Bioinformatics for Farming and Rainforest: An Interview with Bent Petersen

Bent Petersen is a biotechnological engineer with a PhD in bioinformatics and he works as an associate professor at GLOBE Institute. Today, he will talk to us about his precision farming and his rainforest projects, the effect of the pandemic on his work life and how Mailbutler helps him stay organized.

Bent, thanks for taking the time for this interview today! It’s a pleasure having you here. Let’s talk about you, your work, your career, and your life in general. To start with, I’ll ask you to fill in the following blanks:  

If I wasn’t working as an engineer, I would probably have become… 

...a police detective. I have always liked to solve puzzles, but you could say that with my profession as a DNA researcher, this is exactly what I am doing right now.

I hope to spend my retirement… 

...in a warm country. I might be born in Denmark and my wife is saying that I am a Viking, but I really do hate freezing. Maybe this is why I have so many collaborators in Asian and South-American countries ;-)

When I was a kid I always wanted to become… 

...a race driver or a jet pilot, neither of them I turned out to become. Instead, I bought a fast German-brand car and in a normal world, I spend a lot of my working time on aeroplanes.

The most flattering thing a colleague has ever said to me was …

...a colleague told me her little sister found the teaching material we developed for high-school teachers about genome-mining in the rainforest so inspiring, that she now wants to study the same.

What I like most about Copenhagen, the city I live in is …

...the vibe. Denmark is, most of the time, a cold country. So whenever we have a little warmth and the sun is out, you will see the Danes sitting outside everywhere (could be in blankets) with a beer, eating food and enjoying life with a friend or with family. In Copenhagen, we have many small breathing holes, that being green parks, the beach, or other places where you can go to forget your busy schedule for some time. 

Thank you so much for your responses, Bent! Now, let’s dive into your work life. You’re a biotechnological engineer with a PhD in bioinformatics and currently working as an Associate Professor. Please tell us, what are you working on at the moment, exactly? 

At the moment I am working on several projects, with the biggest ones being a precision farming project and a rainforest project. In the precision farming project, we have Maize plants where half of the seeds have been coated with plant beneficial bacteria. We hope to see that the bacteria will be helping the plant to be more resistant to drought. Using machine learning we want to find the biosignatures and key parameters in these more than 500 samples with several terabytes of data in different forms.

In the rainforest projects, we are very interested in looking into the genetic blueprint of the plants hidden in the forest. We are globally facing a situation where, due to deforestation, the rate of species extinction is higher than that of the new species description ~150 species are disappearing​ every day​. Many of the plants, threatened with extinction, contain important​ medical compounds​, which only plants can produce because they are so structurally complex, that they cannot be chemically synthesized. These chemicals are the product of millions of years of evolution for the plant to protect itself against predators - chemicals that we can use for medicines and drugs.

Rainforest plants, therefore, are an enormous untapped source of new genes, new drugs and new valuable/rare compounds and we need to find them and preserve them before they disappear. Besides that, we are also looking for new bacteriophages, or short phages, which are viruses only attacking specific bacteria – including the ones we are unable to kill with today’s antibiotics. They specifically infect and kill bacteria without infecting, or further impacting animal cells. Each phage-type is able to infect and kill a narrow range of bacterial strains, which makes them suitable for development into highly precise antimicrobials. Bacteriophages make great antimicrobials because they have been in an evolutionary arms race with bacteria for more than 3 billion years. As the rainforest is a biodiversity hotspot, we know that there will be many new interesting phages, we just need to find them… 

How would you explain what your work is about to somebody who has no idea of science? 

I use huge supercomputers to look for the golden needles in huge DNA-haystack originating from rainforests, plants, extinct animals, mummies and other interesting environments or species. In my group we use advanced machine learning to find patterns we would otherwise not be able to find with the naked eye and together with our collaborators we translate these patterns into new findings. I also manage the data for one of the worlds largest sequencing projects, where we aim to sequence all 10,000 bird species in the world.

I know that your father runs his own company, and you could have taken it over. You knew pretty soon, though, that you wanted something else, right? How did you get the idea to become an engineer? 

It actually goes back to when I was a kid, after my race driver and jet pilot dream. My childhood friend's father was an engineer, and I thought it was so cool as we got to work on his old computers. To be honest I didn’t really know what an engineer did.

After primary school, I studied at a high school, which had a focus including more physics, maths and natural sciences than the normal high school. I was so fortunate to have a very inspiring biology teacher, who really sparked my interest in biology (we still meet and drink beers once in a while). It then just happened to be that one year after finishing high school, the engineering university started a study line with a focus on biotechnology. It was perfect as I could now combine my interests in biology and computers, with an education that would open many doors for future jobs.

These days, we hear a lot about bacteria, viruses, sequencing, vaccines on the news. Have you, in some way, also been involved in research about COVID 19? 

With other viruses yes, but unfortunately not with COVID-19, yet. I have an idea for a project I would like to pursue in a very near future.

