Tag: Working in the lab

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From the BiLOLogy archives: what’s really going on when I do experiments

This is the first post in a series that i’m calling “From the BiLOLOogy archives.” BioLOLogy was a blog that I created in grad school. My intention was to explain papers and lab life through comics. I won’t re-post everything from BiLOLogy, but this series will feature a few pieces I still like. Enjoy!

ASCB Comic

This post was originally published in October 2014 (my fourth year of graduate school). 

The idea for this comic came from a night when a friend of mine drove me to lab so I could do something “really quickly” (nothing ever takes as long as you think it will in a lab).

As you can see in the comic, that night I was doing something biology researchers do all the time. I was taking bacteria that were resistant to a particular  antibiotic and putting them on plates containing the antibiotic in addition to some food. In this case, the point of the antibiotic was to make it so only my bacteria could grow on the plate. The antibiotic killed other bacteria, but did not kill the bacteria I was studying because they were resistant to it.

This whole process consisted of little more than putting a bunch of clear liquid onto a plate and spreading that liquid all over the plate. On the face of it, as my friend comments in the comic (and did in real life), it seems like a very uninteresting process. However, this is true of a lot of the experiments I do. Most of my days consist of the following:

1. Mixing different clear liquids together

2. Putting white powders into those liquids

3. Adding slightly more opaque liquids containing bacteria to the clear liquids

4. Putting these mixtures into machines that shake, heat, or cool them. Usually this makes the liquids more opaque

5. Putting these mixtures into machines connected to computers and watching the computers spit out numbers

6. Destroying all the bacteria by mixing them with yet another clear liquid (bleach)

On the face of it, this could be very boring, but I certainly don’t think about it that way… if I did, I would probably quit. Instead, I spend my days thinking about all the things going on that I can’t see.

As you can see in the comic, when they are thrown onto the plate, the bacteria spend their energy destroying the antibiotic (or at least producing proteins that make them immune to it) and growing into colonies with MANY MANY individual cells (the cities in the comic). I then come along and subject the bacteria to a bunch of tests that determine things like how fast they can grow, what molecules they can produce, and how those molecules can be used. While I can only see these things through a bunch of numbers on my computer, they’re still awesome to think about!

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Experimental Approaches to the Best Fruit Salad

Diagram of fruit salad experimentA recent episode of Bojack Horseman (love that show) reminded me that most fruit salads are awful. Usually they contain far too much honeydew melon and, really, no one likes honeydew. Of course, one can always look on the bright side. The aspiring entrepreneur might see this lack of good fruit salads as an opportunity.

If you could simply make a good fruit salad, couldn’t you easily take over the fruit salad market and become wealthy beyond your wildest dreams? It’s never quite that simple, but this opportunity leaves us with an interesting question: How do you go about making the best fruit salad?

There are probably lots of ways to make a good fruit salad, but I’ll quickly discuss two possible approaches that are representative of many others. The first approach we’ll call “biased” and the second approach we’ll call “unbiased.” First the biased.

The Biased Approach to Making The Best Fruit Salad

In this approach we’ll use prior knowledge and information to guide the design of our fruit salad. Indeed, the fact that we’re working off of prior information is what makes this approach biased.

To begin this approach, you might poll a bunch of people to figure out what their favorite fruits are. You’d then limit the fruits in your fruit salads to the known favorites. Your decisions on what to put in the final product will also likely be affected by your own preferences. For instance, I would never leave out watermelon because people who don’t like watermelon are clearly nuts.

This seems like a great way to g, and it might even work. However, there are definitely some caveats. Here are a few:

  1. Even if people like certain fruits separately, they might not like them mixed together in a fruit salad. Growing up, my brother was one of those people who absolutely hated to have certain foods touch whereas I would go as far as putting mashed potatoes in my milk…. Clearly preferences about food combinations differ.
  2. People may not have tried all the fruits in the survey prior to taking the survey – you may be missing out on some great fruits simply because most people haven’t tasted them. Friends often give me mysterious and delicious fruits that I can never remember later.
  3. You wouldn’t know what proportions of fruit to put in the fruit salad. Heck maybe even a very small amount of honeydew in a fruit salad is good for some reason… maybe.

