Monday, August 31, 2009

MIT engineers create new school of robotic fish


By Shelby Lin Erdman

  • Story Highlights
  • Engineers at MIT have created a new generation of robotic fish
  • 'Robofish' could be used to map the ocean floor, inspect submerged boats or pipes
  • MIT researchers built their first robotic fish, "Robotuna," in 1994
  • New robofish are modeled after bass and trout and cost only a few hundred dollars

(CNN) -- Schools of robotic fish could one day map the ocean floor, detect pollution or inspect and survey submerged boats or oil and gas pipelines, researchers at the Massachusetts Institute of Technology say.
Nice catch! MIT engineer Kamal Youcef-Toumi displays two of his robot fish.

Nice catch! MIT engineer Kamal Youcef-Toumi displays two of his robot fish.

MIT engineers are showing off the latest generation of so-called robofish 15 years after they built the first one. The latest incarnation is sleeker, more streamlined and capable of mimicking the movements of a real fish.

And it's capable of exploring underwater terrain submersibles can't, said Pablo Valdivia Alvarado, a mechanical engineer at the school.

"Some of our sponsors were thinking of using them for inspection and surveillance," Alvarado said. "Since these prototypes are very cheap, the idea was to build hundreds -- 200, 500 -- and then just release them in a bay or at a port, and they would be roaming around taking measurements."

MIT researchers built their first robotic fish, "Robotuna," in 1994. But Robotuna has gone the way of the dinosaur. Alvarado said the new generation -- modeled after bass and trout -- cost only a few hundred dollars and have only 10 parts instead of the thousands used in R

At five to 18 inches, the new fish is much smaller than Robotuna and built from a single, soft polymer. And unlike Robotuna, the fish is able to be released in the oceans.

"Most of the brains, the electronics, are embedded inside," said Alvarado, who designed the robofish with fellow MIT engineer Kamal Youcef-Toumi. "We have built prototypes with the battery inside, but for my experiments, for simplicity. We have a lot of prototypes that are simply tethered. We have a cable that runs out from the body and connects to a power supply."

The new generation has withstood harsh conditions in the lab, including two years of testing inside tanks filled with tap water, which is corrosive to standard robots, according to Alvarado, who says the Robotuna inspired him to take the technology to the next level.

The oil exploration company Schlumberger helped fund the research, but Alvarado says the U.S. Navy has also expressed interest in the robofish.

MIT's mechanical engineers are now turning their attention to new challenges: A robotic manta ray and a terrestrial robot in the form of a salamander.

Friday, August 28, 2009

Research duo finds cause for disorders



Issue date: 8/28/09
A University professor and graduate student pinpointed a cause of chromosome defects in corn - a major agricultural breakthrough that may further scientific understanding of chromosome disorders such as Down syndrome in humans.

Plant biology professor Kelly Dawe and recently graduated doctoral student Xuexian Li led the research, both spending years on the project, Dawe said.

"This project was one of my ideas I had in my first grant proposal," he said. "It took a while to organize the tools, methods and people."

The pair's hard work paid off, and the research was featured in the advance online publication of the journal Nature Cell Biology this month.

In the study, Dawe and Li found that the loss or degradation of key proteins found in the kinetochore - a protein structure that pulls chromosomes apart - can increase the chance of chromosomes not dividing correctly during meiosis.

Meiosis is the process by which a cell halves the number of chromosomes from 46 to 23 to divide and create sperm and egg sex cells. The final stages of chromosome separation may not happen correctly if the egg is fertilized later in life, Dawe said.

Other researchers are intrigued by the overall implications of the study as well.

"These findings provide new directions on how to conduct similar research in mammals," said Patricia Hunt, Washington State University professor and specialist in reproductive biology and meiosis. "We're riding on the coattails of researchers like Kelly [Dawe] with these big discoveries."

Hunt said Dawe and Li's developments provide new information about the first stage of meiotic division - a complex process scientists are working to understand better.

Since Hunt's interest is in human models, she said analyzing similar structures in human eggs in vitro (examined outside of the body in a laboratory setting) can further enhance researchers' understanding of how some individuals end up with too few or too many chromosome copies.

"These problems arise in the egg. Approximately 10 percent of human pregnancies are chromosomally-abnormal," Hunt said in a telephone interview Tuesday.

"By the time a woman is in her 40s, around half of her eggs are chromosomally-abnormal."

Because women carry their eggs from birth, Dawe and Hunt said eggs degrade and sometimes fail to function properly, much like other aging cells.

Above all, Dawe and Li's research directly influences genetic engineering in agriculture and corn production.

"The research helps to achieve my goal of creating an 'artificial chromosome vector' for crop improvement - a method of adding traits to crops in novel ways," Dawe said. "The idea is to identify all the pieces of a normal chromosome, and then to reconstruct them in a small chromosome that can carry genes of interest."

At the fungal farmer's market, only the best cyanobacteria are for sale


Lichen study has implications for ecosystem research

IMAGE: Cyanobacterial photobionts of tropical cyanolichens of the genera Acantholichen, Coccocarpia, Dictyonema, and Stereocaulon, belong to a previously unrecognized, exclusively lichenized, novel lineage with the name Rhizonema. These photobionts are shared...

Click here for more information.

Lichens are the classic example of a symbiotic relationship. Both the fungal and photobiont components of the lichen benefit from the relationship and often are unable to survive without each other. Recent research by Dr. Robert Lücking (The Field Museum, Chicago), Dr. James Lawrey (George Mason University, Virginia) and a team of colleagues from around the world has put a new spin on this relationship.

In a paper published in the August 2009 issue of the American Journal of Botany (, Lücking et al. explore the possibility of lichens as domesticators, similar to early farmers domesticating grains. By investigating the evolutionary history of a group of cyanobacteria associated with lichens, Lücking and Lawrey and their team have made some surprising conclusions.

