Author: Tyler J. Ford

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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.

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Learning the Game of Life with Biosensors

Cartoon of a DNA Biosensor

There are many ways to learn a new game. You might read the instructions. You might look at diagrams of the game board. You might watch other people playing. You might even play the game yourself.

Similarly, when trying to understand how a cell works, researchers do all of these things. They read the cell’s DNA to learn what it encodes, they use special microscopes to get high definition pictures of cellular components, they watch the cell grow, and sometimes they even try to build new cells.

For all of these techniques to work, we must be able to observe key components of the games or cells under study. For example, if you were trying to learn how to play soccer and couldn’t see what was going on, you’d have a hard time learning the game. To study how a protein works, a researcher must be able to observe the protein in cells. The same is true for chemicals, DNA, and many other molecules a researcher might like to study inside a cell – you must be able to observe, measure and identify these things in order to learn what they do.

What is a biosensor?

Drawing of a protein-protein interaction biosensorA biosensor is one type of tool a researcher can use to observe molecules in cells. Biosensors are devices made of biological components like DNA or proteins (hence bio) and they detect or “sense” when different types of molecules are nearby (hence sensor). Biosensors report that they have detected something through an easily observable signal. You can think of biosensors like friends explaining a game to you for the first time, and showing you clearly what is going on. If the game was soccer, they could point to the goalie and say “That’s the goalie” and also scream “GOOOAAALLLLLL!!!” when a goal has been scored.

Biosensors work in many different ways but they often give researchers visual cues to show that they have detected specific molecules. For instance, some biosensors will start to glow red if there is a particular chemical in a cell. Other glowing biosensors will attach to specific sequences of DNA to show where those pieces of DNA are. Still other biosensors will make cells turn blue only if two proteins interact with each other.

What are biosensors used for?

Cartoon of a biosensor for glutamate

One interesting biosensor that I learned about recently is called iGluSnFr. This cleverly named biosensor glows bright green when it detects a chemical called glutamate. This ability is useful because glutamate is transferred between some cells of the brain when they communicate. You can therefore use iGluSnFr to determine if cells in the brain are talking to each other and even measure brain responses to things like visual cues. In this particular case, detecting glutamate serves as a proxy to tell researchers “Hey! These cells are talking to each other!”

Of course this is just the tip of the iceberg for biosensors. Researchers have produced biosensors to measure levels of toxic waste, to measure the acidity of cells, and even to detect Zika virus. Everyday, scientists are using biosensors to learn the rules of life and, as they get more precise, you may see these cool tools used to diagnose and treat disease!

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The Third Grade Accident

I developed my love for Chicken McNuggets at a tender age (as I’m sure most people do) and, though even now I get intense joy from their fatty, bread-caked flavor, they never quite sit right in my bowels.

In most cases, this isn’t a problem and certainly didn’t keep me from devouring many a Chicken McNugget as a child. Back then, the issue was usually quite acute and only under rare circumstances was I particularly far from a toilet.

Indeed, in those early years, I had no fear of using public restrooms. Heck, I was perfectly willing to roll around in mud and play in street run-off so pooping in one of the many McDonalds around my hometown was far from an issue.

Of course, there comes a time in every person’s life when the closest bathroom is farther than it needs to be. For me, that day was a Tuesday somewhere around third grade. On Tuesdays, the lady up the street whose name I still cannot pronounce (but let’s call her Mrs. S.) used to pick up me, my brother, and her daughter after elementary school so we could go to catholic education class. We used to call these classes “CCD” although I have no idea why.

Mrs. S. also just so happened to be the Avon lady, so, on this day (a bright and sunny Spring day as I recall) she picked me to join her on a cosmetics delivery while my brother, her daughter, and a few other kids played on the school playground for a bit longer. For some reason, I never quite enjoyed playing on the playground and it was a treat for me to be able to drive off with Mrs. S while those suckers were still stuck on school grounds.

When Mrs. S. and I got to the appropriate address, the woman who answered the door saw my cute, bespectacled (and not yet pudgy) face, smiled, and offered me some of her own son’s Chicken McNuggets.

“Could this day get any better?” I thought as I excitedly shook my head yes.

The woman handed over a couple of nuggets which I promptly devoured. Within mere minutes, Mrs. S. whisked me away back to the playground to pick up my brother and her daughter. The afternoon was going so well, a part of me thought maybe something would even stop us from being forced to go to the dreaded, “CCD”…. For being our savior, Jesus sure was boring to learn about.

