After a year of eager anticipation by show viewers, and a year of book readers being annoyed that they’ll no longer know what’s going to happen in the next episode, Season 6 of Game of Thrones is finally upon us. This week has been full of GoT anticipation on my Twitter and Facebook feeds, and I’ve passed several hours in the cell culture lab listening to The World of Ice and Fire audiobook. So with the show and story full in my mind I’ve decided to take a nerdy detour from the last two weeks of practical guides for writing manuscripts to talk about dragons and white walkers.
While perusing through my social media feeds and listening to the Westeros backstories these past few weeks, I’ve pondered why exactly this world and this show is so popular. It’s not the first show to deal with family dramas or power struggles mirroring those in our own history, nor the first one to bring fantasy elements like magic and dragons to life, but this one can strange as it seems, make it feel realistic. Everyone can relate to how love or hate drives people to do crazy things, how sometimes the struggle is not as clear cut as good versus evil, how sometimes the good guys lose, and how everyone’s looking for something that they think they deserve, whether it be retribution or glory or power.
Part of the big attraction, at least for me, is the incredible characters. They have flaws and struggles, they learn from their experiences, and sometimes just can’t catch a break despite being good people (here’s a toast to you, Sansa Stark). We all know people in our lives that mirror these characters, whether they’re vying for the iron throne or just take up all the time during lab meetings. Game of Thrones is such a great story and show because it’s not the perfect fairy tale we were told as kids, but is more of a realistic reflection on the challenges we face in our own world, whether we’re armed with dragons, valyrian steel, or just our own wits.
Graduate school and scientific research can also feel a bit like a Game (of Thesis, in our case most of the time). Whether it’s committee meetings that feel like the Small Council discussing your fate, or daydreaming of being able to graduate using a Trial by Combat, there’s certainly a few ways that the show and the story can reflect on aspects of the lives of scientists and researchers. This week’s post will focus on a few take-home messages from the GoT storyline, talking points that I feel reflect on graduate school and life as a researcher. And while there may not be one Iron Throne of Research that we’re all vying for, we’re all looking for something.
Dragons, prophesies, and steel are good, but a quick wit and hard work ethic can take you just as far. There are several characters and houses that rose to power for obvious reasons. Dragons for House Targaryen, gold for House Lannister, and being really good at shoveling snow for House Stark. It’s easy to see how resources and tools at your disposal can set you apart from the competition, and can make you stand out as a power in your own right. But one of my favorite things about Game of Thrones is that the little guys have a part to play, too, and not an insignificant one at that. Characters like Littlefinger and Varys didn’t come from powerful families (and until we finish the series, we can’t be sure of their honest intentions) but they’ve emerged as players and leaders in the Game through their wits and their knowledge. This is also the case for historically weaker houses such as the Tyrells (read about their back story here) who emerged to power not using, well, power, per se. Through good strategy, patience, and knowing when to stand your ground and when to back down, even minor pieces of the game can emerge to become powerful players.
While scheming or back-stabbing is not recommended in research, you should never compare yourself to what other people have in terms of skills, resources, etc. Never underestimate the power of your own knowledge and abilities, and use your patience and wits to work towards your goals in your career. While you may look at others and only see the things they have that are better than you, whether it be in terms of publications, facilities, or the honorable name of their House (e. g. University), remember that in the end you are the one that can take yourself as far as you want to go. Another thing to remember is that even ‘small’ people can also make an impact, or in the case of Tyrion Lannister, ‘cast a large shadow.’ Don’t lower your own achievements because you didn’t save the world outright. If you make something slightly better, or figure something out that wasn’t known before, then that’s something.
Take-home book quote: Keep your mind and wits sharp! "A mind needs books as a sword needs a whetstone, if it is to keep its edge"
Make things right where you are: avoid blazing ahead and leaving things unfinished behind you. I hear a lot of book readers and show watchers look at Daenery’s storyline and say ‘Come on, girl, get those dragons and fly over to Westeros! What are you waiting for??’ Many criticize Dany’s decision to stay in Essos (and it looks like Season 6 will shed more light on the wisdom of that decision), but I like the reasoning she had here, regardless of all the things that went wrong since then. Instead of blazing ahead to Westeros with her dragons, she saw the problems that a power vacuum had left behind in Slaver’s Bay, and sought to solve the problem of ruthless leadership and a slave-based economy by staying in Mereen as queen. Clearly there has been a learning curve in her success in Slaver’s Bay, but nonetheless her heart was in the right place, and I believe it will end up being a good decision for her personal growth.