Although lichen fungi represent more than 1000 genera, most are associated with photobionts that represent only four genera, one of them believed to be the common and widely distributed cyanobacterial genus Scytonema. However, the identity of photobionts thought to be Scytonema has never been confirmed. Lücking and his colleagues used DNA sequence data to reconstruct evolutionary relationships among free-living members of Scytonema and putative Scytonema photobionts associated with three major fungal lineages.

They discovered that these lichenized photobionts are not members of the genus Scytonema, but form a novel, previously unrecognized, entirely lichenized, lineage of cyanobacteria. The members of this novel lineage, which bears the name Rhizonema, physically appear very similar to free-living members of the genus Scytonema, and members of the two genera can be found close to each other—one lichenized, the other not. Apart from being the first discovery of a completely novel photobiont lineage in lichens using molecular phylogenetics, this find has important implications for ecosystem research because a large proportion of nitrogen-fixing cyanobacteria previously believed to occur in both lichenized and free-living forms now appear to be restricted to lichen symbioses.

Lücking et al. also found that a wide range of lichen fungi that are distantly related with each other but co-occur in the same habitats are associated with members of Rhizonema. This implies that the fungi "share" the cyanobacteria among them, as opposed to evolving in concert with the cyanobacteria, a process that would result in similar evolutionary patterns in the fungal and cyanobacterial components of the lichen.

The authors propose that photobionts are selected based on their compatibility with the mycobionts and their ability to contribute to the establishment and growth of the lichen. This results in an increase in the frequency of particular mycobiont-photobiont pairs, and likewise an increase in the frequency of particular photobionts, which then leads to an increase in the availability of these photobiont strains for other lichen associations. This process may be compared to crop domestication, where farmers develop improved crop varieties and share them with other farmers, leading to higher yields for the farmers and proliferation of the most widely-used varieties. Indeed, the North American lichenologist Trevor Goward has defined lichens as "fungi that discovered agriculture," and this study not only supports this view but adds a further dimension to it.

Aptamer research of Andrew Ellington


My research focuses on using evolutionary techniques to engineer biopolymers and cells. Researchers in my lab select binding species (aptamers) and ribozymes from random sequence populations. We then attempt to apply the selected species to solve real-world problems. For example, we have selected aptamers that can interact tightly and specifically with the Rev protein of HIV-1, and are exploring how these aptamers can be used to block viral replication. Similarly, we have selected ribozymes that can be allosterically activated by a variety of effectors, including proteins, and are using these ribozymes to design and build biosensors that may be useful in diagnosing disease. We also have developed methods for evolving proteins with novel functions, and re similarly attempting to use the evolved proteins in medical or biotechnological applications. For example, we have evolved RNA polymerases that can utilize modified nucleotides. Finally, we have extended our evolutionary approaches to whole organisms, and are attempting to evolve 'unnatural' E. coli (unColi) that can augment their genetic codes with unnatural amino acids. It is hoped that strains of unColi will allow us to generate enzymes with previously unknown or inaccessible structures or activities. While we have largely used evolutionary engineering to effect these changes, we are increasingly relying upon bioinformatics, modeling, and rational design to accelerate evolutionary processes.

Kary Mullis outmaneuvers drug resistant bacteria


Erin Podolak

Nobel Laureate Kary Mullis has developed a new technique for combating deadly drug-resistant bacteria.

Kary Mullis has a way to combat drug-resistant bacteria, he claims, and likens the technique to the illegal possession of marijuana.

“It’s kind of like when you get stopped for a traffic ticket in L.A. and the cop drops a bag of marijuana in the back of your car and then charges you with possession of marijuana,” said the Nobel Laureate. “It’s a very fast, very efficient way to get people off of the street.” Mullis’ technique is comparable to the drug possession scenario because it plants a foreign molecule onto bacteria, which makes the complex an immediate target for an immune response.

The technique is based on the alpha gal epitope, a molecule found in other living organisms that the human immune system does not recognize, and consequently attacks. According to Mullis, this molecule is the reason why organ transplants from pigs are often unsuccessful. However, he claims he has discovered the molecule’s value to humans. “Our immune system can eat it,” said Mullis “The cells in our immune system are always hungry.”

Scientists have not been able to halt the immune response triggered by the molecule. “So why don’t we use it?” said Mullis. According to Mullis, if you can attach the molecule to bacteria, an immune response will eliminate the bacteria, even if the bacterium is resistant to other therapeutics.

Mullis attached an antibody to the alpha gal epitope, which he then attached to pathogenic bacteria. The technique hastened the time needed for the body to produce an immune response to infection in mice. The body can tap into an immune response that is either preexistent or will develop quickly.

Speaking at the annual TED conference in Long Beach, CA earlier this year, Mullis declared success over drug-resistant bacteria. TED is a nonprofit organization that sponsors conferences and talks about controversial or groundbreaking issues. “I feel now like George Bush, mission accomplished,” said Mullis. “I might be doing something dumb like he was at the time, but we’ve gotten it to work.”

According to Mullis researchers from his company, Altermune, tested the technique on mice infected with anthrax. “They all survived. They lived 14 or 28 days until we finally killed them and took them apart to find out what went wrong and why they didn’t die,” said Mullis. ”They didn’t die because they didn’t have anthrax anymore.”

Mullis undertook the project after a close friend died last year of a Staph infection when powerful antibiotics failed to work. Mullis has been working to develop DNA aptamers that can bind to target sites on bacteria. The alpha gal epitope is attached the DNA aptamer, which then binds with the bacteria. The aptamer is programmed to seek out the bacteria and initiate an immune response.

In April, Mullis told an audience of San Jose State University students and faculty that he had a cure for the H1N1 flu. Mullis, who won the Nobel Prize in 1993 for discovering polymerase chain reaction, is a controversial figure in science and known for his strong opinions.

Friday, August 14, 2009

Getting by on six hours of sleep? It’s genetic

updated 4:25 p.m. CT, Thurs., Aug 13, 2009

Most of us need about eight or so hours of sleep a night to perform optimally during the day. But scientists have found a mother and daughter who naturally snooze just six nightly hours, waking up bright-eyed and bushy tailed.

