Blogging about your own work.

Ok, so my titles aren’t nearly as inspired as Cath’s are.  This week hasn’t exactly been encouraging for puns, unless you consider massacring Danish pronunciation as a very complex linguistic joke.

Actually, I only have a glimmer of an idea tonight – but I’m writing because I need something to do to keep me up for an hour or so.  Sorry for the bad pun, but the clock *is* ticking and it’s only three weeks till I’m supposed to be in Denmark – and I still don’t have movers.  It’s driving me completely around the bend.  So, as a therapeutic device, I’m going to write my glimmer of an idea.  Please don’t be too harsh on it.

The idea for the post came from reading Jacquelyn Gill’s blog post, “Why did I start blogging?”  (By the way, please go vote for her to win CollegeScholarships.org Blogging Scholarship. She clearly deserves it!) Her post isn’t quite related, but at the same time, it is – you can go read it to see why, if you’re interested.

One of the things I struggled with for the past two years has been blogging about my own work. Of course, I interpret this as blogging about what you’re currently working on, not the stuff you finished months ago, which is always fair game.  (Blogging your own publications always struck me as blatantly endorsing yourself – something only politicians should need to do.)

Anyhow, blogging your own current work, showing the bumps and warts of science is something I love to do, and as a scientist, something I want to do as often as I can.  However, there are several problems with it.  It tends to tip your hand to the whole world about what you’re working on and that can have some disastrous consequences.

First, if you’re in a medical field, it can be difficult to talk about cases you’re working on, if there’s any form of patient confidentiality.  Many of the projects I’ve been involved in have required me to maintain complete silence about the nature of the project.  Blog + confidentiality = Instant ethics issues, methinks.

Second, if you’re working on a manuscript, presumably you’re going to have to keep everything you do quiet.  Heck, I’ve got a paper in the works for which the journal sent instructions that require absolute silence on whether it’s even been accepted or not, let alone contemplate communicating anything about the topic.  If I say any more about this, I’ll either jeopardize the publication or wind up in jail.  (Have I already said too much?)

Third, if you aren’t working on a manuscript, you’re either not an academic, or you’re working on an open science project.  I was fortunate enough that I my own project was open, allowing me to talk about my Chip-Seq work for the first three years of my PhD – but alas, that work never cumulated into a second paper.   That’s another rant for another day.

That leaves scientists in the awkward position that they either:

  1. blog about someone else’s work – as if they were journalists, describing their own fields,
  2. blog about their own work in vague terms so that their competition doesn’t scoop them,
  3. blog about work they’ve already published.
  4. blog about the unimportant stuff – or the stuff that they don’t plan to publish.

I can think of one exception: Rosie Redfield, who does a good job of writing about what she’s working on, although her recent work has all been about rehashing and verifying (or more accurately not being able to verify) someone else’s results.  (Yes, I’m referring to the arsenic bacteria fiasco.) I have to admit, I don’t follow any other bloggers who discuss their own data in public, but I’m sure there must be some out there…

Still, if this is a problem for academic bloggers, industrial bloggers face an even harder battle to discuss their own data.  I can think of Derek Lowe over at In The Pipeline as a great example of a blogger from industry.  I used to read his blog daily, and back when I was an avid reader, I seem to recall my favorite posts of his were from the lab – but were all about the strange mishaps and challenges faced by chemists, drawn mostly from the past.  Absolutely none of his current work was discussed, unless it ended in spectacular failure. (Those were good stories too…)

So, I often find myself wondering, when I hear people say that scientists should blog more about their own work, who exactly do they expect to follow that advice? (Btw, It’s something that pops up in conversation frequently, although I couldn’t think of a blog entry that makes that case specifically, off hand. If you need a citation, you’ll just have to settle for “personal correspondence.” Sorry.)

Are there a group of scientists who are willing to blog their own work at the expense of getting publications or being fired from their jobs?  Somehow, I have yet to meet this clique – although if I did, I’d have a lot of questions.  And I can’t imagine they’d be in a position to do this for very long.  You don’t get grants renewed without publications – and you wouldn’t have a workplace for very long either, if you kept blogging the secret sauce recipe.

