Tag Archives: research

Moments in Research: A Poster Series

I love poster design. I love decorating my house with See America and WPA posters; I love designing posters about my passions. I haven’t posted any science designs because I find science hard to illustrate. I see lots of designs with beakers and test tubes, atoms, lab coats, and petri dishes. The challenge is that these are the tools of science, but they aren’t what makes science exciting. Science occurs between the ears, and the standards symbols are just tools of the craft. But how do you make posters of people thinking? Even the WPA posters promoting math-related careers are pretty listless, and that is a series of posters that used dinosaurs to promote syphilis treatment.

It occurred to me that the unifying thread of scientific inquiry are the highs, lows, and puzzlements of research. My friends in mechanical engineering have little need for beakers or lab coats, while my friends in biology aren’t (usually) immersed in coding. Different disciplines use different tools, but every discipline knows the elation of a published paper or the frustration of explaining what the heck it is you research to granny.

So, this inspiration broke my science poster designer’s block. I have three designs, but ideas for many more. For the style, I was inspired by World War I illustrator Lucien Laforge. There will be more, but I’m pleased with the start!

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Turing Patterns: What do a leopard’s spots, vegetation in arid zones, and the formation of fingers have in common?

Please excuse my inconsistent posting of late, I have been deep down the rabbit hole of science. Last week, I attended the Society of Industrial and Applied Math (SIAM) dynamical systems conference. What fun!

I learned about Turing Patterns, named for mathematician Alan Turing. Complex patterns can arise from the balance between the diffusion of chemicals and the reaction of those chemicals. For this reason, Turing’s model is also called the Reaction-Diffusion model. In general, these kinds of patterns can arise when there’s some kind of competition.

This sounds abstract, but suspected examples in nature abound. Have you ever wondered how the leopard got his spots or what’s behind the patterns on seashells? We often don’t know the chemical mechanisms that produce the patterns, but we can mathematically reproduce them with generic models.

Image from wired.com discussion of Turing patterns.

Mary Silber and her grad student Karna Gowda presented research on Turing patterns in the vegetation of arid regions. When there isn’t enough precipitation to support uniform vegetation, what vegetation will you observe? If there’s too little water, their model yields a vegetation-free desert. Between “not enough” and “plenty” the model generates patterns, from spots to labyrinths to gaps. Their work expands at least two decades worth of study of Turing patterns in vegetation.

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Figure by Karna Gowda, see the full article at SIAM news.

Silber and Gowda considered an area in the Horn of Africa (the bit that juts east below the Middle East). Here, stable patterns in the vegetation have been documented since the 1950s. They wanted to know how the patterns have changed with time. Have the wavelengths between vegetation bands changed? Are there signs of distress due to climate change? By comparing pictures taken by the RAF in the 1950s to recent satellite images, they found that the pattern were remarkably stable. The bands slowly travelled uphill, but they had the same wavelength and the same pattern. They only observed damage in areas with lots of new roads.

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From google maps of the Horn of Africa! I screen-capped this from here.

Turing patterns have even been studied experimentally in zebrafish. Zebrafish stripes might appear stationary, but they will slowly change in response to perturbations. So scientists did just. Below is a figure from the paper. The left shows the pattern on the zebrafish, the right shows the predictions of the model.

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Experimental perturbations to the patterns of zebrafish are well-predicted by the Turing model. Read more in this excellent Science paper.

The model has been used to explain the distribution of feather buds in chicks and hair follicles in mice. Turing’s equations have even been used to explain how fingers form.

If you want to learn more, the links above are a great start. And if you want to play with the patterns yourself, check out this super fun interactive. These waves aren’t stationary like the Turing patterns I described here, but they arise from similar mathematics. The interactive can make your computer work, fyi.

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Reaction-diffusion pattern I generated with this online interactive. It’s super fun!

The FODMAP Diet: An IBS diet based upon peer-reviewed science

I’m extremely lactose intolerant. What this means, biologically, is that I no longer produce enough lactase to process lactose sugar. Because I can’t process lactose in my small intestine, it moves on intact to my large intestine where bacteria eat the sugar. The byproduct of their digestion, gas, causes bloating, pain, cramping and, well, you know the rest.

What is IBS and what causes it?