I know that you’re a world traveller. In fact, in 2019 you spent 192 hours on planes and covered 136.606 km. Apart from the fact that we all can’t travel, how else has the virus changed your life? 

Yes, those were the times, but now everything has changed. My last travel was to Mumbai in 2019 where I was teaching a bioinformatics workshop. Now I have been working from home like everyone else, and because I work at the university and my workstation is a computer and not the lab, it has not been of utmost importance that I was physically at the office even when we were partly allowed to return. In June I had my first physical meeting at the university in 1,5 years…!

Covid-19 has also significantly changed the way I am working. Zoom has become an integrated part of my daily work life and I have more meetings than I have ever had before. Yes, it is nice that we can have virtual meetings, but on the other hand all the extra meetings just take away the time I have for the job I am hired to do. People have also changed the mentality to “Hey, let's have a meeting, you are anyway just sitting at home..!” … Mentally, having 4-5 back-to-back meetings in a day with only 5 minutes break (if even) is not healthy - and I hope this will be reduced when the world returns to a more normal state.

You have been to countries like Brazil, China, Egypt, India and many more. When you look back, is there a country that particularly impressed you? Would you tell us what you worked on in these countries? 

That is true, I have been around the world, and it's difficult to point out exactly which country impressed me the most. In Malaysia, however, I have been amazed by the accomplishments we have achieved within the past few years. Here we have established a Centre of Excellence for Omics-Driven Computational Biodiscovery, COMBio, of which I am the Joint Deputy Director (https://www.combio-aimst.my).

We have many ongoing projects in Malaysia and in particular,  what I find most interesting, is our rainforest project, where we look for new interesting medical compounds and new bacteriophages to combat antibiotic-resistant phages. We have even been pitching our project to the Ministry of Education. Besides the scientific outcomes, I also choose Malaysia for many other reasons. It has beautiful nature - especially the Belum Royal State Park Rainforest, the food is amazing, everyone we meet is very friendly, and I have some very good friends living there.

You’re involved in 2 rainforest projects, which is wonderful! Are these projects a good opportunity for you to combine your work with your love for nature? 

Absolutely… Except that it does not help with my, hmm let's call it discomfort with small bugs and bloodsuckers. When you are in the rainforest admiring its beauty, the sounds, the plants, flowers and so on, there is also the other side of the beauty, that everything wants to bite or suck your blood. I am in particular not fond of ticks or being chased by snakes (I was once chased by a Malaysian blue coral snake), the latter did get the adrenaline going... And in Malaysia, they have terrestrial leeches which are standing straight up in the forest ground so you barely can see them, just waiting for you to approach them, and when they sense you, they will chase you from all directions.

I am always fully packed up in rainforest clothes, bugs spray and step dancing so I don’t get bitten, and I haven’t so far. But besides that, I absolutely love it and I have tons of pictures from all my travels of plants, animals, sights and so on. 

Besides your passion for nature, you also seem to be fond of writing. Would you tell us a little bit about the blog on your website, please? 

The past year I have unfortunately not been that active at the blog (https://www.bpetersen.dk/), as I wanted to be. Recently I moved it from one provider to another, and before I got to transfer everything Covid kicked in. The overload of work and Zooming has taken most of my energy to expand on the blog. But now is the time to get the writing going again. I have a whole list of subjects I want to add, amongst others I will be writing about our projects, posting in layman's terms about my publications, and posting beautiful pictures from my travels and similar that cross my mind. Amongst others, I have for a long time, been planning some posts about Mailbutler and how I have Mailbutler integrated into my work life as that has really been a lifesaver.

You’ve also written blog posts about Mailbutler! How does Mailbutler help you organize your work? 

Mailbutler has been a fantastic extra tool that I now have fully integrated into my work. Some years ago I started suggesting features I was missing, which has now been integrated into the tool. Absolutely awesome.

One of the features I like the most is the “optimized send” for a specific person. As I have collaborators scattered over the world we are in different time zones. Sending an email at noon to China or Malaysia may not reach the person at the best time, and my email might drown in other emails arriving during the evening/ night for that person. The option of having Mailbutler send the email at the optimal receiving time for that particular contact is simply amazing. This I also use a lot even for people receiving my email in Denmark to make sure they receive the email at the optimal time, depending on when they most often read or reply my email. I am also very fond of the ability to cancel an email, effectively having a sending delay, which has saved me from quite a few email mistakes.

Last question, Bent: If you had 3 wishes for the rest of the year 2021. What would they be? 

1: That we all will be able to return to some sort of normality soon.

2: That funding agencies and/ or philanthropists will realize the need to invest in basic research and that funding agencies will also understand that just because you have not previously published in a specific field, it does not mean you can’t do the search…

3: That my family, friends and collaborators (and everybody at Mailbutler!) will continue to stay safe and healthy.

Thanks so much for taking the time, Bent. We wish you all the best! 

Thank you to you as well. I wish you all the best for you and the entire Mailbutler team. Keep up the good work, you have really developed a fantastic product!