During this years inter-DTC systems biology students conference there was a debate session on the subject “can scientists be multidisciplinary?”. The purpose of the session was to debate whether students are better equiped for scientific research by specialising in a particular field or diversifying across fields. I have heard this debate a number of times since joining the Manchester DTC, which I believe stems from an inherent insecurity in the decision to train in the emergent field of systems biology. Many scientists have the desire to label themselves with an identity through their specialism and join other scientists sharing their label in an almost medieval guild like behaviour. These guilds then form alliances between other like minded individuals within and across Universities. This approach has worked well in the existing reductionist scientific world where research is focused on specific areas of interest, enabling funding bodies to quickly identify and recruit suitably skilled scientists to complete their projects. With the advancements in high throughput automation and computer science an increasing number of projects are pushing towards integrative research projects, combining data and experimentation from diverse scientific fields. These advances have culminated recently in the emergent field of systems biology that is driving a new holistic scientific approach through the integration of many scientific disciplines into multidisciplinary research projects. The existing system of training and recruiting specialist scientists has been adapted to encompass a higher level of organisation, utilizing multidisciplinary teams with a central management body coordinating the multidisciplinary communal effort. Problems arising from this new multidisciplinary group working has been in the area of communication with resistance from each of the parties to work with the other, or a resistance to consider the others ways of working, thought processes, or general scientific rationale. The project coordinators have tackled this by continuing the segregation and coordinating from outside each of the groups, minimizing or eliminating the requirement for the component researchers to interact. More recently however, systems biology has promoted a new, more radical approach of training the individual component researchers with the fundamental key skills of their project colleagues, culminating in the development of pioneering University doctoral training centres such as the MIB where classically trained specialists are re-trained in their opposite fields, combining wet and dry lab skills in a single researcher, and the first wave of “systems biologists” are beginning to emerge.

To return to the point of my post, there were representatives on the conference debate panel from Astra Zenica and Pfizer, and the inevitable question “what are you looking for when recruiting a systems biologist?” came up. I found the answer unsurprising, but disappointing. The large pharma companies are searching for mathematicians who can build them models of biological systems that they can use to direct their research. This statement wasn’t followed up by any of the academic researchers. I was left considering the future and relevance of “multidisciplinary scientists” in the wider world. Philosophically, I believe all scientists should be inherently multidisciplinary, enabling them to investigate the world around them and draw conclusion from whichever realm of science that is relevant to the question. I believe that every individual is capable to a reasonable extent to learn anything, and not just “their field” with the only barrier often being attitude and effort. However, in the real world you have to pay the rent and put food on the table, so the starving scientist must match their skill set with the market demand. Current scientific infrastructure in academia and the private sector is set up to employ the person who has the specific skills to complete whatever task is required that their existing assets in the organisation cannot. A multidisciplinary scientist therefore could be considered a “jack of all trades and master of none” and be continuously out-competed by specialists. Existing academic and industry development frameworks are still configured to develop individuals in a specialist role and multidisciplinary individuals don’t fit in their human resources skills matrix, making employment and development impossible to place within their company hierarchy. In addition, the current “group approach” of systems biology means that multidisciplinary thinking is often only required from those coordinating the project, and not the component individuals facilitating the work, and could be interpreted as an unnecessary diversion, deflecting from the development of a key specialism that would be of value to a potential employer.  It gave me the feeling that the pharmaceutical industry is funding and promoting systems biology development with the aim of using it as a vector to cherry pick mathematicians that can be re-programmed with sufficient biological knowledge to adapt their mathematical skills to simulation of biological interactions, and the development of wet lab scientists an unfortunate by product. Mathematicians, after sufficient training in systems biology can manage the wet lab scientists and systems biology projects sufficiently to deliver the data required to populate the models and drive the biological hypothesis generation, with wet lab scientists a part of the process that is yet to be automated.

Just to qualify the above, I don’t intend for this post to sound of the “sucks to be you chained in the lab” general bench scientist rant. I believe that systems biology is a transitory scientific field born out of the lack of in situ data to build accurate real world simulations of biological systems. The wet scientists are employed purely to gather this data to populate the mathematicians models, which the mathematicians then use to generate hypothesis and direct the research. It is my belief that mathematicians are the multidisciplinary scientists in systems biology, and must be multidisciplinary for it to continue. The biologists on the other hand must continue to focus on specialisation to develop new measurement techniques, physically obtain the required information, and critically to retain their market value and employment. I believe that biological scientists in systems biology will eventually diversify into either their original fields, or new ones particularly synthetic biology, while systems biology retain the mathematicians and to a certain extent chemists who follow the computer science/simulation road.  I believe that adopting a multidisciplinary approach for systems biology is essential for the mathematicians but this approach is detrimental, if not career suicide for biologists, who would be better directed towards classical fields, or for those seeking something new and akin to systems biology – synthetic biology.

I would like to gain comment on this post. I intended for it to be a bit reactionary and maybe inflammatory so I can perhaps incense some response and be proved wrong. I joined the systems biology road trip with the hope of gaining new skills that would drive a new career in biological sciences, and I am hoping for it not to have been a mistake!

