Research Notes

En route to disease-fighting fruit
Nicholas Ewing

Making computers ‘show their work’
Monica Lam

Peering in on privacy
Randy Mayes

Free press falters in overseas coverage
Bill Dorman

Getting a read on testing trouble
Renee Golanty-Koel

Missed diagnosis: ESL as a disability
Celeste Roseberry-Mckibbin

Plotting a soft touch in space
Jose Granda

Projects aims to keep surgeons operating

Could a tomato, one day, keep cholera away? Or produce therapeutic antibodies to treat cancer? Scientists at Sac State have taken a big step toward developing tomatoes as a possible source of edible vaccines and other proteins such as therapeutic antibodies.

Biological sciences professor Nicholas Ewing and a former student have identified and recently patented a portion of a gene that could turn tomatoes into low-cost, disease-relieving agents.

Currently, animal cell cultures are used to produce highly effective but expensive vaccines and anti-cancer antibodies. Since this is such a costly method, a number of groups are using plants as an alternative to produce the antibodies.

The novelty of Ewing’s approach is the choice of the tomato.

His discovery is a genetic “switch” that can be used to trigger the activation of any gene placed adjacent to it. The switch is named Promoter of the Tomato Expansion Gene LeEXP-1. To produce antibodies, the antibody gene is cloned from an animal cell line and placed adjacent to the LeEXP-1 promoter. When this new gene is transferred back into tomato plants, the antibody gene is turned on in tomato fruit, which leads to the accumulation of antibodies. The antibodies can then be purified.

For edible vaccines, a different gene—one from the organism being vaccinated against—would be inserted adjacent to the LeEXP-1 promoter and transferred in the tomato. These fruit would contain the protein of the organism. Consumption of the fruit then could generate an immune response.

Ewing notes that they still have a way to go toward their long-range goal of a tomato-based vaccine. They are just beginning to test the levels of protein they may be able to produce. But if the work comes to fruition, Ewing foresees a great potential for use, especially in developing countries.

“Regular vaccines are often too expensive—they have to be refrigerated and you have to have clean needles,” Ewing says. “While the edible vaccines would still need to be administered by a health professional, they would be much cheaper and not as perishable.

“I’d like to see it used for vaccines that pharmaceutical companies don’t devote much time and money to, such as in developing countries where there’s not a lot of money to be made in fighting diseases that impact large numbers of people.

The discovery of the promoter of the LeEXP-1 gene isn’t the only reason Ewing is pursing the tomato as his potential source. Previous efforts to produce edible vaccines using potatoes would have required subjects to eat the tubers raw, since cooking would alter the chemistry. Ewing decided to try something that people will eat uncooked, so he looked at the tomato.



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Making computers ‘show their work’

Like nervous students who know the right answer but aren’t sure why, computers sometimes know more than they “think.”

For example, a computer using a “neural network” can often reliably pick high-performing stocks. But, like the student asked to explain his answer, the computer often can’t articulate how it came up with the answer. It just “knows.”

“But if you want people to make a decision based on the output, they need to know ‘why,’” said management information science professor Monica Lam.

In search of “why,” Lam developed an innovative way to coax the answer from the computer.

“Now we can explain to customers why we are making a recommendation,” she said. And, she added, that explanation often leads to even more accurate predictions.

While neural networks aren’t new—the first mathematical models were developed in the 1950s—they have become more sophisticated and are being used in a wider range of applications. The networks are modeled after the processes that allow mammals (like that tongue-tied student) to think and learn.

Like people, neural networks learn through training and can apply learning to new situations. The networks are first given data with a known outcome.

In the stock-picking example, company financial data would be input along with the company’s stock performance. The network then processes the data to identify the “rules” that connect the financial data to stock performance. In this example, the network is taught to recognize high, average and low performing stocks. Once it has established the rules, the neural network can analyze any stock and predict stock performance.

Stock selection is a common use of neural networks. Yet investors are often reluctant to invest based on the abstract calculations in a black box, especially since neural networks have not been able to explain the rules.

“The traditional neural net-works couldn’t do that for you,” Lam said. Now they can. Lam created an algorithm that queries the neural networks and reveals the rules the system developed to evaluate the data and make predictions.

“It will figure out what relationships are established during the learning process,” she said. “Then I can judge whether I want to use the results.”

Even better, because her algorithm looks for the most significant relationships, it filters out extraneous or insignificant information.

“The rules then have a higher prediction ability than the neural network itself,” Lam said.

