A. Murat Eren, The Question-Authority Shepherd At MBL– A Scientist’s Unique Story

WOODS HOLE – “Every single day I think about that valley. In my dreams, I am still just a shepherd there. It’s a simple life with vast space to occupy your mind. I miss that life so much.”

Instead of being a shepherd in the Barhal Valley in the mountainous region of northeast Turkey, A. Murat Eren is an assistant research scientist at the Josephine Bay Paul Center for Comparative Molecular Biology & Evolution at the world-renowned Marine Biological Laboratory. He still has a lot to occupy his mind.

Now, his vast space is the world within a world that is microbial ecology, a field he first discovered as a graduate student in New Orleans. “You are an organism and you are a habitat to trillions of other organisms. I had no clue,” he said. “I literally had no idea. Just like we can’t think about the number of stars in the universe, the human mind does not comprehend this.”

Call him “Meren,” he said. “Murat” is common male name in Turkey so he needed a nickname and, he explained, “Nicknames, some of them are not very pleasant when you let other people choose your nickname for you.”

The common American mind almost cannot comprehend the path of Meren.

“Things we realize by the trajectory of our living,” he said, “usually we don’t see it until after it happens.”

He was a shepherd as a child, and later he worked for the Turkish government because he taught himself cryptography as an open source Linux advocate. After arriving in New Orleans and getting humiliated for his English language skills while trying to order food at a Subway Restaurant, the Turkish computer expert pivoted into biology and got a PhD, and then he created a new way – Oligotyping – to differentiate the concealed diversity in microbial populations.

“Oligotyping is a big advancement,” said Mitch Sogin, the director of the Bay Center and the person who hired Meren. “I don’t think the rest of the world appreciates its value yet.”

Meren is a gifted photographer who documented many things, including Occupy Wall Street. “I never classify myself as an anarchist,” he said. “I am interested in uprisings and protests. If I truly want to understand, I have to go talk to the people.”

He owns a bright pink boat. “I have a huge problem with authority. If someone tells me what I cannot talk about, that’s what I want to talk about,” he said.

He played bass in a jazz and blues bands at various places in Turkey, and he has a blog he writes in Turkish featuring, among other things, photography and his political thoughts. “If I go back to Turkey, I can’t be a scientist there. I disturb too many people in Turkey,” he said. He explained that he has upset many Turkish academicians with his calls for stricter standards for plagiarism. In one article he wrote, “Turkey’s bad academia is self-perpetuating.” Though some did not like the criticism, others were happy he spoke up, he said.

“He’s a very high-powered kind of guy,” said Sogin.

Meren is now 33 years old.

As for why he hired Meren in 2011, Sogin said his scientific method came down to, “I decided he had the right look in his eyes.”

 

“I never have plans”

Meren was raised in a city and commuted to the valley where his father was raised every summer until he was 14. The valley was not connected by roads to the rest of Turkey until 1950, he said. Each summer, he lived with his father’s relatives and lived the life of a shepherd – taking care of animals, carrying hay, and harvesting vegetables.

“I ask myself why did I leave there,” he said, of the last time he visited.

He knows it was because he was a city boy, interested in the bigger world. Now, from far away, he said it is heartbreaking to think of home. “I miss those mountains,” he said, as he showed a picture on his computer screen. Out his window was a magnificent view of Eel Pond. “Probably I need this office the least because I never look out the window,” he said. “I just stare at my computer all day.”

He had always wanted to be a civil engineer because of a family tradition. His father was a civil engineer. So were other males in his family. “My father was an authoritarian figure. He influenced many of the males in the family, except me,” said Meren.

More than once, Meren said, “I have a problem with authority.” He left home at 15, he said, declining to explain any further.

When he was in high school, Meren met a friend who was into computer games. He became very good at a game called Quake Arena, “a multi-player game where you could shoot at each other.”

And he realized, “If I became a computer scientist, no one would judge me for playing games all day long.”

So computer science was his plan?

“I never have plans.” he said.

 

Open Source Movement, Then Cryptography

“I realized there was more to computers than just playing games,” said Meren. He became intrigued and then involved in the open source movement, and especially with the Linux operating system.

“The first time I tried to install it, Linux wiped out my hard drive,” he said. “It broke my heart. So I took the challenge, and started playing with Linux.”

He was attending a “a very poor university, from an economic standpoint.” The university did not even have enough email addresses for the students, and Meren wanted to help the school save money and “switch to open source applications and not pay license fees to Microsoft.”

In learning Linux, he learned, “There is a vibrant community in Turkey interested in Linux.” And he also learned, “It’s more mature than the gaming community.”

He wrote a long article for his own blog about the importance of open source, and, two years after he had crashed his hard drive, he was invited to give a seminar on how and why open source is so important.

