Do It Yourself Science

During my master’s program in grad school, I was funded with a lab teaching assistantship for introductory botany. Because this class was a level 1 course, we also covered some basic biology lab techniques. In one particular session, the task at hand was to learn how to extract DNA. The victims were conventionally bred strawberries, which as octoploids, contain such a ridiculously high amount of DNA that a rough extraction technique is sufficient.

How to extract DNA from a strawberry, as understood by my botany students:¹

1) Have your teaching assistant put an amount of isopropanol (aka rubbing alcohol, ~50mls) in the freezer before you know that this lab will exist, because you’ve not done the reading.

2) Make 50mls of extraction buffer by mixing a 1:10 dilution of dish soap (TA says shampoo works as well) with the salt sitting in the weigh boat, located to your right.

3) Place 1 large berry (choose the one with a bit of mold because you plan on eating the rest of them) in an airtight baggie, add extraction buffer and mash thoroughly with your fist.

4) Pour the mash into a beaker through a sieve or whatever to filter out the chunks/clumps/globs and discard by whipping them into the trash all the way across the room. Three points if you make it!

5) Add an equal amount of cold isopropanol and invert to mix. At this point you should see the strands of DNA precipitate out of the solution. This is actually quite neat.

6) Use a glass hook to remove the DNA, and twirl it around like a helicopter before putting it in water.

7) Eat the rest of the berries if you have not done so already, because eating something that is sitting on a lab bench isn’t sketchy at all. Not one bit.

At some point during the lab session, I saw one student accidentally (?) fling a glob of strawberry DNA across the bench with a glass hook. The surrounding students all stared at the white mucus-y gooey pile, before one spoke up.

“Dude, you spilled your DNA.”

Overhearing this, I let out an undignified snort, because I was not mature enough for this job.

Due to the interest in do-it-yourself biology as a larger part of the citizen science movement, the extraction protocol posted above can be readily found on the internet, along with protocols for downstream techniques, such as restriction digest and gel electrophoresis.

The nature of DIY science has changed quite a bit in the last 150 years or so. Between the beginning of the industrial age through the 1960s, forays into citizen science focused on the chemical and mechanical/engineering sciences as advances in these areas became synonymous with American pride. This could be due to the success of the Manhattan Project in ending World War II, the rise of companies such as DuPont and Goodyear offering chemical products to improve our vehicles, our crops, our clothes, our homes, our hygiene, our cosmetics, our foods, our hair, etcetera, etcetera, and, last but not least, advancements in mechanics inspired by, and for the space race.

As it was in society, so it echoed in children’s toys. The 1940’s and 50’s gave rise to an ever-diversifying array of chemistry sets, which provided everything needed to conduct experiments at home. Basic sets typically included a balance, assorted flasks, beakers, and tests tubes, pipettes, thermometers, and most importantly, chemicals. These ranged from the innocuous (potassium chloride) to the eyebrow-raising (hydrogen peroxide, nitric/sulfuric acid) to the “are you kidding me” (U-238 isotope, sodium cyanide) along with other flammable, explosive, and toxic items so that you could carry out the dangerous and awesome tasks on your own.

Admittedly I’m not jealous, because I had Nintendo when I was a kid.

I’m also not jealous because I generally don’t like explosions followed by fire while I am in the vicinity.

You can still get chemistry sets today, but they are quite a bit different. They focus on the creation of inert crystal structures, pretty colors, and things that glow. Neat stuff and all, but what happened to our chemistry sets of old?

The pushback started in the 1960s, as the effects of Agent Orange, Rachel Carson’s Silent Spring, lead poisoning, and growing concern about nuclear proliferation wised us up to the fact that chemistry had a downside. This gave rise to appropriate legislation such as The Federal Hazardous Labeling Act (1960), The Consumer Product Safety Commission (1972), and the Toxic Substances Control Act (1976). More recently, we have our fears about meth labs, chemical warfare, and last but not least, chemtrails. You may not know what it is, but it’s probably controlling your brain waves.

Raise your hand if you know at least one person that won’t eat something if s/he can’t pronounce every single thing in the ingredient list.

Now in the 2010s, we still have a healthy suspicion towards chemicals, manifested in declarations against so-called Big Pharma (GlaxoSmithKline/vaccines/PharmaBro!!!) and Big Food (Monsanto/pesticides/GMOs). And it’s these concerns that have led to a new DIY science movement that centers around biology, or in particular, growing, culturing, fermenting, and preserving your own food. For example, a quick internet search will let you know how to make your own yogurt (step 1: buy yogurt, because you need a starter culture of microbes). Along the same vein, my home state, Oregon, has the honor of being the land of a million microbrews, and it seems like everybody’s grandmother has tried their hand at brewing their own beer. Simply and cheesily put, Do it Yourself has become Brew it Yourself. I’d argue that this is a Good Thing, mainly because it helps us to avoid the extra sugar and salt that is often present in store-bought, processed food.

Another example of wholesome DIY biology/citizen science is wide public participation into ecological and population counting studies. These include bird-counting projects set forth by The National Audubon Society, and the Cornell University Ornithology labs.² A similar project includes algal tracking by the University of Georgia,³ and cicada counting by the National Geographical Society.⁴ I’d argue that this is a Fantastic Thing, as population counts and related studies are so large-scale, it’s a good idea to have mass participation over many years to do the best, most thorough job.

On the computational side, there is an ever-expanding number of databases popping up for organisms that have had their genomes sequenced and annotated. These databases are open-source, which is science-talk for being accessible to the public. A few examples are human, fruit fly, corn, chocolate and most recently, water bears (bizarre), and coming soon, beavers!⁵ Anyone with internet access could go in and poke around, no coding experience necessary. I’d argue that this is an Awesome Thing, as these projects are typically funded by the public, so of course they should be available to the public. The only drawback is that there may be a bit of a learning curve when it comes to drawing a connection from genome databases to figuring out the intricate aspects of the genome that make our critter du jour tick. We in the scientific community are still figuring this one out.

DIY biology has also moved into the realm of recombinant DNA, with the Holy Grail being the creation of a bioluminescent plant. As might be expected, recombinant DNA technology is on the expensive side, requiring a multitude of specific enzymes, cultures, reagents, and equipment such as super cold freezers and centrifuges. This has produced a community effort into creating shared spaces in major US cities, where regular folks can take classes and work on projects in a group environment.⁶

This DIY movement into recombinant DNA technology is what has raised some eyebrows, and has lent itself some unwholesome names such as “BioPunk,” “BioHacking,” and so on, and so forth. The public is terrified of genetically modified organisms (GMOs), which is exactly what this movement creates. Apparently, there is little difference between folks that want to make a fluorescent bacterial culture spell LOVE ☺ in a petri dish, and folks that think creating the next highly virulent toxic cancerous liquefying superbug is first of all, something that can be easily done on an evil whim, and secondly, is a 2nd Amendment right.

As for superbugs, we are doing a fine job of creating them simply through ill-advised and excessive use of sanitizers and antibiotics.

Regular folks studying recombinant DNA technology is a Wonderful Thing, because it is the basis of so many crucial medicines that we use today, not to mention that increased scientific literacy is the Best Thing Ever. If we have the knowledge to create superbugs, it’s likely that we also have the knowledge to stop superbugs. If it makes you nervous, I recommend actually going out, learning about it, and doing it. After all, the best way to get over a fear of flying is to get a pilot’s license.

¹ My botany students were fantastic and talented people. I often times did not do the readings beforehand either.

⁶ http://diybio.org/