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Open Note Databases & the Promise of the Memex

Vannevar Bush’s Memex

In 1945, Vannevar Bush wrote a now famous piece for The Atlantic called “As We May Think.” In it, he proposed the development of a machine called the Memex. This desk shaped machine would be able to display printed and handwritten texts and would be able to record notes made with a special stylus. The machine would be able to record meta-data noting connections between various sources and all of this information could be stored on removable cards.

The Memex served as inspiration in the development of the modern personal computer. Hundreds of articles in the 1990s pointed to the invention of the World Wide Web as the culmination of Bush’s vision, and those comparisons have continued into the new millennium with the modern Internet. But while the stylus-touch interfaces of modern tablets and the proliferation of online media do fulfill much of Bush’s technological vision, the key underlying epistemic concept put forth by Bush has been largely neglected.

The rapid sharing of ideas was an obvious use of the Memex, but Bush proposed that the educational value of the tool would be the ability to retrace the thought processes and connective strands that others had made through the ever growing sea of data. Bush said, “The inheritance from the master becomes, not only his additions to the world’s record, but for his disciples the entire scaffolding by which they were erected.” While academia is slowly moving towards open access models of publication, this deeper level of sharing the cognitive “scaffolding” of our theories has received far less consideration.

On Wednesday, Jeremy Dean and Jon Udell of Hypothes.is joined with Gardner Campbell as part of #openlearning17 to discuss how web annotation is allowing us to record and retrace our thoughts as we move from one website to the next. The collective pooling of reading notes, along with the ability to retrace the steps of an individual go a long way to fulfilling the epistemological vision of Bush’s Memex.

Here though I want to propose a different kind of database as an alternative and complimentary implementation of Bush’s vision. I have been working on an open note database called Situating Chemistry for a couple of years now. The concept is that researchers interested in the history of chemistry (don’t laugh, we exist) can come together to share a wide variety of notes. In addition to reading notes, the system can be used to create a profile of a historical person to record biographical notes compiled from both archival and secondary sources. These people can then be linked to each other to show familial, business, educational or any other type of relationship. Users can also record notes on the places that chemistry was done. A record can be created for a paritcular factory site, a university lab or lecture hall, or the site of an important conference. These sites can be linked back to the people who used them and mapped. Here we see a map from the 18th century of Paris with clustered pins representing the sites in our database:

A screen shot of the world map in the Situating Chemistry database featuring data about 18th century Paris

In addition to people and places, users can use the system to record notes on organizations, events, courses, sources, objects, collections, processes, and theories. The key is that researchers can use the database to take notes on any facet of their studies and then connect that facet to both its particular context and the broader population of notes within the system. Users can choose to put a password on their records, but the default and usual practice is to leave the note sets open to all users so that we can extend each others’ individual records and pool our collective research.

Designing an Open-Notes Database

Web-based databases of historical people like the Prosopography of Anglo-Saxon England (PASE) and the Prosopography of the Byzantine World were produced as conclusive publications of completed research. As such, the developers could accommodate, truncate, or omit problematic pieces of data. Published databases can also choose data visualizations that best highlight key records or insights. Researchers with Stanford’s Mapping the Republic of Letters, put together this beautiful dashboard to explore the correspondence of Enlightenment thinkers.

Screenshot of the Republic of Letters Visualization dashboard

Unlike these published databases, an open note system is designed to accommodate active note taking. Rather than structuring database fields to best present the data already collected, Situating Chemistry was built to be flexible. Because a researcher will more often than not have incomplete data, the only required field is the title of the record. The fields to record dates of birth and death can be partially filled out when only a year or year and month are known. They can also be marked approximate to indicate ambiguity in the historical record. Similarly, visualizations are employed to bring the researcher’s attention to interesting data and suggest new pathways for research.

Within any prosopographical project, the amount of biographical information available for the research subjects can vary widely. One project in Situating Chemistry focuses on the students of the noted Scottish professor William Cullen (1710-1790). In 1756, fifty-nine students attended Cullen’s chemistry course at the University of Edinburgh. Amongst them was George Fordyce (1736-1802) of Aberdeen who would go on to earn his medical degree from Edinburgh and become a lecturer of chemistry and medicine in London. Although there is no monograph length biography of Fordyce, he has entries in the Dictionary of National Biography and the Dictionary of Scientific Biography and is a relatively well-documented individual.

