Author Archives: curiouscat

Dark Cosmos

I just finished reading Dark Cosmos: In Search of Our Universe’s Missing Mass and Energy by Dan Hooper. I found it an enjoyable read. The author writes well for a general audience, that like me, doesn’t have much of an knowledge of the topic. I think he did a good job of providing enough connection to the science but at a level that most interested in science could understand.

Some people think it is a bit too folksy, without enough science. I can see how some might feel this way, I think the balance is good but for those that want to dig into the details around dark matter and dark energy this is probably not the right book. For those that want to get a good idea of the basic concepts though I think this is a good choice. I like discussion of the process of scientific discovery – the uncertainly the adaption of ideas to new experimental results etc.. The tone is similar to Chaos and The Elegant Universe.

Related: science books – Dan Hooper

T-rex Treasure

T. rex remains yield new treasure

Already, the breakthrough has yielded a payoff. Schweitzer and the Harvard scientists found molecular similarities between the Tyrannosaurus rex and modern chickens. They say the finding strengthens a growing case that birds are living relatives of dinosaurs. More tests are needed to see whether the bits of dinosaur proteins match those in other living creatures — including alligators and crocodiles, which, by outward appearances, seem closely related to the ancient species. Molecular maps of proteins in those reptiles are not yet available.
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The very existence of the molecular relics had been unimaginable. Until now, scientists thought such soft stuff survived no more than a million years in animal remains. Usually, tissue degrades and bone gets replaced by mineral, yielding fossils molded precisely like the originals. Although the fossils enable scientists to piece together a skeletal sketch of ancient life forms, they tell only so much.

The discovery of the protein fragments, detailed in the journal Science today, suggests that new molecular clues may be buried in other well-preserved fossils around the world. And those clues could help explain the biology of dinosaurs and other extinct animals. The newly discovered microscopic fragments are not DNA — the inherited code stored in billions of cells that defines every living creature. As a result, no one should expect any Jurassic Park-like replicas of dinosaurs to result from Schweitzer’s finding.

Quake Lifts Island Ten Feet Out of Ocean

Quake Lifts Island Ten Feet Out of Ocean:

Residents of Ranongga island in the South Pacific Ocean sit on a massive coral reef that was exposed by the magnitude 8.1 earthquake that struck in the Solomon Islands last week, sparking a deadly tsunami. The quake lifted Ranongga ten feet (three meters) out of the sea, widening beaches by up to 230 feet (70 meters), according to news reports. The uplift has left some of the island’s pristine coral reefs fatally exposed.

“These are not unusual occurrences for an earthquake of this magnitude,” said Rick MacPherson of the Coral Reef Alliance in San Francisco, California. “During the Asian tsunami two years ago, Banda Aceh [in Indonesia], stretching down almost the extent of the peninsula, experienced similar uplift.”

Universal Blood

Universal Blood by Katherine Bourzac:

Red blood cells have complex sugars on their surfaces; it is these sugars that determine whether the blood is type A, B, O, or both A and B. People with type A red blood cells carry antibodies against type B blood cells. If they are given a transfusion of type B red blood cells, their body will attack and kill the cells. Similarly, people with type B blood will mount an immune attack against a transfusion of type A blood.

Researchers led by Henrik Clausen of the University of Copenhagen have discovered two enzymes that efficiently chop the A and B sugars off of red blood cells, making them universal. The company ZymeQuest, based in Beverly, MA, has licensed the enzymes and developed a machine that can simultaneously treat eight units of blood with the enzymes in 90 minutes.

ScienceMatters@Berkeley April 2007

As usually the latest issue of ScienceMatters@Berkeley includes several intersting articles including, The Protein Machine by Kathleen M. Wong

A large percentage of known antibiotics target bacterial ribosomes, including tetracycline, erythromycin, and streptomycin. Many of these antibiotics have been isolated from microbes themselves. “It’s a byproduct of the chemical warfare that’s been going on among bacteria for hundreds of millions of years,” Cate says. “We want to understand how these natural products inhibit translation. Then, based on what we understand about the ribosome mechanism, we should be able to come up with new ways to stop bacterial translation based on the old compounds.”

Self-Tuning Genes:

Researchers such as UC Berkeley’s Adam Arkin have found that regulatory feedback is associated with chance fluctuations in mRNA or protein levels—a phenomenon called expression noise. “Even though they’re all genetically identical, and grown under the same conditions, yeast clones don’t express certain proteins at exactly the same level,” Brem says. “Some genes are noisier than others. That makes people think the cell is actively tuning the distribution around an expression level set by the regulatory network.” Noise may ensure that a few individuals can handle abrupt changes in their environment. In other words, if a colony is suddenly assaulted by toxic chemicals or high heat, a few individuals will already have expression levels suited to those conditions.

