Greenhouses to Purple Lights; A UCSB Botanist Experience

For the summer of 2015 I have been given the opportunity to be a UC LEADS scholar researching my floral passions in the sunny beach side city of Santa Barbara. Being at UCSB during the summer has been a change from the cavalcade of students going from class to class, though the weather never fails to remained the same. Going to a Univeristy with so many distractions some people might wonder how on earth could somebody go to class when the beach is only five steps into your front yard, or study for a test when there is a plethora of exciting people to socialize with all around in IV or on campus, or be in a lab for 7-9 hrs a day, maybe some weekends, endlessly pipetting countless centrifuge tubes and counting dots on a screen slide after slide after slide when there is a litany of other options in SB. The questions aren’t to hard to answer; It’s fun. It’s not strange to think there are other forms of enjoyment out there, and it just so happens that I enjoy sitting silently looking at pollen grains germinate, and being in awe surrounded by brilliant purple flowers, and learning more and more about such awesome organisms.

My goal throughout my education has been to utilize the knowledge to serve the world in whatever ways that are needed. At the forefront of my service has been to study global warming and provide predictions using experimentation to propel a precautionary  mindset producing sustainable industry and environmental practices. It has been a great honor to be selected by UC LEADS to get a stepping start on my goals this summer by being a part of an evolutionary biology lab with the intent to proliferate cooperation and thought.

I am working in the Susan J Mazer Lab of Evolutionary Biology researching the genetic variations between two sister taxa of angiosperm plants, Clarkia Exilis and Clarkia Unguiculata, in pollen tube growth rate and pollen performance to understand the evolution of mating systems through epistasis with other physiologic genes. The experiment started in the fall of 2015 with ~2000 plants of both species in the UCSB Greenhouses. I have volunteered in the greenhouses before, debugging plants and landscaping with previous experience in other jobs handling delicate seedlings, but I was not quite prepared for what came next. With

Clarkia Ungiuculata

Species from California
Common name: Elegant Clarkia
Photographed on Panoche Road, San Benito County, California

tweezers, an xacto knife, and magnifying glasses we emasculated hundreds buds by carefully plucking small filaments with little red caps, the anthers or pollen producing organ, to assure for no self pollination. Once the white stigmas of the emasculated flowers began to bloom and become fuzzy with tiny papillate hairs we carefully pollinated it with other pollen within the matrix. After 4 hours, we took off the style and preserved it in FAA. It all felt like doing surgery, though thankfully flowers don’t have any blood. All of these styles were then stored for this summer, where an amazing team and myself began preparing them for viewing.

We now count blue dots, callous plugs left behind by germinating pollen grains, every 1mm to determine the rate at which the plugs have been deposited.  It takes quite a long time, and with so many slides being produced each week it becomes a challenge to finish, though through all of it, its worth seeing that big excel chart of data ready for analyzing and screaming for graphs to be made.All of this data will be ultimately used to test the prediction that the outcrossing species of Clarkia will have lower variations in respect to pollen tube growth rates due to selective pressures of competition, while selfing species will maintain a larger genetic variation in pollen tube growth because there isn’t as selective a pathway for competition. The performance of the pollen, tested by how many pollen germinate on the stigma, as we predict, will increase as the pollen tube growth rate increases by epistatic interactions or some other joint mechanism. The goal of the study is not only to perfect the methods for calculating pollen growth rate and pollen performance but to make predictions for the future wildflower populations in the dawn of global warming.


Global warming is no longer a fantastical precaution told by just scientists, but an ostensible fact of the 21st century that cant be considered a future problem any longer as violent storms and insane record highs and lows are becoming more and more frequent as the years progress. Sea levels are rising at an incredible pace throughout the world, flooding not only Balboa Island in San Diego every so often, but decimating villages along the coast line or near delta basins. The greenhouse gases have been accelerating in concentration, causing a gradual heating of the earth, and with it a slow drying of fresh water supplies. The changing physiological conditions of earth also inspire further change in the biosphere, an area that has much importance to my research. As wildflower populations slowly die off due to water dehydration, we want to know what will happen to plants that can survive the heat, but don’t have complete tolerance to drought conditions as much as succulents would for example. Our study sets out to understand the possible implications of a warming climate on the physiological characteristics of Clarkia; pollen tube growth rate, pollen performance, style lengths, and petal size and inversely on the mating system. Selfing plants suffer from a depression in genetic variation, where as outcrossing individuals will produce offspring with a variety of genes that subsequently promote sustainability against disease disasters. As the climate warms and pools dry, we expect to see many plants, Clarkia Unguiculata for example, become smaller in size like its selfing sister ,Clarkia Exilis, and express qualities closer to a selfing plant than an outcrossing plant. Our study is discovering if those selfing physical qualities are genetically tied to self compatibility genes either on the same locus or by epistasis interactions to predict the outcome of outcrossing populations in the future of hotter days.

