Friday, October 28, 2016

10 Years of Omicing!

Today marks a special day - it was 10 years ago that I launched this endeavor.  I'm going to take time today, and perhaps a few times in the near future, to look back on the journey.  Ten years of blogging also happens to be around my anniversary of starting work at Millennium, which means I've been a professional in biotechnology for two decades.  So I must be old; indeed, this summer I celebrated birthday 30 (numeric pedants might make the base charge that I am misleading by not writing that 0x30) and about a quarter century since I launched into bioinformatics full time.  So a bit of nostalgia seems not out of place.

The Genesis

How did this all start?  I had been reading a few science and medicine oriented blogs, but the dominant one was Derek Lowe's In the Pipeline.  I liked his mix of  in depth analysis and commentary.  It was easy to start thinking "I could do something similar".  I've always liked expressing myself through writing and was a bit frustrated that writing at work consisted almost entirely of bullet points and quick emails.

The catch was that I was at Millennium and the company had an explicit and quite restrictive social media policy.  As a public company, that was somewhat understandable, but it was going to be a problem if I wrote on anything in the field.  I could have chosen to stick to dogs and gardening, but that wasn't what I wanted to do.  Perhaps if I was careful I could avoid a hammer coming down, but that wasn't really a risk I wanted to take.  Writing an anonymous blog was an option I quickly rejected; I wanted to have something that was an advertisement of my thinking.  Plus, then there would be a game of keeping from revealing too much and perhaps someone making it their quest to "out" me. 

Then Millennium laid me off, just shy of my 10th anniversary (about two days after getting the pink slip, the "congratulations on your valued service" email arrived).  Here was opportunity!  I could have waited until I actually left the company, but I figured at this point the worst they could do was cut my two weeks short, and besides management was too busy dealing with the chaos of reorganization to focus on one outgoing employee testing the bounds of the policy.  Not that I pushed matters

The name?  I've never found naming things easy.  I was fretting over it, with little progress, when for no particular reason the Roman cartoon character from the Little Caesar's pizza chain (which we almost never ate at) popped in my head, along with the television commercial tagline "Pizza! Pizza!'.  So I aped that.  I've toyed with the idea of having a parody logo drawn -- a double helix replacing the olive wreath around his head and a pipettor instead of a staff, but have never gotten around to snagging an artist (I'm inept at drawing)

Writing Influences

I had rarely thought much of this before, but with the anniversary approaching I started pondering my writing influences.  I read a lot and absorb a lot from what I read, but surely there were definite influences that have affected my style.  These aren't in a particular order, but there are four that spring to mind.  

I've already mentioned Derek Lowe, who was a major influence.  I don't write as well as Derek, and certainly not with such enviable regularity, but I think he has rubbed off on me in some ways.  For example, Derek's obviously far better in the lab than I, but his various tales of chaos there made it easier for me to write about some of my misadventures, both in the lab and at the computer. 

Thinking back, the first blog I ever read was before the concept of blogs existed.  We had a subscription to Byte magazine from the late 1970s until it folded, and there was a long running column there by science fiction writer Jerry Pournelle.  In a magazine aimed at programmers, the most recognizable and engaging writer wasn't one -- he simply was trying to have a system that supported his writing.  He would review different hardware and software and comment on various programming trends and answer mail from readers.  He also created a little bit of an ongoing storyline; the column ended up being titled Chaos Manor.  I think I can trace calling my current work Starbase, my son The Next Generation (aka TNG) and making my shih tzu Amanda a regular character trace a bit back to those Byte columns.

Mrs. Anne Eccles was my ninth grade English teacher.  She was happy to be a bit eccentric; some students found it off-putting but I loved it.  She was also absolutely passionate about teaching.  In that class, more than any other I can remember, we worked on the mechanics of writing.  We spent a bunch of time with descriptive writing, which I struggled with, but even there the focus on choosing words carefully was driven home.  

The other person who deserves nearly infinite credit for making me think about my word choices is my father.  Sometimes he strays into being a pedant and enforcing rules which have fallen by the wayside, but he did make me think when I spoke and wrote.  I've seen some guidelines for helping students that counsel picking only a few major errors to mark, for fear of scarring the psyche of young writers.  Dad didn't subscribe to that viewpoint in the least, and I'm the better for it.  In high school I treasured getting back a draft with red ink all over it; it's a service I missed in college and beyond.  That meant he had read it and thought about it, and my work was always better for it.

Evolution of The Blogging Ecosystem

When I started the blog, an early problem was how to publicize it.  How could I attract readers?  Well, in those days the best way was to find other blogs that were related and contact their writers asking for a plug, or to find a topic to leave a comment on and put the blog there.  When I was looking for a new job, I also printed up business cards that listed the blog and mentioned it in my job talks (though by then, I was already notorious enough that the person introducing me would often mention it).

Over time, the blogosphere has changed.  For example, in those early days there was a regular occurence of "Blog Carnivals", in which one blogger would highlight a bunch of related blog posts.  The theme might even be chosen in advance, with a set of bloggers committing to publish on the same day.  Those lasted for a year or so; I need to look through the archives but I think I may not have gotten around to "hosting" one.

