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I read this Newsweek article about negative results this morning. It's not bad as far as mainstream science and medicine reporting goes, though that's admittedly a low bar to clear.

It's obvious that negative results need to be published. The urgency is especially clear when those negative results could have direct implications for health.

Even so, I was struck by the metaphor used in a JAMA article the Newsweek piece quoted:
“In baseball, it is easy to find out just how well Cal Ripken has hit against various pitchers in the past, at home or away games, in recent weeks or during his career,” Dickersin and Rennie wrote. “Yet in medicine, there is no comprehensive source for finding out similar, accurate statistics for medical interventions. How can baseball be better organized and keep better records than medical science?”
The comparison really triggers some knee-jerk pedandry for me. Yes, the authors are being a bit tounge-in-cheek. It still isn't a fair comparison at all. Baseball has clearly defined rules which haven't changed much over the last century. We can compare batting averages from 1914 with those from 2014 and understand what the values mean in both contexts. There really isn't a way to do that with medical treatments other than whether patients lived or died (even that is a moving target, and a recursive one at that since medical science impacts life expectancy). Truly useful long-term results may take decades to obtain. Most baseball games don't take that long.
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I just found this software called Beaker today - it's essentially a way to mash together several different data analysis and presentation languages, allowing output from one to seamlessly become input for the next. To be fair, this isn't too difficult to do manually as long as the data sets are properly organized, but it's frequently a pain to convert something like R output to a presentable format without a few extra steps. Beaker appears to handle that. It'll even export to LaTeX as far as I can tell, so I can put off learning that for another year or so!

I haven't had a chance to try it out yet, but if Beaker is really as helpful as it seems then it could really save me some time. It would be nice to automatically export sets of R code and output to pretty HTML, at least.

I should have gone to Fire Investigator school: The Work Importance Profiler

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I took another work-related quiz this past week: the Work Importance Profiler. You can take it yourself here. This kind of survey was once called the Minnesota Importance Questionnaire, but despite what the name may imply, it's not about how folks feel about Minnesota.* The survey determines your values in a work context. The theory is this: you may sacrifice your skills and interest to work at an easy, uninteresting job, but you will rarely sacrifice your values. Those values include who you become as part of your job, what you get, who you get to know, and how others regard you.

Here are my results:

OK, to be fair, weighting values like this may be misleading. Working Conditions may rank below Achievement in this list but I still wouldn't work at a job with a genuinely terrible work environment (let's picture a BSL-4 virology lab without proper ventilation, for example). I do tend to value accomplishment above all else. I would never want a job where I don't feel like I'm accomplishing anything.

I'm not sure if it's part of the standard survey, but the values can be converted into career categories. Here are my top 10 matches:

Ah, so I should be an actor! These results don't appear to correlate with those from interest surveys like the Strong so I have to take them with a grain of salt.


*I imagine it would look like this.

The smallest of the small

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The topic of a "minimal bacteriophage" came up in conservation with my lab's PI and postdoc yesterday. I got philosophical about it: what is a phage other than a genome, some structural proteins, and the means to enter bacterial cells? If we began removing items from a phage genome piece-by-piece, at what point would the genome cease to code for a phage? The questions really seem to concern how much genetic information is really necessary to self-propagate. 

There are some incredibly small phages out there, of course. Phage MS2 is a single-stranded RNA phage which infects E. coli and similar species. Its genome is just under 3600 nucleotides and contains just four genes. It was the first full genome to be sequenced - that small size made it a great candidate. It also seems to be used as a model for viruses in water quality studies.

So is MS2 a minimal bacteriophage? At the very least, its single capsid protein self-assembles into capsids and can even be used to encapsulate a protein of choice. If a phage needs to have a capsid then MS2 certainly passes the test. The other MS2 genes also provide basic functions: attachment, replication, and lysis. I'm guessing that the only way to get smaller would be to optimize or completely lose one of those functions (except for attachment, as it still needs to stick to something on its host surface), but would it still be a virus?