Chocolate lovers who think of their passion as rich, sweet, and naturally delicious might want to stay out of Harvard scientist Ben Wolfe’s classroom this summer. Not only is chocolate naturally bitter, Wolfe told students last week, but the way that quality is removed is by fermenting in a heap covered by banana leaves for several days. Wolfe may be taking some of the romance out of chocolate, but he isn’t casting it away. Instead, he’s transferring a bit of its allure to our seldom-appreciated partners in gastronomy: the bacteria and fungi that do heavy lifting, transforming a constellation of foods around the world into edible, flavorful, and even intoxicating creations. Wolfe, who calls cheese his “favorite fermented milk product,” is sharing his enthusiasm for food, drink, and microbes in a new class at Harvard Summer School called “Feast and Famine: The Microbiology of Food.” A postdoctoral fellow in the lab of Bauer Fellow Rachel Dutton , Wolfe created the class as a way to make the study of microbes more accessible to the broad array of students — from high school to graduate school — who people Harvard’s summertime campus. Wolfe is using food as a lens through which students can better understand microbes and the helpful and harmful roles they play in our everyday lives. “People are really into artisanal cheeses and craft brewing. It’s also a really great way to teach undergraduate microbiology,” Wolfe said. “I’m using food as a window into microbial diversity.” Ondine Jean-Baptiste (left) inspected the koji rice, which has mold spores and is used to make sake. The effort is also something of a personal journey for Wolfe, who received his doctorate from Harvard in 2010 and is considering which direction to take his career. His research in Dutton’s lab focuses on something he enjoys — the microbiology of cheese — but he also wanted the experience of designing a class from scratch and taking primary responsibility for teaching its students. The course covers the role of microbes at every step in the food production process, from their beneficial symbiosis on the roots of crop plants, to plant and animal pathogens that can devastate the food supply, to their central role in the transformation of raw materials into the foods we come home to daily. In a recent class, Wolfe spent two hours talking about the creation of cheeses and other fermented milk products that have origins that might raise eyebrows in the West. Koumiss , from Asia, is fermented horse milk. Biruni , from Africa, is fermented camel milk. And phrung , from India, is fermented yak milk. He also reviewed products made from fermented rice and soybeans, used in creating an array of Japanese and Chinese foods and drinks, like soy sauce, miso paste, rice vinegar, and sake. Wolfe outlined lactic fermentation, which converts starches to sugars, and is used in chocolate processing; alcoholic fermentation, which converts sugars to alcohol, and is used in making beer or sake; and acetic fermentation, which converts alcohol to acetic acid to make vinegars. The methods require different microbial partners, though some of those partners, such as the yeast used in beer brewing, Saccharomyces cerevisiae , are used far and wide. “It’s mainly growing things and rotting them in delicious ways,” Wolfe said. He also touched on the fermented vegetables sauerkraut and pickles, kimchi and poi, the fermented skipjack tuna known as katsuobushi in Japan, a pressed cake of fermented peanuts known as oncom in Java, and even the fermented raw meat that ultimately becomes salami. Wolfe brought in an expert to talk about alcohol production. The class’s last hour (Summer School classes run a marathon three hours, twice a week) featured Todd Bellomy , a beer and sake aficionado who brews his own sake and is working to increase its popularity in the Boston area. Bellomy, whose day job involves consumer relations for Boston Beer Co. , led students through the steps of sake brewing, using images from his own exploration of the topic, taking them on a sometimes humorous photographic journey to Japanese sake breweries. A closer look at koji rice used to make sake. Without koji, there is no sake. Other outside speakers who lent their expertise to the class, either in person or via Skype, included Eero Ruuttila of Siena Farms in Sudbury, Mass.; Dan Felder, a chef working on the development of fermented foods; Maryn McKenna, a blogger who writes about food pathogens; and Mateo Kehler, an artisan cheese producer in Vermont. James Palmer, a high school junior from Concord, Mass., whose favorite fermentation is chocolate, said he took the class because he’s interested in biology and thought that subject and food were an interesting combination. Kaitlin McGovern, a junior from Red Hook High School in New York, said she decided to take the class because her father is starting a brewery in Rhinebeck. “I wanted to see how it works,” McGovern said. The class “is different and interesting.”

