history of science

The Pricing of Progress: Podcast interview with Eli Cook

By Contributing Editor Simon Brown

In this podcast, I’m speaking with Eli Cook, assistant professor of history at the University of Haifa, about his new book, The Pricing of Progress: Economic Indicators and the Capitalization of American Life (Harvard University Press, 2017). The book has been honored with the Morris D. Forkosch Book Prize from the Journal of the History of Ideas for the best first book in intellectual history, and with the Annual Book Prize of the Society for US Intellectual History for the best book in that field.

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In The Pricing of Progress, Cook tells the story of how American businessmen, social reformers, politicians, and labor unions came to measure progress and advocate policy in the language of projected monetary gains at the expense of other competing standards. He begins this account with the market for land in seventeenth-century England, and moves across the Atlantic to explain how plantation slavery, westward expansion, and the Civil War helped lead Americans to conceive of their country and its people as potential investments with measurable prices even before the advent of GDP in the twentieth century. He traces an intellectual history that leads the reader through the economic theories of thinkers like William Petty, Alexander Hamilton, and Irving Fisher on the one hand, and quotidian texts like household account books, business periodicals and price indices on the other. Throughout, he shows how the rise of capitalism brought with it the monetary valuation of not only land, labor and technology, but of everyday life itself.   

John Parkinson and the Rise of Botany in the 17th Century

By Guest Contributor Molly Nebiolo

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John Parkinson, depicted in his monumental Theatrum botanicum (1640).

The roots of contemporary botany have been traced back to the botanical systems laid out by Linnaeus in the eighteenth century. Yet going back in further in time reveals some of the key figures who created some of the first ideas and publications that brought horticulture forward as a science. John Parkinson (1567-1650) is one of the foremost in that community of scientists. Although “scientist” was a word coined in the nineteenth century, I will be using it because it embodies the systematic acts of observation and experimentation to understand how nature works that I take Parkinson to be exploring. While “natural philosophy” was the term more commonly in use at the time, the simple word “science” will be used for the brevity of the piece and to stress the links between Parkinson’s efforts and contemporary fields. Parkinson’s works on plants and gardening in England remained integral to botany, herbalism, and medicinal healing for decades after his death, and he was one of the first significant botanists to introduce exotic flowers into England in the 17th century to study their healing properties. He was a true innovator for the field of botany, yet his work has not been heavily analyzed in the literature on the early modern history of science. The purpose of this post is to underline some of the achievements that can be  attributed to Parkinson, and to examine his first major text, Paradisi in sole paradisus terrestris, a groundbreaking work in the field of history in the mid-1600s.

Parkinson grew up as an apprentice for an apothecary from the age of fourteen, and quickly rose in the ranks of society to the point of becoming royal apothecary to James I. His success resulted in many opportunities to collect plants outside of England, including trips to the Iberian Peninsula and northern Africa in the first decade of the seventeenth century. At the turn of the seventeenth century, collectors would commonly accompany trading expeditions to collect botanical specimens to determine if they could prosper in English climate. Being the first to grow the great Spanish daffodil in England, and cultivating over four hundred plants in his own garden by the end of his life, Parkinson was looked up to as a pioneer in the nascent field of botanical science. He assisted fellow botanists in their own work, but he also was the founder of the Worshipful Society of Apothecaries, and the author of two major texts as well.

His first book, Paradisi in sole paradisus terrestris (Park-in-Sun’s Terrestrial Paradise) reveals a humorous side to Parkinson, as he puts a play on words for his surname in the title: “Park-in-Sun.” This text, published in 1628, along with his second, more famous work published in 1640, Theatrum botanicum (The Theater of Plants), were both immensely influential to the horticultural and botanical corpori of work that were emerging during the first half of the 17th century. Just in the titles of both, we can see how much reverence Parkinson had for the intersection of fields he worked with: horticulture, botany, and medicine. By titling his second book The Theater of Plants, he creates a vivid picture of how he perceived gardens. Referencing the commonly used metaphor of the theater of the world, Parkinson compares plants as the actors in the the garden’s theatrum. It is also in Theatrum Botanicum that Parkinson details the medicinal uses of hundreds of plants that make up simple (medicinal) gardens in England. While both texts are rich for analysis, I want to turn attention specifically to Paradisus terrestris because I think it is a strong example of how botany and gardening were evolving into a new form of science in Europe during the seventeenth century.

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Title page woodcut image for Paradisus Terrestris. Image courtesy of the College of Physicians Medical Library, Philadelphia, PA.

The folio pages of Paradisus terrestris are as large and foreboding as those of any early modern edition of the Bible. Chock full of thousands of detailed notes on the origins, appearance, and medical and social uses for pleasure gardens, kitchen gardens and orchards, one could only imagine how long it took Parkinson to collect this information. Paradisus terrestris was one of the first real attempts of a botanist to organize plants into what we now would term genuses and species. This encyclopedia of meticulously detailed, imaged and grouped plants was a new way of displaying horticultural and botanical information when it was first published. While it was not the first groundbreaking example of the science behind gardens and plants in western society, Luci Ghini potentially being the first, Parkinson’s reputation and network within his circle of botany friends and the Worshipful Society of Apothecaries bridged the separation between the two fields. Over the course of the century,  the medicinal properties of a plant were coherently circulated in comprehensive texts like Parkinson’s as the Scientific Revolution and the colonization of the New World steadily increased access to new specimens and the tools to study them.

