the humans that taught me to science

This was originally published on Bold with annotations.

There are three humans that taught me how to science: Justin, Jae and Dee.

This is a story of how we met and how each individual intentionally and unintentionally taught me everything I know about science. We meet a few additional characters along the way.

Justin

When I walked into the first iGEM meeting I couldn’t tell you the difference between proteins and DNA.

I don’t do well in lectures. Denny tried to get my attention for months in our Introduction to Biochemistry course, unsuccessfully. He was unsuccessful because I treated class as nap time. Every day I sat in the very front row of the four hundred person lecture and promptly at fell fast asleep at 10AM.

Eventually a strategy did work for Denny. He sat directly behind me during a study session and threw small pieces of crumpled up paper at my desk. I didn’t notice this until students started exiting the room. My desk was full of paper debris. I didn’t notice because I was fast asleep.

The point is, I didn’t learn anything in lecture. I tend to live in my own world. I make up my own hypotheses. I believe them until the hypotheses are proven false based on personal experience. I failed all three quarters of Physics because I didn’t trust the textbooks and wasn’t dedicated enough to run all the experiments to see for myself. This is a bad strategy for learning.

I wandered my way through university. Then, I met Justin.

Denny deserves a lot of credit for getting me to science and keeping me in science. This is one of the cases. We saw a flier recruiting the iGEM team for 2010. The meeting probably involved free pizza because everyone knows that’s the only way to get students (and especially me) to show up.

Justin is the kind of teacher that will point you in the right direction and then shut up and let your own imagination run wild.

Our task was two fold.

Denny was responsible for designing a biological device to detect the presence of anthrax in any room. This device could be installed in the White House on the wall and notify White House staff if anthrax was present.

I was responsible for designing an orally administered probiotic for patients infected with anthrax. This drug should easily and quickly fight off an anthrax infection without killing any Bacillus species necessary for normal metabolism. Anthrax bacteria is part of the Bacillus family, the scientific name is Bacillus anthracis.

Maybe the other kids in the class paid attention in Intro Biology, I certainly did not. Intro Biology happened during my first summer of undergrad where my number one priority was learning to lucid dream. I was successful at lucid dreaming, but was not successful at much else.

During high school Mr. Androsko told me I was the first student in his AP Biology class to score a 2. The truth is, I fell asleep during the test. As you can see, things didn’t change much once I got to college.

We had until the next iGEM meeting to do a literature search and come up with a proposal and presentation.

I ended up presenting an extremely complex plan for designing a probiotic that could be administered orally.

Justin has this way of using his soft spoken manner to tell you what is realistic without crushing your dreams.

We didn’t make the probiotic. Looking back on it, it was clearly too ambitious for a summer project. Justin gave us another ambitious, but realistic project.

I went through iGEM in a daze. What we’re minipreps? What we’re oligos? How do I use a pipet?

I remember one of my first days in the lab clearly. I was tasked with connecting a bunch of oligos, short for oligonucleotides. After designing our DNA part, we used software to break the DNA up into a bunch of short DNA strands. We ordered the short strands of DNA. My job was to use an enzyme to stick the short strands of DNA together to make our DNA part of interest.

Eager to get started I got the enzyme from the freezer and brought it over to Justin’s lab bench. This was the first time and one of the last times Justin got serious.

Put that on ice!

He said.

Apparently if you bring proteins to room temperature and then refreeze them, the proteins will denature and refold incorrectly. Of course I didn’t know this information because I didn’t pay attention in class. I’m not even certain that class teaches this.

Justin and I never spoke about why this was important. But this experience led me to think critically about what I was doing. I read up on why we need to keep enzymes on ice. This tool, critically thinking about what you are doing and why, is a tool I’ve kept with me ever since that day. I did more investigation and I learned that the scientific community doesn’t actually know how transfection by electroporation works on the molecular level. We just know it works. The scientific community also doesn’t know why using a glass rod to scratch the inside of a beaker containing a pure dissolved chemical causes the chemical to start crystallizing. We just know it works.

This is when I learned that what appears to be known is not always what it may seem. I learned you can always investigate any claim to the root using the peer reviewed paper trail. It is likely that you find gaps in knowledge.

That summer I was funded by Howard Hughes Medical Institute to work full time with Dr. James Bryers on another ambitious project.

I still believed in the project with Justin but knew I did not have the time to devote to it so I recruited the next best person to complete the project, my baby brother Sean. 17 at the time, Sean was the exact opposite of me. Sean loves to read, maintained strait A’s, and avoids social events at all costs. He loves computers and had spent the last summer building his own computer from scratch, something to this day I still don’t understand.

Sean needed something to do over the summer, so I threw him into the mix. Sean ended up spending everyday in the lab from sun up to sun down. He eventually became the first author on our peer-reviewed paper at the age of 18. And, the following year at 19 filed his first patent for a Celiac’s disease probiotic.

