Volume 4, Issue 32 October 2007
Listening for Alien Life
The Allen Telescope Array, dedicated on Oct. 11, 2007, is designed to conduct traditional astronomy and to search for signs of intelligent life elsewhere in the universe. Photo: courtesy of UC Berkeley
In a quiet valley north of California's Mount Lassen stands a peculiar manmade forest. Here, 42 metal dishes, each roughly the height of a two-story building, tilt their bowls toward the sky amid a landscape of green pines and yellow brush. This futuristic assemblage, scattered across UC Berkeley's Hat Creek Observatory, is humanity's leading effort to find intelligent life in outer space.
The Allen Telescope Array (ATA) is the first astronomical observatory designed to search for alien beacons full time. Day and night, its broadband radio receivers scan the skies for "we are here" messages from other solar systems.
The array is the culmination of years of work by husband and wife astronomers Jack Welch and Jill Tarter. A UC Berkeley radio astronomer and professor of the graduate school, Welch served as director of the Hat Creek Observatory for more than 24 years. Tarter leads the SETI Institute, the world's most rigorous search for extraterrestrial intelligence.
Jack Welch examines the feed of an ATA antenna alongside a former student. Photo credit: Rick Forster
Both Welch and Tarter decided early in their careers that the universe might be home to other forms of life. In 1968, Welch helped discover the fact that water molecules are scattered throughout the universe, bolstering the chances of encountering beings elsewhere. "Water is the molecule of life," he says.
Tarter got hooked while still a graduate student at Cal. A professor suggested she read NASA's Project Cyclops study, a plan for building a vast array of large radio telescopes to search for extraterrestrial intelligence. "It's a very dense engineering document, but it was a page turner for me. I learned something I had never thought about before-after all the millennia of asking the priests and philosophers whether we are alone, I lived in the first generation of humans that could try and do an experiment to answer that question. How could I pass up a chance to work on such a profound problem?"
This mutual interest led Welch and Tarter to meet. Welch was asked to fly a guest from NASA Ames Research Center to Hat Creek in his small plane. Tarter came along for the ride. The two have collaborated in work and life ever since.
Astronomer Jill Tarter of the SETI Institute at Arecibo Observatory in Puerto Rico, where she conducted observing campaigns several times a year until 2004. Photo: courtesy Jill Tarter
Tarter spent the first decades of her career relying on scraps of observing time on other people's radio telescopes. It made her research frustratingly slow. She had compiled a list of hundreds of thousands of stars that might harbor life, stars similar in longevity and temperature to the sun, but had managed to examine only 1,000 or so.
Then, in the late 1990s, the SETI Institute held a series of workshops to chart the course of future extraterrestrial intelligence research. The idea for the ATA first arose from these meetings.
The ATA's design balances scientific utility and economy. At 20 feet wide, each dish is a fraction of the size of big radio telescopes, and relatively inexpensive to build. But as a group, they are spread over a square kilometer of real estate. Together, the dishes produce an exquisitely detailed image of a broad swath of the radio sky in any given instant, and promise to make the search for extraterrestrial intelligence hundreds of times faster than before.
Jill Tarter explains the SETI signal processing hardware on the ATA to Steve Trimberger of Xilinx Inc., a generous telescope supporter. Photo: courtesy Jill Tarter
Though inspired by the search for otherworldly civilizations, a partnership between the SETI Institute and UC Berkeley's Radio Astronomy Laboratory has turned the ATA into a multi-tasking radio astronomy facility. Because the array detects signals at an extremely wide range of frequencies, it can perform SETI's searches and collect data for traditional astronomy projects at the same time. These projects include creating a map of local interstellar hydrogen that could shed light on the evolution of the universe, and locating transient radio sources that have been predicted but not yet found.
The 42 dishes in the ATA start observing this month. With additional funding, the project will eventually total 350 dishes. Tarter and Welch know it could take some time to complete the array. But both are convinced it's just the right tool for their search.
Says Welch, "There's got to be life out there in some form. We just have to keep looking for it."
Related Web Sites
The Chemotherapy of the Future
Michael Rape is an assistant professor of cell and develomental biology. In 2007, he was named one of 20 Pew Scholars in the Biomedical Sciences and awarded $240,000 for his cancer research.
If a woman is diagnosed with breast cancer, chances are her doctors will prescribe Taxol. First purified from the bark of the Pacific yew in the 1960s, the drug has since become one of the most prescribed cancer drugs of all time.
Like many other chemotherapies, Taxol stops cancer cells from proliferating out of control. But as these drugs arrest the growth of tumors, they also affect all other dividing cells in the body.
"If you have breast cancer, you don't need to kill all your bone marrow cells," says assistant professor of cell and developmental biology Michael Rape. "If we can find something only needed for cell division in breast tissue, you'll have a better probability for success because the side effects are much less severe, and you can give bigger doses for a longer time."
Rape has plans to exchange the brute force of today's cancer drugs for more fine-tuned therapies. The secret of his optimism: a class of enzymes called ubiquitin ligases. Over 1,000 different versions usher human cells through the steps required before they can divide. If these enzymes aren't functioning right, tumors often result. Taxol and many other chemotherapy drugs hinder these rogues and check cell division.