Maybe, however, this is why some scientists chose to leave the lab bench to pick up the mantle of journalism.  Cue Ed Yong, for instance.  So, the solution isn’t that we need more scientists blogging about their own work, but that we need more scientists to leave science to blog about other people’s work…. or perhaps we should just ask them to stay in science and blog about other people’s work already.

Ahem.  Status quo wins again!

Updates – Oct 2011.

So, my thesis with the requested changes has gone back to my supervisor.  The process we have going is pretty…  unstructured.  At this point, I’m not sure what happens next.  In theory, it should now go to my committee, but who knows when that will happen. My external examiner isn’t scheduled to get it until mid december, which means my thesis defense can’t be scheduled until February at the earliest. Thus, I more or less have  4 months of thumb twiddling penciled in, unless my committee decides they want me to do another experiment. (And I’d probably have some choice words about that plan.)

So, with that said, I have a couple projects to “wrap up”, if you consider it wrapping up to be a) starting a project that won’t appear in my thesis, and b) doing some maintenance work on an open source project that my committee disregards because its not biology.  At worst, that’s about a week’s worth of programming (probably 10-15 hours, really), and getting things organized for someone in the lab.  (Hopefully a few emails I can take care of this afternoon.)

So, that has left me pretty focused on the post-thesis phase.  While I do have plans, I’m just waiting for an airplane ticket to be booked before I announce things. Until there’s an actual date, I’m not sure I feel comfortable spreading the news just yet, just in case everything suddenly crashes down and things don’t work out the way I expect them to.  All I can say, for the moment, is that I’m incredibly excited by the job description and the opportunity to work with the people I have already met, and of course, to meet everyone else there.

(I should mention that I was horribly jet lagged when I met them all the first time, but they all left a great impression, even if I’ve forgotten a few names…)

So, on to blogging, which is the next big thing that I’m mulling over.  First, I haven’t discussed blogging with my prospective employer, so I’m quite sure where things will go.  Of course, I don’t think it’s appropriate to blog about one’s workplace in any great detail, but some corporate bloggers have done a great job of it by discussing issues important to the work place.  In any case, I can see myself doing a few things:

  1. Continuing along the same path, and blogging about next gen sequencing – with a slightly more corporate bent. (which is a hint about what I’ll be doing next.)  There will be plenty of NGS related topics that I’ll be watching, and I’m certain to have an opinion on many of them.  (Who’da guessed?)
  2. Continuing along the same path, but diversifying to other topics in science so as not to focus on science tangential to my work.
  3. Adding on new topics about moving to new lands (is that a hint?).
  4. Adding on new topics about things more personal to me. (photography, music, etc.)

yes, my version of foreshadowing is a bit heavy handed.

And, last but not least, the other two things on my mind:

I’m seriously considering releasing drafts of my thesis on the web.  Now that my supervisor has agreed that my biology project is not likely to lead to a publication (and yes, that was the bulk of my work for the past year), it’s unlikely to meet much resistance.  I won’t do it until I get a go-ahead from those affected by the work, but it’s a project I’m working on, as I’d love to get more feedback.

And, finally, I had plans to write out summaries of some of the papers I’ve read on my way to wrapping up my thesis.  I haven’t decided if I’ll do this yet, but it would probably be a great way to help study for my defense.

In any case, that’s what’s on my mind this afternoon. And now that I’ve gotten it all down, I can clear my mind and get back to some of the other things I’ve been neglecting this past week.  Whee… errands!

Recap for August 2011

So I’m back.  Finally.

About 4 weeks ago, I cut off all of my “time wasting” interests for the sake of completing my thesis and then went all out in writing the damned thing.  As it happens, it was a great way to work.  No twitter, no blogging… no distractions.  I simply sat and wrote for 6-8 hours a day for 3 weeks and two days and banged out a version of my thesis to hand to my supervisor.  Given that I’d already written about 80 pages before pulling the internet plug, that was roughly the equivalent of 100 pages in ~15 days. I’m not unhappy with that.

But, of course, life doesn’t stop while you’re working on your thesis.  I’ve had to do a number of other small projects in the meantime, and a few big projects as well.  The biggest is that I have figured out where I’ll be going after I defend my thesis.  The open question is when that will be, as I still don’t have a defense date, but I am going to push for it to happen as quickly as possible.  For now, I’m going to keep the specifics quiet, but I’ll let everyone know in a few days.