This summer has been amazing outside of the lab as well as I went on a two day seed collection in Sequoia National Forest with my PI. I have always heard about red woods taking peoples breath away, I just never expected such a cliche experience to be so life changing. I felt incredibly humbled by the shear height and volume of this sole organism, while realizing large or small, were all in this whole journey together. Gaining field experience is a lot different than the greenhouse or the lab as its a literal hunt for your data. Keeping eyes pealed is key because its easy to miss a population, and its also simply a shame to miss anything while in Sequoia Forest. It is all a challenging process but seeing all the beauty of the world while making progress is what makes evolutionary and field biology such an amazing career opportunity. The UC LEADS crew has been an amazing eye opener to me as everyone has a prodding mind with interesting personalities that nobody can find anywhere else. Spending time with my colleagues and getting to know their projects deeper and deeper every time we meet, while also reveling in each other successful projects is uplifting and encouraging.

I am having the time of my life in Santa Barbara thanks to the awesome people of UCSB and UC affiliates who have allowed this summer to happen the way it has.

Hotter Than an L.A. Summer

For all my L.A. people, whether you represent San Fernando Valley or downtown, know exactly what that title means. How can anything be hotter than waking up to your pillow drenched with your sweat? Step into the Four Eyes Lab at the University of California, Santa Barbara and see for yourself. Seeing as this lab is full of computer scientists, the heat I refer to exists on a computer monitor, not physically. “Markus, you do realize that the fire isn’t real so how is it hotter than an L.A. summer? Worse thing that happens is that the computer overheats!” First of all, my computer only overheats when I play my music (now that’s hot). Secondly, it was a joke attempting to explain my research, but I quickly gave up on it. Comic relief aside, the fire reference will make sense as I explain the research I have conducted.

This past summer, I had the honor of being able to conduct research at UCSB as a UC LEADS Scholar. I would like to give special thanks to Professor Tobias Höllerer and Professor Matthew Turk for allowing me into their lab. In this lab, I am applying Augmented Reality (AR) in a wildfire scenario to help firefighters maximize their training efficiency.

“Markus….what is augmented reality and how are you applying it?” I was just getting to that person who asks too many questions! Simply put, augmented reality allows human interaction of virtual objects in a real-time environment. Figure 1 illustrates a visual as to the power that augmented reality gives the user. This differs from virtual reality in the fact that virtual reality isolates you from the real world. Having that basic definition, it is appropriate to direct our attention to the problem at hand.

Figure 1. Augmented Reality example from the Four Eyes Lab “HandyAR” project.

Firefighters are out in forests battling wildfires and it is crucial that they are safe while doing so. Part of ensuring their safety requires having top-notch training. As with most things in life, improvements can always be made and that is where we pose the following question: can using augmented reality maximize training efficiency for firefighters battling wildfires?

With that question laid out, the foundation for the research I am helping on has been made. Using Unity3D (software used primarily for making games), a wildfire scene with a burning fire was constructed. Upon my joining of this research, my task was to implement several things to make the scenario more realistic. Spreading the fire was the first task at hand as fires spread very quickly in the wild (hence the term wildfires). While the fire is spreading, a helicopter had to be implemented into the scene carrying some type of fluid to put out the fire. Prior to all of the implementation, I took the time to educate myself on wildfires as well as firefighter procedures for battling them. This was to provide a realistic simulation to mirror the actual situation as possible for training purposes. Figure 2 is one of the many references I utilized while developing a helicopter mimicking real-life functionality.

Figure 2. Helicopter reference I utilized while simulating the helicopter.

All of the C# coding was handled in MonoDevelop, Unity3D’s built-in coding environment. “You made a wildfire and a helicopter, cool for you. How does doing that see if augmented reality would be a good alternative to current firefighter training?” With all these questions, have you considered being a researcher?

By conducting user studies, we can contrast times in the following manner: typical firefigther training or training done in a full-surround environment utilizing augmented reality. The Four Eyes Lab “AlloSphere” immerses the user in this full-surround environment. Going back to the definition of AR, by being in this wildfire world, we can mirror the actual event. Comparing the two will tell us if augmented reality is beneficial for firefighters.


A bear by the name of Smokey once said, “only you can provide wildfires.” Well, Smokey, in case we let you down, we hope that augmented reality can help stop wildfires more efficiently.

