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Derek Lowe The 2002 Model

Dbl%20new%20portrait%20B%26W.png After 10 years of blogging. . .

Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases. To contact Derek email him directly: Twitter: Dereklowe

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January 21, 2014

Throwing Out the Files

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Posted by Derek

Since I'm in the process of moving my office, I've been taking time to do something that's needed to be done for quite a while: cleaning out my files. Somewhere around 2007 or so, I made the switchover to keeping PDFs as my primary filing system, with paper copies when needed. There was a transitional period, which I ended up splicing together by checking through my recent printed copies and backfilling those into my digital archive, but after that, it was all digital. (For the record, I'm still using Zotero for that purpose, although there are several equally valid alternatives, both commercial and freeware).

But I still had a pretty massive filing cabinet full of stuff, and I let that remain undisturbed, even though I knew some of it was surely junk. Only when I started digging into it did I realize just how much of it was little more than that. I'd estimate that I've thrown at least 80% of my files into the recycling bin, an act that would have made me uneasy only a few years ago, and horrified me in, say, 2004. It was easier than I thought, though.

That's because the folders easily fell into several broad categories. In the medical/biological sections of the cabinet, there were "Topics I'm Unlikely to Revisit - And When I Do, It Won't Be With These References". Those went right into the recycling bin. And there were "Topics I May Well Revisit, But When I Do, It Won't Be With These References". Those, after a glance through their contents, went into the bin as well. These were folders on (for example) disease areas that I've worked on in the past, and might conceivably work on again, but a folder full of ten-year-old biomedical articles is not that useful compared to the space it takes up and the trouble it takes to move it. And if that sounds borderline to you, how about the ones that hadn't been updated since the late 1990s? Junk. Nothing in the literature goes out of date faster than a state-of-current-disease-research article.

Moving to the chemistry folders, I was quickly surprised at how many of those I was throwing away as well. The great majority of the printed papers I kept were chemistry ones, but the great majority of what I started out with went into the recycling bin anyway. Digging through them was, in many cases, a reminder of what keeping up with the literature used to be like, back in the day. It was a time when if you found a useful-looking paper, you copied it out and put it in your files, because there was no telling when or if you'd be able to find it again. If you were one of the supremely organized ones, you drew a key reaction or two on an index card and filed that according to some system of your own devising - that's before my time, but I saw people doing that back when I was a grad student. The same sort of pack-ratting persisted well into the 1990s, though, but eroded in the face of better access to Chemical Abstracts (and the rise of competing databases). Finding that reaction, or others like it, or even better references than the ones you knew about, became less and less of a big deal.

So in my files, over in the section for "Synthesis of Amines", there was a folder on the opening of epoxides by amines. And in it were several papers I'd copied in the late 1980s. And some printed-out hits from SciFinder searches in about 1993. And a couple of reactions that I'd seen at conferences, and a paper from 1997 showing how you could change the site of ring opening, sometimes, with some systems. Into the bin it went, despite the feeling (not an inaccurate one) that I was throwing away work that I'd put into assembling all that. But if I find myself wanting to run such a reaction, I can probably set something up that'll work fairly well, and if it doesn't, I can probably find a review article (or two) where someone else has assembled the previous literature.

One of the biggest problems with my chemistry files, I realized, was the difficulty of searching them. I'd gotten used to the world of SciFinder and Reaxsys and Google and PubMed, where information can be called up any way you like. File folders, though, do not speak of their contents. Unless you have the main points of that content committed to memory, you have to open them up and flip through them, hoping for something relevant to pop up. I can well remember doing that in the early 1990s with some of these very folders ("Hmm, let's see what methods I have for such-and-such"), but that style of searching disappeared many years ago. You can now see what methods everyone has, and quickly find out what's been added to the pile since the last time you looked. Younger researchers who've grown up in that world may find it odd that I'm pointing out that water is wet, but my earliest file-cabinet folders were started in another time. File folders are based on tagging (and in its purest form, a physical label), and I agree with people who say that the ability to search is more important and useful than the ability to tag.

