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Statistical genetics, philosophy, and the world seen through the eyes of a 4-year-old

PORTRAIT: For tenure track assistant professor Emre Karaman, his spare time is counterbalanced by anything but the numbers, data and genetics that occupy his research in statistical genetics. Running in the beautiful hills around Viborg, reading philosophy and re-discovering the world through the eyes of his 4-year-old daughter take most of his time when he is away from the office. He has just received the prestigious Sapere Aude grant, which is granted to highly talented, younger researchers.

“- I don’t have any social media accounts,” Emre laughs at the end of the interview, when I tell him I have been searching online for photos of him for the article. “- I don’t need social media, really…” I reply that I think that is a wise decision, not many are able to be that steadfast. But somehow it goes hand in hand with his attitude towards life: Re-discovering the world with a 4-year-old must be so much more fun than spending time on social media.

With an educational background in econometrics and animal science, Emre did his PhD at the Akdeniz University in Antalya in Turkey. In 2016 he joined Center for Quantitative Genetics and Genomics (QGG) for a postdoc position.

What is a Sapere Aude grant?

The Sapere Aude grant is given to research investigators, who are highly talented, younger researchers, ready to lead participants in a research project on a high, international level.

Source: Independent Research Fund Denmark (DFF -Danmarks Frie Forskningsfond)

- What made you choose genetics and genomics?

“- As a statistical geneticist I have always been interested in finding solutions to challenges that arise from genetic and genomic research. One emerging issue in this research field is how to handle genetically admixed populations. If not handled properly, for example in human genetics, it may lead to inefficient medication for patients. In animal genetics, it may lead to inefficient use of genetic resources. Motivated by this challenge, I have gained interest in developing methodologies for the inclusion of genetically admixed populations in genomic research. During those activities, I became aware of the knowledge gap between the current state of the research field and precision medicine/agriculture,” Emre Karaman explains.

- Why did you choose to apply for a postdoc position at QGG and come to Denmark?

“- I had other offers as well when I came, but Aarhus University and QGG is one of the best places that one can work in this area [genetics and genomics]. So, that's the main reason, actually… I mean, it's one of the top universities in the world, and in Europe.”

The Sapere Aude project

- In December 2020, you swopped your postdoc position at QGG with a tenure track position here, and now you have received a Sapere Aude grant from the Independent Research Fund Denmark (DFF -Danmarks Frie Forskningsfond) about halfway into your tenure track position. That is quite an accomplishment. What is your Sapere Aude project about?

“- Genomic research is largely carried out in populations with a single genetic ancestry. On the other hand, populations with multiple ancestral genetic origins (genetically admixed populations) have been increasing in many species,” Emre explains.

- Can you elaborate a bit on how you define single genetic ancestry versus multiple genetic ancestry?

“- Sure,” Emre says, and continues:

“- The multiple ancestry is that if a population has more than one ancestral genetic origin, for example, if the population has had a genetic exchange in the past, for instance a genetic exchange between Europeans and Africans or Asians, these are how we define, at least currently, the populations. So, we say Europeans are one population and Africans are one population, Asians are one population, and so on,” he explains.

“- And multiple ancestral populations are when you have individuals that have, in their line, ancestors from these different populations. So that is what I call multiple genetic ancestry.”

- So, it's actually like one line or many different lines?

“- Yes. I mean, I wouldn't say line… Sometimes describing it in layman’s terms is a bit tricky…” Emre smiles and continues:

“- Handling genetically admixed populations requires novel methods and computational tools, when studying the relationship between the genes an individual have, and its traits. The main research question in my Sapere Aude project is, ‘How to best exploit and account for the genetic diversity among individuals which have multiple ancestral genetic origins, in genomic research?’. The project aims at filling the knowledge gap between the current state of the research field and precision medicine/agriculture, which I became aware of during my earlier research.”

What is a tenure track position?

The position as assistant professor/researcher can be filled as part of a tenure track course, where the employee after a maximum of 6 years moves to an appointment as associate professor/senior researcher. The transfer requires that the employee is assessed as professionally qualified to lecturer/senior researcher level.

(From Act on position structure for academic staff at universities (Retsinformation))

- What are the scientific challenges and perspectives in your project?

“- Understanding how differences at the gene-level are related to differences at the trait-level (for example, disease susceptibility) is a challenging task. State-of-the-art methods in genomic research assume that gene-trait relationship is linear. Complex traits are, however, a result of the interplay of multiple genes. Hence, assuming a linear gene-trait relationship is fundamentally wrong,” Emre elaborates and continues:

“- These multiple genes and their interactions may be more similar among the individuals of the same population, compared to the individuals in different populations. Because individuals in genetically admixed populations inherit their genes from multiple populations, new interactions may arise. Exploiting these interactions requires novel methods and computational tools, which is the focus of this project,” he concludes.

- How do you estimate the impact your project may have to society in the long term?

