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The Scientific Literature

Flipping Through the Pages

I’m traveling today, but as I was scrolling through my RSS feeds on the plane (OK, yeah, I know, but they had free Wi-Fi and why not), I thought about how people of around my scientific generation, maybe a bit younger and certainly the older ones, often talk about how they miss flipping through the physical journals. There was the whole tactile object-in-your-hand thing, of course: I have a Kindle and use it (especially while traveling!), but my wife and I have a ridiculous heap of physical books as well, and we continue to buy more, and both have their points. But the thing that people tend to mention (wistfully) was the serendipity.

You flipped past a lot of other papers while paging through a new issue, and you saw a lot of them while looking things up in the bound volumes, too. Often enough, something would catch your eye, because you weren’t just seeing the title and abstract, you were paging past the figures as well. Most chemists of that era have a story about something they saw while looking for something else that turned out to be useful. It was a real side effect.

That said, it was not a high-percentage side effect, either. The huge majority of the time, you paged right past a bunch of stuff without seeing it that closely, or if you did notice it, you were not exactly excited by it. I’d say that you did get exposed to a broader selection of things that way, during the find-that-paper process, than you would have otherwise, but not efficiently. There’s no denying, though, that the the current click-the-link method takes you past nothing else whatsoever.

At the same time, clicking the link also takes you right to the darn paper, which is something that cannot be said about rooting around in the stacks. Serendipity aside, I think that it’s overall a better use of one’s literature-rooting time to find the thing you’re looking for instantly and seeing if it’s of interest, rather than wrangling bound volumes from the overflow storage room on the lower floor, etc. The “Hmm, look at that” part of the scientific literature is, in fact, pretty well-served by scrolling through RSS journal feeds, as far as I’m concerned. You don’t get the full effect of paging through the whole papers, but you still see a lot of titles and abstracts.

Arguably too many titles and abstracts, true, but there’s always a trade-off. I’m willing to dig through the new articles feeds in order to feel like I’m not missing stuff (although, like everyone else, I occasionally have to Mark All As Read and start over). If you asked me to go back to the table with the new journal issues, next to the shelves of bound volumes, I would, by this point, say Yes to the “Being 25 years younger” part of the deal, but No to the physical paper journal part. . .

34 comments on “Flipping Through the Pages”

  1. A Nonny Mouse says:

    Ha, well said!

    I was looking for a chemical in a Lancaster catalogue when they used to have references/uses and, on the opposite page, was a reaction which lead me on to a process to loratadine by low valent Ti coupling.

    Skimming through a JACS also lead me on to a patent for valcyclovir; it never got used but Roche use the process for valgancyclovir (which I claimed but didn’t exemplify). Pity I wasn’t rich enough to challenge their infringing patents…

  2. Nick says:

    “That said, it was not a high-percentage side effect, either.”

    The same applies to the enterprise of discovering drugs. If the low rate of discovering something valuable through literature browsing is good enough reason to stop, what of the main goal?

    Serendipity need not be a high probability event to be worthwhile (even necessary to success!).

    1. John Trant says:

      But, serendipity happens in the modern ASAPs as well. And faster and easier. I don’t hink anything has been lost honestly. And I am a big physical book reader.

  3. youngun says:

    I’ve never been able to stand reading scientific papers on the screen, and I graduated within the last couple years. I don’t think they’ve really got the layout figured out yet. It’s a lot easier to find corresponding tables and figures referenced in the text in the physical form, and I like to highlight and make notes in the margins. My computer is probably full of thousands of pdfs that I’ve skimmed or not read at all, but if the paper’s on my desk, there’s a high probability that I’ve read the whole thing. Not to mention, it’s a lot easier to find that paper you’re looking for flipping through the physical forms than opening an endless number of arbitrarily named pdfs wishfully thinking “Hey, this might be the one”.

    I can’t speak to having an experience of serendipity that you speak of due to my age and the new nature of the literature, but with the advent of Google Scholar alerts and RSS feeds, I can say there’s not much new in my field that slips through the cracks.