 

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Paradisus terrestris includes many woodcut images of the flowers Parkinson writes about to help the reader better study and identify them. Image courtesy of the Linda Hall Library, Kansas City, MO.

Another thing to note in Paradisus terrestris is the way Parkinson writes about plants in the introduction. While most of the book is more of a how-to narrative on how to grow a pleasure garden, kitchen garden, or orchard, the preface to the volume illustrates much about Parkinson as a botanist. Gardens to Parkinson are integral to life; they are necessary “for Meat or Medicine, for Use or for Delight” (2).  The symbiotic relationship between humans and plants is repeatedly discussed in how gardens should be situated in relationship to the house, and how minute details in the way a person interacts with a garden space can affect the plants. “The fairer and larger your allies [sic] and walks be the more grace your Garden shall have, the lesse [sic] harm the herbs and flowers shall receive…and the better shall your Weeders cleanse both the beds and the allies” (4). The preface divulges the level of respect and adoration Parkinson has towards plants. It illustrates the deep enthusiasm and curiosity he has towards the field, two features of a botanist that seemed synonymous for natural philosophers and collectors of the time.

John Parkinson was one of the first figures in England to merge the formalized study of plants with horticulture and medicine. Although herbs and plants have been used as medicines for thousands of years, it is in the first half of the seventeenth century that the medicinal uses of plants become a scientific attribute to a plant, as they were categorized and defined in texts like Paradisi in sole paradisus terrestris and Theatrum botanicum. Parkinson is a strong example of the way a collector’s mind worked in the early modern period, in the way he titled his texts and the adoration that can be felt when reading the introduction of Paradisus terrestris. From explorer, to collector, horticulturist, botanist, and apothecary, the many hats Parkinson wore throughout his professional career and the way he weaved them together exemplify the lives many of these early scientists lived as they brought about the rise of these new sciences.

Molly Nebiolo is a PhD student in History at Northeastern University. Her research covers early modern science and medicine in North America and the Atlantic world and she is completing a Certificate in Digital Humanities. She also writes posts for the Medical Health and Humanities blog at Columbia University.

Reconsidering Mechanization in the Industrial Revolution: The Dye Book of William Butt

By guest contributor Lidia Plaza

On my way to Covent Garden this summer, I spotted a Muji store and popped inside.  A few months earlier I had picked up a pair of Muji socks in Terminal 5 of JFK, which had since become my favorite pair.  Determined to acquire more, equally lovely socks, I studied the sock selection until I found some in the same style, size, and color as my beloved pair.  I grabbed them and headed to the till.  I didn’t bother to inspect the socks; I assumed the knit tensions were all perfectly even, the densities were consistent, the colors were identical.  I also assumed that they were exactly like the socks I had purchased a few months earlier in New York.  I didn’t compare the socks because I take consistency for granted.  I expect it.  I insist upon it. My expectation that socks I purchase from a Japanese retailer in New York will be identical to socks I find in London months later is a testament to the success of the Industrial Revolution.

In the history of the Industrial Revolution, the mechanization of cleaning, processing, spinning, and weaving textiles has become Chapter One of the gospel, but in this telling there has been undue emphasis put on the mechanization of manufacturing.  The triumph of the Industrial Revolution was not the machines themselves, but the processes that could produce consistent products at a mass scale; machines were just one tool of those processes.  This point is well illustrated in an often-overlooked verse of the gospel: dyeing.

Dyeing’s neglect is partially understandable, as dyeing is almost as difficult for the historian to study as it was for the eighteenth-century apprentice to learn.  Unlike paints, dyes must chemically bond with the textile fibers, and variations in the fibers, the pH of the water, the quality of added mordants and dye-assistants, or even the composition of the containers used can affect the results.  Only in the nineteenth century did chemists begin to understand dye chemistry, and when histories of industrialization include dyes, this, for instance, is often what they highlight. But early modern dyers spent their careers learning to achieve consistent, even dyes, and, more recently, scholars like Giorgio Riello have included dyeing innovations in their examinations of early textile industrialization.  It is now becoming clear that dyers and clothiers like William Butt were making critical strides in early textile industrialization.

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William Butt began his dye book on November 24, 1768.  As a clothier, Butt oversaw the entire process of producing a woolen textile from cleaning the raw fibers to weaving the fabric.  Yet his book, the product of almost daily work, is just about dyeing.  Why then did Butt devote so much effort to just one step in the manufacturing process?  The answer is simple: half the price of a finished textile could come just from the quality of its dyeing.  It was not uncommon for clothiers to set up their own dye houses, unwilling to trust someone else’s work with such a critical step.  William Butt was such a clothier.

Between 1768 and 1785, he recorded 794 recipes, filling over 88 pages with rows and columns of cryptic numbers, strange symbols, bizarre ingredients, and round little pieces of colored felt, stuffing little scraps of paper between its pages.  After weeks and months of pouring over the book in the reading room of the Beinecke Library, I made some sense of the book; each row documents a new recipe, and each column contains a separate piece of information about the recipe.  In this way, Butt recorded the amounts of wool he worked with, the merchant marks of his wool suppliers, and the dyestuffs used in each recipe, always providing samples of the results and assigning a unique recipe number.

