Distributing 3-D Content Through Genomes and Evolutionary Process: A Focus on Plants

Bruce Campbell
March 2001

Introduction

Virtual environments rely heavily on 3-D content to provide aesthetics and meaning. As computer motherboards hold more transistors and pick up speed following Moore’s Law, graphics co-processors increase their specialization in 3-D rendering, and 3-D model demand grows exponentially. Historically, 3D models are loaded into virtual environments from external files hand-crafted by 3-D modelers using popular modeling tools such as 3D Studio Max, Maya, AutoCad, and SoftImage. Model files are either pre-loaded before display (such as in the Virtual Playground system at the UW HIT Lab [1]), or streamed across the network and loaded upon demand (such as in the popular ActiveWorlds platform [2]). Modeling tools implement procedural algorithms for modelers to use in the modeling process, but those algorithms create models that are still saved as the external files that the virtual environments load.

This paper investigates the opportunity to incorporate procedural algorithms directly into the virtual reality rendering systems. Instead of sharing models, participants in a virtual environment can share parameters. These parameters can grow the models inside of the virtual environment instead of loading them from outside. Nature suggests many approaches for parameter driven virtual world building, especially when considering the field of genetics. This paper considers plants as a case study. Lindenmayer Systems (L-Systems) are a popular botanical framework used procedurally by computer scientists for growing sophisticated plants [3] and Cambrian era animals [4] from simple instruction sets. Other techniques include fractals, Gaussian equations, Gerstner waves, and Navier-Stokes equations, all of which are used by special effect movie houses to grow digital images needed for movie scenes.

This paper reviews L-Systems and evolutionary processes before tying them together to create a wide range of 3-D modeled content after a short discussion of the reasons for doing so.

Potential Benefits of Procedural Modeling for Virtual Environments

Shared distributed virtual environments require sophisticated engineering techniques to provide a near real-time experience for all participants. A shared clock keeps participants in synch. Traditional 3-D model loading takes an annoying amount of time and provides delays when new models load in response to participant actions. Distributing model parameters instead of explicit model geometry can cut bandwidth and bus requirements to negligible levels. For example, a plant model with 12,428 polygons spread across 1,222 unique objects (stem segments, leaves, and floral petals) creates a structured VRML97 file sized over 1,000,000 bytes while the equivalent parameters-only file stores in a mere 500 bytes (a 2000:1 ratio). Given that ratio, the same bandwidth communication channel could send one complete plant model file or parameters for 2000 plants to appear in the world.

And, just as life’s DNA instruction set produces the recipe for growing all the elaborate creatures found on Earth, model parameter files can efficiently store the instructions for sophisticated 3-D models. Although the size of model instruction sets today is a miniscule percentage of the genomes for living, respiring plants and animals, savings in storage and information distribution costs are relative. Nature provides a fine example of storage efficiency unmatched by computer graphics file format designers.

DNA combined with evolutionary process creates great variety in beings. Procedural models can similarly create variety from simple changes to the model instruction set. Combinatorial mathematics assures great complexity as long as a significant number of model characteristics are procedurally derived. Even when every parameter lacks a full range of realistic values, a sixteen-parameter model approaches 1018 possible configurations. Procedural models make three important contributions to virtual environment implementation: network savings, model variety, and model complexity.

Procedural Plant Growth Algorithms for 3-D Modeling

Plants have often been at the forefront of genetic research, leaving us with the hotly-debated, emerging, societal issue of so-called ‘Frankenfoods’, genetically altered plants that provide larger yields of edible mass. Gregor Mendel first solved the mystery of inheritance by experimenting with pea plants in the 19th century, leading to the eventual addition of the words allele, dominant, recessive, and diploid to common English vocabulary [5]. Beginning in 1968, Aristid Lindenmayer studied and published works describing the process by which plants develop [6]. Although his work evolved in academic circles for twenty years before computer scientists applied his ideas to generate computer graphics, use of L-Systems in computer graphics blossomed in the 1990s, expanding its reach from 2-D renderings to 3-D models. Dr. Przemyslaw Prusinkiewicz at the University of Calgary and his peers have grown the field of Biological Modeling and Visualization exponentially in the last ten years [7]. More and more pure botanical research has provided inspiration for the development of virtual plants.

