Acids, Bases and the Power of Hydrogen

The 1970’s was the decade that illuminated the threat of acid rain to the citizens of the US. It had been known to exist several years before, but the sources of the problem did their best to suppress the information. It wasn’t until the environmental damage became significant enough to draw national attention that it would lead to the US enacting regulations to stop acid rain.

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Truthfully, most of the public was probably still unaware of what acid rain actually was. The default mental image that comes to the mind of the non-chemist is large drops of battery acid raining down from the heavens and devouring everything. This is not quite the case, however. Pure water has a neutral pH of 7. Normal rain is actually slightly acidic as it picks up CO2 from the air, making carbonic acid. But when this “normal” rain mixes with the byproducts of industrial plants that pump out large amounts of  SO2 (sulfuric dioxide) and NO (nitrogen oxide) into the atmosphere, it becomes even more acidic – down to a pH of 3. This “acid” rain has the acidity of citrus juice, so it’s not going to set the world on fire. But it will wreak havoc on local ecosystems.

The 1990’s brought with it tough government regulations on the output of SO2 and NO by large factories, pretty much eliminating acid rain in the US. The rise and fall of acid rain is a great example of why we should educate ourselves on the basic chemistries that define our lives, even though we might not be actual chemists. In this article, we’re going back to your first year of college and hash out just what defines an acid and base. And solidify our understanding of the pH scale. It is essential for the future biohacker to have this knowledge in their toolbox.

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Chemical Nomenclature

Looking at the ingredient list of some popular processed foods will produce a puzzled look on the typical hacker’s face. Tricalcium phosphate, thiamine mononitrate, zinc proteinate, pyridoxine hydrocloride… just who the hell comes up with these names anyway? It turns out that there is a method to the madness of chemical name structures. Some of them are well known, such as sodium chloride (NaCl) and hydrogen peroxide (H2O2). Others… not so much. In the early years of chemistry, chemical substances were named after their appearance, affects and uses. Baking soda, laughing gas and formic acid (formic is Latin for ant, and responsible for the sting in an ant bite) to name a few. As more and more chemical substances were discovered over time, a more structured naming convention was needed. Today, the above are known as sodium bicarbonate (NaHCO3), nitrous oxide (N2O) and a type of carboxylic acid (R – COOH, think of the “R” as a variable) respectively.

In today’s article, we’re going to talk about this naming structure, so that next time you admire the back of soup can, you won’t look so puzzled. We’ll also cover several common definitions that every novice biohacker should be familiar with as well.

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Chemical Formulas 101

It seems like every other day we hear about some hacker, tinkerer, maker, coder or one of the many other Do-It-Yourself engineer types getting their hands into a complex field once reserved to only a select few. Costs have come down, enabling common everyday folks to equip themselves with 3D printers, laser cutters, CNC mills and a host of other once very expensive pieces of equipment. Getting PCB boards made is literally dirt cheap, and there are more inexpensive Linux single board computers than we can keep track of these days. Combining the lowering hardware costs with the ever increasing wealth of knowledge available on the internet creates a perfect environment for DIYers to push into ever more specific scientific fields.

One of these fields is biomedical research. In labs across the world, you’ll find a host of different machines used to study and create biological and chemical compounds. These machines include DNA and protein synthesizers, mass spectrometers, UV spectrometers, lyophilizers, liquid chromatography machines, fraction collectors… I could go on and on.

These machines are prohibitively expensive to the DIYer. But they don’t have to be. We have the ability to make these machines in our garages if we wanted to. So why aren’t we? One of the reasons we see very few biomedical hacks is because the chemistry knowledge needed to make and operate these machines is generally not in the typical DIYers toolbox. This is something that we believe needs to change, and we start today.

In this article, we’re going to go over how to convert basic chemical formulas, such as C9H804 (aspirin), into its molecular structure, and visa versa. Such knowledge might be elementary, but it is a requirement for anyone who wishes to get started in biomedical hacking, and a great starting point for the curious among us.

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