Watch out, Barbie: Omnivorous beasts are assembling in a 3-D printer near you. A group of graphics experts led by computer scientists at Harvard have created an add-on software tool that translates video game characters — or any other three-dimensional animations — into fully articulated action figures, with the help of a 3-D printer. The project is described in detail in the Association for Computing Machinery (ACM) Transactions on Graphics and will be presented at the ACM SIGGRAPH conference on Aug. 7. In addition to its obvious consumer appeal, the tool constitutes a remarkable piece of code and an unusual conceptual exploration of the virtual and physical worlds. “In animation you’re not necessarily trying to model the physical world perfectly; the model only has to be good enough to convince your eye,” explains lead author Moritz Bächer , a graduate student in computer science at Harvard’s School of Engineering and Applied Sciences (SEAS). “In a virtual world, you have all this freedom that you don’t have in the physical world. You can make a character so anatomically skewed that it would never be able to stand up in real life, and you can make deformations that aren’t physically possible. You could even have a head that isn’t attached to its body, or legs that occasionally intersect each other instead of colliding.” Returning a virtual character to the physical world therefore turns the traditional animation process on its head, in a sort of reverse rendering, as the image that’s on the screen must be adapted to accommodate real-world constraints. Bächer and his co-authors demonstrated their new method using characters from Spore , an evolution-simulation video game. Spore allows players to create a vast range of creatures with numerous limbs, eyes, and body segments in almost any configuration, using a technique called procedural animation to quickly and automatically animate whatever body plan it receives. As with most types of computer animation, the characters themselves are just “skins” — meshes of polygons — that are manipulated like marionettes by an invisible skeleton. “As an animator, you can move the skeletons and create weight relationships with the surface points,” says Bächer, “but the skeletons inside are nonphysical with zero-dimensional joints; they’re not useful to our fabrication process at all. In fact, the skeleton frequently protrudes outside the body entirely.” Bächer tackled the fabrication problem with his Ph.D. adviser, Hanspeter Pfister , Gordon McKay Professor of Computer Science at SEAS. They were joined by Bernd Bickel and Doug James at the Technische Universität Berlin and Cornell University, respectively. This team of computer graphics experts developed a software tool that achieves two things: It identifies the ideal locations for the action figure’s joints, based on the character’s virtual articulation behavior, and then it optimizes the size and location of those joints for the physical world. For instance, a spindly arm might be too thin to hold a robust joint, and the joints in a curving spine might collide with each other if they are too close. The software uses a series of optimization techniques to generate the best possible model, incorporating both hinges and ball-and-socket joints. It also builds some friction into these surfaces so that the printed figure will be able to hold its poses. The tool also perfects the model’s skin texture. Procedurally animated characters tend to have a very roughly defined, low-resolution skin to enable rendering in real time. Details and textures are typically added through a type of virtual optical illusion: manipulating the normals that determine how light reflects off the surface. In order to have these details show up in the 3-D print, the software analyzes that map of normals and translates it into a realistic surface texture. Then the 3-D printer sets to work, and out comes a fully assembled, robust, articulated action figure, bringing the virtual world to life. “Perhaps in the future someone will invent a 3-D printer that prints the body and the electronics in one piece,” mused Moritz Bächer, a graduate student in computer science. “Then you could create the complete animated character at the push of a button and have it run around on your desk.” Photo courtesy of Moritz Bächer “With an animation, you always have to view it on a two-dimensional screen, but this allows you to just print it and take an actual look at it in 3-D,” says Bächer. “I think that’s helpful to the artists and animators, to see how it actually feels in reality and get some feedback. Right now, perhaps they can print a static scene, just a character in one stance, but they can’t see how it really moves. If you print one of these articulated figures, you can experiment with different stances and movements in a natural way, as with an artist’s mannequin.” Bächer’s model does not allow deformations beyond the joints, so squishy, stretchable bodies are not yet captured in this process. But that type of printed character might be possible by incorporating other existing techniques. For instance, in 2010, Pfister, Bächer, and Bickel were part of a group of researchers who replicated an entire flip-flop sandal using a multimaterial 3-D printer. The printed sandal mimicked the elasticity of the original foam rubber and cloth. With some more development, a later iteration of the “3-D-print” button could include this capability. “Perhaps in the future someone will invent a 3-D printer that prints the body and the electronics in one piece,” Bächer muses. “Then you could create the complete animated character at the push of a button and have it run around on your desk.” Harvard’s Office of Technology Development has filed a patent application and is working with the Pfister lab to commercialize the new technology by licensing it to an existing company or by forming a startup. Their near-term areas of interest include cloud-based services for creating highly customized, user-generated products, such as toys, and for enhancing existing animation and 3-D printer software with these capabilities. The research was supported by the National Science Foundation, Pixar, and the John Simon Guggenheim Memorial Foundation.

