Author Archives: Maddie Go

Things that I learned this summer

  1. Science can be slow. And that’s the way it often is. When I started out this summer, I thought I would complete all the 3D modeling needed for my spines within two/three weeks. So when I found myself one month in, still banging my head on the keyboard and trying to figure out how to make the program do what I wanted, I felt incredibly frustrated. I thought that I was the problem, that I was taking too long to learn the material or figure out the software’s ropes. But time and time again, my mentor Jacob reassured me that this is how science goes. A large part of research is spent reading around, absorbing information, and troubleshooting experiments when they don’t work (which they often don’t). And the thing is, the more you tweak and redesign your experiment, the more you learn about your own project, and the better your understanding about your topic becomes. I guess as a newbie, I didn’t really understand the time span involved in doing research. But now I understand that a lot of time is needed in order to produce good work.
  2. Labs can be a community. Back to that point about Jacob reassuring me when I felt frustrated: I feel like the people you’re with in a lab can also make a difference in your own attitude and performance. My mom studied biochem in college, and she once told me this horror story about a lab that was so cutthroat, they wouldn’t allow undergrads to attend meetings because the atmosphere was simply “toxic.” On the other hand, every Patek lab meeting I attended involved listening to the presentations of various lab members while munching on lunch, and were always filled with meaningful feedback and questions sparked from genuine interest. Before BSURF, I imagined research as a mainly solitary activity, where minimal interaction with other human beings occurred. It’s true that majority of the day, everyone in the Patek lab works on their own thing. But there is also a definite sense of community as well. If you have a technical question, you can ask your neighbor about it; if something in your project makes you laugh, you can call everyone over to see. I’m sure not every lab is like this, but now I realize that community and atmosphere is something I greatly appreciate, and that I’ll take into account when figuring out where I want to go in the future.
  3. I’m still not sure what I want to do. Modeling and testing my own spines was a fun challenge, and I loved the way it made me think harder about the way biological structures are shaped in nature. But at the same time, there were also moments when I peered over a graduate student’s shoulder to watch him film the behavior of ants, or watched a visiting high school teacher paint 3D-printed finches for a class, or commented enthusiastically on a popular science video posted in the lab’s casual chatroom.  There are so many ways a person can contribute to science, from research, to education, to communication.  And in research alone, there are different paths you can take, whether you want to study morphology, behavior, both, or something else entirely! I’ve still got a long way to go before figuring out what I truly want to do, and that’s okay. If anything, my experience this summer has shown me that there’s multiple things that can get my mind whirring, which means I have a lot of options to explore. 🙂

A HUGE thank you to the Patek lab for having me this summer, and to Jacob and Dr. Patek specifically for all their guidance and help.   I had a great time!

And of course, thank you very much to the BSURF program for making this eye-opening experience possible!

Throwback to week one…thanks you guys!

(B&W edit by Annika Sharma)

“Why do you do science?”

“To learn stuff…about the world.”

That was the first answer to Dr. Kathleen Donohue’s opening seminar question, given by yours truly. A soft round of chuckles rippled backwards through the seats of the classroom and I lowered my hand sheepishly. Okay, not my most eloquent response given that it was early morning (aka 9am) and I was still processing the much-needed sugar provided by some granola bars.  But still, that was basically the summary of the excited pull I felt in my gut when considering Dr. Donohue’s question. After all, learning new things about the world around us constitutes the very core of science, right?

However, as Dr. Donohue called on other BSURFers, people began giving answers like, “to find cures” or “to solve x problem in society.” Oops. I mean, those are really important too, but I’d be lying if I said they were the first things that came to mind. I felt slightly ashamed. Was I being selfish and, more importantly, impractical with my intentions in research?

It turns out, at a recent convention Dr. Donohue had asked several hundred evolutionary biologists the same question…and many of them had sided with pure curiosity. Dr. Donohue explained that whether you are in basic or applied sciences, it is vital to have the desire to learn things for the sake of learning things, because this is what motivates scientists on a daily basis. “You could be searching for the cure for cancer,” she said, but you’re not going to find it in a single day. Your curiosity and investment in your current tasks, even if what they reveal isn’t the game-changing discovery you ultimately hope to make, is what will carry you in the long run. In other words, pure curiosity is what sustains people who can work years and years on something, and then finally come up for a solution to an important problem. When I heard Dr. Donohue’s words, my shoulders relaxed in relief, and I felt a glimmer of happiness and hope. So I wasn’t going crazy: doing science simply to learn things about the world wasn’t such a bad thing.

