Notes to myself

An effort to extend the time between the recently learned and soon forgotten

November, 2014

Brain algae virus

Robert Yolken, an infectious disease expert at John Hopkins University, recently discovered a virus in the throats of people with psychiatric disease. This virus, ATCV-1, had been identified before but its prevalence was unclear. Literature searches indicated only that this virus infected a species of green algae commonly found in lakes.

The disturbing development occurred when the researchers started looking at healthy people as well as those previously identified as sick. They found this virus in almost half the people they examined, with other tests indicating that those infected with the virus performed 10% worse than uninfected people in tests of their visual processing. As well the attention spans oof infected people seemed to be lower. The effects they identified were not enormous but they were significant.

To distinguish between causation and association, the researchers then infected mice with the virus. The infected animals took longer to find their ways out of mazes and spent less time exploring new objects, suggesting an impact on attention span. An examination of gene expression in the animals hippocampus found changes in the expression of almost 1300 genes.

So the bottom line is this: there is a virus that at least some people have contracted. It may have a connection to mental illness and/or declines in cognitive ability. We have little idea about how widespread this virus might be(the original sample included only 92 healthy people in one geographical area). In the worst case scenario, however, there could be a sickness that is making some or all of us stupider than we would be otherwise. For me at least this is concerning-- to become 10% even dumber would not be a welcome change. Or maybe we all have it already, which would maybe explain a thing or two, such as the popularity of celebrities or reality TV. The story is still unfolding but so far I find the implications pretty troubling.

Additional details are available at the following link

Maps and the mysteries of open source

How difficult would it be to add a map to a website? I might have thought that beyond a simple static images map creation would be pretty tricky, and probably expensive as well. It seems, however, that there is a way to build a powerful mapping application into a webpage, with tool tips, panning, zooming aand all the other interactions that we've come to expect from online maps. Technically it's pretty trivial, requiring only a few lines of JavaScript and a little CSS. Financially the cost is a little less clear, though eventually I'm going to take the time to figure it out.

First let's consider the technical story. I'll use a library that is distributed by a company called mapbox, and they certainly make the process easy. You need only make one call containing 4 parameters ( your starting place on the globe, your level of zoom, an identifier called a map ID, and a selector providing the idea of a DOM object.) You'll also need to create that DOM object, and include enough CSS to hold that DOM object in place. The sum total of the code used in my example is reproduced below:

    
        <div class="map-container">
              <div class="map01">
              </div>
        </div>
    

    
        var mapID = 'examples.map-i86nkdio',
        center = [42.2317, -71.6449],
        zoomLevel = 13;
        L.mapbox.map('map01', mapID).setView(center, zoomLevel);
    

Add a little bit of sizing and positioning with CSS

    
        .map-container {
        position: relative;
        width: 500px;
        height: 500px;
        }

        #map01 {
        position: absolute;
        top: 0;
        bottom: 0;
        width: 100%;
        }
    

And you'll end up with a map that looks like the one below:

And all of this, both in terms of the power of the resulting graphical widget and the straightforward simplicity of the implementation, is most impressive. The tricky part about all of this, however, is whether or not it's actually free. The code itself is mostly open source after all, (apparently a mixture of a volunteer-donated open source, along with code that was commercially developed under an open-source license) so the code should be available for download. The data are also publicly available (some of it coming from NASA satellite imagery, as well as from the massive, fascinating openstreetmap project) so the data are also there for the taking. So is all of mapbox therefore available like air is for anyone to breathe?

Definitely not. Mapbox is a for-profit company and they sell services, server time, processed data, and certain kinds of code. A quick look at their price list ranges from their starter kit (up to 3000 map views per month are available for free), to their Premium plan ($499/month) up to Mapbox Enterprise for $49,000/year. And why, after all, would anyone expect these capabilities to come be free? The company has 25+ employees hard at work developing new code and harmonizing data. I approve of the fact that some large portion of their code is open source, and every company based in open source must address the question of how they sustain themselves. Software is difficult to develop, and if you're going to extend and maintain high-quality code then funding is usually required.

So, for small-end websites there does is in fact seem to be a way to access a well-crafted and well-maintained JavaScript library along with the vast quantities of supporting data necessary to power a zoomable map with a global range. If you want to build a business around a map-related application then you're going to have to pay some money, even if the data and the code originated in the public domain. To me this approach seems like a pretty reasonable compromise, and maybe provides a good model of how a for-profit businesses can adopt an open source approach. I'm not yet familiar enough with the project to endorse it, or even to be confident that I can perceive the project's real strengths or weaknesses yet. At least it sounds like some fun programming for snowy afternoon indoors, however, so I plan to give it another try.