Helping Scientists by Playing Video Games

Growing up with Video Games

Like many people, I grew up playing video games. I can remember when my twin brother and I were ~5 years old and got our first gaming console, which was a Sega Genesis. It came with the “The Lion King,” where we had to jump Simba safely across the Savannah by jumping from giraffe to giraffe. As we got older, we moved to the Sega Saturn, PlayStation I, II, III, etc. One of my favorite games was TimeSplitters 2, when four of us would face off in the multiplayer mode of virtual hide-and-seek. Video games are a fun pastime for people with many different interests.

 Now, scientists are using video games to harness human intelligence to address important scientific research questions.

FoldIt

This online puzzle game was developed by the Center for Game Science at the University of Washington. It involves competition between players trying to work out the 3-D structures of proteins by folding chains of virtual amino acids into optimal configurations. The greater the stability of the protein as zigzags, squiggles, and loops of amino acids are folded into an optimal shape (with the lowest energy), the higher the score. FoldIt also allows players to design new proteins that could have potential therapeutic effects, such as inhibiting influenza virus.

Additionally, FoldIt players can outperform computer simulations to find the lowest energy structures of a protein. They solved a research question that scientists had been studying for decades by determining the structure of a retroviralprotease of the Mason-Pfizer monkey virus (which causes similar symptoms as HIV in humans). Also, FoldIt players redesigned anenzyme to increase the speed of a reaction and increase the production of drugs by ~2,000%.

EteRNA

This game was created by scientists at Carnegie Mellon University and Stanford University. Players arrange colored discs, which represent nucleotides that form RNA molecules, into 2-D chain-link shapes. The best designs, voted for by the eteRNA community, are then generated in the lab and their behavior is observed. The scientists give this information to the players of the game to help them develop new game strategies. This continuous cycle helps researchers understand RNA folding and activity, which can be used to develop new RA molecules to treat diseases. 

Phylo

This puzzle game was created by scientists at McGill University. The goal of the game is to improve genomic sequence alignments of disease-associated genes from multiple species. Players move DNA sequences, illustrated as rows of color-coded blocks, to find the best possible match. Further, 70% of around 350,000 multiple sequence alignment solutions generated by Phylo players are more accurate than a computer algorithm.

The Cure

This card game was created at the Scripps Research Institute to help find predictive biomarkers of breast cancer. Players put together 5 genes from a board of 25 pre-selected genes (based on cancer-relevance). To win, an individual’s gene set produces the best predictive model of breast cancer outcomes.   

EyeWire

This game comes from a lab at Princeton University and uses data from the Max Planck Institute for Medical Research. It challenges players to map retinal neurons by solving puzzles and reconstructing 3D structures of neurons, which helps researchers understand information processing circuits in the brain.  

 Biotic Games

A scientist at Stanford University developed various educational, “biotic games” that help people understand living organisms. In PAC-mecium, players herd a flock of paramecia (single-celled organisms found in ponds), which is represented by a fish. Further, they can see how these organisms swim and change direction in response to electrical stimulation, observe the “fish” eating virtual food pellets, and maneuver it away from predators like zebrafish.

References

"Games for Science" in The Scientist

"Serious Games and Biomedical Research: What Do Game Developers Bring to the Table?" in Biomedical Computation Review

#Mentors

As I started the new year, I reflected back on mentors who have helped me on my career journey. I wouldn’t be where I am today without their support and guidance.

Mrs. Moore

I can still remember one of my first lessons as a 1^st grader in Mrs. Moore’s class at Carson Montessori. She told the scientific story of the formation of the universe. The lights were off and she started quietly. Then, there was the loud pop of a balloon and stars (a.k.a. glitter) scattering across the universe. I didn’t realize it at the time, but she was teaching us the value of communicating science through storytelling. 

Brandt Smith and Ms. Marquard

In Jr. High at Clark Montessori, I learned about the relationship between science and the world from my teachers, Brandt and Ms. Marquard. We went camping for a week each year, where we discussed the ecosystem of the forest. Similarly, in 8^th grade, everyone went to Andros Island in the Bahamas. We studied marine biology by snorkeling around beautiful coral reefs, bright fish, sharks, and more. Experiencing science in the world around me made a strong impact on my life.

