Prologue

When I was in high school, one of the most memorable fieldtrips I had was for a biology class to study the ecosystem of a famed mountain resort in the west coast of Malaysia. It was an overnight trip since the location was quite a distance from our town. Departing in the wee hours of the morning, we arrived just as the sun was up and were quickly organized into teams by our teacher. Each team had to work with their assigned territory and we built quadrants with strings and pegs to map out the space of the botanical and zoological lifeforms found in that habitat.

Besides engaging in the statistical maneuverings of counting and noting of species, we also had to sketch out the organisms (insects) that ‘happened’ to be in our quadrants at that time. Using the data collected at our quadrant, we then schematized and extrapolated the microcosm of the ecosphere we focused on to represent the immediate locale. In other words, we were introduced to a form of scientific diagramming through our work in high school ecology.

A Bit of Prehistory

The diagram in the life (and chemical) sciences can be natural, poetic, and speculative at the same time. It can be as simple as the sketching of a botanical or zoological organism when one goes on a field trip, and the sketch, depending on how good an artist you are, may be life-like or just a schematic outline. Such sketches are performed by naturalists and biologists such as Charles Darwin, D’arcy Wentworth Thompson, and Jakob Üxkull, who were very interested in morphology of organisms; their forms and structure, measurements, and functions, and have written about such studies in their works: The Origin of Species, On Growth and Form, and Theoretical Biology. The latter two men were notable pioneers of the field referred to as theoretical biology, which would later contribute to the development of the field of computational biology, mathematical biology, and biophysics.

While there were also women naturalists who produced illustrations of the specimens they encountered, their contribution through detailed sketches and studies of various plants and insect specimens were less well-documented in the annals of natural history because, like the Bronte sisters, they were not accustomed to having their works published, particularly in scholarly journals or monographs, under their own names.

As they tended to report their work to male ‘professional’ friends, some of their findings would appear in the works of the male scientists that contain only a small line referencing the name of the contributor without necessarily acknowledging her scientific insight. An example of such a scientist is the entomologist Mary Ball, famed for her study of the order of carnivorous insects known as the Odonata.

Additionally, diagramming is not limited to the staining of microorganisms and their photographing through the focal point of the microscope; though, in this day and age, it would take the form of digital imaging with their own color-coded semiotics. Imaging technology has developed to such a cinematic scale that scientific research becomes a form of performance. One such example is research involving a detailed, three-dimensional mapping of the human body through the Visible Human Body Project , both containing volumetric data of CT and MRI scans of two human cadavers, a male and a female.

On a less dramatic scale, one will also find other forms of biomedical and bio-technological imaging to help researchers chart the breadth and length of the biological artifacts they are studying, or to abstract and simplify an otherwise overtly complex biochemical process. We may also equate diagramming with the scientific illustration one finds in magazines, journals, monographs, textbooks and popular writings. After all, one cannot demonstrate a biological or chemical function without actually providing the visuals to show what they are about.

While article journals used sophisticated computer-generated diagrams, many textbooks come accompanied by CDs with animated features that have since become the trend in laboratory demonstration. However, as I will discuss in the third installment of the series, such a trend towards animation did not only emerge with digitalization.

Structuring the Diagram of Life

The 18th century naturalist (and controversial figure) Geoffroy St-Hilaire, was quoted as saying that “organic structure is part of the becoming of an abstract being that is capable of resuming various forms…everything is rendered visible through the grid of natural history.” We think that that divide between classical and quantum happens only in physics (see Part 1 of this series).

However, that is not entirely correct, as the divide happens even with the biology (and chemistry) of the organism. Nonetheless, unlike in physics, such a divide is less clear-cut as the micro and macro-worlds overlap at different points, often also at the macro-level, regardless of our conscious relation to that fact. In other words, it is more intuitive to extrapolate the mechanisms and actions that are invisible to us in the biochemical world than it would be in physics.

The era of the classical diagramming began with Aristotle’s discussion of animal, and human, behaviors that were readily observable, in his The History of Animals. He then extrapolated the effects of the behavior to specific natural causes. However, Aristotle was a pure theorist who never had to cut open any organism, nor built instruments to peer into the invisible world of the prokaryotes and viruses. That happened at a later stage when a naturalist no longer merely observed, but also worked with the specimens of his/her observations.

However, it was only during the 17th and 18th century that naturalists began to gain a better understanding of taxonomy (via Lamarck), not only of zoological and botanical orders, but also of the human body as the sum of its many parts, the parts being the organs constituting the body of the animal and the human. From then, the diagramming of the organism went from an abstract representation to a more physical from. As Foucault discusses in The Order of Things [1], for 18th century naturalists, the organ and its functions “was like a double-entry system which could be read exhaustively either from the point of view of the role it played (reproduction, for example), or from that of its morphological variables (form, magnitude, arrangement, and number): two modes of decipherment coincided exactly, but they were nevertheless, independent of one another - the first expressing the utilizable and second the identifiable (264).”

By this time, developments in the physical sciences started to have an impact in biology, as the naturalists began to consider the nature of force and energy, and their impact, on the shaping and evolution of the biological form. That was when the naturalist-now-biologist became increasingly interested in understanding how energy is transmitted at the most fundamental level of life, and therefore, at the level of the cell. This involved understanding how the thermodynamical process works for an organism, from heat transfer mechanism to molecular transport.