    1. certified millennial says:

      I agree that trying to read through a ton of arbitrarily-named PDF’s is miserable enough to demand a reference manager, and I absolutely print anything I need to be able to explain in detail. However, I actually rather like the infinite-scrolling format of HTML journal articles. Maybe it’s just that it mirrors the way I’ve trained myself to read all the other long-form content the Internet has to offer, but something about the lack of interruption makes it much easier to get “in the zone” of reading. Plus, being able to instantly open all of the interesting references straight from the in-text citation makes for much easier and more efficient hunting.

    2. tlp says:

      That’s kind of surprising and depends on your memory type, I guess. I’ve always had problems organizing my pdf printouts and stopped printing. And keeping the whole journal volume for the few papers you need seemed always very wasteful for me. There are plenty of good pdf organizers that will help you find ‘that cool paper on X that did Y, which seemed relevant for Z’ without remembering the title, journal or author name. But it’s true, sometimes it’s still easier to find that paper again in google than in your own bibliography.
      Agree, electronic ‘reading’ is really different in terms that it encourages one to skim most of the text by following Ctrl+F for keywords. But highlighting and search by annotations are great.

    3. angry about articles says:

      I’ve personally never been able to stand the dual column format. Sure, it made sense in print or whatever, but the up and down, side to side scrolling (or reading something just slightly too small) drives me crazy. Make your articles like every other website on the planet, dammit!

      1. Hap says:

        Lots of synthetic papers (Nicolaou’s in particular) seem to have the tables and text horribly out of sync – a non-page format (continuous) would allow you to place the tables and text in sync better, , but that would have lots of problems, since I don’t read articles on the computer or a tablet.

        1. InfMP says:

          SO TRUE about Nicolaou. I would open 2 copies of the pdf file so I could see the scheme 2 pages away from where they were discussing it.
          But best to just print it and not staple it, and just lay it out on the table.

          1. Hap says:

            I usually put the print in a notebook so I can carry around, and his pagination doesn’t work well enough to look at the pages that way – sometimes it’s the next page (on the back of the one I’m looking at, sometimes not). It’s a PITA.

    4. chimaera says:

      I’ve found multiple monitors (at least two) essential for literature work. I have a reference manager set to automatically scan the folders where I save the pdfs (and I always take the few seconds to save the pdf with the article title as the filename) so they show up there automatically.

      I have one of my monitors set up in portrait orientation and an A4 pdf fits nicely on it for reading. Couple that with a text editor on the other screen for making notes and a notepad on the desk for anything that needs scribbling and I have a system that works nicely for me.

  4. Hap says:

    How do you read journals electronically? I would read some on a Kindle, but the size is a mismatch for journal pages, and I haven’t wanted to buy an iPad for it (I like the reader battery life, though most are no good for color). I don’t like reading on the computer (can’t read in bed, at work don’t like reading off the screens, even though they’re reasonably big).

    1. I highly recommend the Sony DPT-RP1/B (a kind of over-sized 13″ Kindle, but with PDF as primary reader format and other interesting functions, like pen-based annotations).

      1. Hap says:

        It looks neat (a lot of what I would like) but I’d have to think hard about it before I got it (or my work would have to want to cut down on paper enough that I’d need something like that) because of the price.

    2. Ed says:

      I use a Microsoft Surface Pro. Reading PDFs and flipping between pages feels very natural, and you can use the pen to highlight and scribble in the margins. I use Drawboard PDF as the reader/annotator, and Zotero as a reference manager. (Used to use Mendeley but its built in reader/annotator doesn’t play nicely with fingers or pens in a tablet interface.) These days there are a number of decent competitors in various tablet/laptop convertible form factors, most should suffice. The tablets with a 12″+ 3:2 display, a good pen, and a detachable keyboard should be best for paper-substitute functions.