Biofilms may no longer have any solid ground upon which to stand. A team of Harvard scientists has developed a slick way to prevent the troublesome bacterial communities from ever forming on a surface. Biofilms stick to just about everything, from copper pipes to steel ship hulls to glass catheters. The slimy coatings are more than simply a nuisance, resulting in decreased energy efficiency, contamination of water and food supplies, and — especially in medical settings — persistent infections. Even cavities in teeth are the unwelcome result of bacterial colonies. In a study published in the Proceedings of the National Academy of Sciences (PNAS), lead co-authors Joanna Aizenberg , Alexander Epstein , and Tak-Sing Wong coated solid surfaces with an immobilized liquid film to trick the bacteria into thinking they had nowhere to attach and grow. “People have tried all sorts of things to deter biofilm buildup — textured surfaces, chemical coatings, and antibiotics, for example,” says Aizenberg, Amy Smith Berylson Professor of Materials Science at the Harvard School of Engineering and Applied Sciences (SEAS) and a core faculty member at the Wyss Institute for Biologically Inspired Engineering at Harvard . “In all those cases, the solutions are short-lived at best. The surface treatments wear off, become covered with dirt, or the bacteria even deposit their own coatings on top of the coating intended to prevent them. In the end, bacteria manage to settle and grow on just about any solid surface we can come up with.” Taking a completely different approach, the researchers used their recently developed technology, dubbed SLIPS (slippery-liquid-infused porous surfaces) to effectively create a hybrid surface that is smooth and slippery due to the liquid layer that is immobilized on it. First described in the Sept. 22, 2011, issue of the journal Nature , the super-slippery surfaces have been shown to repel both water- and oil-based liquids and even to prevent ice or frost from forming. The word “SLIPS” is coated with the SLIPS technology to show its ability to repel liquids and solids and even prevent ice or frost from forming. The slippery discovery has now been shown to prevent more than 99 percent of harmful bacterial slime from forming on surfaces. Image courtesy of Joanna Aizenberg, Rebecca Belisle, and Tak-Sing Wong “By creating a liquid-infused structured surface, we deprive bacteria of the static interface they need to get a grip and grow together into biofilms,” says Epstein, a recent Ph.D. graduate who worked in Aizenberg’s lab at the time of the study. “In essence, we turned a once bacteria-friendly solid surface into a liquid one. As a result, biofilms cannot cling to the material, and even if they do form, they easily ‘slip’ off under mild flow conditions,” adds Wong, a researcher at SEAS and a Croucher Foundation Postdoctoral Fellow at the Wyss Institute. Aizenberg and her collaborators reported that SLIPS reduced by 96 to 99 percent the formation of three of the most notorious, disease-causing biofilms — Pseudomonas aeruginosa , Escherichia coli, and Staphylococcus aureus — over a seven-day period. The technology works in both a static environment and under flow, or natural conditions, making it ideally suited for coating implanted medical devices that interact with bodily fluids. The coated surfaces can also combat bacterial growth in environments with extreme pH levels, intense ultraviolet light, and high salinity. SLIPS is also nontoxic, readily scalable, and most importantly, self-cleaning, needing nothing more than gravity or a gentle flow of liquid to stay unsoiled. As previously demonstrated with a wide variety of liquids and solids, including blood, oil, and ice, everything seems to slip off surfaces treated with the technology. To date, this may be the first successful test of a nontoxic synthetic surface that can almost completely prevent the formation of biofilms over an extended period of time. The approach may find applications in medical, industrial, and consumer products and settings. In future studies, the researchers aim to better understand the mechanisms involved in preventing biofilms. In particular, they are interested in whether any bacteria transiently attach to the interface and then slip off, if they just float above the surface, or if any individuals can remain loosely attached. “Biofilms have been amazing at outsmarting us. And even when we can attack them, we often make the situation worse with toxins or chemicals. With some very cool, nature-inspired design tricks, we are excited about the possibility that biofilms may have finally met their match,” concludes Aizenberg. Aizenberg and Epstein’s co-authors included Rebecca A. Belisle, research fellow at SEAS, and Emily Marie Boggs ’13, an undergraduate biomedical engineering concentrator at Harvard College . The authors acknowledge support from the Department of Defense Office of Naval Research; the Croucher Foundation; and the Wyss Institute for Biologically Inspired Engineering at Harvard University.

Image: Flag of al-Qaeda in Iraq. Wikipedia Al Qaeda’s Arab Comeback: Capitalizing on Chaos in Syria, Mali — Bruce Riedel, Daily Beast Destroying Timbuktu in Mali, exploiting the turmoil in Syria, successfully attacking in the Sinai—at the operational level, al Qaeda is stronger than it’s ever been, says Bruce Riedel. Al Qaeda has exploited the Arab Spring to create is largest safe havens and operational bases in more than a decade across the Arab world. In the 18 months since the Arab revolutions first began, al Qaeda has grown stronger, despite founder Osama bin Laden’s death and a lack of mass appeal. Like the rest of the world, the terror organization was surprised by the revolutions that toppled dictators in Tunisia, Egypt, Libya, and Yemen. Its ideology of violence and jihad initially was challenged by the largely nonviolent revolutionary movements that swept across North Africa and the Middle East. But al Qaeda is adaptive, and it has exploited the chaos and turmoil of revolutionary change to create bases and new strongholds from one end of the Arab world to the other. Read more …. My Comment: I guess reports of Al Qaeda’s demise were ‘greatly exaggerated’.

Skype Denies Police Surveillance Policy Change — BBC Microsoft’s online message, phone and video chat service Skype has denied making changes to its system “in order to provide law officers greater access” to its members’ conversations. It follows reports suggesting infrastructure upgrades had made it easier to hand on users’ chat data. Skype has now posted a blog saying the changes were made solely to improve user experience and reliability. But it added it would pass on messages to law enforcement when “appropriate”. Read more …. My Comment: But everyone now knows that the technology exists to make it possible …. a fact that Skype will never be able to discount. And while the focus is on police agencies …. no one is discussing what the intelligence agencies are doing.