Reading Natural Science Papers: A Method I Swear By

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Those of who enter grad school in the natural sciences inevitably encounter frustrations with "reading papers." They either seem totally incomprehensible or take forever to get through. When the stars are particularly misaligned, both happen. I've struggled with this for a long time and through talking with my adviser and others' have learned that there is a general system for getting through papers without wasting an entire day, which I outline here in 3 simple points. This strategy has gone through some rigorous training so I'm not going to make excuses for it and say "I hope it works for you." I think it's a good, solid method and should work for just about anyone doing research in the natural sciences. At the same time, I realize the process is one of learning and revising, so I'd love to hear your tips on this subject.

A Caveat for the Young

But first a caveat for those that are just starting to read papers, often those that just started grad school or started research with a group in the late undergrad years. Starting to read science papers sucks at the beginning and there's really no way around it but to keep at it. At the beginning you understand barely anything. There's too much jargon, there may be all kinds of equations you don't understand, you're not clear on what is obvious and what is new in the field, you're not clear on what is important and what is a detail, etc. This is normal. Follow these tips anyways, try your best, pay special attention to the "guess the figures" tip, and keep at it. It will start to make sense sooner than you'd expect.

2 Categories of Papers.

1. Know exactly why you're reading the paper. In my experience, papers in your subject fall into 2 categories: 1) Papers from which you want to extract certain information. 2) Papers that are extremely relevant that you need to read in detail. You read every word of the second type of paper and not every word of the first type. Not heeding the later part of that warning is where most of my time has been wasted. Most papers in your field fall into the first category. And by most, I mean almost all. That makes sense, because if there were a massive number of papers that were so close to what you are doing that you need to read every word of them, you would be getting scooped right and left (scooped = someone else publishing what you're working on before you do). A good strategy for deciding which category a given paper is in is to assume that it's in category 1 and move on. If, as you read, you realize it's very relevant, you will naturally start reading more and more of it and it will fall into category 2. There are only very few papers that fall into category 2. When they do, you know, because you are usually scared shitless that you just got scooped or very excited that you just found out some new, very relevant, information that could really help your project. Category 2 papers are most often ones that you read multiple times.

2. Do the following in order: read the abstract, stop and make a guess as to what the figures will be, look at the figures and captions, read the conclusion, read the introduction if necessary. Minus a few instances where I get bogged down on figures that are interesting for one reason or another, this usually takes no longer than 5 minutes. This is where you get the gist of the paper. The abstract of course should have been read before even downloading the whole paper. The guessing figures step is an extremely handy trick that keeps you engaged. You think "If I wrote a paper with this abstract, I would probably need the following figures to support my claims." Once you do this, each figure becomes a "Yup, of course" or "Hmm, I didn't think of that. Let me think why this is important," and you're 10 times more engaged than if you had kept reading mindlessly. The conclusion is often even more concise than the abstract in stating what about their paper is new and important, and finally, the introduction, should be read if you feel you want more of a sense of context for this work. If you know how the work fits into the larger picture, the introduction is not necessary.

If you feel you've found what you wanted from the paper or what you want is definitely not there, stop here.

3. Move on to discussions of the figures within the text. Know what the most relevant figures to you are, search for where they begin discussing those figures (pdf searching "Fig. 3" or something equivalent works well), and read those sections.

This is all you need for Category 1 papers. If you need to read more, it's probably a Category 2 and it should be obvious by this point. Note there was no mention of the experimental setup and details. These should be skimmed if read at all. The only reason you need to know of these details are when you are comparing your exact experiment with theirs or are working off of their experimental setup, in which case, the paper is clearly a Category 2 and you'll be reading the whole paper probably more than once.

I read Category 2 papers using the same steps above, only after step 3 I start at the introduction and read through the whole thing, skimming parts I just read in detail and understood easily and slowing down at the more interesting sections.

That's it.

