Transitioning from Papers 3 to Bookends: Part 1 - The Why

The Problem

Support for the desktop version of Papers 3, my erstwhile reference management software of choice, was discontinued and sales ceased last November. I have been using some version of Papers on the Mac and iOS for over seven years now, and I have really enjoyed using it on both platforms. The Papers app on iOS was especially useful, with its selective Dropbox-sync and night-reading features. Over the years however, there were many growing annoyances. The lack of significant updates was frustrating, and even when updates were offered, they were largely unable to keep up with operating system advances. Ever since Papers was bought over by ReadCube, I have been worried about the future direction of the software as well as the long-term durability of my reference management system.

Why a reference manager?

Considering the aforementioned problem, a fleeting thought I had was to archive/delete all of my 5000+ PDFs, save a BibTeX file, and give in to the constant connectivity of the attention-economy era: download PDFs from their source whenever I needed it. However, unlike what Spotify does for music (for me), after some thought, I realized that this approach would become troublesome when I’m in the field (>month downtime with no internet, etc.) or traveling. Furthermore, retrieving some hard-to-get PDFs or scans of papers I already would’ve been challenging. I wanted to have access to my papers.

How about simply keeping PDFs somewhere on my iCloud with a fixed naming convention and separately update a BibTeX file with reference information taken from Scholar? I knew I didn’t have to start from scratch because Papers 3 could generate one giant text file with all my references in BibTeX format. This approach was also not entirely appealing. I knew that such a strategy could become unwieldy real quick for an ever-increasing number of papers, especially if I wanted to go inside and edit some references along the way (something that always happens). Also, it would’ve been painful to generate a revised .bib file with a sub-selection of citations for particular projects. Finally, if I ever wanted to use Word or another WYSIWYG editor, citation management would’ve become… a chore. Considering today’s technological umbrella, I don’t think asking for a half-decent reference management software is a tall ask.

What would my ideal reference manager look like?

• Light, powerful, and not prone to crashing
• Ability to attach PDFs to references
• Transparent file handling and archival
• Ability to handle a LOT of PDFs
• Automatically “look” through a PDF and crawl the web for its full reference accurately
• Ability to generate bibliographies or list of references and citations in any format I wanted (preferably customizable)
• Have a PDF-editing interface where I can annotate or make notes on a paper
• Ability to batch processes the references of several PDFs
• Ability to have smart groups and smart search
• Ability to slice and dice my papers in any way I’d like (e.g., view by journal/authors/keywords, etc.)
• Syncs with cloud-service of choice (preferably iCloud so I can get out of the Dropbox ecosystem!)
• Preferably has its own app on iOS via cloud interface
• An affordable payment plan

Although Papers satisfied some of these constraints, as mentioned above, it had severe limitations, the most frustrating of which was its clunkiness and tendency to crash. Moreover, Papers3 used a “virtual library” system where you could choose how files would be named and stored and eventually viewed through its interface (e.g., Author-Year-Journal), but they were actually stored under a machine-readable format (long string of numbers; DDC3-VD2383248.pdf); I was never a fan of this opaque system.

Bookends

Enter Bookends from Sonny Software , a rather unassuming entrant compared to the more well-known platforms (Mendeley, Zotero, etc.) I had first heard of it through the MacPowerUsers forum and then saw some positive things about it on Twitter. Earlier this week, contemplating the long-term home of my PDFs, I decided to take the plunge and see what the fuss was about.

First off, Bookends on Mac costs $60 - it is a one-time buy with updates lasting for two years (at least). The iOS app costs $9.99 as a one-time buy, and then it is another $9.99/year for enabling cloud-sync. To me, this is a very reasonable pricing structure. Bookends does offer a free trial that limits you to 50 references so you can try it out. But first, is it worth it?

Let me start by saying that Bookends ticks off every bullet point that I mentioned above, and does a LOT more. Starting off, the first thing I did was to investigate how well it can capture a reference from a PDF — this seemed to go very smoothly — Bookends had no problem automatically retrieving information (via JSTOR/Scholar/Web of Life, etc.) for a recently published 2019 article or even one published in 1923.

Ok - so it can perform the basic functionality of a reference manager - what else? Well, the field entries to a reference were quickly editable (refreshingly no lag!), and there were many powerful options for global batch edits. More importantly, the citations’ and reference formats were completely customizable and so was the ability to rename PDF files after importing them. Furthermore, Bookends could sync using iCloud!

Oh my, this seemed rather promising at this point. But - what about iOS? This was where Papers3 excelled. Bookends on iOS did not disappoint. It seemed to be fast, light, and also could fully edit and export citations/references. There was functionality to use customizable search engines (Scholar/Web of Science etc.) for finding articles. Also, you could make notes, highlight, or annotate your PDFs, all of which would sync with the desktop version via iCloud. Furthermore, the app supported split screen view for drag and drop!

With this much potential, I decided to take the plunge. The real test was whether it would be able to handle my 5000+ PDFs and perhaps, even more, pressing: could it port all my existing citations from Papers?

Book Review: Digital Minimalism by Cal Newport

Georgetown University’s Cal Newport is back with another book, Digital Minimalism, which extends his outlook on doing more meaningful work in an increasingly distracting world. 