The take-home lesson from Dany is that if you want to learn how to do big things well, you need to start small. A good example of this in academic or scientific research careers is how we need to go through the steps from graduate school, then into post-doctoral training/entry level industry jobs, before we’re ready to lead our own research team or take the helm of a research program within a company or institute. If we try just to get through something for the sake of passing through, without learning lessons along the way or working to make small, impactful changes, then it can leave us unprepared. Becoming a professional scientist is a process, one that works best when you take it one step at a time. That way, you make sure we can get to the later stages and be ready for it. On a similar note, don’t pine too much about progressing to the next level before you’ve seen things through where you are. If you feel like it’s time to move on but you can’t find a way to get there, instead of getting frustrated just focus on what you can do to move forward bit by bit instead of regretting what’s already been done.
Take-home book quote: Keep looking forward! “If I look back I am lost.”
Be strategic and have a plan, but be flexible and get your hands dirty when need be. The battle of Blackwater Bay is a great example of how being well-prepared can seal a victory. Tyrion’s preparedness and forethought helped win the day, despite the numerous challenges in terms of the size of Stannis’ navy. But despite all the extensive planning he did, in the heat of the moment Tyrion had to throw on some armor himself and see to getting the work done that needed to be done.
Being prepared is always a good idea for life as a researcher. Whether it be reading up on literature before you start writing, thinking about your questions and experiments before you dive into work, or having a strategy for networking at an upcoming conference, laying out your goals and ideas ahead of time can set you ahead in your career, especially at an early stage. Do everything you can to foresee any challenges that come along, but know that you’ll have to be ready for a quick change or a leap into action if push comes to shove. It could be a last-minute experiment that you didn’t plan for or a conference presentation you find out about a week before-whatever it is, put some armor on and get out there.
Take-home quote: Go for it! "Can a man still be brave if he's afraid?', 'That is the only time a man can be brave"
Be mindful of broken promises and be diligent in keeping your own oaths. The Red Wedding is certainly a good example of broken promises in the Game of Thrones universe, and it’s not the only time people were led astray or had a promise broken. In work and in life, you’ll meet people who will make promises that they don’t keep, or exaggerate their work and their abilities. This is unfortunately just a part of life. There is a good reason to approach everything in research with a skeptical, scientific eye. Keep up your guard and don’t believe anything until you see the data or see the work completed. On the more positive side of things, in your own work you can strive to be one of those who makes and keeps oaths, establishing yourself as a trustworthy collaborator and colleague. Setting yourself up as a reliable person can mean more collaborations, more supporters, and more allies (see the next section).
Take-home quote: Be mindful of promise-breakers, and strive to be the honorable one. “Give me honorable enemies rather than ambitious ones, and I'll sleep more easily by night.”
We all need allies at our side. We all love House Stark, but no one saw anything good coming from Ned’s single-handed attempt to throw Cersei and her family down. Without support, even if you’re in the right, you can’t hope to make much progress when it comes to big challenges. We all need friends, colleagues, and collaborators on our side to get things done, especially with the challenges we face as scientists today. Similar to being an honorable, promise-keeping person, in your career you should focus on getting and keeping people on your side. Be an engaged and courteous collaborator, and find people you trust that can provide the support or knowledge to make the work you do more impactful. In all your scientific interactions, be professional to the people you meet, and don’t let petty arguments or philosophical disagreements cause you to burn bridges between you and other good researchers.
Take-home quote: None of us can do this alone. “When the snows fall and the white winds blow, the lone wolf dies but the pack survives.”
Knowing yourself and your strengths and weaknesses is the first step towards success. Tyrion gives one of my favorite quotes about this topic: “Never forget what you are, for surely the world will not. Make it your strength. Then it can never be your weakness. Armor yourself in it, and it will never be used to hurt you.” In the Game of Thrones universe everyone has some level of expectation set on them, whether it be to meet up to the standards of their House/family or if they have some hindrance/greatness about them. Some choose to follow their own paths and others to follow the recommendations or expectations of others. Tyrion was despised by his family, and he knew it, but he focused on improving his own mind and his own connections instead of letting it destroy him. Brienne was expected to be the Lady of Tarth, but she went and set on her own course for knighthood and honor. Jamie was seemingly forever known as the Kingslayer, but he set to make things right for the sake of his own entry in the book of the Kingsguard (a theme more relevant for the book, perhaps…).
We already talked about the importance of knowing your own tendencies, work strategies, passions, and all the other ways that you are you. Don’t focus on comparing your skillset or yourself to others, but remember that as a scientist your work is on display for all to see, criticize, and evaluate. Know what you can do and what you can’t, work to fix what you can, and be proud of whoever that person is that you see in the mirror. You won’t be the best at everything, but you are you-and that means something.
