Plausible Accuracy

It actually went better than I had expected.  In some ways it was the baby brother of the important meeting I had with my advisor a month or two back, in which I pretty much said “Look, this is what I’ve got.  Tell me if it’s worthy of a Ph.D.”.  It’s pretty tough to stand in front of learned faculty and lay your past 6 years of work out there like that.

The committee had some good recommendations for experiments to do as I wrap things up, but to be honest they seemed fairly satisfied with my progress to date, and there aren’t really any “must do” items on the list (besides wrapping up what I’ve already got).  We have a couple of ideas for potential experiments that are exciting to me both on a scientific level and also because I’ll get to play with some cool toys.

Everyone keeps asking me if I am relieved or excited.  To be honest, it’s not really either.  It really just feels like there are many many things that need to be done, and now that the timeline is out there I have a ticking clock running.  I’d like to draw an analogy, if you’ll bear with me.

When I was an undergrad, I was in the drinking sailing club. We’d often go out for group sails on our 22′ tub christened the Harmony.  To get out to sea, we would have to sail out through a narrow channel that had been dredged to allow for boats of significant draft to pass.  This was usually not too difficult, and of course once we cleared the channel we could sail wherever we liked.  Eventually, though, we had to bring the boat back in to dock.  Inevitably, both we and the boat would be a bit worse for wear, and it was usually dark.  Regardless, we had to try to get ourselves back up through the channel and into our docking slip.  This was always the most difficult and intense bit of sailing.

Well, I think grad school just entered the channel.  There is not a lot of sailing left to do, but it will likely be the most complicated and pressure-laden section.

Less than an hour to go before my final pre-defense committee meeting.  What am I doing?  I’m glad you asked:

• Making one last-minute figure/slide of an experiment that ran overnight
• Backing up my presentation as a PDF file on a flash drive
• Skimming some of the critical literature
• Worrying… a lot.

Check out this introductory video to Ubiquity, a new web browser concept from Mozilla labs:

Ubiquity for Firefox from Aza Raskin on Vimeo.
I like the idea of using the browser to combine currently disjointed web services, however I’m not certain how well this will come off in practice.

I’ve installed the alpha 0.1 release, and already it’s incredibly useful.  As someone who is fairly comfortable with using a command line, it’s great to be able to call up services like wikipedia, google maps, etc, with just a keystroke.  Since it’s open-source, the real power will be in the new commands that the community (or you yourself) can dream up and implement.

I was preparing for my upcoming committee meeting tonight, and I decided to check the website of our collaborators.  I hadn’t heard from them in a while (it’s sort of a loose collaboration I suppose), and thought it would be interesting to see what they were up to.  At the top of their publications list was a link to an in-press article.

Without going into too many of the boring details, suffice it to say that the content of the article more or less directly dealt with the experiments I’ve been doing for the past several weeks.  It wasn’t necessarily the dreaded “scoop”, but there seems to have been a fair amount of overlapping effort.

This got me thinking about the practice of science again.  Here is a situation in which two groups, which have already agreed on some level to cooperate, are inefficiently duplicating different aspects of work.  It’s especially frustrating because it’s clear that they could quickly clear up some of the difficulties I’ve been having, and I’d hope I could reciprocate.

This metaphor of the miner’s helmet sort of worked it’s way into my thinking.  It’s like we (by this I mean researchers) are wandering about in a cave with a light on our hats.  Sometimes, we point the light in the right direction and find what we’re looking for.  Much of the time it’s just illuminating bare rock.  Other scientists are doing the same, and what might be bare rock to us is exactly what they are hunting for.  The problem is that most of the time you’re too busy to look at what your headlamp is shining on to worry about someone else’s.  What we need are some floodlights.

This is exactly the type of communication that these new web tools I’m always going on about can bring us.  By making it easier to share what you’re doing with others as well as easier to find data that you might be interested in, science will become more efficient and more productive.

I’m working on the presentation for my upcoming committee meeting.  I’ve often been complimented on my slides, so I thought I’d share my personal guidelines for making them.  Most of this is stuff that I’ve picked up elsewhere, but it doesn’t hurt to repeat it.

