Monday, January 22, 2007

What Is "Systems Biology?"

It's an interesting question. One of our departments here at the University of Toronto just renamed itself Cell and Systems Biology so you'd think they would know what "systems biology" is, wouldn't you?

Well, they don't. And neither do I. And neither, as it turns out, does Michael White over at Adaptive Complexity. Read his posting: Is Systems Biology Teaching Us Anything New?. Here's a teaser,
What I find most exciting about basic molecular biology today is the prospect of building a quantitative understanding of how a cell works. Many other scientists are excited about this as well, leading to the current popularity of what's being called 'systems biology.' The idea is that maybe we can understand the design principles behind a cellular process - how the behavior of a cell emerges from all of those detailed physical interactions among proteins, nucleic acids and other components of the cell. If that sounds vague to you, well, that's because it is vague. It's a nice sentiment, but I think biologists still have a hard time defining just what it is we want to learn.


  1. It sounds a lot like adaptive computing, which uses interactions among many sub-units for things like machine learning, inductive inference, pattern recognition, etc.

    Not being a biologist, I have no idea how useful it is in life science areas. I'll leave that to others.

  2. IMO systems biology is mainly a big hype. I guess the appealing thing about SB is that it is presented as catchy graphs in which connections of points with arrows invoke the impression that all connections between data points have been elucidated. The ifs and whens however are rather hidden in the text. At best you will find them in the discussion at worst they are hidden in Materials and Methods or in online supplementary data. I wonder if the quality of available data is sufficient for the ambitious plans of SB proponents. E.g., SB often refers to gene ontologies to group results with reference to gene classes. However, gene ontologies are often just based on sequence similarities and data from expression profiling. Thus, models may be biased due to wrong ontology annotation.
    It is fair to model molecular pathways. However, what is really new about that? Physiologists are doing this for decades. It’s a little bit of the Emperor’s new clothes.
    Seemingly though, it is currently necessary for the head of our institution to jump on the bandwagon and to claim that SB is the future and that it will solve all unanswered questions in biology. Indeed, he claims that SB will automatically generate hypotheses. If this is what SB is about this would mean a dramatic paradigm shift because until now science was hypothesis driven.
    My main concern however is, that SB is currently heavily funded and that this money is lost for old fashioned experimental biology which has been successful for over a century. Unfortunately, funding policies currently shifted in a direction where pure pledges are rewarded and the bigger the pledges the better the funding will be. SB is sold as big science. If it is well done it surely deserves good funding. I am afraid though, that big science is mostly clamored for by small minds who are afraid to miss a train.

  3. What Is "Systems Biology?"

    Physiology done by computer scientists.