Paleontological Research tips V: manuscript writing, research productivity, peer review, and minefield navigation

Other posts in this series:

  

Paleontological Research Tips I: field notes for amateurs and professionals alike

Paleontological Research Tips II: field notes, continued 

Paleontological Research Tips III: a complete idiot's guide to taking decent specimen photographs

Paleontological Research Tips IV: the art and science of maintaining a research notebook

 A recent discussion at SVP revolved around a dear friend asking me how I stay so productive at writing papers. I've been thinking about the next logical step in the paleo research tips series, and this sort of seemed like the next step beyond maintaining a research notebook - translating those notes into a manuscript. I've decided to tack on some ideas about research productivity as well as ideas on peer review, collaboration, and professional conduct. These are all intertwined and perhaps difficult to tease apart into different posts. I won't be going in to figure construction here. Cautionary note: I think the phrase "Life is too short" appears like three thousand times in here. There's a theme here. Fair warning: this one is kind of long.

Writing your first manuscript (or thesis)

So you're a new graduate student or perhaps a particularly enterprising undergraduate, and you're excited to start your first research project! Writing a manuscript is generally not where you start, but day one of the project is precisely where this 'tutorial' begins, because that excitement - that flame - must never be extinguished. We'll get back to that. For now, fast forward to the part where you've collected all the data you think you need to begin writing it up. I'll divide this into two broad categories, since this post specifically covers "paleontological" research tips: 1) anatomical/morphology based data and 2) numerical data of various sorts (my background here is chiefly taphonomic). Each has its own idiosyncracies. Regardless, however, the easiest way to begin a new manuscript is to start with the data - after all, data are the foundation of a scientific study and it is best to let the 'story' build itself from the ground up, even if you think you already know what the narrative and conclusions are - surprises happen during the scientific process, for better or for worse (always better for science-but often worse for your own mental state of affairs).

For the first category, anatomical/morphological description based studies - the bedrock of paleontological research - care must be exercised with regards to how much detail is necessary. The data being presented are new anatomical structures - more than likely it falls into one of the following categories: 1) fossils indicating a new taxon; 2) new fossils of an already described taxon, expanding the knowledge of said taxon and permitting rediagnosis/reevaluation/phylogenetic analysis etc.; 3) incomplete fossils insufficient for taxonomic purposes but nonetheless worthy of reporting; 4) incomplete specimens recording a certain taxon in a new place/time/stratum; 5) specimens revealing a noteworthy anatomical structure; and 6) a faunal survey or description of an assemblage. Categories 1 and 2 are typically those that require gory detail, and monographs fall under these two categories. As much as a new study should attempt to be the 'be-all, end-all' reference for a particular taxon, at some point you have to realize that if you keep adding detail the description will never get completed. Categories 3 and 4 will generally consist of shorter descriptions, and should focus on the features permitting identification (e.g. if the fossil is identifiable as Genus A, briefly list the synapomorphies of Genus A that are preserved and emphasize those in the description). Category 5 is a bit different, as this focuses on a particular structure and the emphasis of the paper is on anatomy rather than taxonomy - gory detail is likely necessary, but only on the structure of focus; for example, the ethmoid labyrinth of extinct cetaceans. Category 6 is dangerous territory, and one I've wandered into several times - because describing an entire fossil assemblage can include categories 1, 2, 3, and 4, and it's important to mentally subdivide each taxonomic section of the manuscript. Yes, consistency is important, but some fossils are more complete than others and warrant longer descriptions - and some assemblages will contain crappy specimens indicating the presence of an interesting taxon (#4) as well as more spectacular fossils of already known taxa (#2) and perhaps even new taxa, resulting in a manuscript-within-a-manuscript naming it (#1). An example of this is my 2013 monograph in Geodiversitas describing the marine mammal assemblage from the Purisima Formation. For methods, things are a bit more lax here: a list of specimens examined is useful, methods used for preparation, photography, and measurements, and of course anatomical terminology (there are often mutually exclusive sets of anatomical terms, and some reviewers will really nail you if you mix them).

Anatomical descriptions should be informative. Biological structures are difficult to describe - make reference to easily remembered shapes, include quantified proportions (e.g. the ulna is long and narrow, approx. 10% as wide as long), and emphasize taxonomically and functionally informative features. If you're naming a new species of whale, don't get hung up on a feature common to all vertebrates ("it has a frontal bone" - congratulations! the reader knows it's a vertebrate). You can't afford wasting any space telling us information the reader likely already knows.