So, what did I keep? Folders on specialized topics that I recalled were very difficult to assemble, in a few cases. Papers that I know that I've referred to several times over the years. Papers that refer directly to things that I'm currently working on. Some stuff that's so old that it falls under the category of memorabilia. And finally, papers on more current topics that I want to make sure that I also have in digital form, but didn't have time to check just now. But that three-inch-thick collection of nuclear receptor papers from 2000-2002? The papers on iron dienyl reagents that I copied off during a look at that chemistry in 1991, and never had a need to refer to after about ten days? A folder of reductive amination conditions from the late 1980s? Into the big blue bin with all of it.

Comments (23) + TrackBacks (0) | Category: Life in the Drug Labs | The Scientific Literature


1. Lisa Balbes on January 21, 2014 8:41 AM writes...

The end of an era.

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2. Dr. Mindbender on January 21, 2014 9:07 AM writes...

I remember categorizing literature for my qualifying exam the way you describe. I'd find a key reaction within a paper, print it, then write the reaction at the top of it so when I flipped through my ridiculous folder full of papers I'd know why I printed that specific one. Oof, I don't miss those days (although I did learn a ton, so it wasn't all bad).

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3. PPedroso on January 21, 2014 9:25 AM writes...

It is clear that you do not work with generics... 1990s papers are gold, due to their never-ever-again published results of animal data.

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4. meshugena313 on January 21, 2014 9:26 AM writes...

While I agree that computer searches are more efficient, better, and much much faster, I really miss the serendipity of opening a bound set of journals in the library and opening to the wrong page and finding something really cool. I find myself now intentionally opening the wrong volume of a journal - especially methods journals - and randomly looking at the papers. Of course paper filing sucks, and when I set up my office a few years ago I insisted on as few filing cabinets and shelves as possible to minimize paper creep. Sorta worked, I still throw out piles of printed PDFs every month or so.

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5. Wheels17 on January 21, 2014 9:28 AM writes...

Rather than discarding the .pdfs, drop them in Evernote. It will do full text indexing on the files, and keep both a local hard disk copy and a cloud copy. The cloud copy can be accessed via a web browser, and will be synched to a local hard disk copy on another computer automatically.

If you have concerns about the printed copies, the Fujitsu ScanSnap series integrates really well with Evernote, including text recognition and indexing. The combination is a very powerful tool, with lots of uses.

Not associated with either of these companies, just a very happy user of the system.

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6. JAB on January 21, 2014 9:44 AM writes...

In synthesis it's my perception that older papers age moderately fast. In my field of nat prods, not so much. A compound isolated from an organism is still there, unless extinction happens. I use a hybrid system dating to when I saw my thesis adviser unable to find stuff in his files. I keep the print copies but they are indexed in Reference Manager by a serial number. The file cabinets are getting pretty large, and I've thought of converting to pdf files, but that's a huge task, even for the papers that are easily accessible online from our scientific library.

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7. Gretchen on January 21, 2014 10:23 AM writes...

I have a visual memory, and I often remember what first page of a paper looked like and can thumb through printouts and quickly find the one I want. When I save online, I have to search for terms and often get 100 hits for a term and don't remember which titles in the resulting list are the ones I want without seeing how they're displayed.

However, filing those printouts often doesn't get done. And going back and chucking the worthless one takes more time than keeping them all.

Some days it seems hopeless.

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8. Gene on January 21, 2014 10:30 AM writes...


As you mention, EverNote is a cloud product, and he probably doesn't want things relating to his confidential company research floating around on the net.

Given all the recent data breaches in things, I no longer trust any company to keep anything confidential. Security appears to be job #961 to most folks nowadays.

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9. watcher on January 21, 2014 10:30 AM writes...

Something that one of my early bosses would say: a month in the lab is worth an hour in the library!

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10. anon the II on January 21, 2014 10:49 AM writes...

It's interesting that you have a folder on the opening of epoxides by amines. I have very few folders these days but I still have that one. I started it over 30 years ago. Controlling the regioselectivity of the reaction based on conditions and substituents is still kind of a black box and results can be counter-intuitive.

Now that I'm enjoying a "geriatric postdoc", I have access to all the online stuff and so I've largely abandoned saving paper for more than few weeks.

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11. anchor on January 21, 2014 10:59 AM writes...

