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Recent Finds

Diseases of the Imagination and Imaginary Disease in the Early Modern Period

Yasmin Annabel Haskell

Brepols Publishers, 2011

“The early modern period was arguably the greatest ‘age of the imagination’ in Europe, and certainly the period in which the powers attributed to that faculty had the greatest consequences – both in theory and in ordinary people’s lives. Theologians and physicians debated the reality of witchcraft (no simple battle between Religion and Science, as believers and doubters could be found on both sides); the existence and pathology of werewolves and vampires; the role of the imagination in influencing the unborn child and in causing disease even in remote others. The imagination was implicated in conditions from plague, lovesickness, and anger through to hysteric and hypochondriac disease – the latter a frightening syndrome of gastric, respiratory, cardiac, and psychiatric problems believed to be epidemic. The essays in this volume, by established and emerging scholars from diverse intellectual and cultural traditions, explore Latin and vernacular, philosophical, medical, poetic, dramatic, epistolary, and juridical sources to expose the tangled conceptual roots of our modern affective, anxiety and somatoform disorders. They confirm that controversies about ‘mad’ versus ‘bad’, ‘real’ versus ‘psychosomatic’ complaints, and the interdependence of perception, emotion, and physical illness are by no means a monopoly of our times. This pioneering, interdisciplinary collection explores the long history of psychosomatic illness from the fifteenth to the eighteenth centuries.”

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Recent Finds

Experiencing Art In the Brain of the Beholder

by Arthur P. Shimamura, Oxford University Press, Oxford, 2013.

“How do we appreciate a work of art? Why do we like some artworks but not others? Is there no accounting for taste? Awarded a Guggenheim Fellowship to explore connections between art, mind, and brain, Shimamura considers how we experience art. In a thoughtful and entertaining manner, the book explores how the brain interprets art by engaging our sensations, thoughts, and emotions. It describes interesting findings from psychological and brain sciences as a way to understand our aesthetic response to art. Beauty, disgust, surprise, anger, sadness, horror, and a myriad of other emotions can occur as we experience art. Some artworks may generate such feelings rather quickly, while others depend on thought and knowledge. Our response to art depends largely on what we know—from everyday knowledge about the world, from our cultural backgrounds, and from personal experience. Filled with artworks from many traditions and time points, “Experiencing Art” offers insightful ways of broadening one’s approach and appreciation of art.”

Check out this review in Science for a sharply critical response.

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Imaginative Fields in protein folding

Here’s a rough abstract for a talk I’m planning to give next spring, plus a back-and-forth discussion between me and Lily H, a friend and colleague at the University of Chicago.

Abstract:

Scientists use landscape visualizations in their study of protein folding as a cognitive tool to imagine new explanations. The landscape metaphor represents the way that a protein folds into its biologically active state as a traversal across a landscape of possibilities. Each shape corresponds to an energy value, and physical forces drive the protein from higher energies (mountains in the landscape) to lower energies (valleys). The landscape metaphor facilitates scientists’ cognitive work by allowing them to relate the many-dimensional process of protein folding to a physical, three-dimensional shape. For instance, different overall topographies of the landscape stand for different scientific theories of how proteins fold. Scientists have also used landscapes to represent empirical measurements of proteins’ behavior in the lab. I argue that these visual representations of natural phenomena link scientists’ abstract conceptual reasoning to their embodied experience by establishing a spatial field for imagination. I also suggest that this role for images in science — as an “imaginative field” — is quite general, and can be found in many places, such as with phase spaces in physics or evolutionary trees in biology.

Will you talk about particular groups/investigations?

–I have in mind a couple major competing theories for protein folding. The most famous is that proteins don’t follow any distinctive pathway to reach their active state but have to pass over a uniform energetic hump involving internal reconfiguration after an initial collapse. Later modifications to this theory allow for certain biased routes analogous to passes in a mountainside. There’s another case of reasoning with landscapes that turned out to be wrong but is particularly clear in setting out the reasoning process.

Will you talk about the historical use of topographical representation-as-explanation in biology?

–I can, but this links up to the larger topic of fitness landscapes in evolutionary biology, which are conceptually distinct from energy landscapes in protein folding. My feeling is that 25 minutes [for the talk] won’t even be enough to do energy landscapes justice…

Just from the abstract it strikes me that your conclusion could go further—for instance, not just a spatial field for the imagination but what kind of spatial field?

–Maybe, but I’m not sure what kind it would be! Any suggestions? 🙂 This is a place where I could probably learn a lot from existing literature and group feedback. The first idea that occurs to me is to differentiate kinds of fields based on dimensionality and the mode of embodied interaction. Landscapes for example depend on the metaphors of traversal, pathways, and topography. Evolutionary trees, however, involve branching and the idea of distance (which may be temporal or also embedded in a morphological space). How might you distinguish between fields?