When in doubt? Fire arrows! Because sometimes that’s all you can do when things get tough, and that’s OK.
So here’s to the next season of our favorite fantasy-family rivalry TV series, hoping that any and all of your favorites are safe, at least for a few episodes. Regardless of how A Song of Ice and Fire finishes or who ends up on the Iron Throne, Game of Thrones will have given us incredible story reflective of the human condition and the flaws and challenges we all face, whether there be dragons or just fire-breathing PhD committee members.
Last week we began our how-to-guide with the key steps that need to be taken before you start writing a manuscript. We stressed the importance of reading, both the scientific literature relevant for your field, as well as the benefits of personal reading outside of science. Reading ensures that you have key information fresh in your mind, and also shows you how other people write and construct a story. You will be the one that makes your own unique manuscript, but other manuscripts can show you what a finished product looks like in terms of organization and structure. We also went into some detail on making an outline, or if you prefer, a storyboard. This provides the framework you will build off as you start putting your story together.
Before jumping into the five steps for writing manuscripts, I wanted to touch briefly on your writing environment. I’ve heard some people say that they can only write in a certain setting, that they write better at home or in the office or in a sound-proof room, or that they have specific needs in order to get writing done (e.g., loud music, complete silence, endless coffee, bottomless pretzels, and really anything in between). It’s good to have a process in place or a tool that can help you write, but be cautious of getting stuck in the mindset of feeling like you can only write under certain conditions.
There will be times in your day or your week when you’ll have some downtime, whether it’s 15 minutes or an hour between running experiments or going to meetings. If you’re thinking about ideas for a manuscript, write them down as they come. Even if it’s a paragraph that you only end up using a couple of sentences from, it’s important to get these ideas out there in a tangible form so you can rearrange and polish them latter. Writing is one of the most important parts of being a scientist. It documents both your thoughts and your hard work and transforms them into a story someone else can learn from-so preparing yourself to be ready to write at any time and in a variety of settings is an important career skill.
Step 1: What’s the story, morning glory?
Going back to Step 0, what do you have at this point? You have a detailed story board/outline of the relevant literature in your field, you have your figures in a mostly finished state…now what? Before you start taking that story board apart and fitting the ideas into text, write the last paragraph of your introduction. In our last post we mentioned that this paragraph describes the ‘Aim of paper, experimental objectives, and also list any specific hypotheses.’
But why do we start here? This is the core of your story: what you’re doing, how you did it, and what you thought you’d get. From a more philosophical viewpoint, this is also a key part of the scientific method, showing the progress between ideas and knowledge and how you use your work to generate new information to shed light on something not known before.
To see this in action, I’ve included the last paper from my PhD, which ended up being one of my personal favorite papers, partly because of lessons learned the hard way in the first two papers. I’ve highlighted the key areas:
'The objective of this study was to evaluate changes in gene expression coupled with in vitro nuclear receptor assays to evaluate the androgenicity of water downstream of the paper mill on the Fenholloway River. Two specific aims were developed: (1) evaluate mRNA levels of vtg, 17βhsd3, and zp2 in the liver, shh in the anal fin, and global hepatic gene expression profiles associated with paper mill exposure, and (2) determine if chemicals in the Fenholloway River could bind to the ligand binding domain of androgen and progesterone receptors. We hypothesized that modulations in gene expression patterns and in vitro analyses would be indicative of androgen exposure and that global gene expression analysis via microarrays would provide insights into the mode(s) of actions of the chemicals present in the effluent.'
The study wasn’t a complicated one, and I strove for clarity and simplicity in how I developed this paragraph. Work on this paragraph before any other part of the paper and have your PI or another graduate mentor review it for you. Then once you’ve got them on board with your idea, print it and keep it off to the side to remind you to focus around this core of the paper. Use this paragraph as a framework for your manuscript. As you write, you should be considering how to address the hypothesis/hypotheses using your specific aims and project objectives.
Step 2: Start from the middle
Once you have the last paragraph of the introduction, you’ll actually want to go to the middle part of the paper next. In the case of your manuscript, the introduction is the beginning of the story, the methods/results is the middle, and the discussion is the end. So before jumping back into the introduction, finish the figure captions and write the materials and methods section (as an added bonus, these are also the two easiest parts of the paper to write). A methods section is essentially structuring your lab protocols and procedures into a narrative form—keeping the most relevant parts in the narrative and citing other papers/protocols to keep the section from becoming too long. Writing this easier section first can help you get into the writing ‘mood’ and can also remind you of exactly what you did in the lab before you write about it.