The other fifty-eight attendees of the course are less known. We know from Cullen’s notes that Robert Cumming was from Edinburgh, that John Richardson was from Northumberland, and that Henry Dunston was from some unspecified part of England. More surprisingly, at least two of the attendees were from Virginia—Thomas Clayton and James Taylor—and one was from Antigua—Christopher Hodge. Clayton, Fordyce, and eight other students would go on to earn their MDs from Edinburgh.

In designing Situating Chemistry database we wanted to ensure that we could capture structured, machine-readable data on someone like George Fordyce, or for that matter William Cullen. Additionally, we also wanted to be able to create records for people like Henry Dunston, for whom we had only a name and relationships of interest, in this case that he was a student in Cullen’s chemistry course, in Edinburgh, in 1756, with these other people, and he was from England.

Screen shot of the Situating Chemistry Database depicting the fields available for recording data about a person

The record for any individual can be linked to other individuals in several different ways. In addition to familial relations, we also have structured fields to collect information on instructor-student relationships and correspondents. There is also a somewhat generic person-to-person connection field that offers a list of relationships that can be expanded when needed. We designed the database such that every individual is the subject of their own record. A field denoting that a person was active in chemistry is automatically checked for every new record, but can be deactivated for familial relations, business partners, and others who are of interest but were not actively ‘doing’ chemistry even in the broadest definition.

In addition to linking a person to other individuals within the system, a person can also be linked to many other kinds of data. The database was initially conceived of as a way to catalogue sites of chemistry. We thus started the database with a table to collect information on apothecary shops, lecture halls, pharmaceutical manufactories, bleach fields, labs, etc. For a given site, the latitude and longitude of the site along with a modern address can be recorded along with information about the ownership and financial history of the site, the chemical activities associated with it, the organizational history, related images, documents, sources, etc. For each individual in the system, we display the sites that they owned and operated and also those additional sites that they were associated with.

After developing tables for the sites and people involved in chemistry, we developed further tables for chemical substances collections, courses, documents, events, images, letters, objects, organizations, primary and secondary sources, processes and techniques of chemistry, and archival and museum repositories. Any two records can be connected with an extensible series of subject-predicate-object relationships. For example a given individual could be a member of an organization or might have studied a particular chemical substance or been a practitioner of a particular process or technique of chemistry. Every record, whether it be for a person or any other type of data, can and should be sourced by linking it to primary and/or secondary sources. For the system as a whole then, we have tables for more than a dozen types of information and hundreds of structured data fields, all strung together into a relational web of information.

Interoperability & Extensibility

In its first conception, the Situating Chemistry database was thought of as a single table for sites with about a dozen fields. However, this variety of tables and fields grew organically through discussion of the research questions and practices that we, as historians of chemistry, conduct. The goal for the project was not to publish a completed set of sites or records, but rather to facilitate active research. A researcher could enter the data that they were collecting for a research project to organize and analyze the information, and they could take the database with them into the archives to continue to collect information. Researchers can access their records and add new records to Situating Chemistry from a laptop, tablet, or even a phone.

To accommodate both offline note-taking and the rapid upload of external data sets, the database has also been designed so that users can upload CSV files (excel-type tables). Any data in the system can in turn be downloaded as a CSV or in other structured formats including XML, RDF, and JSON. Because Situating Chemistry was designed as a research tool rather than a data-publication, the goal of the database is to allow users to both enter and access whatever fields and records sets they consider interesting. Several visualizations including tables, graphs, and a timeline are built into the system. The user can also extract whatever structured data they want to pull from the system, so that she can also generate her own visualizations using tools like Tableau or programming languages like Python and R.

The schema of the database is not specific to our current project, nor to the period 1760-1840. It could be readily adapted for use by other historians of chemistry (and alchemy) and historians of other sciences.  If you were to dump out the 5000 records that we have input into the system, you could convert the project into a Sites of Archeology database and record the digs of the 19th and 20th century.  You could just as easily record the observatories, telescopes, and astronomers of the 16th and 17th centuries or plot the biological specimens collected by Linnaeus’s correspondents.

