research program. It was weird being in Atlanta twice in six months (including the Georgia Aquarium), but in a cool way, and the conference was great for learning about graduate school and how to get there. And at the end of July, I went to another conference at UC Berkeley, where I a) presented my research, b) went out of the Eastern Time Zone for the first time ever, and c) visited San Francisco for a day! (Don’t ever try to do it all in one day. It’s much too big.) My favorite parts of San Francisco were the Golden Gate Bridge (it is NOT overrated) and Lombard Street, the crookedest street in the world. We also got to ride on a traditional trolley to get to Lombard Street, which was so much fun! And traveling is always better with a couple good friends along. If nothing else, they give you something to take photos of.

In short, life has been incredibly busy, but I love research, traveling was really cool, and in just seven short weeks the semester will be over!

Writing

. . . Or, the lack thereof.

Because of all the aforementioned busyness, I haven’t written very much at all. When I left you, I was working quite seriously on editing Circle of Fire, only slightly less seriously on outlining This Hidden Darkness, and I’d given Windsong a break altogether. Now, as ever, things have changed. Windsong has started up again, as a very loosely structured reboot (read: I write when I feel like it, whatever scenes may come to my mind, and I’m hoping a four-book series will magically appear). I got out of the editing groove for CoF sometime before going on vacation in May and haven’t gotten back in yet, though I have some germs of ideas that need sitting down and developing. And unfortunately for the main character, THD has gone entirely to the backburner, to be written “later” when I have more inclination for it.

All this may well seem wishy-washy. It seems that way to me quite often. My perfectionistic mind has been going around and around lately; why am I not writing every day, what’s wrong with me? The answer, of course, is partially that by the end of a day full of science classes and research and so on, my brain is drained. And creativity takes brainpower; I can’t just whip off beautiful writing without staring at the computer screen for a long time. And that’s the other part of the answer, time: between research, coursework, tutoring, and applying for scholarships/fellowships, I’m much too busy to do much writing.

Which is obviously why I’ve created a novel for NaNoWriMo next month.

Stay tuned if you’d like to watch me crash and Burn (the title).

New Plans (As Advertised)

And now, the part you’ve all been waiting for!

So, obviously, I’m resuscitating my blog, and you want to know if it will be just like it was before. The answer is a resounding No, followed by a wimpy But It Will Be Similar. Let’s break this down into categories.

1) Posting Schedule. As you may have noticed, it’s Monday, not Saturday. I will now be posting things on Mondays so I can have the weekend to work on them, rather than scrambling on Friday night to write a post for the next day. I will, however, continue to post weekly (except for this upcoming Christmas, which will be a Monday, so I’ll probably be taking that week off).

2) Types of Posts. Some of these will be the same; for example, Story Starters and My Life This Month will continue to be posted on the first and last Saturdays Mondays of the month, respectively. I will also continue to do science posts, but since I don’t think these were very popular when I was last doing my blog, I want to make them more relevant to writers. My areas of interest and study are plant biology, genetics, and biotechnology, of which the latter two are very popular in sci-fi these days, so I can definitely do some posts on that. If you have any particular topics you’d like to see addressed, drop them in the comments and I’ll take a look!

That leaves one Monday (in most months), which I will probably use for the Beautiful People link-up. I used to do book reviews, and though I enjoyed them, they’re rather time-intensive, so I’m going to stop doing them for now. In months without Beautiful People, which happens sometimes, I’ll probably post a random thought on writing or science or literature, just something of interest. And on those extra-special fifth Mondays, I may do anything and everything: guest posts, special random thoughts, or perhaps book reviews, since those are now out of the regular lineup. That’s just a sampling of what to expect, though!

So I’m back! I had a good summer; how was yours? Did you travel anywhere? Read any particularly good books? Write very much? Do you have any science topics you’d like to see me address? Are you doing NaNoWriMo next month? What are you most interested in seeing on my blog? Share in the comments!

My Life This April: In Which The Semester Winds Down and I Decide to Take a Blogging Break

Hello, everyone! It’s the last Saturday of the month and thus time for my monthly life post. And so I find myself, for the third month in a row, saying that this month was crazy. It’s been a very long semester, between all my classes and research and whatnot, and I’m very excited for next month, when the semester will end and I can hopefully lie around and do nothing for an entire day. That just sounds beautiful to me right now.