For the results section, keep this to a very cut-and-dry overview of what each figure depicts. This part of the paper shouldn’t include data interpretation, just evaluation. As you’re writing these middle sections, go back to your specific aims and hypotheses and see what the data say about them. Work on these questions and use them to help guide what you say in your results section and also to frame what you’ll bring up in the discussion:
Step 3: Set the scene
Now we’re ready to move to the introduction. As we said in our previous post as well as our perfect presentations post, the format of the introduction is presenting a specific problem, its overall importance, and your approach to solving it. We also talked last week about how the outline can look for the introduction (and you already have the last paragraph, so we took that one out):
- Paragraph 1: What is the problem and why should the reader worry/care about it?
- Paragraph 2 (and maybe 3): What’s been done to address/know more about the problem so far
- Paragraph 3/4: Knowledge or tools that can be used to further address the problem
With your outline already sorted, you should be able to fill in a few sentences about each idea. The first paragraph should give a short overview of the problem at hand, including definitions and explanations of key concepts in your research area. This is especially important for people outside your field—those who work in this area will likely skip over this part of your paper, but someone unfamiliar with the tools and concepts you’re looking at will need to get a big picture understanding of your work in a single paragraph. For example, if your work is looking at Gene X and its role in the immune system and how it impacts cancer drug effectiveness, you don’t need to give a broad overview of how the immune system works, but someone coming from the field of neurobiology should be able to understand the basics of what type of study system you’re using and why it’s of relevance for your work.
The second (and potentially also the third) paragraph will be more of a short literature review, which you can expand on more in the discussion as needed. Avoid dumping all of the existing ideas or possibly relevant literature in this section, since it will make it an unreadable series of facts. Start by simply asking ‘Who else is working on a similar topic to mine?’ and work out from there. You don’t need to cover everything slightly related, but for example of Gene X immune system-cancer drug cross-talk, you can summarize the current basis of knowledge for other genes that related to system-drug cross-talk and how your gene emerged as a potential candidate for further study. The length of this section will depend on you, your PI, and also the publisher, if they happen to have limits on the total word count or a word count per section. If it’s on a total word count basis, keep this section shorter and use your words in more important sections such as the discussion.
Step 4: Bring it all together
If the last paragraph is where you start writing for your introduction, the first paragraph of the discussion is where you start writing for this last section (confused already?). This leading paragraph of your discussion is what’s going to set up this crucial section of your paper and tie your new results and previous results all together. In this first paragraph, go back to your specific aims and hypotheses. Describe what you found out through the study in the context of your initial hypotheses, and give a step-by-step overview of what you just presented in the paper. Going back to my PLOS one paper, here’s how the discussion section started out:
'We found that masculinization of female G. holbrooki continues to occur in the Fenholloway River. Paper mill effluent exposure is associated with both anal fin elongation as well as with significantly increased bone segment formation at this site. Additionally, we found an increase in the mRNA levels of vtg, zp2, 17βhsd3, and shh in Fenholloway River G. holbrooki. Through comparison of hepatic gene expression patterns to data from laboratory exposures, we found that paper mill effluent exposure resulted in an increase of genes associated with metabolic pathways, with 62 genes similarly expressed by G. holbrooki exposed to androgens, indicating a similarity between impacts at the molecular level between paper mill and androgen exposure. We also found detectable levels of both AR and PR ligands in the transactivation assay in concentrated water samples collected from both the paper mill impacted and reference sites.'
This opening paragraph can set you up for the rest of the discussion very easily, as you’ll have essentially listed out a topic for each following paragraph in the discussion. In each paragraph, think about how the results you saw fit in with key experiments from the literature and try to connect the two. What proposed pathways or models exist to explain both your results and data already in the literature? What potential ideas could explain discrepancies between your findings and a similar study by another group? It’s in this section that you’ll need to put the most work, which is why it should be saved for the almost last bit of writing.
As with writing anything, though, the one thing you don’t need to do is get it perfect the first time. The discussion is generally the hardest section to write because it requires synthesizing all the results as well as developing new ideas and explanations for what you found. Trying to put this all into writing is not an easy task-but one that you should still give a go anyways. If you feel stuck, try to go one paragraph at a time and send that paragraph to a colleague or mentor to review. Get some feedback from them as to if you’re on the right track, if your scientific logic has any holes, or if there’s a different way you can structure your arguments. The best way to learn how to write is to try, and then try some more-so if anything, don’t be afraid to put words on paper and see how it goes!