While we certainly hope that our database will be used by and be useful to historians of chemistry, the real point of the project is to enable the collaborative epistemology proposed by Vannevar Bush.  History and humanities more generally are dominated by the single-author article and monograph, so a system built to pool research notes may seem counterintuitive. However, we need to remember that the point of these publications is to share our knowledge. If we all share our coffee stained notebooks, idiosyncratic excel files, and shoeboxes full of notecards, we can engage in deeper and more nuanced studies in the history of chemistry and science more broadly. Without sacrificing traditional academic products, we can collectively populate searchable, interlinked reference guides that will accelerate research and model our methodologies for the generations to come.

Please visit our site to learn more about the project and let me know if you would like to set up an account or get a copy of the code.

A Brief History of Alchemy

What is Alchemy?

Alchemy, as a field of study, was thought to answer several different questions making it hard to define. Alchemy was used to study ontology; that is, alchemists asked what stuff is made of and how does that stuff interact with other stuff. Analysis and synthesis reactions along with the more systematic attempts at classification are all concerned with matter theory and the ontological understanding of nature.

Alchemy can also be approached from a more pragmatic angle. We can take that which we find in nature and try to improve it. An alchemist can pick grapes and use the process of fermentation to create wine. An alchemist can take mined ore and smelt it into useful minerals. Alchemists studied the properties of natural materials to find useful ingredients for the creation of medicine and production of a wide variety of craft goods. Thus there is an epistemological use of alchemy as well as a mundane, economical practice of alchemy.

Ancient Alchemy

The alchemists who were seeking to transform base metal into gold were interested in refining and purifying nature.  Those who were seeking to prolong life and to attain immortality were trying to transform their base nature into a more spiritual form, their gross body into a subtle body!
-Peter Marshall

Greece

The four Greek elements displayed as interconnected squaresMany of the well known Greek philosophers were interested in matter theory. Thales of Miletus believed that water was the prime matter. The flow of water and its central role in the growth of plants and animals, convinced Thales that all matter was originally composed of water. The idea that all you needed to grow a tree was a seed and water persisted into the 17th century and the experiments of Jan Baptist van Helmont.

Heraclitus thought that fire was the prime matter and Anaximenes thought it was air. Aristotle proposed that the four terrestrial elements were coequally basic. Earth, water, fire, and air each have two properties and through those properties, they are transmutable. Thus the hot, wet air could be converted into fire if it was dried out. These terrestrial elements were corruptible and impure, but quintessence, the fifth, celestial element was incorruptible and perfect and it was the substance that all of the heavens were made from. Aristotle’s philosophical system became a foundational principle for much of European and Arabic thought for the next two millennia, and his concept of four transmutable elements can be found throughout the writings of subsequent philosophers.

Another part of Aristotle’s matter theory that proved interesting for philosophers was the idea that metals and minerals ‘grow’ over time in a slow progression towards their highest state. In Meteorologica, Aristotle argued that if left in its natural state for long enough, lead would mature through various phases eventually becoming silver and ultimately gold. This theory had immense importance for alchemy. If metals naturally grew more pure over time, alchemists simply had to find ways to speed up nature.

In addition to this Greek interest in matter theory, the Greeks were also interested in the more practical arts. Greeks were smelting copper as early as 2200BCE. Jewelers were interested in producing both genuine gold pieces and in gold-plating baser metals, just as modern jewelers do. Greeks were interested in dyes for clothe produced from plants, animals (beautiful purples can be made from crushing the shells of cochineal insects), and minerals (arsenic can produce a wide variety of oranges, yellows, and reds). Around 200BCE, the Greeks found that urine could be collected and used as a mordant to prepare clothe for later dying.

China

In China, a parallel alchemy grew with a similar interest in both matter theory and the practical application of alchemy. Taoism promotes a matter theory that has five elements known as the Wu Xing.

Diagram of the Wu XingAs with the Greek theory of four elements, the Taoist fivefold matter theory has implications not only for the composition of natural materials, but also for cosmology and medicine and more cultural traditions like martial arts and tea ceremonies.

As with the Greeks, the Chinese were interested in practical applications of alchemy as well as the theoretical. Chinese alchemy is particularly known for its interest in medicine. Taoist beliefs about balance were applied to the composition of medicines. Yang rich substances like gold, jade, and red-blooded cinnabar (mercuric sulphide) could be added into the human body’s natural yin state to reach a higher level of balance. ‘Wai tan,’ codified by Ko Hung in the 4th century BCE focused on drinking elixirs made of yang rich substances to achieve the higher planes of existence.