Otherwise, I do know that my wife and I will be moving out of Vancouver, so we’ve begun the process of winnowing down our possessions.  I’ve given away a few potted plants, sold a lot of stuff on craigslist, emptied out drawers, recycled a ton of paper and even had a (very poorly attended) garage sale.  The fun never ends!

More noticeably to the internet, I’ve also switched internet service providers.  Despite the fact that we’re moving, our previous provider was unwilling to extend our current contract, and instead wanted $50 a month more for the same level of service, which just annoyed me – so I made the call to their competition.  Unfortunately, I didn’t realize that the new ISP actively blocks port 80, which took down my website. By pure fluke, I already had a hosting plan that I had been planning on canceling and they had recently started offering wordpress blogs – So, what you’re now seeing is no longer hosted from the computer in my living room. A big thank you to the staff at namespro.ca who helped make the transition reasonably seamless – other than having to wait over the long weekend for the right staff to come back to work to migrate my account. (=

Of course, the other internet change is that my email is no longer hosted from my home computer anymore – but that’s another long story. (However, the experience of running your own email server is pretty awesome – I highly recommend it if you have the opportunity.)  More to the point: If you tried to reach me over the past week and didn’t get a reply, that was the reason.  Sorry!

I also discovered that 4 weeks of isolation is great for reminding you of all of the blog topics that you should write about.  I have a couple more days of web site migrations to do (such as re-uploading the missing pictures from the blog, moving a few other hosted pages to the web server, etc), but once those are completed, I’ll be back on the blogging band wagon – and I have lots of ideas to write about.

In any case, thanks to everyone for their patience during my disappearance – and thank you for everyone who supported me while I was hunkered down and busy writing.

Interview with the Student Biotech Network

The Student Biotech Network is a really neat organization, and one that has played a big part in my career – both directly and indirectly.  One of the original three founders, Ali Tehrani, sat across the lab bench from me when I was doing my masters degree – and became my “partner-in-crime” during the founding of Zymeworks.  In fact, Zymeworks had some early ties to the SBN in terms of leadership, mentoring and contacts.  Furthermore, it was through my participation in the SBN that I was introduced to entrepreneurship – and that was really the first time I’d considered a non-academic path for my career.

In any case, when the SBN asked, I was very happy to do a quick interview with them via email and share a bit back with an organization that has had a really big influence on my career. If you’re interested in reading it, you can find it here.

If you’re looking for interviews with Ali, here are three that I am aware of (and they’re pretty good too!):  Capitalist Chicks (2007), Business in Vancouver (2008) and BioscienceWorld. You’ll notice that the SBN gets a few mentions there as well. (-;

blogging as practice for thesis writing…

I’ve been telling all of the students around me that they should try their hand at blogging – in fact, I’ve been telling everyone around me that blogging is definitely something you should try if you have a chance. I know that not everyone has a lot to say, but that it’s a great habit to be in. It’s a great way to practice organized writing (without 140 character limits), putting your views out where others can see it, defending your ideas and, of course, it’s great practice at organizing your thoughts. In other words, it’s a microcosm of your final 6-9 months of your graduate studies.

Indeed, I had no idea how much that advice was actually worth till I sat down yesterday afternoon, and started writing out some parts of my thesis. (Yes, I’m now actually writing my thesis!) The brilliant thing was, after spending so much time writing on my blog, the thesis seems SO much easier than the ones I’ve done in the past. (This is actually my 4th thesis.) The text just flowed, which makes the whole process rather fun.. (Yes, thesis and fun in one sentence!)

When I sat down and organized my thoughts on a subject, things just came together and I knew what I wanted to say and how to say it, which I can only ascribe to the endless practice of writing on my blog. Yes, the style is a bit different and less reflective, but other than minor stylistic changes, the process is almost identical.

So, for anyone who’s going to eventually have to write a thesis, I’ll make a suggestion: start practicing for it by starting a blog, even if no one reads it. Keeping your writing skills in shape is invaluable.

My lesson learned.

One shouldn’t often engage in a war of words with people who comment on blogs on the Internet.  It’s rarely productive.  In this case, there are a few points I could clarify by responding to a comment with a particularly ugly tone, especially given that it was written by someone with an illustrious career in a field related to my own.  They’ve held the position of chair and vice chair of multiple departments, have been a professor since before I was born and have hundreds of publications…  And yet, this individual has chosen to send me a message with the identity “fuckhead” – accusing me of intimidating a junior grad student.  Instead of using his real name, I’ll use the moniker “fuckhead” that he chose for himself, and I’ll post fuckhead’s comments below, interspersed with my reply.