What to avoid: Equations, Details, and Reference Chasing

Don't get bogged down in equations. If you really need to know them, you'll get back to their derivations later. The worst thing you could do is start reading the paper from the beginning, word for word, get to equation 1, realize you don't know the derivation, see that it comes from reference 7, look up reference 7, start doing the same thing with that paper and slip down a cycle of never having completed an entire paper because you stop and look at a reference every time you don't understand the tiniest detail. Details are important in science of course, but there is simply too much out there that you don't know to be chasing all the details and all the derivations down the very first time you run into them in scientific literature.

Reading More Papers

I've been using this method (category, abstract, guess figures, figures, conclusion) for months now and it's absolutely dandy. I find I'm exposing myself to more papers now because I know I can get the gist of the paper without wasting an hour. I also don't feel intimidated by not understanding every detail. I used to have this false idea that professors and other experienced scientists understand everything about the papers they read. That's nonsense, of course they don't, that's why papers continue to get published, they're new. I find myself now browsing through Nature and Science magazines' websites expanding my base without feeling stupid about not knowing the details and not wasting too much time. I'm keeping up on the journals in my field a lot more than I used to. And I'm saving massive amounts of time doing literature searches to find information on a specific idea or subject.

What strategies do you use?

How to Act Productive Tip #5: When in Doubt, Check Your Email

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Here at Grad Hacker, we feel that simply being productive is not enough. What good is your inner, clandestine, productivity, if your bosses, colleagues, and you yourself don't really know the extent of just how unbelievably productive, busy, stressed, in a rush, and important you really are? For these, reasons, each weekend we will provide you with a tip on how to act productive.

Let's be honest, productive people get a lot of email, so they have to check it. How could they not? They're productive, so everyone wants a piece. These people often have scores of project they're working on simultaneously (think triple digits), each one producing multiple emails a day that need immediate checking and responding, and they're handling each one better you will probably handle any single project in your whole life. But don't feel bad, feel productive! Check your damn email already.

Most of us check email whenever we feel like it, respond whenever we feel like it, and somehow seem to make it through life with this level of mediocrity. Productive people, on the other hand, feel a deep sense of urgency, and can express this through digital communication like it's going out of style. These are the people that make others say to their friends, "Look at this, he responded to this email in 5 minutes," or "Woah, I sent this at 1am and she responded by 1:30!"They check email at work, at home, on dates, in bed, on the road, driving, biking, jogging, at the movies, at the beach, when they are in front of you and get to the counter at the burrito place that already has a long line. Bottom line is, they check that shit. If you want to be productive you should too. How do you know how often is enough? If you got to the end of this post without checking your email at least once, you're not checking it enough. Go back and try again.

Some good ways to increase your daily email checking: when you're stuck on a difficult project, go check your email; when you really don't want to work on something with a deadline, go check your email; when you get to work in the morning, definitely start by checking your email; when you have that awkward 20 minute break between events, go check your email. You get the point.

How to Act Productive Tip #4: Work Through Spring Break

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Here at Grad Hacker, we feel that simply being productive is not enough. What good is your inner, clandestine, productivity, if your bosses, colleagues, and you yourself don't really know the extent of just how unbelievably productive, busy, stressed, in a rush, and important you really are? For these, reasons, each weekend we will provide you with a tip on how to act productive.

Ah spring break. Sun, skin, MTV video cameras, uninhibited drinking of alcohol. This is what spring break is about - if you're lazy.

We all know the truth about spring break: it's a time to finally get some research done. Maybe you've heard that before, maybe you've ignored it, maybe you're grossly unproductive. But one thing, however, is for sure: even if you don't work through the entirety of spring break telling people how hard you worked all break long is a sure way to increase your perceived productivity. Of course, being productive is an important part of acting productive, and actually working through spring break while everyone else is having unbridled sexual escapades that they won't remember, is encouraged. But we understand that everyone slips up once in a while, that's why we think the most important part about spring break is to prepare for the "how was your break?" conversations, regardless of how hard you worked:

First, make a list of things you got done over the break, review the list (email us, we'll help you with your list at no charge). Try to include items that your friends have been trying to do themselves for a long time but haven't "got around to" doing.