When we got back to the school, Mrs. S. and I hopped out of the car and she marched swiftly off toward the playground to find my brother and her daughter. I would have followed along behind her being the smarmy little goodie two shoes that I was, but as I started to walk after her, something in my large intestine grabbed a hold of me.

“O dear,” I thought, too afraid of God, my parents, teachers, and “CCD”, to use a more appropriate swear word – even in my own head.

Nothing had dislodged, but I was sure it was coming. I had no idea that my bowels could make so many noises and, although there were many kids playing on the playground, I knew they could all hear the cacophony coming from my abdomen.

Luckily, or so I thought, the school was right there. Bathrooms and sweet sweet porcelain salvation were mere steps away. But then I thought about Mrs. S. She wouldn’t have wanted me to go back into the school where she couldn’t see me. I would be disobeying an authority figure if I went inside and so I stopped in my tracks facing the entrance of the school. I was paralyzed between bodily need and fear of the mysterious but powerful adult world.

Another lurch within my stomach destroyed that fear and propelled me into my first act of childhood defiance; I walked through the school doors and began a slow, awkward walk down the hallway. My steps were sometimes over extended, sometimes greatly shortened – my body seemed to know exactly how to contort itself to keep anything from falling out.

However, each step pulled something a little looser and, before I knew it, I had stopped moving. I stopped not because I was holding anything in, quite the opposite. I stopped because there was a great release, but I was still frozen in place until I heard from behind me, “Tyler! What are you doing in here?!? It’s time to go!”

I turned around slowly. I was horrified but had few options. “… Coming!” I said lurching my way forward with increasing momentum and an odd amount of confidence given my situation.

When we go to the car, I sat more than a little uncomfortably next to my dear older brother and we pulled out of the school parking lot.

Not 100 yards into the drive, the questions began.

“What’s that smell?” asked Mrs. S.

… I didn’t answer

“Did one of you fart?!?” she pleaded.

… still I said nothing.

“That’s awful!” she exclaimed in exasperated tones.

My brother leaned over to me and whispered, “Tyler, did you poop your pants?”

I couldn’t make an audible response, couldn’t admit the truth to the whole car, but gave my bro an affirmative nod.

“WE HAVE TO GO HOME!” my brother yelled in response.

“Why?!?” groused Mrs. S., her crinkled and confused brow visible in the rearview mirror.

“TYLER POOPED HIS PANTS!” yelled my brother.

While I don’t doubt that he said this for my own protection, I couldn’t help but detect a little glee in his response and, with the resulting “OH MY GOD! GROSS! YOU’RE TOO OLD FOR THIS! JUST USE THE BATHROOM NEXT TIME!” from the rest of the car, I was a little bitter that my brother had said anything at all.

Nonetheless, my brother got me a ride home where I cleaned up, and, to both our dismay, we were soon on our way to CCD again. The admonishment continued for the 10 minute ride, but, being the only one who had known true discomfort, I was content to be clean.

I sat down at my little desk at CCD (every year those desks seemed to get disproportionately smaller) and within minutes I realized something was still wrong. The squishy rumbling began again.

Normally a supremely shy child, almost ashamed to talk to anyone if it wasn’t 100% necessary, I was surprised at how quickly I shot my hand up to use the bathroom and HORRIFIED that I had the audacity to blurt out before being acknowledged, “CAN I PLEASE USE THE BATHROOM?!?”

The teacher worriedly shook her head yes and I shuffled off to the bathroom.

I had never used the bathrooms at CCD before. The whole building smelled like my grandparents on a bad day and I’d never wanted to know what smells lay hidden in the dank, damp bathroom. That afternoon, however, I didn’t hesitate. I threw open the boy’s room door and rushed into the stall.

I was surprised to discover that, resting on the surface of the murky water were what we used to call “water skeeters” (others call them “water striders” or “water bugs” … utter nonsense if you ask me – they’ll always be water skeeters). Unfortunately I had no time to contemplate the lives of the poor water skeeters or how they came to reside in the toilets in the first place. As my sweet release came, I knew the skeeters were suffering terribly and I felt a few pangs of guilt as I remembered playing with their brethren in the brook behind my childhood home.

I wasn’t worried though. If I learned nothing else from CCD classes, it was that I would be forgiven with a few “Hail Marys” later in the evening.