Also, don’t be afraid of a discussion that goes too long, at least in the pre-submission stages. You can always cut back, and your paper co-authors will likely also have ideas of what should go where and what’s relevant, so feel free to send them a lot and let them cut back as need be. While you as the lead author will do the bulk of the work, don’t be afraid to ask a co-author for additional editorial guidance, especially if they have good paper writing experience.
Step 5: Tie up the loose ends
While you’ll probably have to come back to your paper after your initial few drafts after your co-authors take a look, there are other things you should make sure are good to go before you finally click ‘submit’.
Literature cited: Main hint here? Use a reference tool! If you have access to EndNote then there is a very easy-to-use plug-in; if not there are other free platforms (such as Mendeley) you can use which also have Microsoft Word plug-ins. Whether it’s a long or short paper, regardless of how many references you end up having, using a reference tool will take the tedium out of this section, and will also ensure that everything’s cited in the correct format.
Tables and figures: Each journal should have a guide for authors which will specify the types of files supported and any minimum compression sizes/methods for figures. Remember that these are the part of your paper that people will often look at first-so make sure they are clear, accurate, readable, of a high technical quality, and, of course, stylish.
Acknowledgements: Be sure to thank any lab mates, technicians, or colleagues who helped out with the project but who didn’t do enough work to make it to the author list. If you have co-author who works in a company or government institution, they will likely have to include wording to reflect that this paper doesn’t reflect the companies views (they will probably add it themselves but you can make a note to ensure that they included it). And don’t forget the funding agencies who sponsored your soon-to-be published study!
The key thing to remember about writing is that you won’t get it right the first time around. It takes practice and a lot of trial and error, which can leave you feeling like you’ve been stuck on a paper for ages. That being said, writing is a chance to enable ideas to grow and change over time as part of the creative process, which can bring depth to your arguments and your story. You won’t get a perfect paper the first time around, so envision your time spent writing as constructive practice towards future perfection (or at least publishable perfection!).
We’ve previously touched on writer’s block, and the strategies and tips you can use to get over the initial hurdle of the blank piece of paper. This week I’ve been inspired to revisit the topic of writing, in part because of my own return to science writing after a bit of a break. I greatly enjoyed writing in grad school, perhaps in part because I knew that writing before the end would help me finish my dissertation, but found that picking things up and getting in ‘writing’ mode again after almost two years of lab and computer work as a post-doc was a difficult task. Where do you start when you have nothing but a blank page? How do you go from a few figures to a draft of a manuscript?
As we touched on in our previous post, there are a few ‘blocks’ to get around in order to let the creative juices flow. Just as with presentations, there is no such thing as being held back in your writing by being a bad writer in science. You may not be a naturally prolific writer (just like I am not a naturally confident public speaker), but the great thing about writing in science is that if you stick to a plan and have a goal with what you want to write, you can always get there. In science, it’s not about how big your vocabulary is or how similar your writing is to the great novelists of the 21st century: it’s about sharing your story with clarity and enthusiasm, all laid out in a logical and progressive manner. So don’t let being a ‘bad writer’ bring you down or become a common excuse for you to avoid writing.
As with our easy* steps for a perfect** presentation series, we’ll detail a step-by-step guide to writing, focusing on how you can go from a blank piece of paper to a respectable draft. But instead of calling this the ‘Five Easy* steps for a perfect** paper’, this series will focus on the art underlying science writing. Because in reality, art isn’t only about fanning those flames of creativity, it’s also about getting your tools ready, doing some preliminary sketches, and having the technical knowledge to bring your vision to life. You can’t just be a good artist to make good art—you have to put preparation and thought into the works you create in order for them to be impactful.
Step -1: Read!
Just as with our presentation guidelines, there are things you can and should do before you begin writing a manuscript, grant, science blog, or really anything short or long related to science and to your work. Before you can begin to write and become a better writer, you should read and work towards becoming a better reader. Obviously you’ll read a lot of papers that are relevant to your work, but how many times do you actually read a paper versus just looking at a couple of relevant figures or glancing over the methods section?
If you want to see how science writing works, you need to read the results of science writing. See how manuscript authors lay out their story, how they bring together figures and results to a cohesive conclusion, and what works and what doesn’t in terms of style and structure. You’ll likely find more than a few bad or boring papers in the bunch, so when you do find a paper that sticks with you, keep it around: highlight the key points, see how they laid out their figures, and get a sense of how they developed their story. At the same time, learn how to critique a scientific paper. Focus on both the writing itself as well as the underlying logic. Do the findings they present match up with the conclusion they drew? Do the experiments they did line up with their hypothesis or project objectives? Were there any fundamental flaws in how they designed the study that weakens the conclusions they can draw? While you’re learning by seeing how others write, you can also take the time to become an evaluative, critical scientist, which is crucial at any stage of your career.