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The book shows that Butt was able to dye more wool with better results by systematically experimenting with his dyes.  Starting around 1777, about page 35 of his book, Butt began to treat his book less like a cookbook of collected recipes, and more like a lab notebook to record his experiments.  He started dating his recipes, and the dates suggest that Butt began to intensify his production.  Butt filled 35 pages between 1768 and 1777.  Assuming this was his only dye book, this means he only filled 3 or 4 pages a year during this period.  However, after 1777 he usually filled at least 6 pages each year.

Number of Pages Filled by Each Year in William Butt’s Dye Book Between May 1777-May 1785
Year Approximate Number of pages filled
1777 (May-December) 6
1778 6.5
1779 8
1780 6
1781 7
1782 6
1783 6.5
1784 5
1785 (February-May) 3

Not only was Butt working with more recipes but he also became more meticulous in his work.  He got pickier about how he classified a new dye recipe by assigning a new dye number to recipes that varied only slightly from other recipes in the book.  He began experimenting with his recipes, recreating previous recipes using wool from different suppliers, for example.  In another instance, he experimented with technique, noting that recipe 20129 was the same as 19917, “differing from 19917 in method only.”  His book gets more cluttered as he began recording the merchant marks of the merchants who supplied the wool in each recipe, and as he makes more notes and comments.

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Part of Butt’s success may have come from the fact that he seems to have been a specialist.  He was clearly skilled at using many dyestuffs, but he relied on other dyers to provide him with indigo-dyed wool.  Indigo is a vat dye, which has an entirely separate chemical process for bonding to fibers than the other dyestuffs Butt worked with, which were almost exclusively mordant-dyes.  Not all dyers specialized, but there is evidence that indigo specialists were common, and so it is not surprising that Butt would also specialize in one type of dye.  By focusing on dyes that all required similar methods, Butt was able to refine those methods and increase his efficiency.  By the end of his book, Butt had more than doubled the amount of wool he dyed in each recipe.

Technology was at the heart of the Industrial Revolution, but, as Butt’s dye book illustrates, if all we imagine when we think of technology is machines, we are missing a large part of the picture.  Technology is simply the practical application of scientific knowledge, and in this sense William Butt’s dye book is as much a piece of technological advancement as the spinning jenny and the power loom.  He could not have known the chemistry underpinning his work, but he knew he could maximize his output by systematically experimenting with dyestuffs and applying what he learned to his processes.  All the spinning jennies and power looms in the world would have been useless if all those threads and fabrics could not be consistently and reliably dyed, but dyeing at larger scales required a better understanding of the dyes, not new machines.  Butt and the many others like him understood this.  Hiding in record offices and archives, there are other dye books, all written by clothiers and dyers trying to master dye processes.  It was their mastery of process that achieved the consistency that I take for granted every time I browse a wall of socks.

Lidia Plaza is a PhD student in British history at Yale University. Her research focuses on industrialization and British foreign policy in the late eighteenth- and early nineteenth-centuries.  

GIFs, Archives, and Riverscapes – Process and reflections on Floating Archives

By artist and contributing writer Jacob Rivkin

What are the subtle histories embedded into each landscape? Floating Archives asks Philadelphians to consider our beloved “hidden river” as a source of narratives that tell of the ever-changing borders between land and water. (The original name for the Schuylkill River comes from the Lenni Lenape, Tool-Pay Hanna, which translates to Turtle River. The moniker ‘hidden river’ originates from the name given by Dutch settlers in Pennsylvania.) Some stories show us who shaped the river, and the funds and materials they used to harden its edges. Other stories are more difficult to surface, obscured by centuries of persistent structures of power and displaced ecologies of humans, animals, and plants. Floating Archives playfully and vividly reminds us of these submerged histories.

Floating Archives was a public art intervention on the lower Schuylkill River in Philadelphia. The project was supported through the Mellon Artist-in-Residence program at the Penn Program in the Environmental Humanities, in collaboration with Bartram’s Garden and the Science History Institute. On three Saturday evenings in September 2018, hand-drawn animations based on archival materials were projected on a screen suspended between two canoes. As these floating silent images present traces of the past in vibrant color, they invited us to see still other rivers, as they were, as they are, and as they could be. Specific animations were projected as Floating Archives approached the place that each original image referenced, creating a spectral layering of landscape, history, and wonder, both literally and figuratively. These drawings and animations also provoke us, in times of rising waters and changing coastlines, to consider the labor, capital, and energy that have and will shape the river’s future course.

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Floating Archives on the Schuylkill River, 2018

The inspiration for Floating Archives originally came from making animations for a film on the history of taxidermy, and its contemporary alternative scene, with the Distillations podcast at the Science History Institute. The film, Death and Taxidermy, included animated explanations of the history, process, and personal stories involving taxidermy. The section on history included conducting research on advances in scientific methods of preservation and the buildings and landscapes where these scientific developments occurred. The process of reimagining physical actions and motions of people and animals in these historical spaces proved to be very enjoyable as an artistic practice. I started thinking about how I could bring this sensibility to my own independent research as an artist.

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Clip from Death and Taxidermy, 2016

My work as an artist addresses how we experience and internalize the idea of landscape, and by association, wonder. These include creating devices that record the multi-sensory elements of a landscape through creative coding and physical computing, speculative biological systems, and films which explore the awakening of sentience and complexity within digital images. As an active canoer on the Schuylkill River in Philadelphia, I started thinking about the viewscapes created by the flow of water and the edges that border the river. Taking this as my lead, I started combing through digital archives and was led to reading Redemption of the Lower Schuylkill by John Frederick Lewis from 1924. This book, or perhaps manifesto, which contains a passionate argument for how the river in that time could be improved in cleanliness and recreation, is also filled with photographs and historical images of the river. This is where I would start the process of creating the animations for Floating Archives.

