• Kanna curious?

    Kanna curious?

    The Japanese wooden hand plane, called a kanna, seems a bit more mysterious to the western woodworker. In learning more, one might fall for several misconceptions about these tools. Here, I try to address some of these misconceptions first and then talk about what you should consider when trying to get one to work

  • Putting chisels to the test

    Putting chisels to the test

    Early on in ones journey as a woodworker in the West, one hears the siren song of Japanese chisels. The only reason that one should own western chisels is if you like to sharpen tools. That’s a bit of an exaggeration but has a bit of truth to it. One of the challenges with purchasing…

  • FAQ for Rule-based modeling of cell-level networks in immune-oncology

    FAQ for Rule-based modeling of cell-level networks in immune-oncology

    COVID-19 has limited discourse related to scientific projects. Here we address a number of FAQs related to a proposed rule-based modeling approach for inferring alterations in cell-to-cell communication associated with oncogenesis.

  • Ebonizing wood

    Ebonizing wood

    A formal event calls for the elegance of a black dress or well-tailored black suit. The point of clothing made from black fabric is that it doesn’t have the distraction of a pattern or varying color pallet. In composing your outfit, a fine necklace or tie can provide a singular focal point. In creating a…

  • It’s not you, it’s me

    It’s not you, it’s me

    In looking for love, most people have experienced the “It’s not you, it’s me” breakup strategy. Here I talk in Bayesian terms about this strategy in the context of academic peer review.

  • Darwin’s Hand planes

    Darwin’s Hand planes

    Diversity in nature arises from genetic variation and fitness selection. While evolution applies to biology, the study of how man-made objects disappear or emerge provides insight into fitness landscape of market, or simply the societal context, changes with time. In that light, I think the study of western versus Japanese woodworking hand planes provides an…

  • Montani semper liberi

    Montani semper liberi

    Earlier this summer before going to bed, I decided to turn on the TV and see what still comes over the airwaves. Well Public Broadcasting does and to my delight, it was a show from West Virginia PBS on woodworking. The theme of the show was to embrace Appalachian heritage by examining a regional piece…

  • I have to P

    I have to P

    I get asked frequently by students about career advice. Should they stay in academia or should they look for a job in industry. Most professors have only ever been in academia so their view may be a bit biased. I came to academia through a more indirect route.

  • Trying to not be a hypocrite

    Trying to not be a hypocrite

    At Entelos, a common refrain was that biologist don’t take the right data when it comes to building mechanistic mathematical models of disease. Yet, the company was reluctant to publish primary research articles showing how existing data are used and what kind of data are needed. Over time, this blanket critique of biologists, to me,…

  • [Old Man Yells at Cloud]

    [Old Man Yells at Cloud]

    Creating a mathematical model of disease based on the available literature requires reading a lot of papers. In the 5 years that I was at Entelos, I had read close to 3000 papers.

  • Butterflies and rainbows

    I recently followed my wife to a conference in Denver and I attended a hospitality event. In making casual conversation with someone at the event, the conversation followed the typically script: Casual conversant (CC): “What do you do?”  Me: “I’m a professor” CC: “Oh what in?” Me: “Chemical and Biomedical Engineering” CC scrunches up their…

  • Paper Tales – Klinke DJ PLoS One 2008

    At Entelos, I saw first hand that developing mathematical models of disease requires significant investment before you have a simulation platform that you can market to pharma. These PhysioLab models were complicated and required multiple PhD-level engineers and life scientists working elbow to elbow for 6 months to a year or more before we had…

  • Paper tales – Klinke DJ Journal of Theoretical Biology 2006

    While my graduate work was rule-based modeling of petrochemical-related chemistries, I felt that following graduation I was more interested in applying these computational approaches to biological problems instead of petrochemistry. After a brief post-doc at Sandia National Laboratory in Livermore, I landed a position as a Biosystems Engineer at Entelos, Inc in Menlo Park, California…