Irritable Bowel Syndrome (IBS) is an incredibly common malady, affecting 6-46% of the population, depending upon the study. It’s a diagnosis resulting from the lack of a diagnosis; it’s diarrhea, bloating, stomach pain, and cramping that can’t be explained by celiac disease, lactose intolerance, fructose intolerance, or other understood gut disorders.

IBS is thought to be caused by visceral hypersensitivity, or over-sensitivity to pressure on the intestines. Imagine two people eat broccoli and get a bit gassy: the person with IBS would feel pain and discomfort while the other person might be bloated but otherwise fine.

It’s often implied that IBS is psychological as much as physiological. Anxiety and depression are common in people with IBS. In my experience, the perceived psychological component, the lack of simple treatments, and the lack of life-threatening consequences can lead doctors to be blasé about IBS. They recommend fiber, exercise, and routine, and shrug if that does little. Small wonder that people might feel blue. But gut science is improving, and the FODMAP approach is a new and widely successful strategy for reducing the symptoms of IBS.

What is the FODMAP approach, and what is different about it?

The FODMAP diet is based upon known biochemistry and the hypothesis that visceral hypersensitivity causes IBS. There are many molecules that, like my undigested lactose, tend to be digested in the large intestine and produce gas. The FODMAP diet eliminates a wide range of such molecules.

FODMAP, introduced in 2005 by Monash University, is a peer-reviewed diet based upon a concrete biological hypothesis supported and improved by scientific trials. It is not a weight-loss diet. FODMAP stands for Fermentable Oligo- Di- and Mono- Saccharides And Polyols. Catchy, right? But the concept is simple—FODMAPs are short-chain sugars that we know most people digest poorly (meaning bacteria digest them), and you avoid FODMAPs on the FODMAP diet. (For the biochemists, that means avoiding fructans (oligosaccharide), lactose (disaccharide), fructose (monosaccharide), and all sugar alcohols such sorbitol (polyols).)

Many other diets have questionable scientific bases and are profit driven. The Atkins Diet was published by a cardiologist who never published any peer-reviewed work, but several books. The Paleo Diet was published by an “exercise scientist untrained in paleobiology”. This is not to say that these diets cannot be beneficial in any way. But they have not been tested and refined in the way the FODMAP diet has been, and their fundamental science is hazier. Putting the cart before the horse, they have been developed first for profit, and then researched afterwards, often with mixed results. To be fair, the scientific process is slow and contentious and doesn’t always lend itself well to studies as broad and complex as diet. But FODMAP was developed, tested, and improved using the scientific process. If you’re skeptical of diets, as I am, you can read up and convince yourself that this diet has a reasonable basis and good results.

What’s a FODMAP diet like?

If you are considering a FODMAP diet, you will have to do some research, and be able to prepare food often from scratch. The internet is a phenomenal tool, and there are even some dieticians you can consult online. FODMAP sensitivity is not the same thing as an allergy. You don’t have to absolutely eliminate FODMAP foods, you simply must aim to minimize them for a period of time.

To follow the FODMAP diet, you avoid FODMAP-laden foods for two weeks to two months (different sources vary in their recommendations, and provide rationales). After this time, you re-introduce foods in a controlled manner to identify trigger foods. Most IBS-sufferers are not sensitive to all FODMAPs. Many people report benefits within a few days of starting the diet, and 70% of IBS patients in peer-reviewed studies reported improvements following the diet. I personally had much less bloating within a few days. Following a FODMAP diet revealed that some of my symptoms are due to gastritis, which I’m now treating. I see now that I’ve had gastritis symptoms for a while, but I was unable to separate various gastrointestinal symptoms before this diet. I remain on the full FODMAP diet after three months, but I have eliminated one side issue.

What foods are and aren’t allowed?

Following the most basic level of the FODMAP diet, one avoids all garlic, onion, and gluten-containing foods. It is not a gluten-free diet, but grains containing gluten overlap almost perfectly with grains containing the FODMAP fructan. Beer happily is the major exception; it is FODMAP-free due to the fermentation process.

I consider the FODMAP approach an alternative way of categorizing foods. There is a common perception that vegetables and fruit are healthful, and grains and meat are less healthful. At least from the perspective of IBS, that is not a useful framework. On the FODMAP diet, meats are okay. Roughly half of grains, dairy, vegetables and fruit contain FODMAPs, and these are avoided on the diet. Specifically, greens and squash are okay, but broccoli, leeks, and  brussels sprouts aren’t. Citrus and melon are okay, but peaches, cherries, and figs aren’t. Lactose-free milk and hard cheeses are okay, and ice cream, fresh cheeses, and sour cream aren’t.