The process for creating animations is as follows. I find an image that contains some portion of the Schuylkill River – this can be a photograph, etching, or drawing. All of the images came from archives or images that were digitized. This was necessary because I made most of the drawings and animations while participating in an arts residency at the Fine Arts Work Center during the winter of 2018 in Provincetown, MA. I then study the image for clues of what kind of industry, recreation, labor, or leisure may have taken place there, if it is not immediately apparent. This image is imported into a computer program specifically for hand-drawn animation. The image is cropped to either focus on the action or create a more visually engaging composition. The layer the image is placed onto is then locked, and the opacity is reduced to about eighty percent. On a new layer above, I use a digital pen and tablet to trace over the contours of the image below using a bright pink color with a two-point wide mark. This is so I can more easily delineate between the old and new background and ensure parts of the image below are not missed. A new layer is then created that contains the character or objects that are moving. Separating these different elements out of the image allow for further applications of independent motion or effects. The last elements to animate, also on separate layers, are the atmospheric effects of water, clouds, and smoke. The line drawings of the background layer and animation layers each receive its own independent color layer as well by using a paint bucket to fill in the outlines of the layer above. The process of creating several layers of images, motion, and color allows for the quick rearrangement of timing and compositing because less erasing and drawing is involved than if every image were on the same layer. For example, erasing the outline of a figure begins to erase the color and lines of the background. In the end, a final seamless two-dimensional animation is created.

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Animation is an accessible medium of communication. By translating archival images, many toned by the hue of time, into hand drawn animation containing consistent lines, weights, and vibrant colors, the original cultural currency imbued in the image is transformed into a source of contemplation, more playfulness, and less cultural gravity. The sense of seriousness contained within the original image can become a barrier for imagining the embedded narratives. The language of hand-drawn animation references a childlike association with Saturday morning cartoon series and films produced by Disney, and, by proxy, increases the sense of wonder around an image.

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Shaq vs. Cat GIF

Moreover, the animations take their inspiration from the culture of GIF (Graphic Interchange Format) animations. GIFs are a file type originally associated with rotating logos and website “under construction” signs, which now exist as a quotidian form of communication and expression in digital culture. One important element of GIF animations is that embedded image and actions are on constant repeat, looping, sometimes seamlessly, in time. Each of the animations created for Floating Archives also loop seamlessly. The resonant link between history and repetition, the constant cycle of development and redevelopment, and the ebbing transition of wilderness to the flow of culture, seems analogous to the way images through history depicting the Schuylkill River have portrayed the river as a confluence of labor, resource extraction and transportation, and leisure.

Water, progressing from higher elevations to lower ones, carries the sediment of upper creeks and tributaries to the shores and banks in the wetlands below. The movement is ever forwards. The physical history of a distant, yet interconnected, place becomes present for a brief geological moment, then continues its journey downstream and out to the vast ocean. In animation, one drawing follows another seamlessly. Images move forward sequentially in time to reveal the illusion of movement and convey meaning embedded into each frame. Yet, we cannot hold onto a particular image, as its meaning is conveyed by the images that came before and the images that come afterwards. By placing water and animation, these two vehicles of motion and meaning, in proximity to each other, Floating Archives can offer, for perhaps longer than a moment, a fleeting perspective of history and landscape illuminated by projection, streetlamps, and glimmering reflections in the river below.

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Floating Archives, 2018

Jacob Rivkin is an interdisciplinary artist living and working in Philadelphia, PA. He is a former Fulbright Fellow, a recipient of the Visual Arts Fellowship at the Fine Arts Work Center in Provincetown, and teaches Fine Arts courses at the University of Pennsylvania. His animations have screened at the Japan Media Arts Festival in Tokyo, Japan, Animation Block Party in Brooklyn, NY, Vox Populi in Philadelphia, PA, and the Peephole Cinema in San Francisco. His sculptures have been exhibited at the Vancouver Art Gallery in Vancouver, BC, The Chemical Heritage Foundation Museum, Philadelphia, PA, the Arlington Art Center in Arlington, VA and Julius Caesar Gallery in Chicago, IL. He previously worked with the Penn Program in the Environmental Humanities as an Ecotopian Toolmaker in 2017 with ecological designer Eric Blasco. Their project, the Bio Pool, was described by the Philadelphia Inquirer as “a giant Brita filter for the Schuylkill River.” It continues to filter water and be a habitat for cattails and red-winged blackbirds near the public dock at Bartram’s Garden.

Functional Promiscuity: The Choreography and Architecture of the Zinc Gang

By Contributing Editor Nuala F. Caomhánach

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Zinc Finger DNA Complex, image by Thomas Splettstoesser

 

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Andreas Sigismund Marggraf

The tale about gag knuckles, taz-two, hairpin, ribbons, and treble clef is quite elusive.  Although they sound more like nicknames of a 1920’s bootlegging gang (at least to me) they are the formal nomenclature of a biochemical classification system, known commonly as zinc fingers (ZnF). The taxonomy of zinc fingers describes the morphological motif that the element creates when interacting with various molecules. Macromolecules, such as proteins and DNA, have developed numerous ways to bind to other molecules and zinc fingers are one such molecular scaffold. Zinc, an essential element for biological cell proliferation and differentiation, was first isolated in 1746 by the German chemist Andreas Marggraf (1709-–1782). Zinc fingers were important in the development of genome editing, and while CRISPR remains king, zinc is making a comeback.