For analytical studies, it's actually perhaps less daunting to begin with as you can write this up in a classic methods-results-discussion format and not have to bother with learning how to write anatomical descriptions. For these studies, so long as you're done with the bulk of data collection and processing, you can start by writing the methods section first (I'm only going to speak in general terms I hope are applicable to most analyses; also, if you're here looking for advice on how to write a "methods paper", you won't find any; I've not really written any myself, except perhaps in taphonomy, and am not a great source of wisdom). Then write about the results themselves: describe individual graphs and various statistical metrics. At this point you may start to realize one of four things: 1) your analysis demonstrated everything you hoped for; 2) the analysis sort of did that but showed some unexpected results; 3) the analysis overturns your worldview, by failing to support a favored hypothesis or failing to reject a disfavored hypothesis; and 4) the analysis has results that are inconclusive to a degree that it is not worth publishing them. For starters, I strongly disagree with the philosophy that only positive results are publishable: that idea is antithetical to scientific progress and is perpetuated by the tenure game. I recently had a manuscript turned away from a journal without review because I advocated caution regarding stratigraphic 'certainty' and identification of incomplete cetacean fossils, which seems strange for an admittedly low-impact journal (I'm not going to mince words).

So, if you're in category 1, congratulations - you probably don't need much help. Category 2 is a bit more nuanced, but you will be able to say some words of caution. If you are in Category 3, then you have my highest congratulations - this is a rare opportunity for reflection and intellectual growth as a scientist. It may seem like a pain to reconstruct from the ground-up certain ideas, projects, and manuscripts - but this really is a gift, and moments of realization like this are what drives the science forward (or, alternatively, drags transgressors with false results back where they belong). The trick is whether or not this will trigger the ire of your adviser - so, tread carefully. Unfortunately, for category 4, I don't really have much advice other than to pick another avenue of data collection/analysis. Most analytical studies will have one or two types of analyses, and it should be reasonably straightforward to describe the methods and results. For my master's thesis, I had several sources of data and analyses I preferred to keep all within a single manuscript: 1) a stratigraphic column; 2) a lithofacies analysis based on that column; 3) a multivariate dataset that permitted 4) a number of different comparative taphonomic and taphofacies analyses exploring preservational bias and differential preservation between depositional settings, taxa, and even tissue type. Organizing all of this garbage was quite daunting, and in the process of thesis writing, I really had to mentally remind myself where the mental barriers between topics existed so as to keep each source of information, analysis, and implications in different information 'silos', so to speak (e.g. each analysis will have its own methods section, results section, and discussion section). Eventually I succeeded, and the paper is now published in PLoS One with a healthy number of reads and citations for a taphonomic study

Once you've written up the methods and results section, the discussion is next: this can be somewhat nebulous at first, and requires a solid grasp of the literature (see below). What is new about the results? How are the results different? Does it mean somebody else has been wrong about a particular idea or interpretation? Depending upon how many ideas the new results support or do not support, or how many new ideas it generates, the discussion section can really vary in length. Owing to this I don't really have an overarching theme here, but rather a few choice suggestions. Don't overinterpret your data; it will be very clear to the reader that you had to do mental gymnastics in order to support a particular narrative (especially one you are known to prefer). Follow the Einstein quote: "If you can't explain something simply, you probably don't understand it well enough" - that is not to say that the truth is never esoteric. Don't oversell your results: it's very likely possible that you have in fact not written an earth-shattering paper; it may be difficult when to tell if you're being obnoxious. Reviewers are likely to ding you on this. A degree of boldness is necessary as a young researcher, but hyping up your research, overselling it, and reinventing the wheel comes across somewhere between obnoxious and pathetic, with 'insulting' someplace in between.