Some of the more interesting developments include the consideration of the phenomenon of Spiral Phyllotaxis, aging models for the decomposition of plants over time, ecosystem models for simulating whole fields of wildflowers, and a modular approach to a symbiotic system where environmental parameters affect plant development and plant development effects the environment. A quick survey of work done follows.

In 1992, Deborah Fowler investigated the use of collisions while implementing the process of Spiral Phyllotaxis as a guideline to creating virtual plant models [8]. Phyllotaxis is a well-documented phenomenon in plants that determines where primordia (seeds, petals, nuggets etc.) are located on a recepticle (sunflower, coneflower, corn ear) using a fixed divergence angle of 137.5 degrees. Primordia are packed following the rules of phyllotaxis until they collide with each other. Phyllotaxis has been incorporated into all plant development simulation systems as a result of Fowler and others’ work.

In 1996, Radomir Mech devised a system design where virtual plants could be modularly developed through interaction with other environmental modules [9]. Using such a system, virtual plants don’t grow in a vacuum, but instead have their parameters affected by dynamic environmental parameters. For example, if the environment experiences a drought, plant growth is stunted and body structures wilt. The communication goes in both directions. If a species of plant becomes successful in growing and respiring, additional oxygen is passed back to the environment.

In 1998, Oliver Deussen led a team that focused on realistic modeling of plant ecosystems [10]. Starting with a terrain specification and environmental characteristics such as soil humidity, the researchers’ virtual plant engine distributed plant species across the terrain. With the engine running on a supercomputer array, a computer interface afforded a user the ability to zoom in and zoom out while investigating the component wildflowers that had grown to fill the terrain.

The Vehicles of Evolution

Once procedural plant models are driven by parameters to a virtual plant growth engine, nature can provide additional inspiration in evolving new plants from existing parameter lists. The process mimics nature by repackaging parameter lists into psuedo genomes that then simulate physical plant genomes. Once the parameters are in a genome format, the forces of evolution can be written algorithmically in the virtual plant application engine to provide a variety of plant offspring.

Chris Colby of Boston University classifies observed phenomena of genome evolution into five processes: mutation, recombination, gene flow, genetic drift, and natural selection [11]. All five processes can be simulated in lines of code. A quick mention of each is warranted here.

Mutation occurs when some external process (such as a cosmic ray) interferes with the normal functioning of DNA within live cells and forces a change in its chemical makeup. The changed structure then can change the mutated structure’s function. Mutation usually does more harm than good to the affected entity but in nature, on average, only about 1 x 10-11 mutations occur per base pair of DNA per generation.

Recombination occurs most spectacularly through meiosis during sexual reproduction. During meiosis, the mother provides half the offspring’s genetic material and the father provides the other half. So, the next generation’s DNA varies quite dramatically from that DNA of the mother or father’s individual.

Gene Flow occurs when some process (such as a mosquito drawing blood) transfers genetic material from one species to another and that material makes its way into the DNA of the target species. The process has been documented between species of fruit flies with a parasitic mite as carrier.

Genetic Drift occurs as a purely statistical process. As a gene pool reproduces and survives in an environment where death is caused by events outside its control, chance determines which genes continue to reproduce and which genes die out.

Natural Selection refers to the process where a gene pool's makeup changes based on reproducing and surviving in an environment where the individual does have some control over their survival. Those individuals with genes that are better suited to the environment tend to reproduce more often than those less suited. Volumes have been written about the sub processes of natural selection: ability to feed, ability to avoid predators, sexual selection, etc. as Charles Darwin intrigued the world with his study of life’s struggle in the Galapagos Islands of South America.

My Contribution

To further along research in the area of modeling virtual plants, I chose to make three contributions: to enhance a popular L-Systems engine to take virtual plant genomes as input, to add a vase genome to the plant model to suggest use in artistic expression, and to explore gene pool variety using lessons from evolutionary process. The remainder of this paper explains work done and provides results and discussion.

Enhancing the LParser Engine to Take Virtual Plant Genomes As Input

Figure 1 - Rendered VRML97 output of Flowers1.ls
LParser is a popular virtual plant generation system in the public domain created by Laurens Lapre. LParser reads an L-System description file and processes it into a 3-D form that can then be outputted in several mainstream model formats including VRML, DXF and POV [12]. I investigated the source code looking for opportunities to change the input to a model genome instead of an L-System description. After investigating 50 attractive plant description files, I determined the best for my purposes was one obtained from C.J. van der Mark of Holland. C.J.’s Flowers1.ls file creates the three flowers with reddish stems presented as Figure 1.

