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September 8, 2008

10 Most Beautiful Physics Experiments

Science’s 10 Most Beautiful Experiments by George Johnson

Galileo’s experiment on falling objects

In the late 1500’s, everyone knew that heavy objects fall faster than lighter ones. After all, Aristotle had said so. That an ancient Greek scholar still held such sway was a sign of how far science had declined during the dark ages.

Galileo Galilei, who held a chair in mathematics at the University of Pisa, was impudent enough to question the common knowledge. The story has become part of the folklore of science: he is reputed to have dropped two different weights from the town’s Leaning Tower showing that they landed at the same time. His challenges to Aristotle may have cost Galileo his job, but he had demonstrated the importance of taking nature, not human authority, as the final arbiter in matters of science.

Young’s double-slit experiment applied to the interference of single electrons

Though it is not simply made of particles, neither can it be described purely as a wave. In the first five years of the 20th century, Max Planck and then Albert Einstein showed, respectively, that light is emitted and absorbed in packets — called photons. But other experiments continued to verify that light is also wavelike.

It took quantum theory, developed over the next few decades, to reconcile how both ideas could be true: photons and other subatomic particles — electrons, protons, and so forth — exhibit two complementary qualities; they are, as one physicist put it, ”wavicles.”

Eratosthenes’ measurement of the Earth’s circumference -the librarian at Alexandria in the third century B.C. estimated the circumference of the planet

Assuming the earth is spherical, its circumference spans 360 degrees. So if the two cities are seven degrees apart, that would constitute seven-360ths of the full circle — about one-fiftieth. Estimating from travel time that the towns were 5,000 ‘’stadia” apart, Eratosthenes concluded that the earth must be 50 times that size — 250,000 stadia in girth.

Related: Book, The Ten Most Beautiful Experiments by George Johnson (not the same experiments) - Home Experiments: Quantum Erasing - Particles and Waves - theory of knowledge - scientific experiments

September 2, 2008

8 Percent of the Human Genome is Old Virus Genes

In Our Genes, Old Fossils Take On New Roles

It turns out that about 8 percent of the human genome is made up of viruses that once attacked our ancestors. The viruses lost. What remains are the molecular equivalents of mounted trophies, insects preserved in genomic amber, DNA fossils.

The thousands of human endogenous retroviruses, or HERVs, sketch a history of rough times during the 550 million years of vertebrate evolution. The best-preserved one, HERV-K113, probably arrived less than 200,000 years ago, long after human beings and chimpanzees diverged from a common ancestor.

But these retroviruses are more than just curiosities. They are some of the most important enemies we ever had. They helped mold the immune system that is one of the evolutionary marvels of life on Earth.

I must say there is tons of amazing stuff I learn about but I still find retroviruses amazing.

Related: Amazing Science: Retroviruses - Old Viruses Resurrected Through DNA - One Species’ Genome Discovered Inside Another’s - Our Genome Changes as We Age - posts on genes and genome

August 16, 2008

Dolphin Kick Gives Swimmers Edge

photo of Michael Phelps diving

Dolphin Kick Gives Swimmers Edge

Rajat Mittal, a professor of mechanical and aerospace engineering at the George Washington University, was studying dolphins for the U.S. Navy five years ago. “We were asked to understand how fish swim so efficiently,” Mittal says, “and it seemed like a natural extension to apply this to human swimming.”

They decided to “essentially compare these swimmers to the dolphin, assuming that the dolphin is the ultimate swimmer,” Mittal says. “And the thing that we found is that Michael [Phelps] is able to use his body in a way that is very, very different from the other athletes, and also seems to be much closer to dolphins than we have seen for any other swimmer.”

The dolphin kick first hit Olympic swimming big-time 20 years ago, after Harvard backstroker David Berkoff figured out something fundamental. “It seemed pretty obvious to me that kicking underwater seemed to be a lot faster than swimming on the surface,” Berkoff says.

That’s because there’s turbulence and air on the surface of the water, and they create resistance. The “Berkoff Blastoff,” as it was called, was used at the start and after turns, with long stretches of that underwater undulating kick.

Follow the link for a video of Michael Phelps demonstrating the technique and more interesting details. Photo by A. Dawson shows Michael Phelps diving into the water at the 2008 U.S. Olympic Swimming Trials.