While Lam looked specifically at stock picking, neural networks and the algorithm could be applied to a variety of problems in business and other fields—including medicine.

Her work was published in the IEEE Transactions on Knowledge and Data Engineering and the proceedings of the first International Conference on Electronic Business last year. She holds a copyright on the computer code that implements her algorithm, though the algorithm itself is in the public domain.

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Peering in on privacy

Since 9/11, Americans seem willing to tolerate a greater degree of surveillance. That doesn’t surprise philosophy professor Randy Mayes.

“A person’s rights aren’t being fundamentally violated by being watched,” he says. “Sometimes people misinterpret me as saying I think privacy isn’t important. I just use ‘privacy’ differently.”

Mayes says the concept of the “right to privacy” began in the late 1800s as the right to be left alone. But as technology progressed, it began to be considered a violation of privacy if a person just looks.

That goes too far, says Mayes, who presented his findings at a conference on “Terror and Justice” in May.

“There’s a great deal of good in observation,” he says. “If you think about it, in a liberal culture, knowledge is one of the things you value in and of itself.

“The reason you don’t like people knowing about you is because you’re afraid of what they might think or do. It needs to be stipulated when it doesn’t harm, you can’t say your privacy has been violated.”

The harm comes when information gathering violates a person’s rationality, the privacy of one’s mind. Mayes defines privacy as the freedom to keep people out of your consciousness.

“If someone is spying or eavesdropping on you, and you aren’t aware of it, that’s very different,” he says. “Even a peeping Tom hasn’t hurt anybody, except himself in a moral sense, until he’s discovered. Then he has intruded into the personal space of the person he’s watching. The right to privacy doesn’t prevent people from looking. It requires them to be discrete.”

Mayes also makes a distinction between privacy and the right to privacy. “The right to privacy doesn’t mean you get to keep everything private,“ he says. “It’s like liberty—people have a right to it, but they still can’t do anything they want. ”

“What is important,” he says, “what you really have a right to, is a space to think, to use practical rationality.”

Sac State government professor Bill Dorman often asks his students a pair of related questions. The answers offer a quick introduction to his quarter-century of research into war, peace and the American mass media.

What would happen, Dorman asks, if a U.S. president suddenly issued an executive order making abortion illegal? And what did happen when a U.S. president declared it was necessary to invade Grenada or Panama, or to send 150,000 troops to the Persian Gulf?

His students generally agree there would be a major national debate in the first case, Dorman says. They also readily agree that few Americans questioned the military actions.

Dorman says that during the last half century, Americans have lost their say in foreign affairs and military action.

In large part, he says, that’s because the nation’s major news outlets now tend to report on international relations simply by printing assertions of fact provided by the U.S. government. There is very little journalistic independence. Instead, he says, there is a “journalism of deference,” reporting that assumes the government has provided a complete and accurate representation of a situation.

And Americans are highly dependent on the media for information about foreign and military issues, Dorman says, unlike issues such as taxes or abortion. For domestic issues, Americans also get information from friends at work, church, social organizations and the like. The media is just one source.

“The media in essence waits for permission from political elites,” he says. “And political elites too often don’t open up debate until it is too late, until the fighting started.”

Dorman says this wasn’t always the case. Before World War II, he says, American media and American citizens were much more likely to question military options. Once any fighting began there was always the same “rally effect” in which citizens unite behind their leaders, he says. But before any fighting there was much more debate.

Dorman says the change came with the Cold War—45 years of intense competition with the Soviets and the threat of nuclear war.

“It created a kind of nationalism this country had never known,” Dorman says. “There was this permanent rally effect that you usually only see during armed conflict, and the media and political elites in general didn’t question things.”

Now semi-retired after 35 years at Sac State, Dorman is currently reviewing recent research on the American media’s international coverage for the Center for War, Peace and the News Media at New York University.

This spring, he was honored with a Wang Family Excellence Award from the 23-campus California State University system. The $20,000 award honors exemplary contributions and achievements to an academic area and university.

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Getting a read on testing trouble

The overemphasis on test scores and standards–to the exclusion of everything else–may be turning teenagers off to reading, warns education professor Renee Golanty-Koel.

The former high school English teacher says the literature used in English classes can affect motivation to read. She has presented her findings at the European Conference on Reading.

“English teachers don’t always select material that resonates with adolescents. So students can become disengaged with literature,” she says. “It’s especially difficult in California because literature standards require students to read ‘historically and culturally significant works’—the classics that are often taught to the exclusion of everything else.