Sally Lamping

I was lucky to have Sally as my freshman and sophomore English teacher in high school. She was so supportive of her students and encouraged our creativity. I remember being in her class and acting out Shakespeare scenes that we re-worked into a hip hop setting, having a mock trial with the characters from The Great Gatsby, and writing poems inspired by artists of the Harlem Renaissance. She helped me become a better writer, and helped me understand the power of the written word.   

Doc Brock

My high school chemistry teacher at Clark Montessori, Doc Brock, was an amazing mentor. He was passionate about the subject and made chemistry exciting. I chose to study science in college because of his class. He fostered my interest in chemistry. In fact, the school didn’t offer AP chemistry, so Doc Brock formed a club where he was willing to teach it after school. He really started me on a scientific career path.

Dr. Jody Modarelli

My academic advisor and undergraduate research mentor at Hiram College, Jody, had a profound impact on my life. She gave me the opportunity to start doing laboratory research in biochemistry as a freshman. I could always go to her for support and guidance, and she encouraged me to consider applying to graduate school for science. She was very smart, yet down-to-earth. Jody always listened to her student’s ideas and encouraged us to test our hypotheses. She was my role model and I wanted to be just like her. I really miss her since she passed away from pancreatic cancer in 2013, but I know her spirit lives on in all of the lives she touched.

Dr. Carol Shreiner

My organic chemistry professor, Carol, was a great teacher and mentor. I know most people groan when they hear the word, “O-chem,” but Carol made it interesting. It seemed more like art when she was drawing structures on the board. She was supportive of her students (including me) and always willing to help them understand chemistry concepts. Also, she was passionate about chemistry and shared her love of science with the campus. I was a member of the chemistry club, which she advised. Carol encouraged us to communicate science in fun ways. We did demos, such as the electric pickle and liquid nitrogen ice cream, for National Chemistry Week, worked on science projects with children who had special needs at Hattie Larlham, and holiday themed experiments, such as a green flaming pumpkin for Halloween. I was lucky to have her as one of my mentors.

Dr. Erin Lamb

Erin was my teacher for a Biomedical Humanities course on “Genetics and Popular Culture” at Hiram College. In that course, I learned the importance of the public perception of science. For example, we discussed how Gattaca and Chromosome 6 promote fear of laboratory experiments and biotechnology. We also debated issues surrounding biospecimens, including the story of Henrietta Lacks and HeLa cells. This class allowed me to understand the importance of sharing science with everyone. Erin also helped me improve my writing skills by providing constructive feedback about my work.  

   

Dr. Patricia Sime

My PhD advisor at the University of Rochester was Tricia. She is a great role model for young scientists and clinicians. She takes care of patients, mentors students and oversees research in a lab, chairs the Pulmonary and Critical Care Division, and spends time with her family. She was a wonderful mentor who supported me when I chose to go towards a science communication career. Writing and revising drafts of papers, presentations, and abstracts with her taught me about the creative process.

Dr. Jim Hsiao

Jim was an older graduate in the Sime Lab who took me under his wing. He trained me in laboratory techniques and experimental design. Moreover, he became my big brother. He supported me throughout graduate school and continues to give me encouragement from far away. If my experiments weren’t working, he helped me troubleshoot. When I was feeling confused about my future, he reminded me to follow my heart.

Dr. Tracey Baas

I was lucky to be a part of the Broadening Experiences in Scientific Training (BEST) program at the University of Rochester (UR), which gave me the opportunity to learn about careers in science communication. As the director of the program, Tracey helped me (similar to many others) pursue a post-doctoral path in science writing. For example, she gave me opportunities to write for the UR BEST newsletter, which allowed me to build up my writing experience. She is always there for graduate students who need career advice. 

What to Wear at Scientific Conferences

Along with science, I’ve always had an interest in fashion. I love watching project Runway and reading tweets about the latest trends. This may be one reason that I always got excited about scientific meetings in graduate school. They gave me a chance to dress up, compared to my daily outfit of jeans and gym shoes in the lab.

Here are some of my tips about chic and comfy conference wear:

• I recommend packing some cute wrinkle-free dresses or shirts. This will help you save time in the morning, so you can focus on a day of exciting science. 