I did accomplish some stuff this month, though. The proposal I wrote and submitted last month was accepted, but with revisions, so I learned how to revise a research proposal, which is not a bad skill for someone planning to go on to grad school. I also had the madness of collecting, analyzing, and presenting preliminary research data, all within one week. It worked out well, though, particularly because my organic chemistry teacher (an absolutely brilliant man) stopped by my poster and said my project was really cool. That really made my weekend! It was also great walking around the poster session and seeing all the cool research other students have been doing, including some of my friends.

Class-wise, I took a lot of exams this month–seven, which comes out to one-and-a-third every week on average, if my math is correct. One of those was a laboratory practical spanning two weeks, which was very exciting, because as of this past Wednesday the end of that practical marked my completion of organic chemistry lab; I never have to take it again! Yay! I also registered for my fall classes, none of which are organic chemistry or physics, which is delightful. I’m happy to have a slightly less hectic schedule next semester, though I’m not sure how much I’ll be in the lab.

This brings me to my final point, in my final blog post for a while. Because of all the craziness, I’ve had very little time for writing. I think I’ve worked on Circle of Fire for a total of four hours out of this whole month, if that, and Windsong and This Hidden Darkness have gotten zero formal attention. I’ve realized that, if I’m going to finish any writing, something has to give, and that thing, unfortunately, is my blogging. I’ve really loved making this a part of my routine, and interacting with all you followers has been a joy, but I’m going to have to take an indefinite hiatus. I hope to come back when I have more time in my life and maybe have actually finished a novel; I wish I could give you a definite date, but I really don’t know how long it’s going to take at this point. It will be at least a few months. Do look for a post from me sometime in the future!

Until then, I’ll miss blogging and interacting with you, and I wish you all the best of luck in your endeavors. Thank you all so much for liking, following, commenting, and supporting my blog in general!

I’m so sad to leave you! But unfortunately that’s how it has to be. How was your month? Did you do more writing than I did (hopefully)? How are your projects coming? Are you also wrapping up a busy semester? Tell me in the comments!

Your Questions Answered, Part 2: General Biotechnology

Hi, everyone! Today I have Part 2 of a genetics/biotechnology/general life science post for you. You can check out Part 1 here. Again, thanks to H. Halverstadt for asking these fantastic questions! Let’s get right to it:

How do you think CRISPR and the gene drive will change the future of genetic engineering?

I am of the opinion that CRISPR is one of the most revolutionary advances in biotechnology of our time. The precision with which genes can be edited due to the specificity of the system is just incredible. I would certainly predict that its popularity (with scientists, not necessarily with the general public, especially the uninformed) will soar in the future, although at least for a short time, “conventional” genetic engineering will still be practiced. But given public outcry about GMOs (even if not warranted—a topic for another time), the ability to improve an organism without bringing in genes from another organism could be more popular and, indeed, simply easier, with fewer steps required.

The gene drive is more specific; I think it has a lot fewer potential applications than CRISPR. Whereas CRISPR can be used with most any current genetic engineering application, I really can’t think of an application for the gene drive that is really different from its current uses, combating insect-vector diseases and pesticide/herbicide resistance. They might try to tackle antibiotic resistance with it next, but I don’t think it will have broad-based applications after that. I would predict that CRISPR will be by far the more influential technique in future.

What gradual, irreversible changes to the human genome might happen?

My best idea is that, according to the principles of natural selection, any beneficial-to-survival changes made to a majority of people by genetic engineering (and propagated through the germ line) could eventually become fixed in the population. I’m going to stop there, since I don’t have quite the human or population genetics knowledge to go on.

Can you see cells from certain people being in high demand? What kind of people?

This is a very interesting question. First, instead of cells, I think we’d be talking about DNA sequences; why bother taking the whole cell if you can get just the DNA you want? I also assume here that the question is asking about acquiring copies of someone else’s DNA for non-gene-therapy genetic enhancement. In this case, I expect that genes from athletic people (there are some known genes related to athleticism—I know of one specific case in which a certain allele of one gene is associated with endurance running) and intelligent people (if such genes could be identified—to my knowledge there are none currently) might be popular for making “designer babies” and so forth.

What laws do you think might be passed to regulate genetic engineering?