You don’t just have to turn to the scientific literature for reading inspiration, though. Your job as a writer is essentially to tell a story: a story with a beginning, a middle, and an end. Just because your story is crafted on data instead of imagination doesn’t mean that the methods used by authors from outside of science aren’t relevant. Take a break and pick up a new novel or read a non-fiction book on a topic you’re interested in. How does the author keep your attention? How do they transition between ideas or paragraphs? What words or phrases do they use that stick with you? We pick up a lot of our vocabulary and our way of phrasing ideas from listening and reading, so by enjoying more good writing you can also become a better writer.
Step 0: Make a story board
Sound familiar? That’s because it’s the same piece of advice we gave in our perfect presentations series. Before you open up that dreaded empty Word document (or the boilerplate ‘.tex’ file for those Latex nerds out there), do some ground work and set yourself up for success by drafting your outline or, to use the analogy from last time, a story board. As with the presentation guidelines, the purpose of the storyboard is to provide some structure for your ideas and to let you be creative while at the same time helping you guide your creativity in a logical manner.
So what exactly do you need to create your story board for science writing?
Figures. These should be in a 90% final form before you begin writing your paper. Maybe you’ll add something else in that was initially lacking, maybe you’ll change the label on some axes or change the color schemes, but overall they should be static the moment you begin writing. The figures should be able to tell a story on their own, the story that you’ll craft into words around these core figures.
You may think that the place to start with a manuscript is the introduction, but in reality you should focus on your figures before thinking of any other part of the paper. If you are a pen-and-paper type of person like me, print off each figure as its own separate sheet of paper. Around the sides, make notes about the figure. What do the bars show, on a very basic level (e.g. ‘Number of eggs per brood’)? Is everything labeled appropriately? Someone should be able to look at the figure, even without the caption, and have a basic understanding of what’s going on (such as ‘ok, there’s an increase in the number of eggs based on the dose of the treatment’).
Once you’ve had a thorough evaluation of the figures themselves, draft a caption for each one. Start with bullet points of the take-home messages for each figure. What does the figure show, on a more advanced level (e.g. ‘Differences in nutrient uptake in treated versus control animals’)? What should someone understand about this figure that they can’t figure out just by looking at the image itself (such as how many replicates are in each measurement)? Take these bullets as the starting point for your figure caption, and when back on your computer go ahead and write a full paragraph for each figure based on these bullet points. So now you’ve now got your figures and figure captions, which in reality what most people will turn to first in your paper-so you’re off to a good start!
Experimental protocols. Once you know the basics of what you’re going to show with your figures, start working on an outline for your experimental methods. This is generally the easiest (and also most boring) part of a paper, but from a scientific perspective is the most crucial. As you put together all of your relevant figures, dig out your lab notebooks and protocols to get all the details of your experiments. Make note of any steps of an experiment that fall outside the scope of a more standard operating procedure, or if a group of samples from one analysis was processed in a different way that the others.
Have your lab notes and protocols on hand and give them another read-through before you start writing. You can also look at methods sections from other manuscripts (even ones from your own lab) to get a feel for what information is important and what is superfluous. But be careful not to just copy-paste the methods section from another group’s manuscript, or even your own group (or your own previous manuscript). Even without any malintentions, simply reusing a section may be plagiarism or self-plagiarism. Rewriting the methods section ensures it is current, and it may end up being more clear or concise.
A pile of papers that have already been read. This is again a spot that can trip people up in the writing process. Once you’ve got your figures and protocol in place, the next step is to think about how to craft the story around them. You used the protocols to generate the data that you’ll present in your figures. But what’s the contribution to the existing body of knowledge? What’s the context of why that work was done, and how does it fit into what other data is out there already? How does this help your field understand a problem/scientific question?
As with step -1, it’s hard to be a good writer if you don’t read. And while you may have a basic understanding of what’s going on in your field or within this topic, you need to take a closer look at the literature before you start writing in order to craft your story and lay out the logic in the most appropriate way. So before you start writing, read in detail any of the manuscripts that you’ll most likely cite: the papers with the experiments that inspired your work, the papers that did similar types of experiments but with perhaps different systems or questions, and the papers that challenge your result at some level. Even if you’re read them already, read them again and make notes on the important findings or concepts that you’ll need to construct your paper.
Once the literature review is done, you can use this pile of knowledge to construct your storyboard. Think of your introduction and conclusion not as two separate components, but instead as a continuation of one to the other. The introduction is the beginning of the story, the methods/results is the middle, and the discussion is the end.
