Paper: A Top-Down Approach to a Complex Natural System: Protein Folding

Alan Levin has published the paper “A Top-Down Approach to a Complex Natural System: Protein Folding” in Axiomathes. The abstract:

We develop a general method for applying functional models to natural systems and cite recent progress in protein modeling that demonstrates the power of this approach. Functional modeling constrains the range of acceptable structural models of a system, reduces the difficulty of finding them, and improves their fidelity.  However, functional models are distinctly different from the structural models that are more commonly applied in science.  In particular, structural and functional models ask different questions and provide different kinds of answers.  As we clarify these differences and articulate how to use these models jointly, we extend our ability to do science and gain insight into the proper use of the terms organization, order, and emergence when describing systems in nature.

A copy of the paper can also be downloaded from Alan Levin’s website.



[1] 2009. Levin, A. “A Top-Down Approach to a Complex Natural System: Protein Folding”. Axiomathes. DOI 10.1007/s10516-009-9093-0.



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3 Responses to Paper: A Top-Down Approach to a Complex Natural System: Protein Folding

  1. Alan Levin says:

    Apologies for bumping my own article, but I have posted a presentation about my research given to a computer science and system engineering colloquium at USC last Friday. It is available at my website along with the paper.

    If there are any questions or comments, I would be happy to address them here.


  2. Peter C Marks says:

    I had originally posted this message at Alan’s website but I just noticed that he would like comments posted here.

    A comment (edited original):

    I read your paper with great interest. It’s not often that one finds a practical application of some of Robert Rosen’s ideas. I, too, wish to use his ideas in biological research. I came across Life Itself several years ago. My response to reading and trying to understand this book was to steer my career towards biological applications. I’ve been involved in software for over forty years, mostly in the area of commercial applications. I have just succeeded – two months ago – in a getting a Research Associate position at MMCRI here in Maine.

    With respect of Relational Biology, I find myself drawn towards the idea of functional modeling rather than data (plus differential equations) modeling. There are some ideas rattling around in my head. They mostly center on developing a modeling application whose unit of modeling would be Rosen’s (M,R) Systems. I have this idea that one could build biological mechanisms out of these (M,R) systems, each representing a functional component. Because of your paper, I am studying the FFBD approach to functional modeling because it offers the connecting and timing elements that one would need in a model.

    I look forward to reading more about your work.


    Peter C Marks

  3. Alan Levin says:


    Thanks for the kind words. I would suggest that you use care when you “combine” things into models, vs. thinking about how different models and/or different types of models help to understand the same natural system.

    For instance, to the extent that your functional flow block diagram (ffbd) is an input/processing/output timing sequence, it will not be capable of entailments that one would find in a more general architecture that would correspond to an augmented abstract block diagram in LI. In particular, I expect that an ffbd is not rich enough to model an (M,R) system. OTH, exploring an ffbd as one of the many aspects of a relational model or functional component might be more promising.