      The Surface is even more expensive than the previously mentioned Sony digital paper tablet, but since it doubles as very nice ultraportable computer it might be worth considering.

      Like other posters, I used to skim through papers on a computer screen but the only papers I truly *read* were stacked on my desk and covered with scribbles. Now the papers I’ve *read* are still PDFs when they’re scribbled and annotated, but they’re neatly organized within a reference manager. Papers I haven’t read yet or have just skimmed are also in my reference manager, but I’ve tagged them as such.

  5. Peter S. Shenkin says:

    I do have younger colleagues who can read complicated technical papers on a screen, but I certainly can’t. I need to scribble on them, particularly if I’m a reviewer. I’ve used a kindle (early model) for reading novels, and I have to say it saved my life when I was trying to finish Lonesome Dove on a trip back from London to JFK when we were stranded on the tarmac in JFK for 3 hours waiting for a gate. I took the kindle version as backup for the tome that traveled in my checked baggage. My kindle is useless for charts & illustrations, but maybe they’ve improved.

    I do find serendipity in web browsing. I’ll go to Wikipedia to look something up and that will take me to something else, which takes me….

    Just reading all the blogs and articles (well, not a huge number) that I’m informed of via RSS, I can, at the touch of a button, go look up a paper that’s mentioned, or learn more about the subject on Wikipedia, which takes me…. These things would each have taken a serious commitment of time and energy back before “click education” became possible, and the list of peripheral subjects I explore may be different from the list I’d have explored back when there were only libraries and an encyclopedia on the shelf, but it’s actually a larger list and covers a broader domain. As with library serendipity, of course, major relevant discoveries are rare.

  6. Anonymous says:

    I am a big fan of flipping through the pages. I would go to the lib with my lit notebooks and work thru the new journals, 1 x 1, taking notes. I would put a tiny mark on the cover so I would know if I had read it or not. It was fun to open the bound journals and see my little marks on the covers years later. Those bound journals have now been discarded to be burned or sent to landfills.

    But there are many things that you still cannot find by searching electronically and only by using an eye-to-brain filter.

    Example 1: topologically non-planar molecules. Those hit the literature ‘big time’ in the early 80s with papers by Walba, Simmons / Paquette, Siegel, et al. I had noticed, by eye, some topologically non-planar peptides, usually not even IDed as being “non-planar” with text or any other searchable term or searchable structural constraint. By “flipping through the pages”, I started collecting references to visually clear but otherwise non-searchable non-planar peptides (and other non-planar molecules not recognized as such in the source articles). [long story deleted] I eventually sent my bibliography lists to a famous prof who was able to publish a couple of papers on non-planar peptides and an algorithm for searching for them (no acknowledgement to me at all). I also took notes on a variety of natural products or synthetic intermediates that were “one bond” away from being non-planar.

    Example 2: Since carrying it out as a grad student, I have been interested in a particular rearrangement reaction (Org Synth, but rarely cited). It turns out that there are dozens and dozens of isolated examples of the same reaction type (mechanism, that is) in the lit but never recognized as such:
    linear version, endocyclic version, exocyclic, hetero atom substitution, … etc. You cannot find these papers in that context using any electronic search that I ever came up with, and I had the papers in-hand and knew exactly what to search for. There is nothing in the title, abstract, text, or ref list to make them stand out for “my” purposes. You have to see the reactions and process them eye-to-brain to see something that, sometimes, the authors didn’t even see.

    I have other examples. Maybe I’ll add them later.

    I used to have an excellent bibliographic memory linked, I am sure, to the tactile journal, color of the binding, the geography of the lib (“red binding, middle section, left side, eye level, … must have been Helvetica”; balcony, blue binding, bottom shelf = Synthesis), and other cues. Today, every PDF looks so similar. Angew or Chem Eur J? I haven’t yet found enough tiny cues (clues) to make the specific source stick in my brain.