This is when I learned that anyone anywhere could do real science. If I could take my brother who had little interest in biology and make him a real published scientist within a summer that was really something.

What iGEM really gave me was confidence. After the summer was over and the team had discovered a potential anthrax therapeutic someone had to present the findings. If you met me after starting Experiment you might think of me as an extroverted human but I can assure you that was not the case. That is certainly still not the case.

Justin helped me find the courage to face my biggest fear, public speaking.

Three people were selected to present our work at the largest synthetic biology competition in MIT the fall of 2010. Luckily no one but Chris volunteered and it gave me a few moments of silence in the room to get the true courage to volunteer myself.

If you knew me in elementary school it would be hard to believe that I am the person I am today. I was shy to the point where my friends’ parents would ask my parents if I spoke English. I once wrote my friend Alison a note telling her how to be like Cindy. The first tip was don’t talk. The second tip was don’t raise your hand in class. The next tip was don’t tie your shoe laces. I feared speaking. What I feared more than that was speaking to a live audience.

Presenting on stage at MIT to a room full of a few hundred people was one of the scariest things I’ve done. I’m grateful for the opportunity because guess what I have to do that nearly everyday now? It is still terrifying, but it is one of the most effective ways of sharing our mission.

While Sean was working on the project in the Health Sciences Building during the day, I was one building over trying to engineer cell based immunotherapies. In the evenings I headed over to join Sean and the team.

Our dream was that one day we could take the blood out of your body, filter out your white blood cells, culture your cells, feed your cells a unique RNA specific to any disease, your cells would learn this sequence and become immune to the specific disease. Then, I could put your cells back into your body and voila! You’d be cured.

The dream was a universal vaccine. That was the dream. It is still just a dream.

Jae

I met Jae by way of Dr. James Bryers. We call him Dr. Bryers.

I met Dr. Bryers in a very roundabout way. After Denny got my attention in study section by throwing a bunch of crumpled pieces of paper at me, we became fast friends.

At the time I was working in Dr. Lali Ramakrishnan’s zebrafish lab. Her research focus was Tuberculosis and zebra fish was the model organism. In a nutshell my job was to grow sea monkeys and rotifers and feed them to the zebra fish fry. Though extremely grateful for that experience I felt ready to actually do research instead of just being someone’s lackey.

I shared with Denny that I wanted to apply for this grant funded by Howard Hughes Medical Institute through my department. Denny was oddly earnest and offered to help me with my application. I don’t know if I would have submitted the application without his support.

This Howard Hughes Medical Institute funded program was designed specifically for undergraduate students that had zero experience in research. Now I know it was an experiment to see if institutions, like the University of Washington, could develop a program to create scientists. They followed us for many years and may still be following us today. The grant funded a student’s stipend for three quarters. If awarded I would be paid to choose any lab that I wanted and get paid to do research for three quarters. It sounded like a sweet deal. It was a sweet deal.

Lo and behold a few months later, I got an email. I got the grant. Brian was the lecturer for the program that consisted of me and fifteen other students. He taught me everything I know about reaching out to Professors. It turns out that this would come in handy when starting Experiment. I wrote terrible email drafts with the intention of reaching out to Professors. I’d send them to Brian and Brian would coach me on all the things I was obviously doing wrong.

One professor I emailed was Dr. Buddy Ratner. My email, which was largely crafted by Brian at this point got me a meeting. Dr. Ratner’s lab was full, but he had a joint NIH R01 with Dr. Bryers. Dr. Ratner recommended I email Dr. Bryers. So, I did.

I guess at the time it was a pretty good deal for the Professor. I was offering to work and I was coming in with my own funding.

I meet Dr. Bryers. If you know Dr. Bryers, you he is a real character. He gave me the silliest research presentation in his office on hospital acquired infections and described his plan to recruit the patients own immune cells to fight off biofilms. Hospital acquired infections are the fourth leading cause of death in the United States. I try to avoid hospitals as much as possible.

I read a lot of Dr. Bryers’ papers before coming in for the meeting. I told him my ambitious plan. I wanted to use the data he had to model how the immune system works. I wanted to create a computer simulation of the realities of what is happening in the human immune system. I don’t know why he said this, but he said he would teach me how to make this a reality.

Like Justin, Dr. Bryers had a way of diverting your attention without crushing your dreams. He introduced me to Jaehyung or Jae.

Jae would then become one of the three most influential scientists in my life. I spent more time with Jae than any other human during my last two years of college.

I was Jae’s puppy. He trained me to do everything I know about science. Together we designed the first protocol in our lab for culturing dendritic cells. I was then responsible for babysitting our cells for over two years.

I learned how to measure cell confluence, passage cells, treat cells with difference chemokines, stain cells with specific antibodies, and measure the presence of specific markers using the flow cytometer. My work with Jae later gave me the confidence to ask Dr. Bryers to let me start my own independent project.

