Category Archives: Education

Science and the City: Science Barge

Science and the City is (among other things) an excellent podcast series from the New York Academy of Science. The latest podcast discusses the science barge project we posted about earlier. They discuss looking at commercially viable urban farms (on rooftops in NYC) and the establishing educational gardens at schools.

See the Curious Cat Science and Engineering Podcast Directory for some great resources for podcasts. Don’t miss the naked scientists from the BBC.

University Web Presence Rankings

The Webometrics Ranking of University Web Sites provides some interesting data. I don’t remember reading this last year, but they state on the site now: “The original aim of the Ranking was to promote Web publication, not to rank institutions. Supporting Open Access initiatives, electronic access to scientific publications and to other academic material are our primary targets.” I support those goals, I am not totally convinced this is the most effective measure to do that but it provides one way of ranking web presence of universities. I am not that convinced this does a good job of ranking the web presences of universities but I think it is of some interest so I decided to post on the results.

graph of universities web presence

Country	% top 200	% top 500	% World Population	Jiao Tong top 101
USA	53	37.8	4.6	54
Germany	7.5	9.4	1.3	6
United Kingdom	5.5	7.2	0.9	11
Canada	8.5	5	0.5	4
Australia	3	2.8	0.3	2
Italy	0.5	2.8	0.9	1
Japan	1.5	2.4	2	6
France	0.5	2.4	0.9	4
Netherlands	4	2.2	0.3	2
Sweden	3	2	0.1	4
Switzerland	2	1.6	0.1	3
Taiwan	0.5	1.6	0.4	0
Finland	0.5	1.4	0.1	1
China	0.5	1.2	20.1	0
Portugal	0	1.2	0.2	0

Life After the Chernobyl Nuclear Accident

Silent Spring by Lauren Monaghan, Cosmos

Ever since, a 30 km ‘exclusion zone’ has existed around the contaminated site, accessible to those with special clearance only. It’s quite easy, then, to conjure an apocalyptic vision of the area; to imagine an eerily deserted wasteland, utterly devoid of life.

But the truth is quite the opposite. The exclusion zone is teeming with wildlife of all shapes and sizes, flourishing unhindered by human interference and seemingly unfazed by the ever-present radiation. Most remarkable, however, is not the life buzzing around the site, but what’s blooming inside the perilous depths of the reactor.

Sitting at the centre of the exclusion zone, the damaged reactor unit is encased in a steel and cement sarcophagus. It’s a deathly tomb that plays host to about 200 tonnes of melted radioactive fuel, and is swarming with radioactive dust.

But it’s also the abode of some very hardy fungi which researchers believe aren’t just tolerating the severe radiation, but actually harnessing its energy to thrive.

“Our findings suggest that [the fungi] can capture the energy from radiation and transform it into other forms of energy that can be used for growth,” said microbiologist Arturo Casadevall from the Albert Einstein College of Medicine at Yeshiva University in New York, USA.
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Taken together, the researchers think their results do indeed hint that fungi can live off ionising radiation, harnessing its energy through melanin to somehow generate a new form of biologically usable growing power.

If they’re right, then this is powerful stuff, said fungal biologist Dee Carter from the University of Sydney. The results will challenge fundamental assumptions we have about the very nature of fungi, she said.

It also raises the possibility that fungi might be using melanin to secretly harvest visible and ultraviolet light for growth, adds Casadevall. If confirmed, this will further complicate our understanding of these sneaky organisms and their role in ecosystems.

Pretty amazing stuff. It really is great all that nature gives us to study and learn about using science.

Learning How Viruses Evade the Immune System

photo of Naama Elefant

MicroRNA genes are a class of very tiny genes found in a variety of organisms. First discovered in 1993 and at the time considered relatively unimportant, they are now recognized as major players in diverse biological processes.

