Tuesday, September 13, 2016

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


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 V: manuscript writing, research productivity, peer review, and more


I’ve taken half a year off from blog writing, ostensibly to catch up on manuscript writing. It’s been somewhat useful, but now it’s gotten to the point where I just feel bad. So, Paleo research tips returns to Coastal Paleo. I hope to keep this up at a more regular pace than before. This post is likely to be useful to anyone conducting exploratory natural history research – but may be less useful to those whose research consists entirely of statistics (though, read to the end). 

Continuing the “underpants gnomes” joke from south park, we’re sort of at this stage:

Step 1: fossils
Step 2: get data
Step 3:???
Step 4: paper (profit)

This blog post gives some more subjective tips on what to do after you’ve recorded data/field notes and how to organize that information using actual pen and paper and distill it down into a coherent story you can type up into a manuscript.


All of my research notebooks - two notebooks dedicated to eomysticetids from my Ph.D. (look for New Zealand beer labels), an entire notebook just on Herpetocetus (Blue Moon label), and an entire notebook on marine vertebrate taphonomy.



Why bother with an actual notebook?

For some of my readers, there is no doubt that this post may sound like it was written by a Luddite. We’ve got computers, tablets, iphones, apple watches, and refrigerators with twitter installed on them (I’m seriouslynot kidding, and I really, really wish I was) – so why should we bother with keeping a physical notebook for research? Why not just keep everything as MS word documents on your computer, or in cloud storage?

There are a number of reasons for/against, and I’m not going to pass judgement on one side or the other; both sides – traditional notekeeping, and digital notekeeping – have compelling arguments to be made, and so it largely boils down to picking options based on personal preference and the sort of science you’re doing. Recent cloud storage hacks raise the possibility of losing data. Hard disk drives are not permanent, and generally last about seven years. I almost lost ten years of data, unwritten manuscripts, and digital photographs when my hard drive died this summer, and as my hard disk was slowly dying, I realized I did not have enough money to pay for a new one. Eventually I saved up some over the summer and picked up a new one, meanwhile adding a solid-state drive and an upgraded power supply, and I got very, very lucky. I’ve gone through a dozen flash drives over the past decade, with various drives either getting corrupted somehow or being lost. Requiring a device to work on research can be impractical at times: you very likely will run into a situation where a dank museum basement may not have an appropriately placed plug, let alone a wireless (or wired) internet connection. Digital research notes have their upsides – you can instantly share information with coauthors. There are also digital calipers out there which can be set up so that measurements are automatically entered into a spreadsheet. Large spreadsheets are much, much easier to work with electronically than rather than on a sheet of paper; recording many sorts of data are easier to do digitally. Notebooks can also get a bit heavy; I’ve filled up over half a dozen moleskine notebooks since I started using them eight years ago, and I need to remember to grab the correct one with me – this is obviously not a problem with a laptop or a tablet. Lastly, at some point, we are no longer sending handwritten manuscripts (or even typewritten, for that matter) in to journals, and we’re all using MS word or a similar program to write the end-result of our research with – so why not go digital all the way?

But what about “real” notebooks that aren’t written in binary? For starters, time and again I see in the news new studies being published indicating that notes written by hand being stored more firmly in your memory. Full disclosure: I’ve not bothered to read any of these studies first hand, mind you, but since they reinforce my own biases and personal experience they sound eminently plausible. I personally have a much easier time recalling information I’ve written out by hand. Colleagues, friends, and my dear wife routinely make fun of me for my abnormally sharp memory for unimportant things like fossils (my brain is a library of fossils and their morphology & locality details) and Star Wars, and yet in school I could never remember when my damn homework was due. Point is, if memory is an issue for someone like me who can recall the date, time, and location of a particular fossil I collected six years ago down to one meter – then likely it is an important issue for everyone.