Sleep logs revealed the 44-year-old woman and her 69-year-old mother have been "natural short sleepers" for most of their lives. They both go to bed at about 10 p.m. and rise at 4 or 4:30 a.m.

While that might sound a lot like your schedule, there's a catch: Besides catching fewer Z's, the two family members are also very active. For instance, the mother travels internationally often and dances three or four times a week.

"They really have shorter sleep requirements," said study researcher Ying-Hui Fu, a professor of neurology at the University of California at San Francisco, Mission Bay.

It turns out, the pair are genetically programmed for such abbreviated sleep. They both carry a genetic mutation to the gene DEC2 that Fu and her colleagues found is at least partly responsible for the sleep pattern and probably contributes to so-called sleep homeostasis (how much sleep we need).

Scientists think sleep is controlled by at least two processes, one called circadian rhythm that sets the timing of when we go to sleep and when we wake up, turning some into night owls, for instance. The second is a homeostatic process, which regulates the length of shut-eye.

Though Fu isn't sure how many people carry such a genetic mutation, she said it's probably rare as the researchers found no other carriers in a sample of 250.

To figure out how the genetic mutation impacts sleep, Fu and her colleagues genetically engineered mice to have either two copies of the mutant gene or just one copy.

Compared with the normal mice, those with one mutant gene slept about 1.2 hours less, and mice with two mutant genes slept 2.5 hours less. The mutant mice also bounced back faster than the normal mice from sleep deprivation.

While the results, which will be detailed in the Aug. 14 issue of the journal Science, may not let the habitually late snoozers catch fewer snores, they could ultimately lead to treatment for individuals with sleep disturbances, the researchers note.

Next, Fu and her colleagues hope to find other genes related to sleep homeostasis.

"This is something that gives us a clue that there is a gene that is regulating human sleep homeostasis," Fu told LiveScience. "After we find several [genes], we can get a picture of how this sleep homeostasis mechanism works, how our body regulates how much sleep we need."

Computer Scientist Reveals The Math And Science Behind Blockbuster Movies


ScienceDaily (Feb. 27, 2007) — On Feb. 19 at the annual meeting of the American Association for the Advancement of Science in San Francisco, movie lovers got a behind-the-scenes glimpse at the physics-based simulations that breathe life into fantasy.

"It is an exhaustive task to prescribe the motion of every degree of freedom in a piece of clothing or a crashing wave," says Ron Fedkiw, an assistant professor of computer science at Stanford who will speak about computations used to make solids and fluids more realistic in feature films. "Since these motions are governed by physical processes, it can be difficult to make these phenomena appear natural. Thus, physically based simulation has become quite popular in the special effects industry. The same class of tools useful for computational fluid dynamics is also useful for sinking a ship on the big screen."

Fedkiw's talk is part of a symposium titled "Blockbuster Science: Math and Science Behind Movies and Entertainment," which brought together leaders from industry and academia. The other speakers included Tony DeRose of Pixar in Emeryville, Calif., and Doug Roble of Digital Domain in Venice, Calif. Math Professor Tony Chan of the University of California-Los Angeles will moderate the symposium.

Science at the Oscars

This year, two of the three movies nominated for a special effects Oscar--Poseidon and Pirates of the Caribbean: Dead Man's Chest, both made by Industrial Light & Magic (ILM)-- required heavy numerical simulation, says Fedkiw, who has consulted for ILM for six years. Most recently, the PhysBAM (for Physics Based Modeling) core math engine he developed helped to create realistic water in Poseidon and Davy Jones' tentacles in Dead Man's Chest.

Computer graphics (CG) experts used to have to make a Catch-22 decision. They could run inferior algorithms on many processors or run the best algorithm on only one processor. The problem is that many algorithms do not scale well to larger numbers of processors. But about a year and a half ago Fedkiw figured out how to run a star algorithm on many processors, resulting in special effects unprecedented in their realism.

He designs new algorithms for diverse applications including computational fluid dynamics and solid mechanics, computer graphics, computer vision and computational biomechanics. The algorithms may rotate objects, simulate textures, generate reflections or mimic collisions. Or they may mathematically stitch together slices of a falling water drop, rising smoke wisp or flickering flame to weave realism into CG images.

Fedkiw received screen credits for his work on Poseidon, on Terminator 3: Rise of the Machines for the liquid terminator and the nuclear explosions and on Star Wars: Episode III--Revenge of the Sith for explosions in space battle scenes. "My first love is computational physics and most of my career has been dedicated to that," says Fedkiw, who has published more than 75 research papers in computational physics, computer graphics and vision, as well as a book on level set methods with UCLA's Stanley Osher. Recently he has grown interested in applying computational physics to virtual surgery and modeling of the human face.

Fedkiw is the recipient of a National Academy of Sciences award for innovations in the modeling and numerical simulation of flows and pioneering contributions to physically based computer graphics. He also received a David and Lucile Packard Foundation fellowship for simulations of humans and a Presidential Early Career Award for Scientists and Engineers, the nation's highest honor for professionals at the outset of their independent research careers.

Going Hollywood

Research universities like Stanford play big roles in training the next generation of CG specialists and developing the science and technology that gets applied in movies in innovative ways.

"The simulation of gases, liquids and combustion for scientific reasons quickly translates into the ability to make animations of smoke, water and fire," Fedkiw says. "Similar statements hold for soft biological tissues, muscles, fractures and other solid material problems. Once the scientific numerical simulations are worked out, interesting animations can be made shortly thereafter."

Most of Fedkiw's students double-major in math and computer science. "Graphics itself is a bit less important, and many of them don't take their first graphics class until their junior or senior year of college," Fedkiw says. "I started [learning computer graphics] rather late, working in pure mathematics until I was 23 years old, and then switching to applied mathematics after that. I didn't know anything about computer graphics until 1998. And although I did work on engineering-related problems, I didn't do any work in computer science until I started working with a company in 1998 to learn more about graphics."