Summon spirits and you will be able to change
cinnabar powder into yellow gold.  With this yellow gold you may make vessels to eat and drink out of.You will increase your span of life, you will be able to see the hsien of the Pʼeng-lai [home of the immortals] that is in the midst of the sea. Then you may perform
the sacrifices fang and shang and escape death.
-Li Shao-chun to Emperor Wu Ti in 133 BC

Unfortunately, drinking elixirs that have mercury or gold in them often proved fatal, and eventually this form of alchemy lost favor. From the 6th century CE, Wai tan was replaced by ‘Nai tan’ which focused instead on finding the inner elixir. Physiological techniques focused on breathing, controlled movement, and sexual exercises could be used to purify ones own body and thus achieve higher planes of existence.

Arabic Alchemy

islamspread

The Islamic world was a melting pot of the world’s people. In the 8th and 9th centuries, the Islamic empire was amongst the largest in the history of the world with partial control of lands from modern day Afghanistan in the East to Spain and Morocco in the West. Mirroring the equally brutal Pax Romana that was now collapsing, the Caliphs often ruled by law over a broad variety of people and they actively sought to bring together the accumulated knowledge of the world. Thus, Greek philosophy was translated into Arabic as was Indian mathematics, Chinese medicine, Egyptian mathematics, and Persian astronomy and religion.

Jabir ibn Hayyan

15th century European portrait of Jabir from wikimedia

One of the most noted Arabic alchemists was Jabir ibn Hayyan (721-815CE), known in the west as Geber. Jabir ibn Hayyan developed a theory that said that all metals and minerals were composed of two more fundamental elements: sulphur and mercury. Historians initially thought this was an adaptation of Aristotle’s mineralogical theories from Meteorologica, but more recently they have come to believe that Jabir drew more from Chinese and Indian sources. Whatever the origin, Jabir’s theory proved influential for alchemists and chemists well into the eighteenth century as they classified metals and minerals along this spectrum of sulphur and mercury. The more sulphureous elements were thought to be more brittle. Actual sulphur and other minerals far on this end of the spectrum (arsenic for example) would vaporize on heating. Metals and minerals with more mercury were more malleable and shiny. Transmutation could be performed by adding or removing these two constituents through complex alchemical procedures.

Jabir’s theory proved influential in the understanding of metals and the pursuit of the philosopher’s stone, but his practical experimentation may be even more influential. He used a wide variety of apparatus that modern chemists would still be comfortable with and used reagents that are still common in the modern lab. Jabir’s work is a wonderful example of historical science that was done under a different theoretical paradigm that shares the experimental epistemology and material practices that span a much broader span of time. His work clearly contributed to the development of what we would now comfortably call chemistry.

Arabic Pharmacy

Medicine advanced dramatically during the Islamic Golden Age. Because of the geographic span of the empire and the extensive translation efforts promoted by various caliphs and wealthy doctors, pharmacists had access to European, African, middle-Eastern, Indian, and Chinese biological and mineralogical materials. The great works of Galen and Dioscorides were translated along with Indian toxicology. These traditions were synthesized and extended by Jabir ibn Hayyan in his book On Poisons and their Antidotes.

A professional pharmacy (Saydanah) developed from the 9th century, and one could find numerous pharmacies in major cities like Baghdad. Pharmacists had to go through specialized education before sitting for board-review style examinations. The polymath doctor al-Razi compiled a book called al-Hawi which listed 829 simple and compound recipes.

European Renaissance Alchemy

During the 13th through 16th centuries, translators were extremely active in the centers of trade and cultural overlap between the Islamic Caliphates and the growing European states. Islamic advances in astronomy, natural philosophy, and medicine were translated and retranslated into Latin and studied in both the courts and universities. The reintroduction of various Greek texts along with the sharing of the newer works by al-Razi and Jabir amongst many others contributed to intellectual Renaissance.

Debates about the natural world and man’s ability to improve upon it through study and art transcended works on theology and natural philosophy. Noted theologians like Albertus Magnus and Thomas Aquinas wrote on these issues. At various times the universities debated the relationship between Aristotle’s theories and the Catholic doctrines.