I’m not as knowledgeable about the legal side of biotech, but currently, I know labeling laws for GMO foods are a big deal. A quick search revealed to me that GMOs are put through testing processes by a few federal agencies before being put on the market to determine their safety. It’s conceivable that a law prohibiting non-gene-therapy engineering of humans could be passed, although presumably not in the kind of society most sci-fi/dystopian writers who read this will be interested in. Besides that, I apologize, but I can’t come up with much.

Is inter-species gene editing something that is possible for humans?

Technically, yes. Ethically, it’s complicated. Personally, I don’t see this as acceptable, but I’m sure some bioethicist out there could make the case that improving human welfare by adding nonhuman genes would be worth the (hypothetical) cost in our humanity.  (A technical note: this seems to me to be less gene editing, and more transgenic expression. Gene editing is messing with a gene that’s already there; transgenics are organisms containing genes from other species.)

Do you see genetic engineering ever being something smart high school students can do in their kitchen?

Absolutely. In fact, this kind of thing is happening today among a DIY biologist or “biohacker” movement that believes science shouldn’t be for academia alone. So far, though, they’re not that scary; national and worldwide organizations like DIY Bio (https://diybio.org/) have been good about organizing events regarding safety and bioethics. It’s not being done to humans, or even vertebrate animals as far as I can tell; there are still too many ethical issues in that area. But yes, as long as you can afford the reagents and equipment, you can genetically engineer a plant or a (nonpathogenic) microbe. I believe even CRISPR is currently accessible for DIY biologists (though it costs about $500—I’m sure the price will go down as it becomes an established part of biotech).

If inter-species gene editing is possible for humans, how about humans and a different category of animals, like birds? 

Again, absolutely; you could put a plant gene in a human cell if you wanted, or vice versa. And I’ve read about glow-in-the-dark animals being created by expressing a jellyfish gene.

Please comment on the feasibility of these fantastical forms of genetic engineering. Winged humans, mermaids, elves, centaurs, giants, dwarves, humans able to breathe lower oxygen air. Do you think any other traits would bleed through? (Like for example, if winged humans had eagle genes, would they have other eagle traits as well?)

First, let me say that “dwarves” already exist; we know them as “midgets.” There are a variety fo forms of dwarfism, some dominant, some recessive, but none require genetic engineering. By “elves” I assume you mean basically humans with pointed ears. I expect this would most easily be done surgically.

As for “giants,” height is an extremely complex trait. It is quantitative, meaning that it follows a bell-curve distribution in the population, and there are currently thought to be about 700 genes that influence it. So engineering really tall people could be possible, but I suspect it would be inefficient in the incredible amount of effort it would take. Here is my source (http://time.com/4655634/genetics-height-tall-short/) for that, and I recommend you look up more detailed information on that trait if it’s something you’re interested in using in your story. I just don’t know enough about it to be of much help.

The others would be difficult, but theoretically doable in the far future given a masterful understanding of cellular physiology and probably lots of trial and error. For the humans with animal parts (winged, merpeople, centaurs), geneticists would need an almost perfectly complete understanding of development, which, once again, is incredibly complicated and controlled by many, many genes. It is possible that cells could be induced (“programmed”) to differentiate in such a way as to generate animal limbs on a human body, or to replace human limbs with animal ones, but this would also likely require detailed knowledge of the role of epigenetics in development, and complete knowledge of both human and animal development, which would simply take a very long time to achieve. And even then, it’s completely possible that scientists assembling and applying all this knowledge could miss something essential and make some terrible mistakes. Not to mention all the trial and error—what if a limb grew in the wrong place? etc. So, possible, but not probable to begin with, and would need to be masterfully executed.

The “bleeding through” of other traits mentioned in this question is, I would say, almost certainly not realistic. Giving someone wings will not automatically give them, say, sharp eyesight; that would be controlled by other genes (as well as environmental factors). It makes for interesting fiction, but as far as I know, there is no scientific basis for it.

As for the last one on the list, the pertinent process is cellular respiration. You would need to somehow increase the efficiency of this (again) complex process, which is only 39% efficient at capturing the energy in glucose into ATP (look up the basics of the process). I will say tentatively that this could be one of the more feasible things on this list, if only because cellular respiration is already fairly well understood (i.e. it’s not one of the great mysteries of our time) and preliminary studies could be carried out with bacterial or yeast cultures before progressing to human and mouse cultures, mouse trials, and finally human trials.