 

Strings of amino acids fold and pleat into complex secondary and tertiary structures (for an overview, see this video from Khan Academy).

 

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Fig. 1: The folding funnel

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Fig. 2: The energy landscape

Proteins with zinc finger domains—meganucleases—act as molecular DNA scissors, always ready to snip and organize genetic material. The return of these biochemical bootleggers, an older generation of genome editing tools, is due to the problem of exploring the invisible molecular world of the cell. In this age of genomic editing, biologists are debating the concept of protein stability and trying to elucidate the mechanism of protein dynamics within complex signalling pathways. Structural biologists imagine this process through two intermingled metaphors, the folding funnel (fig. 1) and the energy landscape (fig. 2). The energy landscape theory is a statistical description of a protein’s potential surface, and the folding funnel is a theoretical construct, a visual aid for scientists. These two metaphors get scientists out of Levinthal’s Paradox, which argues that finding the native or stable 3-dimensional folded state of a protein, that is, the point at which it becomes biologically functional, by a random search among all possible configurations, can take anywhere from years to decades. Proteins can fold in seconds or less, therefore, biologists assert that it cannot be random. Patterns surely may be discovered. Proteins, however, no longer seem to follow a unique or prescribed folding pathway, but move in different positions, in cellular time and space, in an energy landscape resembling a funnel of irregular shape and size. Capturing the choreography of these activities is the crusade of many types of scientists, from biochemists to molecular biologists.

 

Within this deluge of scientific terminology is the zinc atom of this story.  With an atomic number of 30, Zinc wanders in and out of the cell with two valence electrons (Zn2+). If Zinc could speak it might tell us that it wishes to dispose, trade, and vehemently rid-itself of these electrons for its own atomic stability. It leads with these electrons, recalling a zombie with outstretched arms. It is attracted to molecules and other elements as it moves around the cytoplasm and equally repelled upon being cornered by others. Whilst not as reactionary as the free radical Hydrogen Peroxide (H2O2), it certainly trawls its valency net in the hope of catching a break to atomic stasis, at least temporarily. In this world of unseen molecular movements a ritual occurs as Zinc finds the right partner to anchor itself to. Zinc trades the two electrons to form bonds making bridges, links, ties and connections which slowly reconfigure long strings of amino or nucleic acids into megamolecules with specific functions. All of this occurs beneath the phospholipid bilayer of the cell, unseen and unheard by biologists.

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Model of a Zinc atom

The cell itself is an actor in this performance by behaving like a state security system, as it monitors Zn2+ closely. If the concentration gets too high, it will quarantine the element in cordoned-off areas called zincosomes. By arranging chains of amino acids, such as cysteine and histidine, close to each other, the zinc ion is drawn into a protein trap, and held in place to create a solid, stable structure. They connect to each other via a hydrogen atom, with hydrogen’s single electron being heavily pulled on by Carbon as if curtailing a wild animal on a leash. In the 1990s, when the crystal structures of zinc finger complexes were solved, they revealed the canonical tapestry of interactions. It was notable that unlike many other proteins that bind to DNA through the 2-fold symmetry of the double helix, zinc fingers are connected linearly to link sequences of varying lengths, creating the fingers of its namesake. Elaborate architectural forms are created.

Like a dance, one needs hairpins, or rather beta-hairpins, two strands of amino acids that form a long slender loop, just like a hairpin. To do the gag knuckle one needs two short beta-strands then a turn (the knuckle), followed by a short helix or loop. Want to be daring, do the retroviral gag knuckle. Add one-turn alpha-helix followed by the beta hairpin. The tref clef finger looks like a musical treble clef if you squint really hard. First, assemble around a zinc ion, then do a knuckle turn, loop, beta-hairpin and top it off with an alpha-helix. The less-complex zinc ribbon is more for beginners: two knuckle turns, throw in a hairpin and a couple of zinc ions. Never witnessed, biologists interpret this dance using x-ray crystallography, data that looks like redacted government documents, and computer simulated images.

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X-ray crystallography of a Zinc Finger Protein, image from Liu et al., “Two C3H Type Zinc Finger Protein Genes, CpCZF1 and CpCZF2, from Chimonanthus praecox Affect Stamen Development in Arabidopsis,” Genes 8 (2017).

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Aaron Klug

In the 1980s, zinc fingers were first described in a study of transcription of an RNA sequence by the biochemist Aaron Klug. Since then a number of types have been delimited, each with a unique three-dimensional architecture. Klug used a model of the molecular world that required stasis in structure.The pathway towards this universal static theoretical framework of protein functional landscapes was tortuous. In 1904, Christian Bohr (1855–1911), Karl Albert Hasselbalch (1874-1962), and August Krogh (1874-1949) carried out a simple experiment. A blood sample of known partial oxygen pressure was saturated with oxygen to determine the amount of oxygen uptake. The biologists added the same amount of CO2 and the measurement repeated under the same partial oxygen pressure. They described how one molecule (CO2) interferes with the binding affinity of another molecule (O2) to the blood proteins, haemoglobin. The “Bohr effect” described the curious and busy interactions of how molecules bind to proteins.