Fedkiw earned his doctorate in applied mathematics from UCLA in 1996 and did postdoctoral work at UCLA in mathematics and at Caltech in aeronautics before joining Stanford's Computer Science Department in 2000. He wrote his first two papers for the 2001 SIGGRAPH (short for Special Interest Group for Computer Graphics), an annual CG conference convened by the Association for Computing Machinery (ACM). In 2005, ACM SIGGRAPH honored him with its Significant New Researcher Award for contributions to the computer graphics community.

Getting research experience is important for anyone applying to Stanford's computer science doctoral program. "Connecting with a research group is quite important to do in addition to taking classes," Fedkiw says. He and his students have worked closely with ILM, Pixar, Intel, Honda and Sony Imageworks. "This collaboration with industry is a two-way street and has produced a number of academic papers--as well as some screen credits," he says. "Both the companies and group at Stanford think of this as a highly synergistic relationship."

Fedkiw's favorite movie employing CG is Revenge of the Sith. "When I watched the first [Star Wars movie] at 9 years old, I never dreamed that I'd eventually be helping to make the last one."

Math In The Movies Mathematicians To Thank For Great Graphics


May 1, 2007 — 100 powerful supercomputers perform geometrical, algebraic and calculus-based calculations to animate Pixar's characters. The laws of physics that inform the dynamics of fabric movement are most used in the computations.

Most students in high school dread their math classes and wonder when they will ever use the information in "real life." Now, with so much work being done on computers, the algebra and trigonometry learned in high school is actually being put to good use.

The animation industry is one that can be a math teacher's best friend. It is high school math that can actually help bring animated movies to life. Tony DeRose, a computer scientist at Pixar Animation Studios, realized his love of mathematics could transfer into a real world, real interesting job by bringing the pretend world of animation to life. He told DBIS, "Without mathematics, we wouldn't have these visually rich environments, and visually rich characters."

Advances in math can lead to advances in animation. Earlier math techniques show simple, hard, plastic toys. Now, advances in math help make more human-like characters and special effects. DeRose explains the difference a few years can make, "You didn't see any water in Toy Story, whereas by the time we got to Finding Nemo, we had the computer techniques that were needed to create all the splash effects."

How exactly do the high school math classes help with the animation? Trigonometry helps rotate and move characters, algebra creates the special effects that make images shine and sparkle and calculus helps light up a scene. DeRose encourages people to stick with their math classes. He says, "I remember as a mathematics student thinking, 'Well, where am I ever going to use simultaneous equations?' And I find myself using them every day, all the time now."

The American Mathematical Society and the Mathematical Association of America contributed to the information contained in the TV portion of this report.

BACKGROUND: Pixar Animation Studios is undergoing a digital revolution thanks to advances in areas such as computer technology, computational physics, and approximation theory. Tony Derose provided a behind-the-scenes look at the role that geometry plays in the revolution using examples drawn from Pixar's feature films, such as Toy Story I and II. Upcoming movie characters will be animated using a new advancement in geometry recently developed at Pixar.

ABOUT ANIMATION: The term animation refers generally to graphical displays in which a sequence of images with gradual differences results in the same effect as a photographed movie. Computer generated animations are getting more and more common, replacing hand drawn images and other special techniques. There are several ways to generate dynamic changes in computer graphics. Geometry animation is the most complex, and requires changing the geometric elements of a scene dynamically. This is also what most people generally refer to when using the term "animation," evidenced by motion pictures like "Toy Story" and "A Bug's Life."

HOW PIXAR DOES IT: Perhaps the most difficult aspect of animation is making people and clothing look real. Pixar's software is based on complex studies of how cloth moves when draped on a character, based on the laws of physics. For instance, drape a bedsheet between two points, and the center will hang downward, adjusting itself until it comes to rest in a state of pure tension. The animators begin with drawings of the characters, which they use to build computer puppets, later adding digital "strings" that correspond to various geometric points on the puppet. These strings serve as animation controls, ensuring that as each string is "pulled," the puppet's movements reflect what would occur in real life. Color and lighting effects are added last before the puppet is "animated." Pixar uses 100 powerful supercomputers that run 24 hours a day, seven days a week. It still takes the computers five to six hours to render a single frame lasting 1/24th of a second. For every second of film, it takes the computer six days.

WHAT IS GEOMETRY? Geometry is the field of mathematical knowledge dealing with spatial relationships. The earliest written records -- dating from Egypt and Mesopotamia about 3100 BC -- demonstrate that ancient peoples had already begun to devise mathematical rules and techniques useful for surveying land areas, constructing buildings, and measuring storage containers. Beginning about the 6th century BC, the Greeks gathered and extended this practical knowledge and from it generalized the abstract subject now known as geometry, from the combination of the Greek words geo ("Earth") and metron ("measure") for the measurement of the Earth.

'Bacterial Computers': Genetically Engineered Bacteria Have Potential To Solve Complicated Mathematical Problems


ScienceDaily (July 24, 2009) — US researchers have created 'bacterial computers' with the potential to solve complicated mathematics problems. The findings of the research demonstrate that computing in living cells is feasible, opening the door to a number of applications. The second-generation bacterial computers illustrate the feasibility of extending the approach to other computationally challenging math problems.

A research team made up of four faculty members and 15 undergraduate students from the biology and mathematics departments at Missouri Western State University in Missouri and Davidson College in North Carolina, USA engineered the DNA of Escherichia coli bacteria, creating bacterial computers capable of solving a classic mathematical problem known as the Hamiltonian Path Problem.

The research extends previous work published last year in the same journal to produce bacterial computers that could solve the Burnt Pancake Problem.