1. Less text, more figures.  I’ve heard this repeated many many times, but I still see people giving talks with slides full of bullet points.  PUT THE BULLET POINTS DOWN AND STEP AWAY.  My perfect slide is a large figure with absolutely zero text.  This is tough to accomplish with scientific talks, but really ask yourself “do I need this text for this slide to make sense?”  If the answer is not an emphatic “yes”, get rid of it.  Another good question is “can I change the figure so that the text isn’t needed?”  One thing I try to do is put the bare necessities on the slide; perhaps a sentence fragment describing what the figure is showing.  This is intended as a memory jog in case the audience forgets or misses the slide introduction, not as a full descriptor of what is there.
2. Spend time on your figures.  This ties in directly with rule #1.  If you are going to be relying on your figures to get your message across, they need to be good.  Make sure that they are high resolution, so you don’t get “jaggies”.  Remove any superfluous labels or text on the figures.  Use clear & consistent coloring.  If possible, match the font to your presentation (see rule 3).  I tend to re-draw my figures for every presentation, because I want that figure to match exactly the role it will be filling on a particular slide.  Usually this means a different orientation, different labels, new colors/fonts, or something that requires me to redo it from one presentation to the next.  It’s time well spent, and pays off in clarity and coherency of the talk.
3. Pick a good font, use it consistently.  Do not use Comic Sans, and avoid black Times New Roman on a white background.  The font I’m using for my committee presentation is DistrictThin.  It’s free and looks great.  I’m sure you have many on your computer, so cycle through them once when you are making your first slide.  By “use it consistently”, I mean that all the elements in your presentation should use this font if possible.  Many presentation packages have a “replace font” ability, so you can run this when your presentation is finished.  A good idea is to replace the default (Arial or Times New Roman, perhaps) with the one you selected.  Then make sure that everything still looks OK.
4. Budget enough time for your slides.  If I’m giving an hour talk, 30 slides is my hard limit.  28 is even better.  This can seem daunting, allowing 2 minutes for a slide that isn’t much more than a single figure, but trust me it’s good for several reasons.  First of all, it makes you slow down and fully explain the slide.  Secondly, it gives your audience time to take in all of the information and digest it.  Finally, this ensures that there is ample time for questions.
5. Minimal, but not incomplete.  This is probably the toughest guideline.  You want everything about your talk to be a solid and complete summary of your work, and nothing more.  The hard part is making sure that this includes all the relevant details.  It’s remarkably easy to go too far one way or the other (leaving important facts out or going on about extraneous points that don’t strike at the core).  I probably err on the side of leaving things out, and hope that the audience will ask about anything that they need clarification of or expanding upon.  Too often I’ve seen people throw everything but the kitchen sink into a talk and end up just confusing the audience or sending the discussion down an unimportant side track.

In the end, I want my slides to be something like a series of bridge supports.  Alone they don’t get you across the water, but when the talk is overlaid the whole thing becomes a functioning entity.

Those are my personal suggestions.  What are yours?

We just moved out of our house into an apartment while we finish up here.  Easily the worst part of this is the kitchen.  It’s roughly the size of a shoebox.  The stove has no timer or indicators of any kind.  The left-hand side of the stove is so close to the wall that using those burners makes the paint bubble.  The venting is poor, and using the oven to make some biscuits caused the smoke detector to go off.  There wasn’t any way to easily shut it off, either, so I’m sure the neighbors appreciated that.

I feel like this kitchen is almost designed to force the inhabitants of the apartment to rely on pre-made, microwaveable (heavily processed!) food or else eat out all the time.  As someone who would much rather have homemade dishes made from organic ingredients from the local co-op, this is a problem.

I didn’t realize until we moved just how much influence your residence can have on some habits that seem basic.  At least it’s only for a few months, then it’s off to somewhere new.

In an effort to make good on my promise in the last post to spend more time discussing the stuff that’s going on here at the end of graduate school, I thought I’d write a bit about “what makes the end so hard”.  I think the central issue is one of time management/multitasking.  To give you a sense of what I’ve got going on, here is a rough breakdown (off the top of my head) of my current priority tree:

• Short-term (daily work)
  • Wet lab experiments. Obtain data for committee meeting in 9 days
  • Computational experiments. Obtain data for committee meeting in 9 days
  • Work on presentation for aforementioned meeting
  • Unpack/settle in at new apartment
  • Clean out old house. Yard sale to get rid of things we aren’t taking
• Medium term
  • Read papers from potential postdoc labs. Think about contacting them
  • Look for independent funding sources for postdocs, to improve chances of getting a position in a lab of my choosing
  • Think about/plan for Mrs. PA’s move to Vancouver
  • Think about what papers need to be written before I defend
  • Write my thesis

Individually, or even in small groups, these tasks aren’t that bad.  The struggle comes when you have to deal with all of them at once.  It’s easy to slip into a form of immobility, where your mind just focuses on the mountain of things to do rather than productive cogitation which actually leads to doing them.  It’s also a bit tough to prioritize, because every item on that list is IMPORTANT, and it’s not going to work to let any one of them slide a bit.

It doesn’t help that there is this constant lurking fear, a sort of waiting for the crisis to hit.  Any one of these items could run into a major roadblock suddenly, and that would upend the cart as it were.  It feels a bit like running along juggling priceless vases while also trying to keep an eye out for overhangs that you might toss one of them into.  A bit on the side of nerve-wracking.

It doesn’t help that I’ve never been terribly brilliant at serious multitasking.  I find that dividing my attention on important matters on a timescale shorter than a day tends to have a detrimental effect on productivity.  The deep insights and “eureka” moments tend to come when I can really dive into something, rather than work on it for a few hours and then put it aside for another task.

In a way, however, I feel that this is the best sort of preparation for moving onward in science.  My guess is that in order to be a decent research professor, a keen multitasking ability is key.  One has to handle teaching responsibilities, laboratory management (both personnel and research issues), grant writing, and service, all in addition to anything going on in your personal life.  It’s no surprise to me that the cliche of the “absent minded professor” is so pervasive.  Who wouldn’t be a bit forgetful in such a situation?

