The Basic Science Research Concept

“So are you trying to make plants more defended?”

This is often the first question I encounter when I share my research questions with anyone that does not spend their work life thinking about plants. Before the conversation can get much further, I find it helps to introduce the difference between basic science research and applied research.

Both are important, but it is easier for people to connect with applied research: research designed to improve the way humans live. However, many of the solutions we use today came as a result of discoveries from basic science research: research designed to understand the way something works for the sake of understanding.

Like what?

PCR: the technology that lets us duplicate tiny amounts of DNA, was only possible because a scientist was curious about how acidic and hot Yellowstone hot springs could be for bacteria to survive. Bacteria flourishing at high temperatures have DNA too, and the enzymes that could replicate DNA despite the heat were eventually extracted and were able to withstand the hot temperatures in PCR.

Efficient building design: scientists were curious about the structure of termite mounds, which can maintain a constant temperature despite the heat of the desert. The results from these studies were used to construct a building in Zimbabwe (The Eastgate Centre) that uses 90% less energy.

Velcro, the ubiquitous adhesive found on light-up shoes, was inspired by plant hook-shaped hairs.

And the list goes on. The moral of the story is that technology gets along well with natural selection, but first we have to understand how it all works.

My research goal is to understand how plant-insect interactions change as a result of the chemistry within the plants that have a symbiotic relationship with nitrogen-fixing bacteria. I spend my time at my desk wondering about how and when plants will use their resources to make the stuff that protect them- either directly by making poisonous chemicals, or indirectly, by sending volatile compounds into the air to communicate with the predators of their attackers.

Instead of trying to get plants to do anything, my goal is to understand what they actually do on their own- to understand the unknown aspects of their biology.

Do these bacteria play an important role in the food web by altering plant-insect interactions? My research will let you know.

The Front of the Train

One major goal in science education is to teach students how to think like a scientist. In many cases, this means teaching science the way we do science, which is often through inquiry and research. But before students can strike out in the lab on their own with a pipette and a new question to answer, they need to learn the foundational information that came from research before them.

I like to think of this challenge using a visual from Zen and the Art of Motorcycle Maintenance. The front of a train represents the interface between the past experiences we carry with us and the unknown track ahead. Even while being hung up on a past memory or anxious about what may come, the front of the train is what we continually witness: here and now, moving through time.

Science research is also the front of the train, where discovery happens. The challenge in science education is starting at the back of the train and working forwards to cover all of where we have been (which is usually presented in textbook format), in order to get students to the front of the train, asking their own questions and making their own connections.

However, covering the entire textbook before getting to the inquiry and connecting part creates a problem: we are training students to passively ride along like a train car as we move forward in what we know, until suddenly, students make it to the front and come up against what we do not yet know. If students have not practiced asking questions or thinking about how to figure out the next step, when they do conduct research, they are not prepared to discuss it.

A true discussion explains how this new piece of information fits into our understanding of the world—how the shape of our overall understanding changes with this new dimension. To connect new observations to the big picture requires not only extensive background knowledge on the subject, but also creativity. Drawing lines that never existed or imagining a differently-shaped perspective are essential skills in science.

I watched this happen as a high school student I was mentoring in research presented her work to her high school. She was able to introduce complicated biology topics: plant secondary metabolism and symbiosis with nitrogen-fixing bacteria, describe what she did in the lab, and even interpret a few graphs. But then she pulled up a slide titled “discussion” and she listed potential sources of error, including the size of the pots, and even “human error” in her count data. I was baffled by this until a colleague reminded me that the science most students do in school has a known outcome, and if data do not match that outcome, students are trained to explain why not by citing sources of error that caused results to stray from what they were supposed to find.

This is an important paradigm shift. A well-designed, controlled experiment does not have sources of error because the result is not yet known. So how should students discuss and interpret unknown results?

A true discussion explains how this new piece of information fits into our understanding of the world—how the shape of our overall understanding changes with this new dimension. To connect new observations to the big picture requires not only extensive background knowledge on the subject, but also creativity. Drawing lines that never existed or imagining a differently-shaped perspective are essential skills in science.