Actual notebooks don’t run on electricity, and don’t take a minute to boot up. They also don’t have annoying pop-up windows telling you that your free McAfee antivirus trial ended 11 months ago (no, I’m not going to give you any money for something that works half as well as freeware, now piss off McAfee!). I’ve never heard of a notebook breaking if you dropped it. Notebooks also won’t become corrupted, or crash, if used improperly or left on the shelf for too long.But just like electronics, notebooks have their limitations. Both will be lost permanently in a house fire or natural disaster; both will be completely screwed if you spill enough coffee on them (as I type this, I nervously push my coffee mug further away). Both will be ruined if your checked bag busts open on the tarmac at SEATAC; of course it’s raining, it’s Seattle (this did happen to me, but ironically it was a checked box with part of a fossil whale skull inside; the box was damaged but the whale was in a concretion, so it was fine). As a result of these very real fears, whenever I travel my top priority is to have ALL notebooks I’m traveling with inside my carry-ons. On my way back from New Zealand, this meant I had ~15 field and “lab” notebooks in my two carry-on bags, which was a bit ridiculous.
Another issue is that of “language”. Storing certain information digitally has long term problems, and the most prominent problem I’m thinking of starts and ends with file extension. Try opening certain file extensions in MS Word 2010 – sometimes it’s impossible. Sure, Microsoft puts out file compatability packs, but what about when we’re on MS Word 2015, and they decide to stop supporting software/file types that are older than 10 years? I hate MS Word 2007 & 2010, and still use Word 2003 whenever possible as it is by far the most intuitive to me. My dad is an attorney and has used Word Perfect since the 1980s, and until the last five years it was the typical word processor of choice for those in law. The version of Word Perfect he uses is now 15 years old, and he has to run a Windows XP emulator in order to even run the software – he dislikes the newer version, paralleling my frustration with Word 2007/2010. This is not just a matter of poor choices – many of his older legal files are accessible only using Word Perfect and not through Word, and attorneys are required to save all documentation for a long period of time (10 years, I believe). 

Likewise, this problem of having the information but being helpless to actually read it is not unique to electronics and software that are constantly being updated and tweaked, often at the expense of existing products. Notes must be written neatly enough and in a comprehensible language in order to be useful. I used to have terrible handwriting, and I realized when I was a Freshmen in college that I could no longer write in lower case, and began writing in all-caps with a sort of easy-to-read block printing. I can open up notebooks from my master’s program and still read everything. I can’t say the same for class notes from high school, written in incomprehensible chicken-scratch. Can I read anything in cursive? Only if it’s immaculate. I was probably one of the last cohorts of students to be taught how to write in cursive; I stopped using it as soon as I was no longer being graded on it, and so my skills are very rudimentary, frozen in time from third grade. During my Ph.D., Morgan Churchill and I started researching a fragmentary fossil called the Waipunga seal (our eventual research was just published in NZJGG). When we took the specimen on loan from GNS in Wellington, we were generously sent along Dr. J.A. Berry’s (Napier, NZ) notes on the fossil. I was excited to see them – a time capsule of thoughts on a completely overlooked fossil from the early 20th century, when many “modern” ideas of pinniped relationships we take for granted did not exist. Morgan and I opened up the folder and were disappointed to see an inch thick stack of loose sheets of paper with messy, cursive-esque squiggles – the notes were completely useless, probably readable only to Dr. Berry. I could make out perhaps one or two individual words on every two or three sheets. 20th century pinnipedologist Dr. Judith King published on several other specimens Berry worked on, and remarked in each case that Dr. Berry deserved credit for his correct identifications, but that his manuscripts were not in a state to be published; I doubt that Dr. King had much more luck deciphering Dr. Berry’s cuneiform than I had, and I assume that she was being nicer about it than I am currently.




Utterly gorgeous entry from one Leonardo Da Vinci's notes, one of the most famous pages of any scientific notebook in history.

