Live from Egypt: ASU grad reports on protests

February 1, 2011

"Cairo in the morning looks like a war zone. The ruling party's headquarters is still burning." 

When Ian Lee graduated with a bachelor's degree in journalism in 2008, he was among 12 ASU graduates who had been awarded a prestigious Fulbright scholarship to study and conduct research abroad. Download Full Image

With his degree in hand, along with certificates in Islamic Studies and Arabic, Lee headed to Cairo, Egypt to spend a year at American University, studying the reporting differences between newspapers written in English and those written in Arabic. He also would be monitoring Arab satellite networks for the Adham Center for Electronic Journalism while producing freelance stories for American media outlets.

Fast-forward to more than two years later, and Lee is living in downtown Cairo working for The Daily News Egypt and Reuters. His tireless reporting on the current protests in Egypt have contributed to recent CNN reports – heard in this target="_blank">live interview and in this target="_blank">article.

However, perhaps even more compelling are Lee's live" target="_blank">Twitter updates, chronicling his journey from the streets of Cairo to the events in Suez – as he engages in the kind of reporting he said he aspired to while studying at ASU's Walter Cronkite School of Journalism and Mass Communication.

“I want to go to conflict zones and report from there,” said Lee, in 2008, before embarking on his Fulbright year. 

While helping to organize the opposition, social media such as Twitter also have served journalists like Lee in helping provide minute-by-minute, on-the-scene reporting. Just as telling as his status updates, Lee's offline periods – when Twitter and Facebook fall silent – further illustrate the unprecedented widespread Internet and mobile service outages.

Lee's story of the recent protests begins Jan. 22, in Cairo, from a cab (his favorite form of transportation in the city) via Twitter. Follow Ian Lee at" target="_blank">

January 22 (via Twitter)

Our cab driver hadn't heard about the 25th. That will be the organizers' biggest problem. Getting the word out beyond facebook#Egypt

Egyptians began taking to the streets Jan. 25 to protest rampant unemployment, poverty, government corruption and the 30-year rule of President Hosni Mubarak.

January 25

Wow, downtown Cairo is on lock down. Riot police are everywhere, guarding every street. Will today be battle on the Nile? 

And here we go. Heading to Supreme Court for first of many demonstrations #jan25 #Egypt

Police and protesters clashing downtown. Police struggle to control.

People leaving buses and cars to join protest. Roughly 2000 people.

Police beating protesters, protesters respond with rocks.

Police officer tried to arrest me while I was filming a man in custody being beaten.

Reports of protesters in Ramses Square being beaten and fired upon with tear gas.

January 26

Protest scheduled for 9 AM in Tahrir square. On my way to cover it.

Reports coming from Suez, live bullets, molotov cocktails. Things seem to be deteriorating very quickly there.

Protests still taking place downtown. Tomorrow I will be traveling to Suez to cover events there.

January 27

On my way to report on the events in Suez. Hopefully I won't be turned around at a police checkpoint.

My cab driver says he isn't protesting because he needs to make money for food. But Friday he plans to hit the street.

Almost in Suez, heard rumors cell phones aren't working. Might be last tweet for a while. If not, I'll keep tweeting.

El Giesh street looks like a war zone. Burnt out tires and rubble litter the street. Police checkpoint destroyed.

Finished talking with opposition party leaders. They say EVERY party is united in Suez to overthrow the govt if demands aren't met.

Families of the dead in Suez say they are afraid to talk because of the possible retaliation from the government.

Contrary to reports cell phones are working in Suez. Protests breaking out.

Large numbers of protesters outside al arbaeen police station in Suez. Situation is violent

Rocks fill the air. Protesters charging. Suez. Reports of live rounds being used. 

Protesters angry that I am a foreigner, they think I am a spy. Left area.

I'm shooting video from rooftops, too dangerous for foreigners on street. Numbers in thousands.

January 28

With the largest protests planned thus far, the government responds by blocking all Internet services in the country – Lee's Twitter included.