For those considering the diet, this is my favorite exhaustive list of allowed and disallowed foods.

TL;DR

In short, the FODMAP diet requires research and it’s a pain to follow, but it offers real promise to the numerous people suffering from IBS. If you’re considering the diet yourself, good luck. I hope this provided a better explanation of the topic than the sources I encountered when trying to understand this diet. To others, maybe this will help explain why your friend has such a fiddly diet, and why you should support them.

What is an engineering PhD?

Sorry I have fallen way off of schedule. Since my last posting, my husband defended and graduated with his PhD, and we visited out new city and bought our first house. So it’s been extremely exciting and hectic.

But I promised to write about what a PhD is, and so I shall. During  our seven years of graduate study, I’ve encountered a lot of confusion about what a PhD in science and engineering is. Getting a PhD is really really different from other forms of graduate education, such as law, business, and medical school. A PhD in fields like English can vary some from the science experience I describe here, but pursuing a PhD in English is more similar to pursuing a PhD in Physics than it is to law school.

Why you never ask a PhD student when they will graduate

Law school takes 3 years. Med school takes 4 years. A PhD takes ???? years. In science and engineering, it takes about 4-7 years, depending upon whether you go in with a masters, how hard you work, who your advisor is, and luck. Very little of the timing is directly within your control.

When you start with your bachelor’s degree, the first year focuses mostly on classes, the second year is a balance between classes and research, and most of the time after the second year is totally devoted to research. (A student starting with a master’s degree gets to skip most of the classwork.) In science and engineering, you might TA (teaching assist) for a semester or two. In other fields like Spanish and English, you might teach every semester. For them, this is often a good thing since teaching comprises a lot of their post-graduate opportunities. Teaching also pays the bills.

There are three big hurdles in grad school: qualifying exams, proposing your dissertation, and finishing your dissertation. Qualifying exams vary by school and department. If you fail your qualifiers, you won’t get your PhD. Many people who fail their qualifiers leave with a masters. Some departments have terribly difficult qualifiers, others don’t.

Your dissertation tells the story of your research. It describes experimental and mathematical techniques, the state of the field, shows results, and talks about future research possibilities. A dissertation is typically 100-300 pages, depending upon your field. You and your advisor work together to develop a central narrative to your dissertation. A PhD student must propose this avenue of exploration to their proposal committee, a panel of five professors, in a formal presentation. The professors give their feedback and criticisms on the proposed work. They may reject the proposal.

A PhD student graduates when they successfully defend their dissertation. But typically it’s writing the dissertation that is the hardest part after a successful proposal. It takes a long time to write 200 pages, and your advisor will expect a lot of things out of the document. You may also be expected to publish peer-reviewed papers. You can incorporate these papers into your dissertation, but the papers alone don’t count toward the dissertation directly. Papers are even harder to write than dissertation chapters. Papers may involve collaborations with researchers on other continents with other native languages and time zones.

All of the above is why a PhD student’s graduation date is hazy. So don’t ask a PhD student when they will graduate—they are wondering the same thing!

PhD students get paid

Unlike other types of grad school, you get paid to study towards a PhD. The teaching and research you do pay your tuition and salary. Your salary is never a lot, but unlike other post-graduate educations, you earn rather than pay. Depending upon the school and your area of study, a grad student earns between $15k-30k a year. You sometimes get benefits like health insurance as well (this might be universal now).

Your advisor: the master of your grad school experience

Every graduate student has an advisor. An advisor is the professor that funds you and your research project. Your advisor is the most important person in your grad school experience. Your advisor pays your salary and tuition, determines the area of your research topic, and influences your connections within your field.

An advisor can make your life miserable. If they run out of funding, you might have to teach more. They can slow your graduation. They are more than just a boss; they control your access to your doctoral degree. If you are five years into your PhD, you can’t do much if your advisor jerks you around short of quitting sans degree. And you may have noticed that professors are sometimes difficult people. Most grad students can name the difficult professors in their department.

Research

This simple cartoon explains the significance of your research in grad school. Your research is why you get paid to go to grad school. Your research could address industrial issues or basic science. Your advisor gets money based upon the kind of research he promises to do. In grad school, you produce research output, but more importantly, you learn how to do research. You learn how to solve problems and learn to identify interesting questions.