Meren graduated with a degree in computer engineering. He wrote his undergraduate thesis on cryptography. “Cryptography is a way to establish secure connections online, No one knew anything about it. There were no resources in Turkish, and I didn’t know any English. So I’m the guy who learned English from a cryptography textbook.”

He taught a couple of courses because, “I wanted to teach. I wanted to be the person I couldn’t find when I tried to get into the university.”

And then, with his cryptography degree he began a security consultancy that led to him working for The Scientific and Technical Research Council of Turkey (and for Turkish National Research Institute of Electronics and Cryptology) to develop a Linux-based operating system for the use in Army and other government agencies, he said.

“Even though it was Turkish Army, I couldn’t say no to this opportunity to make Linux more accessible to the Turkish people,” he said.

But the government changed, he said. “When the government changes in a country like Turkey, the new government feels the urge to change every single person in the government. We did a very good job for years. The project is now dead, because the government have changed the entire administrative core of these institutes which affected the project. At the beginning, the project was a big success.”

He had spent 15 hours a day in front of a computer screen.  “I started to realize that life is about more than just doing work.”

He met a woman. Her name was Duygu. “She is a lovely biologist. One night, I stumbled upon her blog, and decided to marry her,” he said.

She had plans to come to the USA, to New Orleans specifically, and pursue her PhD in biology at Louisiana State University. “I was very impressed. I didn’t want to let her go.” They got married.

“I quit my job and moved here to the U.S without any particular plan,” he said.

 

The New Orleans Pivot

So the Turkish guy who learned English from a cryptography book found himself in New Orleans. One day, when he first arrived, his wife asked him to get her a sandwich at a Subway Restaurant. In truth, he spoke hardly any English, but he had a strategy. He would repeat whatever the person in line in front of him ordered.

The restaurant was crowded and when he got to the front he did not hear what the person in front of him ordered. He panicked a little when the person behind the counter asked him a question. He didn’t understand, “so I figured I’d just say, yes.”

The person asked the question again, this time annoyed.

“ ‘Yes’ didn’t work, so I tried ‘No.’ ”

That didn’t work either.

He later learned that he was being asked what kind of bread he wanted. “I lost my pride,” said Meren of that memorable day at the Subway Restaurant.

That was 2007. Only seven years later, his English is flawless.

He attended the University of New Orleans and began pursuing a PhD in computer science. While Meren was there, working at Children’s Hospital in New Orleans, a Louisiana State University microbiologist named Mike Ferris walked into the computer lab looking for someone to help him with a problem cataloging large sequences of data.

“I knew if I can’t do it, shame on me,” recalled Meren.

“He said he’d do it,” recalled Ferris. “But he said, ‘I really want to know what you are doing, research-wise.”

Ferris explained about the world within a world that is the world of microbes. “He invited me into his lab, said Meren. “He explained his research to me and I realized I had no idea what he was talking about.”

Because Meren did not understand, he switched fields. He moved down one floor in the same building and began working with Ferris.

“To most people, it was ridiculous to walk away. But I don’t do things if I’m not interested in doing them. Your gut feeling tells you the truth the way it is. If you keep talking about only the things you have an idea about, you are stuck with only the things you can comprehend,” said Meren.

“In the limited time I have on this planet, all I can do is have these experiences,” he said.

“It’s impossible that I’ll ever see that kind of student walk into my laboratory again,” said Ferris. “He went from not knowing a word of English to becoming a PhD in a field he had never heard of before.”

 

Microbial Ecology, And Oligotyping

“I started telling him about microbes and he wanted to hear more,” said Ferris. “I told him how they were the only life on the planet for 3 billion years, how they can survive in boiling water, and how there are millions more bacteria in your body than there are actual cells in your body.”

He learned that “there are 10 trillion cells in your gastrointestinal tract,” said Meren. “That’s ten times more cells than in your entire body.”

And these microbes exist all throughout nature. Although they can appear to be similar, there are differences, some extremely subtle. Trying to sort those differences in trillions of cells is an enormous task, and Ferris was looking for some help in his specific research area.

After helping Ferris, Meren began learning all he could about microbiology and focused more specifically on microbial ecology, “the study of microbes and their interaction with their environment,” according to his dissertation, which he posted online.

Meren said an example is the microbes at different levels of a human’s gum line in their oral cavity have subtle differences, even though they are very close to each other in, essentially, the same environment. Understanding those subtle differences in similar microbes could be a key to understanding many things, he said,

The problem has been that there is so much data and there had been no way to identify the concealed diversity between very similar organisms until Meren developed a computational method called, Oligotyping. “It simply increases the resolution of understanding,” said Meren.

“Up until he did it, no one had looked at that small a difference in the genetic data,” said Ferris.. “He wrote a computer program to do it. He showed you can find interesting patterns by looking at subtle variations.”