–And could this working image have been otherwise?

Depends on what “otherwise” means. 😛 There are considerable variations in the depiction of folding landscapes, much like what David Kaiser describes for Feynmann diagrams in particle physics. There are also other ways of imagining mechanisms for protein folding, such as a divide and conquer process by which parts of the protein fold locally and then combine modularly to form the whole. My impression is that there is no settled, general answer for whether one is “right” overall. A different answer to that question might point to the recent discovery of chaperones that assist protein folding and the historical assumption that landscapes always have a unique lowest point independent of environmental context. (In other words, protein folding involved the motion toward a global minimum specified intrinsically by the amino acid sequence alone.) The idea of a global minimum corresponding to the active state was historically central to the original popularity of the landscape visualization. I’m not sure what would happen if physicists decided the global minimum was no longer explanatorily important.
–What does this particular visualization explain better than others, and what does it not explain?

The main alternative visualization for protein folding is to draw the atoms in three dimensions and watch them move around. This keeps the physical description of the protein’s state concrete, but makes it harder to identify general physical processes. The hydrophobic forces that cause many proteins to collapse, for example, do not have a distinctive signature at the atomic level other than the protein getting more dense, which can also be caused by other forces. The landscape formulation is aimed at describing generic features to all protein folding rather than the particular motions of individual amino acid sequences.

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Recent Find

Image and Reality: Kekulé, Kopp, and the Scientific Imagination

University of Chicago Press, May 15, 2010 – Science – 416 pages

“Nineteenth-century chemists were faced with a particular problem: how to depict the atoms and molecules that are beyond the direct reach of our bodily senses. In visualizing this microworld, these scientists were the first to move beyond high-level philosophical speculations regarding the unseen. In Image and Reality, Alan Rocke focuses on the community of organic chemists in Germany to provide the basis for a fuller understanding of the nature of scientific creativity.

Arguing that visual mental images regularly assisted many of these scientists in thinking through old problems and new possibilities, Rocke uses a variety of sources, including private correspondence, diagrams and illustrations, scientific papers, and public statements, to investigate their ability to not only imagine the invisibly tiny atoms and molecules upon which they operated daily, but to build detailed and empirically based pictures of how all of the atoms in complicated molecules were interconnected. These portrayals of “chemical structures,” both as mental images and as paper tools, gradually became an accepted part of science during these years and are now regarded as one of the central defining features of chemistry.  In telling this fascinating story in a manner accessible to the lay reader, Rocke also suggests that imagistic thinking is often at the heart of creative thinking in all fields.

Image and Reality is the first book in the Synthesis series, a series in the history of chemistry, broadly construed, edited by Angela N. H. Creager, John E. Lesch, Stuart W. Leslie, Lawrence M. Principe, Alan Rocke, E.C. Spary, and Audra J. Wolfe, in partnership with the Chemical Heritage Foundation.”

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Images and imagination

I’ve been reading Benoit Mandelbrot’s recent autobiography, The Fractalist. For anyone who hasn’t run across fractals, the famous mandelbrot set, or Julia sets, Wikipedia has a good starting point. You can also enjoy this video:

If you’re still here, Mandelbrot was the mathematician who coined the term fractal and brought their visual beauty to life. His work has no doubt resonated far beyond academic mathematics precisely because it is so graphic and engrossing. Although I’m still in the early days of his autobiography, Mandelbrot has already introduced a couple themes he sees as central to the course of his life: his early predisposition to think geometrically, and his varied interests — what some people would call unfocused, but which he sees as different angles on a common topic.

As Mandelbrot grew up, he moved from Poland to France to escape growing anti-semitism, and then spent much of his adolescent years hiding in rural France during the Nazi occupation of World War II. Somehow Mandelbrot learned to think about mathematics in terms of shapes and geometries: he credits some early textbooks that were sufficiently introductory they hadn’t eliminated pictures in favor of equations and algebra. Already as he prepared to enter college, he ran up against this same obstacle: the common mathematical culture that values the ability to manipulate equations over using diagrams. Fortunately, Mandelbrot had sufficient presence of mind to be able to translate difficult algebraic problems (such as triple integrals) into geometric terms quickly, so that he still excelled on major scholastic exams.