As I was wrangling with a couple of protein models last night, I saw an email notification come in.  Almost invariably when something arrives in the box during the evening hours, it’s some manner of spam/junk.  I clicked over intending to hit delete, but quickly realized that this was no spam.

It was an email from a professor in response to my post from a bit over a week ago soliciting comments on how to land a postdoc.  The email stated that the professor was sending it directly in order to avoid offending anyone at UBC, where I’ll be heading (since the email contained specific comments/recommendations on some faculty there, I understand).

Also included were some general comments on what this professor in particular is looking for in post-docs.  Since these are more broadly applicable, I thought it would be fine if I posted them here.

Everyone is different, but I’m looking for:

• a very good scientist, which you show by knowing the lab’s literature cold and in presenting your own work clearly & thoroughly
• a team player, which you show by asking good questions of people in the lab in one-on-one or small group meetings
• a person who’s interested in working/living here, which is also demonstrated by one-on-ones
• a responsible addition to my team, shown by having done a little bit of checking into postdocs that will work for you as you move to Canada (something the other Dr. PA will need to be doing too, saving you both some effort)
• a colleague who’s interested in taking advantage of training/opportunities as a postdoc to get to the next level, which you show my discussing your career objectives with your PI (and again annually, of your own initiative if not required by your employer)

Some of these things I had given priority, some I hadn’t considered as much.  I find it interesting that a professor looking to hire a postdoc would immediately be interested in “getting them out”, as the last point of advice indicates.  Of course postdocs are generally considered to be short term appointments, however it’s my experience that it’s usually the postdoc and not the professor who provides the inertia impetus for leaving.

I think that the “insider information” from a real live professor is great, and I deeply appreciate the consideration shown in writing me an email.  Not only the general comments above, but the specific thoughts and supportive tone of the message really mean a lot to me.  It makes me a bit chagrined that I’m heading to a different area of the world to postdoc… Perhaps he’ll let us know if he’s looking for candidates himself.

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On a somewhat tangential subject, you may (or more likely may have not) noticed a reduction in the frequency of posts here at PA.  Don’t run away yet, this is not a “sorry I haven’t been posting” monologue (mostly).  I have been incredibly busy with moving apartments, research, and everything, but that’s no real excuse.  When I started this blog, I intended for it to be at least a partial record and forum for discussing the trial and travails of finishing up graduate school, finding postdocs, and moving forward in life.  In short, the things that I’m working on now and not writing about.  Mainly I’m struggling with a way to do this that doesn’t descend into the navel-gazing that blogging is infamous for (you know, like the way this post is going at the moment).  I suppose I should just write what I want to write, and let you readers decide if you care enough to spend time on it.

I was moving this weekend, so I’m a bit late to broadcasting the arrival of the Praxis blog carnival.  The posts that I’ve had a chance to read so far are great, and it seems that there will be something interesting to almost everyone in academia (or perhaps even outside of it).

Kudos to Martin and Bora for getting it off the ground, and I look forward to future installments.

The August 8 issue of Science published an article which examined what happens to scientists who are found guilty of research fraud.

As the authors point out, even the accusation of unethical conduct is considered very damaging to a scientist’s career.  Indeed this is the reason cited for extreme secrecy in the conduct of investigations prior to the guilty verdict being issued.  A finding of actual guilt should (and is presumed to) deep-six a research career thoroughly.  Interestingly, the findings of this paper do not necessarily back up this commonly held belief.  The authors examined in 2003 the publication records of 43 scientists (Ph.D.s, M.D.s, and M.D./Ph.D.s) who were found guilty of research misconduct between 1994 and 2001.  From the paper:

Thirty-six of these scientists were found guilty of falsification or fabrication, 10 were guilty of plagiarism, and 12 were guilty of “misrepresentation.” Seventeen scientists had committed only one infraction, and the remaining 26 had committed multiple breaches.

They go into the specific details of “where are they now” extensively in the paper itself.  A fair number of these scientists were found to still be employed in academia, with others in industry or at non-profit organizations.  Perhaps more surprisingly is that a majority continued to publish papers after their “determinations”.  In spite of hardship when they were first found guilty, “most reported that they had recovered or sustained useful scientific lives after initial shocks to their reputations”.

In my opinion, this means that the punishments are not strict enough.  I have seen firsthand the incredibly inhibitory/damaging effect that research misconduct perpetuated by a faculty member can have on the lives and careers of the graduate students in the lab.  In such a tight funding/publishing environment, I think there are more than enough ethical scientists to utilize the available resources.

It disturbs me deeply that although I and my fellow students were completely unaware/innocent of our advisor’s misconduct (much of which happened before he became a professor), yet all of us have had our careers, earning potential, lives, and relationships adversely effected while he may resume a “useful scientific life” after a couple of years.  If that makes me sound bitter, so be it.

hat-tip to Nobel Intent