Here, to make a long answer longer, I want to make a general note about the approval process for human studies. I feel that the “evil scientist does unethical experiments on humans” trope is both overused and inaccurate. Every university, as far as I know, has an Institutional Review Board (IRB) that convenes solely for the purpose of evaluating and approving human-subject studies. This applies not only to clinical trials, but to interviews and surveys in psychology studies, and even to education studies that take class data and use it for research. Even if there is no perceptible risk at all, researchers are absolutely required to provide the subjects with knowledge about risks, so that they can be informed when they sign the form they must sign (even for a harmless survey!). This applies very much more to genetic engineering and so forth. Under this system, it’s very difficult to conduct an unethical study regarding human subjects, and unless social mores shifted in the future, it’s conceivable that the system will stay like this, making it difficult for any of these ideas to get off the ground, due to possible unforeseen consequences of the alterations.

If yes for the above, would reversal be possible, not just for the offspring but for the person in question? For example, if a winged human wanted to be a regular human again, would she be able to be one after extensive surgery and gene therapy?

I would say yes, although it’s completely a guess since I’m not a medical expert. The gene therapy might not even be necessary; though the genes might still be in the rest of her body, if they weren’t being expressed, she could be a “normal” human with nonhuman DNA, as long as her wings were removed. My bet is that the removal could be done with a surgical procedure (albeit complicated, probably, to remove the whole wing skeletal structure).

 

 

Your Questions Answered, Part 1: Biomedical

Hey, everyone! A couple weeks ago, I put out a call for questions from writers about sci-fi genetics things. Genetics and biotechnology are becoming really popular in science fiction, going right along with the scientific revolution they’re currently undergoing, and as a genetics major, I really like to see these topics accurately portrayed in fiction. Thank you so much to Victoria Howell and H. Halverstadt for asking these questions!

Is it possible in the future that a compound could be invented to speed up healing of all tissues?

The short answer is: anything’s possible, right? Actually, tissue regeneration, which is kind of similar to this question, is becoming a big thing; I knew someone once who was applying to a tissue regeneration master’s program at Brown University. As this article explains, though, speed healing is a tradeoff for accuracy in rebuilding tissues (the article also has some other great thoughts about regeneration, more than I can tell you, if anyone’s interested).

How do you think people in the future would respond physiologically to bacterial and viral infections?

I would say essentially the same way they do today, and presumably the same way they’ve been responding for thousands of years. Evolution (or adaptation, if you prefer) is a really slow process. It’s very difficult to imagine that, even in a thousand years, humans will have evolved something radically different from the current immune system; think of the expression, “If it ain’t broke, don’t fix it.” (But if a really aggressive disease swept through and wiped out everyone who couldn’t cope with it . . . who knows?)

In a society where human genetic engineering is commonplace, how do you think sickness would be affected? What kind of diseases can’t be eradicated by genetic engineering or vaccines?

This is a difficult question. In theory, humans could master the incredibly complex immune system and ramp it up somehow by genetic engineering, but that’s a far-off possibility. I don’t think genetic engineering would impact infectious diseases so much as terminal illnesses, and certainly genetic diseases. (Sure, if someone had a genetic predisposition to an infectious disease, someone could use gene therapy to reduce their risk of that disease, but I’ve actually never heard of a case like that.)

As far as eradication, some kinds of diseases are easier to eradicate than others. Smallpox was a good candidate for eradication for a couple reasons: 1) it has no animal vector (i.e. doesn’t spend part of its life cycle in an animal or an insect somewhere, which makes diseases very difficult to control—think malaria), and 2) when you’ve had smallpox once, you don’t get it again. Anything that doesn’t fit these criteria (which is a lot of diseases!) is difficult to eradicate, although the gene drive is being tested against malaria and other mosquito-vector diseases (see this post). Any kind of parasite (think tapeworm) could probably be eradicated with good living conditions (you don’t hear about Americans getting parasitic worms, do you? But they’re all over third-world countries). So bottom line, it’s hard to say, but it really depends on the kind of disease, what resources are available, and how much time is available to develop those resources.

