Biological Venn diagrams: Where do math and biology intersect?

Posted on December 20, 2016 by Briana K. Whitaker

Think back to some of the core materials you learned from a biology course, either in college or high school. What do you remember? Maybe you remember something about human anatomy, or the carbon cycle, the structure of cells, or how DNA is replicated? But do you ever immediately think about how math and biology overlap? Mathematical tools and concepts are used by a large number of biological scientists, but the connection between math and biology isn’t always visible.

For example, in my work, I use statistics to test hypotheses about how species interact in nature, and I have used computer-programming tools to analyze genetic sequences from the microbial species I study as part of my research. But what kinds of tools do other biologists use? Below is a brief survey of IU biology professors who merge biology with math in a lot of surprising ways. How can we use computers to help solve the mysteries of fruit flies and use mathematical models to simulate chopping down a forest? Find out below! (more…)

Branching out with interdisciplinary science

Posted on December 13, 2016 by Ed Basom

A theoretical chemist and a biochemist walk into a bar. They both speak the same language, yet it’s difficult for them to have a conversation about each other’s research. They’re both intelligent, educated scientists who have at least a basic understanding of the other’s field, so what’s the problem?

The first post from the ScIU blog asked the question: what is science really? The answer: it’s broad and complicated, but science can roughly be separated into “basic” and “applied” sciences, and both encompass many disciplines, such as chemistry, astronomy, and psychology.

A illustration shows the words "biochemistry" and "theoretical chemistry" separated by walls, but arrows pointing from the words over the walls lead to "something new". — By catapulting over the walls of jargon which complicate scientific collaboration, exciting new ideas can be formed.

But even these disciplines themselves are quite broad. For example, there are numerous subdivisions under the field of “chemistry”. While some chemists specialize in creating novel molecules (synthetic chemists), others pursue challenges in biologically relevant chemistry (biochemists), and still others use computational models to study the fundamental forces that explain chemical interactions (theoretical chemists). There are many other sub-disciplines (which are disciplines in their own right) under the “chemistry” umbrella as well, each with their own particular ensemble of jargon.

Each of these disciplines brings a unique perspective to the broader scientific community, but it is sometimes challenging for one researcher to discuss the impact of their work with someone from a different discipline. Hence, the theoretical chemist and biochemist may have communication difficulties unless they carefully rephrase their language and avoid discipline-specific jargon. Working to make their research accessible to a broader audience is one way in which communication between colleagues in different fields can also be improved. (more…)

Hands, tools, and words, oh my!

Posted on December 6, 2016 by Lana Ruck

It is relatively easy to list things that make our species, Homo sapiens, unique. From modest biological traits like hairless bodies and walking on two feet, to amazing things like culture, technology, and language, it is quite clear that we became some pretty quirky animals over the course of our evolution. Exactly how and why our lineage became ‘human’ is a much more difficult matter to investigate, especially when we consider some of the more complex behaviors on our list.

A hand holding a triangular stone tool, which was made millions of years ago. — Caption: “Hand axe” by serious but unabashed is licensed under CC BY 2.0

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Fuel for the future: The evolving process of making hydrogen

Posted on November 29, 2016 by Josey E. Topolski

Hydrogen gas (H₂), which is currently used in world-wide production of ammonia, is also being considered as an alternative fuel. But how is hydrogen gas made? Carbon monoxide (CO) and water (H₂O) can be combined to form hydrogen gas (H₂) and carbon dioxide (CO₂) in a process known as the water-gas shift reaction. The water-gas shift reaction is one of our primary sources of hydrogen. Several other processes of producing hydrogen exist and are being developed, such as electrolysis, direct solar water splitting, and microbial biomass conversion.

For efficient production of hydrogen using the water-gas shift reaction, a catalyst is necessary. A catalyst is a substance that will increase the rate of the reaction. For example, the catalytic converters in cars use platinum in order to catalyze the conversion of carbon monoxide to carbon dioxide. Scientists have developed catalysts for the water-gas shift reaction containing a range of metals such as iron, platinum, gold, copper, and nickel. More recently, (more…)

Harnessing the therapeutic benefits of marijuana: Research findings from Dr. Andrea Hohmann’s laboratory at Indiana University presented at international neuroscience conference

Posted on November 23, 2016 by Rachel Skipper

Last week, over 32,000 neuroscientists met in San Diego for the annual Society for Neuroscience (SfN) conference. Joining them were members of IU’s Program in Neuroscience, including Dr. Andrea Hohmann, who is also a professor in the Department of Psychological and Brain Sciences in the College of Arts in Sciences and a Linda and Jack Gill Chair of Neuroscience in the Gill Center for Biomolecular Science.

Scientific conferences like SfN bring together scientists from all over the world to discuss their findings. Researchers attend SfN to discuss a wide variety of topics related to brain function and mental health. At the conference, Dr. Hohmann met not only with her colleagues, but also members of the press, who were interested in her lab’s research on the neurochemistry of pain. She described how the endocannabinoid system, a complex network of cells and receptors in the brain, is involved in pain perception and may be a useful target for pain relief drugs. The endocannabinoid system is currently a hot topic in neuroscience, partly because receptors in this system are targeted by THC, the psychoactive ingredient in marijuana and other synthetic marijuana-like compounds. When THC and other synthetic cannabinoids reach the brain, they act on cannabinoid receptors to elicit both psychoactive and pain-relieving effects. Marijuana is currently being considered for legalization in the US. (more…)

Math on a clock: Exploration in mathematics

Posted on November 22, 2016 by Steve Hussung

I want to give you a sense of what it’s like doing math “in the wild”. Doing mathematics is not just about learning what other people have already done: it’s about exploring and playing around with a system to figure out what’s going on. Let’s give it a go!

