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.

Microcosm by Carl Zimmer

cover of Microcosm by Carl Zimmer

Microcosm: E. Coli and the New Science of Life by Carl Zimmer is an excellent book. It is full of fascinating information and as usual Carl Zimmer’s writing is engaging and makes complex topics clear.

E-coli keep the level of oxygen low in the gut making the resident microbes comfortable. At any time a person will have as many as 30 strains of E. coli in their gut and it is very rare for someone ever to be free of E. coli. [page 53]

In 1943, Luria and Delbruck published the results that won them the 1969 Nobel Prize in Physiology or Medicine in which they showed that bacteria and viruses pass down their traits using genes (though it took quite some time for the scientific community at large to accept this). [page 70]

during a crisis E coli’s mutation rates could soar a hundred – or even a thousandfold… Normally, natural selection favors low mutation rates, since most mutations are harmful. But in times of stress extra mutations may raise the odds that organisms will hit on a way out of their crisis… [alternatively, perhaps] In times of stress, E coli. may not be able to afford the luxury of accurate DNA repair. Instead, it turns to the cheaper lo-fi polymerases. While they may do a sloppier job, E coli. comes out ahead [page 106]
Hybridization is not the only way foreign DNA got into our cells. Some 3 billion years ago our single-celled ancestors engulfed oxygen-breathing bacteria, which became the mitochondria on which we depend. And, like E. coli, our genomes have taken in virus upon virus. Scientists have identified more than 98,000 viruses in the human genome, along with our mutant vestiges of 150,00 others… If we were to strip out all our transgenic DNA, we would become extinct.

I highly recommend Microcosm, just as I highly recommend Parasite Rex, by Carl Zimmer.

Related: Bacteriophages: The Most Common Life-Like Form on EarthForeign Cells Outnumber Human Cells in Our BodiesAmazing Designs of LifeAmazing Science: RetrovirusesOne Species’ Genome Discovered Inside Another’s

Bionic Vision

Micro Machines and Opto-Electronics on a Contact Lense

Fiction now meets reality with prototype contact lenses developed by Babak Parviz at the University of Washington, in Seattle. Dr. Parviz’s prototype lenses can be used as biosensors to display body chemistry or as a heads up display (HUD). Powered by radio waves and 330 microwatts of power from a loop antenna that picks up power beamed from nearby radio sources, future versions will also be able to harvest power from a cell phone.

In his early 2008 lab tests, rabbits safely wore contact lenses with metal connectors for electronic circuits. The prototype lenses contained an electric circuit as well as red light-emitting diodes for a display. The lenses were tested on rabbits for up to 20 minutes and the animals showed no adverse effects.

Contact lenses as replacements for smart phone displays — even to monitor blood glucose levels — might best be done while not operating heavy equipment. “The true promise of this research is not just the actual system we end up making, whether it’s a display, a biosensor, or both,” comments Dr. Parviz. “We already see a future in which the humble contact lens becomes a real platform, like the iPhone is today, with lots of developers contributing their ideas and inventions. As far as we’re concerned, the possibilities extend as far as the eye can see, and beyond.”

Related: A Journey Into the Human Eye3-D Images of EyesScientists Discover How Our Eyes Focus When We Read

Soren Bisgaard 1951-2009

photo of Soren Bisgaard

Soren Bisgaard died earlier this month of cancer. Soren was a student (Ph.D., statistics) of my father’s who shared the commitment to using applied statistics to improve people’s lives. I know this seem odd to many (I tried to describe this idea previously and read his acceptance of the 2002 William G. Hunter award).

Most recently Soren Bisgaard, Ph.D. was Professor of technology management at Eugene M. Isenberg School of Management at the University of Massachusetts – Amherst. He was an ASQ Fellow; recipient of Shewart Medal, Hunter Award, George Box Medal, among many others awards. Soren also served as the director of the Center for Quality and Productivity Improvement at the University of Wisconsin-Madison (founded by William Hunter and George Box) for several years.

I will remember the passion he brought to his work. He reminded me of my father in his desire to improve how things are done and provide people the opportunity to lead better lives. Those that bring passion to their work in management improvement are unsung heroes. It seems odd, to many, to see that you can bring improvement to people’s lives through work. But we spend huge amounts of our time at work. And by improving the systems we work in we can improve people’s lives. Soren will be missed, by those who knew him and those who didn’t (even if they never realize it).

The Future of Quality Technology: From a Manufacturing to a Knowledge Economy and From Defects to Innovations (pdf) by Soren Bisgaard. Read more articles by Søren Bisgaard.