The Unbiased Approach to Making The Best Fruit Salad

To get around these issues, you could instead take an unbiased approach (see drawing above). In this approach, you might start off with huge piles of many different types of fruit. You would then use these fruits to fill many different salad bowls as randomly as possible, record the contents of each bowl (recipes for each bowl), give them to many different people, and ask the people to eat/rate the fruit salads. After collecting the ratings, you would then make a list of the most highly rated salads and use their recorded recipes to remake them. You would then distribute these new salads to many more people and repeat the process again and again until you found the very best 1-3 salads.

This approach doesn’t have any of the caveats of the biased process and will likely lead you to a better fruit salad than the biased approach. What’s the drawback? It’s a HUGE undertaking. It will take tons of fruit, tons of time, and tons of people to make sure you’ve sampled enough combinations and preferences to get to the few salads that are generally well rated. Were I an entrepreneur trying to make a new salad, I might avoid this technique simply because of the sheer amount of time and money it would take.

Combining the Biased and Unbiased Approaches

There are many ways you could modify these approaches to make them better and/or use them to answer different questions (for instance, what’s the worse salad I could possibly make?… all honeydew… duh). You may have noticed that you could also combine the biased and unbiased approaches.

You could add a little bias to your unbiased method by limiting the initial number of types of fruit. You might use a survey to find the best fruits and then only make random combinations with these. Alternatively, you might only use the cheapest fruits available to you. This would make the entire process less expensive and more doable.

Why Are We Talking about Fruit Salad?

Good question! Mostly because of Bojack Horseman, but also because these biased and unbiased approaches are used by experimental biologists everyday. Luckily for many biologists, the unbiased approach can be far more practical in a biology lab than in our fruit salad example – it’s just easier to get the large numbers of cells and other small biological things needed for unbiased biology experiments.

Whether or not a biologist chooses a biased or unbiased approach will be determined by a variety of factors. Just like our fruit salad example, these factors can include time, money, and level of prior knowledge. Importantly, both biased and unbiased methods can lead researchers to discover answers to big questions. For example, researchers recently used the biased approach to make pigs impervious to a particular type of virus (this could be useful for organ transplants from pigs to humans or for making better chimeras), and the unbiased approach was recently used to make viruses that infect specific parts of the human central nervous system (these could be very useful research tools).

 

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Jargon – The Expert’s Delight and the Novice’s Bore: Supernatant

Check out this post on scientific jargon that I wrote for my friend Matthew Niederhuber’s blog .jargon.

A drawing of turtle floating in an inner tube

Every field has jargon. Marketers talk of leads and conversions, cyclists speak of cadence and derailleurs, and programmers speak of grooming, for-loops, and much more. Jargon is everywhere. Both a boon and bane to understanding, jargon makes it difficult for any novice to get started in a field but makes it easy for experts to quickly communicate complex ideas to those in the know. Any word used only by experts in a field can be considered jargon. Scientists however, are perhaps the most egregious users of jargon.

My good friend Matt Niederhuber recently started thinking about how scientists use jargon and has been working on a blog where he introduces readers to the history of scientific jargon. Interestingly, few scientists know where many of the words they use come from, but learning about a piece of scientific jargon’s history can both provide one with a new way to get someone interested in science and reveal something about how science has advanced – the artistry of language serves as a proxy for the story of discovery.

Supernatant

The word “supernatant” is a fantastic example of scientific jargon. I’ve used it a million times but, the first time I saw it I probably thought it meant powerful vapor or something… I was very wrong. Simply put, the supernatant is the liquid portion left on top when a process produces solids and liquids or multiple distinct liquids.

For example, say you put a bunch of muddy water in a glass and let it sit. After a little while the mud would sink to the bottom and the water would sit on top of it. The water would be the supernatant.

On the face of it, supernatant appears to be a boring, mechanical word, but it has power in its specificity. When doing experiments, researchers often use procedures that separate complex mixtures into liquid and solid portions or multiple distinct liquid portions. The liquid that rests on top is the supernatant. Separating the supernatant from its counterpart may make it easier for a scientist to isolate something for an experiment. For example, when finished growing a bunch of cells, a researcher could separate the solid cells from their liquid waste (the supernatant). The researcher could then continue growing/using the cells while measuring chemicals in the supernatant. If you tell a fellow researcher to remove the supernatant from a mixture, she will know precisely what you’re talking about.

