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3D visualization of biological processes

Today the entire sequence of the human genome is known, as well as that of several other organisms; the knowledge of biochemistry and cell biology has reached a point of unprecedented detail and the interactions among proteins, small molecules and cellular structures is quite well defined. Yet most people, including professional scientists, would not recognize the model of an actin molecule from that of Picachu, if they were scaled to similar size. We human beings have developed special skills in the visual system, and what we see, we know much better than what we acquire from other senses, as filmmakers and advertising professionals very well know and implement.

Imaging techniques in biology, including X-ray crystallography, atomic force microscopy, scanning and transmission electron microscopy, even molecular simulation programs and others, are providing a large amount of material related to the shape and movements of single molecules and multi-molecular structures. However the complex system of interaction that takes place in what could be called the ‘cellular landscape’, is still far from being considered in a comprehensive view.

The industry of entertainment has developed an impressive array of tools for the representation and animation of objects in 3D, starting from the building of models, to their movement in space and the interaction among many of them. The representation of surfaces is so sophisticated that viewers can be easily convinced of the physical properties of the represented virtual objects. Shading, illumination, colour and surface rendering tools are available for the development of complex scenes with convincing landscape and background, and even more convincing characters interacting as main actors.

We propose that representing cell biology in a visual, 3D animated motion, can be of great value for several reasons.

  • The modelling effort can offer a new perspective on cell biology that will enable the formulation new questions that can be addressed experimentally.
  • From an educational perspective, being able to show how cells work, how they are made inside, what a virus or a cytokine looks like, will help the understanding of science in a more immediate way, and attract students to the field of molecular and cell biology.
  • Last but not least, representation of nature, also in its most minute details, can be assimilated to the work of an artist, and indeed some creative skills will be necessary to develop ways to represent physical-chemical properties of the various cellular components. We thus expect the final product to be visually beautiful.

It is important that the main feature of the project is that every effort is made to represent molecular events as close to reality as possible, as described by the modern scientific techniques. Therefore, proteins are modelled according to the real atomic co-ordinates (where known), structures such as ribosomes and the cytoskeleton to the microscopy and structural studies. Events in turn are modelled respecting biochemistry and the most recent modelling studies (as example, see Nature 22 Jan 2004, describing the fusion of membranes at viral entry in the cell).
To reach the aim described above, the interaction among specialist of several disciplines (scientific and artistic) is of paramount importance.

Cell biology and virology are the basic subjects for the plot and the ‘set’ (the cellular environment).

Structural biology is the field from which most of the information regarding protein shapes and activities are retrieved.

Information technology and programming skills are needed to develop a ‘link’ between the biological sciences and the 3D animation software.

Communication and 3D animation experts will help in the development of standards for the visual delivery of concepts such as pH, hydrophylicity and -phobicity, electro-chemical potential gradients etc. In the elaboration of the project, new instruments will be developed for the manipulation of structural, chemical and biological information.

If we can ask new questions, then new answers can be found.

 

Monica Zoppè, 2005

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