“I believe English should be taught very differently in high school than it is in college. We need to examine literature with students beyond the conventions usually taught in the classroom such as theme and symbolism,” she says. “Trying to make them literature critics has a paradoxical effect of turning them off. We need to find a way of engaging adolescents.”

Golanty-Koel notes teens go through several phases that affect their sense of identity at a time when they’re asking themselves, “Who am I?” and “Who will I become?” When students can identify with literature, the teacher can encourage better verbal and written response, opening their imaginations, allowing rediscovery and stimulating emotions.

“I’m not negating the necessity for adolescents to write in a coherent manner, to increase their vocabulary, to give good oral explications. Those skills are, of course, necessary. But because of the pressure of standards–not the standards themselves–and the pressure of test scores, what is quite human and life-supporting in being an adolescent gets lost in other things,” she says.

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Missed diagnosis: ESL as a disability

Children learning English as a second language are often mistakenly singled out for special education, says a Sac State speech pathology and audiology professor, putting additional demands on an already overburdened system.

Celeste Roseberry-McKibbin says non-native English speakers are being referred to special education for communication disorders more often than primary English speakers, though the incidence of communication disorders is the same across ethnic groups.

She first noticed the problem years ago as a school speech therapist working with bilingual children, and she continues to see it in her consulting role with a local school district. The question is: Do the children have underlying speech and language learning problems or do they just need more time to learn English?

“Often, the children are referred because they aren’t progressing academically and have been slow to learn English,” says Roseberry-McKibbin, the author of The Source for Bilingual Students with Language Disorders, a book for English speaking clinicians. “It’s important to differentiate a language difference versus a disorder.”
If the child’s skills in his or her primary language are normal, but he or she is behind in English, it may be a language difference issue. But if the child is slow in both, it could be an underlying disability.

“I look at patterns that are atypical for both languages,” Roseberry-McKibbin says.” If a child has underlying language issues they may not be able to express themselves in appropriately long sentences or comprehend and remember what they hear. They may have difficulty with articulation, pronouncing their sounds. They may stutter.”

She says one reason kids learning ESL are referred more often may be because many teachers aren’t familiar with the English acquisition process. “For example, when exposed to a new language many children go through a ‘silent period’ where they won’t talk in either language,” Roseberry-McKibbin says.

Cultural differences may also play a factor. Many cultures don’t expect children to do as much for themselves as soon as Americans do, she says. n

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Plotting a soft touch in space

The biggest test of Jose Granda’s software will come sometime in April, when a U.S. space shuttle docks with the International Space Station.

That’s when Granda will know how well his Computer Aided Modeling Program (CAMP-G) helped engineers create computer models of the flexible structure in space. Granda, a Sac State mechanical engineering professor, was awarded a NASA Faculty Fellowship over the summer to work with engineers and scientists who model the station.

If all goes well–and a battery of tests on Earth and in space say it will–then the station will hardly quiver as the shuttle attaches itself. If everything goes incredibly badly, the station could shake itself into space debris. That isn’t likely, but …

“When you do these simulations, the biggest question is what happens at the time the shuttle attaches to the station, which has a flexible structure,” Granda explains. “Obviously, you don’t want to produce resonance—the vibrations could destroy the station.”

Granda introduced his software to NASA over the summer, when he was at Langley Research Center in Virginia and working with mission control operations at the Johnson Space Center in Houston.

The software translates engineering ideas directly into computer code, allowing engineers to more easily enter information into simulation software such as MATLAB and SiMULINK.

Writing the code manually can require long, tedious hours of work, and is subject to error. And in the space station’s case, those hours were multiplied several times over. It’s still under construction and changes weight and shape all the time, so NASA has had to complete new mission simulations every time a space shuttle is scheduled to attach to the station to drop off new parts.

“CAMP-G uses Bond Graph Modeling technology and produces the code automatically. It’s a way of making the step between reality and the computer a quick step,” Granda says.

Granda is internationally recognized for his research. He is the chair of the Bond Graph Modeling Committee of the Society for Computer Simulation and is chair of the upcoming ICBGM’2003 International Conference on Bond Graph Modeling and Simulation.

NASA scientists were impressed enough with Granda’s CAMP-G to look into using the software for future missions. He and NASA scientist Raymond Montgomery have begun testing models from Zvezda, the original space station. Their goal is to continue through other space station configurations until they reach mission A12, which is expected to be in April.

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