A more famous example, of course, is Leonardo Da Vinci, who wrote backwards – and many believe this was done to keep others from reading his notes. However, I’ve also seen others note that he was left handed and did this to keep ink from smudging. If you want your data to outlive you, please don’t turn your notebook into the Voynich Manuscript

Other reasons exist for using real notebooks. It’s much, much easier to include sketches interspersed with handwritten notes, for example, and I’ll wager that most people can produce a sketch (or reproduce one, if in class) much faster with pen and paper than with mouse (or a touch screen for that matter). Sure, the software does exist for quickly adding sketches into text, but it comes across to me as less convenient. There is certainly an aesthetic element to it as well – it feels damn good to look through old notes when working on research, seeing carefully written text associated with annotated photographs and sketches, cross-referenced to other sections in the notebook (and indeed, other notebooks) – having a well-organized notebook can be a thing of beauty. This may seem shallow and superficial, and there are certainly sci-hipsters out there who will get all uppity about notebook brands (moleskines are expensive, moreso than when I started – perhaps thanks to hipster assholes – but I am anal retentive enough that I want all of my notebooks to match one another). However, keeping a properly organized notebook is the best way I know of to organize and consolidate all of my thoughts on a particular research subject, and permit me to convert disconnected observations into a cohesive story and help me feel like an organized person (which is now a 31 year-long effort that is finally succeeding). If you can get this same feeling from digital note-taking, great! I don’t know how you do it, and if that accurately describes you, then you can stop reading here. Lastly, and perhaps most fundamentally, I dislike staring at computer screens for too long and I get distracted easily – I also am very susceptible to headaches, and suffer from them almost daily. Bright screens trigger headaches after a couple of hours (and on that note, it’s time to go take a break and check on our 3D printer and fossils sitting in acid baths). Writing in notebooks solves all of the above problems (which are NOT universal!) and for me, and surely many others, mark a critical stage in the condensation of ideas between the nebulous conditions in the brain and the refined format of a manuscript and resulting journal article.


What sort of notebook?

This section is by far and away the most subjective, and owing to that I’ll keep it short. There are some heinously expensive notebooks out there – I use Moleskine notebooks, which are moderately priced, and have increased in price by ~30% since I bought my first in 2008. They come in a number of sizes, have nice college-ruled lines, a decent page thickness that keeps ink from bleeding through, and come with a page-marker ribbon and a pocket on the back cover for scraps. I keep printed photos in here if I’m working on a large project and have a lot of photos to paste in. If you don’t want to spend 20$ on a 10x7.5” notebook, there are plenty of knock-offs at half the price that are probably of similar quality. Some colleagues of mine just use those funny composition notebooks with the speckled black/white covers; my undergraduate adviser, Dr. Dave Varricchio, had a single monograph written out in four of these notebooks. I started with hardcover, smaller moleskines, and within a few years was a bit tired of the small format and upgraded to somewhat larger and more expensive notebooks. Moleskine does make much, much larger notebooks (like 12x20” or so) but these were 50$ when I saw them in New Zealand (although, that’s just how much any book costs down under). As far as what sort of notebook to pick, you should weigh 1) line ruling 2) paper thickness (if you use ink that bleeds, a lot of your notes will be unreadable), 3) notebook size (larger notebooks can fit larger diagrams & annotated photos; my handwriting is also messier in smaller notebooks), and of course 4) your budget. Most scientists are academics of course, used to living off of bread crumbs. My view was that a 20$ purchase would give me more than a year’s worth of notes; indeed, I have perhaps spent only 100$ on notebooks over the past 8 years. Most techies would surely drop several times that amount at the slightest announcement of the newest Iphone (It’s got headphones without a cable! You’ll feel better than everyone!).




Table of contents from my first notebook on cetaceans; most of this has all been published by now.

Where to start? Basic organization

At the very beginning of course, it’s a very good place to start. In all seriousness, the first page should include some brief description of what will go into the notebook, if for example you’re like me and have different notebooks for different topics. Name, affiliation, contact information, and a reward in dollar amount in case it goes missing. My guess is that a thief or good Samaritan are more likely to swipe an Ipad over a research notebook filled with labeled pictures of bones. 100$ is a good bet for a reward, in my opinion, though that’s entirely a guess as I’ve never had to worry about that problem.
Next up should be a table of contents. I block off the first few pages for the TOC to give room for expansion – a typical entry will be 5-15 pages in length. If you anticipate your entries to be longer, you can always subdivide it and include those subdivisions into the TOC – or just allot fewer pages for the TOC. My TOC has “subject” on the left and “page #s” on the right, and I even use little dots like in an actual TOC/index in a book. Whenever I start a new entry, I’ll add it into the TOC and indicate the starting page, leaving room of course for the last page. And that means numbering every single damn page in the notebook; you don’t need to do it all in one go – I add in page numbers as I write.

