PainScience.com Sensible advice for aches, pains & injuries
 
 

About the Design and (odd) Tech of PainScience.com

updated (first published 2013)
by Paul Ingraham, Vancouver, Canadabio
I am a science writer and a former Registered Massage Therapist with a decade of experience treating tough pain cases. I was the Assistant Editor of ScienceBasedMedicine.org for several years. I’ve written hundreds of articles and several books, and I’m known for readable but heavily referenced analysis, with a touch of sass. I am a runner and ultimate player. • more about memore about PainScience.com

PainScience.com readers often ask things like:

This site is mostly my own custom work. I have been publishing webpages since the dawn of the web in the early 90s. And the secret to publishing so much is an obsession with publishing automation and efficiency: creating both quantity and quality with as few keystrokes as possible, based on about 30,000 lines of weird custom code and a truly unique content-management system (CMS).

The focus of that system is on making it as easy as possible to publish good footnotes. The best parts of it were originally written by a friend of mine, a programming prodigy who now works for Apple. We still have lunch every week.

I chuckle when people ask, “How can I get a website like yours?” You really just can’t.

A thing of highly abstract beauty

Top-notch referencing is important to me, so I manage this site’s huge bibliographic database using an obscure database format used by academics, BibTeX and a wonderful free app called BibDesk. (My own articles are also stored in the database, and so they can be organized and cited like any other reference.)

The system parses (reads) the database, which then uses the data to make web-ready citations in many styles. For instance, I can create an inline citation versus full bibliographic details for a footnote, all pulled from the BibTeX database and turned into complex HTML. (Footnote formatting is all automated too.1) If I tweak a citation format, every usage on the site changes in one stroke! Or if I change the summary of an item in the database, it automatically changes everywhere it’s used on the site.

And so I can write like a writer and cite on the fly with extreme efficiency that would make any scholar cry. It’s a thing of highly abstract beauty. I get fan mail from librarians. (I am not kidding.)

The tools

I’m old school: I write PHP, HTML, Perl, and prose in the venerable, insanely powerful Mac text editor, BBEdit, and a fleet of other power-user tools:

The need for speed (and security)

I also have a really lean, mean custom blogging machine: publishing software I wrote that really gets out of my way and lets me write, write, write. Making websites is so complex and tricky that even the best tools available — and there are some amazing ones — are missing many features I consider essential, and include much more that I don’t need or like. There has always been a serious disconnect between my priorities and the nature of most web publishing tools.

After years of getting frustrated by content-management systems and blogging platforms of every description, I decided the only hope was to write my own — as every writerly geek must eventually do. And so my production workflow is now faster than any other blogging platform I’ve ever used or heard of. All kinds of publishing and formatting chores that are a bit of a pain with all other CMSs are reduced to a few keystrokes. A short post can be written and uploaded in less than a minute, and yet look richly formatted. The files are plain text, highly readable and editable (Markdown and more) and highly resistant to obsolence.

And it makes unhackable, fast pages made of pure, organic, free-range HTML5 and CSS and nothing else: no Javascript frameworks, no SQL database, no accounts and logins, no code that can be exploited or rev up the server’s CPU.


Appendix: The making of a footnote (many hours of science wrangling to create one small footnote about hot kneecaps)

As you can see from the above, I take my footnoting really seriously technologically. But I also take them very seriously as a matter of scholarship.2 There are a lot of ways to do referencing wrong,3 so I work hard to understand and correctly explain relevant science. Preparing a new footnote recently — just a single, “minor” footnote for my IT band syndrome book — I was struck by what a huge process/ordeal it is for one teensy little number, both technologically and in terms of scholarship.

They’re like icebergs: there’s a lot more to them than you can see.

So this is the life cycle of a typical show-me-the-science footnote: one that’s interesting enough to deserve some real effort, but still not important enough to end up as anything much more than a wee footnote. It begins easily enough…

I do something like this two or three times per week, and have for many years now. And that’s how a typical footnote is born — in this case, one which shows (among other things) that about half of people with unexplained anterior knee pain have “hot” kneecaps.4

Notes

  1. And, of course, the footnote itself links nicely back to the document body. You can imagine what a headache it would be to “manually” create and rearrange thousands of footnotes. Imagine a large, heavily footnoted document … and then trying to add a new footnote somewhere in the middle! Yikes. Software handles all that: specifically, a custom Perl filter, quite powerful, inserting and renumbering new footnotes with the press of a button. Return to text.
  2. For an example, here’s a very serious citation:

    Patton D, McIntosh A. Head and neck injury risks in heavy metal: head bangers stuck between rock and a hard bass. BMJ. 2008;337:a2825. PubMed #19091761.

    It turns out that head-banging, “a popular dance form,” constitutes “a definite risk of mild traumatic brain injury” and the study “helps to explain why metal concert goers often seem dazed, confused, and incoherent.” I can think of other reasons! Part of the reason I wanted to share this beautiful piece of science is that I grew up in a youth culture dominated by heavy metal — a small industry town in northern Canada, Prince George. I was surrounded by head bangers, and they were definitely dazed, confused, and incoherent. And worse! But there is a strong possibility that the daze preceded the heavy metal in many cases.

    The risk of neck injury also increases with head banging intensity — although less than one might expect, which we can infer from the way people are able to keep doing it.

    BACK TO TEXT
  3. PS Ingraham. Bogus Citations: 13 classic ways to self-servingly screw up references to science, like “the sneaky reach” or “the uncheckable”. PainScience.com. 3119 words. BACK TO TEXT
  4. Näslund J, Näslund UB, Odenbring S, Lundeberg T. Comparison of symptoms and clinical findings in subgroups of individuals with patellofemoral pain. Physiotherapy Theory and Practice. 2006 Jun;22(3):105–18. PubMed #16848349.

    Researchers bone scanned and x-rayed 80 patients diagnosed with PFPS and with many common similar diagnoses eliminated, a nice “pure” selection of unexplained knee pain patients. They divided them into three groups: 17 with pathology, 29 with “hot” kneecaps (metabolically active), and 29 without any findings (5 dropped out). All patients and 48 healthy subjects without any knee pain were then interviewed and examined by a surgeon and a physical therapist.

    They could not diagnose the pathologies without the scans — all patients with pain tested about the same, and their symptoms were indistinguishable. Q-for-quadriceps angles were about 4˚ bigger in the afflicted, but the authors carefully explain that 4˚ too small to be reliably detected. The most interesting result of the study is that almost half the PFPS patients had kneecaps throbbing with metabolic activity — that’s a fairly strong pattern.

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