Related: Science of the High Jump - Sports Engineering - Physicist Swimming Revolution - Swimming Robot Aids Researchers

August 13, 2008

How Humans Got So Smart

Cooking and Cognition: How Humans Got So Smart

For a long time, we were pretty dumb. Humans did little but make “the same very boring stone tools for almost 2 million years,” he said. Then, only about 150,000 years ago, a different type of spurt happened — our big brains suddenly got smart. We started innovating. We tried different materials, such as bone, and invented many new tools, including needles for beadwork. Responding to, presumably, our first abstract thoughts, we started creating art and maybe even religion.

To understand what caused the cognitive spurt, Khaitovich and colleagues examined chemical brain processes known to have changed in the past 200,000 years. Comparing apes and humans, they found the most robust differences were for processes involved in energy metabolism.

The finding suggests that increased access to calories spurred our cognitive advances, said Khaitovich, carefully adding that definitive claims of causation are premature.

Nice example of scientific discovery in action. The direct link from cooking to brain development is far from proven but it is interesting. I also like “the same very boring stone tools for almost 2 million years” - maybe that is because I am too cynical (but while evolution is amazing - sometimes it is amazing how slow progress is).

Related: Brain Development Gene is Evolving the Fastest - Mapping Where Brains Store Similar Information - posts on science and out brains

August 7, 2008

Viruses and What is Life

Viruses are generally considered not to be alive (they must use a host cell of something else to reproduce). However, defining exactly what life is, is not as easy as you might think.

The debate about what counts as a living thing is fuelled today by the discovery of the first virus that is able to fall “ill” by being infected with another virus.

the discovery of a giant virus that itself falls ill through infection by another virus seems to suggest they too are alive, highlighting how there is no watertight definition of what exactly scientists mean when they refer to something as “living”.

“There’s no doubt, this is a living organism,” the journal Nature is told by Prof Jean-Michel Claverie, director of the Mediterranean Institute of Microbiology in Marseilles, part of France’s basic-research agency CNRS. “The fact that it can get sick makes it more alive.”

Related: People Have More Bacterial Cells than Human Cells - Bacteria Feed on Earth’s Ocean-Bottom Crust - Retroviruses - Bacteriophages: The Most Common Life-Like Form on Earth

August 6, 2008

Werner Heisenberg

photo of Werner Heisenberg

Read a very nice biography from Center for History of Physics of the American Institute of Physics for Werner Heisenberg, the founder of quantum mechanics, and the Heisenberg uncertainty principle:

Heisenberg set himself the task of finding the new quantum mechanics upon returning to Göttingen from Copenhagen in April 1925. Inspired by Bohr and his assistant, H.A. Kramers, in Copenhagen, Pauli in Hamburg, and Born in Göttingen, Heisenberg’s intensive struggle over the following months to achieve his goal has been well documented by historians. Since the electron orbits in atoms could not be observed, Heisenberg tried to develop a quantum mechanics without them.

He relied instead on what can be observed, namely the light emitted and absorbed by the atoms. By July 1925 Heisenberg had an answer, but the mathematics was so unfamiliar that he was not sure if it made any sense. Heisenberg handed a paper on the derivation to his mentor, Max Born, before leaving on a month-long lecture trip to Holland and England and a camping trip to Scandinavia with his youth-movement group. After puzzling over the derivation, Born finally recognized that the unfamiliar mathematics was related to the mathematics of arrays of numbers known as “matrices.” Born sent Heisenberg’s paper off for publication. It was the breakthrough to quantum mechanics.

Related: 1932 Nobel Prize in Physics - photo, 1927 - Uncertainty: Einstein, Heisenberg, Bohr, and the Struggle for the Soul of Science by David Lindley - 2007 Nobel Prize in Physics - posts on physics

July 24, 2008

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.”
(more…)

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.

Related: Baseball Pitch Designed in the Lab - Engineering Sports at MIT - Randomization in Sports

July 21, 2008

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.

Related: Vega Science Lectures: Feynman and More - How flowering plants beat the competition - What Are Flowers For?

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.

Related: Mystery of High-Temperature Superconductivity - Superconducting Surprise - Florida State lures Applied Superconductivity Center from Wisconsin

July 20, 2008

DNA Passed to Descendants Changed by Your Life

How your behaviour can change your children’s DNA

Until recently that would also have been the opinion of most scientists. Genes, it was thought, were highly resilient. Even if people did wreck their own DNA through bad diet, smoking and getting fat, that damage was unlikely to be passed to future generations.

Now, however, those assumptions are being re-examined. At the heart of this revolution is a simple but controversial idea: that DNA can be modified or imprinted with the experiences of your parents and grandparents.