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Jacques Monod and François Jacob, image by Agence France-Presse

In 1961, Jacques Monod and Francois Jacob extended Bohr’s research. The word ‘allosteric’ was introduced by Monod in the conclusion of the Cold Spring Harbor Symposium of 1961. It distinguished simultaneously the differences in the structure of molecules and the consequent necessary existence of different sites across the molecule for substrates and allosteric regulators. Monod introduced the “induced-fit” model (proposed earlier by Daniel Koshland in 1958). This model states that the attachment of a particular substrate to an enzyme causes a change in the shape of the enzyme so as to enhance or inhibit its activity. Suddenly, allostery erupted into a chaotic landscape of multiple meanings that affected contemporary understanding of the choreography of zinc as an architectural maker. Zinc returned as the bootlegger of the cellular underworld.

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The “induced-fit” model

Around 2000, many biologists were discussing new views on proteins, how they fold, allosteric regulation and catalysis. One major shift in the debate was the view that the evolutionary history of proteins could explain their characteristics. This was brought about by the new imaginings of the space around the molecules as a funnel in an energy landscape. When James and Tawfik (2003) argued that proteins, from antibodies to enzymes, seem to be functionally promiscuous, they pulled organismal natural selection and sexual selection theory into the cellular world. They argued that promiscuity is of considerable physiological importance. Bonding of atoms is more temporal and more susceptible to change than thought of before. Whilst they recognized that the mechanism behind promiscuity and the relationship between specific and promiscuous activities were unknown they opened the door to a level of fluidity earlier models could not contain. Zinc fingers, thus, played an important role in being a “freer” elements with the ability to change its “mind”.

These ideas were not new. Linus Pauling proposed a similar hypothesis, eventually discarded as incorrect, to explain the extraordinary capacity for certain proteins (antibodies) to bind to any chemical molecule. This new wave of thinking meant that perhaps extinct proteins were more promiscuous than extant ones, or there was a spectrum of promiscuity, with selection progressively sifting proteins for more and more specificity. In 2007, Dean and Thornton, reconstructed ancestral proteins in vitro and supported this hypothesis.  If the term promiscuity as it has been placed on these macromolecules sticks, what exactly does it mean?  If promiscuity is defined as indiscriminate mingling with a number of partners on a casual basis, is zinc an enabler? A true bootlegger? This type of language has piqued the interest of biologists who see the importance of this term in evolution and the potential doors it opens in biotechnology today. Promiscuity makes molecular biology sexy.

To state that a protein, or any molecule, is not rigid or puritanical in nature but behaves dynamically is not the equivalent of stating that the origin of its catalytic potential and functional properties has to be looked for in its intrinsic dynamics, and that the latter emerged from the evolutionary history of these macromolecules.  The union of structural studies of proteins and evolutionary studies means biologists have not only (re)discovered their dynamics but also highlights the way that these properties have emerged in evolution. Today, evolutionary biologists consider that natural selection sieves the result, not necessarily the ways by which the result was reached: there are many different ways of increasing fitness and adaptation. In the case of protein folding with zinc fingers, what is sieved is a rapid, and efficient folding choreography. These new debates suggest that what has been selected was not a unique pathway but an ensemble of different pathways, a reticulating network of single-events, with a different order of bond formation.

If the complex signalling pathways inside of a cell begins with a single interaction, zinc plays a star role. Zinc, along with other elements such as Iron, are the underbelly of the molecular world. Until captured and tied down, the new view of proteins offers to bond mechanistic and evolutionary interpretations into a novel field.  This novelty is a crucial nuance to explain the functions and architecture of molecular biology. As the comeback king, zinc fingers are used in a myriad of ways. As a lookout, biologists infected cells with with DNA engineered to produce zinc fingers only in the presence of specific molecules. Zinc reports back as biologist looks for the presence of a molecule, such as a toxin, by looking for the surface zinc fingers rather than the toxin itself. Zinc fingers are obstructionists. In 1994 an artificially-constructed three-finger protein blocked the expression of an oncogene in a mouse cell line. As informants, they capture specific cells.  Scientists have experimented by creating a mixture of labeled and unlabeled cells and incubated them with magnetic beads covered in target DNA strands. The cells expressing zinc fingers were still attached to the beads. They introduce outsiders into the cell, such as delivering foreign DNA into cells in viral research. In tracking these bootleggers, scientists have pushed the limits of their own theories and molecular landscapes, but have landed on promiscuity, a culturally laden, inherently gendered word.

“To seek God in all things”: The Jesuit encounter with botany in India

By contributing writer Joseph Satish V

Only a month after India gained independence from the British in 1947, the Indian botanist Debabrata Chatterjee wrote of his

hope that in the new India the Government will… effect among other things the early revival of the Botanical Survey of India. If it is possible to recruit men of knowledge and qualities of those giants of the past… no man of science in India need doubt that the revival of the Survey would be of the greatest help and of far-reaching benefits to India.

In 1954, the first independent Government of India appointed the taxonomist Hermegild Santapau as its Chief Botanist and Director.  Santapau had a PhD in Botany from the London University, had worked at the Royal Botanical Gardens in Kew (England), was a Fellow of the Linnean Society of London, editor of the Journal of the Bombay Museum of Natural History, and a Professor of Botany. His services to reviving botany and science education in the country were recognized with the award of the Padma Shri from the Government of India. But this “giant” was neither British nor Indian — he was a Catholic Jesuit priest from Spain. Fr. Santapau was only one of the many Jesuits who established a legacy of “Jesuit science” in India after the religious order was “restored” in 1814.