Second, have at least one event in mind that you were invited to attend but skipped out on to ensure you aren't perceived as a loser. Multi day events in tropical locations are encouraged. Mentioning the event was attended by very attractive and rather out-of-your-league peers is very strongly encouraged.

Third, what should be a fundamental skill if you've read any of the tips in this series, always start the conversation off by asking about their break was, mentioning how you wish you could say the same, and expressing a resigned acceptance that it was so much more fun than yours.

Finally, if there is one person you have this conversation with, let it be your boss. Your boss is probably not cool enough, attractive enough, nor lazy enough, to have spent spring break at some tropical location, they were probably working too, but expected that you weren't. But you were, and you should say so. Or you weren't, but you should still say so. Set yourself apart from your peers and tell your boss.

Happy Spring Break.

How to Act Productive Tip #3 - Work All Weekend

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Here at Grad Hacker, we feel that simply being productive is not enough. What good is your inner, clandestine, productivity, if your bosses, colleagues, and you yourself don't really know the extent of just how unbelievably productive, busy, stressed, in a rush, and important you really are? For these, reasons, each weekend we will provide you with a tip on how to act productive.

What did you do this past weekend? Hang out with friends? Drink alcoholic beverages? "Oh but I did a little bit of work on Sunday morning" you say. Unacceptable. Who do you think you are, Cal Newport? Stop being lazy, start being productive, work the entire weekend.

Productive people don't have weekends. Weekends are when the office is quiet, there are no classes if you are a student or professor, the phones aren't ringing, the email volume takes a dip, so why would any sane, productive person waste this time gallivanting around town when they could be making progress on the million projects on their plate? Don't get me wrong, you can do that, it's your life, just don't expect to be productive at the same time.

Now, in the vain of the How to Act Productive series, I must add the final ingredient to acting productive by working all weekend long: tell people what you did over the weekend. You need people to know how productive you were over the weekend. You need to inspire them. Last week I mentioned how you must carefully slide your lack of sleep into conversations to preserve some social tact. Such rules seemlessly extend into this week. Don't start by talking about your productive weekend, ask about their lazy weekend first: "So what did you do this weekend." "Oh it was awesome, we took the boat out on Saturday, the weather was beautiful, hung out for a while, hit up this party in the evening. Then on Sunday..." "Oh, that must have been nice, I was here working the whole time." Oh yes.

So towards the end of this week, when you start to think about what you'll do this weekend, ask yourself this simple question: Am I a productive person?

Zotero Review

On its website, Zotero is described "is a free, easy-to-use Firefox extension to help you collect, manage, and cite your research sources." Even though it’s been out for a while, I somehow didn’t run into it until a few months ago. I’ve used it for a while and have switched over from using Endnote because I like it that much, below is my review.

Here is my two sentence review of Zotero: If Evernote and Endnote had sex and made a baby, Zotero would be that baby. It would then outdo its parents in so many ways.

If that is all you need to know, go ahead and try it out, it's free for crying out loud. Otherwise, here is my longer review organized in list form of my opinions of its features. The part about Evernote in my two sentence review is about how Zotero can do more than just manage research articles, but I can’t write about everything (that’s what it’s website is for) so this review will just be about using Zotero to manage research papers.

1. Autofind - This is perhaps the coolest thing about Zotero. Zotero recognizes when you're looking at a summary, abstract, citation, and/or list of articles and puts a little icon next to the url. When you click on the icon, it automatically stores the citation information for that article in the database. My experiences with this feature have been pretty damn good. I'm in the natural sciences, so results in other fields may vary, but in the databases that I use, and most surprisingly at the vast majority of individual journals' websites, Zotero knows when I'm looking at an article. It isn't perfect though, and it can be annoying when you're cruising along and just want to store a citation and move on and Zotero doesn't recognize it. I've had this problem when checking who cited a given paper in Web of Science. But overall, this is a positive feature and a hell of a lot faster than exporting to Endnote. Which leads me to...