I do need to acknowledge that my tone in my “Advice to graduate students” was somewhat condescending, due to some rather unfortunate word choices on my part.  I have since edited the post for tone, but not for content.  That said, fuckhead’s comment (and unfortunate choice of moniker) was still inappropriate and deserves a reply – and yes, it is a great cathartic release to reply to a negative comment once in a while.

“Coming on the heels of the previous “why I have not graduated yet” post, this is telling”.

Oddly enough, the point of my post on why I haven’t graduated yet was because I’m unable to find any clear signals in the noise in my data set, while my point on advice to other graduate students was about respecting your colleagues, even if it wasn’t necessarily obvious in my first released version of the post.  Putting the two together might allow for a few interesting conclusions – although I would suggest that it is not the ones that are suggested in the comment.

“It’s one thing to intimidate a student out of the way (rather simple, actually, if you have the slightest clue what you are doing), but what you espouse here will poison you. So you’ve been working on the topic for a while, and some meatball comes along and asks you about the topic, and your reaction is ‘get bent’? What will you tell people when they ask what you spent X years of your life on in graduate school? ‘Get bent’?”

It should be clear right away that fuckhead really doesn’t know me well.  I run a blog to share information and help other people, I have more than 200 posts (answering questions) on seqanswers.com, all of the code I’ve written towards my thesis has been available freely on source forge for 3 years, I’ve dedicated countless hours to helping other bioinformaticians online and always make time to help out my fellow students. (My resume is online somewhere, if you want more than that.) I probably have told a few people to “get bent”, as it were, but in this case, I most certainly didn’t.

It’s rather telling to me that fuckhead didn’t take the time to find out who I am before jumping to the conclusion that I’m obstructive and surly towards my colleagues.  I can be gruff when people don’t take the time to think through their questions, but I always take the time to listen to my colleagues and help them find the information they need.  If my tone is a bit gruff sometimes, we all have off days – and it’s an inherent danger of insufficient blog editing as well.

“Do you think that you are going to cure cancer, or are you trying to make a little tiny dent in the vast universe of ignorance that surrounds humankind?”

Wow… leading question.  While I do joke that my job is to “cure cancer”, I’m fully aware that expectations for graduate students are low and making a “little tiny dent in the vast universe of ignorance” is where the bar is normally set.  In case it wasn’t clear, no one expects me to cure cancer while working on my doctorate.

That said, who’s to say that neither myself nor the incoming graduate student can’t be the one who does find an important cure? Why hobble myself by agreeing to do no more than meet your base expectations.? Fuckhead doesn’t say why he thinks I shouldn’t have big goals – or why he thinks I’m incapable of meeting them.  Nor does he explicitly state his underlying assumption, which is clear here.  To paraphrase: “You’re just a lowly graduate student, and thus you aren’t the one doing the important work.”

For the record, I like to think big – and I like to achieve my goals.

“And if you are after the latter, why not start off with the ignorant student that approached you?”

Ironically, since fuckhead’s main point is that he thinks I’m intimidating junior colleagues, his tone is oddly lacking in self reflection.  The implication that I haven’t helped the graduate student already is plain – and plain wrong.  However, that is between myself and the student, and we are in the process of establishing a better relation on stronger co-operation where my time is respected and the students needs are better met.  After all, that is the goal:  By getting the student to ask more focused questions, he’ll get better answers.

Further, given that I am fuckhead’s junior colleague, I have to ask why he chose to respond to my post with such venom.  He could have taken the time to set me straight by leading me to see his point, rather than writing a biting comment that chastises me for being rude to those who have less experience than I.

Irony, anyone?

“If you have lots of good ideas, some dolt stealing one of them won’t hurt you.”

I’m not afraid of people stealing my work, but one should recall the context of my comments.  Frankly, I am a strong believer in open source and collaborative work and if you want to see the code I’m working on this week, all you have to do is download my work from source forge.