According to this new science, known as epigenetics, your ancestors’ diet, smoking habits, exposure to pollutants and levels of obesity could be affecting you today. In turn, your lifestyle could affect your children and grandchildren.

If we drink heavily, take drugs, get fat or wait too long to reproduce, then epigenetics might start tying up some of the wrong genes and loosening the bonds on others. Sometimes those changes will affect sperm and egg cells.

It seems to me this area is still far from having conclusive proof. But it is another great example of scientists seeking to improve our knowledge of how things work.

Related: Nova on Epigenetics - Epigenetics: Sins of the fathers, and their fathers - Evidence for Transgenerational Transmission of Epigenetic Tumor Susceptibility in Drosophila - posts on DNA

July 15, 2008

2 Mysterious Species in the UK

Plane Bug - UK

Mystery insect found in Museum garden

This mystery bug has not been seen in the UK before and has made the Natural History Museum’s Wildlife Garden its home. The tiny bug is baffling insect experts at the Museum who are still trying to identify the mystery newcomer. The almond-shaped bug is red and black and about the size of a grain of rice

Experts checked the new bug with those in the Museum’s national insect collection of more than 28 million specimens. Amazingly, there is no exact match.

The bug closely resembles the fairly rare species Arocatus roeselii, which is usually found in central Europe. However, the roeselii bugs are brighter red than this new bug and they are usually associated with alder trees rather than plane trees.

However, the National Museum in Prague discovered an exact match to the mystery bug in their collections - an insect that was found in Nice and is classified as Arocatus roeselii. ‘There are two possible explanations,’ explains Barclay. ‘That the bug is roeselii and by switching to feed on the plane trees it could suddenly become more abundant, successful and invasive. The other possibility is that the insect in our grounds may not be roeselii at all.’

The Museum is working with international colleagues to analyse the bug’s body shape, form and DNA to see whether it is a newly discovered species or if it is in fact Arocatus roeselii.

Here is a green bug from my trip to Clifton Gorge Nature Preserve that is probably easier to identify. Or how about this insect from the Forest Glen Preserve, Illinois. Or how about this one at Our Lady of Gethsemani Abbey, in Kentucky.

Related: posts on invasive species - articles on invasive plants - Ballast-free Ships

Help us find out more about the mysterious alien “Ghost Slug”
(more…)

July 11, 2008

Too Toxic for Microorganisms - Not

The Pit of Life and Death by Richard Solensky:

The water became as acidic as lemon juice, creating a toxic brew of heavy metal poisons including arsenic, lead, and zinc. No fish live there, and no plants line the shores. There aren’t even any insects buzzing about. The Berkeley Pit had become one of the deadliest places on earth, too toxic even for microorganisms. Or so it was thought.

the researchers identified it as Euglena mutabilis, a protozoan which has the remarkable ability of being able to survive in the toxic waters of the Berkeley Pit by altering its local environment to something more hospitable. Through photosynthesis, it increases the oxygen level in the water, which causes dissolved metals to oxidize and precipitate out. In addition, it pulls iron out of the water and sequesters it inside of itself. This makes it a classic example of an extremophile.

Related: Bacteria Frozen for 8 Million Years In Polar Ice Resuscitated - Bacterium Living with High Level Radiation - posts on Microbes

July 7, 2008

How Prozac Sent Science Inquiry Off Track

I post often on examples of scientific inquiry in action. I think it is an important way to see how science works while searching for answers. The process is not a simple one, but after a solution is found it can often be presented as obvious. But while trying to find answers it is quite difficult.

How Prozac sent the science of depression in the wrong direction

But the success of Prozac hasn’t simply transformed the treatment of depression: it has also transformed the science of depression. For decades, researchers struggled to identify the underlying cause of depression, and patients were forced to endure a series of ineffective treatments. But then came Prozac. Like many other antidepressants, Prozac increases the brain’s supply of serotonin, a neurotransmitter. The drug’s effectiveness inspired an elegant theory, known as the chemical hypothesis: Sadness is simply a lack of chemical happiness. The little blue pills cheer us up because they give the brain what it has been missing.

There’s only one problem with this theory of depression: it’s almost certainly wrong, or at the very least woefully incomplete. Experiments have since shown that lowering people’s serotonin levels does not make them depressed, nor does it does not make them depressed, nor does it worsen their symptoms if they are already depressed.

In this sense, Prozac is simply a bottled version of other activities that have a similar effect, such as physical exercise.

