Dennis Bray Podcast on Microbes As Computers

Carl Zimmer interviews Dennis Bray in an interesting podcast:

Dennis Bray is an active professor emeritus in both the Department of Physiology and Department of Neuroscience at the University of Cambridge. He studies the behavior of microbes–how they “decide” where to swim, when to divide, and how best to manage the millions of chemical reactions taking place inside their membranes. For Bray, microbes are tiny, living computers, with genes and proteins serving the roles of microprocessors.

William Kamkwamba on the Daily Show

Pointy haired bosses removed the video. Argh!

William Kamkwamba on the Daily show. I first posted about William’s great work in 2007 – Home Engineering: Windmill for Electricity. What a great example of what can be done by sharing scientific and engineering ideas with those who will make the effort to create workable solutions.

William has written a book on his life: The Boy Who Harnessed the Wind.

Learning Design of Experiments with Paper Helicopters

Photo showing the helicopter test track by Brad

Dr. George E.P. Box wrote a great paper on Teaching Engineers Experimental Design With a Paper Helicopter that can be used to learn principles of experimental design, including – conditions for validity of experimentation, randomization, blocking, the use of factorial and fractional factorial designs and the management of experimentation.

I ran across an interesting blog post on a class learning these principles today – Brad’s Hella-Copter:

For our statistics class, we have been working hard on a Design of Experiments project that optimizes a paper helicopter with respect to hang time an accuracy of a decent down a stairwell.
…
We were to design a helicopter that would drop 3 stories down within the 2ft gap between flights of stairs.
…
[design of experiments is] very powerful when you have lots of variables (ie. paper type, helicopter blade length, blade width, body height, body width, paperclip weights, etc) and not a lot of time to vary each one individually. If we were to individually change each variable one at a time, we would have made over 256 different helicopters. Instead we built 16, tested them, and got a feel for which variables were most important. We then focused on these important variables for design improvement through further testing and optimization.

Friday Fun: Dancing Parrot

Birds show off their dance moves

Footage revealed that some parrots have a near-perfect sense of rhythm; swaying their bodies, bobbing their heads and tapping their feet in time to a beat. Previously, it was thought that only humans had the ability to groove. The researchers believe the findings could help shed light on how our relationship with music and the capacity to dance came about.
…
Dr Patel told the BBC: “We analysed these videos frame by frame, and we found he did synchronise – he did slow down and speed up in time with the music. “It was really surprising that he had this flexibility.”

The Nobel Prize in Physics 2009

The 2009 Nobel Prize in Physics honors three scientists, who have had important roles in shaping modern information technology, with one half to Charles Kuen Kao and with Willard Sterling Boyle and George Elwood Smith sharing the other half. Kao’s discoveries have paved the way for optical fiber technology, which today is used for almost all telephony and data communication. Boyle and Smith have invented a digital image sensor – CCD, or charge-coupled device – which today has become an electronic eye in almost all areas of photography. The Nobel prize site includes great information on the science behind the research that has been honored:

The first ideas of applications of light guiding in glass fibers (i.e. small glass rods) date from the late 1920’s. They were all about image transmission through a bundle of fibers. The motivation was medicine (gastroscope), defense (flexible periscope, image scrambler) and even early television. Bare glass fibers were, however, quite leaky and did not transmit much light. Each time the fibers were touching each other, or when the surface of the fibers was scratched, light was led away from the fibers. A breakthrough happened in the beginning of the 1950’s with the idea and demonstration that cladding the fibers would help light transmission, by facilitating total internal reflection.
…
Optical communication of today has reached its present status thanks to a number of breakthroughs. Light emitting diodes (LEDs) and especially diode lasers, first based on GaAs (800-900 nm) and later on InGaAsP (1-1.7 ïm), have been essential. The optical communication window has evolved from 870 nm to 1.3 ïm and, finally, to 1.55 ïm where fiber losses are lowest. Gradient-index fibers were used in the first optical communication lines. However, when moving towards longer wavelengths and longer communication distances, single-mode fibers have become more advantageous.