In your introduction, you set up the coming tale. As with our presentation guidelines, you can use the following format: your paper, just like your presentation, isn’t a series of facts, but is instead a means of presenting a specific problem, its overall importance, and your approach to solving it. You can consistently keep this to anywhere from 4-5 paragraphs by using the following layout:
- Paragraph 1: What is the problem and why should the reader worry/care about it?
- Paragraph 2 (- 3): What’s been done to address/know more about the problem so far
- Paragraph 3/4: Knowledge or tools that can be used to further address the problem
- Paragraph 4/5: Aim of paper, experimental objectives, and also list any specific hypotheses
The methods and results section are pretty cut and dry, and don’t need much of an outline apart from what’s in your experimental protocols and the bullets you jotted down while working on your figures. Keep any specific or detailed interpretations of figures (such as ‘the decrease in egg production is related to an increase in temperature’) for the discussion. The results section should be very cut and dry, with one paragraph of results per figure. Focus on the basics of what each figure is telling you and save the juicy, exciting bits about what it all means for the discussion.
In the discussion, you continue the story started in the instruction, but now you have a new factor to accommodate for: the data you generated in the manuscript. How does your new data fit in with what was known already? Does anyone have data that disagrees with yours? Frame the discussion as a way of addressing the questions you presented in your introduction, how your results fit in with your hypothesis, and what the limitations/future directions of your work are.
As you make your outline, put as many ideas, relevant citations, and things to mention in the paper in your storyboard as you can think of. You likely won’t use half of them, but laying out any potentially relevant findings can help provide context for what you should discuss and how you should frame your writing. One way to do this is to break down each paper into a series of bullet points. List out relevant methods, rationale, hypotheses, findings, and if you think results were interpreted correctly. Another alternative is to have bullets ranked by topic, and then list papers and relevant results under that topic, and see where the similarities/differences lie. I’ve tended to use a mixture of both, and then while writing used color-coded notations to help me keep track of what sections were written where.
For my own dissertation, before I began writing the introduction and conclusion sections, I first laid out the literature and the key points I wanted to address in a very long outline. While in the end I only used about half of what I put into the outline, when I was ready to begin writing I was able to jump into it quickly, without having to go back and forth between reading and writing and disrupting the flow of my ideas and thoughts. Being ready to write means being more efficient at writing, because you can let your ideas come to life without having to jump back and forth between different tasks, thoughts, or distractions.
It may seem like a lot of work before you even start writing more than just a few bullet points. But think about it this way: How much preparation work do you put into a big experiment? How much time does it take you to code something that’s never been done before? How much washing, chopping, and reading recipes do you need to do before you cook a nice dinner? A lot of the things we do, both in lab and in life, take a lot of pre-work in order to come out at a high quality and to be done efficiently. The work you put in before you start writing will allow your work to take off once you are ready to get started-and will make the task less tedious and tiresome, since at that point all you’ll have to do is to tell the story.
Next week we’ll go more into detail of how to take the outline and figures and construct a story around them. Until then, happy storyboarding!
Some of my recurring blog themes include topics such as knowing yourself, your working style, and your strengths and weaknesses. By knowing yourself and your tendencies, you can better figure out how to get yourself out of ruts, how to ask for help, or how to make it through a difficult situation in the lab or in the office. As part of my interest in scientific ‘self-help’, I love reading about personality assessments and combing through the theories about my own or my colleagues’ ‘types’. I use the information to think about how to communicate with other people better and also how to recognize my own shortfalls and to work to correct them.
My mother and I share the same interest in observing people and their personalities. Recently she talked to me about Gretchen Rubin’s four tendencies, a personality test that distinguishes people by the way respond to internal and external expectations. I enjoyed the simple and clear presentation, and, while I was initially skeptical of its applicability (probably due to the type of tendency I fall into), I feel it’s relevant for understanding how we work in the lab and in a research setting.
You can read all about the theory behind Rubin’s tendencies on her website, but in a nutshell a person’s tendency boils down to how he or she follows instructions. In her book ‘Better than Before’, Rubin focuses on applying this theory towards changing habits, whether it be to exercise three times a week or to call your mom more often so you can discuss your entire family’s Rubin tendency distribution. It’s probably not initially clear what relevance this personality test could have in your scientific career, but as with most jobs, you spend a good portion of your day handling a lot of instructions: what your principal investigator wants, what your company/university wants, what you want, and at some point you’ll also be the one giving out instructions to others. At the same time that we receive information and instruction from various sources, we also make decisions on when do we decide to take breaks and how we decide which tasks to prioritize.