There were others who contributed to publicizing the blog.  GenomeWeb would graciously highlight my pieces at times in their coverage of the web, which was always very nice. Other bloggers would put me on their blog roll, or sometimes write commentaries on what I had written.

I never imagined when I started the blog that companies would reach out to me and offer me in on breaking news.  That was quite an honor; I realize they aren't doing it out of pure goodness, but it is still something that they are willing to have senior scientists and executives spend an hour talking to me.  I've always tried to observed the embargoes, and only once have I messed up -- but 10X Genomics was very nice about me publishing an hour before the agreed time (a stupid mental slip; I got the time wrong in my head).  Those pieces have often driven huge traffic to the blog, particularly if a more conventional media writer such as Matthew Herper mentions it.

These days most of the publicity for the blog is through Twitter.  There are still a number of other active genomics blogs, though I think none of the ones that existed when I started are still around (or at least they are very quiet).  I didn't keep a record of my original roll of other blogs, so I can't check my memory.

That Regularity Issue

I'd probably do a lot better in general if I'd keep up a more uniform and regular pace.  I really pushed hard the first year, getting out 35 pieces in those two months and change at the tail end of 2006 and then 136 in 2007.  But that was a high water mark that I haven't come close to; I would like to beat my second highest total of 79 from 2009; this post makes 57 for 2016, which is within striking distance of #4 (59 in 2010) and #3 (64 in 2011) and not so far from getting to 80 and passing 2009.

There are, sadly, a multitude of ways I find to not blog. Sometimes there are hard reasons, such as family vacations.  Sometimes work involves late nights to hit a deadline, leaving little time or energy for writing. But all too often, I just don't prioritize writing.  Then there's also dark times, when something else is going haywire in life and I can't find enthusiasm to write.  There's a terrible cooperativity to inactivity; once you haven't written for a while it is easy to find excuses to keep not writing.

The worst part is that I've never had a shortage of ideas on what to write; many a potentially interesting piece has been procrastinated until I forget it or it is no longer timely.  Perhaps the worst example of this was with Theranos; when so many media outlets were singing its praise, I took a look at the Board of Directors and was struck in a very negative way by all the political heavyweights.  If I had written something about that, I might have looked prescient; now you just have to take my word for it.  

A Confession

When I started the blog I had some lofty goals.  For example, it was supposed to be revenue-neutral, a stance that held out until this year (it is impossible to have a cheap MinION habit).  Another was to not have the blog interfere with my day job (and especially, not cause me to exit said job!)  But another one was to be very transparent; my goal was for my readers to always understand my biases.  

I do try to work to that goal, but a little bit at Infinity and then frequently at Starbase I've run into a conflict between my desire to openness and my responsibilities at work.  A simple way to put this: you can assume at all times that I may be under a confidentiality agreement  via my company with just about any company in the genomics space.  I treat these very seriously, sometimes avoiding topics that are too close to what I am privy to and also checking rigorously with public sources when I do write in the vicinity.  Getting access to non-public technologies is key to my professional mission, so I have to live with these rules.


I really should steal some time to go back and skim over everything I've written.  Sadly, I rarely read later what I've written, unless I'm reference the piece in a new entry or on Twitter.  The worst sins have, as noted above, sins of omission from putting off a topic too long, or those cases where I leave information out that I can't prove I can get from a public source.  But I've made a few other mistakes, annoying people unnecessarily or getting details wrong.  My goal is to get them right!

I also suspect that if I look back through the early years of the blog that I really didn't write as much about Illumina as the topic warranted.  I don't believe I wrote much at all about "next generation" sequencing in the first few years of the blog, which seems odd.  I was also slow to realize that Twitter was a useful source of information.  I didn't cover AGBT for quite a while, which might not be awful since so many early "belle of the ball" technologies were total fizzles.

I really kick myself for not trying to get to more of these meetings.  I got in the habit of being a bit averse to business travel; I think I didn't go to any meetings while at Codon (other than the sales folks, hardly anybody did) and I suspect Infinity would have supported me going to AGBT, but I never thought to try.  Nowadays I'm constantly sheepishly telling people who ask that I won't be going to X or Y; I'd love to attend AGBT, London Calling, ISMB, the PacBio user groups, the CSHL Genome Meeting, the ONT New York Community Meeting, ASHG and a bunch of others each year, but the company likes me to get work done and will spring for one meeting a year. 

Thanks and Onward!

Above all, I do treasure the feedback I get on the pieces, so long as it is constructive (okay, I like just hearing that people read it, which technically isn't constructive).  Comments are moderated to reduce spam (so please don't type twice!), but any that are on target I okay. One of the stated goals for this space was to put my ideas out for critique and to learn from those comments, and sometimes I've done more general dredging of the collective wisdom of my readers.  

Somehow, and it's not just me looking for posts to cite (nor just robots), I've accumulated over 1.5 million page views.  So thank you readers, especially those who come here regularly.  I throw at you puns. too clever titles and awful dog jokes, yet still you come back. That you are willing to spend some of your time reading my output is high praise, and I do appreciate it very much.  Now to the second decade of Omics! Omics!

1 comment:

Rick said...

I have been reading since close to the beginning and have enjoyed the ride. Most of the time I receive notice of a new blog via email and then immediately go to the web page because I am anxious to get to the meat of the the blog. Thanks for the inciteful thoughts and the clear writing.