I would argue that you also learn patience. As an undergraduate student, few tasks take more than a week. The longest tasks take is a semester. You can get help from other students or professors in many cases. If you phone it in, perhaps you’ll get a lower grade, but the task goes away. Your research in grad school is a multi-year problem solving exercise. No one in the world may know the answer to your problem. Few people in the world may even understand the significance of your problem. You can try to go in a different direction, but at some point, you will bang your head against a problem for months. You learn an appreciation for what advancing human knowledge entails. And you advance human knowledge. This may damage your ability to speak English with everyone else.

Why get a PhD?

Because you are curious. Because the type of work described above appeals to you. Don’t start a PhD because you don’t know what to do next, or because you want to make more money. A PhD in science and engineering will get you a decent paying job, but you will deal with a ton of frustration and low-income years. Law school or business school are way faster, and engineers with these skills are valuable.

I started my PhD because it seemed like an interesting thing to do next. Like a lot of students, I found the middle of the process very discouraging. School seemed like it would never end, and I didn’t know what I would do after school. But I still liked my research. I still woke up thinking of ideas of things I could do. I felt more capable as a person with the skills I was developing in grad school. Grad school will feel aimless at some point for most; it’s your innate passion that helps bridge the gap and get you to the end.

The fun stuff

Grad school can also be a lot of fun. Other members of your research group help you learn and help you cope with setbacks. Your fellow prisoners well understand your challenges. Many schools have vibrant grad student communities apart from the undergraduate communities, in which you will meet grad students studying crazy and amazing things. Almost any eccentric nerding that you enjoy will be enjoyed by some other grad student. You’re all old enough to drink at bars, and most college towns will have some fun ones. Grad students get into their beer and drinks and most long-standing grad students can tell you a lot about them. Many grad students learn to be great cooks. The resources available for the undergraduates, such as gyms, sporting events, and social clubs, are still available to you as a grad student. While you’re pulling your hair our trying to get your degree, you will be in the middle of a community with some fun distractions when you need them and some really fun peers.

Hopefully that’s a useful summary of the PhD school experience, and not rendered too incoherent by my own state of disorganization. I’m happy to provide further info to those with questions as well!

Science communication

Science communication is hard, but it’s something scientists should always be striving to improve.

Specifically, we often see the difficulty in communication between scientists and the general public. The concepts discussed are often complex and not fully settled. Scientists often use jargon or scientific methods of communication that don’t translate to the public well. The final result is that scientists and the public don’t understand one another as well as they might, which is a loss for all of us.

On Friday I went to a science communication workshop run by The American Association for the Advancement of Science (or AAAS) to learn about science communication. The AAAS tries to help scientists communicate in all ways–such as with policy makers, with other scientists, and with members of the public. They outlined three points of emphasis to improve communication. We then practiced talking about our research following these guidelines (perhaps I’ll post my spiel in some future post).

  • Communication structure: Scientific papers first provide the background material before stating the outcomes or results of a paper. Popular writing starts with the results and then provides the supporting arguments. In discourse with the public, scientists must follow the conventions the public uses.
  • Audience: A scientist must understand the communication’s audience. Jargon may work within the field, but even scientists from nearby disciplines probably won’t know it. The general public or children definitely won’t.
  • Message: A brief talk or article cannot communicate an entire field. It must communicate two or three salient points. It can be tempting to explain everything to an interested member of the public, but it simply isn’t possible.

In particular, I think the public might be surprised to learn of the difficulties different scientists have in communication. I recently earned my PhD in chemical engineering. When I was writing my final dissertation, I asked my father for help with editing. He has a PhD in chemical engineering as well, and works on advanced data management. It might seem strange, but he struggles to understand my work, and I struggle to understand his. With effort, I made the more general parts of my dissertation accessible to him, but the truly technical parts would have taken him much longer to understand. This graphic of what a PhD is partially illustrates the nature of this problem.

The difficulty two people with the same kind of PhD face in communication highlights the need for us to discuss science communication. As I initially said, science communication is hard. But many important problems today have a scientific aspect or could be examined in a scientific way. As scientists learn to articulate their concerns and findings better, that paves the way for better discourse with the public.

Science is Creative!