Once the discussion is done, now you have the necessary guts to form the remainder of the manuscript around: abstract, introduction, conclusions. Each of these serves different purposes: sometimes the discussion and conclusions can be combined, especially if while writing the conclusions section you feel really repetitive. Some repetition is OK; it's also OK, and perhaps a bit more effective for a paper discussing a multitude of topics, to list conclusions as a set of simplified bullet points. I write the abstract and introduction dead last. The abstract should be somewhat sterile, and a recap of the entire paper in 250ish words: 1-2 sentences introducing the problem, 1-2 sentences on methods, brief summary of results, and the implications of the results. The introduction is a bit of a different beast altogether: it can start with a completely different but at least tangentially related topic, a brief review, something to act as a 'hook' for the audience. This, along with the discussion, is perhaps the most creative part of the scientific writing process. Make it interesting - but don't you dare make it too long. There is a tendency, especially for graduate students converting their thesis into a paper - to dump their literature review into the introduction. Don't do it! Cut that shit out. We don't care you know the entire background. You're supposed to know it, and we implicitly assume that you do. All it does is waste space by retreading crap everyone has already read about. Summarize prior work with as little text as possible, unless the point of the paper is quite literally a literature review. If you're really proud of how much you've read and want to cite everyone who deserves it, do so in the discussion instead and cite everyone deserving of it as the breadth of your results and interpretations dictate.

Acknowledgements

Here's where it's really possible to mess things up. Many journals request that you avoid overly flowery acknowledgments; that's fine. But don't you dare forget anyone, because you'll hear about it. And not necessarily in ways that you'll like. If a piece of thesis work you are publishing yourself, thank your adviser. Thank any other official/informal mentors. Always thank the reviewers, either by name or if anonymous; thank the editors. Thank all who gave you the gift of red, bleeding drafts (below), even if they were an asshole. Always thank the kind folks who helped you in innumerable ways: museum collections managers, curators (sometimes you're supposed to thank both, even if the friendly manager was the only one who lifted a finger; you may not be invited back to visit collections again if the curator did not actually help you was not thanked as well; just bite the bullet and thank them anyway). Most importantly, thank the folks who collected and prepared the fossils you're reporting: collection and preparation involve a lot of effort, and I've heard a multitude of comments from colleagues along the lines of "I'm a bit pissed off I wasn't acknowledged by Student/Colleague X, given that I collected/prepared that goddamn specimen they were so pleased about publishing on." Almost nothing in paleontology paints you as an out-of-touch elite as failing to thank the people who most fundamentally made your scientific research possible. Speaking of, don't forget to thank funders. Anyone else who let you borrow their car, let you stay on their couch, fed you, discussed research with, etc. also deserves thanks. None of this needs to be particularly long, and while flowery language ought to be avoided, it does not mean you can't have some fun with it.

Embrace the tyranny of the red pen

Your first draft is probably going to be garbage, and that's OK. Self-editing is a difficult skill to learn, and usually you're going to learn it from others; a good adviser will know to be critical but not nasty. You'll probably learn the most from them and their comments. Unfortunately, bad advisers teach bad habits and breed bad scientists. If comments on a manuscript piss you off or make you sad or distressed, don't despair - ask yourself "why"? You've spent all this hard work just to see a manuscript bleeding to death with red marks. Sometimes you focus entirely on those red marks - or sections completely crossed out - and panic. That's fine. Take a day off. Go see a movie. Hang out with friends. Have a few drinks (the number of drinks might end up being proportional to the amount of red ink) with friends (not by yourself). After a day or two, think about why you're so upset; I find that knowing why allows you to separate the emotion from logic and gives you a way forward. Are you upset because you are not used to dealing with criticism? If so, I don't really have anything insightful to say other than accepting criticism and not getting hurt feelings over it is difficult to learn and takes a lot of conditioning; ignoring emotions is unnatural, and 10 years of research later I'm still learning. It takes time and practice. Are you upset because the comments are nasty? It happens, and several things are important here. 1) &%$# them. If at all possible, do not ask this person for review comments again. They are a bad scientist and cannot divorce logic from emotions. 2) Try to separate the useful comments from the shit ones; try taking a marker and literally cross out the hurtful garbage. There may be some genuine insight, and it's best not to throw the baby out with the bathwater. 3) If this is your adviser, then you're in trouble. Learn to live with it for now, and try to learn from it: try to learn it as something to avoid rather than emulate. Everything is a learning experience, and unfortunately, sometimes learning from negative example can hurt but reveal to you a positive alternative. If you think you can speak frankly about it with them, then do so; it is fully within your rights to respectfully demand to be treated with respect. If your adviser is capable of a heart to heart discussion, then you've made a good choice for graduate school. If not, I'd start thinking real quick about how to complete your thesis soon or find an alternative. At one of my alma maters, there was some seriously messed up adviser-student antagonism and students secretly switching advisers and committee members like baseball cards.

