by Bonnie DeVarco and Eileen Clegg
The tree is history’s most enduring symbol, one that demonstrates beautifully how our visual representations are shaped by human perception. We use shapes to visualize knowledge. These visualizations, in turn, shape the way we perceive the world. Using the Shape of Thought Approach , we can see how history and the leading edge meet in a universal image that has transformed as humanity has transformed.
Traveling through history in a short series of images and visualizations of the tree, we can see a very different story about human perception than that told in the text-based, historical record. Looking at how humans have used the tree structure as a communication tool, we can see how humanity’s perception of who we are and how we fit in the Universe changed through the centuries.
The following three tree stories - The Tree of Life, The Tree of Human Relationships and The Tree of Knowledge - demonstrate how our perception of ourselves and our relationships is not static. Instead, it is a dynamic, ever-changing visual conversation between generations
The Tree of Life to the Superorganism
The World Tree
The tree is one of the oldest, most enduring visual metaphors in human history. Because of its dense networks of roots, branches and foliage, the tree is often used to visualize relationships between species, languages, families and social groups. For at least the past 2000 years, it has also been used to map hierarchies of knowledge and ideas.
The tree is central to the way many cultures understand the cosmos. It also represents the source of life. Every sacred practice and religion used tree myths to tell origin stories, from the oral tradition of the Icelandic Edda to the Tree of Life in the Judeo Christian Bible. The tree also holds answers to future-oriented questions about information management, because its growth pattern involves fundamental properties of geometry, including the Golden Mean, which can be applied as a design approach or used in algorithms for digital design.
Ancient cultures throughout the world used the tree as a symbol to represent the construction of the universe. The oldest symbolic use of the tree was the “World Tree” or the “Tree of Life.” Mircea Eliade, renowned historian of myth, religion, ritual and symbol, traced the World Tree idea to the navel of the Earth, a symbol found in the folklore, stories, rituals and architectures of numerous indigenous cultures around the world. The Tree of Life is also referred to as “axis mundi” or the cosmic axis - literally the point of connection between the sky and earth.
In Norse mythology the world tree is called “Yggdrasil”, an oak tree that connects all nine worlds of Norse Mythology together. Visualized as a colossal tree, the Yggdrasil connected the heavens to the Earth with its roots extending deep underground.
For pre-Columbian cultures of Mesoamerica (the Aztec, Izapan, Mixtec Maya and Olmec) the World Tree was central to the origin of the Cosmos. Their reverence for the Milky Way was linked directly to the World Tree, the center of the Earth-Sky.
Since ancient times, we have represented humanity and the gods or higher powers as part of the tree of life. More than three millennia ago in Mesopotamia, the tree of life was depicted on bas-reliefs as both a symbolic and literal image capturing the force that connects all life.
To the ancient Egyptians, the “tree of life” was an Acacia tree from which the first couple, Isis and Osiris emerged; they called it the “tree in which life and death are enclosed."  In the Judeo-Christian Bible, the book of Genesis introduces two trees—the Tree of Life and the Tree of Knowledge of Good and Evil. The fruit from the tree of life gives immortality. When Adam and Eve eat from the Tree of Knowledge of Good and Evil, they lose their innocence and are banished from the Garden of Eden. A more abstract Tree of Life can be found in the Hebrew Kabbalah. Called the “Sephirot” it is a mystical diagram with ten sephirot (spheres or emanations). Between the 10 spheres are 22 sacred pathways used to “map” creation—wisdom from the direct understanding of the nature of God.
The Tree of Life in the religious or symbolic context encapsulated the idea that everything is related, from the cosmos to the tiniest atoms in our bodies. In the nineteenth century we witnessed the emergence of a different tree metaphor, the scientific tree of life.
Charles Darwin, a naturalist who spent a decades carefully charting the variations among animals of the same species in different environments, helped ground the fledgling field of evolutionary biology in a more exacting science. He published his remarkable scientific work, On the Origin of Species in 1859. This book contained only one illustration - an abstract diagram showing Darwin’s theoretical “tree” of multiple species related to a common genus.