“- The outcome of this project will facilitate research within precision medicine and precision agriculture, by providing novel methods and tools for scientists within those research areas. By facilitating prevention strategies based on more accurate disease risk scores, the effectiveness of medication will increase. With its expected potential of increasing the accuracy of selection in agriculture, it will help plant and animal breeders to further increase the genetic gain. Not only can increased genetic gain help breeders, but it can also improve the value chain in the production sector, and the rest of the entire food sector. It will help to increase output and quality for the same or reduced input levels, which corresponds to millions of Euros. This will result in consumers benefitting from improved efficiency and lower costs, and the environment due to improved resource efficiency.”

- How do you expect the Sapere Aude grant to impact your career as a researcher?

“- I am truly grateful for achieving this highly prestigious Sapere Aude grant, which is a key stepping stone in my career advancement. This grant will allow me to become an independent researcher and to form my own research group, whose focus will be on development of novel approaches for genomic research, with a special focus on admixed individuals. I believe that the establishment of my own research group in this emerging research field will create outcomes that will allow me and my group, and thereby Denmark, to maintain our leading position in statistical and quantitative genetics”.

The world seen through the eyes of a child

For the 41-year-old statistical geneticist, his spare-time is anything but numbers, data and genetics. Since he moved from Turkey to Denmark with his wife in 2016, the couple has had the immense joy of becoming parents of a baby girl. For Emre, he is currently re-discovering the world with her and trying to be a good guide.

- How old is your daughter?

The simple question sparks light in Emre’s eyes:

“- She is four-and-a-half years old.”

- How do you re-discover the world with her?

“- Actually, we do a lot of things automatically in our life, right?” Emre starts rhetorically.

“- So even things like reaching for a bottle or reading or eating, they are quite normal to us. But when you look at a baby, everything is new to them. So, they just want to understand. They don't just pull everything, you know. It's a learning process. As you see them grow, you notice that the things you miss or you think that is quite normal to you, actually could be amazing to a kid. Because they get really amazed. I mean, the first time they can eat themselves, or they can walk themselves, or they can do things, where you think that's so easy. It is very interesting. You know, there's a lot of things that you have to appreciate. You have to appreciate it in your life. When she asks me good questions, or sometimes is annoying, if she corrects my Danish, for example.” He pauses a bit, and then continues:

“- We learn a lot of things from each other. And trying to be a good example is the tricky part. For example, I have to eat things that I normally don't like. Because she needs to have an open mind. These kinds of things.”

The philosophical perspective

- Other than spending time with your daughter, you read philosophy books, when you have time. What kind of philosophy books do you read?

“- I just read biography books, or sometimes mainly books about certain persons. Because sometimes I read a book and then they mention other philosophies, and then I become interested in that quote to better understand what that person thinks in general. I don’t feel like I am so interested in one person specifically, because they say a lot of things, some of which I don’t think the same way. Sometimes it's just one part or one angle they look at different things, is interesting.”

- Literature and philosophy are quite opposite to what you do in your professional life. Is reading philosophy like a counterweight to your professional life, where it is all about data and statistics?

“- I don’t think that is true. Philosophy is about thinking and questioning. Sometimes it's beyond the level of general thinking. And science is motivated by thinking and asking questions. You think about a problem, and you ask questions. So, philosophy, I think, is the same principle. You find something, find a problem to think about. Not necessarily a problem, but some topic to think about in depth and ask questions. Not general questions, but maybe detailed questions. It helps how you approach a problem, because sometimes even unnecessary and stupid questions may lead to better thinking. And they help you to approach from a different angle.”

Cultural differences

- Moving to Denmark, what is the biggest cultural difference you have experienced?

”- Cultural difference?” Emre reflects for a moment, and then continues:

“- I think here the professional life and the private life is very well respected, or maybe well separated. They are more entangled in my home country. So, your private life is also shaped by your work environment, and your relationships therein. Of course, you have some other life outside but here I think it's more professional, and more distinct. Work is at work and private life is private life. Sometimes you want to be able to talk with a friend that understands the situation at work. For example, if you have a bad meeting or whatever... That's the main thing. But with time you learn. This is the way it is. Either you accept it, or you just leave. It's just the way it is,” Emre says.

“- Another thing is the respect and trust, people have in each other. Because I grew up being suspicious of everything. But here, if you say something people trust you, people believe you. And then you follow the same principle. You know that nobody will cheat or treat you in a different way. That is a good difference. So, it makes life much easier actually. That you don't have to think about other things. I feel life is much easier here.”

“- Social life is totally different for example,” Emre begins. “- Because you leave everything. All your relationships. And then you move to a new country. So, the social life is affected like 100%. But I think work life is affected 100% in the opposite way. Finding the right balance between social life and the work life is the most challenging part. Because you have your professional life improved, social life reduced. So, you just try to figure out how to bring that up as well. That's the most challenging part.”

- We hear that many times. People in Denmark are really reserved. You don't make friends easily here…

“- Yes, exactly! So, when Covid came, they were saying ‘you have to have two meters distance’, right? And everywhere there were stickers and other things. But in Denmark you don't need that because there is always a two meters distance. Even in a corridor. So, we always have this distance,” Emre jokes, before he concludes:

“- There are cultural differences but it's not always negative. There are positive and negative things.”


This portrait article is partially based on background replies from Emre Karaman to the Independent Research Fund Denmark (DFF - Danmarks Frie Forskningsfond)