Related: The Work of Peter ScholtesMistakes in Experimental Design and InterpretationThe Scientific Context of Quality Improvement by George Box and Soren Bisgaard, 1987 – William G. Hunter Award 2008: Ronald Does

Obituary Søren Bisgaard at ENBIS:
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Briggs-Rauscher Oscillating Reaction

video showing the Briggs-Rauscher Oscillating Reaction. From Wikipedia:

The first known homogeneous oscillating chemical reaction, reported by W. C. Bray in 1921, was between hydrogen peroxide (H2O2) and iodate (IO3−) in acidic solution. Due to experimental difficulty, it attracted little attention and was unsuitable as a demonstration. In 1958 B. P. Belousov in the Soviet Union discovered the Belousov–Zhabotinsky reaction (BZ reaction), is suitable as a demonstration, but it too met with skepticism (largely because such oscillatory behavior was unheard of up to that time) until A. M. Zhabotinsky, also in the USSR, learned of it and in 1964 published his research. In May of 1972 a pair of articles in the Journal of Chemical Education brought it to the attention of two science instructors at Galileo High School in San Francisco. They discovered the Briggs–Rauscher oscillating reaction by replacing bromate (BrO3−) in the BZ reaction by iodate and adding hydrogen peroxide. They produced the striking visual demonstration by adding starch indicator.

The detailed mechanism of this reaction is quite complex. Nevertheless, a good general explanation can be given.
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Monkey Bridge

Monkey see Monkey do

When you visit Diani Beach, Kenya’s version the Florida keys, look up and you’ll see 20 rope bridges swinging over the highway – what’s that little bulge with a tail? Before you flash by, you will realise that it’s a monkey sitting up there. Yes it’s watching you! And then, a burst of action as an entire troop of black and white might start galloping across the wildly swaying bridge!

Being naturally shy, the colobus initially stared at the bridges gadgets with disdain until the more inquisitive and daring Sykes monkey began to see the logic. Once the Sykes and even vervet monkeys started using the bridges, the colobus followed suit, and are now very comfortable with their arboreal walkways.

Related: Colobus TrustEngineering a Better World: Bike Corn-Sheller‘Refrigerator’ Without ElectricityMassive Gorilla Population FoundOrangutan Attempts to Hunt Fish with Spear

Unless We Take Decisive Action, Climate Change Will Ravage Our Planet

Lake McDonald, Glacier National Park photo by John Hunterphoto by John Hunter at Glacier National Park.

Tomorrow 56 newspapers, in 45 countries, are taking the unprecedented step of publishing the same editorial. The editorial will appear in 20 languages, as the United Nations Climate Change Conference is set to begin in Copenhagen.

Unless we combine to take decisive action, climate change will ravage our planet, and with it our prosperity and security. The dangers have been becoming apparent for a generation. Now the facts have started to speak: 11 of the past 14 years have been the warmest on record, the Arctic ice-cap is melting and last year’s inflamed oil and food prices provide a foretaste of future havoc. In scientific journals the question is no longer whether humans are to blame, but how little time we have got left to limit the damage. Yet so far the world’s response has been feeble and half-hearted.

Climate change has been caused over centuries, has consequences that will endure for all time and our prospects of taming it will be determined in the next 14 days. We call on the representatives of the 192 countries gathered in Copenhagen not to hesitate, not to fall into dispute, not to blame each other but to seize opportunity from the greatest modern failure of politics. This should not be a fight between the rich world and the poor world, or between east and west. Climate change affects everyone, and must be solved by everyone.

The science is complex but the facts are clear. The world needs to take steps to limit temperature rises to 2C, an aim that will require global emissions to peak and begin falling within the next 5-10 years.

Few believe that Copenhagen can any longer produce a fully polished treaty; real progress towards one could only begin with the arrival of President Obama in the White House and the reversal of years of US obstructionism. Even now the world finds itself at the mercy of American domestic politics, for the president cannot fully commit to the action required until the US Congress has done so.

the rich world is responsible for most of the accumulated carbon in the atmosphere – three-quarters of all carbon dioxide emitted since 1850. It must now take a lead, and every developed country must commit to deep cuts which will reduce their emissions within a decade to very substantially less than their 1990 level.

The transformation will be costly, but many times less than the bill for bailing out global finance — and far less costly than the consequences of doing nothing.

Many of us, particularly in the developed world, will have to change our lifestyles. The era of flights that cost less than the taxi ride to the airport is drawing to a close. We will have to shop, eat and travel more intelligently. We will have to pay more for our energy, and use less of it.

Kicking our carbon habit within a few short decades will require a feat of engineering and innovation to match anything in our history. But whereas putting a man on the moon or splitting the atom were born of conflict and competition, the coming carbon race must be driven by a collaborative effort to achieve collective salvation.

The politicians in Copenhagen have the power to shape history’s judgment on this generation: one that saw a challenge and rose to it, or one so stupid that we saw calamity coming but did nothing to avert it. We implore them to make the right choice.

