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  1. Do bacterial species exist?

    Any of my friends or colleagues who have had the "pleasure" of talking about science with me for more than a few hours know that I am prepared, at the drop of a hat, to rant extensively about several standing debates in biology which I consider merely semantic. For instance:

    Q: Are viruses alive?

    A: Who CARES!? Viruses do what they do. Cellular organisms do something else. What difference does it make if we decide to allow our middle-schoolers to draw little dotted lines around animals, bacteria, and viruses? And I don't even want to hear the word "prion".

    I have a similar level of disdain for people who try to decide on a single definition for "species". Ultimately I am a pluralist: the definition should be tailored to the scientific question. Paleontologists, you have your morphological species concept, because what else do stony fossils allow? Are you studying speciation …

  2. You, too, can host this website

    Loyal readers of this blog (of which I am sure there are exactly zero) might have noticed that things are looking a little different since yesterday. That's because I've finally developed my own Pelican theme to the point that it's functional, and not too embaressing to look at.

    It doesn't appear too different—it's certainly still inspired by the sample theme—but now I understand 95% of the code, instead of 5%. My goal was to simplify the template files and css to the point that I could customize just about anything with a minimum of work. I also attempted to maintain compatability with all of the configuration options supported by the default theme.

    Not that I know why you would want to, but you can read and copy the content and configuration files on Github. The theme source code is there as well.

    By putting everything up on Github …

  3. Even pathogens hate a cheater

    I would like to apologize for the long delay since my last post. The excuse (I keep telling myself) is that, having already written too many computational articles, it was time to prove that I could write about biology too. Unfortunately I'm not nearly as good at reading the literature as I should be. Anyway, it's done. You can stop complaining now.

    One barrier to engineering bacteria for biofuel production or any other human endeavor is that evolutionary rates are scaled by population sizes and growth rates. For an organism with massive population sizes (trillions of individuals or more) and doubling times on the order of hours, evolution can occur quite quickly. Genetic variants within the population which are capable of growing faster will quickly take over. For an organism which is, for example, wasting a huge fraction of its energy producing your future gasoline, you can bet this months …

  4. Compiling SciPy on RHEL6

    Within the past two years I've discovered something interesting about myself (...actually really, really boring about myself): I can be happily entertained for hours on end setting up my computational environment just right. I find that it gives me a similar type of satisfaction to cataloguing my music collection. I guess you could call it a hobby.

    Usually this entails installing the usual suspects (NumPy, Pandas, IPython, matplotlib, etc.) in a python virtual environment. When I'm particularly into it (which is always), I'll also compile the python distribution itself. I've had several opportunities to indulge this pasttime, most recently in setting up my research pipeline on the Flux high-performance compute cluster at The University of Michigan.

    Installing NumPy is usually no trouble at all, but for some reason (if you know, please tell me), SciPy has always given me a "BlasNotFoundError" when installing on the Red Hat Enterprise Linux distros …

  5. PyMake I: Another GNU Make clone

    (Edit 1): This is the first of two posts about my program PyMake. I'll post the link to Part II here when I've written it. While I still agree with some of the many of the views expressed in this piece, I have changed my thinking on Makefiles.

    (Edit 2): I'll post a new post about the topic when I take the time to write it. I've written a tutorial on using _Make for reproducible data analysis_.

    I am an aspiring but unskilled (not yet skilled?) computer geek. You can observe this for yourself by watching me fumble my way through vim configuration, multi-threading/processing in Python, and git merges.

    Rarely do I actually feel like my products are worth sharing with the wider world. The only reason I have a GitHub account is personal convenience and absolute confidence that no one else will ever look at it besides me …

  6. Hello World!


    This is mostly a test post and a chance to get some real content on my brand-new blog.

    Inspired by C. Titus Brown's tireless pressure to make more graduate student clones of himself—and the fact that a pretty damn good domain name was still available—I started this website/blog over the weekend.

    I hope that it will turn into a place for me to share my excitement and views on microbiology, microbial ecology, mathematical ecology, bioinformatics, python, (very) amateur software development, etc. But I will be satisfied if it turns out to just be writing practice. Heaven knows I need that.

    In case you're curious, setup took me about 3 hours (plus some waiting for DNS updates). Largely, this is because I'm shamelessly mirroring Titus's well trafficked blog by using a nifty python application called Pelican. And at $15/year for the domain (using Hover1 …

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