Category Archives: Students

Items for students and others, interested in learning about science and engineering and the application of science in our lives. We post many of the general interest items here.

Darwin’s Jellyfishes

Palau’s marine-lake jellyfish actually diverged very quickly from their common ancestor, the spotted jellyfish. Like other jellyfish, the spotted jellies are cnidarians, a scientific grouping that includes reef-building corals. The spotted jellyfish drift in Palau’s lagoon, zapping the occasional zooplankton with their stinging nettles and absorbing the sugary by-products of photosynthesizing algae living in their tissues.

Like many jelly species, the spotted jellyfish has a multi-stage life cycle. Adult males and females with the familiar bell-shaped bodies are called medusae, but you would not recognize very young jellyfish as jellyfish at all. After medusae release eggs and sperm into the water, fertilized eggs hatch as larvae that drift for a few days before attaching to solid objects, such as rocks. The larvae morph into polyps resembling tiny anemones. Polyps can bud off into more polyps or, when conditions are right, into new young medusae.
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the jellyfish do not “eat” algae. Like their lagoon ancestors, the jellyfish simply absorb their algae’s photosynthetic leftovers. The jellies get about three-fourths of their energy from algal excretions and the remainder from prey. In essence, the jellyfish are landlords that hunt a bit on the side.

The jellyfish-algae partnership did not originate in the lakes, either. Ancestral spotted jellyfish brought the arrangement with them. “Spotted jellyfish in the lagoon have basic behaviors that help ‘sun’ their algae,” Martin explains. “They move eastward in the morning. The lake jellies have adapted this migration to each individual lake. The most spectacular migration is in Jellyfish Lake.”

The jellies’ migration delicately balances time in the sun (to benefit their algae) and predator avoidance. The gelatinous masses of peanut-shaped Jellyfish Lake begin their day in the western basin. As the sun rises they pulsate eastward toward the rising sun—but not too far east, because the lakeshore is covered with jellyfish-eating anemones. The jellies stop swimming east when they hit the shade cast by mangrove trees lining the shore.
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At nightfall the jellies switch to a vertical migration. Jellyfish Lake reaches depths of 100 feet, but only the top 45 feet contain oxygen. The bottom is a toxic vat of hydrogen sulfide. Bacteria do a brisk business at the interface, metabolizing both the oxygen above and hydrogen sulfide below. Every night the jellies bob up and down from the surface to the bacterial layer. Besides helping the jellyfish stay in place, dipping down treats the jellies’ algae to a midnight snack of nutrients excreted by the microbial masses.

Very Cool.

Open Science: Explaining Spontaneous Knotting

Shedding light on why long strands tend to become knotted

Anyone who has ever put up Christmas lights knows the problem: Holiday strands so carefully packed away last year are now more knotty than nice. In fact, they have become an inextricable, inexplicable, seemingly inevitable mess. It happens every year, like some sort of universal law of physics.

Which, it turns out, it basically is. In October, two UCSD researchers published the first physical explanation of why knots seem to form magically, not just in strands of Christmas lights, but in pretty much anything stringy, from garden hoses to iPod earbud cords to DNA.
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“We’re not mathematicians,” Smith said. “We’re physicists. Physicists do experiments.”

UCSD researchers constructed a knot probability machine that involved placing a single length of string in a plastic box, sealing it, then rotating the box at a set speed for a brief period of time.
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The experiment involved placing a single length of floppy string into a plastic box, sealing it, then rotating the box at a set speed for a brief time. The researchers did this 3,415 times, sometimes changing variables such as box size and string length.

Open access research paper: Spontaneous knotting of an agitated string by Dorian M. Raymer and Douglas E. Smith.

Above a critical string length, the probability P of knotting at first increased sharply with length but then saturated below 100%. This behavior differs from that of mathematical self-avoiding random walks, where P has been proven to approach 100%. Finite agitation time and jamming of the string due to its stiffness result in lower probability, but P approaches 100% with long, flexible strings.
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As L [length] was increased from 0.46 to 1.5 m, P increased sharply. However, as L was increased from 1.5 to 6 m, P saturated at 50%.
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Tripling the agitation time caused a substantial increase in P, indicating that the knotting is kinetically limited. Decreasing the rotation rate by 3-fold while keeping the same number of rotations caused little change in P.
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We also did measurements with a stiffer string and observed a probability of finding a knot would approach 100% with an substantial drop in P.