With each entry, I try to include the full title on the first page, and on subsequent pages simply write a shortened title followed by “cntd.” There will come a time when you will have to abandon an entry, begin a new entry, and return to the former subject and therefore split an entry; on the last page, I write “continued on page…” and fill in the page number when I get back to it. This requires diligent revisiting of older sections on occasion. For a split section, I tend to also add that in as a separate TOC entry – e.g. “Description of a Cambrian rabbit fossil part 1…….p. 84-96; Description of a Cambrian rabbit part 2…….p.109-121.”

Occasionally I might have multiple notebooks where I might refer to an observation I have made that is not yet published – in which case I will reference the notebook title (I also number all of my notebooks in roman numerals, I-VIII at present) and page number. This also works if you need to refer to field notes. When appropriate, I will often completely copy field note entries for a particular fossil description entry. It may also be important to note the date each entry was – in case, for example, a museum visit opens your eyes to some new pattern and you have to reevaluate all of your assumptions and biases regarding some aspect of the fossil record (such as my 2013 visit to the Cooper Center in Orange County did about fossil pinnipeds).




Labeled fold-out photograph of the holotype skull of the eomysticetid whale Tokarahia kauaeroa.

Including illustrations and photographs

This is where you can get a bit creative, and can blur the lines between science and scrapbooking. Paleontology and many other branches of natural history research are visual, and there’s no better way to make your work accessible to your future self than supplementing written notes with hand-drawn sketches/diagrams or photographs. My undergrad adviser Dave Varricchio would take photos in the field with a Polaroid camera, shake the picture, and tape it directly into his field notebook – carefully annotating the position of individual bones and sedimentary contacts/bedding and burrows as he excavated a site (this is precisely how Dave painstakingly documented the den of the first burrowing dinosaur, Oryctodromeus cubicularis). I remember helping out at a marine crocodile excavation in the Thermopolis Shale in 2009 as Dave took his last few polaroid shots – the company had just stopped producing the film, and he ran out (I believe they make the film again now, though). I took that idea and ran with it – it’s not quite as efficient, but if I know I’ll be writing about a particular fossil, I’ll snap some digital photos, quickly edit them in photoshop, and arrange them into a single image and print them off on a laser printer. I used to print everything off on photo paper, but I found that A) photo paper is heavy and thick and B) the ink rubs off after only a few months of notebook use. My laser printer images, however, are all still sharp 5-6 years later. I annotate these using a different colored pen (red for annotations, black/blue for the main text). I treat these as the proto-figures for a project – often by the time I am done with the entry, I’ve figured out what works and what doesn’t and edit the final images accordingly. If a specimen or other image is too big for a single sheet, I fold them in half and glue (old fashioned glue sticks work well) one side down – and now you’ve got a cute flip-out image that is appropriately sized. Any images that will help you consolidate your thoughts can be included – I tend to include maps, labeled anatomical & comparative photographs, and when relevant even graphs.




An example of photo paper beginning to smudge after years of use - the notes (circa 2008) from my very first research project on the fur seal Callorhinus, published in JVP in 2011.

If you are artistically inclined, sketching directly into the notebook is a great way to supplement your text. If you find yourself in a descriptive field within natural history, sketching is an eminently useful skill – it improves your powers of observation and attention to detail. If art is not your strong suit, I recommend setting aside some time and learning – practice makes perfect, and artistic talent is a myth. “Talent” is nothing other than investing time into artwork and practicing regardless of how many crappy drawings you produce at first. My art used to be terrible, and it wasn’t until High School when I took four years of drawing classes; that much practice will turn anybody into a serious artist. Many people I’ve met believe that art is quickly done – and it can be, given the medium – but more often than not those wishing for instant gratification will lose interest or become discouraged when they do not get instant results. I recommend those people take up photography instead (and then, why not re-read Paleo Research Tips Part III: fossil photography?). In all seriousness, at the very least I recommend taking up art as a hobby to keep yourself sane during graduate school; I taught myself watercolor so I wouldn’t go insane during my Ph.D., and taught myself acrylic on canvas when I got my first job and could afford the supplies, as well as being a rite of passage as an “adult/grown-up” artist).




