Collaboration and convergence

For British researcher Steve Oliver, the complete DNA sequencing of the Xylella fastidiosa bacteria initiative, supported by FAPESP, did not only mean the introduction of biocomputing in Brazil, but it also revolutionized the country’s cooperative scientific culture

By Fábio de Castro

Agência FAPESP – In 1999, the use of internet-based software made reaching a great landmark in Brazilian science possible: complete DNA sequencing of the Xylella fastidiosa bacteria, which causes Citrus Variegated Chlorosis (CVC), popularly known as the praga do amarelinho (yellow plague).

For British researcher Steve Oliver, who was part of the directing committee for the sequencing project performed by the FAPESP Genome Program, the initiative did not only mean the introduction of Biocomputing in Brazil, but it also revolutionized the country’s cooperative scientific culture.

Oliver, who is director of the Cambridge Systems Biology Centre (U.K.), participated in the Workshop on Synthetic Biology and Robotics on February 24, organized by FAPESP and the British Consulate in São Paulo as part of the Brazil-United Kingdom Partnership in Science and Innovation.

At the event, Oliver spoke on applying automation to metabolomics—the study of the metabolic diversity existent in biological systems—and to chemo genomics, or the genomic reactions of chemical compounds with the goal of identifying new medicines and therapies. Robot scientists developed at the University of Wales in the U.K. are used in these studies.

In an interview with Agência FAPESP, Oliver analyzed the profile of the scientists that will work in the emerging field that unites robotics and synthetic biology. The scientist also commented on the evolution of Brazilian science that currently involves computer science applied to biology.

In one of his more recent collaborations with Brazilians, Oliver and Fábio Costa from Universidade Estadual de Campinas’ Biological Institute (Unicamp-IB), unraveled the mechanism of action for violacein. The compound, isolated by Costa in bacteria from the Amazon River, is effective against malaria. But, without understanding the mechanism of action, it would be impossible to transform it into a new drug.

Now, with the help of a robot scientist, researchers will be able to test other drugs against the same target identified in violacein’s mechanism of action. The work performed from a single compound can be tested, thanks to automation, in entire libraries of other compounds, accelerating the process and increasing the chances of discovering a new drug against malaria exponentially.

Agência FAPESP – Have you maintained your partnerships with Brazilian scientists since your involvement with the Xylella fastidiosa genome mapping project over ten years ago?
Steve Oliver – Yes, I have had contact with the Brazilian scientific community for a long time, even before I was invited to participate in the committee for the Xylella Genome project. But it was from that point on that I had the opportunity to develop a strong network of contacts in the country and carry some cooperative research projects forward.

Agência FAPESP – How do you see the current evolution of the integration of biological sciences and computer technology in Brazil? Has there been growth?
Oliver – The Genome projects, in my opinion, transformed Brazilian science, especially in the state of São Paulo. In many ways, I think that in this period there were advances in development of new skills, in the formation of talented scientists and improvement in infrastructure of both installations and equipment.

Agência FAPESP – What was it that made these projects transformational?
Oliver – Mostly the manner in which the project was carried out. It was something similar to what happened in Europe with the large genome mapping projects. The fundamental aspect is that in these projects, scientists have to work together. I remember, in my first projects with Brazilians, the lack of cooperation between laboratories caught my attention.

Agência FAPESP – The Xylella Genome project brought about scientific cooperation in a new way?
Oliver – Yes, it was fundamental for creating this culture. Before, money was harder to come by and people were very possessive of the things they achieved. This brought about ridiculous situations: there were times when researchers came to me asking for reagents that they could have gotten from colleagues in their own departments by just crossing the hallway. With regard to this, the Xylella Genome project changed things completely, generating more access to resources and new equipment, which facilitated cooperative work. Today, the cooperative situation between scientists in Brazil is much healthier. People have started to work together. It’s silly not to cooperate. 

Agência FAPESP – Has this interaction also increased among international groups?
Oliver – Without a doubt. In this respect, FAPESP, which had already made the difference on the Xylella Genome project, made the decisive contribution in recent years by intensifying its international relationships. Such is the case with the agreement FAPESP made with the U.K. Research Councils (RCUK). Actions like this are part of the general growing context of international cooperation in Brazilian science. 

Agência FAPESP – Is it important  for Brazil to invest in automation technology for synthetic biology? Or is it not worthwhile to focus on infrastructure resources of this type?
Oliver – I think it is important. Some could argue that there is enough available labor in Brazil that automating processes is not worthwhile. But I don’t believe so. First, because there is a lack of talent, considering the demand. Especially at a time when the economy is growing and access to installations where vanguard science can be practiced is more and more available. Second, because we need experiments that are highly reproducible more all the time. Robots can do this much better than human scientists. Brazil has the conditions to develop automated science, which is fundamental in being able to apply data from one experiment to innumerous others. Robotization has a multiplicative effect on science.

Agência FAPESP – Automation applied to synthetic biology is an area that requires scientists with a very special profile. How do we educate these people?
Oliver – I can speak to the United Kingdom, where the biggest problem is that biology students in general aren’t usually good at mathematics. At many large universities, they aren’t motivated to perfect their knowledge of math. At Cambridge, it’s different. We insist on this quite a bit. But if I look back at my own education, I remember that I never thought that I would need to know more mathematics or chemistry. Today we have biologists with backgrounds in mathematics, physics or engineering, and this is very good. 

Agência FAPESP – But is it possible—and necessary—to have high knowledge in two areas? 
Oliver – Yes, I do think it is possible. But I don’t think everyone needs to do this. Some individuals can explore these talents very well, like a student from my lab that earned a degree in mathematics at Cambridge and is now doing a doctorate in the biological sciences. The important thing overall is that a specialist has sufficient knowledge to communicate with specialists in other areas. At Cambridge, we try to motivate this dialogue, even between individuals that don’t have the aptitude to work deeply in two or more areas. 

Agência FAPESP – How do you incentivize this? 
Oliver – To begin with, at Cambridge we start with an interdisciplinary course program for fourth year students. We receive students with backgrounds in mathematics, computer science, physics and biology. The course begins before the regular academic year and offers intensive courses in all these areas. We promote this situation so that a dialogue occurs that helps people connect. The important thing is putting them into contact with each other. I believe that students learn more from each other than they do from professors. I think it’s working very well. It’s important not for incrementing their curriculum, but for making it possible for them to know and teach each other.