Difference between revisions of "Team:EPFL/Engagement"

So we will conduct this interview in two parts. In the first part we would like to know a little more about you and how you got into synthetic biology specifically, and then we’ll get to the part pertaining to ethics and community outreach.

What can you tell us about yourself? How did you get into sciences, did you have a straightforward path into it, or did you have different turns?

Well I started biochemistry and microbiology at ETH Zurich. I directly felt that I liked protein engineering and found that engineering biological system was very cool. But synthetic biology was at the very start, and during my studies I didn’t hear much of it. There wasn’t any iGEM team in ETH yet. Then I did my PhD at the University of Cambridge where I performed directed evolution of proteins and also worked on methods for doing this efficiently, namely using microfluidic water-in-oil droplets.

In each droplet you can have a separate compartment, so instead of having a 96-well plate you can have like a million droplets. So basically, in each droplet you can have a different library member. For example, if you want to create a library on an enzyme, you introduce mutations then you select out the members out that do want you want. But then, you have to find a method for screening them.

So we took a quick look at your publications on google scholar. (giggling) We noticed that the past couple papers you published are really pertinent to synthetic biology. One in 2015 about the changing expression in gene regulatory networks when you introduce new links between pathways and another one in 2014 where you were able to create an AND gate. How did you move from doing something more like biochemistry into synthetic biology?

So after my PhD, I wanted to move from engineering individual proteins to engineering gene regulatory networks. My main post-doc project was published in 2014 (A unified design space of synthetic stripe-forming networks) where I built stripe-forming gene regulatory networks. We first used computational methods to screen every 3-node topology and asked if this network could form a gene expression profile of a single stripe in a gradient of inducer. Once we have we had all the possible topologies, I build like 4 representative topologies that achieved the same phenotype but with different dynamical mechanisms.

After that I moved to Zurich as a junior group. In my group we use synthetic biology to improve our understanding of gene regulatory networks and their evolution. For example one of the question I am asking is “do networks with different dynamical mechanisms have different potentials to produce novel phenotypes?”

To answer this question we introduce mutations in the regulatory region of the networks and ask what kind of phenotype we get now. We do that for different networks and what we find is that depending on the network we start with we get a different a distribution of phenotypes. This implies that the dynamical mechanism puts a constrain to what it can evolve to.

We use synthetic biology to address evolutionary questions. I think it’s a nice approach because you can easily build different topologies. It is actually also known in nature that the same phenotype can be caused by quite different gene regulatory networks but of course it is much harder to study this in let’s say fly development than with synthetic networks in E. coli.

In January I’ll move to the Department of Fundamental Microbiology at the University of Lausanne and where I’ll start as an assistant professor in synthetic biology.

And do you see you research going in the same direction?

Yes, similar to what I just explained. We will build synthetic gene regulatory networks to improve our understanding of them and their evolution.

We would like to start by trying to tie this into the ethical part. So our first question for you is whether you are ever faced with suspicion about the application of your work.

Dimitri: I’m from the US and I know that in the US specifically there is a lot of tension between the scientific community and the general public especially when it comes down to genetic manipulation or regulation people are skeptical, to say the least, and suspicious most time.

So our first question is; are you ever asked about if your research falls into the realm of the unethical and how do you respond to those question if they come up?

I see what you mean, but personally I don’t think I had any such situation. The research I do is really basic research. It stays in the laboratory, so I think that people don’t mind that much if it stays in the lab. Currently, it is not intended for any application and no modified organisms are released. And I work on bacteria, where ethical questions are less of an issue.

But I see the issue, the public can be skeptical. This is our job to communicate to the general public and explain what we are doing.

How do you personally go about this? Or in other words, do scientists that have the obligation to explain what is going on - in their view - or is that something that should be dealt with politicians, by social groups of organizations of this nature?

I think it is part of the scientists’ job. I guess we should actually educate scientists better because we never learned how to communicate with the public. But apparently [the rapport has] changed. You are the proof by doing this interview that communication becomes more and more important.

I think public outreach is important. We need to try to speak to the public. In the end they’re paying our research, right! They should have a right of deciding what we are doing and at least we should explain to them what we are doing. We should have more open discussion on where the new technologies should be applied and how far should we go.

Actually, last year’s EPFL iGEM team did little interviews in the streets of Lausanne. They explained to the passengers willing to give them their time what synthetic biology is and all the different applications. People thought it was really interesting. But when they started talking about genetically modified organisms they were reluctant on the idea. What is your opinion on that?

With GMO it is kind of a difficult subject anyway. When the techniques initially emerged it was really badly handled by the scientists I would say. Now, this word has a sort of stigma. As soon as you mention GMOs, people don’t like it. I think we should learn from what happened then and do better this time. What better opportunity than now with synthetic biology?

On the other hand, I also think it is not something really specific to synthetic biology generally it is every emergent technology has potential risk and also benefits.

Maybe the problem with synthetic biology is that it’s something complex enough so people within the general public may not truly understand it, but it’s relatable enough that they have opinions about it. Maybe other emerging technologies doesn’t always face the same barrier. For example, work in physics. People may not understand it but they don’t relate to it either.

And I also think that there are several different aspects to be considered:

There is a safety aspect: for example, whether we should release modified organisms in the environment or maybe even inject them in tumor of a patient. There are also social aspects: who should get the patents? Should the techniques be open? who has access to the technology? Finally, there is the third level, the ethical aspect. That’s more about what’s our relation to the natural world. Should we engineer the living creatures around us?