2. It Lives in Firefox - An absolute plus. Firefox is where I find articles, often look at the pdf of articles I've found, find other articles related to a given article I'm reading, so it only makes sense that my database of papers also live in Firefox. When you click on the icon in the address bar, the whole world doesn’t stop for Endnote to startup and you don’t have to click 5 other screens to allow Firefox to download the file, pick the library, etc. It just pulls up a little “Saving item…” tab in the bottom corner of the Firefox window, does its business, and removes the tab. The whole process, when working properly (which is the vast majority of the time) takes maybe 10 seconds. You do have to be careful about which folder you left highlighted in Zotero, because it will automatically save citations into that folder. I find this more of a plus than a minus though, because often I’m searching for a bunch of articles about one research subject, so I can just keep clicking the icon in the address bar and Zotero will keep saving citations right where I want them.

3. Folders – Does Endnote have folders inside a given library? I don’t think so, but maybe. Is it useful and fast enough for me to have known about? Evidently not. The folders and subfolders list is extremely useful and a breath of fresh air. Research papers aren’t emails. Throwing them all in one folder and searching for them is often not the best way to find what you’re looking for. You also seem to be able to place a given entry into more than one folder, which rocks. Drag, drop, drag, drop. Ooooh, it’s easy.

4. Tags – If folders aren’t enough for finding the articles you want, you can also add tags to papers, which work exactly like Gmail labels. Personally, I find that since I can place an entry into multiple folders already, tags aren’t particularly useful. But I use this occasionally. For example, when I’m doing a search on a given subject, it’s often convenient to keep adding entries to the list, but mark the especially pertinent ones as “to read” via a tag and go back and make sure I read all of them later. I wish I had learned this trick earlier because it’s one hell of a time saver. I’ll write more about this and other opinions about doing literature searches later.

5. Search as you type – Awesome. The search function of Zotero is so convenient. It’s fast, and it’s built, unobtrusively, right into the little screen. Endnote’s search worked well for me too, but it brought up a second screen and results didn’t show up as I typed; minor details, I know, but I’m just listing what I like here.

6. Notes – Oooh this is convenient. I’ve started to keep all of my notes and summaries of papers in Zotero in the notes option. It’s right there with the paper always. Besides actually taking notes on the paper though, the fact that the notes are included in searches means that I can type a list of “keywords” or random ways that I remember a paper into the notes to increase my chances of finding it later. Why not use tags or folders for this? Because often the ways I, and many others, remember a paper is through odd characteristics like: “that one paper by those British guys”, “the one with the blah blah technique in it”, “the one with that blah blah figure in it”, etc. I don’t want those random thoughts about every paper to have their own folder or tag, that’s ridiculous.

7. Importing from Endnote – So, if you’ve been using another reference software, how easy is it to switch? Good question. I used Endnote, so that’s all I can talk about. I went through their method of importing my references from Endnote and it worked with one weird quirk: it turned all kinds of Endnote keywords of some sort into tags, which is really annoying. So now I have all these tags that I don’t want and I don’t know how to delete all tags at one time, so I’m just not using tags much, eh, oh well. Otherwise the papers seem to enter just fine.

8. Citing as you type – I haven’t written a paper using Zotero for citations and don’t plan on it because my colleagues, and most importantly, my adviser, don’t use Zotero, so collaborating on a paper requires that I still use Endnote for that. I don’t forsee that being a problem though because the papers we write have maybe 20 or so citations max, and I can export them as RIS and make a little Endnote library for that particular paper. Maybe I’ll use Zotero for citations in a paper when I have to write the dissertation. I’ll let you know.

9. Free – Endnote costs money, this doesn’t. How do you beat that?

10. Open Source – Zotero is actively being worked on, which means bugs and kinks, and compatibility issues are constantly being fixed. This is a huge plus. Think Google; it responds to users’ requests by constantly improving its products, that’s so useful.

Overall, I’m quite happy with Zotero, and I find myself saving more papers than before and doing literature searches a lot faster and a lot more efficiently than before, which is a plus. Recommended.

What do you think of Zotero? Share your thoughts!

