Chapter 2 Cartoons as Models in Molecular Biology A picture is worth a thousand words Unknown RP JK to Readers The present draft should be viewed as having the basic structure of the ultimate final version of this chapter On the other hand as it currently stands there is much that is incomplete i the figures when in their final form will ALL be drawn in the same style and will resemble fig 2 25 ii many sections are incomplete in particular one of our main ambitions is to try and complement each section and each cartoon with some quantitative insight As yet these insights are present at best in skeletal form We are interested in hearing your views on the level of presentation what is assumed of the reader whether the concept is clear your views on the logic basically everything Thanks for your time 2 1 Cartoons and Models RP each cartoon needs an Biological Cartoons Select Those Features of the Problem Thought associated estimate and an associated set of equations to Be Essential This chapter and the one We have argued that the fine art of model building ultimately reflects a that follows are after reviewtasteful separation of that which is essential for understanding a given phenom ing all of ECB the two prienon from that which is not One of the key reflections which struck both of mary sources of much of bius while trying to learn something about the beautiful subject that is biology ological phenomenology We was the profound and subtle way in which biologists have learned to confront need to do a beautiful job the enormous complexity of their problems In particular we were struck with in this chapter of organizthe fact that the visual representations in biology whether drawn from the im ing that phenomenology acpressive cartoons that are a mainstay of biological pedagogy or those found on cording to spatial and temthe pages of the most recent research reports exhibit precisely those features of poral hierarchies and in the next chapter on the basis of model building that have been exploited with success in the physics setting particular models that have catapulted forward our un41 derstanding of biological systems Also make sure not to forget that the chapter has some parallel aims 1 prove that cartoons serve as models 2 introduce biological phenomenology especially stu we will try 42 CHAPTER 2 CARTOONS AS MODELS IN MOLECULAR BIOLOGY 1 2 mm 0 1 0 5 mm 2 D view of mitochondrion outer membrane inner membrane intermembrane cristae space matrix baffle model crista junctions crista junction model Figure 2 1 Several generations of structural cartoons illustrating the properties of mitochondria JK wonders if we should have history thread like the Pollard and Earnshaw picture on membrane cartoons show images with the cartoon As argued in the previous chapter a model must contain the essential features of a system while not containing so much detail as to make it intractable As an example of the role of cartoons in conveying the essential features of biological structure fig 2 1 shows cartoons meant to convey several generations of structural understanding concerning mitochondria Though cryo electron microscopy has o ered some refinements of the original picture the essential conceptual elements are present even in earlier cartoons namely a the mitochondria are closed membrane bound organelles b the inner membrane is decorated with a series of protrusions which segregate di erent regions of the mitochondria and might also serve as the seat of reduced dimensionality di usion In this chapter our intention is to put together a case that biological model building is practiced without abandon in the form of cartoon making From its earliest inception as an experimental science biology has been built around the role of visual descriptions Whether in the form of classification of species or the study of human anatomy or the representation of microscope observations see fig 2 2 or even the structure of macromolecules biology has been unapologetically visual Even in this modern era of fluorescent labels for di erent biological molecules and high speed cameras to record them often the results of such images are framed in the form of cartoons which guide the viewer in their RP cartoons are in fact interepretation of what from the image is important and what is not very subtle because they have to have enough of a resemblance to reality so that everyone knows which reality is being described presidents always look enough like presidents to be recognizable In biology cartoons are a fantastic separation of wheat and cha 2 2 DIAGRAMMATIC REPRESENTATIONS IN THE PHYSICAL SCIENCES43 Figure 2 2 Sketches of Leeuwenhoek and Hooke of the results of their microscope observations 2 2 Diagrammatic Representations in the Physical Sciences Physics Also Has a Rich Tradition of Using Cartoons to Represent Phenomena Thus far we have made it sound as though biology is somehow unique in its exploitation of visual representations in the context of model building On the other hand the physical sciences are similarly replete with historic examples of the role of visual representations As will be described briefly below one of the most profound chapters in the history of physics concerned the discovery of the connection between electricity magnetism and light The two figures that tower over the field of electromagnetism perhaps more than any others are Michael Faraday a bookbinder s apprentice with probably less mathematical equipment at his disposal than a college biology student has today and James Clerk Maxwell one of the most successful theoretical physicists of all time 2 2 1 Faraday and Lines of Force Though a discussion of Michael Faraday and the emergence of the concept of the electromagnetic field in the context of biological cartoons may seem like making a round the world flight to get from San Diego to San Francisco i e a stretch the relation between the work of Faraday and Maxwell serves as an example of precisely the sort of integration of visual and quantitative representations that is now taking place in biology and which is the backdrop of the present book In addition electric fields and potentials are one of the cornerstones of biological phenomenology Indeed as will be shown in section the notion of 44 CHAPTER 2 CARTOONS AS MODELS IN MOLECULAR BIOLOGY Figure 2 3 Cartoon from the Experimental Researches in Electricity of Faraday which helped usher in the field concept action potentials is central to our
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