Most of the newspapers have taken the unusual step of featuring the editorial on their front page. Even with the overwhelming evidence and tremendous consequences I don’t expect politicians to make the right decisions. We know full well what the choices are. We just decide to avoid the unpleasant choices. To bad so many that don’t get to choose are going to suffer. The politicians will be weak. They will play to those that pay them money. They will delay taking important steps now. We have chosen to elect non-leaders for quite some time. We can’t really expect them to act with courage, vision, wisdom and leadership given who we elect. The politicians are responsible for their failing but we are more responsible for electing them. Some politicians, even now, do possess fine qualities but not nearly enough. Maybe I will be proven wrong, but I doubt it.

Related: What’s Up With the Weather?Arctic System on Trajectory to New, Seasonally Ice-Free StateScientists Denounce Global Warming Report EditsDeforestation and Global WarmingMIT’s Energy ‘Manhattan Project’Global Installed Wind Power Now Over 1.5% of Global Electricity DemandBigger Impact: 15 to 18 mpg or 50 to 100 mpg?Solar Thermal in Desert, to Beat Coal by 202076 Nobel Laureates in Science Endorse Obama

Zubbles – Get Your Colored Bubbles

photo of blue bubblephoto of blue colored bubble.

I first posted on this in 2005: Colored Bubbles. Now you can order your own via Zubbles. Colored Bubbles Have Landed (and Popped and Vanished)

Having solved the colored bubble dilemma, we spent most of 2006 trying to refine our dyes and the manufacturing process. We had invented several completely new dyes and a few derivatives of existing dyes. But the manufacturing process was long, tedious and expensive. It took three days just to make a few grams of each dye. It quickly became apparent that we needed to radically streamline the production process in order to have a viable product.

The complexities of the chemistry resembled a pharmaceutical more than a toy. So I enlisted the help of Gary Willingham, and the Belgium development team, at Fisher Scientific. Fisher is a pharmaceutical chemical manufacturer with the equipment and expertise needed to manufacture tons of our dyes.

Due to the complexities of the chemistry, Jamm decided to stay close to the production process and manufacture Zubbles in the US. The first bottles rolled off the line this week. Jamm presented me with the very first case of Zubbles. And it was a very strange feeling to finally hold the product in my hand—15 years after I mixed my first batch of dishwashing detergent and food coloring.

Being an entrepreneur is a challenge any time. When your product requires complex science and engineering that adds additional challenges. It is great to see this product is now available.

Related: Making Magnificent Mirrors with Math1979 “iPod-like” Music PlayerThe Glove – Engineering Coolnessscience and engineering gadgets and giftsBuild Your Own Tabletop Interactive Multi-touch ComputerAwesome Cat Cam

Ants Counting Their Step

Ants That Count!

Most ants get around by leaving smell trails on the forest floor that show other ants how to get home or to food. They squeeze the glands that cover their bodies; those glands release a scent, and the scents in combination create trails the other ants can follow.

That works in the forest, but it doesn’t work in a desert. Deserts are sandy and when the wind blows, smells scatter.

It’s already known that ants use celestial clues to establish the general direction home, but how do they know exactly the number of steps to take that will lead them right to the entrance of their nest?

Wolf and Whittlinger trained a bunch of ants to walk across a patch of desert to some food. When the ants began eating, the scientists trapped them and divided them into three groups. They left the first group alone. With the second group, they used superglue to attach pre-cut pig bristles to each of their six legs, essentially putting them on stilts.

The regular ants walked right to the nest and went inside. The ants on stilts walked right past the nest, stopped and looked around for their home…

I posted about this back in 2006: Ants on Stilts for Science, but the webcast by NPR is worth a new post.

Related: E.O. Wilson: Lord of the AntsHuge Ant Nestposts showing the scientific method of learning in action

Disrupting Bacterial Communication to Thwart Them

Interrupting Bacterial Chatter to Thwart Infection

To measure their own numbers, bacteria produce, release, and detect chemical signals called autoinducers. As a population of bacteria grows, it releases more autoinducer into its environment. When individuals detect that a threshold level of autoinducer is present, they change their behavior – by releasing a toxin, for example.

Bassler and her colleagues disrupted these lines of communication by interfering with molecules called acyl-homoserine lactone (AHL) autoinducers, which drive quorum sensing among a kind of bacteria known as Gram-negative bacteria. Gram-negative bacteria include Pseudomonas, E. coli and Salmonella, and other disease-causing microbes. In the study, the team focused on Chromobacterium violaceum, which rarely infects human, but can be lethal to other organisms. C. violaceum lends itself to studies of quorum sensing because it produces a readily detected, bright purple dye when it detects that its population has reached a critical mass.

The experiment shows that interfering with quorum sensing may provide an alternative to traditional antibiotics, Bassler says, and circumvent the problem of resistance that antibiotics foster by killing off susceptible bacteria but allowing resistant ones to survive and propagate.

Related: Bacteria Communicate Using a Chemical Language (quorum sensing)Disrupting Bacteria Communication (2007)Electrolyzed Water Replacing Toxic Cleaning SubstancesGram-negative Bacteria Defy Drug Solutions