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Human-pig chimeras

In a pair of recent publications, scientists showed the following:

  • Mouse pancreatic cells produced in a rat can cure diabetic mice
  • Human stem cells can contribute to tissues in pig embryos (i.e. it’s possible to make human-pig chimeras)

In the future, scientists hope to combine these findings to determine if it’s possible to make human pancreatic cells in other animals. These cells could be used to treat diabetes.

What is a chimera?

Photo of a chimeric mouseYou can check out the wikipedia chimera page for the description of a mythological chimera (essentially a beast consisting of a lion, goat, and snake). While cool, that’s not what we’re talking about here. In biology, a chimera is a single organism composed of genetically distinct cells.

We normally think that all the cells in an organism have the same DNA sequences. This is true most of the time. Yet, there are a few natural cases where cell’s change their DNA sequences (in the production of B cells for instance). In addition, humans can be born with patches of cells that have non-identical DNA (check out this Scientific American Article for more information).

Beyond these natural cases, scientists use stem cells to create chimeric organisms. To do so, they implant foreign stem cells into developing embryos.  These grow along with the embryo. Ultimately, they will make up some fraction of the cells in the adult.

Scientists routinely make chimeric mice composed of cells from genetically distinct mouse strains. Scientists use these chimeric mice to produce new strains with particular traits (see chimeric mouse image above).

It’s also possible to create chimeras between different species (like between mice and rats). However, it’s unclear how different the two species can be. Furthermore, while most would argue that creating chimeras within a single species is okay, it’s ethically questionable to produce chimeras with cells from different species.

You might ask – why make interspecies chimeras in the first place? The answer: chimeras may allow us to cure disease.

Indeed the combined results from two papers (one published in the journal Nature, the other in the journal Cell) show that it may be possible to use chimeras to grow replacement cells for those with diseases.

Growing a replacement pancreas for a mouse

The first paper showed that, if you take a rat embryo that’s unable to grow a pancreas and give it stem cells from a mouse , the mouse stem cells will form a pancreas in the rat. This rescues the developing rat which would otherwise die.

You can then take the pancreas cells from the rat and use them to replace broken cells in a diabetic mouse. This mouse will essentially be cured of its diabetes.

Now you might say, “Why grow a mouse pancreas in a rat? Couldn’t you just taken pancreas cells from another mouse?”

In the case of mice, you have a point. Scientists could easily harvest the necessary pancreas cells from another mouse. However, researchers would like to use similar techniques to cure human diabetes. You can’t just take one person’s pancreas cells and use them to treat a different person with diabetes. If, however, you can grow a human pancreas in another animal, you could potentially use it to treat diabetes.

This sounds far-fetched, but the next paper makes it seem more likely.

Making human-pig chimeras

The second paper set out to determine if human stem cells can contribute to embryos of other animals (specifically pigs). TLDR – Yes, the process is inefficient and requires the stem cells to be prepared in a particular way, but it does work.

In this work, the researchers did not allow the chimeric pigs to fully develop. It’s unclear if they even could. Yet these results do provide evidence that it’s possible to grow human organs in pigs.

There are a number of important issues that need to be considered before similar research moves forward:

  1. Ethics – We have to ask the question, should we be making chimeras to treat disease? In my mind, chimeras have two major ethical issues:
    • Unintended consequences: Just one example, we don’t have good ways of directing human stem cells to particular pig tissues yet. This raises questions like – If some of the human cells contribute to the pig’s brain, will that affect the pig’s cognition? What other attributes might the chimeric pig gain?
    • Animal welfare: What about the welfare of the pig? A pure utilitarian might argue that the ends, curing human disease, justify the means. However, there may be other ways to achieve the same goal. For example, should we focus our efforts on growing organs in the lab?
  2. Human pancreas formation – The papers discussed above are very interesting and demonstrate important first steps towards the production of viable human-pig chimeras. However, these researchers did not show whether or not a fully grown pig could be formed using this technique. New techniques may be required for the creation of fully functional organs.
  3. Immune rejection – In the mouse/rat experiments above, researchers suppressed the mouse immune system. As a result, the mice didn’t have drastic immune responses to the replacement pancreatic cells. If replacement human pancreatic cells were taken from a pig, how would the human immune system respond to them?

Final thoughts on chimeras in research

These are the 3 biggest challenges that I can think of at the moment. I’m sure there are many more, but these shouldn’t dissuade researchers from at least thinking about pursuing this work. Keep in mind that pig valves are already used to replace human heart valves. Pigs were also once a major source of insulin for Type I diabetes. In a way, human-pig chimeras have been around for a long time.

