Skip Navigation LinksHome > February 2009 - Volume 57 - Issue 2 > Training Interdisciplinary Scientists for Systems Biology
Journal of Investigative Medicine:
doi: 10.231/JIM.0b013e31819825e3
Symposium and Meeting Reports

Training Interdisciplinary Scientists for Systems Biology

Facciotti, Marc T. PhD

Free Access
Article Outline
Collapse Box

Author Information

From the University of California, Davis, Department of Biomedical Engineering and U.C. Davis Genome Center, University of California, Davis, CA.

Received December 5, 2008.

Accepted for publication December 9, 2008.

Reprints: Marc T. Facciotti, PhD, University of California, Davis, Department of Biomedical Engineering and U.C. Davis Genome Center, One Shields Drive, University of California, Davis, CA 95616 (e-mail: mtfacciotti@ucdavis.edu).

Funding: This symposium was supported in part by a grant from the National Center for Research Resources (R13 RR023236).

The author declares no conflict of interest.

Collapse Box

Abstract

The rise of interdisciplinary research programs in recent years has spawned numerous questions regarding the best way to organize interdisciplinary programs and how to best train new interdisciplinary scientists in ways that will catalyze novel discoveries in biology. Systems biology, a relatively new branch of science, can be considered in many respects a poster child for modern interdisciplinary science. It not only requires that people from different traditional disciplines work closely together but it also requires the development of unique training environments to educate the next generation of systems biologists. The unique scientific and training challenges associated with the development of systems biology are certainly faced across the spectrum of interdisciplinary endeavors. Therefore, it is useful for scientists interested in building interdisciplinary research programs to consider the merits of successful systems biology initiatives. Institute for Systems Biology is one such example, and in the following, several key aspects of Institute for Systems Biology that make it both a unique and successful interdisciplinary science and training center are discussed.

Interdisciplinary research programs have gained popularity in biology and in medicine during the last decade. It has been suggested that this new organizational emphasis may be traced to the success of the human genome sequencing project in which numerous engineers, biologists, computational scientists, and mathematicians worked together to achieve this well-defined goal. Its success, and that of many other sequencing projects, has catapulted the biological sciences forward to a point at which it is very difficult indeed to imagine biology proceeding without the firm grounding of numerous genome sequences. The emphasis on interdisciplinary science has, however, provoked some in the research community to question the very nature of interdisciplinary science. For instance, there appears to be some degree of confusion about how to best define interdisciplinary science and how to fit more traditional disciplinary science within the new research model.1 Another important issue being considered is understanding how established academic training centers-typically academic Universities that are organized by and teach students by discipline-should adapt their programs to this interdisciplinary future2,3 and whether their students' careers will ultimately benefit from this type of training.4 Despite these questions, it seems that the general notion of promoting interdisciplinary sciences is still popular and will in one incarnation or another be with us for the foreseeable future. Therefore, it is productive to consider, if even briefly, examples of successful interdisciplinary endeavors to apply lessons drawn from these models might help promote interdisciplinary research elsewhere.

Systems biology is an intriguing new interdisciplinary science that can serve as a good example of how to establish good training environments for interdisciplinary science. It seeks to "discover, model, understand and ultimately engineer at the molecular level the dynamic relationships between biological molecules that define living organisms."5 Eventually, its practitioners hope to use the knowledge and techniques developed by systems biology to engineer living systems and treat complex diseases. Although the philosophical underpinnings of systems biology (eg, the holistic approach to whole systems) are old ideas that have resurfaced, today they are distinguished from past incarnations by focusing clearly on understanding the complex and dynamic molecular-level phenomena within cells. The resurgence of systems biology has been catalyzed through advances in global measurement (eg, microarray, proteomics, metabolomics, etc.) and DNA sequencing technologies that have finally enabled us to more fully interrogate the molecular-level happenings of the cell. Despite this recent progress, it should be noted that we are likely still at the beginning of the development of this technological wave and that much more technology development will be required to deliver the grand promises of this new discipline. It is hoped, in health care for instance, that systems biology will impact not only new discoveries regarding complex diseases but also health care delivery, participation by patients, and even aspects of social behavior.6 The precise route to this future is not known but it is very likely that the technological and philosophical foundations being laid by early practitioners of systems biology will play a major role in bringing about this change.