Software Patents – Bad Idea

MIT League for Programming Freedom on Software Patents, including: Why Patents Are Bad for Software, No Patents on Ideas by Thomas Jefferson and letter from Donald E. Knuth to the U.S. Patent Office

In the period 1945-1980, it was generally believed that patent law did not pertain to software. However, it now appears that some people have received patents for algorithms of practical importance–e.g., Lempel-Ziv compression and RSA public key encryption–and are now legally preventing other programmers from using these algorithms.

This is a serious change from the previous policy under which the computer revolution became possible, and I fear this change will be harmful for society. It certainly would have had a profoundly negative effect on my own work: For example, I developed software called TeX that is now used to produce more than 90% of all books and journals in mathematics and physics and to produce hundreds of thousands of technical reports in all scientific disciplines. If software patents had been commonplace in 1980, I would not have been able to create such a system, nor would I probably have ever thought of doing it, nor can I imagine anyone else doing so.

Math and Nature

Can’t Knock It Down:

Give mathematicians such a toy, and they’re liable to turn it into a math problem.

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Next, the pair began to investigate whether all three-dimensional shapes have at least two stable and two unstable balance points. They tried to generalize their two-dimensional proof to higher dimensions, but it didn’t hold up. Therefore, it seemed possible that a self-righting three-dimensional object could exist. Such a shape would have only one stable and one unstable balance point.
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Once the pair had built their Once the pair had built their self-righting object, they noticed that it looked very much like a turtle. They figured that wasn’t an accident, since it would be useful for a turtle never to get stuck on its back., they noticed that it looked very much like a turtle. They figured that wasn’t an accident, since it would be useful for a turtle never to get stuck on its back.
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The mathematicians still face an unanswered question. The self-righting objects they’ve found have been smooth and curvy. They wonder if it’s possible to create a self-righting polyhedral object, which would have flat sides. They think it is probably possible, but they haven’t yet managed to find such an object. So, they are offering a prize to the first person to find one: $10,000, divided by the number of sides of the polyhedron.

And Now for Something Completely Different

Macavity the cat

Too cool. Mystery cat takes regular bus to the shops:

The cat was nicknamed Macavity after the mystery cat in T.S Elliot’s poem. He gets on the bus in front of a row of 1950s semi-detached houses and jumps off at a row of shops down the road which include a fish and chip shop.
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Driver Bill Khunkhun, 49, who first saw the cat jumping from the bus in January, said: “It is really odd, the first time I saw the cat jumping off the bus with a group of passengers. I hadn’t seen it get on which was a bit confusing. “The next day I pulled up on Churchill Road to let a couple of passengers on. As soon as I opened the doors the cat ran towards the bus, jumped on and ran under one of the seats, I don’t think any of the passengers noticed. “Because I had seen it jump off the day before I carried on driving and sure enough when I stopped just down the road he jumped off – I don’t know why he would catch the bus but he seems to like it. I told some of the other drivers on this route and they have seen him too.”

Here is T.S. Eliot’s poem:

Macavity’s a Mystery Cat: he’s called the Hidden Paw-
For he’s the master criminal who can defy the Law.
He’s the bafflement of Scotland Yard, the Flying Squad’s despair:
For when they reach the scene of crime-Macavity’s not there!

Macavity, Macavity, there’s no one like Macavity,
He’s broken every human law, he breaks the law of gravity.
His powers of levitation would make a fakir stare,
And when you reach the scene of crime-Macavity’s not there!
You may seek him in the basement, you may look up in the air-
But I tell you once and once again, Macavity’s not there!
Continue reading →

Changing the Circadian Clock with the Seasons

Changing the Circadian Clock with the Seasons:

The findings – gleaned from work on the fruit fly Drosophila – have broad implications for understanding how innate behaviors such as mating, migrating, and hibernating are stimulated by environmental cues. Dan Stoleru, the lead author of the Cell paper and a postdoctoral fellow in Rosbash’s laboratory at Brandeis University, adds that the study reveals insights into possible causes of seasonal depression as well as other forms of mood disorders that respond to light therapy.
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Rosbash is a leader in the field of circadian research. For the past 25 years he has been defining the machinery that underlies the nearly universal pattern of circadian rhythms in insects, animals, and humans. He employs the tools of Drosophila genetics to understand how the circadian clock ticks and which master neural circuits underlie circadian activity patterns.

Lego Autopilot Project Update

An update to, The sub-$1,000 UAV Project from Chris Anderson – Lego Autopilot is Working!:

Our summer project is to create a sub-$1,000 UAV as a proof-of-concept for a drone competition for kids. This weekend we passed a major milestone with a successful ground test of the key elements. The video below shows the prototype working.

We’d initially intended to do all the autopilot functions in Lego, but the gyro programming turned out to be beyond our abilities. So we switched to a commercial stabilization unit to keep the plane level and just use the Lego Mindstorms for waypoint navigation.

Very cool.