On the “quilt plot”

One of the big blow ups on twitter last week (at least in the circles that I follow) was the “quilt plot”, an article recently published in PLoS ONE. The quilt plot is actually just a heat map. Not a heat map with other bits removed, but a heat map. The article itself says that “they produce a similar graphical display to ‘heat maps’ when the ‘clustering’ and ‘dendrogram’ options are turned off”, but that misunderstands what a heat map is. While the wikipedia page for heat maps has a hierarchically clustered heat map as the example image at the top, the examples farther down do not. To claim that there is something new here is to fundamentally misunderstand what already existed.

It’s not really new, but scientists can’t be familiar with the entirety of the literature, and often “rediscover” old techniques from other fields. What one would hope, however, is that the journal itself is able to spot this, and respond appropriately. PLoS ONE actually has guidelines for whether new software methods should be published. Briefly, they say they must have

  1. Utility
  2. Validation
  3. Accessibility

Continue reading On the “quilt plot”

Keeping Busy

Sometimes, despite all my best planning, I run out of tasks that need to be done. This seems to happen to me most often in the experimental phases of a project, where I first need to do experiment A, and see what A looks like, before deciding whether experiment B or C is the most appropriate direct follow up.

There are, nevertheless, things I can do during this time while I’m waiting for A to finish (other than wasting time on Facebook or the like).

Continue reading Keeping Busy

Grad Students Aren’t Stupid…

…but maybe there should be fewer of them anyways.

I think perhaps I’m late to this game, but there’s been quite a bit of discussion about “Thinning the Ph.D. Herd”, a Slate piece by Rebecca Schuman about Johns Hopkins University’s plan to reduce enrollment in PhD Programs.  Sean Carroll, for instance, says “I’ll believe we should accept fewer grad students when I hear it from actual undergrads applying for grad school.”  There is quite a strong strain of people arguing that people should be allowed to freely choose what to do, and that reducing PhD enrollment is paternalistic on the part of JHU. People seem to think that by downsizing programs, JHU is saying “you only think you want a PhD, but you are mistakenly signing yourself up for a life of penury, so we’re saving you from that”.

Responses to the Slate article

Responses to the Slate article

It’s worth recalling Braess’s Paradox, however.  In essence, it says that people might be making locally optimal choices that lead to globally sub-optimal outcomes for everyone (including themselves), and limiting choice may actually improve results for everyone. Nobody in the hypothetical scenario is acting irrationally or without having considered all the options, but things are worse than if someone stepped in to constrain choices.

There’s two questions we need to ask: is the current PhD system the globally optimal system for the students in it, and if not, would unilaterally reducing the number of grad students improve the results. In the sciences, I’m actually not sure that we’re too far off—most people I know of (in my Tier 1 R1 highly ranked program) live comfortably on our stipends, receive health insurance and various perks, and typically don’t have trouble finding jobs that use their research skills.  I suspect the same is true for the students in Profs Carroll’s, Krugylak’s, and Booty’s departments as well.

The same is not obviously true for the humanities, even from top tier institutions.  My partner is in a highly ranked, unusually well funded humanities program, and the horror stories I hear are chilling.  Her stipend is, in a good year, 75% as much as mine (although $2-5k more than many other programs in the humanities), her program has a shockingly high attrition rate, jobs outside academia are considered outright failure, and a significant number of people end up as adjuncts, earning wages below the poverty line.  Having gotten her PhD in German, I suspect this is much the world that Rebecca Schuman is from as well.  Is this the globally optimal situation for graduate students? I think not.  Would reducing PhD enrollment help, especially if stipends are redirected to the ones that remain? I’m not certain, but I think it’s worth a shot.

Finally, I just want to make clear that reducing PhD enrollment isn’t the only way to improve the lives of grad students, nor even necessarily the best one.  But it is an option in the arsenal, and seems likely to have at least some positive effect.

New Year’s Resolutions

  1. Blog weekly.  It seems to be true that part of being a successful academic is in getting my name out there. Plus, the more you write, the better your writing tends to be, through a strange and little understood process that some call “practice”. To that end, I’ve created this blog shaped thing that I will attempt to write in with some regularity. See here for entry 1.
  2. Publish. I’ve got one small story that a roton worked on which the Boss thinks could be a small paper, and lord knows we probably aren’t going to do much else with it.  I’ve also got big plans for the next couple big experiments in my thesis project, which if I’m reasonably productive this spring while TAing, I ought to be able to get out the door by the end of summer, and hopefully in print by Christmas, assuming I come across nothing unexpected (ha!).
  3. Line up the next thing.  I’m expecting to graduate May 2015, and am currently researching potential post-doc labs. The timing is both flexible and in flux, depending in large part on 2-body problem considerations, but also on funding arrangements that I’m also in the process of researching.
  4. Relax. I’m often pretty bad at overscheduling myself, so the other resolutions notwithstanding, I’m hoping to keep as much downtime open as possible.