    Like others, I now collect PDFs but don’t always read them. I also find it hard to read Org Chem on a small computer screen. When I was in the stacks, I would read enough to have to decide whether or not to lug a heavy volume to the copier. When standing at the copier, I would read more to decide whether or not to pay for a copy. And I annotated my copies with underlines, marginal notes, etc.. I know that I did some very good and effective reading under such “urgent” circumstances.

    Have psychologists studied that “urgent reading” thing at all? Maybe I can find a paper on that if I go to the stacks and start flipping through the pages…

    1. drsnowboard says:

      I postdoc’d for Prof. Marc Julia way back when . One whole wall of his office was filed papers.
      When I used to wander in with a question, his eyes would light up ‘ah, monsieur’ , walk to his wall of papers, and rifle through maybe 2 folders before handing me a relevant paper. It may have been just luck, but I doubt it. He knew that wall.

      1. Anonymous says:

        As an undergrad, I learned to use many of the indexes and to search the literature fairly well even if I did not yet have a good knowledge in the context of org syn. I began my first year as a grad student with a big famous guy who is known for his excellent knowledge of the literature. Like many profs back then, his office was floor to ceiling with shelved journals (and books).

        The first short project to get my feet wet was based on some old Trost chemistry. It went well. A few weeks later, I was tasked to develop a parallel route to a natural product that had gotten stuck at a biphenyl coupling. I had to make a similar but brominated aromatic intermediate to facilitate the coupling. I returned with my lit search and recommended route and he was impressed. I was rather thorough. He asked, as if surprised, “How did you find this stuff?” Eh … Chem Abs, Beilstein, … My suggested route worked very well but the non-bromo path finally worked and my effort was moot.

        After that, I got my “real” project and was shown his route to a recently reported natural product and I took good notes in the office meeting. As I was about to leave, he said, “Wait. How will you make starting material A?” I’ll find it in the literature. “No, no. … Over there. JOC, 1976, January. Check the author index for XXX.” Bingo! The exact compound I needed. I was REALLY impressed! But I soon came to realize a few things:

        1. Most important papers (back then) were TL, JACS, JOC and few others. You can guess one of those journals and be right most of the time.
        2. I later found out that my boss and XXX were good friends. Of course you tend to follow the work of such colleagues.
        3. It is most likely that my boss refereed that paper for JOC (friends, some overlap in research areas; never confirmed that with him, though).
        4. It was HIS proposal! He had researched it before he ever showed it to me!

        It is kind of like an astrologer or mind reader. “I see a starting material! It is in an important journal! TL – no. J-something. J JA? JO? JOC, perhaps? The year, the year … I refereed that paper … it can’t be 1955 … not 65 … 75! No? Try 76. I am smelling something citrus. Limes? Lemons? It was written by a man with an interest in terpenes, perhaps Prof XXX. The page is … the spirits are tired. I must rest. I have led you down the path. Find the page on your own.”

        You still need to know the lit really well to be a good “astrologer.” I have known many who try to fake it but fail miserably.

      2. Nick K says:

        Back in the day Professor Tony Barrett apparently used to have the entire literature of Organic Chemistry on standard file cards. I once asked him if one could use 1,2-benzoquinones as Diels-Alder dienes. “Sure!” he remarked, and in ten seconds unerringly pulled out a file card with just such a reaction on it. I was stunned.

        1. Anonymous says:

          Barrett’s File Cards: Another comment / theory on the way we learn things. Multiple sensory inputs are alleged to improve learning. SEEING writing go up on the blackboard, in concert with HEARING the explanations, and WRITING contemporaneous notes (brain-to-hand coordination) … and the smell of the demo in a chem class or hearing the music in a music class, etc.. Writing actual notes (lit notebooks, index cards, marginal and in-text on photocopies, on your tablet, …) should enhance learning and memory. (What says the latest research? I don’t know.)

          As Old Timer said (above), overly passive students today just learn to look up an answer using google rather than deeply incorporating new information. Incidental vs Intentional learning.