What are the possibilities of a pandemic happening?

So a “pandemic” is defined as a disease outbreak that becomes prevalent over an entire country or internationally. This actually has happened and will probably happen again; H1N1 (swine flu), Ebola, HIV, and (I believe) Zika all count as pandemics. What I think this question is actually getting at is the probability of a world-decimating pandemic, and that’s hard for me to say with my limited medical knowledge. My guess is that it could happen, and if it did, it would devastate third-world countries with few public health efforts first, and unless it was an extraordinarily fast-spreading pathogen, advanced countries like the US would have plenty of time to prepare vaccines and minimize cases.

Cyber limbs are becoming more common every day. What limitations might someone with cyber technology face?

This is really more a computer science thing, as far as I can tell, but I’ll do my best to give thoughts from the biology side—just take everything I say here with a grain of salt. J So my guess is that cyber limbs would require some kind of wiring into the brain, for starters, and that would require some really tough, non-rustable wires (they would have to be metal coated in nontoxic plastic or something). Also, the body often rejects foreign objects, like nonsimilar organ transplants, as being “nonself,” causing the immune system to go on full attack mode and eventually making the person very sick. I expect this would happen with cyber technology as well. (I’ve actually heard of research projects dealing with the difficulty of creating bioadhesives compatible with the body, for transplants and what have you.) So my guess is most of the problems would be during the implantation phase.

Do you see new disease mutations happening to replace any that are eradicated? What kind of diseases do you think they would be, and how do you think people in this future world would physiologically respond to them?

To the first part of the question, I say absolutely. Disease organisms, like all organisms, mutate all the time. To give some background information, the average error rate per DNA replication cycle (which is all the mutation rate is, really) is one error per 106-108 nucleotide base pairs. That’s one error per 1 million-100 million bases, which is pretty low, really, but when you consider how large the genome is, and how many copies of the genome are present in multicellular organisms, it’s staggering. Taking the 100 million number for the human body, 37.2 trillion cells in the body, and a genome of about 3 billion bases, that comes out to about 1.1 quadrillion mutations in the human body every cell cycle, which is staggering! The moral of the story is, mutations happen in every organism, all the time, so yes, new disease mutations could certainly happen, whether in bacteria, viruses, or fungi.

With regards to human disease response physiology, humans aren’t exactly my specialty, but I expect it would be much the same as today. Evolution is a really slow process, unless humans sped it up by somehow engineering themselves with better immune systems, which is theoretically possible, but I’ve heard the immune system is so complex that I doubt this would be feasible without a technological breakthrough similar to that of next-generation sequencing (which revolutionized genetics and actually created the whole new field of genomics).

How do you think aging would be affected by genetic engineering and advanced medicine?

This is an intriguing and highly relevant question. Aging is one of the great scientific mysteries of our time, and as you can imagine, there are many scientists out there who are devoted to conquering it. To give some background, there are several current hypotheses about how aging happens. First, and perhaps most prevalently, the telomere theory: telomeres are the ends of our chromosomes, which shorten with each successive DNA replication. There is an enzyme called telomerase which re-lengthens them, but eventually, as we age, our telomeres shorten further and further, and the theory is that this contributes to the decline of our cells as we age. (This hypothesis is supported by the fact that cancer cells’ and germ-line cells’ telomeres don’t shrink at all.) Another hypothesis is called “antagonistic pleiotropy,” the idea of mutations accumulating in body cells (see above question), eventually reaching a detrimental level. Of course, one’s environment also plays into aging; people who eat healthy and so forth “age better” than those who don’t.

With that very long background discussion, we can get to some of my educated guesses. Perhaps humans would be able to engineer some kind of hyperactive telomerase to prevent the degradation of telomeres, or an extra-corrective DNA polymerase that could go back and fix its mistakes at a higher rate than normal DNA pol. And it might eventually be considered a form of gene therapy to go back and “fix” a person’s aged genes and try to make them younger again (although it’s a long shot that this would work, in my opinion). Environmental factors, of course, can always be improved; good diets, for example, might become more prevalent in the future.

***

That’s it for me today!

What do you think? Does this apply to any of your writing? Have you thought about these questions before? Do you have any follow-up questions? (I might not be able to answer them all, but I’ll give it my best shot!) Tell me in the comments!