Ignatius at the River Cardoner - By Dora Nikolova Bittau in Chapel of St Ignatius, Seattle University

Ignatius at the River Cardoner .By Dora Nikolova Bittau, in the Chapel of St. Ignatius, Seattle University

The Society of Jesus is a religious congregation of Catholic clerics founded by Ignatius of Loyola (1491-1556) in 1540. Only two years later, Francis Xavier (1506-1552), one of Ignatius’ first companions, reached Goa on the western coast of India. When Ignatius died sixteen years later, the number of Jesuits had grown to a thousand members around the world. With a unique “way of proceeding“, the Jesuits established themselves firmly in secular culture — arts, astronomy, anthropology, even naval architecture — all “for the greater glory of God“. However, the growing influence of the Jesuits in the Church, State, and society caused resentment in many of Catholic Europe’s nations (chiefly Portugal, Spain, and France), which led to the Suppression of the Jesuits by Pope Clement XIV in 1773. Forty-one years later though, Pope Pius VII restored the Society in 1814.

Scholarship in the history of the Jesuits has witnessed a significant shift in the past few decades. Since the 1980s, the number of non-Jesuit (also non-Catholic) scholars interrogating what has come to be called “Jesuit science” has increased. Historians of Jesuit science have generally explored the relationship between the Jesuit missionary goals and their scientific activity in the sixteenth and seventeenth centuries, often portraying the Jesuits as ‘transmitters’ of European science to the colonies in the New World. Steven J. Harris’s description of early modern Jesuit science continues to be used as a universal description of Jesuit science across space and time. But some scholars have begun arguing the case for a more nuanced engagement with regional variants of Jesuit science.

Dhruv Raina explains that the European Jesuits who arrived in South Asia not only transmitted European science but also discovered, collected, and interpreted indigenous knowledge in the colonies. Agustin Udias argues for a broader exploration of Jesuit science in the post-Restoration period beyond Europe. It is worth exploring, even briefly, why post-1814 Jesuit science is considered different in comparison to early modern Jesuit science.

After 1814, the “new” Jesuits of the restored Society found themselves in an alien scientific landscape, which, among other things, was characterized by the emergence of specialized disciplines and “professionals” who were paid to pursue science. Subsequently, the Jesuits reinvented themselves as a teaching order in schools and colleges across the world. But they were forced to shift from the eclectic scientific tradition of their past to the new disciplines like seismology in North America and the “new botany” (laboratory-based botany research) in England and Germany. It was also in this period that the Jesuits returned to India – a group of Belgian Jesuits came to the eastern coast and set up the Bengal Mission in 1834. Later in 1837, the French Jesuits established the Madurai Mission in southern India. While the sixteenth-century Jesuits interacted with Hindu kings and Mughal emperors, now the Jesuits were obligated to cooperate with the British Empire. However, one feature remained common to the scientific enterprise of the “old” and the “new” Jesuits in India: collecting plant specimens.

Harris notes that medical botany – identifying local plants and their benefits for health reasons – was fairly consistent across all the early Jesuit missions. In India, the Jesuits in early modern Goa acquainted themselves with the native medical traditions – the Portuguese physician Garcia de Orta (1500-1568) provided the first instance of the exchange between European and Ayurvedic medical systems. The early Jesuits to India lived as pilgrims, moving between villages and kingdoms, and evangelized the natives. In the process the Jesuits gained knowledge about the local customs, including that of native plants which they consumed as food or medicine. The restored Jesuits were no longer evangelizers but educators of the evangelized. They established training houses (novitiates) for teaching candidates for the priesthood (novices) in subjects that included philosophy, theology as well as the natural and physical sciences. Training in the natural sciences included collecting, identifying and preserving different flora and fauna. Yet, the focus on nature and the sciences was not only necessitated by the educational mission of the Jesuits; it was an integral part of their “spiritual” training.

Ignatius of Loyola believed that one could experience God in the natural world. He writes in his autobiography that he had spiritual experiences while gazing at nature, be it the stars in the night sky or the Cardoner river in his native Spain. Ignatius maintained notes of these experiences, reflected upon them, and later felt that “some things which he used to observe in his soul and found advantageous could be useful also to others, and so he put them into writing”. This took the form of a series of contemplative exercises called the Spiritual Exercises which later became the foundation for the compulsory spiritual training of the Jesuit novices and continues to be so.

The goal of the Spiritual Exercises was (and is) to help the Jesuit to identify his vocation in life. Guided by a spiritual director in solitude, the novice was urged “to use his senses, particularly sight to fix their mental gaze upon the scene of the meditation” during each exercise. Following this, the novice was expected to write down notes of his contemplative experience, like Ignatius did, and maintain an “observational” record of his spiritual experiences. The acme of the exercises was the ‘Contemplation to Attain Love‘ in the Fourth Week where the novice was asked to consider: “… how God dwells in creatures; in the elements, giving them existence; in the plants, giving them life; in the animals, giving them sensation; in human beings, giving them intelligence …” This tradition of contemplating “how God dwells in” nature remained unchanged in the restored Society. This along with an emphasis on silence and solitude encouraged Jesuits to establish their formation houses amidst pristine natural habitats. It was for this reason that the French Jesuits established their novitiate in Shembaganur (1877) close to Kodaikanal, a south Indian hill station favored by the British.

