Micro-Institutions Everywhere: Virus Naming

Giant stuffed microbes make the lethal loveable

Giant stuffed microbes make the lethal loveable

The alphabet soup of naming new viruses rivals Pentagonese. AIDS. SARS. MRSA. Where do these names come from? One major source of influence in this area is the International Committee on Taxonomy of Viruses (ICTV).

Their latest innovation is MERS, referring to a new form of coronavirus that was first reported in September, 2012. In the meantime the virus has gone by the various abbreviations hCov-EMC, HCOV, NCoV, and nCoV (the last two referring to a “novel coronavirus”).

Coming up with a good name is tricky. It should be descriptive and memorable, but naming a virus after a geographic area has major downsides:

Historically, many infectious disease agents—or the diseases themselves—have been named after the place where they were first found. But increasingly, scientists and public health officials have shied away from that system to avoid stigmatizing a particular country or city. When a serious new type of pneumonia started spreading from Asia in 2003, officials at WHO coined the term severe acute respiratory syndrome (SARS) to prevent the disease from being named “Chinese flu” or something similar. (As it happened, the name ruffled feathers in Hong Kong anyway, because the city’s official name is Hong Kong SAR, for special administrative region—a fact that WHO had overlooked.)…

The new name is only a recommendation—one which the study group hopes will be adopted widely but which it has no power to enforce, Gorbalenya says. That’s because ICTV has the authority only to classify and name entire virus species

For more, check out this post from Science.

Wednesday Nerd Fun: Oximetry with Ruby and R

These posts are getting pretty esoteric, which may be a sign that I should put the series on hold for a while. Feed back is welcome. In any event, here’s some midweek entertainment for the coders among you:

A popular and fast way to effectively get the heart rate is pulse oximetry. A pulse oximeter is a device placed on a thin part of a person’s body, often a fingertip or earlobe. Light of different wavelengths (usually red and infrared) is then passed through that part of the body to a photodetector. The oximeter works by measuring the amounts of red and infrared light absorbed by the hemoglobin and oxyhemoglobin in the blood to determine how oxygenated the blood is. Because this absorption happens in pulses as the heart pumps oxygenated blood throughout the body, the heart rate can also be determined.

We are not going to build an oximeter, but in this post we’ll use the same concepts used in oximetry to determine the heart rate. We will record a video as we pass light through our finger for a short duration of time. With each beat of the heart, more or less blood flows through our body, including our finger. The blood flowing through our finger will block different amounts of the light accordingly. If we calculate the light intensity of each frame of the video we captured, we can chart the amount of blood flowing through our finger at different points in time, therefore getting the heart rate.

Continue here.

Dangers of low blood sugar

Right now, my conscious-but-still-dumb choice to skip lunch is causing me to send a lot of links to my one of my new favorite apps, Instapaper, instead of just reading them right away.

If you’re in an Israeli prison seeking parole, low blood sugar can be even more dangerous. At right is the percent of favorable rulings for parolees, shown before and after the judges’ mid-morning snack break and afternoon lunch. Read more at The Economist or check out the study here.

Yes, this originally came out in April. Refer back to paragraph one for why I don’t feel like coming up with anything new right now. Continuing this discussion of food and politics might be worthwhile…