    2. Anonymous says:

      I remembered an example of a natural product starting material from which to make a K3,3 non-planar product: ryanodine. It was commercially available and also being researched by GSK at the time. Using the wikipedia structure, you can see 4 OHs on the alpha face. If you connect two of them correctly as, e.g., a diester using suberic or azelaic or other diacid, you have rendered the compound topologically non-planar. (I modeled the diester to check the length. I don’t remember which diester made the best fit.) Yeah, you might need some protection / deprot steps. I had several other examples of proto-non-planars that you cannot find any other way than by flipping through the pages.

    3. Uncle Al says:

      Topologically non-planar molecules’ skeletal graphs are non-planar by Kuratowski’s theorem. A graph is planar if and only if it has no subgraph homeomorphic to K5 or K3,3.

      https://iopscience.iop.org/article/10.1088/0953-8984/27/35/354101
      … (g). It ties itself.

      https://www.tandfonline.com/doi/abs/10.1080/00268976.2018.1434247
      “[6.6]Chiralane: a remarkably symmetric chiral molecule,” Symmetry: Culture and Science 19(4) 307-316 (2008)

      Also point group T fullerenes C44, C52, C92, C100
      Also point group I fullerenes C140, C260

      In late 1999 Petitjean had published a computable quantitative measure of geometric chiral divergence normalized zero (achiral) to 1 (perfectly chiral) in N dimensions. His most divergent example was CHI = 0.76. Our paths crossed. For the next 18 months I spent some lunch time being clever with HyperChem, he calculated the results. [6,6]-chiralane finally appeared, along with a trivial strategy. All pairs of enantiomorphic space groups are asymptotically perfectly geometrically chiral divergent with increasing lattice ball radius.

      Onerously calculate increasing radii…or measure one angle and calculate CHI = mx + b directly for a radius, contributed by mathematician Dr. Smith then at at Lehigh University. She wickedly declined to tell us why that works, nor did we ever divine it. It is exact,
      log(1 – CHI) = -2[log (radius, Å)] +(pi)[2 – (α/60))] where α, is the the three atom angle in degrees. Four (later discovered) misassigned crystal structures gave CHIs greater than one. How did it know?

      1. Anonymous says:

        1. That iop link to Molecular Knots includes a reference to Sauvage’s Angew cover story on the first synthesis of a trefoil knot, “proven” by chiral NMR. However, they had failed to consider a non-knotted D2 twisted ring conformation that would also produce a chiral mixture by NMR; hence NOT a proof of the first knot synthesis. Their subsequent paper had an X-ray that nailed the knottedness.

        2. The Novak paper (Mol Phys, 2018, 116(12), 1565-1572) is behind the Taylor and Francis paywall. I can’t see if he cites Andre Dreiding for a 6,6-chiralane. … I first stumbled upon Chiralanes via Uncle Al’s (note: that’s Uncle ay-el AL, not uncle ay-eye AI) website years ago. Amazing concept. Uncle Al treated them as a class with different ring sizes.

        A few years later, while “flipping through the pages” (trying to stay on topic, you know!), I came across 6,6-chiralane in a pre-Uncle Al paper by Dreiding, made a copy and put it in one of my “symmetry” folders. That folder (and the reference) got lost during an office move. An extensive lit search of every Dreiding ref I could find did not reveal the source. I think it must have been a book chapter, research summary, long abstract … something not indexed … that I was flipping through in the library. I wrote to Dreiding (RIP, 2013) and brought his attention to the Uncle Al’s chiralanes but he didn’t recall and couldn’t find his own paper that had 6,6-chiralane. Dreiding did not use the term chiralane and his paper with 6,6-chiralane is something that may only be found by “flipping through the pages.” (Is Dreiding cited in the Novak paper, anyone?)

        I hope that the current generation of DIGITAL-only page flippers can have as much fun and luck finding new ideas and their correlations and ramifications.