Digital Minimalism is one-part manifesto and one-part popular science. In essence, it is a discourse on the critical disadvantages of constant connectivity and the advantages of being intentional about using today’s technologies. By documenting several studies as well as anecdotal examples of how mobile applications and social media have become deeply interwoven into the fabric of society, Newport makes an excellent case for minimizing the usage of most things digital to (a) break free from screens and (b) regain control of intentionality in communication. Newport contends that finding tools for a problem at hand is a far superior strategy to first gathering tools for hypothetical future issues. This philosophy resonates throughout the book and in particular, hits home concerning today’s smartphone ecosystem, with countless (many unnecessary) mobile applications and innumerable (unconscious) sign-ups for the shiniest new social media platform. 

Newport, unsurprisingly, goes quite deep into providing concrete examples of methods and strategies for assimilating into the digital minimalist’s mindset. Newport showcases read-later apps and blocking apps, but most effectively, demonstrates how social media companies prey on addictive tendencies to develop their platforms (swipe down for refresh = slot machine; bright red notifications, etc.) The book details many suggestions and techniques to offset such tactics and lists the many disadvantages of continually glancing at Twitter or Facebook. Ultimately, Newport asks us to reclaim our time because “our time = their money.” In doing so, he delivers a stark warning about the impact of addictive digital media in today’s attention economy.

At the same time, Newport, who is a computer scientist by profession, also emphasizes that digital minimalism is not an anti-technology movement. The book outlines why careful curation and consideration of apps, as well as their intentional usage, can actually elevate efficiency and efficacy in the workplace (“dumb down your smartphone”). Much of this builds on concepts described in Newport’s earlier book, Deep Work. Concerning the minimization of screens altogether, Digital Minimalism goes a step beyond Deep Work’s ethos of emphasizing “value in boredom” and contains an additional dimension of focus: leisure. Newport pulls together examples of how ‘leisure’ activities, which is easily distanced from the activity of endless scrolling on an app, can contribute to wellbeing and how technology itself can foster such ‘crafty’ activities. 

It’s at this end of the book where I felt that Newport begins to meander and briefly loses sight of the bigger picture. Perhaps unwillingly, the tone morphs into one with a somewhat preachy demeanor and extols the virtues of activities that do not appeal to most readers (e.g., Crossfit) nor extend to their day-to-day realities (e.g., emphasis on handiwork), and importantly aren’t relevant to the message at hand. At times I also felt that the balance between scaremongering and hard facts became fuzzier than at a comfortable level. 

Regardless of these setbacks, Digital Minimalism is an important book on an important topic. Whereas Deep Work was a tour de force on honing intentionality in the workplace, Digital Minimalism is Newport’s effort to extend this perspective to overall wellbeing and personal nourishment. By highlighting some alarming ongoing trends in digital addiction as well as offering tangible solutions to minimize screen use, Digital Minimalism is a compelling read.

[Thanks to Chris Maupin for gifting me a copy of this book!]

Book Review: Indica by Pranay Lal

Balancing the nuanced and involved intricacies of the scientific method versus proselytizing the fantastic “factoids” of popular science is a tough act. Having to straddle this line to focus on the geology and geobiological history of the Indian subcontinent, an ambitiously multidisciplinary topic, on which there are scant accessible texts (popular science or not), is an even tougher act to follow. Fortunately, Pranay Lal manages to achieve such a balance and convey his infectious enthusiasm about the subject matter rather effectively for the most part of Indica’s ~400 pages.

It was refreshing and enjoyable to learn about new geological and paleontological information of the Indian subcontinent - a topic dear to my heart. The detailed place-markers and the McPhee-esque narratives of sites where geological features are found scattered throughout India was highly interesting. The accompanying photographs and schematics are also very nicely done. You can quickly see that Lal put in hours and hours of (non-book-based) research into Indica — it shows. It felt as if Indica was an attempt to channel Sagan or Bryson or Winchester but with a focus on the history of the Indian subcontinent — a fantastic idea. However, it becomes apparent through Lal’s reporting that it is challenging to piece together and chronicle information on such a vastly “big-picture” topic, especially, when construction, urban expansion, and apathy are on their path to eroding many of India’s geological marvels.

Lal is a geneticist by training and his disposition towards anthropology, biology, and paleontology becomes discernible as his writing on these topics shines. For example, his narrative on the evolutionary history of the recently discovered Indian purple frog (Nasikabatrachus sahayadrensis), its evolutionary ties to another frog found in Seychelles, and its parallels to the tuatara or kiwi was a treat to read. Moreover, the lengthy descriptions of India’s Phanerozoic paleoenvironment and the medley of dinosaurs that walked on the subcontinent were entertaining. The closing chapters on hominid evolution and India’s potential contribution to this story were thought-provoking.

As a downside to Indica, there are many small inaccuracies conveyed with certainty that are really more uncertain than presented. My friend Suvrat Kher has an excellent blog post on many problematic sections dealing with sedimentology, tectonics, and mantle dynamics. I can echo Suvrat’s concerns in the paleomonsoon and paleoclimate domain where, amongst other things, Lal makes it seem as if we have a more concrete picture of the vagaries of the monsoon, its initiation, and its intensification than we actually do. Many of these points amount to more than sheer nitpicking. Ultimately, these inaccuracies are a significant downside to Indica, and I wonder about errors revolving around geobiology and other realms removed from my own field. Nevertheless, these inaccuracies did not prevent me from puzzling about them for a few minutes and moving on, driven by Lal’s ardor (one day, on my second read, I might find the time to write down my concerns as well and as thoroughly as Suvrat did).

As a closing statement, Indica is for anyone and everyone interested in the geological natural history of the Indian subcontinent. For students/workers who do read it, I recommend trying to spot the inaccuracies and perhaps making a list.