Once you're able to ignore shitty comments, you can get over them quickly and take action to insulate yourself: don't keep it a secret if you get a shitty peer review with ad hominem attacks back from a journal; write to the editor and politely request that the editor not pick that reviewer again, or edit the review for content. A surprising number of unhappy people end up in academia and it's best to avoid them, and warn others which bridges have trolls.

After you've learned some tips for editing, you can self-edit more effectively. Can you shorten a sentence? Does anything seem out of place? Does it belong in a different sentence/paragraph/section? Or, a completely different manuscript? Is anything repetitive? How is the flow of the paper - are the large breaks needing more efficient paving? All of these factor into what Ernest Hemingway called the "shit detector". Personally, I will repeatedly print off a manuscript and mark it up myself several times during the process. If a section seems totally disjointed, you can quite literally cut out thematically contiguous passages of text out of a printed copy, lay them out on a table, and try placing them in alternative orders (I did this several times during graduate school). Once you've figured out a more logical order, tape them together and use that as a guide for copy/paste/cut into the new order. One last tip about editing: it helps to wait a few days after you've written something to edit it. If it's still fresh in your mind, nothing will seem amiss. Give it a few days, and the details you articulated will become fuzzy and eventually forgotten to a point where it will read like anything written by a different person. For example, if you read something you wrote years ago, you may have zero memory of writing it to begin with. My golden standard is about one week: after this period of time I have no misgivings about editing my own work and 'crap' becomes much more obvious.

Keeping up with current research - the literature review

This is a crucial part in the early stages of any scientific writing. I'm including it here, after the section on writing your first paper - to emphasize that it usually doesn't belong anywhere in the published literature. Often this is a check box you need to tick off during the stages of thesis writing, and many theses include one; actually including it within a scientific body of text, UNLESS you're writing an actual review paper, is a waste of time. Unless your adviser requires it for the thesis, don't bother (see below). It is, however, important to read everything and distill it somehow. I knew I did not want a big literature review, but I needed to go through the process anyway - so I filled up an entire moleskine notebook with notes and figures from papers on marine vertebrate taphonomy. This took me about a year - maybe 3-4 papers a week. I would write anywhere from 1/2 to 2 pages of notes, and if possible include a photocopied figure pasted into the notebook - try to find the single most important figure from the paper, and pick only that one - and ask yourself, why is this one most important? Boil every paper down into a series of 4-5 bullet points. What is truly new? Ironically, you won't be summarizing the lit review sections of those papers and before you know it you'll skip over those sections wholesale. When you're new, you're probably going to be googling a LOT of definitions, which will in all likelihood not be in a dictionary and will force you to disappear down the rabbit hole of other background work. Once you've gotten good at this you can distill a 10 page paper into a few bullet points in about a half hour or less.

One last point - don't fail to cite anyone who deserves citing. Being not cited by someone really hurts, especially if you did hard work going unrecognized and they get a bunch of fanfare for something you published several years before. There's no better way to show the community you are sharp than by hitting all the proper notes; if you neglect to cite something relevant, you risk pissing off that researcher (who may review your work in the future) and showing the world you're not very competent. When I do peer reviews, I routinely suggest additional citations if the authors have not included them. Often they listen; sometimes they don't.

Walking the tightrope: how many side projects?

Don't put all your eggs in one basket. My master's thesis was not published until three years after I graduated. It was a reasonably tight thesis but a pretty hefty manuscript. My biggest advice on here is to start out a small number of side projects, once you're comfortable enough. These should not include your adviser, if, for example, your adviser is responsible for holding up research. If they are able to acknowledge "this is a short side project, we work together well, and we can get it out quickly" then there's not a problem. But ideally, start making early collaborations with other graduate students - these projects are often the seeds of lifelong collaborative partnerships with other researchers and friends. All projects will have stopping points and slow down; maybe you're waiting on somebody for data, access to a specimen, etc. - if you have something else you can work on in the meantime, then you can keep the motivation train going. So how many side projects? You want to leave graduate school with at least one paper already published. As in, something you can put down for Ph.D. program applications. Not in press, not in review, published. So, have as many as you can manage - I juggle anywhere from 3-4 active projects at a time, with several additional 'off in the distance' projects I will incrementally update and 'open up' once enough active projects are completed. This is a critical part of planning for the future: always have extra rounds to load into the chamber. Do not take on so many side projects you cannot complete them all or be a burden to your coauthors - be responsible. I've met many researchers who have taken on too heavy a load; it's OK to be responsible and decline project invitations. More below.