We are all familiar with the 12 hour system for counting time on a clock. The numbers count each digit from 1 to 12 and then circle back to 1. Since 12 is the number just before 1, we can think of 12 just like 0. We will ignore AM/PM for all of this.

One of IU's red clocks, surrounded by red flowers. The picture was taken on campus. — One of IU’s red clocks.

We don’t usually talk about it this way, but we could say that adding 2 and 3 o’clock gives 5, in that 5 o’clock is 2 hours after 3, or 3 hours after 2.

We can ask what 7 + 7 would be. The answer is 14, but this is the same as 2, since 12 is a whole circle around the clock. That is, since 12 is the same as 0.

The next few examples are a little more complicated. Math is a much more interesting subject if you interact with it. It’s rare to find a mathematician reading without something to write on. Find a pencil and paper if you don’t have them around already. (more…)

Catching brainwaves

Posted on November 15, 2016 by Noah Zarr

Graduate students prepare an eeg cap resembling a shower cap exuding wires. — Graduate student Nancy Lundin sets up on EEG cap on fellow graduate student John Purcell.

If your family is anything like mine, you have that one crazy uncle with his tin foil hat, purportedly to prevent the aliens from electromagnetically manipulating his brain or to prevent his precious brain waves from being read by the government. While few take such fears seriously, significant confusion persists regarding ‘brain waves.’ What are they and where do they come from? Can they be picked up and decoded like radio signals, perhaps even useful for telepathy (or alien-monitoring of your thoughts)? (more…)

Proactively combating the continuing threat of pesticide resistance

Posted on November 8, 2016 by Mark Juers

A researcher sits at a workbench surrounded by many dozens of small weigh boats. — Research associate Dylan Siniard carefully setting up but one batch of dozens of experimental units in his pesticide resistance assays.

Consider briefly the process of evolution and you might imagine a lumbering process, splitting lineages and bringing new species forth from old, or the gradual formation of morphological novelties like wings. While it’s true that evolutionary processes such as the formation of new species are generally slow by our standards, other effects of evolution that cannot be seen with the naked eye (but are no less important) can often develop over the course of a human lifetime.

In only a few decades, we have seen the proliferation of pesticide-resistant strains of a number of important crop pests through the differential reproduction of individuals bearing molecular traits that allow them to avoid succumbing to pesticides. Organisms, in this case crop pests, have some variable number of offspring each generation that can survive and reproduce themselves. If a lineage of crop pests has a greater number of viable offspring because it is better able to withstand the pesticides that killed other insects, its descendants will come to represent a larger portion of the population. The population of pests will then have, in aggregate, more of the attributes of the successful lineages, including those that lent increased reproductive success–in this case, pesticide resistance. This is the essence of evolution by natural selection. (more…)

Measuring the mass of Goldilocks molecules: not too big, but not too small

Posted on November 1, 2016 by Benjamin E. Draper

Line graph showing peaks at ~3.8 and 5 megadaltons for the mass of the virus capsid — Figure 1. Mass spectrum obtained using Charge Detection Mass Spectrometry showing the relative amounts of empty, filled, and partially filled viruses from a gene therapy sample. Here the bottom axis shows the mass of the virus in megadaltons, which are very small units (for scale, one megadalton is equivalent to the mass of one million hydrogen atoms). Interestingly, CDMS discovered partially filled capsids in the 3.5-4.0 MDa range that are not readily detectable by other techniques. [1]

Finding out how much you weigh is simple–just step on a scale and see the answer within seconds. Weighing ourselves is easy, but how do we weigh the microscopic things in our world that are too small to see? By using mass spectrometry.

Mass spectrometry has been around since the early 20th century, and researchers have gotten very good at measuring the small atoms and molecules that make up our world. Mass spectrometers work by adding a charge to a molecule or atom of interest and then using sophisticated electric fields to accelerate that charged molecule. Because the moving particle’s energy depends on its mass, measurements of the energy allow researchers to deduce that mass. Mass spectrometry works well for atoms and small molecules, but what about biological complexes–like viruses–which are still small, but have masses millions of times larger than a single hydrogen atom? (more…)

An event like no other: Science Fest 2016

Posted on October 20, 2016 by Briana K. Whitaker

A child, 10-12 years of age, is surrounded by the inner components of a computer, while a volunteer stands by watching. — A young student gets his hands on the inner workings of a computer, while a volunteer stands by.

You’d have to wonder what could bring close to 600 students, faculty, staff, and parent volunteers to the IU campus on a Saturday morning. They could instead be home mowing the lawn, enjoying a nice stack of pancakes at the Runcible Spoon, or sleeping in…..but no. This team of people is on a mission to guide young children and their families to a better understanding of the natural world using inquiry and hands-on discovery. For this reason, they wake up early and head to IU on a Saturday morning. (more…)