I dissected the Flowers1.ls description file to determine which statements (also called rules) in the file influenced which part of the final plant model form. My conclusions were as follows:

Description File Rule . . . General Conclusion


q
q=&(30)p^(30)p^(10)p
p=[t(-0.2)!Ft(-0.2)!Ft(-0.2)!Fo]
o=>y>(60)y>(60)y>(60)y>(60)y>(60)>y
a=[&(10)s]a
y=[a&(125)w]
w=Z[d][h]'^(30)cw
d=[+d{.].x.}
h=[^(5)-h{.].x.}
x=^(5)ggx
s=[c(5)^(60)!'Ft(0.6)ZZt(0.6)?(10)ZZ]
F='(1.3)F'(.77)

The Axiom (all descriptions begin with the Axiom)
q sets the number of stalks and their placement
p creates the stalk (with t providing a gravity force)
o sets the number of petals around the flower
a sets the overall shape of the petal
y is a component of the petal shape
w is a component of the petal shape
d is the right hand side of the petal
h is the left hand side of the petal
x pushes the vertex formation of the petal forward
s creates the stamen
F directs the overall size of each forward instruction
(at) is the end of file marker

Because L-Systems incorporate recursion, the processes by which petals and leaves are generated are similar with the difference being that leaves are created in earlier iterations and are colored green, while petals are created in later iterations and are brightly colored at the red and violet ends of the color spectrum (not that virtual plants have to conform to the stereotypes of physical plants). Thinking that through, I realized that I could add an additional set of rules to the Flowers1.ls description file that would generate the plant leaves independently of the flower petals.

I then generalized the description file to substitute variables where fixed coefficients had been used by C.J. and added interesting features from other description files in order to provide a wider possibility of form from the genome input engine. I put component plant parts into for loops to be able to vary the number of parts that would be created. For example, to calculate the number of stalks in the model, I wrote the following snippet of code 

for(counter=1;counter<=numstalks;counter++) {
    strcat(rule[0], "^(20)S");
}

where the first rule would concatenate one stalk (represented by S for each additional stalk up to the number of stalks stored in the model genome. I then derived the positioning of the next stalk from the previous (represented by ^ from another value stored in the genome. I continued adding coding branches and loops, replacing coefficients with variables, and adding new features from other L-System description files until I had produced a rich enough system to let each component of my plant genome affect a wide-range of possible plants.

An example plant genome is stored as a single line text string like:

YY|NN|3|0.3|0.3|0.0|0.5|YY|NN|YN|NY|2|4|YY|NN|YN|NY|3|0.2|0.6|0.15|10|1|YY|NN|YN|NY|4|0.6|0.2|0.1

where each pipe symbol separates an allele pair or simulated gene from its neighbors. Form that is driven by dominant or recessive alleles is stored as a series of NN, NY, YN, or YY pairs where Y is the dominant trait and N the recessive. Form that supports color is stored in three floats contributing red, green, and blue components of light in that order. All other values are single floats or integers that substitute into rule variables in the virtual plant generation process.

Figure 2 lists the mapping of the stored genome by responsibility during virtual model development. The genome focuses on three of many potential plant body parts: The stalk; the leaves, and the petals.

Figure 2 - My Virtual Plant Genome
Each component plant part in the left column of Figure 2 is derived from data stored in the format specified in the right column of Figure 2. The right column may be more understandable after reading the section entitled ‘Exploring Gene Pool Variety in Virtual Plants’ below.

Adding a Vase Genome

In order to differentiate my work from those who thoroughly understand botany, I decided to create a vase genome as well to suggest application in creating objects of artistic expression. Virtual plants need not be realistic to be interesting or entertaining. My vase genome is stored as a simple single-lined text string like:

750^25^50^75^100^-90^-80^-70^-60^-50^-40^-30^-20^-5^5^5^5^5^5^5^5^Male^0.8^0.8^0.2^1.0^0.8^0.2^YN

where each value is substituted into a vase generation process I added to the LParser engine. Female vases are completely circular in any top view cross-section while male vase top view cross-sections have corners. Much of the vase genome simply stores the radius of the vase at different heights in the model. The two sets of RGB color values at the end are identical if the vase carries two recessive alleles for stripes (and then the second triplet is ignored). The complete vase genome is shown in Figure 3.