The dreaded writer's block and random tips for maintaining productivity and sanity

Everyone will get to a point where they've gotten sick of research or academic bullshit. Just accept that this is probably going to happen. It often comes down to interpersonal relationships - if you can, minimize (or eliminate) these interactions and for those you can't, grin and bear it. If it's something that can be avoided without being detrimental to your graduate school graduation prospects (or job for that matter) - life is too short for toxic bullshit. There are a lot of bullies in academia, and it's OK to tell yourself that they can go blank themselves. It may not be the best thing to actually say to their face - but make a pact with yourself to avoid them. If they're not on your committee, and they really really suck, they are of zero consequence. I encountered these sorts of personalities during each of my graduate programs - I avoided them, and instead spent time with labmates who I enjoyed being around. More below.

Note that I'm talking about general assholery here and not actual harassment. Actual harassment - verbal, sexual, physical - should be immediately reported, damn the torpedoes.

If the source of writer's block is not related to general assholery, then it's important to figure out what it is precisely. In my case it has often been a series of conflicting ideas within a paper, or perhaps the paper is hung up because some analysis/equipment/data is not quite available. Can you find a workaround? Often workarounds will come at odd moments of brilliance - I often got ideas while muttering to myself on long walks home in the rainy suburbs of Dunedin NZ, immediately calling my wife at home to discuss the proposed solution. As with many other parts of this post, creativity is important - working your way through nonscientific problems is just as important a set of skills you will need as a scientist, particularly when working as part of a research team.

I do not profess to have all the answers or even many of them - but I'll share my perspective on motivation. I wanted to be a paleontologist since I was very young, and the modus operandi of my career has been keeping research fun. So long as I am enjoying it, I will surmount most challenges and keep trucking. I make decisions about what to work on in order to maintain that fun - which also ensures that productivity is maintained. I will shift from project to project to fight boredom. I'll share a particular strategy I learned during my undergraduate. I am a millennial, and grew up playing computer games, and I shamelessly continue to do so as do many of my peers (many baby boomers don't get it). Gaming can be quite addictive, and resulted in some lackluster grades during my freshmen year of college. When taking calculus I and II during summer school, a particularly addictive game had just came out - but my computer was a bit out of date and could just barely run it. So, between missions, the computer would have a loading screen for about 20 minutes - during which I would solve 1-2 calculus problems. After a few hours, my homework was done, and I got my gaming fix in. That was ten years ago - and this strategy still serves me well. I'll do something fun for about an hour or less, then switch to writing/figure editing/formatting/data entry/analysis for a bit. Another tip: if you're on a roll writing, I find that a drink or two really helps - relax, have a beer or a glass of wine; you second guess yourself less and less and write more. You can go back and edit it later, but I tend not to sweat the small stuff so much if I'm ever so slightly tipsy.

Another tip: when you get a bit sick of a particular project, halt work on it and switch to a different one that is more fun and easy to stay motivated about. Eventually you'll get to another stopping point and can switch back to the other project. Your own attitude towards a project can be a stumbling block of its own.

Yet another quick tip: use a shit load of check lists. I have an entire tiny notebook that is devoted only to checklists! Each page represents about 2-3 weeks worth of tasks to complete. Write out everything and accomplish as much as you can; on days I don't teach, I try to check off 2-3 items a day. This is an easy and effective way of tracking progress and keeping tabs on what task is next.