 

MB-Something

He and his wife divorced, but they remained best friends, he said. She showed him an ad for someone studying the leaves on tomato plants looking for a post-doc to help out.

“I sent an application to MB-something,” he said.

He came north. It was spring. He rented a car but couldn’t find his parking spot even though his name was on a reserved spot. He met Sogin, someone Ferris called “a big name in the field.” Meren had no idea who he was but when they met, Meren said, Sogin was, “a pleasant guy.”

Meren met other scientists, and then as part of the application process he gave a talk to, among others, Sogin. “I gave my talk, a talk coming from a very novice person,” said Meren. “I said, ‘I don’t like how clustering ruins the data sets. There must be a better way.’ ”

At the time, said Meren, he didn’t know that Sogin had something to do with clustering, which was the only way, at the time, to deal with the enormous data sets that sequencing the genetics of microbial populations was producing.

Before he left Woods Hole, the scientist who was researching tomato plants suggested Meren was not a good match. But then Sogin pulled him aside and asked for ten minutes of his time.

“Of the people I have hired in my laboratory, If they tell me they have spent any time traveling by themselves, in a foreign country and not as part of a group, that is the biggest indicator of success, “ said Sogin. “That is the most essential screening question I can ask them. It shows initiative. Traveling in another country, shows self-confidence and the ability to take care of themselves. They grew up.”

Of course, the science helped too.

“He said, ‘You can come to my lab if you want. You are going to be able to work with anyone you want. This is what makes this place very special.’ “

“I thought this guy was taking pity on me,” said Meren.

He returned to New Orleans and, Meren said he consulted Ferris about Sogin. “He’s like, everyone knows him. He’s the pioneer.”

Ferris said he recalled writing a recommendation letter for Meren. “I said it would be a huge mistake not to hire him.”

Sogin hired Meren, even though Meren criticized clustering of data sets. “The first thing you realize is that good scientists are the ones that can take criticism and change their mind just like that,” said Meren.

He moved from New Orleans to Woods Hole in spring in 2011.

“No one told me that this place gets cold,” he said.

 

A Very Pure Goal

“The curiosity part is very pure,” said Meren. “You want to learn; it’s a very pure goal. The scientist should be disconnected from the potential application of the findings.”

It is research for the sake of research. Let others do with it what they will.

“Once you have a well-defined goal, even if its helpful, you think a little too far ahead for your research,” he explained. Goals define your perspective.

He lets the research lead where it will, he said. “My goal is to sequence this data set and see if there is a long-term pattern. When you are completely open-minded, you do the research without a long-term goal.”

On Presidents Day, his goal appeared to be to work on a holiday. After a three-hour interview with Cape Cod Wave, he resumed his seven-day work week.

As his colleague and friend, Tom Delmont, a post-doc at MBL who recently studied algae in Antarctica said, “There’s no rest for science.”

On this holiday, Meren, Delmont, and Sogin were all in the building.

“When I was hired, Mitch asked me if I want to negotiate,” remembered Meren. “The question didn’t make any sense. I’m going to do what I like. Why would I want to negotiate?”

Despite not knowing exactly what MBL was when he applied, Meren said he now understands, “There are 54 Nobel Prize winners associated with MBL. The history of MBL makes it a unique place. You can do biomedical stuff with a well defined goal, or can do pure exploratory research stuff, he said.

And he added, “Failure is an option in the MBL.”

 

Life of Meren

“Twelve years ago I was touring with a band in Turkey,” said Meren. Now, he has no desire to play music. “I get a little too much satisfaction from science,” he said.

“His background is really unusual,” said Delmont. “Most people go to a university and stay with a topic.” But Meren changed directions completely more than once.

“I don’t see him staying here for decades. This guy can jump to another life. Possibly in another life, he will jump to astrophysics,” said Delmont.

“He’ll probably end up being famous for something,” said Ferris. “The Internet, some protest, something unpredictable. There’s a good chance he’ll be famous in science.”

“He works hard. He’s highly ethical, a highly-principled individual,” said Sogin.

“The way I live,” said Meren, “I don’t ask long-term questions to myself. I’m going to do what I want until I don’t want to do that anymore. When I am satisfied with my output, probably I would slow down.

Speaking of slowing down and his life on Cape Cod, he said, “I don’t like summer because it’s so much fun.”

For scientists, said Meren, work isn’t work. But distractions are distractions. Still, he doesn’t seem to care. His mind goes where it goes, just as it always has. He still thinks about the Barhal Valley, and he has proven his ability to change directions many times.

“I’m not making plans,” said Meren. “If you ask me if I want to go back today, probably not. I have a presentation in a week.”

 

— Brian Tarcy