However, Dr. Donohue also reminded us of the reality that, while curiosity may motivate scientists, practical applications are what interest most of society—including many funding organizations. So it’s really important to be able to communicate the value of your work to non-scientist contacts. That’s when Dr. Donohue said something that struck me: “whomever you are talking to is perfectly capable of understanding you, if you are perfectly capable of communicating to them.” Communicating science needs to be a dialogue: you need to know what the other party cares about, what they already know (or think they know), what their concerns are, and more. If you know this, you’ll know what to say and do in order to engage them in your work. This was good food for thought for me, because I’m interested in communicating science to the public but am sometimes unsure how to go about it. Understanding where the other party is coming from, and integrating these insights into how I explain science, is a tactic I’ll be keeping in the forefront of my mind from now on.

I know a major aspect of these faculty seminars is learning about each scientist’s specific research topics. But honestly, I think that Dr. Donohue’s more general discussion about the nature of scientific research and communication made one of the strongest impacts on me. It didn’t just reassure me that curiosity still plays a key role in driving science forward, but also acknowledged that the desire for practical solutions cannot be ignored and must also be satisfied. I think a good scientist has to be able to balance both of those motivations when doing research, and I hope that’s what I’ll be able to do in the future.

Abstract Draft

The effect of serration angle on spine puncture mechanics

Spines, defined as rigid biological structures that come to a point, are physical features found across a wide range of organisms; however general relationships between spine structure and function remain unclear. This study explores a specific aspect of the form-function relationship of spines, by investigating the influence of serration angle on spine puncture mechanics. Autodesk Fusion 360 was used to 3D-model spines with differing serration angles, which were then printed out with hard resin. The models will undergo materials testing as they are punctured into and retracted from ballistics gel. The maximum force needed for both puncture and retraction will be recorded and analyzed to see whether a change in serration angle leads to a change in puncture mechanics. Maximum puncture force is expected to increase with serration angle, as serrations angled more towards the front of the spine will increase the surface area on which the ballistics gel can resist the spine’s entry. An inverse trend with maximum retraction force is also expected, as similar gel-spine interactions will occur but in the reverse direction.

The Fly Matchmaker

Rebecca’s not really a matchmaker in the lab, but that’s the first thing I thought of when she described her project to us during her chalk talk.

Rebecca’s looking into how certain genes (or lack of) may impact the ability of fruit flies to learn courtship behavior. Specifically, she’s looking at a particular olfactory gene called Or47B, and how knocking this gene out might affect a male fly’s ability to learn courtship cues from other flies. A lot of her lab work seems to consist of raising these knockout flies (and others) and putting each male together with a group of females. Then at specific times she takes each male, puts them alone together in a chamber with one female, and sees whether they’ve picked up on how to pick up a lady from their time interacting with the group.

One thing that struck me during Rebecca’s talk was how this courtship behavior of flies, which I thought was an intrinsically innate instinct, could potentially be “erased”. But then again, what does innate mean? In Rebecca’s case, she’s working with things on a genetic level, literally going down to the DNA that defines a fruit fly, and seeing whether removing/adding components to this molecule changes anything about the whole organism. If we say that any behavior stimulated by characteristics/physiological traits encoded in DNA is innate instinct, then I guess fly courtship behavior still counts. This behavior is apparently learned through things such as olfactory receptors; and when you take away the right olfactory receptors, you block the pathway to learning the behavior. Not only was this project an interesting discussion of what counts as innate and if we can alter innate behavior; it’s also a really interesting example of how behavior and physiology/genetics can be, essentially, directly linked (though I assume that the actual relationship is far more complicated than I just stated!)

Speaking of the link between genetics and behavior, I’ve always been fascinated by how genetics studies often have to utilize both ends of the spectrum in order to gather data. For example, a study like Rebecca’s can start out by deciding what genes they want to leave in or out (resulting a control group and other experimental set-ups). But then, to determine what the presence/absence of this gene signifies, they have to observe the resulting phenotype(s), which includes a physiological and/or behavioral change. Again, this link between what has happened at the molecular level and what is going on in the whole organism fascinates me.   I’m sure that elucidating the exact nature of genotype-phenotype relationships is not always (if ever) clear-cut. But it’s still an interesting way to try to learn more about different genes and the roles they play, whether in flies, humans, or across a whole range of Earth’s organisms (we all share some bit of DNA after all!)

Thanks Rebecca for sharing your project with us, and great job to everyone on their awesome chalk talks!

My Average Itinerary

9:00am (Mon & Fri) / 10:00am (Tues-Thurs)

  • Arrive at lab.
  • Say good morning to everyone. Receive a friendly round of nods/verbal greetings back.
  • Check in with my mentor Jacob. Exchange our plans for the day, and confirm any meetings we might have.