Nowadays, long-distance optical communication uses single mode fibers almost exclusively, following Kao’s vision. The first such systems used frequent electronic repeaters to compensate for the remaining losses. Most of these repeaters have now been replaced by optical amplifiers, in particular erbium-doped fiber amplifiers. Optical communication uses wavelength division multiplexing with different wavelengths to carry different signals in the same fiber, thus multiplying the transmission rate. The first non-experimental optical fiber links were installed in 1975 in UK, and soon after in the US and in Japan. The first transatlantic fiber-optic cable was installed in 1988.

2009 Nobel Prize in Chemistry: the Structure and Function of the Ribosome

graphic image of the components of a cell

Cross section of a cell by the Royal Swedish Academy of Sciences. A ribosome is about 25 nanometters (a millionth of a millimeter) in size. A cell contains tens of thousands of ribosomes.

The Nobel Prize in Chemistry for 2009 awards studies of one of life’s core processes: the ribosome’s translation of DNA information into life. Ribosomes produce proteins, which in turn control the chemistry in all living organisms. As ribosomes are crucial to life, they are also a major target for new antibiotics.

This year’s Nobel Prize in Chemistry awards Venkatraman Ramakrishnan, Thomas A. Steitz and Ada E. Yonath for having showed what the ribosome looks like and how it functions at the atomic level. All three have used a method called X-ray crystallography to map the position for each and every one of the hundreds of thousands of atoms that make up the ribosome.

Inside every cell in all organisms, there are DNA molecules. They contain the blueprints for how a human being, a plant or a bacterium, looks and functions. But the DNA molecule is passive. If there was nothing else, there would be no life.

The blueprints become transformed into living matter through the work of ribosomes. Based upon the information in DNA, ribosomes make proteins: oxygen-transporting haemoglobin, antibodies of the immune system, hormones such as insulin, the collagen of the skin, or enzymes that break down sugar. There are tens of thousands of proteins in the body and they all have different forms and functions. They build and control life at the chemical level.

Details from the Nobel Prize site (which continues to do a great job providing scientific information to the public openly).
Continue reading →

2009 Nobel Prize in Physiology or Medicine

This year’s Nobel Prize in Physiology or Medicine is awarded to three scientists who have solved a major problem in biology: how the chromosomes can be copied in a complete way during cell divisions and how they are protected against degradation. The Nobel Laureates have shown that the solution is to be found in the ends of the chromosomes – the telomeres – and in an enzyme that forms them – telomerase.

The long, thread-like DNA molecules that carry our genes are packed into chromosomes, the telomeres being the caps on their ends. Elizabeth Blackburn and Jack Szostak discovered that a unique DNA sequence in the telomeres protects the chromosomes from degradation. Carol Greider and Elizabeth Blackburn identified telomerase, the enzyme that makes telomere DNA. These discoveries explained how the ends of the chromosomes are protected by the telomeres and that they are built by telomerase.

If the telomeres are shortened, cells age. Conversely, if telomerase activity is high, telomere length is maintained, and cellular senescence is delayed. This is the case in cancer cells, which can be considered to have eternal life. Certain inherited diseases, in contrast, are characterized by a defective telomerase, resulting in damaged cells. The award of the Nobel Prize recognizes the discovery of a fundamental mechanism in the cell, a discovery that has stimulated the development of new therapeutic strategies.

Scientists began to investigate what roles the telomere might play in the cell. Szostak’s group identified yeast cells with mutations that led to a gradual shortening of the telomeres. Such cells grew poorly and eventually stopped dividing. Blackburn and her co-workers made mutations in the RNA of the telomerase and observed similar effects in Tetrahymena. In both cases, this led to premature cellular ageing – senescence. In contrast, functional telomeres instead prevent chromosomal damage and delay cellular senescence. Later on, Greider’s group showed that the senescence of human cells is also delayed by telomerase. Research in this area has been intense and it is now known that the DNA sequence in the telomere attracts proteins that form a protective cap around the fragile ends of the DNA strands.