Let’s Get Down to Business, to Defeat… Senior Year?


Graduate school applications are approaching…must…survive.

This is definitely how I’m feeling currently. I’m in the calm before the storm (which is funny cause it’s raining  in Riverside, CA where I am). But before I discuss the storm, let’s talk about how nice things are right now!

I have to say summer research is the best. Not that research during the school year is bad (it’s just as awesome all year-round, trust me), but its hard to enjoy the cutting edge science as much when you’re stressed about classes, midterms, grades, projects, and all the other responsibilities that come during the academic year (which again, are really awesome but when put together all at once can be a bit overwhelming).

Anyway, this summer I’m conducting research as a part of the Yin Group at UC Riverside! This is my second summer as a part of the UC LEADS Program, and it’s been great! I am working on some really cool research, which I won’t get into too much but in short: I am working on a materials system that changes color upon stretching or when under mechanical stress. Yeah, materials chemistry is basically magic. It’s been a really cool project and I hope that I am able to finish it before I leave! I’ve also been working very independently this summer, which has been nice to help me prepare for (*crosses fingers*) graduate school. Though it also means that when there’s an issue that arises, I am solely in charge of finding the solution, which is pretty crazy!

As for the program, I’ve loved all the people I’ve been able to meet! Many of the other undergraduate researchers here are from UCR, but a good number of students like me who are from other institutions. I’ve been able to do some pretty fun stuff outside of research, last Wednesday I even went Salsa dancing with a group of friends from the program. Overall it’s amazing. And I won’t forget to mention the apartment and meal plan that my internship pays for (in essence, I feel super spoiled).

And after this amazing program, I will be one of the Resident Assistants for the Summer Institute of Mathematics and Science (SIMS)! I’m incredibly excited for this, we have an outstanding group of scholars this year and I really want to do my best to help them feel prepared for UCSB, STEM, research, the whole shebang. I’m stoked to meet them and I’m hoping I can really impact them positively as one of the RAs. I seriously cannot communicate my enthusiasm, SIMS!

And then I’ll have a short break before…SENIOR YEAR.

Senior Year

That means on top of classes, there will be:

  • SACNAS and oSTEM Co-Chairing and Co-Presidenting, respectively
  • oSTEM Conferencing in Pittsburgh, PA
  • Undergraduate Researching AWESOME SCIENCE
  • Potential Graduate School Previewing (let’s hope so on this one)
  • Fellowship Applying (NSF, yay!)



Honestly, I’m pretty scared. But I also feel really fortunate, I’m happy that I’ve made it this far and I’ve had so many spectacular opportunities on the way. I’m looking forward to it all, even the graduate school applications will be really exciting. It’s going to be a busy year, but an exciting one. I’ll be working hard, but it’s going to be awesome, I’m essentially preparing for a new chapter of my life. More than that, it’s all towards my overall goal: I want to make a difference in the world, and I can do a great job at that with my passion for science and engineering.

Wish me luck, cheers!



Going With the Flow at UCSB

I, like most people, have a very difficult time remembering names; however people tend to remember mine. Maybe it is the association with the delicious soft cookies known as Fig Newtons or maybe it is the association with my field of study, Geophysics. I am often asked if I chose my field because of the fact that I was named after Isaac Newton and the unit for force but the answer is a not very profound “maybe?”. I chose Geophysics because I believe it is beautiful how we can model what we observe on Earth and other planetary bodies with the equations of physics. I am saying this while religiously stalking the New Horizons Pluto Mission.

Coming to UCSB, I traded the fog of the bay area for the sunshine of Santa Barbra. The first things I noticed were that everyone wears flip-flops, everyone bikes and skateboards, and everyone skateboards and bikes wearing flip-flops. Although it is my fourth week at UCSB, I still laugh to myself when I walk into my office and smell the ocean.

At UCSB, I work under Professor Frederic Gibou in the Computational Applied Sciences Lab (CASL) creating and analyzing algorithms for nonlinear dynamical problems. In other words, I am writing code in C++ to efficiently compute the calculation of problems that change in both space and time. This applies to the crystallization of multicomponent alloys for use in the aerospace industry and image processing algorithms for use in some futuristic medical surgeries. My favorite application is its use in the field of Computational Fluid Dynamics. This is the study of the way fluids behave and how one can simulate it on computers.

Newton, why do we care about the way water moves? Isn’t that what plumbers are for?