(Whenever I arrive) – 12:30pm

  • Plop my stuff down at my lab table quadrant. Pull out the beautiful, sci-fi looking, high-speed processing laptop that Dr. Patek lent to me.
  • Spend most of my time on said laptop working in 3Ds Max to create 3D spine model prototypes. Rotate between sketching designs in my notebook, scrutinizing actual stingray spine samples, modeling spines in 3Ds Max, crash-coursing 3Ds Max tutorials/troubleshooting, and recording my modeling procedure in my notebook.*
  • (*This routine will change soon, once prototyping is finished and we move on to ballistics-gel making and puncture tests)

12:30pm

  • Get lunch. If I have a finished spine prototype by this time, send to the lab’s Makerbot to 3D print. (Depending on the load, printing can range from 30 minutes to a few hours.)
  • On all days except Thursday: lunchtime varies between going out together with other interns, and grabbing a quick bite from Au Bon Pain before returning to tackle some modeling problem I just can’t let go of.
  • On Thursdays: eat lunch during weekly meeting with the entire lab. Be the audience (along with everyone else) for various lab members’ presentation practice. Learn cool things about their projects. Give feedback. Low-key worry about what will happen when it’s my turn to go up front. Watch fellow lab members be genuinely engaged and give meaningful advice to the presenting group. Realize that no matter what, I will be in good hands.

1:20pm—6:00pm

  • If spine has printed, look at result and ask Jacob for feedback. Discuss potential improvements with the aid of a whiteboard. Begin designing next prototype.
  • Potentially, repeat itinerary from “(Whenever I arrive) – 12:30pm”
  • If a break from modeling is needed: read literature on spines and their cutting/puncturing mechanics.
  • If a meeting with Jacob is in order: convene at the lab’s whiteboard. Usually, meetings are called because Jacob is a great person and is happy to review things like my previous blog post and chalk talk. Potentially go off tangent and just start talking with him about cool spiny animals or his other ongoing research.

6:00pm

  • If this is the time when I finish a prototype spine(s), set to print overnight.
  • Leave lab. Say goodbye to anyone who remains. If I am the last one, double-check that the door is locked.
  • Return to dorm. Chill out and look forward to tomorrow. 🙂

Spines: what’s the point of it all?

When you hear the word “spine,” your first thought is probably a backbone: that familiar stack of vertebrae running from the base of your skull to your tailbone. At least, that’s what popped into my head when I first discussed my project with my mentor Jacob Harrison, a PhD student in the Patek Lab. However, there’s another type of spine that is often overlooked, one that is far more prevalent in nature than you might think.

Note: drawings are not realistic depictions of species

My research focuses on spines in the spiky sense. For my project, spines are defined as rigid biological structures that come to a point (J. Harrison). Barbs, quills, thorns, spines… these are all different names used across the literature for fundamentally similar structures (J. Harrison). Many of us are aware that spines exist in nature, because we’ve experienced (or tried to avoid) painful run-ins with them. However, until now I never appreciated just how diverse spines are across biology. Some organisms such as sea urchins have conical toothpick-like spines, while other species like stingrays have flattened barbs reminiscent of knife blades. Some spines are smooth, like the stingers of scorpions, while other spines display serrations of varying size, number, and orientation. For instance, while both the sea urchin and stingray have many small serrations on their spines, these serrations run in opposite directions (see Fig. 1)! Furthermore some structures, such as the raptorial appendages of spearing mantis shrimp, contain several spines at once (see Fig. 1).

Aside from being diverse in structure, spines vary widely in their function. Stingrays use their barbs defensively, embedding their spines in the bodies of predators (and sometimes, the feet of unwary beachgoers!). Meanwhile, spearing mantis shrimp use their spines for predation, skewering prey that swim above their sand burrows. This large difference in function occurs, despite the fact that both species utilize the same underlying tool of the spine.   This suggests that small changes to the structure of a spine play a role in how it is used, and ultimately begs the question: how do changes in spine morphology (or structure) influence spine function?

Fig. 1 – The structures of a sea urchin spine, stingray barb, and a spearing mantis shrimp dactyl (foreclaw)

To better understand the relationship between spine form and function, we’ll be investigating how spine structure affects puncture and draw mechanics. We decided to use 3D modeling for this project, because this will allow us to perform more controlled comparisons of changes in spine structure. First, we’ll design a basic underlying spine shape as a control, and then manipulate different aspects of that spine’s morphology (ex. serration number, size and angle) in set increments. After printing the resulting variations using the Patek lab’s 3D printer, we’ll then record the force required for each of the spines to pierce ballistics gel using a Material Testing System (MTS), which measures forces in tension and compression. This will allow us to see whether/how changes in the spine’s morphology affect its puncture/draw mechanics (i.e. how it pierces or retracts from the gel).