Many years earlier Darwin had drawn the genesis of his tree of life idea as a simple network structure. A sketch next to his earliest thoughts on this tree of relationships and speciation was drawn 22 years before his legendary book was finally published. This sketch is considered to be the very first “network diagram” - his first depiction of a scientific “tree of life” next to his now famous words, “I think.”
In the 19th century, biologist and physician Ernst Haeckel, a protégé of Darwin’s, was the first to describe and codify the “phylogenetic tree” into five branches. Charles Darwin knew it was important to visualize the relationships among groups of organisms for his theory of evolution. Integrating Darwin’s idea of an abstract branching diagram with Haeckel’s own ideas about genetic evolution, Haeckel animated this vision using a literal tree structure as a natural metaphor and as a structural diagram of relationships. Forty years after Darwin’s sketch, Haeckel published the first official image of the genetic “Tree of Life”. At the time, the notion of human progress was deeply embedded into the theory of evolution and humans were considered the pinnacle of the Tree.
As both artist and scientist, Haeckel is best known for his beautiful illustrations of the morphology of microscopic life forms. He named thousands of new species and coined many terms for biology including “phylogeny”. His tree was called the “phylogenetic tree.”
The evolving morphology of the scientific “tree of life” through the next couple centuries tells a story about our increasing knowledge of life. In the 20th and 21st centuries, biologists have acquired a greater understanding of the genetic relationships among the species. Haeckel’s literal image of the tree with roots still limited our way to diagram genetic relationships. The Tree of Life was not a direct or hierarchical lineage, but rather a radial branching of various species from a common ancestor. By 1960, the Phylogenetic Tree image organized the species’ into five different “Kingdoms.”
Throughout most of the 20th century, the tree of life still had five kingdoms; we still shaped our understanding of life into an anthropomorphic framework by the use of the word, “kingdoms.”
More recently, the work of scientist Carl Woese started a revolution in the way we classify life by taking out the hierarchy where humans represent the pinnacle of evolution. He did this by organizing the tree of life into only three domains.
At this point, the plant and animal “kingdoms” were seen to be part of the Eucarya family, and the name “kingdoms” had been changed to “domains.” The new tree of life’s three domains were dominated by microscopic life - bacteria and archaea. Lynn Margulis, who championed a new way of looking at evolution in the theory of symbiogenesis, originally proposed by cell biologist Boris Kozo-Polyansky created the first dendrogram showing these trees in the 1970s.
With Haeckel’s 19th century conception of dominant branches of life being animalia, protista and plantae we look back to see this as a time when scientists considered humans and meso-scale life to be the dominant life form on the planet. Today, we understand a vastly different story about life on Earth. Humans have been knocked off their pedestal.
Mapping Life on Earth
Last century, the burgeoning of genetic knowledge and a concern about the many threats to biodiversity gave rise to a project to map all life on Earth. Using the power of the World Wide Web to link the work of hundreds of biologists from around the world together, the “Tree of Life web project” (ToL) was launched in 2002. In its first five years, this project has networked together the collective work of professional scientists, teachers, students and amateurs. Over 1.7 million species are identified and searchable on more than 10 thousand web pages. 
In 2006, a new, interactive genomic tree of life was completed by the European Molecular Biology Laboratory (EMBL) showed us a different picture of the relationship of humans to other forms of life. It is considered the most accurate tree of life to date.
The evolution of tree imagery demonstrates how, through a new generation of science centered around genomics, we are reframing the way we look at our place on our planet. New research by Princeton biologist Bonnie Bassler demonstrates that, genomically speaking, 99 percent of our bodies are comprised of bacteria that actually talk to each other using a chemical language called quorum sensing. With new views based on the burgeoning field of genomics we are forced to further to rethink our place in the tree. Humans have become a “footnote in the story of bacteria” and life looks more like a vast “superorganism” from this genomic point of view.
These new visualizations of the tree of life convey a far more accurate "whole systems" view of life on Earth. We see the dominant branches of the tree the very modest place humans, and all mesoscale life hold in a living system dominated by microscale life. As scientists map more and more of the diversity of life, we need bigger, and more dynamic “tree” maps to contain the hundreds of thousands of life forms on the tree.