So how do we teach these skills if we have to cover sufficient background info for students to grasp the current state of science knowledge with enough proficiency to draw new connections? A formal answer to this question is a recipe for grant funding, but I think any educator intuitively knows the secret ingredient:

Learning how to ask questions.

Question confidence is where science progresses- where the massive train of knowledge comes up against the wind at the front. This also explains why many funding agencies highlight the importance of scientists coming from diverse backgrounds: to ask diverse questions, use creativity to draw conclusions and serve as role models for a diverse group of students learning how to gain their own question confidence.

Feel free to offer resources or ideas about how to help more students think like a scientist.

Armed and Delicious.

Go to your spice rack, make a kale smoothie, have a cup of coffee. Just about everything we use to add flavor to our lives comes from a co-evolutionary battle between an herbivore and a plant protecting its leaves.

That bite on your tongue from an arugula salad? The sulfur-containing cyanide molecules you taste are the result of glucosinolates, a characteristic defense of the mustard plant family. Mustard plants—e.g. horseradish, wasabi, mustard—all use this metabolic pathway because the burning sensation, which many people enjoy with oysters, actually works as an effective anti-herbivore toxic defense. When bugs break open cells, the enzyme myrosinase cuts a precursor to release nitriles, isothiocyanates, and other various bioactive toxic compounds. Plants in a population that are slightly more toxic survive the constant herbivore attack better and can pass on their genes to the next generation. Ah, bittersweet natural selection.

How do we know it is the bugs that put the pressure on? This paper (also summarized in a great article here) swapped mustard plants from Colorado and Montana, and found that not only did the unique spice of each plant stay consistent, but bugs preferred the visiting treat—plants that did not adapt to the local suite of herbivores. The difference in plant survival in this case is an example of local adaptation, all starting from bugs preferring the new mustard spice.

Just like these bugs and everything else in nature, we choose what we eat based on the flavors we like and what won’t kill us.

So why do we intentionally eat so many compounds plants use to make feeding difficult? Often these same toxins are essential for nutrition. The darkest green vegetables, pungent garlic, soothing mint—all play a health benefit role because of the energy plants put into making defense compounds. Bioactive toxins in low doses continue to do their toxic, bad-self thing: the alkaloid caffeine in your coffee stimulates the nervous system, the indole-3-carbinole in your kale salad degrades excess hormones that can lead to cancer, and the terpenes in oak barrel-aged wine rich in phenolic tannins can prevent carcinogens from binding to DNA and reduce the risk of harmful blood clots. The underlying theme here is that many toxins are reactive, for better or for worse.

Disclaimer: Some plant defenses are toxic to humans in high concentrations, and some plants are just plain poisonous at any dose. Don’t start eating everything toxic. Instead, appreciate the nutrients plants invest in creating highly reactive compounds in order to protect themselves, as well as the coevolutionary arms race that made plants with these exciting products succeed.

Wings on Fire

I had always dreamed of going to the Amazon. The rainforest was a dream that breathed new life into me the way it breathes oxygen into the planet. As indescribable as the awe that comes from being amongst such biodiversity may be, the rainforest enchanted me in the movement of a toucan awkwardly wielding its beak, and in the flapping of wings on fire in the sunset as the faithful scarlet macaw streaks across the sky in its squeaky calling out to all below. Some moments brought forth vulnerabilities- the surprise of a snake’s delicate flicker of its tongue interrupting our gaze, and some brought forth grace, such as meeting the long-dreaded tarantula and experiencing not fear, but its majesty. Walls of rain sing in the rainforest upon giant sheets of leaves and dance on the surface of the turbid river. There is promise in the sunrise through the canopy mist, and in the sigh of achievement in the last orange glows on emergent branches, awaiting the stars and tree frog songs. I believe in this feeling of awe, and in its power.  Because of this, I live with more connection to the earth, more affinity for discovery, and more passion for sharing this awe with the global community. Dr. Kelly Swing, the director of the research station, quoted an Amazonian tribe leader in a presentation to visiting students, “We only know what we see; we only love what we know; we only care about what we love”. This has become my personal mission statement.