Unfortunately, in academia, one generally doesn’t release data until it’s published – that is the default position – and one I have openly questioned in the past.  But, if I want someone’s unpublished results, I go to them with the respect for the work that went into it.  It is as simple as that.

Besides, as someone with an entrepreneurial past, I’m well aware of the value of ideas. One does not disclose the “secret sauce” to competitors without an NDA (non-disclosure agreement), but when it comes to investors, you have to respect their time and effort and be aware that your idea has no value until you’ve done something with it – and even then, it’s still not the idea itself that has value.

However, the proof is in the pudding, as they say.  If I were afraid of people stealing my ideas, would I be blogging them?

“If you don’t have lots of good ideas, how the hell will you survive on your own as a researcher?”

I haven’t the foggiest clue.  I’ve never found myself lacking in ideas, although I’m shying away from the academic career path for this very reason.  I know the value of sharing ideas and of working in a group to combine and improve ideas.  Unfortunately, I don’t see that kind of environment being created in academia where professors competing for a small pool of grant money hoard their findings so that others will be less effective in competing with them.

If there’s one thing that I hate, it is wasting time reinventing the wheel.  Unfortunately, that appears to be an inherent part of the academic process.  (I’m not talking about independently confirming results, which is an inherent and important part of the scientific method.)

To wrap things up, yes, I’ll go quietly back into my little bubble of the universe in which I will quietly battle the raging sea of ignorance around me, but I can’t promise that I’ll stay there.  However, even as I fade quietly back into obscurity, I do plan to learn from my mistakes and to let others learn from them as well.

The hard lesson I learned today was to watch my own tone when communicating on the Internet, to keep myself from unintentionally sounding arrogant and condescending.  I’d be happy to pass the same lesson on to you, fuckhead.

New developments…

I’ve not been blogging lately because I have managed to convince myself that blogging was taking time away from other things I need to be doing, which I feel I need to focus on.  The most important thing at the moment is to get a paper done, which will be the backbone of my thesis.  Clearly, it is high priority, however, it’s becoming harder and harder not to talk about things that are going on, so I thought I’d interrupt my “non-blogging” with a few quick updates.  I have a whole list of topics I’m dying to write about, but just haven’t found the time to work on yet, but trust me, they will get done.  Moving along….

First, I’m INCREDIBLY happy that I’ve been invited to attend and blog the Copenhagenomics 2011 conference (June 9/10, 2011).  I’m not being paid, but the organizers are supporting my travel and hotel (and presumably waiving the conference fee), so that I can do it.  That means, of course, that I’ll be working hard to match or exceed what I was able to do for AGBT 2011. And, of course, I’ll be taking a few days to see some of Denmark and presumably do some photography.  Travel, photography, science and blogging!  What a week that’ll be!

Anyhow, this invitation came just before the wonderful editorial in Nature Methods, in which social media is discussed as a positive scientific communication for conference organizers.  I have much to say on this issue, but I don’t want to get into it at the moment.  It will have to wait till I’m a few figures further in my paper, but needless to say, I believe very strongly in it and think that conferences can get a lot of value out of supporting bloggers.

Moving along (again), I will also be traveling in June to give an invited talk, which will be my first outside of Vancouver. Details have not been arranged yet, but once things are settled down, I’ll definitely share some more information.

And, a little closer to home, I’ve been invited to sit on a panel for VanBug (the Vancouver Bioinformatics Users Group) on their “Careers in Bioinformatics” night (April 14th).  Apparently, my bioinformatics start-up credentials are still good and I’ve been told I’m an interesting speaker.  (In case you’re wondering, I will do my best to avoid suggesting a career as a permanent graduate student…) Of course, I’m looking forward to sitting on a panel with the other speakers: Dr. Inanc Birol, Dr. Ben Good and Dr. Phil Hieter – all of whom are better speakers than I am.  I’ve had the opportunity to interact with all of them at one point or another and found them to be fascinating people. In fact, I took my very first genomics course with Dr. Hieter nearly a decade ago, in an interesting twist of fate.  (You can find the poster for the event here.)

Even with just the few things I’ve mentioned above, the next few months should be busy, but I’m really excited.  Not only can I start to see the proverbial light at the end of the tunnel for grad school, I’m really starting to get excited about what comes after that.  It’s hard to not want to work, when you can see the results taking shape infront of your eyes.  If only there were a few more hours in the day!