Tag Archives: Science

Prion Proteins, Without Genes, Can Evolve

‘Lifeless’ prion proteins are ‘capable of evolution’

scientists transferred prion populations from brain cells to other cells in culture and observed the prions that adapted to the new cellular environment out-competed their brain-adapted counterparts. When returned to the brain cells, the brain-adapted prions again took over the population.

Charles Weissmann, head of Scripps Florida’s department of infectology who led the study, said: “On the face of it, you have exactly the same process of mutation and adaptive change in prions as you see in viruses.

“This means that this pattern of Darwinian evolution appears to be universally active. “In viruses, mutation is linked to changes in nucleic acid sequence that leads to resistance.

“Now, this adaptability has moved one level down- to prions and protein folding – and it’s clear that you do not need nucleic acid (DNA or RNA) for the process of evolution.”

He said: “The prion protein is not a clone, it is a quasi-species that can create different protein strains even in the same animal. “The abnormal prion proteins multiply by converting normal prion proteins.

“The implication of Charles Weissmann’s work is that it would be better to cut off that supply of normal prion proteins rather than risk the abnormal prion adapting to a drug and evolving into a new more virulent form.

Related: Challenging the Science Status QuoClues to Prion InfectivitySoil Mineral Degrades the Nearly Indestructible PrionBdelloid Rotifers Abandoned Sex 100 Million Years Ago

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

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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Cuts for British Science

Cuts mark ‘sad day for British science’

Britain’s physics community is reeling from a “disastrous” day of funding cuts that will force scientists to withdraw from major research facilities and see PhD studentships fall by a quarter. Space missions and projects across astronomy, nuclear and particle physics are being cancelled to save at least £115m, the Science and Technology Facilities Council (STFC) said today.

Fellowships and student grants for PhD projects will be cut by 25% from next year. The announcement has appalled senior physicists who warn the cuts threaten Britain’s future as a leading player in science.

In February, Gordon Brown delivered his first speech on science in Oxford and stated: “The downturn is no time to slow down our investment in science but to build more vigorously for the future.”

Politicians like to talk about funding science investment. And they do so to some extent. However, they are more reluctant to actually spend money than to talk about the wonders of science. Several countries in Asia are not just talking, they continue to invest, large amounts of money. The USA seems to be willing to put some money (not the kind of funds paid to protect bankers bonuses but significant amounts). Still the amounts the USA is investing is, I believe, falling as a percentage of global investment.

Related: posts on funding investments in scienceBritain’s Doctors of InnovationEconomic Strength Through Technology LeadershipScience and Engineering in Global EconomicsScience and Engineering Workforce IndicatorsThe value of investing in science and engineeringSaving FermilabNanotechnology Investment as Strategic National Economic Policy

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

Feynman “is a second Dirac, only this time human”

Oppenheimer recommendation of Feynman, page 1

Great quotes from Oppenheimer’s recommendation of Richard Feynman

“He is by all odds the most brilliant young physicist here, and everyone knows this. He is a man of thoroughly engaging character and personality, extremely clear, extremely normal in all respects, and an excellent teacher with a warm feeling for physics in all its aspects. He has the best possible relations both with the theoretical people of whom he is one, and with the experimental people with whom he works in very close harmony.”

Bethe has said that he would rather lose any two other men than Feynman from this present job, and Wigner said, ‘He is a second Dirac, only this time human.”

Oppenheimer recommendation of Feynman, page 2

Images of letter from Oppenheimer to the University of California – Berkeley Recommending Richard Feynman for a position, November 4, 1943 (from Big Science at Berkeley).

via: He is a second Dirac, only this time human.

Related: Vega Science Lectures: Feynman and MoreThe Feynman Lectures on Physics by Richard P. Feynman and Robert B. Leighton and Matthew Sands – posts on physics

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