I’m glad you asked! When we picture a fluid, we think of water and the contents of our glasses we drink with a big group of complete strangers at the end of a long week; however, the definition of a fluid is more general than that. Fluids take up whatever shape they are contained in. An example of this would be gases such as air.

xkcdFluids also exhibit this behavior called turbulence. If you want to make a million dollars, get a Fields Medal in Mathematics, and get automatic tenure at a university of your choosing, you can create a statistical model for the behavior of turbulence. It is a Millennium Math Problem. Turbulence is why the emergency seatbelt sign turns on  mid-flight when you are waiting in line to go to the bathroom or heaven forbid, already in the bathroom. Turbulence is chaos, and I mean this in both the context of being stuck in an airplane bathroom and math. It is one of the great unsolved problems in physics.

That’s so interesting Newton, but what does this have to do with Geophysics?

Great question! The research being done in CASL can be applied to Multiphase Flows. A multiphase flow is a flow is defined as multiple fluids with different densities flowing in one system without mixing. This applies to the interaction between the atmosphere and oceans. By understanding the chaotic interactions between the atmospheric and oceanic systems, we can better understand our weather, climate, and how humans are affecting them. The ocean covers 70% of the Earth so it is rather important in how the atmosphere behaves. With that knowledge, we can better understand how changes in the atmosphere affect changes in the oceans and how changes in the oceans affect changes in the atmosphere. This is what I hope to study for my PhD but maybe my heads are just in the clouds.


A Frenzy of Research


I still remember the excitement I had when I was accepted into UCLeads. I was in line at the UCSB arbor buying a bottle of water and a bag of dark chocolate M&Ms and I felt my phone buzz. As soon as I read my email I could not believe that I had been accepted and If I remember correctly I held up the line by rereading the email about 5 times until the cashier yelled at me. At the time the summer program had seemed far away, but now that I am fully immersed in the program it feels a research roller coaster! I am currently working in Dr. Reich’s Lab which is primarily involved in the study of DNA modifying enzyme mechanisms (how they behave on DNA) and also characterizing the ability to deliver drugs (mRNA and siRNA) to cancer cells using novel particles. I am working directly with Dr. Reich, my faculty mentor, and my undergraduate mentor, Brigitte Naughton. I am also very fortunate to have Clay Woodcock as my grad mentor who often gives me advice but I am primarily being trained by Brigitte who has been very helpful and resourceful! As of right now Brigitte, Dr. Reich, and I are working on our manuscript in anticipation of submitting it for publication! It feels great to see the fruits of hard work as Brigitte and I have spent time working on the project.

This is what a Page Gel looks like when it is being used to analyze the outcomes of the experiment. Notice how there are no bubbles between the glass plates. Mine usually have a lot!

This is what a Page Gel looks like when it is being used to analyze the outcomes of the experiment. Notice how there are no bubbles between the glass plates. Mine usually have a lot!

Working in the lab has been a great experience and everyone is wonderful and friendly to each other. Going into undergraduate research I had expected an office setting for the lab but it is mostly a group of friends running experiments, interacting, and doing other activities together. It is also immensely helpful that my faculty mentor, Dr. Reich, is very friendly and helpful. He has a sort of open door policy and anyone can go in to get help or talk. Even though the atmosphere is very friendly hard work is expected of us.  It was a little hard for me transitioning from the summer to working full time in the lab as sometimes i might be in here for 10 hours a day. I have found that the one thing i dislike the most about research is not getting the right results! But I am sure that this is the same for everyone. In our lab we use PAGE Gels to check to see if the enzyme has worked on the DNA substrate in the way we expect it too. To use a Page Gel one has to cast the liquid solution between 2 glass plates without forming any air bubbles that may be trapped in the gel. I have found out that this is something I am absolutely terrible at. It takes me 4 tries at times to cast the gel and it is both amusing and disappointing at the same.


So I guess I should talk about my current project as it is quite exciting and nearing the end. I am focusing on an enzyme called Dam also known as DNA Adenine Methyltransferase. Essentially Dam methylates (adds a methyl group) to the N6-Adenine on DNA and can alter the expression of genes. Right now I am involved in a bioinformatics project on the E.coli Dam and the T4 Bacteriophage Dam. The bacteria E.coli uses Dam in chromosome replication, mismatch repair, and for regulating virulence genes. The T4 bacteriophage which infects E.coli has a Dam of its own for which we do not know its purpose. So my project hopes to shed some light on what this purpose could potentially be. I am using  a variety of exciting computer tools to see my project to completion. I have put up a video of E.coli Dam which what I am studying and I am soon going to be transitioning towards conventional lab bench experiments and am excited to see my research go forward!