Lastly, don't give up your personal life. It's only science. It'll be there waiting for you if you take the weekend off. Stop and smell the roses. During my last year of graduate school I became really frustrated on a number of fronts, the specifics of which I won't repeat. I took more time for myself; I left campus every day right at 5 o clock regardless of what I was doing. I spent more time at home with my lovely wife and cat. I decided to do more artwork - and to hell with it, I wanted to learn to paint! So I taught myself watercolor since it was reasonably affordable. Once I started my first job, I could afford more expensive materials and taught myself to paint on canvas as a gift to myself. Set aside a certain number of hours every week for something fun, something that doesn't overlap with research at all. Don't neglect your significant other, family, and friends; they understand you're busy, but don't overdo it. Life is too short. And, most importantly, life as a professional is going to be busier than graduate school, if you can believe it - so find something that works. Mental health is really important, and don't mess around with it. On that note, so is physical health: many Ph.D. students gain a bit of weight. Living in a foreign country with a budget too paltry to afford meals in restaurants or travel, I had a lot of spare time so I worked out a lot - I channeled much of my negative energy into exercise. Jogging, lifting weights, etc. Take care of yourself.

Thesis v. Publication

This is going to be short: nobody cares about your thesis. It's probably great. But, nobody is going to read it (unless of course you don't bother publishing it, and somebody desperate might cite something from it). Write your thesis in such a way that makes converting it to a scientific manuscript easy. Or, better yet, write the manuscript first, and convert it into thesis format second; that way, you won't have the laborious task of having cut off all the thesis fat to make a solid, lean manuscript that will survive the hellfire of peer review. Many schools now offer a manuscript option for the thesis, where you can write some sort of synopsis and then quite literally copy and paste the text from two or more different manuscripts into the body of the thesis (you may have to combine the references cited list, though). This is a great option. Unfortunately, my master's thesis was too monolithic and had no easy dividing line, so I published it as a single, enormous paper. My Ph.D., on the other hand, had 10 chapters - all of which are now published as six papers (several of which I combined).

A brief guide to peer review

Once you start publishing papers, you'll start getting invitations to review articles for journals. Holy crap! Somebody cares about what I have to say? It's one of the most satisfying - and sobering - moments in your academic career. Hopefully by this point you have learned by positive example how to edit your own work - and if by negative example, you may already have a short list of things you really didn't like seeing. I would not profess to be good at peer reviewing, *but* during my Ph.D. a senior colleague whom I had reviewed a paper for wrote me a polite letter thanking me for the best peer review he had ever received - so I'll try to not mess this up. There's a number of rules I put in place.

1) In a word, don't be an asshole. Nobody cares about your feelings, so keep them out of the review - unless of course they're positive. It's OK to have nice, warm fuzzy feelings if you read something amazing - then, goddamnit, tell the author how damn talented they are. Glowing reviews are OK if the work is good. But if it's not, then you should be careful - even if it's somebody you dislike. First off, if it's a researcher you do not particularly care for, or has mistreated you in the past, it is probably best to recuse yourself as you are unlikely to offer an objective review. Watch your tone, stay away from ad hominem bullshit. If you wonder about a particular passage offending the writer ask yourself if everything you wrote is factually or objectively defendable. If not, make it that way. Make sure your reviews are always constructive.

2) Be detailed. Short statements painting things with broad strokes doesn't help anyone - don't skimp on details and don't be a lazy ass. We've all gotten reviews where the reviewer basically did not like something but did not really explain it in enough detail - they did not really have enough time to review it and have thus failed you and the scientific process. Don't fall into that trap; explain things precisely in order to give the author a 'road map to success'.

3) Avoid saying "we don't really know enough for you to claim/propose hypothesis X". That's a bullshit cop-out, and when you see this, this is the translation: "I don't really like this work, out of my disdain for the authors or out of laziness." One exception is if you truly do not believe a proposed hypothesis is testable - and if you don't think so, then say it. One example comes to mind - the "Triassic kraken".

4) Make sure the authors have not skipped any steps. A classic example in taphonomy is "these bite marks are best interpreted as coming from shark bites" without exploring alternative hypotheses. Multiple working hypotheses should be evaluated given that we are in a historical science. Ensure that the authors have gone from one logical step to another without cheating (knowingly or unknowingly).

5) Save rejection for only the worst cases.

6) If an author continually has papers rejected from regular journals, only to be followed by publication in non-peer reviewed journals without incorporating your comments, then consider refusing to review for them.