The Hamiltonian Path Problem asks whether there is a route in a network from a beginning node to an ending node, visiting each node exactly once. The student and faculty researchers modified the genetic circuitry of the bacteria to enable them to find a Hamiltonian path in a three-node graph. Bacteria that successfully solved the problem reported their success by fluorescing both red and green, resulting in yellow colonies.

Synthetic biology is the use of molecular biology techniques, engineering principles, and mathematical modeling to design and construct genetic circuits that enable living cells to carry out novel functions. "Our research contributed more than 60 parts to the Registry of Standard Biological Parts, which are available for use by the larger synthetic biology community, including the newly split red fluorescent protein and green fluorescent protein genes," said Jordan Baumgardner, recent graduate of Missouri Western and first author of the research paper. "The research provides yet another example of how powerful and dynamic synthetic biology can be. We used synthetic biology to solve mathematical problems; others find applications in medicine, energy and the environment. Synthetic biology has great potential in the real world."

According to Dr. Eckdahl, the corresponding author of the article, synthetic biology affords a new opportunity for multidisciplinary undergraduate research training. "We have found synthetic biology to be an excellent way to engage students in research that connects biology and mathematics. Our students learn firsthand the value of crossing traditional disciplinary lines."

Journal references:

  1. Jordan Baumgardner, Karen Acker, Oyinade Adefuye, Samuel THOMAS Crowley, Will DeLoache, James O Dickson, Lane Heard, Andrew T Martens, Nickolaus Morton, Michelle Ritter, Amber Shoecraft, Jessica Treece, Matthew Unzicker, Amanda Valencia, Mike Waters, A. M. Campbell, Laurie J. Heyer, Jeffrey L. Poet and Todd T. Eckdahl. Solving a Hamiltonian Path Problem with a bacterial computer. Journal of Biological Engineering, (in press) [link]
  2. Haynes et al. Engineering bacteria to solve the Burnt Pancake Problem. Journal of Biological Engineering, 2008; 2 (1): 8 DOI: 10.1186/1754-1611-2-8
Adapted from materials provided by BioMed Central, via EurekAlert!, a service of AAAS.

Algebra Adds Value To Mathematical Biology Education


ScienceDaily (Aug. 3, 2009) — As mathematics continues to become an increasingly important component in undergraduate biology programs, a more comprehensive understanding of the use of algebraic models is needed by the next generation of biologists to facilitate new advances in the life sciences, according to researchers at Sweet Briar College and the Virginia Bioinformatics Institute (VBI) at Virginia Tech.

VBI Professor Reinhard Laubenbacher and Sweet Briar College Mathematical Sciences Professor Raina Robeva have highlighted algebraic models as one of the diverse mathematical tools needed in the professional development of up-and-coming life scientists in a new article in Science. Despite this critical need, the authors explain, algebraic models have played a less substantial role in undergraduate curricula than other methods.

Future generations of biologists will routinely use mathematical and computational approaches to develop and frame hypotheses, design experiments, and analyze results. Sound mathematical models are essential for this purpose and are currently used in the field of systems biology to understand complex biological networks. Two types of mathematical models, in particular, have been successfully used in biology to reproduce network structure and dynamics: Continuous-time models derived from differential equations (DE models) focus on the kinetics of biochemical reactions, while discrete-time algebraic models built from functions of finite-state variables focus on the logic of the connections of network variables. According to Laubenbacher and Robeva, while DE models have been included more often in undergraduate curricula integrating mathematics and biology, algebraic models should also be viewed as an important training component for students at all education levels.

"Discrete-time algebraic models created from finite-state variables, such as Boolean networks, are increasingly being used to model a variety of biochemical networks, including metabolic, gene regulatory, and signal transduction networks," says Laubenbacher. "Often, researchers do not have enough of the information required to build detailed quantitative models. Algebraic models need less information about the system to be modeled, making them useful for instances where quantitative information may be missing. All the work that goes into building them can then be used to construct detailed kinetic models, when additional information becomes available. In addition, algebraic models are much more intuitive than differential equations models, which makes them more easily accessible to life scientists."

Using algebraic models is a relatively quick, easy and reliable way for students to integrate mathematical modeling into their life sciences coursework. Creating algebraic models of biochemical networks requires only a modest mathematical background, which is usually provided in a college algebra course. Without the complexities involved in teaching students how to construct more complicated models, algebraic models make the introduction of mathematical modeling into life sciences courses more accessible for faculty members as well.

According to Robeva, "The exciting thing about algebraic models from an educational perspective is that they highlight aspects of modern-day biology and can easily fit in both the biology and mathematics curricula. At the introductory level, they provide a quick path for introducing biology students to constructing and using mathematical models in the context of contemporary problems such as gene regulation. At the more advanced level, the general study and analysis of such models often require sophisticated mathematical theories. This makes them perfect for inclusion into mathematics courses, where the biology can provide a meaningful framework for many of the abstract structures. As educators, we should actively be looking for the best ways to seize this opportunity for advancing mathematical biology."

World's Smallest Computers Made of DNA and Other Biological Molecules Made to 'Think' Logically

ScienceDaily (Aug. 3, 2009) — Biomolecular computers, made of DNA and other biological molecules, only exist today in a few specialized labs, remote from the regular computer user. Nonetheless, Tom Ran and Shai Kaplan, research students in the lab of Prof. Ehud Shapiro of the Weizmann Institute’s Biological Chemistry, and Computer Science and Applied Mathematics Departments have found a way to make these microscopic computing devices ‘user friendly,’ even while performing complex computations and answering complicated queries.

Shapiro and his team at Weizmann introduced the first autonomous programmable DNA computing device in 2001. So small that a trillion fit in a drop of water, that device was able to perform such simple calculations as checking a list of 0s and 1s to determine if there was an even number of 1s. A newer version of the device, created in 2004, detected cancer in a test tube and released a molecule to destroy it. Besides the tantalizing possibility that such biology-based devices could one day be injected into the body – a sort of ‘doctor in a cell’ locating disease and preventing its spread – biomolecular computers could conceivably perform millions of calculations in parallel.