Yet another interesting case of scientists explaining the world around us (and the value of open science).

Macropinna Microstoma: Fish with a Transparent Head

That is a pretty awesome fish. The eyes were believed to be fixed in place and seemed to provide only a “tunnel-vision” view of whatever was directly above the fish’s head. A new paper by Bruce Robison and Kim Reisenbichler shows that these unusual eyes can rotate within a transparent shield that covers the fish’s head. This allows the barreleye to peer up at potential prey or focus forward to see what it is eating.

Deep-sea fish have adapted to their pitch-black environment in a variety of amazing ways. Several species of deep-water fishes in the family Opisthoproctidae are called “barreleyes” because their eyes are tubular in shape. Barreleyes typically live near the depth where sunlight from the surface fades to complete blackness. They use their ultra-sensitive tubular eyes to search for the faint silhouettes of prey overhead.

Full press release

Study Shows Weight Loss From Calorie Reduction Not Low Fat or Low Carb

A Randomized Trial Comparing Low-Fat and Low-Carbohydrate Diets Matched for Energy and Protein

The preliminary results presented in this paper are for the first four of six postmenopausal overweight or obese participants who followed, in random order, both a VLC [very-low-carbohydrate] and an LF [low-fat] diet for 6 weeks. Other outcome measures were serum lipids, glucose, and insulin, as well as dietary compliance and side effects. Our results showed no significant weight loss, lipid, serum insulin, or glucose differences between the two diets. Lipids were dramatically reduced on both diets, with a trend for greater triglyceride reduction on the VLC diet. Glucose levels were also reduced on both diets, with a trend for insulin reduction on the VLC diet. Compliance was excellent with both diets, and side effects were mild

Essentially the study showed that the calories had an impact on weight loss but the makeup of those calories did not. Don’t forget this is just one study. Listen to interview with the Author, Frank Sacks, on Science Friday on NPR.

Problems Using Corn as Biofuel

The pluses and (mostly) minuses of biofuels by Robert Sanders

one ripple effect from the stampede to create more ethanol from corn in the United States. As corn prices skyrocketed several years ago, soybean fields were converted to corn, and the price of soy rose. As a result, farmers in Brazil, one of the main countries with the soil, climate and infrastructure to make up the difference, began to bulldoze rainforest to grow more soybeans.

“If reduced U.S. soybean production results in a parallel increase in Brazilian soybean production, a potential net release of 1,800 to 9,100 Tg (trillion grams) of CO2-equivalents of greenhouse gas emissions due to land-use change is possible,” Coe wrote in a summary of his talk. That is equivalent to more than 9 billion metric tons of carbon dioxide.

Canadian Oil Sands

Photograph by Peter Essick, National Geographic

Canadian Oil Boom

To extract each barrel of oil from a surface mine, the industry must first cut down the forest, then remove an average of two tons of peat and dirt that lie above the oil sands layer, then two tons of the sand itself. It must heat several barrels of water to strip the bitumen from the sand and upgrade it, and afterward it discharges contaminated water into tailings ponds like the one near Mildred Lake. They now cover around 50 square miles.
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The Alberta government estimates that the province’s three main oil sands deposits, of which the Athabasca one is the largest, contain 173 billion barrels of oil that are economically recoverable today. “The size of that, on the world stage—it’s massive,” says Rick George, CEO of Suncor, which opened the first mine on the Athabasca River in 1967. In 2003, when the Oil & Gas Journal added the Alberta oil sands to its list of proven reserves, it immediately propelled Canada to second place, behind Saudi Arabia, among oil-producing nations. The proven reserves in the oil sands are eight times those of the entire U.S. “And that number will do nothing but go up,” says George. The Alberta Energy Resources and Conservation Board estimates that more than 300 billion barrels may one day be recoverable from the oil sands; it puts the total size of the deposit at 1.7 trillion barrels.
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But the free market does not consider the effects of the mines on the river or the forest, or on the people who live there, unless it is forced to. Nor, left to itself, will it consider the effects of the oil sands on climate. Jim Boucher has collaborated with the oil sands industry in order to build a new economy for his people, to replace the one they lost, to provide a new future for kids who no longer hunt ptarmigan in the moonlight. But he is aware of the trade-offs. “It’s a struggle to balance the needs of today and tomorrow when you look at the environment we’re going to live in,” he says. In northern Alberta the question of how to strike that balance has been left to the free market, and its answer has been to forget about tomorrow. Tomorrow is not its job.