In the late 1990's, CAIDA's WALRUS, a large graph mapping too, enabled us to visualize the structure of the Phylogenetic tree as we know it today through a 3D hyperbolic space through a computer screen.
Even today, 3D visualization gives us a glimpse of what might be possible when we are able to fly in and around a 3 dimensional virtual or augmented genomic tree and to “feel” where we fit into the whole. We see in the biological Tree of Life, the progression from a linear, hierarchical vision of relationships to a circular, radial and eventually spherical image of the tree. As we’ll see below, the metamorphosis of the family tree paralleled the evolution of the Tree of Life as humans began to think less traditionally and linearly in our use of metaphors.
A Metaphor becomes an Algorithm
The tree in nature as a visual metaphor and symbol has become more and more abstract when we use its image as a structural principle to organize social relationships and knowledge. But can the tree as a visual metaphor drawn directly from nature somehow also lead us directly back to nature’s own geometry? Could we decipher a “code” that would allow us to automatically generate virtual 3-dimensional trees as realistic as those in the real world? Although most people are unaware, we are already well on our way to doing that. It is part the most recent history of our visual languages: the history of visual math (fractals) and the emergence of virtual worlds.
In the 1970s biologist and botanist, Aristide Lindenmeyer created a formal grammar – a computer language to model the growth processes of plant development in order to study plant growth. His language is called “L-Systems” and it has been used since that time to generate lifelike branching structures. 
Amazingly, the tree takes us right back to our very special symmetry. When Lindenmeyer began his work, mathematicians had already discovered two things: (1) math could be used to understand complex systems that are self generative and these could be visualized as geometric objects or “fractals” and (2) The Fibonacci series  has the special property of “fivefold symmetry” that is an important property of organic forms of life. Lindenmeyer applied the Fibonacci series to fractal algorithms in order to create this new “language.” L-systems could generate and model the morphology of branching organisms that look and act like real trees. Certainly he, as those before him understood and used a type of geometric “code” derived from Nature. The Fibonacci series approximates the Golden Mean.
Today L-Systems are used by botanists, physicists and ecologists to better understand the natural world. But L-Systems has already had a huge effect on computer programmers, 3D designers and virtual world developers today. Lindenmeyer’s computer “language” inspired a new field within artificial life. Artificial Life, commonly called ALife studies evolutionary agents or populations of computer simulated life forms in artificial environments. ALife researchers use three fundamental concepts essential to our understanding of structure and processes of life: symmetry, complexity and self-similarity. They apply the tools of L-systems to generate “life” in cyberspace as evolving virtual worlds. 
The Tree of Human Relationships
Trees of our Forefathers
The tree has been used for hundreds of years to organize our genealogical histories. Our forefathers are the “roots” of our branching family line, and the branches reflect our relationships to each other with a similar, hierarchical beginning. Trees showed heritage to be related to royal bloodlines and religious figures. By the 12th century, the Christian religion emphasized the connection between the New and the Old Testament by visually codifying the line of Jesus back to King David in illuminated “Jesse Trees”. The Jesse tree is envisaged to demonstrate the direct lineage between Jesus and the Prophets of the Old Testament to prove he was a direct descendent. It is based on the prophecy of Isaiah, "there shall come forth a rod out of the stem of Jesse, and a branch shall grow out of his roots."  Yet even in biblical Jesse Trees, a pagan female figure, the Cumaean Sybil was also included with the Prophets because she had predicted the birth of a “messiah.”
The Jesse Tree of the Judeo-Christian Bible, depicted in countless illuminated manuscripts, paintings and stained glass windows chronicled the genealogy of Jesus up to the Father of King David. The Jesse Tree as a structural metaphor continued to be used through the centuries by Royal families. Royalty used consanguinity trees to understand lines of descent and to determine whom they could marry.
Visually, these trees progressively went from a literal to a more abstract form. In the tradition of the “Jesse Tree,” royal consanguinity trees perpetuated the royal status of bloodlines by conflating royal blood with religious and royal decree. Consanguinity trees were theoretical diagrams of blood relations showing who may marry and who may inherit.