@ 10-After layoff, While I was on the job block not knowing what was in store for you (still going to be medicinal chemist or who knows?)frustration was building up in that you do not know whether to keep many files that you have accumulated over the years that you brought it with you when you were let go! This was the hardest decision on me and am sure many were in a similar situation. Eventually, I had to junk most of it and retained only those schemes and ideas that I casually scribbled in my note book in late-eighties. I share your sentiment.

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12. Rhenium on January 21, 2014 11:54 AM writes...

I went to my modern university library last night, because I enjoy the quiet and because I never know when I might dig up a new idea.

I became very despondent, because just about any book I picked up off the shelf felt as if it already outdated, no matter how new it actually was.

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13. WGC on January 21, 2014 1:20 PM writes...

Moving your office is very good from the standpoint of keeping useful files. If they aren't important enough to box up and move, they aren't that important. When I moved after being in the same office for 12 years, I found myself looking at the minutes of a committee meeting from ten years previous. I asked myself, "Should I keep this report considering that I probably didn't even look at it when I received it?"

I filled one and a half recycling bins.

I am now going through the same process you are going through with respect to paper copies of articles, asking myself "Do I need to keep these together, or can I find the important references easily enough using PubMed?"

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14. Anonymous on January 21, 2014 1:23 PM writes...

I remember using google book search to find a sentence I briefly remembered I read in a book somewhere. Within seconds had the right book and the page number!

I can't live without microsoft onenote now. It really is amazing. I can drag together any piece of information I want and have it all classified and searchable. It's much better than evernote as a note taker, as well as allowing shared documents on your shared drive. Not a cloud in site if you don't want it to.

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15. Anonymous BMS Researcher on January 21, 2014 1:58 PM writes...

One of my grad school profs kvetched about how cheap photocopies had caused our note-taking skills to atrophy: "when I was a grad student, I would read each article in the library and capture enough on a few 3x5 cards that I would never need to look up that paper again."

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16. DCRogers on January 21, 2014 2:28 PM writes...

You left off the most difficult group - papers I will never conceivably use, but are written with such beauty that you could not bear to condemn them to the bin.

In fact, your entire cleanup process comes to a pause as you take 5 minutes to re-experience the deep joy of a well-written scientific argument.

Turing's 1950 "Mind" paper [where he proposes the Turing Test] nearly derailed my last cleanout...

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17. An Old chemist on January 21, 2014 3:57 PM writes...

How about books, like Fiesr and Fieser; Compendium of synthetic methods; etc. When I moved from one town to another,I sent these books for recycling. My company also sent all their volumes of Fieser and Fieser to recycling bin. I am wondering as to what others have been doing???

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18. anon the II on January 21, 2014 4:09 PM writes...

Speaking of... I've also got like the first 16 volumes of Fieser and Fieser in a box in the garage. What do I do with them?
And I have a CRC Handbook from the 30's that my uncle had as an undergrad. He's 94. It's actually handbook size. I'll keep it.

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19. David on January 21, 2014 8:18 PM writes...

Anon the II/anyone,
If you are in the Boston area, I'd be happy to take any Fieser/Fieser books or other similar references off your hands. I'm building a little library for our group by scrounging these types of things.

Many thanks,

David (

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20. Andy on January 21, 2014 10:14 PM writes...

I hope you're not moving your office because your shop is switching to an "open concept" workspace floor plan like we are doing...

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21. a. nonymaus on January 22, 2014 10:11 AM writes...

Re: 16
I keep a separate file for those, as well as another one with epic pissing contests and burns on the mendacious. In the first go things like Woodward's beautiful description of one of the tetracyclines as a "diabolical concatenation of functionality". In the other go classics such as the fight over higher-order organocuprates, along with the alleged and real syntheses of hexacyclinol and Cornforth's studies on the Chatterjee demethylation. These latter ones are also useful reading that I give to new students in the lab while saying "and these days, the internet never sleeps."

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22. Anonymous on January 22, 2014 10:26 AM writes...

the first 9 volumes of fieser & fieser came to me by way of a company tossing them out. i use them as shelf dressing and have cracked them open out of curiousity a few times, but i can't see them competing with an electronic literature search

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23. Adam on January 24, 2014 11:28 AM writes...

I hope you didn't throw away your copy of "The Chemical Properties of Dioxygen Difluoride"...

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