How to Act Productive Tip #2 - Talk About How Much You Haven't Slept

Photo by: Al-Fassam [Online! :D]

Here at Grad Hacker, we feel that simply being productive is not enough. What good is your inner, clandestine, productivity, if your bosses, colleagues, and you yourself don't really know the extent of just how unbelievably productive, busy, stressed, in a rush, and important you really are? For these, reasons, each weekend we will provide you with a tip on how to act productive.

If you think you can be productive and sleep well, you've got another thing coming. Busy people don't sleep. How could they? They're too busy. If you want to be a productive, important person you need to start losing sleep. More important than just your sleeping patterns, however, is your reputation around the office. You don't want people to think you're a lazy, 8-hours a night sleeper. You want them to know just how much you haven't slept in the past week or year. So you need to tell them. Often, it can be awkward simply inserting a sentence about your lack of sleep mid-conversation. So you must learn to be adept at more subtle tricks: "Yeah, that really was a good game last night, so what did you do afterwards?" "Went to bed" "Oh, that must have been nice. I was up till 4 working on the TPS reports." "Really? Wow..." You see, your lack of sleep impresses and inspires people. Maybe your friend will think twice the next time she plans on simply going to bed after the game.

A more advanced trick is to cite multiple-day averages instead of just a single night. Why? Because many people lose sleep every once in a while, but really important people don't sleep on a consistent basis. You need have these numbers on hand for when someone else tries to seem harder-working than you. Often, inserting a little sympathy in your phrasing can really make you sound like a winner: "Man, on Tuesday, I was up till 4 working on the TPS reports." "Oh, I hear you, that must have been rough. I've slept maybe 20 hours in the past week." "Total?!" "Yeah, total." "Woah..."

So this week, try to work more and sleep less. But if that's hard, don't worry about it, just make sure you tell people how little you've slept.

How to Act Productive Tip #1 - Walk Fast

Photo by: Hamed Saber

Here at Grad Hacker, we feel that simply being productive is not enough. What good is your inner, clandestine productivity, if your bosses, colleagues, and you yourself don't really know the extent of just how unbelievably productive, busy, stressed, in a rush, and important you really are? For these, reasons, each weekend we will provide you with a tip on how to act productive.

Walking fast is slowly becoming a lost art form (except maybe in certain parts of New England). As our level of affluence grows to a point where we can spend time at work reading about how to work more efficiently on the internet from other people that are writing about it instead of actually working, we find that simple things like walking from point A to point B have really lost their sense of urgency. Today you observe people leisurely taking strolls at work instead of really going somewhere with a sense of purpose. Document printed? Okay, I'll stroll over to the printer, maybe grab some coffee on the way, chat with Jon about the game, take a nap, who knows. So with their hands in their pockets thumbing through loose change, their heads down watching their feet drag, and a soft tune whistling from their lips, they walk around, listlessly, from printer to coffee machine, from Jon to Jan, from unproductive to really unproductive.

This is most people, but not all people. In every organization you have a few, the really productive ones, that walk fast. These people are getting things done. Period. How could they not be? Look at how fast they're walking. These people are at the printer before the document has finished printing. They're heads are up. They're going somewhere. Often a slight frown or scowl is on their face as they walk that reminds everyone they're in deep thought, troubled by the enormous quantity of problems they solve every day.

They have no patience for waiting. If the microwave is full at noon, they can often be seen looking around to see what slow feet-dragger is using it and intends on wasting their time by showing up a minute after their food is done. Often they will return at 12:30 when the lunch crowd has subsided. Or, if they are really hungry, or more likely have a meeting in 10 minutes, they will keep their hand on the door-open button for the last 3 to 5 seconds and immediately open the door, take out slow-person food, and start heating theirs.

God forbid there be slow-walkers in front of them when they're in a tight hallway or corridor. Fast-walkers don't have time for "excuse me". Maybe, just maybe, they have time for a grunt, heavy breath, or other humanly sound that let's the other people know there is a fast walker around...but not for long. Before the feet-draggers know what happened, they are gone. That is fast-walking. That is productivity.

So this coming week, try to keep your head up, put a slight scowl on your face, and walk fast. Don't hide your inner productivity. Display it. Your boss will love you for it.