• Personally, I think it’s good to have some outfits that are bright and colorful. Many business clothes at conferences are grey and black. Thus, a pop of color, like red, or a cool print can help you stand out.

• Coordinate with your presentation. For example, if you have a poster that is blue, you could wear a matching dress/shirt/tie. Also, if you have a talk in a large, dark room, you may want to wear a light color.

•          Some female T.V. characters with style that would be great for scientific meetings include Claire Underwood in House of Cards, Olivia Pope in Scandal, Alicia Florrick in The Good Wife, and Jessica Pearson in Suits.    

 

  

• Male T.V. characters wearing nice suits that would work well at scientific conferences are Mike Ross and Harvey Spector in Suits, Walter O’Brien (business attire) in Scorpion, Don Cheadle in House of Lies, and Rafael Barba in Law and Order: SVU. 

• "Let’s get some shoes.” When I’m giving a presentation, I prefer to wear heels. The added height makes me feel taller and more confident. However, it’s also important to have comfortable dress shoes at scientific meetings, especially if you have to walk a lot. I recommend bringing a couple pairs that would work with your clothes, whether it’s flats, men’s dress shoes, high heels, or wedges.

My Red Power Heels

• My last tip is to wear what makes you feel good and expresses your own, individual personality. I love dresses, so that’s what I bring for conferences. A fellow graduate student in my lab liked to wear bow ties at scientific meetings. Some people like to add accent jewelry. #YouDoYou and dress in a way that will make you feel like the scientific expert that you are.     

#Startstruck by Scientists and Science-Related Writers

As a trainee in science, you often have the chance to attend talks and meetings where you see world-renowned experts in the field. Similar to a person who spots their favorite celebrity (movie/tv/music star) IRL, you can’t help but be #startstruck. Here are a few of my #startstruck moments when I got to see amazing researchers and science communicators:

1) Rebecca Skloot – I remember attending a talk by Rebecca Skloot, the author of “The Immortal Life of Henrietta Lacks,” as an undergraduate at Hiram College. I was so excited to see an author who changed the way both scientists and the public think about medical ethics (including informed consent and patient privacy) and the history of cell culture. I can remember her talking about sitting in a biology class where she learned about HeLa cells, where she wondered, “Who did these cells come from?” She is one of my role models, since my career goal is to be a science writer.  

 2) Tracy Kidder – The common reading for Hiram College one year was the book, “Mountains Beyond Mountains,” which was written by Tracy Kidder. The book describes the work of Dr. Paul Farmer, who improved the diagnosis and treatment of tuberculosis in under-served areas throughout the world. Based on the use of his book in the curriculum, Tracy Kidder came and gave the opening convocation. It was cool to have the chance to see a Pulitzer Prize-winning author and famous literary journalist in person. Looking back, I wish I had recorded his inspirational speech.

3) Peter Barnes, MD – As a graduate student studying inflammatory lung diseases, I remember reading a lot of reviews and manuscripts by Dr. Barnes. He is a respiratory researcher in the U.K. who is an expert in the areas of asthma and chronic obstructive pulmonary disease (COPD). The first time that I saw him was at the American Thoracic Society (ATS) Annual Conference in Philadelphia, where he gave a talk about non-smokers with COPD. I can remember just being in awe of him since he is such a leader in the field. This past May, he actually introduced me at a conference. I may have looked calm and collected as I walked up to the podium, but I definitely did an internal #startstruck squeal.  

 4) Stephen Gordon, MD – I was able to attend great talks by Stephen Gordon at ATS conferences, and even got to meet him in person. He is a respiratory researcher who studies respiratory infectious diseases and the health effects of household air pollution from cooking fires. He is one of the world’s experts on lung diseases related to biomass smoke exposure and cookstove interventions in low-and-middle-income countries. He also received the World Lung Health Award from the ATS for his research and training efforts in Malawi.   