I’ll leave the details of the theory and the typologies to Rubin to describe in detail, but let’s get some context for what these four tendencies are, how they may manifest given that you work in a research-type setting, and what the potential strengths and weaknesses are in the lab for each type. But first thing’s first: take the test. No, really, it’s crucial for the rest of this post! It’s a short questionnaire and only a few questions long. And as with any personality test: be sure to answer truthfully to yourself. Respond as you would respond in that situation, and try to really picture yourself in the setting for each question.
Assuming that you have now taken the quiz and have been assigned your personality, we can discuss its implications. Rubin’s four personality types first came to be in 2013 and have now grown in detail and structure. The tendencies are also part of Rubin’s The Happiness Project, where she goes into detail of strategies for changing habits based on what types of expectations you follow the most. These descriptions come directly from her website and are referred to as either the Rubin Personality Index or the Rubin Tendencies. We like Rubin Tendencies, so we’ll stick with that one. The four tendencies are obligers, upholders, questioners, and REBELS. In the quote below, ‘rules’ also refer to instruction, or really any type of expectation.
“Upholders respond to both inner and outer rules; Questioners question all rules, but can follow rules they endorse (effectively making all rules into inner rules); REBELS resist all rules; Obligers respond to outer rules but not to inner rules.
- Upholders wake up and think, “What’s on the schedule and the to-do list for today?” They’re very motivated by execution, getting things accomplished. They really don’t like making mistakes, getting blamed, or failing to follow through (including doing so to themselves).
- Questioners wake up and think, “What needs to get done today?” They’re very motivated by seeing good reasons for a particular course of action. They really don’t like spending time and effort on activities they don’t agree with.
- REBELS wake up and think, “What do I want to do today?” They’re very motivated by a sense of freedom, of self-determination. They really don’t like being told what to do.
- Obligers wake up and think, “What must I do today?” They’re very motivated by accountability. They really don’t like being reprimanded or letting others down. “
Quoted from Gretchen Rubin blog, 27 March 2013
So now that you’ve done the quiz, what do you think of this short assessment of yourself? Do you wake up every morning thinking about what your Rubin tendency says you do? You can read in more detail about your own Rubin Tendency if you’re interested. After reading the detailed reports for the four Rubin tendencies, here’s our own shortened interpretation of them:
- Upholders are great doers and achievers, but may struggle if there’s no clarity or no plan.
- Questioners are very internally motivated, but may run into issues if they can’t accept worthwhile direction or advice from others.
- REBELS have great ambition and creativity, but may resist following direction if they don’t feel like they can do what they want on their own time.
- Obligers are reliable and dependable, but may have issues with being too self-sacrificing and spend time building up others before themselves.
While Rubin focuses on how types related to habits and her books show you how to create good habits based on what your type is, in this post I instead wanted to highlight some common scenarios that can come up in research and how each type might get caught up with and a potential solution/approach.
Upholders: The to-do list masters who may run into progress speed bumps with things like:
What can upholders do? You’ve already got a great work ethic, now you just need to figure out how to think on your feet and think outside the box:
Questioners: Good at critically evaluating everything…except sometimes themselves! Here are the issues that these constant wonderers of ‘why’ can fall into:
What can questioners do? Asking a lot of questions is a good tendency in science, as long as that critical evaluation is evenly distributed and fair. To give yourself a fair assessment, work on the following:
REBELS: Will challenge ideas and reach for the skies…but may have a hard time getting there if they don’t listen to others. Here’s what trouble REBELS can run into in the lab:
What can REBELS do? It may sound like a hard sell to be a good REBEL scientist at first, but one of the things that makes rebels great is that they go against the grain-think of all the great paradigm shifts in science that came from looking at the status quo and saying ‘no’! Nonetheless, you do have to play by the book, at least a little bit:
Obligers: You’re everyone’s favorite, most helpful lab mate, but your own work will go un-worked on if you have a job to do for someone else. Here are some other situations that an obliger may run into:
What can obligers do? It’s hard to put yourself first, so here’s some tips on how you can look at your internal obligations with an external focus:
The thing I like about the Rubin tendencies in the context of research is that it highlights the need for teamwork. There is no one perfect personality type for academic research: we all have to challenge currently held perceptions, knowledge, and ideas, but also have to know when to follow the rules and respect the knowledge already in play. We have to strike a balance between working towards our own goals and recognizing the value of working with others. The key with integrating the tendencies in your own research career is first to recognize which tendency you follow the most and to work towards ensuring that you stay on task for your own career goals. Additional life hack: find friends and collaborators who exhibit different tendencies than you have to balance out the scales. Whoever said that psycho-analyzing your friends and co-workers couldn't be fun or useful!!