  7. AQR says:

    In an effort at “directed serendipity”, I used to pick up old volumes of Organic Reactions and read articles on reactions I had never used or even never heard of before. I found it especially interesting to read the mechanistic parts of those articles from the perspective of what was now known but wasn’t at the time the article was written. I can’t say I ever put anything I learned about to use, but it was a stimulating exercise.

  8. loupgarous says:

    My days in biomedical engineering introduced me to Louisiana Tech’s excellent library, and just the sort of serendipitous learning you talk about, Derek. I was exposed not just to the matter I sought, but unsuspected troves of knowledge.

    I found bound collections of symposia on Marburgvirus and Ebola long before they became popularized by Douglas Preston’s The Hot Zone, and more recently, the waves of Ebola, Marburg and other hemmorhagic viruses through Africa. Then I’d go home to the wife and kids, past the Lincoln Parish library and revel in the newest copy of Bulletin of the Atomic Scientists and treats like Iben Browning and Nels Winkless’ Robots on your Doorstep.

    My time at Lousiana Tech formed my Googling habits indelibly. I’m not as efficient a researcher as some, but I get more joy from it than the more focused hot shots. Riffling through electronic pages, always.

    1. Hap says:

      Richard Preston. I think they’re brothers, though. Douglas Preston writes more thrillers, while Richard writes mostly nonfiction (he finished a book of Crichton’s).

      1. loupgarous says:

        Wups, you’re right. I had the novelist brother, not the reporter. Thanks!

  9. Scott says:

    I suppose I should be thankful that HR isn’t as literature-intensive as some fields of effort, though you really should be on good terms with your corporate counsel (if you have one). Because reading case law makes my eyes bleed!

    My bad habits are wikipedia, atomic rockets, and heaven help me if I get a link to TVTropes. It will be days before I come up for air then!

  10. Lambchops says:

    I guess the great thing about serendipity is you never know when it’s going to strike. My supervisor once gave me the vague instruction to “think about topic X and go do some some experiments” I skimmed RSS feeds, I did some searches, I printed out some seemingly relevant articles and scribbled all over them. Did I come up with an idea over the course of a couple of months? Did I hell as like. I forgot about the topic for a bit and focused on other things.

    Fast forward three months later I’m sitting in the department watching a guest lecturer, see a neat reaction related to topic XX and scribble “asymmetric version?” in my notebook. Sure the project results were mediocre (proof of concept at best), but inspiration had struck and as it turned out a good chunk of my thesis was based on my decision to go to a fairly innocuous sounding lecture.

    So if I based things on an n of 1 I’d be advising you all that journals are overrated, if you want directed serendipity go to as many lectures as possible!

  11. jb says:

    I can’t stand reading articles electronically. The worst is when reading on a digital platform and the article will refer to a figure. You can’t look at the figure while reading because it is on a separate page and you have to scroll back and forth between them. Of course you can always use a setup with two screens, but that’s not very mobile. I always print out articles. Study after study has shown that you also retain more by having physical text in your hands.

  12. Old Timer says:

    I believe this is referred to as incidental learning vs. intentional learning. Most people over 25yo have lots of experience of incidental learning and the ability to “soak in” information as they quickly scroll through graphical abstracts. The problem is that for the current generation of students, most haven’t experienced incidental learning (e.g., Google instead of Dewey Decimal). This makes them terrible problem solvers and constant answer seekers. Why think when you can google? I have a friend in Big Pharma who is an organic chemist because he got lost and walked into an auditorium where an Organic Chemistry lecture was going on. Incidental learning at its finest!

  13. I was a grad student during the paper-to-bytes transition and I don’t think that kind of literature-serendipity ever hit me during the journal era as much as it does now via Twitter.

    1. loupgarous says:

      Twitter strikes me as a narrow hose, technical serendipity-wise. nextbigfuture.com is much better, that way (though Twitter does have good bioscience poop, nextbigfuture.com has better coverage of everything else in new science and technology).

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