John Balmes, MD - I was able to meet Dr. Balmes at ATS conferences. He is a well-known respiratory researcher who studies outdoor air pollution, household air pollution, asthma, and cardiopulmonary diseases. He has received many awards throughout his career, including the ATS Public Service Award in Recognition of Outstanding Contributions in Public Health in the area of Respiratory Disease and Medicine, The John M. Peters Award in Appreciation of a Lifetime of Leadership, Research, and Devoted Service to the Pursuit of Respiratory Health from the ATS's Assembly on Environmental, Occupational and Population Health, Rutherford T. Johnstone Award for Exemplary Contributions to the Field of Occupational Medicine, and more. He also likes to support and promote trainees. I can remember feeling a good type of shock when he recognized me at an ATS assembly meeting.

5) Joe Palca, PhD – I took a graduate school course called “Careers in Science Communication.” Different speakers in science communication would come and tell us about their jobs. One week, Joe Palca, a science correspondent for NPR came to our class. He gave really good examples and tips about communicating science to the public. Later that evening, I was a part of a small group from the class who got to join him for dinner. It was a great experience to hang out with a nationally-recognized science journalist.  

6) Enid Neptune, MD - The keynote speaker for the University of Rochester's Lung Biology Research and Trainee Day in January 2017 was Dr. Enid Neptune. I was able to see her present her research on Marfan syndrome and inflammatory lung diseases, specifically COPD. I also had the opportunity to attend a career development round table with her, where she gave advice to graduate students, post-docs, and clinical fellows about planning for the future. I'll never forget that she said, "It's your life. You have to do what's right for you." It was helpful to learn the experiences and perspective of an important translation researcher in pulmonary medicine. 

7) Dinah Singer, PhD – As a science writing fellow, I was able to meet Dr. Singer, the director of the Division of Cancer Biology at the National Cancer Institute (NCI). She is also a Senior Investigator and Chief of the Molecular Regulation Section of the Experimental Immunology Branch of the NCI intramural research program. She is a well-known scientist, serves on various advisory and scientific boards/committees, and an important leader at NCI. As a woman in STEM, I look up to her as a role-model. Further, even though she is this amazing and accomplished researcher, she is very down to earth. For example, when I met her, I said, “Nice to meet you Dr. Singer.” She quickly replied, “You can call me Dinah.”

8) Douglas Lowy, MD – I was able to sit in during a meeting that was led by the (then) acting NCI director, Dr. Lowy. I was in the same room as one of the scientists who won the 2017 Lasker-DeBakey Clinical Medical Research Award. His research led to the development of the human papillomavirus (HPV) vaccines, which help prevent cervical cancer.  

9) Diana Galbadon, PhD – I was able to go to the National Book Festival this year with a lecture by Diana Galbadon. She is the author of the “Outlander” series, as well as a PhD in Quantitative Behavioral Ecology. I am a huge fan of the “Outlander” books and T.V. show, so it was a great chance to see her in person. Since I am interested in science communication, it was interesting to hear her perspective on science and writing during her talk. According to her, in both science and writing you are trying to draw out patterns from chaos. The only difference is that one is external (science) and one is internal (writing).  

Feel free to share your own science-related #startstruck moments in the comments!

Great Books Related to Science and Medicine

Since I have started a science writing internship, I have reflected back on books related to science and medicine that inspired me to pursue a career combining scientific knowledge and creative writing. Here is a list of works, both nonfiction and fiction, that I recommend for individuals with an interest in science who love to read.  

Call the Midwife (by Jennifer Worth)

This memoir describes healthcare, especially related to pregnancy and birth, for people living in the low-income area of the East End slums of London during the 1950’s. If you like the PBS show based on the book, I highly recommend reading the book.

Cider House Rules (by John Irving)

A fictional story about an orphan who grows up, leaves home, and eventually becomes a doctor. It also discusses medical ethics related to reproductive rights.

Complications: A Surgeon’s Notes on an Imperfect Science (by Atul Gawande)

The stories in this book show the complexities and uncertainties related to the science of surgery. It gives us a view of hard choices and fatal mistakes from the surgeon’s perspective.

Cooked: A Natural History of Transformation (by Michael Pollan)

In this book, Pollan describes cooking as it relates to four elements – air, earth, fire, and water. It describes the scientific aspects of cooking, as well as both ecological and social connections to food.

Cutting for Stone (Dr. Abraham Verghese

This fictional novel describes the lives of twins growing up in Ethiopia (during political turmoil), their medical training throughout childhood, and experiences as they grow up and travel.