Trees become Structures & Charts
A new symbol system was created in the field of anthropology as an abstract diagram used to demonstrate the many types of familial relationships within different cultures. In the 20th century, anthropologists studying familial relationships through “kinship charts” began to find numerous non-hierarchical and patriarchal familial formations of bloodlines.
Cultural practice such as matrilineal and avuncular family structures made us rethink our linear, hierarchical categories and appreciate the diversity of family structures and lines of descent.
Interest in ancestry began to grow in the latter part of the 20th century. The power of the World Wide Web in the 1990s unleashed an explosion of interest in personal genealogical research that could be carried out from anyone’s home. Digital census records and historical collections were brought into ancestry web sites for broad access to information on the Internet.
Genealogy networks and software tools enabled thousands of people to trace their ancestry and link to others with the same lineage. Family tree templates, charts and software make it easy to input family information, share and display it with others. Many of these contemporary family trees use more radial abstract tree diagrams than the elaborate heraldic structures of the past.
Dynamism and Dimension
The Internet revolution has changed the basic nature of our personal and community relationships. Humans are collaborating and communicating with each other; mapping relationships has gone beyond genetic heritage and geographical locations on Earth to include complex and overlapping sets of networks. As we communicate globally and instantly with each other through email and social media, our game consoles, PDA’s and IPhones, our relationships increased and global communities of students, scientists, friends and international business colleagues have emerged.
Our hierarchical trees of human relationship were turning ever more radial with the rise of global communities coming out of enhanced synchronous and asynchronous communication via the Internet, Now we have numerous dynamic graphs of social networks, where we can see “communities” linked by affinity rather than by geography or blood.
Social groups are now linked by interest, affinity and knowledge. These groups can include thousands of people. We can learn about our transforming culture by analyzing these new social groupings. We now want to “see” how our new communities congregate in cyberspace compared to relationships in the physical world, and how subgroups arise, branch off and change through time. As Web 2.0 applications, social networking and microblogging hubs like Twitter, FriendFeed and Facebook scale out, each and every one of us can now see affinity “friendship networks” of our contacts in the real and virtual environments.
New visualizations such as Twitter’s tweetmaps and Facebook’s friendwheels are based on branching tree structures that have become increasingly abstract, nonlinear, and dynamic. These radial wheels also show how our networks of associations are interconnected, demonstrating that we are all linked to each other by less than “six degrees.”
With the advent of social networking and blogging, digital mapping tools are now being merged with blogs and network hubs such as Friendster, LinkedIn and Facebook. In 2006 IBM released ManyEyes, a Web 2.0 site a number of visualization tools anyone can use to visualize their own data and share it with others. 
Since that time, the toolset behind ManyEyes has been integrated with interactive news hubs such as the New York Times Visualization Lab. This way, users can create and share their own visualizations with up-to-the-minute statistical data from New York Times Stories. Social network tools are now changing rapidly with an explosion of shared data and locative information from myriad sources. Expectations for the emerging Semantic Web suggest that this new level of ontologically networked information will enable us to visualize even larger meta-networks of relationships. These visualizations will provide new insights about the complex, emergent organization of our growing communities and the knowledge these communities share.
The Tree of Knowledge to Mapping Knowledge Domains
Structuring Knowledge with Arboria
In addition to mapping relationships, humans have also used trees or “arboria” to structure knowledge and organize ontologies. Going back Aristotle’s categories of logic, third century Neoplatonist philosopher Porphyry visually codified these categories into a tree structure that was later called “Porphyry’s Tree.” The terms ‘genus’ and ‘species’ used by Darwin and Haeckel for their scientific Tree of Life derived their use from the more ancient practice Porphyry used to trace relationships between abstract dichotomies (genus differentia) and their sources (species).