In the US, science is regarded as valuable, but dry and a bit stiff. As a student, it’s easy to get this impression, studying rigid facts first explored centuries ago. The math, chemistry, physics, and biology we learn in high school and college are about recreating long-known answers by well-established methods. But the process of making new science and math is inherently creative, and new ideas require letting the mind run wild a little. In this post, I’ll talk about how I develop my ideas.

I work with populations of oscillators. The idea of this research is that the complexity of the whole (the population) exceeds the complexity of each element (the oscillator). The human brain is a good example of such a system–each neuron is fairly simple and well-understood, but overall brain behavior arising from the interactions of many neurons is not understood. My research tends to work by observation–I notice something I find interesting and I explore that further. Other researchers work on what they suspect they will find, based upon other work. All research works within the context of its field. There are many interesting behaviors I have noted in my experiments, but I explore the ones I might explain. Really random observations are cool, but hard to frame in a way which is meaningful to the community.

The above may not sound particularly creative. But the key to experiments like I do is imagining what might happen when one explores slightly beyond what is known. It requires extrapolating from the areas we know, in the context of the rules we know, to the areas we don’t know. Some of the rules we know are pretty absolute, like thermodynamics, but others may be flexible. (As a note on this point, the stable chemical oscillations I study were once considered thermodynamically impossible. Someone had to bend the established understanding of thermodynamics to explain these oscillations. Einstein had to bend Newton’s Laws for relativity, and he arrived at that conclusion by logic rather than by observation.) In an experimental apparatus like mine, thousands of experiments are possible. It is up to the experimentalist to pick from the possibilities, in the context of what might work in his imagination, to demonstrate something hitherto unknown.

In some ways, the process is similar to writing. There are rules that must be obeyed, and the process of finding something new or interesting is very indirect. With science and writing, I develop some of my best ideas drinking a beer or taking a walk. Sitting at a desk focusing is required at times, but so too is active contemplation. The rules of science are broader and more rigid and take longer to learn, but there are similarities.

A lot of historical scientists were fascinating people, akin to historical artists. Van Gogh got his ear cut off in a fight. Astronomer Tycho Brahe lost his nose in a duel. Salvador Dali shellacked his hair. Electrical engineer Nikola Tesla fell in love with a pigeon. Mathematician Paul Erdos lived itinerantly for decades. In one visit to a colleague, he couldn’t figure out how to open a carton of juice, so he instead stabbed it open (among many, many other oddities). Physicist Richard Feynman used to work on his physics at strip clubs. Artists may share their eccentricities more in their works, but I would argue that scientists have every bit as much oddness.

I hope this post illustrates a little what it is like to be a research scientist, and how science at the cutting edge works. For more science posts, check out my fun science list.

Fun Science: Gravitational waves

Gravitational waves were first predicted in 1916 by Einstein’s general theory of relativity; today we are trying to directly observe them. A gravitational wave is a tiny oscillation in the fabric of space-time that travels at the speed of light; all other findings from general relativity predict its existence. Many objects will create minuscule gravitational waves, and even the largest objects create ones we just barely hope to see (such as binary stars and black holes). From the LIGO wikipedia page “gravitational waves that originate tens of millions of light years from Earth are expected to distort the 4 kilometer mirror spacing by about 10−18 m, less than one-thousandth the charge diameter of a proton.”

What would we gain from this? Astronomers believe that gravitational waves could eventually become another mode of imaging by which to analyze the universe, like gamma ray, x-ray, and infrared imaging.

Example of gravitational wave distortions (from wikipedia)

The LIGO (Laser interferometer gravitational-wave observatory) ran from 2002 to 2010; it was unsuccessful in its hunt for gravitational waves. It is being recalibrated to restart in 2014. The two observatories in Louisiana and Richland, Washington record the same events and compare the time at which they arrive. Below is a schematic of this set-up. LISA, the laser interferometer space array, has been discussed for years as an orbiting detector with greater length scales (and therefore greater accuracy) than LIGO; a proof-of-concept is due for launch in 2014.

Laser interferometer set-up (wikipedia)

If you want to learn more, Einstein Online, which is run by the Max Planck Institute, is a great resource (the Max Planck Institute is involved in great cutting edge research, perhaps comparable to NASA). The above link is for info on gravitational waves, but there is also great info on other concepts related to relativity if you are interested.