The heavy emphasis on technology development places a burden on the discipline to recruit and develop skilled engineers who are also well versed in the nature of biological systems. The ever-growing data sets also require biologically minded people with training in computer sciences, mathematics, and statistics to analyze and discover biological meaning from the mountains of data that the increasingly efficient high-throughput instruments are generating. Systems biology must also include people who have a deep understanding of biology and specific biological systems-from ecology to diseases-to provide fundamental insight into the systems in question. Thus, from both philosophical and technical perspectives, the challenges facing systems biology make it an interdisciplinary science.

In the last few years, a number of institutions have begun to emphasize systems biology and support its development into a distinct discipline. There seem to be as many models about how to organize such initiatives as there are efforts. The lack of a common approach to developing programs in systems biology seem to stem from difficulties in arriving at a completely generic and precise definition of what constitutes the field. There is, in general, a similar problem associated with finding mutually agreed upon definitions of what endeavors constitute interdisciplinary science. For example, working definitions of interdisciplinary science might be significantly different in one area of biology, for instance clinical science, than another, microbial ecology. In the first case, interdisciplinary science may work best when, like the genome project, teams of scientists representing different traditional disciplines work together toward the resolution of a common and well-defined research/clinical outcome. In the second case, individual research laboratories working on projects that do not easily find homes within traditional disciplines could be considered interdisciplinary science. Semantics on defining the interdisciplinary science aside, there are some techniques and approaches used by successful centers of interdisciplinary work that can be learned and applied elsewhere regardless of a strict definition.

Institute for Systems Biology (ISB) is a nonprofit research institute located Seattle, WA that was founded in the year 2000. It is widely considered a successful example of developing a good environment for interdisciplinary science and in particular for training new interdisciplinary scientists. Since its founding, ISB has been a pioneer and leader in the ongoing development of systems biology. Collectively, the faculty has diverse research programs ranging from disease processes to model prokaryotic systems. However, despite the diversity of specific research interests, they have all rallied under the umbrella of P4 medicine-a vision of medicine that is more predictive, personalized, preventative, and participatory that what we have today. A precise definition of what this means to faculty at ISB and some of the broader ramifications associated with its practice can be found on ISB's Web site (www.systemsbiology.org). It is sufficient, however, to summarize that the faculty collectively believe in the enormous potential for systems biology to significantly transform health care as we know it. United by this common goal, scientists at ISB are constantly challenged, whether they are working on cancer, yeast, computation, or model prokaryotes, to measure the success of their projects against the goal of revolutionizing medicine in the P4 context. In addition, although the goal of transforming medicine is a key organizational principle at ISB, it is applied in a manner that allows for individuals to explore areas of biology that they are most fascinated by, thereby maintaining the exploratory spirit that drives most researchers careers. This organizational principle allows ISB to adopt a unique research agenda that is sometimes characterized as a mix between private industry, where goal driven, team science is king, and academia, where research driven by individual curiosity reigns.

In the context of training, ISB recognizes that its trainees come to the Institute from a variety of professional paths. Some come to the Institute as well-established scientists, programmers, or engineers. These individuals have developed specific skills and want to leverage those to advance novel projects in biology. Their initial training challenges are to learn new vocabulary and the key problems that colleagues are trying to address. People with less prior experience, such as students and postdoctoral fellows must also be trained and may have different professional goals than the more established individuals. Students and postdoctoral fellows generally want to become known as masters of the new discipline. All trainees though, will need to learn a broad new skill set and theories that span various aspects of traditional disciplines in order to be successful. Specific subsets of skills are often project specific and summoning the resources to effectively meet the needs of the wide variety of students presents a unique training challenge.

Addressing these complex training requirements imposed by the diversity of trainees at ISB is accomplished by adopting 2 training modalities-formal and informal training. Formal training largely includes coursework and formal instruction from peers on specific aspects of the job. At ISB, formal training includes regular peer mentoring and a series of formal courses that cover both the theory and practice of systems biology and its core technologies (eg, gene expression technologies, proteomics, and data visualization/integration). These courses provide an opportunity, for employees and outsiders alike, to learn about core technologies in the field, irrespective of primary research interest. These courses provide a common experience and theoretical grounding among ISB scientists, engineers, and programmers that they all can refer to when working collaboratively.