Many scientists speculated that telomere shortening could be the reason for ageing, not only in the individual cells but also in the organism as a whole. But the ageing process has turned out to be complex and it is now thought to depend on several different factors, the telomere being one of them. Research in this area remains intense.

The 3 awardees are citizens of the USA; two were born elsewhere.
Read more about their research at the Nobel Prize web site.

Molecular biologist Elizabeth Blackburn–one of Time magazine’s 100 “Most Influential People in the World” in 2007–made headlines in 2004 when she was dismissed from the President’s Council on Bioethics after objecting to the council’s call for a moratorium on stem cell research and protesting the suppression of relevant scientific evidence in its final report.

Webcast of Dr. Elizabeth Blackburn speaking at Google:
Continue reading →

Test it Out, Experiment by They Might Be Giants

Put It to the Test is one of the songs on the great new Album and animated DVD from They Might Be Giants: Here Comes Science.

Are you sure that thing is true, or did someone just tell it to you.
Come up with a test. Test it out.
Find a way to show what would happen if you were incorrect. Test it out.
A fact is just a fantasy unless it can be checked.
Make a test. Test it out.

A fun song on fundamentals of experimenting to the scientific method.

Movie Aims to Inspire College Students With Tales of Successful Minority Scientists

African American women are still rare in many science professions, despite their increasing representation in undergraduate science classes. The documentary – Roots to STEM: Spelman Women in Science—seeks to explore how these women were able to succeed and to hold them up as role models.

Tarsha Ward remembers begging her mother for a stethoscope so she could be the star of career day at her kindergarten class in Charleston, S.C. Her mother presented her with something that proved more prophetic: a white lab coat.

“For me that was the beginning of a career,” said Ward, who is working toward her doctorate in biomedical sciences at Morehouse School of Medicine in Atlanta, Ga., focused on cancer research. “Ever since then everything was about science.”

“If you get into a bind you have to think it out yourself,” she said. “A Ph.D. has really taught me to think on my own. You’re here thinking in the midnight hours and there’s no book to tell you what’s right. You just have to see if it works.”

Such struggles have already paid off. “In seven months, I published my first paper. I worked on it day and night,” said Ward, a 2004 Spelman graduate. “I (loved) the fact that I could find something no one else could find and actually publish it.”

Read the full press release

Why do we Need Dark Energy to Explain the Observable Universe?

Why do we need dark energy to explain the observable universe?

Against all reason, the universe is accelerating its expansion. When two prominent research teams dropped this bombshell in 1998, cosmologists had to revise their models of the universe to include an enormous and deeply mysterious placeholder they called “dark energy.” For dark energy to explain the accelerating expansion, it had to constitute more than 70 percent of the universe. It joined another placeholder, “dark matter,” constituting 20 percent, in overshadowing the meager 4 percent that make up everything else—things like stars, planets, and people.
…
An accelerating wave of expansion following the Big Bang could push what later became matter out across the universe, spreading galaxies farther apart the more distant they got from the wave’s center. If this did happen, it would account for the fact that supernovae were dim- they were in fact shoved far away at the very beginning of the universe. But this would’ve been an isolated event, not a constant accelerating force. Their explanation of the 1998 observations does away with the need for dark energy.
…
And Smoller and Temple say that once they have worked out a further version of their solutions, they should have a testable prediction that they can use to see if the theory fits observations.

Another interesting example of the scientific inquiry process at work in cosmology.

Shouldn’t the National Academy of Science (NAS), a congressionally chartered institution, promote open science instead of erecting pay walls to block papers from open access? The paper (by 2 public school professors) is not freely available online. It seems like it will be available 6 months after publication (which is good) but shouldn’t the NAS do better? Delayed open access, for organizations with a focus other than promoting science (journal companies etc.), is acceptable at the current time, but the NAS should do better to promote science, I think.