Interestingly, supernatant can also be used as an adjective to describe one thing floating on top of another. So, if you wanted to describe the whipped cream floating on top of your hot chocolate, you could call it the “supernatant cream.” While this seems somewhat superfluous (we just expect the cream to float after all), it does add a bit of flourish and specificity to the sentence.

Like the noun form, the adjective has been used extensively in scientific settings. For example, one could say “mix these two solutions together and then remove the supernatant liquid.” However, I don’t really remember anyone using it this way in the lab. This is possibly because you could just say “remove the supernatant” and there’s really no need for the adjective form. Indeed some of the adjective forms like “supernatant fluid, supernatant oil, supernatant liquid, or supernatant water” peak in their usage prior to “supernatant” according to google books so it’s possible that this use is going out of style.

Floating above – The Supernatant Breakdown

Supernatant’s two latin roots, “super” and “natant” make perfect sense for its scientific meaning.

  • Super – An interesting word on its own with a bunch of different meanings. Here it means “above” as opposed “great” as in “I’m super, thanks for asking!”
  • Natant – I didn’t actually realize this was a word before, but natant means swimming or floating. Natant has fallen out of popular usage, but the next time you go to the local pond, you might spot some natant ducks or, my personal favorite, a natant turtle.

Put these together and you get the adjective form “floating above.” When supernatant is used as noun, it’s just a thing that floats above. In our mud-water example, the water was “floating above” the mud – it was the supernatant.

Nonscientific Uses of Supernatant

Possibly because it’s meaning is so specific, you don’t hear supernatant being used much in nonscientific speech. However, it’s Latin progenitor (also supernatant) is just the third person present conjugation of the verb supernatō which means “to float.” Presumably you could use it to say something like “The ducks float down the river” if you were speaking latin. In this sense, it’s usage wouldn’t be that uncommon if we all still spoke latin. Alack we do not and must therefore look to other more contemporary uses.

Searching through the news, it was difficult to find examples of supernatant being used outside of science. One recent Market Watch article did use it to describe the current heights of the stock market: “Such a preternatural period of supernatant trade is bordering on insane….” Here supernatant is an adjective used to denote market growth without any apparent foundation – the market just seems to float upwards. Uses like this are rare, but perhaps they will pick up as scientific advances and scientists themselves seep ever further into the public eye.

Future Evolution for Supernatant

With the practicality of its roots, supernatant is, in some ways, an ideal word. It has only one definition with a very clear meaning. However, supernatant’s lack of use outside science and the outdatedness of it’s roots makes it a rather blatant case of jargon. If you’re a scientist writing a piece for the general public, trying to communicate your work to friends and family, or explaining a procedure to a lab novice, you’d be wise to avoid this word. Nonetheless, it’s interesting that supernatant displays the practicality and functionality that many scientists try to exhibit when designing their experiments. Why come up with a random word for the “liquid that floats above” when supernatant has that exact meaning and serves it’s purpose so well?

As scientists move out of their labs and into other careers perhaps we’ll see the specific meaning of supernatant applied in non-scientific but perfectly apropo situations. The next time I travel to San Francisco for work, I’ll be sure to point out the supernatant fog coming over the bay. The next time we hear about an oil spill maybe we’ll learn of the supernatant oil oozing over the ocean. Both of these uses, while true to the very specific definition of supernatant, serve to drive home the point that the fog and the oil each loom over their counterparts distinctly separate, distinctly unattached, distinctly other. The precision of supernatant’s definition gives us a means of describing anything the floats above and without any real attachment. If supernatant makes its way into common language, it may give people means to more easily describe ideas knocking around in their heads – the things that are above but separate. Supernatant leaders? The supernatnat 1%? Supernatant values? Even a seemingly boring word like supernatant, which already has great power is describing lab procedures, could have even greater power outside the lab because of its clear and specific meaning.

You’ll see this same theme come up again and again in scientific jargon. A personal favorite – while the name “sonic hedgehog” may have seemed totally appropriate for the name of a gene discovered in the 90s, even now it doesn’t quite hold up.