The Immortal Life of Henrietta Lacks (by Rebecca Skloot)

A great book that discusses bioethical issues related to patient consent for biomedical research, issues of race in clinical research, and the development of cell culture.

Lab Girl (by Hope Jahren)

In this memoir, Hope Jahren describes how her childhood experiences led her to become a scientist, as well as describes her triumphs and disappointments throughout her research career.

Mercies in Disguise: A Story of Hope, a Family's Genetic Destiny, and the Science That Rescued Them (by Gina Kolata)

This is the only book on the list that I haven’t read; however, it is currently on my Amazon wish list. A friend in science communications told me about this book by NY Times writer Gina Kolata. It describes the story of a family that discovers that they carry a genetic disease, and discusses issues related to genetic testing.

Mountains Beyond Mountains: The Quest of Dr. Paul Farmer, a Man Who Would Cure the World (by Tracy Kidder)

An inspiring book about Dr. Paul Farmer, who started Partners in Health, a global health organization. It addresses healthcare disparities and describes Dr. Farmer’s work in researching and treating infectious diseases in low-income areas throughout the world.

My Own Country: A Doctor’s Story (by Abraham Verghese)

In this memoir, Dr. Verghese writes about his experience as a young, infectious disease doctor in Tennessee, who becomes the local expert on AIDS. It shows the important relationship between a doctor and his/her patients, as well as the impact of social views on medical treatment and research.

Oryx and Crake (by Margaret Atwood)

This fictional, post-apocolyptic novel makes the reader think about the ethics of bioengineering, the impact of businesses and money on science, the role of the media in social perception, etc.

Outlander (by Diana Galbadon)

This historical romance with a sci-fi twist tells the story of a British nurse in 1946 who travels back in time to 18^th century Scotland. Throughout the book, the main character uses her 20^th century medical knowledge to solve health-related problems.  

 Silent Spring (by Rachel Carson)

If you are interested in toxicology and/or environmental health, you should read “Silent Spring.” This book describes the harmful effects of DDT, and played an important role in the environmental movement of the 1960’s. 

The #SimeLab is Searching for Lung Disease Cures

As I was working on my thesis defense slides, I started listening to Lady Gaga's new song, "The Cure." Honestly, I am a total fan of Lady Gaga and love her music. Replaying the song many times over the weekend, I was inspired to write lyrics related to respiratory research projects in the #SimeLab. I hope you like this science-related song.

#SimeLab

Lady Gaga – “The Cure”

The #SimeLab is Searching for Lung Disease Cures

Sung to the lyrics of Lady Gaga’s “The Cure”

Lyrics:

Lung scarring makes you breathless

And it will result in death

Since there are few effective treatments

No drugs can reverse scarring

Or stop patchy lung hard’ning

“When you can’t breathe, nothing else matters”

So many knowledge gaps

The Sime lab keeps researching

So many knowledge gaps

That need to be addressed right now

So many knowledge gaps

The Sime lab keeps researching

To help those with lung disease

We want to find the cure, We’ll

We’ll try and fix the lungs

We research the bio,

We’ll try and fix the lungs

Doing experiments each day

Trying to make some good headway

Finding a new therapy

Keep searching for the cure (for the cure)

Breathing smoke from fires and cigs

Harms and damages the lungs

And suppresses immune defenses

Yet, there are few therapies

To help these communities

With smoke induced health consequences

So many knowledge gaps

The Sime lab keeps researching

So many knowledge gaps

That need to be addressed right now

So many knowledge gaps

The Sime lab keeps researching

To help those with lung disease

We want to find the cure, We’ll

We’ll try and fix the lungs

We research the bio, We’ll

We’ll try and fix the lungs

Doing experiments each day

Trying to make some good headway

Finding a new therapy

Keep searching for the cure (for the cure)

We’ll try and fix the lungs

We’ll try and fix the lungs

We’ll try and fix the lungs

We’ll try and fix the lungs

We want to find the cure, We’ll

We’ll try and fix the lungs

We research the bio, 

We’ll try and fix the lungs

Doing experiments each day

Trying to make some good headway

Finding a new therapy

Keep searching for the cure (for the cure)

Keep searching for the cure (for the cure)

We’ll try and fix the lungs