Now, Shapiro and his team, in a paper published online August 3 in Nature Nanotechnology, have devised an advanced program for biomolecular computers that enables them to ‘think’ logically.

The train of deduction used by this futuristic device is remarkably familiar. It was first proposed by Aristotle over 2000 years ago as a simple if…then proposition: ‘All men are mortal. Socrates is a man. Therefore, Socrates is mortal.’ When fed a rule (All men are mortal) and a fact (Socrates is a man), the computer answered the question ‘Is Socrates Mortal?’ correctly. The team went on to set up more complicated queries involving multiple rules and facts, and the DNA computing devices were able to deduce the correct answers every time. At the same time, the team created a compiler – a program for bridging between a high-level computer programming language and DNA computing code. Upon compiling, the query could be typed in something like this: Mortal(Socrates)?. To compute the answer, various strands of DNA representing the rules, facts and queries were assembled by a robotic system and searched for a fit in a hierarchical process. The answer was encoded in a flash of green light: Some of the strands had a biological version of a flashlight signal – they were equipped with a naturally glowing fluorescent molecule bound to a second protein which keeps the light covered. A specialized enzyme, attracted to the site of the correct answer, removed the ‘cover’ and let the light shine. The tiny water drops containing the biomolecular data-bases were able to answer very intricate queries, and they lit up in a combination of colors representing the complex answers.

Prof. Ehud Shapiro’s research is supported by the Clore Center for Biological Physics; the Arie and Ida Crown Memorial Charitable Fund; the Phyllis and Joseph Gurwin Fund for Scientific Advancement; Sally Leafman Appelbaum, Scottsdale, AZ; the Carolito Stiftung, Switzerland; the Louis Chor Memorial Trust Fund; and Miel de Botton Aynsley, UK. Prof. Shapiro is the incumbent of the Harry Weinrebe Chair of Computer Science and Biology.

Wednesday, August 12, 2009

How 6 people accidentally found a fortune

  • Story Highlights
  • Man buys Martin Johnson Heade painting for $30 and sells it for $1.2 million
  • Woman with metal detector found crucifix priced at more than $63,000
  • Arkansas park is the only diamond site in the world that's open to the public
  • Possible Jackson Pollock painting bought for $5 may be worth $100 million

By Rob Lammle
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Mental Floss

(Mental Floss) -- We've all been there: a week until payday, the rent is due, and you're rummaging in your parents' attic to find Dad's Mickey Mantle rookie card.

Only 36 of 200 official copies of the Declaration of Independence have been found intact since 1820.

Only 36 of 200 official copies of the Declaration of Independence have been found intact since 1820.

If you're in need of some quick cash, here are six stories of people who found a fortune when -- and where -- they least expected it.

1. Lose a hammer, find a horde

In November 1992, a farmer living near the village of Hoxne in Suffolk, England, lost a hammer in one of his fields, so he asked Eric Lawes to use his metal detector to search for it.

While looking for the hammer, Lawes happened upon something else of interest -- 24 bronze coins, 565 gold coins, 14,191 silver coins, plus hundreds of gold and silver spoons, jewelry, and statues, all dating back to the Roman Empire.

As required by British law, the so-called "Hoxne Hoard" was reported to the local authorities, who declared it a "Treasure Trove," meaning it was now legally the property of Britain.

However, the government is required to pay fair market value for a treasure trove, meaning the farmer and Lawes split a cool £1.75 million (about $2.8 million).

The Hoxne Hoard is now on permanent display at the British Museum, drawing thousands of people every year.

Sadly, there is no word on whether or not the hammer was ever found.

2. Arkansas is a girl's best friend

W.O. Bassum found a giant of a gemstone in 1924 -- a 40.23 carat diamond.

It might surprise you to hear that he wasn't digging in one of the famous South African diamond mines at the time, but was near Murfreesboro, Arkansas, at a site that is now the Crater of Diamonds State Park.

Sitting on top of a volcanic pipe (a geologic tube formed by an ancient underground volcanic explosion), the park is the only diamond site in the world that is open to the public.

Best of all, the park's policy is: "You find it. You keep it. No matter how valuable it is."

Bassum's big find -- nicknamed "The Uncle Sam Diamond," the largest diamond ever discovered in North America -- was later cut down to 12.42 carat and sold for $150,000 in 1971 (About $800,000 today).

But his wasn't the last valuable rock dug out of that Arkansas soil.

In 1964, "The Star of Murfreesboro" was discovered at the same site, weighing in at 34.25 carat.

Then, in 1975, came the 16.37 carat "Amarillo Starlight Diamond."

The 6.35 carat "Roden Diamond" was found in 2006.

And the crown jewel of the park has been the "Strawn-Wagner Diamond," a comparatively small 3.09 carat diamond, that was dug up in 1990, and expertly cut down to 1.90 carat.

Despite its smaller size, the Strawn-Wagner stands out because it was given a "Perfect" rating by the American Gem Society -- the first diamond to ever receive such a high grade.

But don't think this list of big gems means the site has been tapped out. On average, two diamonds are found every day at Crater of Diamonds.

They're not all as big as The Uncle Sam Diamond, but maybe you'll get lucky. There's only one way to find out... Mental Floss: 10 diamond-encrusted things you don't need

If getting your hands dirty isn't your idea of fun, maybe you should start hitting garage sales and thrift stores to find valuables buried among the castoff bread machines and Members Only jackets.

Sometimes, one man's trash really is another man's treasure.

3. The Declaration of (financial) Independence

We've all heard of the man who bought a $4 painting at a garage sale, found an original copy of the Declaration of Independence inside, and sold it for $2.4 million. A once-in-a-lifetime story, right?

Not so much, actually.

Michael Sparks was visiting a Nashville thrift store, where he bought a candleholder, a set of salt and pepper shakers, and a yellowed print of the Declaration of Independence.

Sparks figured the document was a worthless, modern reprint, so he paid the asking price -- $2.48 -- and headed home.