The Tree of Life and Porphyry’s Tree further influenced medieval thinkers to use trees to identify relationships between different categories or types of knowledge. In the 6th century, Bishop Isidore of Seville used trees to organize his encyclopedia, “Etymologiae” and Catalan mystic and philosopher Ramon Llull followed suit by using Porphyry’s structure to depict the disciplines of knowledge as Ars Sapientiae, or Tree of Knowledge. The model of Porphyry’s Tree was also used in tree diagrams for medieval religious books. Trees of Virtues and Vices were used to visually diagram moral stories in the life of Jesus, dichotomizing good and bad.
Trees were also used by later writers, delineating the structure of book sections or geometric classes such as Luca Pacioli’s Tree of Proportions in his book on the Divine Proportion, De Divina Proportione, published in 1509.
Over the following several centuries, trees continued to be used to organize categories of knowledge, topics and subjects in encyclopedias.
Organizing the Data Deluge
In today’s digital culture, the current profusion of data requires us to find new ways to organize vast amounts of information: to see more at once, to allow for numerous the points of view (POV), and to introduce dynamism in our models. In order to do this, the metaphor of the tree has brought us from linear trees to cone, spherical and hyperbolic trees. The use of the tree structure continued through the 19th, 20th and 21st century as a way to organize knowledge and our web site directories.
In 1991, Stuart Card and his team at Xerox Parc introduced dynamism to the tree structure by creating “cone trees” that could be rotated. These trees moved away from the top down linear structuring, but allowed multiple views and the ability for the user to spin the cone tree around to see all the data.
Three university students who worked at Xerox Park—including visualization pioneer Ramana Rao—were inspired by the nonperiodic tilings-based artworks of artist M.C. Escher to try to create a dynamic way to visualize a tree of related information or content. Influenced by the hyperbolic math that MC Escher used (which was actually enhanced by Escher’s discussions with geometer Donald Coxeter while he was creating his artworks), Rao and his colleagues created a browser interface that would enable each chosen node to become the center around which all the other connected nodes would be organized. This became the first hyperbolic tree browser through Rao’s company, Inxight Software, Inc.
Along with social relationships, the nature of human knowledge began to change with the advent of the World Wide Web. Today, we have too much data and it is changing too fast for us to stay current. It is important to have simple ways to navigate and visualize connections between ideas, information and domains of knowledge. We can do this by revolutionizing the way we look at data by visualizing its larger patterns.
As our knowledge increases on the Internet and access to massive databases of information must be analyzed, classified, accessed and understood, we need new structures to envision broader swaths of knowledge, its creation and evolution. In the first decade of this century, Dr. Katy Borner, Chaomei Chen and Kevin Boyack pioneered a new direction for visualization as applied to “domains of knowledge” by mapping the growing domain structure of scientific disciplines through citations indexes.
Boyack’s work with Richard Klavans has undergone almost a decade of refinement in the visual metaphors used for these structures, becoming less and less hierarchical and more natural, almost biological in shape. These new science maps are based on hundreds of thousands of citations and are analyzed and visualized to identify emergent paradigms of scientific knowledge domains.
Now that visualizations can illustrate the radial patterns and connections between different types of knowledge, we are able to see relationships between disciplines again. The branching connections and overlaps between research is highlighted in a new kind of mapping developed by a cluster of scholars and leaders in the field of information visualization. These are called “Knowledge Domain” maps. 
A New Aesthetics for Knowledge Visualization
“Knowledge domain” visualizations have become a growing genre now known as “Science Maps.” A new information aesthetics defines the way to show metrics across a broad range of source material. More cross fertilization between disciplines is seen. More data is being generated collaboratively in the public domain. Using a public Wikipedia “data dump” in 2007, Borner, et.al. applied knowledge domain visualization methods to understanding how science, math and technology are represented in Wikipedia - showing where they cluster and where they overlap.
Although the Wikipedia map of science is just a snapshot of Wikipedia at a moment in time, eventually such “maps” will be able to be used as dynamic interfaces into huge repositories of shared information. As we move further into the dynamism and non-linearity of collaborative information, visualization tools are being created to visualize knowledge “flows” over time through new kinds of visualization such as those by Moritz Stefaner’s Well-Formed Eigenfactor.