But it seems to me that here we already have a common split in the imagination of mathematicians and the pedagogy of mathematics. On the one hand, symbols, equations, and algebra. On the other hand, pictures, visualization, and geometry. Both are central to the history and development of mathematics over millennia, yet there is a consistent prejudice in at least the last hundred years (probably longer) toward the “pure” formalism of symbols over the “dirty” concreteness of images. The tension is epitomized in the simple story that no triangle we could draw on paper is ever a “true” triangle of mathematics. In real life, when I draw a triangle it has irregularities instead of perfectly straight edges, the three angles probably don’t actually sum to 180 degrees, and the figure has a finite resolution limited by the grain of the paper. The triangle as a mathematical object is distinct from these material features, and is properly known only abstractly.

Is a visual approach to mathematics necessary? One way to think of this, which I think tilts the issue in favor of symbolism, is to ask whether images would be part of a final, ultimate theory of mathematics. If we went forward in time a thousand years, or ten thousand, and collected all the theorems of mathematics available, would we need pictures to state or prove any of these theorems? If the answer is no, then one could argue that any use of visualization today is more like a crutch than a permanent feature of mathematics.

Alternatively, we might object to this “ultimate” notion of mathematics. Where did we get this crystal ball from anyway? How convincing is an argument that entirely depends on predicting what math will look like in a thousand years? By comparison, a thousand years ago mathematicians didn’t even have the concept of algebra as a system of abstract variables that we do today. (This was one of the great innovations of Descartes in the 16th century.) Maybe in 3013 mathematicians will prove theorems using a five dimensional flight simulator running on some bioengineered brain in a box.

One thing we do know is that visualization has mattered to at least some mathematicians and some areas of mathematics consistently over time since Euclid. This suggests that geometric imagination is here to stay. Under this view, symbolic and geometric approaches are complementary heuristics: imperfect ways of thinking that have characteristic strengths and weaknesses that can compensate for each other when used in tandem. This cooperation between styles can operate at the level of a mathematical problem, a subfield or topic area, the career of a mathematician, or even mathematics as a whole discipline. The most interesting question in this situation is how different modes of mathematical imagination can work together, and hopefully Mandelbrot’s autobiography will have some ideas about this I can write about here soon.

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Energy Landscapes: Images of Protein Folding

Here is an image of a protein folding landscape. It’s a pretty complicated one to start with, but I found it looking through my archive and you have to start somewhere. The landscape itself is recognizable in the top middle of the diagram, with the topographic lines. The height of the landscape is colored from lowest — dark blue — to highest — bright red. The 3D landscape is projected onto the flat XY plane below. (Imagine taking a 3D topographic map of a mountain range and smushing it flat on a table.)

Arrayed alongside the energy landscape are pictures of what proteins at certain places in the landscape look like. These images are really composites. Imagine taking a long photographic exposure of someone dancing on a stage. You would see faint versions of their arms, legs, and body as they moved around all superimposed in the same image. In the places where they spent more time — either because they lingered there or came back multiple times — the image would be stronger and less transparent. In this case, we’re looking at the superposition of images of a single protein over time. The protein itself is just a thin cylinder colored red at one end and blue at the other, with white in the middle. But depending on how much the protein moves, we can either see one coherent pattern (Basin b3) or a big jumble (Basin b2, although notice the red part of the protein doesn’t move much). So the analogy with the photograph is close but not perfect, since every snapshot of the protein is drawn as opaque in the diagram in order to highlight the presence and absence of variation in its shape over time.

The energy landscape diagram therefore offers us a way of visualizing and imagining the relationship between a global property of the protein — its energy level — and what three dimensional structure it has. I’ll be surveying more images of protein landscapes to describe how the diagram functions as a way of imagining new hypotheses about how proteins fold as well as summarizing and testing these hypotheses.

Screen Shot 2013-03-20 at 3.05.30 PM

From: Carlo Camilloni, Daniel Schaal, Kristian Schweimer, Stephan Schwarzinger, and Alfonso De Simone. “Energy Landscape of the Prion Protein Helix 1 Probed by Metadynamics and NMR.” Biophys J, 2012 vol. 102 (1) pp. 158-167.

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Science and Imagination

Collecting some pieces from the past:

How Intuition and the Imagination Fuel Scientific Discovery and Creativity: A 1957 Guide. From Brain Pickings (Maria Popova)

Science IS imagination. From Bad Astronomy (Phil Plait, now here)

Imagination According to Science, Engineering, and Philosophy. From The Science of Imagination (Jim Davies)2@@@2

Life on Mars and the Imagination of Scientists. From Only Human (Virginia Hughes)

Is science just imagination in a straitjacket? From TED Conversations (Swetha Chandrasekar)

Imagination and Science. A video lecture from CornellCast (Bruce Lewenstein)

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