This is a good article by National Geographic. We need energy. We also need to protect the environment. The trade-offs societies decide to make are often not easy. But open discussion of the issues is important.

Gram-negative Bacteria Defy Drug Solutions

Deadly bacteria defy drugs, alarming doctors by Mary Engel

Acinetobacter doesn’t garner as many headlines as methicillin-resistant Staphylococcus aureus, the dangerous superbug better known as MRSA. But a January report by the Infectious Diseases Society of America warned that drug-resistant strains of Acinetobacter baumannii and two other microbes — Pseudomonas aeruginosa and Klebsiella pneumoniae — could soon produce a toll to rival MRSA’s.

The three bugs belong to a large category of bacteria called “gram-negative” that are especially hard to fight because they are wrapped in a double membrane and harbor enzymes that chew up many antibiotics. As dangerous as MRSA is, some antibiotics can still treat it, and more are in development, experts say.

But the drugs once used to treat gram-negative bacteria are becoming ineffective, and finding effective new ones is especially challenging.
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For the most part, gram-negative bacteria are hospital scourges — harmless to healthy people but ready to infect already-damaged tissue. The bacteria steal into the body via ventilator tubes, catheters, open wounds and burns, causing pneumonia, urinary tract infections, and bone, joint and bloodstream infections.

Pseudomonas is widely found in soil and water, and rarely causes problems except in hospitals.

Friday Duckling Fun

This duckling seems imprinted on this puppy in China.

Why Does Hair Turn Grey as We Age?

A team of European scientists have learned why our hair turns gray as we age. Despite the notion that gray hair is a sign of wisdom, these researchers show that going gray is caused by a massive build up of hydrogen peroxide due to wear and tear of our hair follicles. The peroxide winds up blocking the normal synthesis of melanin, our hair’s natural pigment.

“Not only blondes change their hair color with hydrogen peroxide,” said Gerald Weissmann, MD, Editor-in-Chief of The FASEB Journal. “All of our hair cells make a tiny bit of hydrogen peroxide, but as we get older, this little bit becomes a lot. We bleach our hair pigment from within, and our hair turns gray and then white. This research, however, is an important first step to get at the root of the problem, so to speak.”

The researchers made this discovery by examining cell cultures of human hair follicles. They found that the build up of hydrogen peroxide was caused by a reduction of an enzyme that breaks up hydrogen peroxide into water and oxygen (catalase). They also discovered that hair follicles could not repair the damage caused by the hydrogen peroxide because of low levels of enzymes that normally serve this function (MSR A and B). Further complicating matters, the high levels of hydrogen peroxide and low levels of MSR A and B, disrupt the formation of an enzyme (tyrosinase) that leads to the production of melanin in hair follicles. Melanin is the pigment responsible for hair color, skin color, and eye color. The researchers speculate that a similar breakdown in the skin could be the root cause of vitiligo.

Weissmann added. “This study is a prime example of how basic research in biology can benefit us in ways never imagined.”

See full press release

Mental Pick-Me-Ups: The Coming Boom

I am not a fan of lifestyle drugs. People seem to forget that drugs have side effects that are quite large. Being surprised when a drug has adverse consequences shows a failure to understand the risks. You should assume adverse effects and take them only when that risk is outweighed by significant tangible benefits. A Boom in Memory-Enhancing Drugs?

A whole generation has come of age using attention-deficit drugs such as Adderall and Ritalin, a category valued at nearly $4.7 billion in 2007. A lot of teenagers have used them casually as study aids, often buying them on the Internet. And now, overworked professionals are seeing the appeal.

And when they almost certainly have significant adverse effects on many people, then people will get upset. Granted the drug companies pushing sales for negligible benefits do deserve condemnation. However, the larger problem is people that choose to risk their health as though they don’t have the ability to learn and can just ignore evidence of risks.