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Science Brought Us Beer and Other Thoughts on Science Communication

Signs from the March for Science

Yesterday (April 22, 2017) I attended a march for science. If you’re not familiar with the marches, head over to my friend Stephanie Hay’s blog post to learn a little about why scientists decided to march. TLDR: There were lots of reasons, but, more or less, people want knowledge and facts to become stronger forces behind the decisions that guide government action. It was invigorating to see so many people out there in support of knowledge, but there are a few things we need to keep in mind as we try to make science and knowledge effective forces for change.

1. Empathy, Empathy, Empathy

Many scientists are angry about the way decisions are being made in the US and throughout the world. This is understandable. After having done my PhD work in renewable energy and climate change, it frustrates me to no end to see these fields pushed aside. BUT, no amount of angry chanting, slogan writing, sign making, or even informative explaining will convince people that the problems so many scientists work so hard to solve are important.

If you lived in a small coal mining town where it was once possible to work in the coal industry your whole life and make a comfortable living, you wouldn’t be supportive of regulations that shut down coal-fired power plants. In fact, seeing few other options available to you and believing your entire livelihood was about to be destroyed, you’d probably be happy to see mining jobs come back; even if the long-term costs could be problematic, at least you could live with some chance of adapting to the problems later. Don’t fool yourself into thinking that you can start a conversation about science with a coal miner who disagrees with you using a snarky, science-y, anti-Trump sign. How could you possibly expect that person to relate to you?

Now, you might ask, why do I need to relate? Shouldn’t the truth be able to convince people? I wish it could, but, as a recent study on protest tactics showed, movements are more likely to succeed and recruit followers when people can relate to them (see NPR article segment on the study). The more you can identify with someone you are trying to convince, the more likely you are to convince them.

2. Extreme Rhetoric and Extreme Protesting Are Probably Not Useful

Despite common belief, people don’t necessarily avoid behaviors that are believed to be extremely or insurmountably risky. I’ll call this the “Screw it, I’m doomed anyway” principle. For example, work in Malawi showed that if men believed they had a 100% chance of contracting HIV by having sex with someone who was already infected, they were far less likely to use condoms than if they knew the actual, much lower, 10% chance. In a recent NPR report, the authors explain this as a kind of fatalistic approach to risk. If you’re told that you’re doomed, you don’t bother to change your action because, hey, you’re doomed anyway.

This has important consequences for the ways we talk about challenges facing the global community. If we simply start yelling “THE ECONOMY WILL IMPLODE WITHOUT NAFTA” … we’ll probably shut people off. Instead we might say, “I love being able to get fresh tomatoes for cheap at any time throughout the year, don’t you? …. Did you know that NAFTA is part of the reason you can get fresh tomatoes so cheaply? Pretty cool huh?”.

“Okay,” you might say, “but people will only start listening if I get extreme.” While it may be true that extreme protests get more news coverage, the same study on protest tactics I mentioned above found that protests using more extreme tactics are less likely to recruit people to a cause and may, in fact, have the opposite effect (again, you gotta be relatable!).

3. Jargon Sucks

I work at a biotech non-profit and many of my coworkers are not scientists. Despite the fact that they work around biologists and biology jargon everyday, we recently discussed the fact that many, many times they get lost once a scientist starts talking. This wasn’t unexpected – biology and molecular biology in particular is choc full of words that either a) have no meaning outside of biology or b) have biological meanings that make no sense when compared to their more general meanings (a good example, the term “gene expression”). Jargon makes my co-worker’s jobs more difficult and makes it harder for them to speak up in meetings for fear of looking stupid or making the meeting run too long.

What does this have to do with science advocacy or science marching? Researchers need to remember that, when they get around groups of peers, they are prone to start using alienating jargon that is nonsensical to people outside their specific fields. One of the quickest ways we make ourselves un-relatable and even a bit pretentious is to use jargon. So, while many of the more science-y signs at the march were quite cool and the messages were very good (loved the “Be like a proton, be positive” signs) they could have been more alienating than many of us realized (go ask a random group of ten people what a proton is). It’s certainly possible to make a relatable science march sign with a positive message: “Science brought us beer!” (slightly altered version of one of the great signs above).

Before I go, I’d like to reiterate that many people at the March for Science Boston (and I assume elsewhere as well) seemed to understand these points and did a great job. Hopefully we’ll see more positive science communication that will bring about effective policy change and community interactions in the months to come.