After looking over the document for a few days, he wondered if it might be older than he initially thought.

So he hopped on the Internet to do some research and soon realized he had purchased one of only 200 official copies of the Declaration of Independence commissioned by John Quincy Adams in 1820.

Of those 200, 35 had been found intact; he had number 36.

It took a year for Sparks to have the print authenticated and preserved, and then he put it up for auction, netting a final sale price of $477,650.

The salt and pepper shakers, on the other hand, were still worthless.

4. A good Heade for bargains

One day, an employee at a tool-and-die company in Indiana spent $30 for a few pieces of used furniture and an old painting of some flowers.

When he got his new stuff home, he decided to strategically hang the picture to cover up a hole in the wall that had been bugging him.

Some years later he was playing a board game called Masterpiece in which players attempt to outbid one another for artwork at an auction.

Much to his surprise, one of the cards in the game featured a painting of flowers that looked a lot like the one he had on his wall.

So he went online and found that his painting was similar in style to the work of Martin Johnson Heade, an American still-life artist best known for landscapes and flower arrangements.

Through his research he found the Kennedy Galleries in Manhattan, which handles many of Heade's works, and asked them to take a look at his painting.

They agreed and were able to verify that the piece of artwork covering the hole in his wall was a previously unknown Heade painting, since named Magnolias on Gold Velvet Cloth.

In 1999, The Museum of Fine Arts in Houston purchased the painting for $1.2 million dollars.

I emailed the Museum to ask if the painting was covering a hole in the wall, but I didn't get a reply. Mental Floss: 6 really strange truck spills

As you go in search of your nest egg, keep in mind the old adage: "It's only worth what the market will bear."

Sometimes finding treasure is the easy part; finding someone willing to buy it can be the real challenge.

5. It's nice, but it's no Middleham Jewel...

Every Sunday afternoon for the last seven years, Mary Hannaby had gone for a walk with her metal detector.

She'd never really found anything of value, but she liked getting the exercise, so she kept at it.

On one Sunday in June 2009, her detector beeped, and she bent down to dig up what she thought was going to be another common coin or old nail. Instead, she uncovered a postage stamp-sized gold pendant featuring an intricate carving of the crucifixion of Jesus.

Maybe she had finally hit the jackpot.

Upon inspection by the British Museum, the pendant was described as "an important find," and they estimated the market value to be around £4,000 (about $6,600).

Still, they decided not to purchase it for their collection, so Mary took the pendant to Sotheby's.

The experts at the auction house felt the piece was much more valuable, because it was believed to be one of only three similar items known to exist. Their initial estimate was £250,000 ($415,900), but said it could easily sell for as much as £2.5 million ($4.1 million) thanks to its resemblance to another English treasure also found with a metal detector, the Middleham Jewel.

But as the saying goes, "Never count your millions until the auctioneer bangs his gavel."

Sotheby's put the pendant up for auction on July 9, 2009, making it the highlight of a large lot of antique sculptures.

Clearly the expectations were high. The bidding started at £30,000 (about $49,900), but as the final call was made, the best offer was only £38,000 (about $63,200) -- far below the reserve price to make a sale. Mental Floss: 6 articles of clothing that caused riots

6. A possible Pollock

In 1992, Teri Horton, a retired truck driver, went to her local thrift store to buy a depressed friend a gag gift.

She found a rather large painting -- 66 inches by 47 inches -- that she thought was pretty amusing because it was, in her opinion, so ugly. When she asked the thrift store employee the price, they said $8. She haggled and only paid $5.

In the end, her friend didn't want it (she, too, thought it was ugly, plus it wouldn't fit through the door of her trailer), so Teri took it home and tried to unload it at her garage sale.

A local art teacher saw the painting and suggested it could very well be a Jackson Pollock. In response, Teri famously asked the teacher, "Who the f*** is Jackson Pollock?"

Since that day, Teri Horton has been struggling to prove that her thrift store treasure is a lost piece of artwork potentially worth well over $100 million.

However, due to the painting's lack of verifiable history of ownership (called "provenance"), the piece is disputed by many fine arts experts as simply another artist's work inspired by Pollock.

To find proof of Pollock, Teri had the work examined by a forensic specialist who claims to have found a fingerprint that matches one in Pollock's studio.

But even the fingerprint evidence has been disputed by the art world, leaving the painting, as yet, unsold.

Teri, her painting, and her battle with the art world elite became the subject of a 2006 documentary called, appropriately, Who the *$&% is Jackson Pollock?


Thursday, August 6, 2009

Apple cakes save home from foreclosure

Story Highlights
New Jersey actress turned to baking apple cakes to avoid foreclosure
The idea came from brainstorming with a consumer credit counselor
She resolved to sell 100 cakes in 10 days at $40 each to pay mortgage, debts
So far, she's sold about 200 cakes, attracting the attention of an Internet retailer

By Allan ChernoffCNN Senior Correspondent

TEANECK, New Jersey (CNN) -- Actress Angela Logan has played many roles off-stage to earn a living. She's worked as a teacher, model and hairdresser and is studying to be a nurse.

A contractor promised to renovate Logan's home. Instead, she says he took the money and left the job unfinished.