7) Always sign your review. Doing this ensures two things: it ensures you keep the review constructive and is something you can stand behind; it also gets your name out there, and writing good reviews helps you get taken more seriously. Eventually you may come across a paper written by a colleague where you feel they have been led down the wrong path and owe it to them to write a firmly worded review saying certain things that need to be said - it's an uncomfortable position to be in, and I've been there - and that's perhaps the one example where it is politically best not to sign your review. Note that some journals not only make your name aware but publish your name and reviews; others keep everything anonymous. Each has their pluses and minuses, and truth be told there is not a one-size-fits-all approach that works universally. You'll always end up reviewing something that is just kind of f-d up, poorly written dreck, and it takes calm nerves and a steady hand to politely dissect it.

8) If you have a stronger grasp of the literature than the author (possible even as a grad student) then suggest alternative works to be cited.

9) If you want to phrase something politely to the authors, but wish to be firm about it, do not hesitate to say to the editor "The authors NEED to do X,Y, & Z in order for me to endorse this work" in no uncertain terms. This will give your review teeth.

10) Most importantly, you have to spend the rest of your career sharing the field with these people. You gain more from being friendly and honest than being a vindictive asshole. Trust me: I've watched people systematically burn their bridges, one by one, and it's not pretty. Don't poison the well.

11) Don't be a parasite. You should be, bare minimum, reviewing at least one manuscript for every one you submit. My Ph.D. adviser suggested three per every manuscript you submit - I think that's a fine number, if you get that many requests. By the third year of my Ph.D., I was reviewing on average 2-4 for everything I submitted.

12) Know when to recuse yourself. If there's a scientific paper with some data you really shouldn't be seeing, owing to a conflict of interest - recuse yourself. I've been asked for unpublished data by an unscrupulous colleague, and then subsequently had that data unwittingly shared with said individual by an editor who did not bother to read my reasons for excluding said individual from reviewing.

13) Get it done on time! Don't take more than a few weeks at most. Don't be the asshole who sits on a manuscript for four months.

Minesweeper

As nice a picture as I've painted academia is not always so nice and rosy. Survival in academia relies upon being able to navigate minefields. I'm not going to say much here - but to quote a famous 80s cartoon, knowing is half the battle. Keep a mental record of attitudes, goings-on, etc. - keep tabs on things. Know which way the wind is blowing. Do a lot of listening. Having 'feelers' out will help you avoid toxic individuals, avoid saying the wrong thing to the wrong person, etc. Identify friends who are good confidants and know the score, so to speak, and you can safely discuss ideas and concerns with. Being able to predict things before they happen is a useful skill to have. Being a researcher has a surprising number of parallels with being an intelligence analyst. Some degree of secrecy is important: there may always be some shitty person out there incapable of independent creative thought and takes your idea and publishes it themselves. Think about information circles and the movement of information; who can you trust with what information? If individual X should not hear some critical piece of unpublished data from your research, it probably should not be shared with somebody in their circle: students, departmental coworkers, external coauthors/collaborators. People talk, and they do hear things. I hate saying it, and people (even who this applies to!) roll their eyes when I say this, but most effective researchers think like spies do. And I don't mean illicit acquisition of information - I mean in the sense of just being alert, taking lots of mental notes, and doing mental gymnastics regarding the flow of information - going through 'what if' scenarios in your head. My advice to all graduate students is to read spy fiction by John Le Carre and others; I wish I had earlier, it would have saved me from a number of early blunders in my career. Loose lips sink ships!

Parting note

Nobody gives a flying # about your ego. We're young researchers, and we're going to be working together for a long, long period of time. Some of us have gotten some decent papers out there already and made some great discoveries. But check your ego at the door. Quite frankly, nobody wants to see it; it's like that annoying dog your friend has that they obsess over a little too much and show off all the time but in reality it's kind of ugly, barks too much and eats its own poop. Nobody wants you to bring that dog to a dinner party.

At a regional conference I recently saw some speeches made about the career of a recently 'retired' paleoherpetologist who I was not quite familiar with - they emphasized positive relationships with colleagues over a long career, mentored many (successful) students, and nurtured quite a number of paleontologists. Try to be that person who everyone speaks of in glowing terms. Life is too short to be a miserable loner surrounded by enemies. And most of all, when you've finished your climb up the education ladder, be nice to students: if not, they will remember. I was that student once, and I remember everything.

Further Reading

11 steps to structure a scientific paper editors will take seriously

Writing a Scientific Research Article

Peer Review: how to get it right - 10 tips

What I learned about surviving graduate school

9 Brilliant productivity tips for researchers