Rough idea of a base spine and resulting variations. We chose to model the spine after a stingray barb because 1) it’s an easily replicable shape, and 2) we know that it is definitely used to puncture things that the stingray views as a threat.

Currently I’m in the process of designing prototype spines using the 3D-modeling software 3Ds Max. Below are some printed models!

Feelin a bit like Tony Stark looking at his Hall of Armors

Because these spines aren’t precise replicas of ones found in nature, we have to be careful about what conclusions we can draw about ecological/evolutionary functions. However, the effects we observe with our basic models can still give us insight into the fundamental influences that spine structure can have on function.

The Patek Lab focuses their research on the intersection between physics and evolution, which is an inherent part of my project. I’m really excited to see what we might learn, not only because I am curious about the nature of spines and the organisms that wield them, but because I think our findings could have practical applications to people’s lives. After all, wouldn’t you want to know the structure of a stingray barb if it revealed an easier way to get it out of your foot?

Of course, there’s a lot more to explore, prepare, and test before I can say anything for sure. But still, I’m excited to take a stab at this investigation and see how it goes!

The Path of a Scientist

(Warning: long post ahead.  I didn’t realize it, but we talked a lot!)

Dr. Patek in the aquarium part of the lab. Image Source: Jon Gardiner/Duke University Photography

So here’s the thing: I’ve been lucky to have numerous role models in my life, many of them female, ranging from my seniors to peers in the same grade as me. The problem is, every time I look up to someone, my ability to talk to them just goes down the drain. I stumble over words, trail off sentences and avert my eyes—more often than usual. So when I was assigned to interview Dr. Sheila Patek—a biologist who has spoken at a TED conference, defended the value of her research when politicians called it a “waste,” and also happens to be my PI—I freaked out big time. Fortunately, Dr. Patek is one of the friendliest people I’ve met at Duke. When I knocked on her office door she invited me to sit down with a smile, leaning back casually with her mug of tea. Even with the relaxed atmosphere I still stuttered my way through the interview. But in the end I learned a lot of interesting things about Dr. Patek, and also gained valuable insights into the nature of scientific research.

I was surprised to find out that Dr. Patek and I share a few similar experiences. For one thing, we first developed our love of the marine world by exploring it firsthand. While attending middle school in Japan, Dr. Patek’s class took a field trip to the island Miyake-jima. That was the first time Dr. Patek went snorkeling, and although everything appeared blurry without her glasses, the moving colors she saw underwater blew her away. As an avid scuba diver, I couldn’t agree with her more about how marine life can leave anyone in awe of the natural world. I also discovered that, like me, Dr. Patek has passions in both the sciences and the arts; and she too had to face the struggle of choosing between them career-wise. While I’m mainly interested in visual art and creative writing, Dr. Patek was hugely invested in orchestra during college. She loved playing the clarinet, and remarked during our interview that she could have actually continued down the path of a professional musician. However, during college she realized something about herself: while she worked hard in both her scientific and musical pursuits, she “couldn’t stand being beat up in music performance, but somehow it didn’t bother (her) in science.” She guessed that this might be because there’s something less personal about criticism in the sciences. Afterwards, she finally became set on being a scientist in her senior year. While I still hope to combine my artistic and scientific interests—for instance, through communication of science to the public—it was amazing to hear the story of someone who had once been in a position similar to mine, and hearing about her decision-making process provided insight into how I might make my own choices in the future.

We also talked at length about Dr. Patek’s development as a scientist. One big lesson I took away was that research involves a lot of hard work, tough decisions, and a bit of luck. While completing her postdoc at UC Berkeley, Dr. Patek initially aimed to study hearing in mantis shrimp. However, after a whole year of hard work, she realized that she wasn’t going to be able to answer her research question in time, and made the tough choice to switch studies. The turnover was definitely not an easy one. Dr. Patek’s next plan was to study the mantis shrimp’s strikes, however these ultra-fast movements could not be recorded by any of the university’s cameras. By utter chance, a BBC crew visited Berkeley around the time Dr. Patek was facing this dilemma, and were kind enough to rent out a ~$3000 high-speed video camera for her in exchange for filming her and other scientists doing research. It was only then that Dr. Patek was able to study the mind-blowing mechanism of the mantis shrimp’s strike. My jaw dropped when thinking about how important sheer luck was to Dr. Patek’s career trajectory; had the BBC crew not visited when they did, Dr. Patek herself admits that she would not be researching on mantis shrimp today. However, she also adds that she would’ve eventually found something else; and that reminded me that this luck was really only a bonus to all the labor Dr. Patek had already put in as a scientist. I’d like to think this adds weight to the idea that chance opportunities are great, but they’ll only really start arising once you’ve put in work yourself.