Portrait of Paracelsus by Quentin Matsys courtesy of Wikimedia CommonsIn the sixteenth century, Paracelsus came onto the scene and ultimately became one of the best known alchemists in history. Philippus Aureolus Theophrastus Bombastus von Hohenheim called Paracelsus was a self-educated doctor who moved around what would now be Switzerland, the low countries, France, and Germany. Unable to ever gain acceptance from the various medical guilds/faculties of the cities he visited, he was an iconoclast who called for medical reform.

Paracelsus learned in his travels about mineralogy and developed mineral-based liquid medicines as part of what he would call the ars spagyrica. His medical alchemy was at the same time practical in that it was administered to patients and theoretical in that it challenged all prior matter theories. Paracelsus proposed a blend of the four Aristotelian elements with his own tria prima of chemical principles: salt, sulphur and mercury. This philosophical conglomeration of Greek and Arabic elements, combined with Paracelsus’s aggrandizing claims of medical supremacy elevated him to a legendary status amongst those who would study alchemy for the coming centuries. Stories of Paracelsus discovering the philosopher’s stone or the elixir of immortality drove alchemical research amongst his students in France and later by government administrators in Germany and even the scientific elite of the Enlightenment.

A baker is an alchemist when he bakes bread, the vintner when he makes wine, the weaver in that he makes cloth.  Thus the individual who harvests natural fruits useful to humans in ways prescribed by nature is an alchemist.
Now all crafts are founded on imitating nature and experiencing the properties of nature, so that crafts people know that in all their work they follow in the path of nature and bring out what nature is in her. 
– Paracelsus

Paracelsus was less concerned with chrysopoeia (the conversion of base metals into more valuable metals like gold) than with the medical and practical aspects of alchemy. However, Paracelsus was interested in one of the more far-fetched goals of alchemy, the homunculus. In De natura rerum (1537), Paracelsus denied that the mandragora root which can at times look like a small human was of any importance. Instead he suggested that the key to producing alchemical life was to combine sperm with blood in a warm, artificial womb. He argued that by removing women from the process or human reproduction, you could shield the offspring from Eve’s original sin and thus create a perfect human. In some writings, this concept of the homunculus was thought to promise a second Christ.

German Betrüger

Tara Nummedal has documented a wonderful story about a group of alchemists who claimed to be disciples of Paracelsus. In her article “Alchemical Reproduction and the Career of Anna Maria Zieglerin,” Prof. Nummedal talks about how Zieglerin and her husband Heinrich Schombach came to work for Philipp Sömmering in the court of Duke Julius of Braunschweig-Wolfenbuttel (in modern day Germany) in 1571.

Anna ingratiated herself to Duke Julius with the claim that she had studied alchemy from Count Carl von Oettingen, whom she said was the illegitimate son of Paracelsus. Anna claimed that Count Carl had taught her all of Paracelsus’ secrets and that she would both write down these recipes and produce their products for Duke Julius. Amongst these products was a powdered ‘tincture’ that could turn base metals into gold, ie the Philosopher’s Stone. Even more fantastic was a product called the ‘Lion’s Blood’ that could accelerate the growth of biological things like fruit or even animals. In fact Zieglerin claimed that she could take the ‘Lion’s Blood’ to shorten the process of giving birth from the usual 9.5 months to 1 month.

Anna, Heinrich, and Philipp worked for Duke Julius for three years and during that time they produced small samples of various alchemical goods and wrote several of the recipe books that they had promised. However, in the summer of 1574, they were brought to trial for murdering a courier, attempting to poison the Duchess, failing to fulfill their alchemical promises, and fraud in their claims to alchemical expertise. In particular, Zieglerin was charged with making up the entire story about Count Carl von Oettingen. Upon conviction, the two men were flayed, drawn and quartered. Zieglerin as the fabricator of the lie, was also flayed and then burnt alive while strapped to an iron stool (Nummedal 56).

There are a couple of things to take away from this trial. The first is that alchemists sought employment at the courts of Europe, and Duke Julius along with many other rulers sought to bring alchemists into their courts.  Duke Julius entered into a contract with his alchemists laying out the terms of their work. He promised them room and board, he brought them under his protection, and at times he gave them a currency or other valuable goods. In return the alchemist promised to deliver a good or a set of goods like a proscribed volume of a medical remedy or a given weight of worked metals. Zieglerin and Schombach promised to deliver a recipe book for the philosopher’s stone, ‘Lion’s Blood’ (a product that would cause fruit to ripen or even speed up human gestation), and various other alchemical wonders along with samples. Zieglerin grounded her promises in her own expertise and training.