Informal training encompasses all of the other training employees receive. In addition, ISB has, in my opinion, found a number of ways-whether by design or by accident-to make this form of training the most valuable that they offer. The critical benefit of extended informal training is that its inherently flexible nature provides a great variety of individualized training opportunities that can be tailored to meet the needs of the diverse trainee set. Informal training at ISB is extensive and is greatly facilitated by the Institute's physical plant; the most important feature is the laboratory spaces which have been designed with minimum physical boundaries. This means that members of numerous faculty laboratories effectively share a common laboratory space, which encourages people from different scientific backgrounds to frequently exchange ideas, practical knowledge, and discuss other aspects of their work. Core instrumentation facilities are, for the sake of the instruments, housed in their own rooms. However, even these spaces sit at the center of the common work areas. This increases the interactions between core facility operators and others are the institute, providing easy opportunities for interaction between the people who are experts in these technologies to interact with those who would like to learn about them. The open facilities have also encouraged the close of grouping people with different backgrounds. For instance, although my formal training was in structural biology, I shared space with microbiologists, an astronomer, a biostatistician, and a biogeochemist. These day-to-day interactions contributed significantly to my personal development as a scientist by allowing me to develop a new breadth of ideas that would not have gained from formal training alone.

Besides facilitating interactions among people of varying backgrounds, there are also organized activities that contribute to informal training. For instance, a yearly all-employee retreat provides an opportunity for everyone to share research updates with a broad Institute audience. This encourages a culture of idea exchange that facilitates interdisciplinary work. In addition to the yearly retreat, ISB hosts a yearly symposium that spotlights external guest speakers conducting research at the forefront of systems biology. This provides breadth and context to the work of ISB employees. In addition, even at ISB, a pioneering home for systems biology, the continuously evolving nature of the field is evident in a lively weekly discussion group. The success of this specific discussion group is tied to the flexible format its organizers have instituted-a format that reflects the dynamism of the field. Some weeks the group takes the form of a journal club, other times a topic of relevance to ISB culture is debated/discussed, and other times the hour is designated as a brainstorming session regarding key questions in systems biology and how to best apply resources at ISB to answer them. The flexible group provides a way for the community culture at ISB to evolve along with the field by providing a venue to learn about it and to solicit new ideas about how to make future progress. The ever-changing format and topics discussed in this group also ensures that a broad variety of interests are represented and that the discussions continue to be relevant to people of different backgrounds and professional goals at ISB.

These examples of both ISB's formal and informal training mechanisms are just some examples of the how ISB trains its employees in a rapidly changing scientific environment. In some respects, these simple tactics are implemented in other professional and academic settings. It seems, however, that ISB has made a significant effort to adopt the philosophy that communication (in this context the transfer of knowledge for training) is most effective when done face-to-face and to institute measures to facilitate this.

This training environment can be contrasted to that which is typically found in a University setting. Somewhat unsurprisingly, some of the primary hurdles to overcome when training interdisciplinary scientists are the artificial boundaries imposed by existing departmental/disciplinary structure. Some of these academic boundaries have organizational merit-for instance, organizing like-minded people into departmental structures can have a significant impact on developing a greater breadth and depth of knowledge in a particular scientific field on campus. Departments are also important for organizing core resources for their members and for developing a complete and meaningful academic curriculum for their students. However, the same barriers that help to strengthen the foundations of a discipline may also tend to inhibit the development of new research areas or discourage interactions among colleagues across different departments. One barrier to fostering interdisciplinary sciences in traditional academic settings is the existing merit and reward structures at universities that typically encourage individuals to conform within the boundaries outlined by departmental visions of a specific field. That is, one of the major criteria used to judge an individual's academic performance is to ask how outstanding their contributions are to the advancement of an existing discipline. This obviously runs counter to the idea of promoting research outside of disciplinary boundaries and discourages faculty, particularly junior faculty, from seeking research projects out of their departmental disciplines. A second barrier is the prioritization of university resources by campus administrators on a departmental basis. This creates artificial competition among faculty from different departments rather than encouraging them to work across departmental boundaries. Finally, although necessary for fostering community within a department, grouping departmental faculty into separate common spaces, particularly on larger campuses, results in the geographical sequestration of faculty from different disciplines and decreases the potential for face-to-face communication.