Figure 3 - The Vase Genome

Exploring Gene Pool Variety in Virtual Plants

Having succeeded at generating 3-D plant models from plant genomes, I decided to put in place a process to generate new plant genomes from existing plants. I added three new processes to simulate gene pool processes described earlier.

To implement mutation, I represented each numeric value in the genome as a base two binary number and flipped random bits. An interesting example was one where an orange petal genome and red petal genome produced next-generation petals that were brown. I implemented an averaging process (with mild noise) to create offspring petal color and looking at the results came to the conclusion that the most-significant bit of the child petal’s red color component had been flipped from 1 to 0 (thus reducing the amount of red dramatically).

To implement recombination, I created a merging process where two plant genomes could come together to create a new plant genome. Those traits driven by dominant and recessive alleles simulated meiosis by each randomly providing one of the two base alleles to the next-generation plant. Non-allele specified traits were merged using an averaging process with noise. I adjusted the noise threshold such that most of the time the offspring trait value would fall between the range of both parents. Yet, values outside of the range (especially for narrow ranges) were statistically possible at two standard deviations from the norm.

To implement genetic drift, I ran multiple generations and watched for drift. When values drifted toward too narrow a value (symptomatic of poorly designed code) consistently, I reworked the engine to provide a wider range of potential drift.

In considering Stephen Rooke's process for genetically evolving art paintings, I agreed human like and dislike were representative forms of environmental pressure simulating natural selection [13]. Although I haven't personally applied my aesthetic as a genetic pruning mechanism, I watch the process in action when I installed my engine at a booth during April 21-May 6, 2001 at the Boston Cyberarts Festival [14] in Boston, MA. More than 700 visitors to the booth were able to mate two virtual plants and decide if the offspring should survive to mate themselves.

Visitors experienced the plants by using the University of Washington HIT Lab's Magic Book technology. The Magic Book allows for a mixed reality presentation so visitors will be able to see the 3-D virtual plants overlaid on video processed from their real world perspective [15]. Figure 4 shows a participant placing two plants together to mate them at the Boston Architecture Center exhibition on April 26, 2001.

Figure 4 - Mating Two Plants at the Boston CyberArts Festival

Examples

Figure 5 shows the visual effects of recombination from alleles that define leaves on stem or not. The first two columns show the visual effects of the allele contribution from both parent plants. The third column shows the visual effect in the child. Since having leaves on the stem is a dominant trait in the system, a plant must possess two recessive alleles in order to display the recessive trait (lack of leaves on the stem).

Figure 5 - Effect of Recombination of Alleles on Stem Leaves
Figure 6 shows the effect of mutation in a color parameter. The left most flower has orange petals. The center flower has red petals. Their offspring flower is brown through the effect of mutation flipping its most significant bit in the petal red color component.

Figure 6 - Example of Mutation in the Red Color Component
Figure 7 shows an example of engine output. The engine creates standard VRML97 output files that can be viewed with a VRML97 compliant viewer. Figure 7's example demonstrates a male vase with a three-stalked flower model. The model shows most dominant traits, yet is simplified by the limited numbers of each body part. Plant models generated by the engine can be significantly more crowded as the number of stalks, leaves, and petals increases.

Figure 7 - A 3-D Model Created by the Engine

Conclusions and Future Work

I found playing with parametric model generation engines intoxicating and innately creative when the goal was not much more than exploration. Many of the decisions I made and implemented in code are arbitrary in their purpose. The process felt more like artistic expression than scientific discovery and yet the process was inspired by readings in the sciences. Though there are 1020 possible models generated by my simple genomes (before applying noise algorithms), I still have only touched an infinitesimal percentage of all possible plants generated from L-System rules. Playing with L-Systems has taught me to more deeply appreciate nature and the variety life process produces without any necessary conscious guidance.

Speculation that evolutionary process can evolve new processes in the digital realm appears to be a hot topic based on the number of books one can find related to the subject. Investigators such as Tom Ray of the University of Oklahoma continue to opine that great things will come of digital evolution seeded properly and left to its own device [16]. Such popular science discussion often overshadows the significance of what we already know how to do. Generating a wide variety of complex 3-D models to enhance our virtual environments in a real-time system seems to be a worthwhile goal on its own accord.