This contractual record is really interesting in that it suggests that when an alchemist failed to deliver on their promises, they were sued for breach of contract. However, it was only in rare cases like that of Zieglerin and her colleagues, that they were killed for these failings. Normally you might only require repayment or simply fire an alchemist. However, Zieglerin was found to be a charlatan who had committed fraud in her basic claims. Her story about Count Carl and her own ability to birth alchemical children both brought her great respect and admiration and ultimately caused her brutal end.

The contractual record also describes the extensive facilities at the court of Duke Julius and the variety of activities that his various alchemical workers were pursuing. Through her extensive archival work, Nummedal has found blueprints for alchemical workshops and shown how these facilities and contracts were used to structure alchemical work. The work contracts, architectural plans, and inventories of these labs shed insight on the day-to-day practice of alchemy. She has also found many contract proposals that were dismissed as impractical or never pursued because of cost.

That the Germans had a word for such charlatan alchemists, Betrüger, shows that not all alchemists were charlatans. Many fulfilled their basic promises of creating a medicine or improving the process for refining metals or producing jewelry or other goods. People with alchemical expertise were hired to manage mines and mints, run pharmacies, refine sugar, or set up textile bleaching and dying operations.

The End of Alchemy?

I will write a second post about alchemy after 1600 in the coming days.

Sources and Further Reading

This sketch of alchemy was compiled from my readings of Bruce Moran’s Distilling Knowledge: Alchemy, Chemistry, and the Scientific Revolution; Tara Nummedal’s Alchemy and Authority; Pamela Smith’s books The Business of Alchemy & The Body of the Artisan; and the wonderful corpus of Bill Newman and Larry Principe. The scholarly journal Ambix, edited by Jennifer Rampling, is devoted to the history of alchemy and chemistry, and is another wonderful resource. Please read any of these works for a more thorough analysis of the history of alchemy.

How-to sign up for Wiki Edu Courses

Wikipedia Education Foundation is a fantastic program that helps integrate the writing of wikipedia articles into courses. Wiki Edu spun off from Wikipedia proper a couple of years ago, and they’ve done a ton of work in that time to put together training materials for students and teachers and organizational tools to help manage classes.

However, it can still be a little confusing as to how to get started in Wiki Edu. Below is a step by step process to help your students join your Wiki Edu Course and navigate back and forth with Wikipedia.

1. After an instructor has joined Wiki Edu and set up a course, she receives an email with a link for their course dashboard. The link that Wikipedia sends will have an enrollment code built in, so that your students can automatically join the course. If students navigate to the page without following the link, they will likely need the enrollment code which can be found at the end of the link. For example, here’s a link for the course dashboard for Remembering the Asian Pacific War:  https://dashboard.wikiedu.org/courses/OU/Remembering_the_Asian_Pacific_War_(Spring_2017)?enroll=xxxxxxx. You can see at the end of the link a bit of text that says “enroll=xxxxxxx.” Whatever comes after the “=” is the code for enrolling in the course.

2. Once a student reaches the course dashboard, she can log in to her account using the button at the top right:screen shot of the wiki edu dashboard for a course with the login link highlighted

3. After she logs in to Wiki Education Foundation, she should click on “join course” in the actions tab on the right hand side of the screen. If it asks for a passcode, she uses the enrollment code.

screen shot of the wiki edu dashboard for a course with the 'join course' button highlighted

4. The student should now be a member of the course. When you are in Wikipedia reading an article, you can return to the course by first clicking on your username at the top of the screen:

screen shot of the wikipedia page for an article with the user name highlighted

5. On your user page, you should have our course listed at the top of the page. Click this link to go to the Wikipedia page for our course.

UserPage2

6. From there you can return to the Wikipedia Education Foundation dashboard for the course.

WikipediaCoursePage

For more information on Wikipedia assignments and the Wiki Edu program, you can check out my posts below or wikiedu.org

http://www.johnastewart.org/dh/wikipedia-in-the-classroom/

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