Notes from my taphonomic literature review from my master's thesis; depicted here are notes on phosphogenesis and Osedax bioerosion.

Literature review

Maintaining a research notebook may not completely revolve around primary research at first. When I started my master’s thesis on marine vertebrate taphonomy, I quickly realized that I had a firm grasp of most of the available literature (hint: there’s not much) and that having a solid grasp on all of the relevant literature was within arm’s reach. Aside from reading, I was unsure how to proceed. Type up bullet points? Again, I found that such activity did little to maintain mental permanence. Then I thought, why don’t I buy another moleskine and write notes on each paper I read? I started another notebook and recorded notes on most of the relevant papers on marine vertebrate taphonomy. Certain ideas are best communicated through diagrams, graphs, and photographs – so I photocopied the most important figures from each paper and pasted them into the notebook. In each entry, I distilled each paper into a series of bullet points – and in some cases, I noted where certain papers on whale taphonomy were simply reinventing the wheel and making a big deal out of recycled ideas from 20-30 years ago. “Calling bullshit” is an important part of the literature review process, after all. Six years later and most of these papers and the most relevant bullet points are still somewhat fresh in my memory – and if not, I can go back to my distilled notes and save myself the trouble of doing it all over again. This sounds quite a bit like revisiting notes from college courses [confession time: I did not bother keeping many of my notes from college; so long as it pertained to sedimentary geology or paleontology, the act of writing it down and re-reading it once or twice prior to exams has burned most of it into my uncanny memory].




Labeled tabs (up to date for most of these) allow easy and quick location of relevant entries.

Miscellaneous Tips

-To keep super organized, I add in little colored plastic tabs and write (with a fine point micron pen) for each entry. I can quickly refer to that topic when necessary.

-This might be my anal retention showing, but I tend to edit photographs prior to pasting them into notebooks because I strongly dislike including photographs with the background left in. It introduces a bit of extra work, particularly if you’re using “working photographs” (as they’re called in the Fordyce Lab) which will not be used in the final publication, meaning that two rounds of photo editing are needed. This also, however, means that you can do a faster, sloppier editing job if it’s just going into your notebook.

-The utility of this sort of activity is not relegated to primarily descriptive work. When interpreting graphs and charts of taphonomic data, I’ve found that being able to lay out all possible interpretations and relevant observations within a notebook permits me to pick and choose the more relevant points to include in the eventual paper.

-Not really a tip, but more of an observation that is better shoehorned in here than elsewhere in the post: I find that when I’m done writing an entry in one of my notebooks, the manuscript is already 75% written, and can be typed up directly from the notebook.

-I've included a few tips for embellishing notebooks. There's an entire webpage dedicated to modifying moleskine notebooks. Check out the "Moleskine hacks archive".

-Have other tips for maintaining research notes in a traditional manner? Let me know, and I’m more than happy to include it here!

This entry in the paleontological research tips series is admittedly quite a bit more open-ended than the field notes section. After all, there are many more guidelines about what should be written in the field, given that in some cases field notes belonging to certain geologists may be subpoenaed for legal purposes. For field paleontology, there are some very black and white rules as to what information needs to be recorded. As far as research in the laboratory or museum goes, it is admittedly much more subjective and revolves around what works best for individual researchers; I’ve outlined my own methodology in the hopes that it might give ideas or inspiration to students in my position eight years ago – knowing which direction to go with research, but unclear about how to organize thoughts between the “get data" and "profit" stages of research.

1 comment:

George said...

Great post. Having a notebook makes it very personal. With a good handwriting and drawing skills, a notebook can turn to a valuable treasure passing knowledge from generation after generation.