Through my explorations for this paper, I have gained a deeper understanding of how digitally produced movie sets, such as the one used recently in The Grinch Who Stole Christmas, will continue to evolve to become more interesting and more realistic at the same time. If variety truly is the spice of life, these parametric modeling engines are worth their weight in gold. As long as bandwidth continues to be a limiting bottleneck in real-time, shared virtual environments, research in this field should be considered important and invaluable. Other processes of nature in the chemical and physical sciences should be reaped as inspirational models for engine development.

Certainly both the plant and vase genomes could continue to be expanded to enact an even finer level of control during virtual plant generation. But, perhaps, improvement of the engine itself should come first. Currently, the engine produces plant body parts that have no mass and thus can intersect in unfortunate places. Often, the output in that case appears immediately ugly to the eye. Sometimes, the effect is desirable, especially when the intersecting polygons are near the same plane or are of the same color. Collision detection techniques that are well understood algorithmically today could be incorporated to preclude those situations where the virtual plant immediately appears unattractive.

Of final interest are the comments made by participants who mated plants at the Boston CyberArts' Festival. Suggestions participants were especially keen on seeing realized included:

References:

[1] Schwartz, Paul et al, Virtual Playground: Architectures for a Shared Virtual World, http://www.hitl.washington.edu/publications/r-98-12/ (Accessed 12 February, 2001)

[2] ActiveWorlds, Welcome To The 3D Internet, http://www.activeworlds.com (Accessed 24 February, 2001)

[3] Przemyslaw Prusinkiewicz et al, Visual models of plant development. In G. Rozenberg and A. Salomaa, editors, Handbook of formal languages. Springer-Verlag, 1996. To appear.

[4] Karl Sims, Evolving Virtual Creatures, Proceedings of SIGGRAPH ’94 (Orlando, Florida, July 24-29, 1994) pp 15-22.

[5] MendelWeb, Mendel’s Paper, http://www-hpcc.astro.washington.edu/mirrors/MandelWeb/ (Accessed 26 February, 2001)

[6] Aristid Lindenmayer, Mathematical Models for Cellular Interaction in Development, Parts I and II. J. Theoretical Biology, 18: (1968), pp. 280-315.

[7] The University of Calgary Web Server, Biological Modeling and Visualization, http://www.cpsc.ucalgary.ca/Research/bmv/index.html (Accessed 24 February, 2001)

[8] Deborah R. Fowler, Przemyslaw Prusinkiewicz, and Johannes Battjes A Collision-based Model of Spiral Phyllotaxis. Proceedings of SIGGRAPH '92 (Chicago, Illinois, July 26-31, 1992), In Computer Graphics, 26, 2, (July 1992), ACM SIGGRAPH, New York, pp. 361-368.

[9] Radomir Mech and Przemyslaw Prusinkiewicz Visual Models of Plants Interacting with Their Environment. Proceedings of SIGGRAPH '96 (New Orleans, Louisiana, August 4-9, 1996).

[10] Oliver Deussen et al. Realistic Modeling and Rendering of Plant Ecosystems. Proceedings of SIGGRAPH '98 (Orlando, Florida, July 19-24, 1998).

[11] Chris Colby, Introduction to Evolutionary Biology, http://www.talkorigins.org/faqs/faq-intro-to-biology.html (Accessed 25 February, 2001)

[12] Laurens Lapre, LParser, http://www.xs4all.nl/~ljlapre/lparser.htm (Accessed 20 January, 2001)

[13] Steven Rooke, The Genetic-Evolutionary Art Process Employed by Steven Rooke, http://www.azstarnet.com/~srooke/process.html (Accessed 14 February, 2001)

[16] Boston Cyberarts Festival, Boston Cyberarts Festival, http://www.bostoncyberarts.org/ (Accessed 1 March 2001)

[15] Mark Billinghurst, The Magic Book, http://www.hitl.washington.edu/magicbook/ (Accessed 1 March, 2001)

[16] Tom Ray, Beyond The Turing Test, Lecture at The Digital Biota 3 OWorlds Conference (San José, CA, November 6-7, 1999)