January 29

Cairo in the morning looks like a war zone. The ruling party's headquarters is still burning.

Phone service in Cairo back up but Internet is mostly still down. 

Protesters say they won't go home until President Hosni Mubarak steps down.

A group called the Egyptian Youth Movement is organizing to protect public property from looters. Cairo is lawless.

Each day I've seen the protests get larger. I'm anticipating the same for today. Curious how the army will react.

Moment of truth for protesters and the army as a curfew is scheduled for 4 PM.

State TV reporting the Army is going to be strict about the curfew

I am back from the battle at the Ministry of Interior. Police used live rounds, tear gas and rubber bullets to disperse protesters.

I saw several people dragged away bleeding. One man said he wasn't going to give up until the ministry was taken.

The streets of Cairo are in a state of anarchy. Groups of men protect neighborhoods with sticks, dogs, and few guns.

During the siege on the Interior Ministry, reports of at least 5 people killed. Saw funeral procession 30 minutes ago.

Reports that Mubarak's sons, Gamal and Alaa are in London. Does this mean Mubarak will follow soon?

Local mosque saying telling people not to be worried, the military is here.

It is now 12:30 AM and we are currently listening to a running gun battle in the distance.

With the reports about mobs attacking wealthier neighborhoods, makes me glad I live downtown.

January 30

Reports that Al Jazeera is being banned in Egypt. This isn't good news for the press.

Amazing scenes of camaraderie in Tahrir today. People were volunteering to pick-up trash and handing out free food and water.

I am hearing more gunfire outside tonight. Neighborhood watch told me last night they shoot sometimes to keep people alert.

Back from Tahrir, the crowd is starting to grow. Currently in the low thousands.

January 31

I believe this is a revolutionary moment but not quite a revolution. Tomorrow's "million man march" could be tipping point.

7 days into the uprising and social change is already sweeping Egypt.

Breaking curfew to get a feel for what's happening on the street. I'll tweet what I see when I return.

Back from Tahrir, numbers when I left in the tens of thousands. All talk about tomorrow's million man march.

The Egyptian army says it won't resort to violence against the people. Is this "game over" for Mubarak?

Rumors that cell phones are going to be down in a half an hour. Let's hope not.

If protesters march to the presidential palace tomorrow, something's gotta give.

Driven by his fascination with Cairo's complex history, Lee has analyzed both Arabic and English press in Cairo, comparing coverage of major historical events over the past 10 years. He also has learned Cairene dialect, different from the Jordanian dialect he had learned in the United States.

Britt Lewis

Communications Specialist, ASU Library

New quartet of ant genomes advanced by experts

February 2, 2011

“Look to the ant thou sluggard and consider her ways and be wise.” This proverbial wisdom was taken to heart recently by an international group of ant experts who have published the genome sequences of four ants in a series of coordinated releases in the online early edition of the journal Proceedings of the National Academy of Sciences (PNAS).

The quartet includes the genomes of the red harvester ant Pogonomyrmex barbatus; the Argentine ant Linepithema humile; the fire ant Solenopsis invicta, and the leaf-cutter ant Atta cephalotes, whose genome will be published Feb. 10 in Public Library of Science (PLoS) Genetics. Ant genome research at ASU Download Full Image

Perhaps drawing insights from their study organisms, the scientists' distributed, coordinated effort sped the advancement of these genome projects from sequencing to assembly to annotation to interpretation in less than two years.

Ants are dominant members of almost all terrestrial ecosystems; they are master architects, voracious predators, farmers, ranchers, scavengers and come in a fantastic array of shapes, sizes and colors. Almost all humans have come into contact with ants in one fashion or another. There are fire ants in yards, Argentine ants in kitchens, harvester ants in ant farms, and trains of leaf-cutter ants dismantling forests in documentaries.