It is jarring to think of depression in terms of atrophied brain cells, rather than an altered emotional state. It is called “depression,” after all. Yet these scientists argue that the name conceals the fundamental nature of the illness, in which the building blocks of the brain - neurons - start to crumble. This leads, over time, to the shrinking of certain brain structures, like the hippocampus, which the brain needs to function normally.

Related: Lifestyle Drugs and Risk - Overrelience on Prescription Drugs to Aid Children’s Sleep?

July 1, 2008

Protecting the Food Supply

A few weeks ago we posted about Tracking Down Tomato Troubles as another example of the challenges of scientific inquiry. Too often, in the rare instances that science is even discussed in the news, the presentation provides the illusion of simple obvious answers. Instead it is often a very confusing path until the answers are finally found (posts on scientific investigations in action). At which time it often seems obvious what was going on. But to get to the solutions we need dedicated and talented scientists to search for answers.

Now the CDC is saying tomatoes might not be the source of the salmonella after all: CDC investigates possible non-tomato salmonella sources.

Federal investigators retraced their steps Monday as suspicions mount that fresh unprocessed tomatoes aren’t necessarily causing the salmonella outbreak that has sickened hundreds across the USA.

Three weeks after the Food and Drug Administration warned consumers to avoid certain types of tomatoes linked to the salmonella outbreak, people are still falling ill, says Robert Tauxe with the Centers for Disease Control and Prevention. The latest numbers as of Monday afternoon were 851 cases, some of whom fell ill as recently as June 20, says Tauxe, deputy director of the CDC’s division of foodborne diseases.

The CDC launched a new round of interviews over the weekend. “We’re broadening the investigation to be sure it encompasses food items that are commonly consumed with tomatoes,” Tauxe says. If another food is found to be the culprit after tomatoes were recalled nationwide and the produce industry sustained losses of hundreds of millions of dollars, food safety experts say the public’s trust in the government’s ability to track foodborne illnesses will be shattered.

“It’s going to fundamentally rewrite how we do outbreak investigations in this country,” says Michael Osterholm of the Center for Infectious Disease Research and Policy at the University of Minnesota. “We can’t let this investigation, however it might turn out, end with just the answer of ‘What caused it?’ We need to take a very in-depth look at foodborne disease investigation as we do it today.”

I am inclined to believe the FDA is not enough focused on food safety. Perhaps we are not funding it enough, but we sure are spending tons of money on something so I can’t believe more money needs to be spent. Maybe just fewer bills passed (that the politicians don’t even bother to read) with favors to special interests instead of funding to support science and food safety. Or perhaps we are funding enough (though I am skeptical of this contention) and we just are not allowing food safety to get in the way of what special interests want (so we fund plenty for FDA to have managed this much better, to have systems in place that would provide better evidence but they are either prevented from doing so or failed to do so). I am inclined to believe special interests have more sway in agencies like (NASA, EPA, FDA…) than the public good and scientific openness - which is very sad. And, it seems to me, politicians have overwhelmingly chosen not to support more science in places like FDA, CDC, NIH… while increasing federal spending in other areas dramatically.

Related: USDA’s failure to protect the food supply - FDA May Make Decision That Will Speed Antibiotic Drug Resistance - Food safety proposal: throw the bums out - The A to Z Guide to Political Interference in Science

June 26, 2008

Our Genome Changes as We Age

Our Genome Changes Over Our Lifetime

For the new study, researchers first collected DNA samples collected in 1991 and again between 2002 and 2006 from 600 participants already enrolled in the AGES Reykjavik Study. The AGES study is renowned for its value to genetics research because of the historic isolation and reduced number of genetic “variables” among Iceland’s population, making certain patterns of genetic information easier to identify.

Among the 600, the research team measured the total amount of DNA methylation in each of 111 samples and compared total methylation from DNA collected in 2002 to 2005 to that person’s DNA collected in 1991.

They discovered that in almost one-third of the subjects, methylation changed over that 11-year span, with some gaining DNA methylation and others losing it.

“The key thing this part of the study told us is that levels changed over time, proof of principle that an individual’s epigenetic profile does change with age,” said M. Daniele Fallin, Ph.D., an associate professor of epidemiology at the Johns Hopkins Bloomberg School of Public Health.

Still a puzzle, though, was why or how, Fallin said, “so we wondered whether the tendency to those changes was also inherited, right along with our DNA sequences. That would explain why certain families are more susceptible to certain diseases.”

Related: Genetic Information Nondiscrimination Act - Learning About the Human Genome - Genomics Course For College Freshman Supported by HHMI at 12 Universities

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