MicroRNAs are important regulators of protein production. Proteins, the building blocks of the cell, must be produced precisely at the right time and place. MicroRNAs specifically latch on to other genes (their targets) and inhibit the production of the protein products of these genes. Hundreds of microRNAs have already been discovered, but the identity of their target genes remains mostly unknown and presents a great challenge in the field.

Elefant developed a computer algorithm that predicts the targets of microRNAs. Her algorithm, named RepTar, searches the thousands of genes in the human genome and through sequence, structural and physical considerations detects matches to hundreds of microRNAs.

For her work in this field, Naama Elefant, a student of Prof. Hanah Margalit of the Faculty of Medicine at the Hebrew University and an Azrieli fellow, was named one of this year’s winners of the Barenholz Prizes for Creativity and Originality in Applied Computer Science and Computational Biology. This discovery also was declared by the magazine Nature Medicine as ”one of the ten notable advances of the year 2007.”
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Science Based Triathlete

The Making of a Olympian by Arianne Cohen

In a break with training orthodoxy, Potts and his coach have created a regimen called feedback training in which the training plan is reassessed every 24 hours based on the constant monitoring of three variables: wattage (the power Potts’s body produces), cadence (the tempo of his arm and leg movements) and heart rate. No lap times. No mileage. No grand training schedules planned months in advance. Only raw biological data. “My coach and I talk a lot about engines,” Potts says. “In auto racing, you want to put out the highest amount of power with the least amount of fuel. We do the same thing. My heart and lungs are my engine. The goal is to always increase the efficiency of the engine.”

Every night, Doane analyzes his athlete’s response to the day’s training. He’s looking for the best way to expand Potts’s aerobic capacity, power output and lactate threshold, without overtraining. If Doane sees that Potts’s heartbeat has been sluggish—say, beating 140 times per minute while Potts is trying to produce 410 watts—that means his body is struggling to recover from earlier training, so he’ll dial back the intensity of his workouts. If, on the other hand, his heart rate stays in the sweet spot around 165 while he churns through a series of 360- to 400-watt intervals, that means he’s fully recovered and ready to be pushed again. “We’ve created a feedback loop,” Doane says. In other words, Doane subjects Potts to a careful dose of punishment, and Potts’s body tells Doane, through empirical data, what he needs to do next.

Nice article. As it mentions really almost all Olympic athletes today use a great deal of science in their training.

Why ‘Licking Your Wounds’ Works

Why ‘Licking Your Wounds’ Actually Works

scientists found that histatin, a small protein in saliva previously only believed to kill bacteria was responsible for the healing.

To come to this conclusion, the researchers used epithelial cells that line the inner cheek, and cultured in dishes until the surfaces were completely covered with cells. Then they made an artificial wound in the cell layer in each dish, by scratching a small piece of the cells away.

In one dish, cells were bathed in an isotonic fluid without any additions. In the other dish, cells were bathed in human saliva. After 16 hours the scientists noticed that the saliva treated “wound” was almost completely closed. In the dish with the untreated “wound,” a substantial part of the “wound” was still open. This proved that human saliva contains a factor which accelerates wound closure of oral cells.

Because saliva is a complex liquid with many components, the next step was to identify which component was responsible for wound healing. Using various techniques the researchers split the saliva into its individual components, tested each in their wound model, and finally determined that histatin was responsible.

Awesome Robot: uBot-5

Cool video on the uBot-5 from UMass Amherst.

The uBot-5 is dynamically stable, using two wheels in a differential drive configuration for mobility. Dynamically stable robots are well suited to environments designed for humans where both a high center of mass and a small footprint are often required.

via: Pop Culture and Engineering Intersect

Toyota has long been interested in personal robot assistants. And the uBot-5, under development at UMass-Amherst, is also looking to meeting that need: Robot developed by computer scientists to assist with elder care:

Baby boomers are set to retire, and robots are ready to help, providing elder care and improving the quality of life for those in need.
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The uBOT-5 carries a Web cam, a microphone, and a touch-sensitive LCD display that acts as an interface for communication with the outside world. “Grandma can take the robot’s hand, lead it out into the garden and have a virtual visit with a grandchild who is living on the opposite coast,” says Grupen, who notes that isolation can lead to depression in the elderly.