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But when she fell into foreclosure on her Teaneck, New Jersey, home, Logan turned to baking an apple cake her family had always loved.
"It was a flash of desperation," Logan said. "I thought, 'Wow. We could sell these cakes, they're so good.' "
Logan named her delicacy Mortgage Apple Cake and resolved to sell 100 in 10 days at $40 each to meet a mortgage payment, pay off bills and qualify for a federal program that could lower her monthly payments.
She advertised the cake to everyone she knew, including her classmates.
"The hardest part was saying, 'Can you buy my cakes, this is my problem,' because admitting to your friends that you're in foreclosure, and that you need their help, that's a hard thing to say," Logan said.
Two years ago, a contractor promised to renovate Logan's brick-and-stucco home. But instead, Logan says he took the money and did only a portion of the work -- leaving the entire second floor bare to the beams and plastic wrap still covering much of the exterior.
Don't Miss
In Depth: Money & Main St. Home sweet home: How Angela Logan saved her house by baking
Logan's financial squeeze tightened when one of the actress' talent agencies shut down without paying her for commercial work.
The 55-year-old divorced mother of three fell far behind on her mortgage and other debt payments, leading her to seek help from Consumer Credit Counseling of New Jersey. Counselor Pamela Glass brainstormed with Logan to envision potential extra sources of income.
"We put our heads together to make extra money," Glass said. "I said, 'Take a look at what you can do.' She said, 'I bake once in a while'. I said, 'Well, maybe you can do some baking.' "
When Logan asked, neighbors, fellow church congregants and classmates responded. Soon she was baking night and day, two cakes at a time. Al Hamdi, general manager of the Hilton in nearby Hasbrouck Heights, heard of Logan's plan and offered the hotel's four giant ovens, letting her accelerate production.
"She was going to do something out of the box to save her home and her family. That was the inspiring part for us," Hamdi said.
Logan figures she's baked about 200 cakes -- double her goal. And since qualifying for the federal Make Home Affordable program, her monthly mortgage payment is dropping by nearly 20 percent
Other Americans in a financial bind can also find creative answers to their cash crunch, Logan said.
"Find your talent. Find something you can do that will help," she said. Watch as Logan describes the circumstances that led her to bake the Mortgage Apple Cake »
Many hobbies have the potential to generate extra cash: teaching a skill like playing an instrument or speaking a foreign language; home repairs for those who are handy; even dog-walking or pet-sitting for animal lovers.
"Some people have extra skills they don't use," Glass said.
Internet retailer Bake Me A Wish! got a whiff of the Mortgage Apple Cake and is preparing to mass-produce it and share the proceeds with Logan. The company says it already has 650 Mortgage Apple Cake orders.
"We're going to be baking cakes together, develop a whole line of cakes, Angela Logan Cakes," said Josh Kaye, president of Bake Me A Wish!
Escaping foreclosure could propel Logan to a new career in baking. But she's still studying nursing, knowing from experience never to depend upon just one role.


Monday, August 3, 2009

Six things to do if they take the job offer back

Story Highlights
With recession, job offers are rescinded or starting dates pushed back
Be professional -- how you react may determine if the offer returns
Expert: Do not stop looking for work until your first day at a new job
Before accepting a job, ask about the employer's financial health

by Rachel writer

Editor's note: has a business partnership with, which serves as the exclusive provider of job listings and services to

"Your reaction to the retraction of a job offer may determine whether the offer is ever returned.

Fired before you're hired
is a trend that's becoming more common as with the stagnating. As companies downsize and institute hiring freezes, job seekers are finding start dates pushed back and job offers withdrawn completely.

"Job offers are rescinded for a variety of reasons. Some [are] external, such as the overall economy, some [are] internal such as a department's funding is cut," says Laura George, author of "Excuse Me, Your Job is Waiting." "There are also times when it's determined that a person is needed but it would be more cost-effective to hire one person to work in two or more departments and spread the costs."
No matter the reason your job offer is repealed, experts agree that you should respond to the situation in a professional manner and get to the bottom of what happened.
"If your offer has been rescinded, you must find out what the exact reasons behind the decision were. Were they economically based or due to a background, drug or reference check?" says Jonathan Mazzocchi, partner and general manager of the New York accounting and finance division of Winter, Wyman. "As hard as it is, gather the facts. Try to separate the people you interviewed with from the organization's decision, and keep all of your interactions professional."
In Graham's case, for example, when the first offer was revoked, the company never explained what was going on; they just said the paperwork was in and they were waiting. In the meantime, she lived off her savings and put her job search on hold. The second company, which told her the job was placed on hold "indefinitely," said they would keep her mind for the future, but she hasn't heard anything yet.
"Once I found out that my offer was no longer viable, I quickly started to search for another position, but it was more difficult to find something by that time," she says.
Now what?
Unfortunately, you don't have many legal rights in this situation. Most states have employment-at-will policies, which means employees can be terminated at any time, for any reason. You should think long and hard before pursuing legal action if a job offer is revoked -- litigation costs will be extensive and you will undoubtedly burn bridges with your would-be employer. Consult an HR expert or lawyer in your area about your options.

It's important to handle the situation professionally if you find yourself with a rescinded job offer. Here are six steps you can take to protect yourself:
1. Find out why
Find out the exact reason behind the withdrawn offer.
2. Be open and honest
" If you are still interested in the job, let them know your finances. Can you wait six months to start?"
Or, let the employer know you will wait for the full-time position.
"If you simply can't wait for the position to re-open, don't be shy about it," Luzar says. "You came looking for a job because you needed one. Respectively tell them so that if you are looking for a job again in the future, they will still have a high opinion of you."
3. Prepare yourself
"Graham says the biggest lesson she learned was that nothing is a done deal until you are sitting in your new office or cubicle.
4. Do your homework
Doughtery says, "Before accepting a job offer, it's important to ask if the position is approved, Ask if an offer was ever withdrawn and if so, what was done in the past. If the withdrawal of a vacant position is a real threat, ask if your offer letter can state what the company will do if the job offer is withdrawn."
5. Negotiate
If you left an old job to work for a new company , you can try to negotiate unemployment benefits or a severance package from the employer, Mazzocchi says. Or, you can try negotiating for a lower salary or position.
6. Move on
Roberta Chinsky Matuson, president of Human Resource Solutions, says"If nothing comes from negotiating with your would-be companies others taht expressed interest in the past and let them know you are still available". Don't badmouth the organization that pulled back your offer.
In the meantime, continue your job search, going to school to maintain and enhance your skills, volunteering with nonprofit organizations and growing your own business.
"Keep positive. Something viable will eventually come your way if you don't give up."
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