While physics is also interested in the same thing, the former’s preoccupation has more to do with how it is consistent with certain physical laws and states, while in the life sciences, there is more concern with how such a mechanism is able to allow for the sustenance of biological life while also ensuring that the synchronization of important functions are maintained.[2] This is particularly the case in the study of neurosciences and the function of the brain, since time is an important material point for tracing certain cortical processes, especially that involving the sensory perception and attention, as MRI scans and the electroencephalographs research in these areas will tell you.

The life sciences have gone on a paradigmatic shift but the physical character undergirding its study has not undergone drastic change. As we go from the classical ‘behaviorism’ of Aristotle (no disrespect to BF Skinner) for ascertaining causality in organisms to tracing how time impacts the mechanism of life, we have moved between different scales, from the concrete to the abstract, the observable to the extrapolated, the macro to the micro worlds. I would suggest that the onset of modern life sciences also reconfigures the map of hierarchy: what was one top-down now becomes a circular whorl that spins in and out as each of the binaries of scales feed continuously into each other. Models are now web-like nodes rather than standalone absolutes.

Conceiving the (In)Organic

The model has finally appeared in this discussion, and as scientists of all stripes would know, is intrinsic to how modern sciences across different fields work. How it works is another contentious matter. In the early years, in the nineteenth century to early twentieth-century particularly, the development of mathematical modeling in biology was not as readily accepted because of fear of reductionism to only physico-chemical processes while not sufficiently considering the complexity and more subjective aspects of biology.[3]

Simply put, modeling is a method for creating hypothetical or speculative frameworks usually based on statistical or other forms of mathematical functions, with either data simulated from theoretical predictions or from prior experiments/research performed. Modeling can take the form of abstraction, fictionalization, idealization, and also approximate representations of what is observable from nature.

Modeling has been around long before the age of the analog and digital computer. The easiest representation would be the tactile models built and produced by chemists to aid with their visualization and analysis of various chemical bonds and isomers in stereochemistry. Carefully placed among the history of science special collections at the Oregon State University are the chemical models belonging to the Nobel Laureate Linus Pauling. An example of it can be found at their website dedicated specifically to the scientific work and life of Linus Pauling.

However, the advent of modeling software and the increasing sophistication of programming languages built for the production of simulations enable biologists and chemists to simulate a potential experiment beforehand, and even to work out sets of imaginaries and thought experiments depicting the what-ifs of certain manipulations or interventions. This has, of course, revolutionized the way certain pre-tests are done in the medical sciences, particularly in the deployment of new drugs or surgical procedures. There is a slew of literature, including of a more philosophical nature, about modeling. While many of these tend to focus on the physical sciences, developments in theoretical biology and chemistry, synthetic biology, genetics, and bioinformatics have made modeling as a part of the computational processes more integral. In going from the single specimens and classical models explicated by Foucault to more data-generative research, models are needed to make sense and categorize (as well as compartmentalize) the streams of data pouring in so that a more intuitive representation can be derived out of them. For those of you sufficiently interested in delving more deeply into the subject, I would suggest checking out Fictions in Science: Philosophical Essays on Modeling and Idealization edited by Mauricio Suárez.

Concluding Part II and Peeking into Part III

There are other areas of the sciences where diagrammatic thinking is involved, such as in climate studies, geology/geophysics, oceanography, environmental science, etc, that I have not covered in this post. However, much of the examples I have discussed in terms of taxonomic mapping and modeling apply just as much to them, since, like the life-sciences, these areas of the sciences are interested in mapping the abstract to very concrete, possibly life-changing events. But, before I end this post, and as a taster for the next and final part of the series, I will like to mention briefly an interesting area of history of science that I will expand in greater detail later.

When I mentioned early modern to nineteenth century natural history, I did not include another curious area of history of science, which is the Wunderkammer or chamber (cabinet) of curiosity. In fact many of the natural historians of that period maintained their specimen collections, together with other objects of curiosities, in such cabinets, which can come in many shapes and sizes. What is interesting about the wunderkammer is that it can also contain objects that were constructed and created as forms of experimental play to test out certain scientific theories in circulation at the time.

These items were housed together with more mundane curiosities such as special occasion cards, memento moris, miniatures, ancient coins, semi precious stones, models depicting human and animal anatomies, and other objects of collectable value to the owners. Some of these collectors may use some of these objects to create early ‘animated’ versions of books depicting their interests in the organic world, as well as the inorganic world of mechanical objects. Out of these came flap books, cut-up books, hollow books, and volvelles. There were instruments of scientific instruction and knowledge dissemination to the public from the ‘Age of Enlightenment’ onwards.

To be continued…

References:

1 Foucault, M., 1994. The Order of Things: An Archaeology of the Human Sciences, New York: Vintage Books.

2 Buonomano, D.V., 2007. The biology of time across different scales. Nat Chem Biol, 3(10), pp.594–597. Available at: http://dx.doi.org/10.1038/nchembio1007-594.

3 Twardy, J.C.S. and C. & Twardy, J.C.S. and C., 2009. The Cambridge History of Science, Cambridge University Press.

Images: Cameron Highlands; Darwin; Uexkull; ; Corix striata; surgical modeling; Wunderkammer; Wunderkammer 2.