Enzymes called ubiquitin ligases are involved in cell division. Their job is to flag substrate proteins with a protein called ubiquitin. The structure of the ubiquitin flag determines whether the substrate is destroyed or recycled. Image credit: Michael Rape
"Many ubiquitin ligases are required for cells to divide, and they are often expressed in a tissue-specific manner. That gives us evidence that inhibiting them might affect cell proliferation in one tissue and not another," Rape says.
In a cell, ubiquitin ligases operate like tiny meter maids. They tag molecular machinery involved in cell division with a small protein called ubiquitin. The ligases may also link ubiquitin molecules into long single or branched chains. The structure of these chains determines whether the protein is destroyed or recycled for other purposes.
"We know that specific linear chains are important, but don't know what branched chains do.If you understand this reaction mechanistically, you can look for inhibitors at specific stages and get good tools for interfering with the process," Rape says.
Until now, Rape has focused on studying a handful ubiquitin ligases linked to breast, colon, and other cancers. He examines how these enzymes interact with other cell components, and how they build their ubiquitin chains. His ultimate goal is to find drugs that block these enzymes when they malfunction.
Ubiquitin ligases such as E3 have been linked to cancer. The red and green blocks show that E3 production often shifts in tissues with cancer. Image credit: Michael Rape
Rape's research is about to enjoy a dramatic expansion in scope. In September, he received a $1.5 million National Institutes of Health New Innovator Award. The award will help him screen the entire human genome for ubiquitin ligases expressed only in a specific tissue.
Rape will complement this work with a new method to find enzyme substrates. With it, Rape can screen every human protein for a match in just a few weeks. Once he finds a promising substrate-enzyme pair, he can then look for drugs that block it. The result could be that holy grail of cancer treatment—a tissue-specific chemotherapy.
Related Web Sites
The Mathematician and the Genome
Lior Pachter is at the leading edge of a new generation of mathematics and biologists. He is not only a professor of mathematics and computer science, but also a QB3 faculty affiliate and a member of Berkeley's Center for Computational Biology. Photo credit: Robert Fisher
The completion of the Human Genome Project in 2001 was hailed as a major breakthrough in science. For the first time, humans could look at their DNA and discover traits ranging from their propensity to alcohol addiction to the likelihood that their children will have blue eyes.
In fact, research into our biochemical blueprints had only just begun. Since then, scientists have added the rat, cow, chicken, dog, and even platypus to the list of creatures whose genes have been read like a biochemical book. Each species has shed new light on the structure and function of our own genetic code.
Darwin's first sketch of an evolutionary tree from his First Notebook on Transmutation of Species (1837). Source: Wikipedia
Lior Pachter has been at the forefront of these new genomic analyses. Officially a UC Berkeley professor of mathematics and computer science, Pachter considers himself a mathematical biologist. He uses the power of mathematical modeling and statistics to evaluate the vast quantities of data in DNA.
Pachter first got interested in biology as a graduate student in mathematics at MIT. There, he began using mathematical techniques to find functional genes within the so-called "junk" sequences in human DNA. Later, while biologists sequenced the mouse genome, he developed methods to compare where the mouse and human genomes were similar by chance versus selection.
Pachter has big plans for his sequence analysis work: he seeks to do nothing less than map the ancestral tree of life. "I want to understand how each one of the 3 billion nucleotides in the human genome arose in the course of evolution," Pachter says. "To make sense of how the genome works, we have to understand its history. That means understanding what we share in common with other organisms, both with other humans and primates but also all other animals."
To date, the genomes of nearly 30 vertebrates with genes relatively similar to ours have been sequenced. Each has made the task of comparing sequences exponentially more useful and complicated. "It's no longer possible for biologists to analyze these results by hand; there's just too much data," Pachter says. "Here, mathematics helps make sense of the data and also provides models of how the actual molecular components work."
Pachter's research comparing genomes has helped define relationships among vertebrate species. The lengths of the branches on this phylogenetic tree, which are based on DNA sequence comparisons, show how closely each animal is related. The numbers next to each species name indicate the amount of sequence (in megabases) that was analyzed. Image credit: E.H. Margulies et al., "Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome," Genome Research (2007).
Pachter likens genome studies to recreating plans for an existing building. "Until now, we've just been labeling the parts, the doorknobs and windows. Only recently have we started to ask about the function of the parts, and how these functions are related to each other."
A genotope representing genetic relationships among individuals. Each point corresponds to an individual from one of four distinct populations. Image credit: P. Huggins et al., "Towards the human genotope," Bulletin of Mathematical Biology (2007).
In addition to sequence data, a profusion of other genetic information is now flooding the field. Measurements of gene expression in different tissues, ways to measure gene variations between individuals, and other information can all help make sense of how our DNA makes us who we are. "Mathematics and statistics provides a good means for synthesizing the data in a reasonable way," Pachter says.
Just this year, Pachter began collaborating on the Human Microbiome Project. This new initiative from the National Institutes of Health seeks to analyze the microbial flora that lives in and on the human body. Scientists estimate that each person carries around 10 times more bacterial than human cells, species ranging from helpful gut microbes to pathogens like streptococci. The project will generate a jumble of gene fragments from both known and new species. Pachter's role is to help determine the rough number of creatures represented in the mix.
"It's fun for me that I can combine both mathematics and biology and participate in these major enterprises," Pachter says. "The best thing is, I get to do a lot of beautiful math to go along with it."