Blending the human genome with art

An unusual collaboration between scientists and artists leads to the creation of a "human search tool."

Tech Industry
"What is the nature of life?" and "Who am I?" are questions that cut across science, religion, art, philosophy and even computer science.

Yet type those questions into a search engine like Google or Yahoo and, interspersed with academic papers, you're likely to find a site selling nutritional supplements or one like that evaluates your looks.

In the name of art and science, a group of Southern California-based academics have tapped into a specialized search database used widely by the scientific community to shed a more meaningful light on the subject.


What's new:
A collaboration between artists and scientists has led to a "human search tool" that they hope will shed more meaningful light on how one becomes what one is.

Bottom line:
The project relies on search tools that use Blast, a standard mathematical algorithm in comparative genomics, to illuminate and visualize the links between human genes and those of other organisms.

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The result is "Ecce Homology," an artistic rumination on the nature of life that will be on display next week at Siggraph, an international conference in Los Angeles for creators of .

The project relies on search tools that use Blast (which stands for Basic Local Alignment Search Tool), a standard mathematical algorithm in a field called comparative genomics, to illuminate and visualize the links between human genes and those of other organisms.

"We actually use the scientific algorithm to drive the aesthetic process of the piece," said Ruth West, lead of Ecce Homology and director of visual analytics and interactive technologies at the University of California at San Diego's National Center for Microscopy and Imaging Research.

In more ways than one, Ecce Homology can be thought of as a human search tool.

When someone first walks into its darkened gallery space, he or she will see projected on a far wall a shimmering light that's 3 feet wide and 12 feet tall. Once the visitor stops moving, the light condenses into a ball. Move again, and the light particles trace a person's gestures in calligraphic forms, or human pictographs, across a wall that's 40 feet wide and 17 feet tall. Move an arm in a circular fashion, for example, and the light will form a circle.

Behind the scenes, the computer-vision system is "looking" at the person's movement and is running a simple pattern-matching algorithm to discern whether the pictograph resembles shapes that are part of the human gene protein, which have been given a calligraphic value in the system.

Ecce Homology

If a match is found, then that gene will be the basis for a Blast search and analysis. Blast will mine for a match between the human gene and the rice genome--a symbolic choice for the biological process of cellular respiration represented in both the plant and humans. Cellular respiration is the process of oxidizing food molecules.

When an overlap between the human and rice genome is determined, the project displays a human pictograph superimposed over the rice pictograph. It's a metaphor for the unity of life, West said, given that the rice genes have an estimated 30 percent overlap with human genes.

If a match is not found, then the light will condense again in preparation for another search.

In scientific terms, the team created what they call a "virtual calligraphic brush" that can generate an artistic, high-dimensional visualization of genomic data, which means that it condenses different scientific data to extract value in the form of a visual image. That the light scopes out to 40 feet is meant to represent the enormity of data that's processed and created by genetic research of humans and other organisms.

One of the biggest goals of the project is to harness the ever-expanding body of data from genetic research so that people can better understand comparative genomics. Comparative genomics is one of the chief methods scientists use to understand who we are and how we evolve, by examining the similarities, or homology, of our genes against the structure of other organisms.

"We actually use the scientific algorithm to drive the aesthetic process of the piece."
--Ruth West, head of Ecce Homology

In other words, we study ourselves by studying others.

However, in the digital age, an abundance of data produced by research can prove a hindrance as much as an asset. Before research can turn to breakthroughs in medicine, genetics, or even anti-terrorism, it must be pooled, interpreted and understood. In many cases, it also must be evaluated against other types of data or knowledge sets.

Scientists believe so-called visual analytics and high-dimensional visualization will help make data more comprehensible. The disciplines have long been a focus for researchers, but they are gaining more attention lately as a means to transform science and answer big questions.

The Department of Homeland Security, for example, established the National Visual Analytics Center as a means to abstract meaningful leads in the fight against terrorism from the disparate, voluminous data they've collected from e-mail, bank records, Web sites and phone communications. In February, it chose Stanford University as its first university partner to aid in information analysis.

"If you're going to solve big problems, you need to bring together people who wouldn't normally work together," said West, who trained as a microbiologist and began her career in medical genetics. "Combining disciplines you may not have combined otherwise, you can answer questions from a broader perspective."

That was ultimately the feat of Ecce Homology.

The seeds of the project were planted three years ago when West was teaching a college science lab for non-science majors at UCSD. Students were using the Web version of Blast to complete homework on comparative genomics, without fully understanding how the algorithm works or scoring the genetic sequences to ascertain right answers.

"It relates to a broad spectrum of people (from little kids to scientists) and gets them thinking of the relationship between science and art."
--Carmela Cunningham, director, UCLA's office of information technology

When she asked various colleagues about the tool, she learned that it had become a de facto standard in the scientific community, often the first place researchers went to run queries on gene sequences. Tens of thousands of biologists run DNA sequences into Blast daily. They typically submit 200 to 400 base pairs, or letters, of genetic code to be matched against the billions of letters for known genes.

Despite its ubiquity, many researchers didn't fully understand it either, or blindly accepted the default settings or learning aids of the search tool.

That sparked West's artistic curiosity about a technology that's broadly influencing so much knowledge but is little understood by the public.

That eventually led to a collaboration between 10 other scientists and artists from three universities--UCSD, the University of California at Los Angeles, and the University of Southern California. The group represents the fields of molecular biology, new media, computer graphics, computer science and engineering, performance and bioinformatics. Technology companies including Intel and NEC also signed on to sponsor the work.

The project itself is named after Friedrich Nietzsche's Ecce Homo, an autobiographical book that expounds on how one becomes what one is.

In order for the project to be useful to scientists it needs more work, West said. She and her group, who work on a volunteer basis, plan to eventually include calligraphic DNA data in Ecce Homology, which will essentially require creating a new language. Right now, the software maps only the protein data of gene sequences.

For Siggraph, the software was updated to enhance the visual interface and improve the responsiveness of the tool for the tens of thousands of people expected to interact with it at the conference.

The project originally debuted at UCLA's Fowler Museum in November 2003 to great public interest, according to Carmela Cunningham, a director at UCLA's office of information technology, which supported the project.

"It relates to a broad spectrum of people (from little kids to scientists) and gets them thinking of the relationship between science and art," Cunningham said.

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