Hand painted plate by Anglade 1919 - Courtesy Rapinat Herbarium Trichy

Hand painted plate by Anglade, 1919. Courtesy Rapinat Herbarium Trichy

Less than a decade before the Shembaganur novitiate was established, the British taxonomist Joseph Dalton Hooker had completed his botanical expedition in the Himalayas and published several illustrated flora (1871). The Royal Botanical Gardens at Kew outside London became “the center of a worldwide network of colonial gardens”. Acknowledging these developments, the French Jesuits (who had already received some training in the natural sciences in Europe) promoted the teaching and learning of the biological sciences at Shembaganur. A part of the novice’s education also included plant taxonomy; the novices had to venture into the nearby Palni hills to identify and collect plant specimens. The young novices had several Jesuits to guide and inspire them. Pierre Labarthere (1831–1904)  cultivated botanical gardens on the novitiate premises (of course, with the help of the novices). Emile Gombert (1866–1948) collected orchids and established a garden dedicated to orchids (which survives till date). Louis Anglade (1873–1953) documented local plants through a collection of nearly 2000 paintings. George Foreau (1889–1959) assembled a collection of mosses, lichens, algae, and fungi while Alfred Rapinat (1892–1959) collected flowering plants and ferns. These Jesuits and the young novices often sent plant specimens to the Royal Botanical Gardens at Kew for proper identification. Santapau, though not a resident of Shembaganur, had begun his life’s work at the Kew Garden. Soon enough, the French Jesuits encouraged the young novices to interact with Santapau, who was then in the Jesuit college of St. Xavier’s at Bombay (1940). It was only expected that the younger Jesuits would follow his botanical legacy.

Jesuits with the oldest tree on the Palni Hills 1903 - Courtesy Rapinat Herbarium Trichy

Jesuits with the oldest tree on the Palni Hills, 1903. Courtesy Rapinat Herbarium Trichy.

As a young novice at the Sacred Heart College, KM Matthew (1930-2004) was acquainted with botanical surveys in Shembaganur. With the nomination of Santapau to the Botanical Survey of India, Mathew was encouraged to pursue his doctoral research with the senior botanist. In 1962, under the supervision of Santapau, KM Matthew became the first Indian Jesuit to acquire a PhD in botany, focusing on the alien plants of the Palni Hills. In 1963, another pupil of Santapau, Cecil Saldanha (1926-2002) was awarded his PhD for his thesis on Taxonomic Revision of the Scrophulariaceae of Western Peninsular India. Like Santapau, both the Jesuits made significant contributions to plant taxonomy: KM Mathew published the four-volume Flora of Tamil Nadu Carnatic (1981-1988) while Saldanha published Flora of the Hassan District, Karnataka (1976).

Matthew and Saldanha were among the first Indian Jesuits to engage with science in a globalized, industrial era, where science and technology came to be seen as intertwined with “social, political and cultural issues of societal relevance”. Observing the wider implications of modern science and technology for the Catholic Church, its bishops observed at the Second Vatican Council (1962-65) that “if these instruments (of science and technology) are rightly used they bring solid nourishment to the human race”. After Vatican II, the Jesuit Superior General of the Jesuits, Pedro Arrupe (1907-1991) named the first delegate for what came to be known as the “scientific apostolate” of the Jesuits. In 1979, the Jesuit scientists of India, Nepal and Sri Lanka came together to organize the first ever meeting of south Asian Jesuit scientists. Responding to a report of this meeting, Arrupe noted the “apostolic aspect of the Jesuit [s]cientist’s work” and emphasized the need for Indian Jesuits “to reflect more on Indian problems”. This provides a hint of how the “new” Jesuit scientific activity became “localized” in the backdrop of the Catholic Church’s wider embrace of modern science and technology. Further investigation of how Jesuit science is manifested locally in the context of a global missionary ethos is required, especially with respect to Jesuit botany in southern India.

Contemporary Jesuit botanists in India have widened their horizons beyond the plant taxonomy of their French mentors. This engagement has extended into specialized terrains like molecular systematics and agricultural biotechnology for solving “Indian problems” like drought, crop pests and diseases, extinction of native flora, and deforestation. While Jesuits have also ventured into the twenty-first century (and contentious) disciplines like genetic engineering, there is little scholarship on how the trajectory of Jesuit biological sciences evolved in India. The establishment of the Shembaganur novitiate and the arrival of European Jesuits like Santapau signify a milestone for exploring the dawn of post-Restoration Jesuit science in southern India.

The election of the first Jesuit Pope (Francis) in 2013 has renewed interest in Jesuit studies. Historians of Jesuit science and historians of post-colonial science could consider stepping into this uncharted domain of why the quintessential Jesuit botanist did what he did in independent India. Young historians of Jesuit science must wonder why then Prime Minister of India, Indira Gandhi observed after Santapau’s death in 1970 that:

In Rev. Fr. Santapau’s death we have lost an eminent scholar who has served education and science for over 40 years. His deep love for India urged him to become a citizen of the country. He had a great knowledge of, and concern for, our plant wealth and wrote intensively on it for experts and laymen. May his memory long continue to inspire all those interested in our flora.

Joseph Satish V is a PhD student in Science, Technology and Society Studies (STS) at the Centre for Knowledge, Culture and Innovation Studies (CKCIS), University of Hyderabad, India. His research focuses on the work of Jesuit scientists in the botanical sciences in independent India.