In the case of systems biology, some of these issues have begun to be addressed at certain academic institutions. Some institutions, most notably Harvard University, have formed a Departments of Systems Biology (http://sysbio.med.harvard.edu/). This is clearly an attempt not only to bring people together under a common academic umbrella but also to mitigate some of the merit/advancement and departmental resource issues noted earlier. Other institutions have opted to foster alternate nondepartmental incarnations of interdisciplinary biology by grouping faculty from different departments together in common facilities. At University of California, Davis for instance, a multidepartment Genome Center (http://genomics.ucdavis.edu/) has been formed in recent years. Rather than form a new department, this effort seeks to make formal links, via individual faculty, to existing academic departments to help build bridges over traditional campus boundaries. This core set of department-crossing center faculty is also paired and cohoused in a single building with a host of cutting-edge technologies. Together, it is hoped that these 2 attributes (faculty linking various departments and novel technologies) will sufficiently lower the energy barrier for other individual faculty to spur significant advances in interdisciplinary biology on campus.

The Harvard, Davis, and ISB models are but three examples among many that have appeared in recent years to foster interdisciplinary biology. Each is still relatively new, and it is unclear which, if any, will be most effective at fostering the development of systems biology. Nevertheless, most of these institutions have implemented a number of common organizational principles that have already been discussed (i.e. open laboratory structures, optimized training for individuals of different backgrounds). However, some features that continue to distinguish ISB still remain. The first is that ISB has been able to form a culture of research and training that supports both goal-oriented research (eg, the development of P4 medicine) and that still enables individual creativity. This balance may be difficult to completely emulate at either a traditional academic institute or in private industry. Another is ISBs reward structure that rewards not only individual achievement but also for contributions to the common mission of the Institute. Only time will tell if enabling a balance between rewarding individual achievements and those that significantly advance team goals is also important to the development of systems biology and to the training of its practitioners. However, on this front, it would seem possible that some amendments to current faculty merit review criteria might be made that would encourage more collaborative/interdisciplinary work in university settings. That said, the precise recipe for success is still elusive and will very likely be institution specific.

In the meantime, a few lessons from ISB's current success that have some potential to be universally applied follow. First, define a large-scale and meaningful mission that gives individuals the flexibility to creatively explore the areas they are most excited about. Second, support work that is collaborative by rewarding both unique individual contributions to science and those that advance the common goal. Third, promote as much face-to-face interaction and communication as possible-this enables interdisciplinary work to happen but also is an important component in the training of new researchers. The latter can be accomplished by mechanisms that can include physical infrastructure considerations and by supporting dynamic discussion opportunities for trainees. Finally, reinforce informal training with formal educational opportunities. These basic ideas have been important for ISBs current success and should be, at least in part, useful to other institutions looking for positive models to follow in their own efforts to encourage interdisciplinary science.

Back to Top | Article Outline

REFERENCES

1. Eddy SR. "Antedisciplinary" science. PLoS Comput Biol. 2005;1(1):e6.

2. Chang S, Hursting SD, Perkins SN, et al. Adapting postdoctoral training to interdisciplinary science in the 21st century: the Cancer Prevention Fellowship Program at the National Cancer Institute. Acad Med. 2005;80(3):261-265.

3. Rhoten D, Pfirman S. Women in interdisciplinary science: exploring preferences and consequences. Research Policy. 2007;36(1):56-75.

4. Rhoten D, Parker A. Education. Risks and rewards of an interdisciplinary research path. Science. 2004;306(5704):2046.

5. Facciotti MT, Bonneau R, Hood L, et al. Systems biology experimental design-considerations for building predictive gene regulatory network models for prokaryotic systems. Curr Genomics. 2004;5:527-544.

6. Hood L. [Institute for Systems Biology Web Page]. 2008. Available at: http://www.systemsbiology.org/Intro_to_ISB_and_Systems_Biology/Predictive_Preventive_Personalized_and_Participatory. Accessed August 21, 2008.

Keywords:

systems biology; interdisciplinary science; training

© 2009 American Federation for Medical Research

Login

Search for Similar Articles
You may search for similar articles that contain these same keywords or you may modify the keyword list to augment your search.