Grupen studied developmental neurology in his quest to create a robot that could do a variety of tasks in different environments. The uBot-5’s arm motors are analogous to the muscles and joints in our own arms, and it can push itself up to a vertical position if it falls over. It has a “spinal cord” and the equivalent of an inner ear to keep it balanced on its Segway-like wheels.

Such robots have a huge market waiting for them if engineers can provide models that can be useful at the right price. The future of such efforts looks very promising.

Microbes Beneath the Sea Floor

This stuff is cool. Here is the full press release from Penn State, Microbes beneath sea floor genetically distinct

Tiny microbes beneath the sea floor, distinct from life on the Earth’s surface, may account for one-tenth of the Earth’s living biomass, according to an interdisciplinary team of researchers, but many of these minute creatures are living on a geologic timescale.

“Our first study, back in 2006, made some estimates that the cells could double every 100 to 2,000 years,” says Jennifer F. Biddle, PhD. recipient in biochemistry and former postdoctoral fellow in geosciences, Penn State. Biddle is now a postdoctoral associate at the University of North Carolina, Chapel Hill.

The researchers looked at sediment samples from a variety of depths taken off the coast of Peru at Ocean Drilling Site 1229. They report their findings in today’s (July 22) online issue of the Proceedings of the National Academy of Sciences.

“The Peruvian Margin is one of the most active surface waters in the world and lots of organic matter is continuously being deposited there,” says Christopher H. House, associate professor of geoscience. “We are interested in how the microbial world differs in the subsea floor from that in the surface waters.”

The researchers used a metagenomic approach to determine the types of microbes residing in the sediment 3 feet, 53 feet, 105 feet and 164 feet beneath the ocean floor. The use of the metagenomics, where bulk samples of sediment are sequences without separation, allows recognition of unknown organism and determination of the composition of the ecosystem.

“The results show that this subsurface environment is the most unique environment yet studied metagenomic approach known today,” says House. “The world does look very different below the sediment surface.” He notes that a small number of buried genetic fragments exist from the water above, but that a large portion of the microbes found are distinct and adapted to their dark and quiet world.

The researchers, who included Biddle; House; Stephan C. Schuster, associate professor; and Jean E. Brenchley, professor, biochemistry and molecular biology, Penn State; and Sorel Fitz-Gibbon, assistant research molecular biologist at the Center for Astrobiology, UCLA, found that a large percentage of the microbes were Archaea, single-celled organisms that look like Bacteria but are different on the metabolic and genetic levels. The percentage of Archaea increases with depth so that at 164 feet below the sea floor, perhaps 90 percent of the microbes are Archaea. The total number of organisms decreases with depth, but there are lots of cells, perhaps as many as 1,600 million cells in each cubic inch.
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Science and the Excitement, the Mystery and the Awe of a Flower

Pleasure of Finding Things Out by Richard P. Feynman is a great explanation of how scientists think: “The science knowledge only adds to the excitement, the mystery and the awe of a flower”

I did post on this before. Related book: Classic Feynman: All the Adventures of a Curious Character.

Pseudogap and Superconductivity

MIT physicists shed light on key superconductivity riddle

Hudson’s team is focusing on the state of matter that exists at temperatures just above the temperature at which materials start to superconduct. This state, known as the pseudogap, is poorly understood, but physicists have long believed that characterizing the pseudogap is important to understanding superconductivity.

In their latest work, published online on July 6 in Nature Physics, they suggest that the pseudogap is not a precursor to superconductivity, as has been theorized, but a competing state. If that is true, it could completely change the way physicists look at superconductivity, said Hudson.

“Now, if you want to explain high-temperature superconductivity and you believe the pseudogap is a precursor, you need to explain both. If it turns out that it is a competing state, you can instead focus more on superconductivity,” he said.