Finally, we also discussed Dr. Patek’s current work and life.  Surprisingly, one thing that my PI stressed to me was that research is a “ruthless” career. Obtaining grants and publishing papers is a highly competitive process, and many qualified people with PhDs aren’t able to succeed in a scientific career. The grants Dr. Patek receives are also the main thing keeping her lab running, so my PI spends a lot of her time writing grants. Dr. Patek also describes her job as “all-consuming,” as she often works all day and sometimes has to take work home with her. But at the same time, she notes that it grants her a degree of flexibility that most jobs don’t have. For instance, she’s able to attend her son’s kindergarten graduation at eleven in the morning, or be home at six for dinner everyday with her family, and do work later at night. She also says that it’s a huge privilege to be doing what she does: paving the way for new knowledge on subjects that she cares about, and working closely with others who have similar interests. And with regards to the job being “all-consuming,” she also notes that “sometimes the best things in life are like that.” Yes, research is a job that can demand total investment; but if it’s investment into something that you love, that you already have an “overwhelming fascination and passion” for, then this type of career can be pretty amazing. Through her voice and animated gestures, it’s very clear that Dr. Patek has this very passion she speaks of. I can’t help but feel in awe of how my PI balances the ups and downs of her career, and ultimately takes great joy and pride in what she does.

After half an hour, I finished the interview and thanked Dr. Patek for making time for me out of her busy schedule. We still ended up chatting about random things as we headed back to the lab.

I don’t know if this has gotten across already in my writing, but this interview was truly inspiring. I was genuinely surprised at the similarities Dr. Patek and I shared, and was amazed at the challenges she faces as part of her life as a researcher. Learning that someone I can relate to has experienced what she did, and made it to where she is now…that inspires hope in me that I can do the same, and has given me a greater awareness about how I may approach my own future. I’m honestly so glad I’ve been given the chance to work in her lab this summer!

Printing Things and Poking Stuff

When I found out that I had been placed in Dr. Sheila Patek’s lab for BSURF, I almost burst with excitement. As a scuba diver who has grown up swimming around the islands of the Philippines, I’ve fallen in love with marine life, and with animals in general! The Patek Lab is one of the few labs on Duke’s main campus that studies marine animals, studying things such as the acoustics and fast-movement systems of the amazing mantis shrimp, as well as other organisms like fungi and trap-jaw ants. Coming in this summer I already had a broad idea of what I might be doing for my research project: studying the spines* of mantis shrimp and other animals, and seeing how the structures of these spines affect their puncture mechanics. In other words, printing model spines out and poking ballistic gel.

One of the things I hope to do this summer is gain more technical knowledge on the procedures I use in my project. For example, my project involves a fair amount of 3D modeling and printing, neither of which I had ever done before. However, for the past week I’ve had the good fortune of being able to practice operating the Patek Lab’s Makerbot 3D Printer, and try my hand at a few different modeling programs. This meant that by Friday afternoon, I was grinning down stupidly at a 2-inch lionfish spine that I had isolated from a CT scan and printed out myself, and my initial doubts about my ability to handle my project had been sizably quelled. I’m hoping that I’ll continue to make progress in learning different scientific and technical techniques; and in the end, I hope to come out not only with a toolkit of skills that I can use in future projects, but also with more confidence in my ability to conduct research.

Left: my work at the lab’s computer.  On the display you can see a lionfish skeleton and an isolated lionfish spine ready for printing. Right: The spine has been printed!

I also hope to gain a better idea about what life is like in the lab, both in terms of working with other lab members and in terms of workload. The discovery of new knowledge about the natural world is an inherent part of research, and this enticing prospect is what causes me to seriously consider research as a career path. However, I don’t believe that I can dive into research without at least making an effort to learn about how it may (or may not) change my work habits, work-life balance and other aspects of life. By interacting with/observing my fellow lab members and asking lots of questions, hopefully I can gain a more accurate picture of what it means to be a research scientist, and decide whether that is truly the life for me.

Overall, through BSURF I hope to learn more about methods for exploring science, learn more about a living a life dedicated to research, and in the process, learn more about myself and my capabilities as a scientist. And no matter what I discover or decide by the end, I hope that this summer will be a fun and eye-opening one!

The Patek Lab members (+ the two Patek kids) over at Dr. Patek’s for dinner last Friday!

 

*The stabby bits, not the backbone 😀