Some days I feel powerless. Numbers can be defeating—statistics on global carbon emissions, deforestation rates, biodiversity loss, increased poverty, inequality in human rights, and school shootings lead me to question whether I can have a positive impact. Science gives me hope; through science more people have a reason to care. My goal is to create research to discover new results, my findings will allow deeper understanding, and through understanding my work will facilitate an affinity for ecology. Through practice I know I have the power to connect as a science instructor and I have the power to connect across cultural boundaries. Of course I am still refining the art of connecting people from many different backgrounds to science, but luckily science inquiry is a task that always brings me joy.

-A

Santa Claus is Comin’ to Town!

In the spirit of Christmas, a time for giving, I find it fascinating that one concept perplexing many scientists is the number of species that help each other. This is called a mutualism in science speak, and is confusing to many scientists because the underlying rules of natural selection (Darwin, 1859) intuitively work against spending energy or valuable resources helping others. Remember, fitness= grow and reproduce (although this kind of fitness is also fun). Any trait involved in spending the currency on an unrelated organism that would otherwise go towards kids theoretically would not last for many generations (because it takes having kids to make a new generation with those traits). But mutualistic traits do last, even when other organisms evolve ways to cheat and take more than they provide, further baffling evolutionary ecologists.

Which is why I think this paper is so cool.

The scientists used a creative strategy to assess how plants deal with the extra loss of sugars without any return of nitrogen when the symbiotic bacteria in their root nodules cheat. The creative part is forcing bacteria to cheat: rhizobia, which take the inaccessible, triple-bonded nitrogen from the air and turn it into a useful, organic molecule for the plant are not able to provide this service when there is no nitrogen in the air! Dr. E. Toby Kiers and her team kicked out all of the nitrogen by flooding chambers with roots and nodules with oxygen, 20% (rhizobia need oxygen too), and argon, 80% – a stable gas that is heavier than nitrogen.

Plants with “cheating” rhizobia on their roots cut off the oxygen supply to those nodules!

This concept of punishing cheaters (aka host sanctioning) to maintain a fitness benefit from the relationship is a huge help in solving the evolutionary questions about two-way beneficial relationships (mutualisms!) in nature.

It’s kind of like how Santa keeps you on your best behavior so you don’t get coal in your stocking.

Merry Christmas (or whatever you celebrate)!

-A

What is plant defense?

Let’s start with plant defense in general. To follow this blog, here are some key things to know:

Plants can’t run away from their attackers. Instead, over evolutionary time, plants have developed secondary metabolism (aka, not photosynthesis- that is primary metabolism) to make toxic, tough, unpalatable, or otherwise unpleasant experiences for the bugs that try to eat the plants (I use the term bug here loosely to include all herbivorous arthropods, fully knowing that technically a true bug belongs to the phylogenetic order Hemiptera). Plant defense is when plants resist being eaten by bugs.

Plant defense has many flavors:

Chemical defense: the toxic and bitter stuff. We like to consume many of these things that plants designed in order to kill their opponents. (Small apology- I will only minimally anthropomorphize plants throughout my blog.)

Mechanical defense: the tough stuff. Usually this comes in the form of thicker and rougher leaves, or leaves covered in trichomes (fancy word for hair, and very effective: picture walking on velcro as an aphid… difficult right?).

Direct defense: the plant makes a toxic or tough compound that deters bugs.

Indirect defense: the plant relies on predators to provide the defensive service. (This is my personal favorite!) Here is how it works: plants under attack send out a cry for help either as a sugar reward or a signal in the air to attract predator bugs (ants, wasps, or spiders) that fill a hit-man role and kill or evict the herbivore from the plant. Badass! Can you attract ants to be your bodyguards? Didn’t think so.

Inducible defense: This is the on/off switch for plant defense. Usually it behooves the plant to use energy defending themselves when herbivores are around, and to save that energy when they are not under attack.

Constitutive defense: Leaving the secondary metabolite lights on all the time, even when there is nobody home (aka no herbivore attack)

That’s all for vocabulary today. I know, plant biology can get pretty crazy exciting. Get ready for the underlying evolutionary tradeoffs and hypotheses explaining why, how, and when plants defend themselves.