Jae is one of the most idealistic scientists I know. He is also one of the hardest working humans I know. He believed in what we were engineering. He believed that given the right conditions we could reprogram the dendritic cells with enhanced efficiency at recognizing foreign pathogens and delivering the message for our bodies to develop immunity.

Jae is an optimist. I think part of the reason why I’ve believed in our model for funding science at Experiment is because of Jae.

I must have run the same experiment for Jae hundreds of times. Each trial took over a week. I screwed up so many times. Every time Jae would buy me a cup of coffee and just tell me to try again.

I lived in the lab. I lived in the lab because by osmosis through Jae I also wanted so badly for our hypothesis to be correct. What we were building was an engineering project, not a pure research project. When you are creating you have to believe.

We ended up publishing and it wasn’t some grand Nature paper. This is when I learned it is not about the final discovery. The magic is in the process. I watched as the system would only ever reward Jae if he got a paper in a high impact journal.

The system didn’t care about the learning. The system didn’t care unless we got results. The system didn’t care about the ambitious plan that we had and the incremental progress we were making towards making cell based immunotherapies a reality.

The system only cared about publications and so that is what Jae prioritized. The system was not optimized for rewarding the best science or the best scientist. The system was broken and Jae and everyone around him was a victim of the system.

Then, I met someone silently fighting the system. That person was Dee.

Dee

Where do I even begin with this one. Let’s go way back. When I was five years old I went on my first date. I went on my first date with a boy named Terry. His aunt took us to the local McDonald’s in her red convertible and I tried a milkshake for the very first time in my life.

Terry ordered strawberry and I ordered cherry. Strawberry was the clear winner. Terry was a keeper.

Terry and I, we were inseparable at recess. We spent every recess catching bugs. My favorite we’re the stink bugs and I loved finding caterpillar eggs under the leaves of trees. If you looked behind the portable buildings that’s where the daddy long legs lived. I didn’t like them too much. I very much admired Terry because he was better at me at two things: identifying bugs and drawing.

The first thing I wanted to be when I grew up was a bug catcher. I would later find this profession is Entomologist.

Dee, she was running a course where every Friday was a full day field trip. I didn’t have the pre requisites for her class but that never stopped me before. I asked her over email to let me in. She said yes.

I remember the first day of class clearly. Dee definitely has a memorable presence. We all knew she wasn’t messing around. It was clear this course would not be easy. The class was small, maybe a dozen people. It wasn’t until this course that I felt like I started actually learning how to learn.

We did a lot of things that quarter. We measured the nearest neighbors of the dandelions on the Foege Building lawn, we watched the behavior of the local ducks, we counted the number of bumblebees on Ceanothus bushes. The most valuable thing about going into the field was going into the field.

We went to the potholes in Eastern Washington two times. I went three. There we observed red-winged blackbirds, set out different kinds of seeds for the native mice, fed the ants different concentrations of sugar and measured the temperature of their hills, we put on waders and caught baby dragon flies still in their larval stage. For the first time I was certain I was doing real science. So this is what sciencing is like.

Dee taught me three things.

Determination can take you very far. She taught this by leading by example.

Explaining the natural world is possible with science. You can form a research question and measure what you observe to come up with an answer. This was the recipe for finding the truth.

Literature search. She showed me the body of knowledge that is peer reviewed papers.

Beyond that I learned that she had the opportunity to be promoted within the university to chair of the department and maybe even president of the university. She said no to all that so she could be with her first love, penguins. Watching Dee do science is where I found jelly.

Internally at Experiment we obsess over jelly. Jelly is an English word we created to mean the collective feeling of a shared moment of discovery.

This is the feeling that Dee gave me and my peers watching her hike up under bluffs to observe the cliff swallow nests. This is the feeling that I got when she gave me the permission to be fearless and hike up to the top of a steep ravine in flip flops with nothing but a bug net and jar of ethyl acetate to catch bumblebees. I found a new sense of what is “safe” and found the adventure that I had been searching for with Terry every day at recess.

This was jelly. This is the feeling that we’re obligated to share with everyone around us.

Through her career she focused on the science. She did everything in her power to stay focused on the science. She silently stopped playing the traditional grants game and found an individual group of donors to support her work every year. She repaid the donors by sending them content, updates on the progress of the science. Dee was living and breathing proof that Experiment already existed even before Denny came up with the idea.

This is how I know the destiny of Experiment is inevitable. Dee was the first person I called when we were at Startup Weekend trying to validate our idea. I called by phone. Calling by phone is trick I learned from Dee herself.

Science itself is universal. Science knows no borders. Science knows no age. The best way to learn how to science at any age is to watch others science. We create more scientists by showing the world how scientists science. Good science is reproducible. It is not in the final discovery, but in the process that we move humanity forward. When the process is open and transparent we will see an exponential rise in the understanding of the universe around us. Then and only then will the world be able to truly science.