All these different aspects should be discussed.

Do you have any like opinion specifically on what you just said, like on the patent and the access of synthetic biology? I guess you are referring to certain companies wanting to patents gene as intellectual property.

I don’t have a solution. I guess it is a complicated problem. Especially in synthetic biology there is this open source movement. Which I welcome greatly, especially on the academic side. On the other hand, I also see that companies need to have some kind of protection of their research and development, therefore the patents!

There is some fear that those new technologies just make the gap between poor and rich people bigger. Because the rich people are those who get direct access to the new technologies; an example are the plants that don’t produce their own seeds. Farmer have to buy seed from the same company each year. This is an issue.

I like that you mentioned the open source community because one of the questions we had prepared for you was regarding biohacking and kind of where ... And what the first thing that might come into your mind when you think about kind of... Well I am not sure if this is where you were taking this question when you were talking about open source. Maybe you were talking about everybody getting involved. But when you think about small maybe members of the general public running their own small experiments in synthetic biology, do you see that as an issue? Because these people usually aren’t’ regulated to the same level as an institution might be.

Dimitri ;Taking this back to where I am coming from (United States), this was a big issue after 9/11; they shut down a ton of people running their own biohacking experiments.

That’s a good question. In general, I think that it’s great that people not doing this as professionals are interested and can play around with it. It is also a form of public engagement.

But then of course, if they don’t treat the waste and release genetically modified organisms that’s not a good idea. There should be some basic safety level ensured. Basically the same rules should apply independent of where the experiments are performed.

But in this case I guess the limit to which biohacking might be available to the general public is under the umbrella of an open laboratory. We have something similar here in a town nearby called Renens. We went there to present our project. They have a small laboratory called “Hackuarium” which is open to the members of the public who want to run their own biological experiment.

I imagine they must have the possibility for proper waste disposal, for example using an autoclave. And there should be somebody responsible to control this.

Our last question regarding biohacking is whether even if it is open to the pubic if there should be some sort of regulation of who should do it about who can do it. Basically, if whether in your estimation It should be regulated - now we are balancing public safety and community engagement.

Do you mean like bioterrorism, or things like this?

Not specifically, also that an interesting thing to talk about. Imagine I have a small lab in my garage, because it is something I am interested in. Of course these places would have to have an autoclave, for example. Does the government have or do we have a responsibility to make sure that people that run those sorts of experiments have certain equipment? Or is that something that we should trust people to follow?

Trust is usually not enough, I guess. It depends on what thing you do. Even in a real lab, there are different levels of safety. I don’t think anyone would mind you doing a miniprep in your garage.

But for your research you need the approval of a safety committee. So I don’t think there should be a different regulation if you are doing this in a company or in your garage. The same rules should apply. But then it is really hard to check everything.

A follow up question to that is “do you or other scientist you work with have to find yourself taking supplementary steps to make sure you are following safety and ethical guidelines?”

For example, do you insert kill switches into networks? Or do you screen the DNA sequence you use to be sure that they aren’t compatible with human DNA or such things?

First of all, if you apply for a grant for funding there is always a form to fill in for all safety and ethical issues. If they see that your project is dangerous or not ethical, it would not be approved.

And then, if you order DNA from companies they have to check that there aren’t belonging to certain genes. Like we mention before bioterrorism that is actually checked at this level so you can’t order some bird flu virus…

Those are standardized in the process. It is not in the responsibility of the researcher.

And it depends on the application. If you want to release synthetically modified organisms into the environment, I think you should make sure it does only what you want and it doesn’t mutate. It might be necessary that you insert a kill switch. Or maybe the modified organisms can only live if you supply a modified amino acid that doesn’t occur in nature. Imagine, modified cells are injected into your body for some medical application. You really don’t want them to go wild on you. If modified bacteria stay in a fermenter for drug production you probably mind less.

When we talk about medical uses, it’s the epitome of the conflict between safety and benefit. So you were saying before that most research doing is more on the structural level of how the network function. Maybe you are not looking at medical app.

Do you see the conflict between the safety and the benefit being such a barrier that it might take decades for this technology to be applied or did you find in your research that there is a way to predictably create networks already that might be able to make safe medical application?

In my research no, but I think the field is quite far in this question. For example Prof. Fussenegger at the ETH Zurich, does a lot of work for medical applications. They already proved in mice that they can fight different diseases for example diabetes or skin diseases. To be honest, I don’t know, how far they are to get the approval to do human trials.

Another thing to consider is how bad the disease is. If it the last hope, then people are willing to take more risk that than if the disease can already be cured by some existing drug.

Last question! Do you see a world in the future with everything around us that could be engineered? Like where everything is modified, like food is more nutritious. Etc.

Last question! Do you see a world in the future with everything around us that could be engineered? Like where everything is modified, like food is more nutritious. Etc.

It’s a bit scary no? But, to be honest I think there is not much different between this and breeding right? We ‘ve been doing this for centuries, we are just getting better at it! EPFL:

The difference, I guess, is we were doing it without knowing the mechanism behind it, and now we know. Like carrots weren’t orange until the 1800s, so we clearly changed their genes, but now we could do it much, much faster.

I think that’s it for the interview. Thank you very much. We won’t take more of your time! It was really informative and interesting discussing with you.

And good luck and enjoy the Jamboree.