Ants originated more than 100 million years ago, their ecological dominance and evolutionary success, complex societies, variation in form and function, and the diverse roles they play in ecosystems, collectively contribute to the scientific rationale behind scientists’ efforts to sequence their genomes. With more than 14,000 described ant species, and with many thousands yet to be described, it is the diversity of ants, matched with many genome sequences, that researchers believe can solve some fundamental questions in biology.

Much of the impetus behind these collaborative efforts grew out of a workshop on ant genomics that took place at the Center for Social Dynamics and Complexity at ASU in 2009.

“Our goal was to sequence 10 ant genomes across the ant family tree and we are well on our way,” said Chris R. Smith, an assistant professor at Earlham College in Indiana. “The pace of our progress was also advanced by employment of the same annotation pipeline, MAKER, developed by Mark Yandell’s group at the University of Utah.”

Smith co-organized the ASU workshop with his P. barbatus co-author, Jürgen Gadau, a professor with ASU’s School of Life Sciences. These publications bring the total number of sequenced ant genomes to six, all released since 2010.

Lead authors of the four studies, in addition to CR Smith and Gadau for P. barbatus, were Christopher D. Smith (San Francisco State University) and Neil Tsutsui (University of California, Berkeley) for L. humile; Yannick Wurm and Laurent Keller (University of Lausanne), Ioannis Xenarios (Swiss Institute of Bioinformatics) and Dewayne Shoemaker (USDA ARS) for S. invicta; and Garret Suen and Cameron Currie (University of Wisconsin-Madison) for A. cephalotes.

Gadau’s team at ASU included School of Life Sciences doctoral students Joshua Gibson, Rick Overson, Elizabeth Cash, and postdoctoral fellows Martin Helmkampf and Florian Wolschin. Their studies, and those of co-author CR Smith, were supported by a grant from the National Science Foundation.

"These publications open the gates to entirely new and highly significant research ventures,” said Bert Hoelldobler, Pulitzer Prize-winning co-author of “The Ants,” with Edward O. Wilson, and a professor in ASU’s College of Liberal Arts and Sciences.

Among these four newly sequenced ant species are two of the world’s most damaging invasive species, the Argentine ant, L. humile, and fire ant, S. invicta. Control of these two pest species is a multi-billion dollar per year industry. Both are native to South America, but now can be found worldwide. The ant research community hopes that having the fully sequenced genomes of these ants will help researchers decode both the secrets of their success as invasive species and open avenues for new means for their control. 

“Controlling invasive ant populations has long involved pesticides that also hurt native competitors including ants and other insects,” said Wurm, lead author on the S. invicta genome. “The genome sequence represents a crucial milestone towards understanding how the members of an ant colony communicate. Ultimately, reverse engineering their communication system might facilitate the development of pesticides that specifically induce workers of a given species to kill their nestmates, while minimizing impact on other species and the environment.”

“Argentine ants may seem like only a nuisance to many since they don’t sting humans like their compatriot fire ant invaders, but studies have shown that they decimate native arthropods wherever they invade,” added CD Smith, lead author of the L. humile genome. “They also protect crop pests, leading to pesticide use that contaminates waterways and probably human health. With luck, the genome will shed light on how to short circuit the destructive behaviors of both invasive ants.” 

The other two ant species in this quartet, the harvester ant, P. barbatus, and leafcutter ant A. cephalotes, were sequenced largely because of their unique biology. These two species have queens and workers that differ greatly in size, morphology, physiology, behavior and longevity. Researchers hope to illuminate how ant colonies manage to produce such genetically similar, but vastly different individuals. For example, harvester ant queens may live several decades, but workers only six months. Similarly, the range of sizes of leaf-cutter ant workers varies from smaller than a grain of rice, to as large as a peanut.

Scientific studies of these ants already have offered insights into molecular pathways that enable the ants to produce individuals with such differences and allow researchers, such as Gadau and CR Smith, to find those genes that ultimately distinguish queens from workers. CR Smith notes that, “these are the quintessential genes for advanced sociality, the genes that fate an individual to a life of royalty or drudgery.”