The talks were divided into sections covering many aspects of systems biology ranging across application to theory.  There were a number of interesting keynote speakers.  Dieter Weichart talked on “from ‘omics’ to systems biology, and David Broomhead gave an intriguing lecture on applying fractal maths to simulate the complex composition of the cell cytoplasm.  Professor Broomhead has an excellent way of communicating complex theorem to the most mathematically inept (me!).  Pedro Mendes presented a history of simulating biochemical reactions taking us back to the early days of punch cards and drive through size computers crunching away and amusingly producing the same graphs your quad core Intel 8gb DDR-3 powered nvidia SLi carbon footprint behemoth produces

The students presented a diverse range of projects representative of the style of the doctoral training centre in each University.  Oxford University gave an impressive visual presentation of their progress modelling blood vessels within the heart, building on the existing model of the heart by Noble.   There were a number of talks ranging across modelling cell signalling, tracking cell movements, and bioengineering of microorganisms for potential biotechnology applications.  In addition, there was also 2 interesting talks that diversified from the cell biology / microbiology themes, on modelling / “decoding” epilepsy EEG seizure data to provide new understanding of the underlying cause of the condition and provide potential technologies for predicting and managing seizures.  One talk focused on absent seizures while the other focused on grand mal seizures, bother using different mathematical and statistical methods to search for patterns in the inherantly complex and chaotic brain activity.

The event was a great way to encourage students to communicate between systems biology DTC’s as well as building links for current and future research.  I enjoyed the opportunity to meet with students working on areas similar to my own, as well as their supervisors who could give their own incite on the work that I was doing.  This helps to broaden your understanding, as well as gain fresh ideas from people outside of your usual research group.  After the conference we went for an excellent meal hosted by Professor Westerhoff and had a chance to interact in a more relaxed social environment.

Next year’s conference hopefully will be hosted by Oxford University, which would be a unique and priviledged opportunity to visit their prestigious campus, and experience their own blend of systems biology research.

I particularly enjoyed the talks from Roger Brent from Berkeley, CA and Ron Weiss of Princeton as these were particularly relevant to my work in synthetic biology.  The electrical engineering approach of Ron Weiss was very useful in conceptualising the design of synthetic gene circuitry and his work in mamalian cells was inspiring.  Roger Brent provided some practical methods of measuring outputs of gene circuits and some useful open source software tools and lab methods that will greatly benefit my project.

There was also some very good talks from Eda Klipp on the mathematical modelling of biological pathways, and combined with practical copasi sessions with Frank Bruggerman modelling MAPK signaling pathways.  There was a lot of practical worked examples combining wet lab experimentation with mathematical modelling that gave a real incite into the development of systems biology and the application of it’s approach.

Denis Noble popped in for a keynote lecture on his development of the heart model and provided a unique opportunity to gain an understanding of the processes he went through in building one of the pioneering projects in systems biology.  There was also a nice opportunity to meet with him and we received a signed copy of his book - the music of life.  It is always an inspiration to hear Denis Noble speak and I would recommend any scientist to take a look at his talks on youtube.

I will update more info as I get time, as it’s full steam ahead on my return to Manchester.

This year our DTC studentship will be attending the FEBS systems biology advanced lecture course in Alpbach, Austria.

I have booked in for the “physiological systems biology” and “modeling cell biology workshops”.  Hopefully both courses will provide valuable training for the dry component of my project.

I will be updating from Austria if I can get internet access.

The lectures began with Mike White of Liverpool University on temporal and spatial information encoding by the NF-kB system and continued with Olivier Pourquié (Kansas City) on periodic patterns in embryonic development: the vertibrate segmentation clock. Following this lecture we had Andrew Millar of Edinburgh on unwinding the biological clock, and finally Béla Novák of Oxford on the systems biology of the cell cycle. Béla Novák’s lecture was of particular interest and delivered with great enthusiasm. It was clear that we must dispense with reductionist approaches if we are to understand the true essence of biological systems. It is the understanding of the interplay between the various components that defines the behaviour of the system, and not the individual key components. The reductionist approach to the components is still crucial to understanding the working of the component parts, but cannot be used to describe the emergent properties of cellular processes when working as part of their overall function in the cells life cycle.

The afternoon continued with seminars on systems biology from microbe to planet: understanding lots of data through comprehensive models, advanced concepts and techniques in array informatics, and clinical genomics of cancer.

I chose to attend the systems biology modelling lectures and we had Masaru Tomita (Keio) on multi-omics analysis and integrative systems biology, Steve Oliver (Cambridge) on yeast systems biology, and Matthias Reuss from Stuttgart on unravelling regulatory networks in hepatocytes on the basis of time-series data.

The afternoon finished with David Richardson of Norwich who presented an interesting talk on the global nitrogen cycle, detailing the effect of nitrogen fixing bacteria on the environment and how it fits into the current issues around the environment, particularly its under-reported importance next to the levels of carbon in the environment.

The conference was concluded by an excellent lecture from Hans Westerhoff of Manchester/Amsterdam entitled “from genomes to systems… dealing with the networks”. Professor Westerhoff presented some interesting theories on the future of systems biology, together with some new mathematics on fragility that went with his theories on control coefficients and robustness.

I found the conference very interesting, and it was a great opportunity to be immersed in the community of systems biology. It was inspiring to see so many people working in the field without the usual question of “what the heck is systems biology?”… although I don’t think anybody had a clear definition of what the heck it is anyway!