A new aesthetics of data visualization is emerging. The universal image of the tree has transformed from a natural form that was used as a mythical image, a visual metaphor, a symbol, a dynamic organizing structure for information, and finally, an algorithm that generates lifelike trees in virtual space.
The tree structure has morphed from a static image to a dynamic way to look at the changing patterns in large amounts of data. As we used the tree to map relationships between humans and knowledge, our tree patterns evolved from a linear 2-dimensional tree to radial tree to a 3-dimensional sphere tree. Now we can return to the original mythical images of the World Tree and the Tree of Life and take these tendrils out further to the Global Mind.
The rapid growth of social media and knowledge domain mapping is changing the way we communicate our relationships, our knowledge, and our relationship to our planet. As the streaming, conversational network of the realtime global community grows, the only way we can see our organizational forms from a “satellite view” is to use visualization tools.
These dynamic tree structures and new visualizations can be thought of as a small world networks. These are mathematical graphs of networks. In the burgeoning field of network theory, which builds on early work by social psychologist Stanley Milgram in 1967, everyone is connected to everyone else by no more than six degrees. Milgram postulated that networks of clusters are connected to other clusters with very few bridges, connecting all the nodes between. We can think of this as a number of linked or nested tree clusters. In the “Six Degrees of Kevin Bacon” game, this idea was born out and popularized.
The “Oracle of Bacon” game was more than just a popular game. It influenced mathematician/physicists Duncan Watts and Steven Strogatz to establish the mathematical principles whereby Small World Theory could be rigorously proven as a class of random graphs. This complex systems algorithm initiated the new “science of networks” that allows scientists to better understand collective dynamics through graphing techniques or complex tree structures. Similar dynamics can be seen in any type of network. Physicist Albert-Laszlo Barabasi later proved that the distribution of these networks follows a specific power law, and this common blueprint can be seen in a vast array of networks – from intra-cellular protein networks to human social networks. Network theory is now able to be put to pragmatic use for everything from computer viruses to human behavior. Scientists led by Alessandro Vespignani have recently used network algorithms to map how patterns of global transport networks can help us quickly respond to pandemic outbreaks. 
From the Kevin Bacon game to a game changer for humanity, small world network theory and its emerging class of visualization technologies offer new ways of thinking and “seeing” that amplifies our human ability to share knowledge for global self-reflexivity. What began with the tree metaphor has become instead a dynamic language of patterned networks of whole systems behavior – systems of life, knowledge and relationship.
“These patterns are biological, they are scale independent – the patterns we see when we use our powerful lenses to explore the outer reaches of the cosmos and the inner dimensions of the cell. Visionary language mirrors the history of knowledge, the neurostructure of synaptic behavior, the self-assembly of crowd consciousness, the ubiquitous mobility of swarm behavior, the ephemeral architecture of smart mobs. But it does more – it mirrors the span of self-awareness to mass introspection by engaging our emotional intelligence through the act of seeing our reflection. In the words of biologist Barbara McClintock, it offers us “a feeling for the organism.”"
Through the evolution of the Tree of Life, the Tree of Human Relationship and the Tree of Knowledge, we see the story that brought us to today’s visualization technologies reflecting the ‘superorganism’ of collective thought.
FOOTNOTES: See more about the Shape of Thought Approach "What is the Shape of Thought?" Clegg & DeVarco
 From the online New World Encyclopedia – Judeo Christian Tree of Life
 Lindenmeyer, Aristid and Przemyslaw Prusinkiewicz. 1990. The Algorithmic Beauty of Plants. Springer-Verlag
 Storyboard for UCSC Virtual High School Complexity Gallery
 Isaiah 11:1. The New International Version of the Bible
 See more about ManyEyes
 Borner, Katy, R. Schiffrin, "Mapping Knowledge Domains," Proceedings of the National Academy of Sciences (PNAS), Jan. 23, 2004.
 See more at: Scholarly Networking to Stop Disease which features the work of A. Vespignani, S. Sherman and K. Borner.
 DeVarco, B. “A Visionary Language.” Scale Independent Thought Blog Jan 2, 2009.