Access to the leaf-cutter genome also offers opportunities to study the molecular underpinnings of a highly complex mutualism. Leaf-cutter ants evolved agriculture more than 10 million years ago. They not only cut leaves as a substrate to grow fungal gardens, but they also use bacteria to increase the intake of nitrogen and fight off harmful (parasitic) fungi. 

“The intricate and obligate relationships between the ants and their symbionts are reflected in gene losses in the leaf-cutter ant genome, especially in pathways related to nutrient acquisition and storage, as would be expected when other organisms obligately supply nutrients,” said Suen, one of the lead authors of the A. cephalotes genome. “As one of the most ancient forms of non-human agriculture, having access to the leaf-cutter ant genome will also help us understand how this complex behavior evolved. This ant-fungus association led to the development of the immense colony size in these ants, which can contain hundreds of fungus gardens and millions of workers.”

Colleague and co-author Currie also noted that “having a genome for a leaf-cutter ant will greatly facilitate our ability to understand the molecular underpinnings of this complex agricultural symbiosis.”

Ultimately, however, the insights to be gained from the combination of these social insect genomes outweighs the individual contribution of each study, CR Smith said, in keeping with the ant genome researchers’ collective, ant-like approach to “the greater good.” 

Smith’s co-author, Gadau, agreed, noting that “large scale genomics analysis within a group of related organisms will also allow the identification of new functional non-coding DNA sequences that play a critical role in the organization of insect societies and phenotypic plasticity in general. This allows social insects to contribute to our understanding of how the environment and genome interact to generate an intricately intertwined society. At the same time, such studies also help us to understand how genomes in general interact with the environment to generate adaptive phenotypes or complex diseases like diabetes which are the result of an interaction between the environment, individual behavior and genes.”

For example, these four genomes, taken together, have revealed that the brand of sociality that evolved among ants is different from, but similar to, that which has evolved among bees. By comparisons to the previously published honey bee genome, researchers have independently found that ants have much expanded odorant receptor genes, whereas honey bees have a contracted set, relative to other insects. Ants have the most odorant receptor genes of any insect described to date and this difference likely reflects an increased dependence on and sophistication of chemical communication. On the other hand, both the bees and ants have a relatively depauperate set of innate immunity genes, as compared to other insects, which seems to reflect an increased reliance on social immunity – the processes whereby individuals of a society rely on others to clean and ‘de-bug’ each other and the nest. All of the ant genomes also contain a complete DNA methylation toolkit. DNA methylation is known to modify the expression of genes, independent of changes in DNA sequence, and is involved in differentiating the developmental pathways of queens and workers in honey bees. Analyses in some of the ant genomes suggest that DNA methylation is also involved in making ant queens and workers different.

The studies’ authors noted, “We know bees use DNA methylation to execute caste programs and now have the first hints that ants may too. But even while they appear to have the same genes as bees, it is already clear that they use methylation differently, and that both species use it differently than humans.”

The researchers believe that epigenetic processes such as methylation likely also contribute to the astonishing life-span differences between queens (that live more than 20 years) and workers that typically die after several months.

Myrmecology, or the study of ants, has entered the genomic era, according to these four studies’ authors. Such advances in genomics will, they believe, allow scientists to ask questions related to pest management, phenotypic plasticity, evolutionary novelty, the interaction of environment and genotype in the production of adaptive phenotypes, kinship and the evolution of sociality, reproductive conflict, disease management in social environments, and other fundamental questions in development, ecology and evolutionary biology. However, the scale of integrating genome knowledge across so many species will also require “databases, new software tools, data-sharing policies and the continuation of the kind of unprecedented cooperation offered by the authors and institutions in these four studies,” said Gadau and CR Smith. Perhaps scientists, by following the principles of their social study organisms, by sharing information and resources to tackle complex problems, can hope to fully resolve how ants reign as some of the most successful organisms on Earth.

Margaret Coulombe

Director, Executive Communications, Office of the University Provost