Category Archives: Research

At the Heart of All Matter

The hunt for the God particle by Joel Achenbach

Physics underwent one revolution after another. Einstein’s special theory of relativity (1905) begat the general theory of relativity (1915), and suddenly even such reliable concepts as absolute space and absolute time had been discarded in favor of a mind-boggling space-time fabric in which two events can never be said to be simultaneous. Matter bends space; space directs how matter moves. Light is both a particle and a wave. Energy and mass are inter- changeable. Reality is probabilistic and not deterministic: Einstein didn’t believe that God plays dice with the universe, but that became the scientific orthodoxy.
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Most physicists believe that there must be a Higgs field that pervades all space; the Higgs particle would be the carrier of the field and would interact with other particles, sort of the way a Jedi knight in Star Wars is the carrier of the “force.” The Higgs is a crucial part of the standard model of particle physics—but no one’s ever found it.
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The Higgs boson is presumed to be massive compared with most subatomic particles. It might have 100 to 200 times the mass of a proton. That’s why you need a huge collider to produce a Higgs—the more energy in the collision, the more massive the particles in the debris. But a jumbo particle like the Higgs would also be, like all oversize particles, unstable. It’s not the kind of particle that sticks around in a manner that we can detect—in a fraction of a fraction of a fraction of a second it will decay into other particles. What the LHC can do is create a tiny, compact wad of energy from which a Higgs might spark into existence long enough and vivaciously enough to be recognized.

Previous posts on CERN and the Higgs boson: The god of small things – CERN Prepares for LHC Operations – CERN Pressure Test Failure – The New Yorker on CERN’s Large Hadron Collider

Funding Medical Research

Cheap, ‘safe’ drug kills most cancers

It sounds almost too good to be true: a cheap and simple drug that kills almost all cancers by switching off their “immortality”. The drug, dichloroacetate (DCA), has already been used for years to treat rare metabolic disorders and so is known to be relatively safe. It also has no patent, meaning it could be manufactured for a fraction of the cost of newly developed drugs.

Evangelos Michelakis of the University of Alberta in Edmonton, Canada, and his colleagues tested DCA on human cells cultured outside the body and found that it killed lung, breast and brain cancer cells, but not healthy cells. Tumours in rats deliberately infected with human cancer also shrank drastically when they were fed DCA-laced water for several weeks.

DCA attacks a unique feature of cancer cells: the fact that they make their energy throughout the main body of the cell, rather than in distinct organelles called mitochondria. This process, called glycolysis, is inefficient and uses up vast amounts of sugar.

Until now it had been assumed that cancer cells used glycolysis because their mitochondria were irreparably damaged. However, Michelakis’s experiments prove this is not the case, because DCA reawakened the mitochondria in cancer cells. The cells then withered and died

The University of Alberta is raising funds to further the research. Some look at this and indite a funding system that does not support research for human health unless there is profit to be made. Much of the blame seems to go to profit focused drug companies. I can see room for some criticism. But really I think the criticism is misplaced.

The organizations for which curing cancer is the partial aim (rather than making money) say government (partial aim or public health…), public universities (partial aim of science research or medical research…), foundations, cancer societies, private universities… should fund such efforts, if they have merit. Universities have huge research budgets. Unfortunately many see profit as their objective and research as the means to the objective (based on their actions not their claims). These entities with supposedly noble purposes are the entities I blame most, not profit focused companies (though yes, if they claim an aim of health care they I would blame them too).

Now I don’t know what category this particular research falls into. Extremely promising or a decent risk that might work just like hundreds or thousands of other possibilities. But lets look at several possibilities. Some others thoughts on where it falls: Dichloroacetate to enter clinical trials in cancer patients, from a previous post here – Not a Cancer Cure Yet, The dichloroacetate (DCA) cancer kerfuffle, CBC’s ‘The Current’ on dichloroacetate (DCA), Dichloroacetate (DCA) Phase II Trial To Begin (“Like hundreds (if not, thousands) of compounds being tested to treat cancer, DCA was shown by Michelakis’ group earlier this year to slow the growth of human lung tumors in a preclinical rodent model.”).
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Your Inner Fish

photo of Neil Shubin

Your Inner Fish: A Journey into the 3.5-Billion-Year History of the Human Body by Neil Shubin. A great piece from the University of Chicago, Fish out of Water, provides a good preview to the book:

What are the leading causes of death in humans? Four of the top ten causes—heart disease, diabetes, obesity, and stroke – have some sort of genetic basis and, likely, a historical one. Much of the difficulty is almost certainly due to our having a body built for an active animal but the lifestyle of a spud.
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The problem is that the brain stem originally controlled breathing in fish; it has been jerry-rigged to work in mammals… This works well in fish, but it is a lousy arrangement for mammals.
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The example from microbes is not unique. Judging by the Nobel Prizes awarded in medicine and physiology in the past 13 years, I should have called this book Your Inner Fly, Your Inner Worm, or Your Inner Yeast. Pioneering research on flies won the 1995 Nobel Prize in medicine for uncovering a set of genes that builds bodies in humans and other animals. Nobels in medicine in 2002 and 2006 went to people who made significant advances in human genetics and health by studying an insignificant-looking little worm (C. elegans). Similarly, in 2001, elegant analyses of yeast (including baker’s yeast) and sea urchins won the Nobel in medicine for increasing our understanding of some of the basic biology of all cells. These are not esoteric discoveries made on obscure and unimportant creatures. These discoveries on yeast, flies, worms, and, yes, fish tell us about how our own bodies work, the causes of many of the diseases we suffer, and ways we can develop tools to make our lives longer and healthier.

Two of my more controversial posts have been: Evolution is Fundamental to Science and Understanding the Evolution of Human Beings by Country. Evolution is not controversial scientifically. Just as gravity is not. Obviously this understanding is far from universal however.

But it is just a matter of time: similar to Galileo Galilei and heliocentric cosmology. See: Galileo’s Battle for the Heavens – Copernican System – Galileo). We now sit maybe 100 years after Galileo’s death (based on the evidence available in support of each scientific theory). At some point the evidence is accepted and life continues. Though I must admit it, I find it a bit disappointing how long it is taking for some people to accept the evidence of evolution. But I probably need to learn to be more patient – I have been told that more than once. All I can do is try to help present some small amount of the great work so many scientists have done to advance our knowledge. And here I am talking about evolution – for the 28% of those in the USA that couldn’t provide the answer that earth revolves around the sun, in 1998, well, they need much more help than I can provide.

Bacteria Can Transfer Genes to Other Bacteria

From page 115 of Good Gems, Bad Germs:

Microbiologists of the 1950’s did not appreciate the stunning extent to which bacteria swap genes… In 1959 Japanese hospitals experience outbreaks of multidrug-resistant bacterial dysentery. The shigella bacteria, which caused the outbreaks, were shrugging off four different classes of previously effective antibiotics: sulfonamides, streptomycins, chloramphenicols, and tetracyclines… In fact, the Japanese researches found it quite easy to transfer multidrug resistance from E. coli to shingella and back again simply by mixing resistant and susceptible strains together in a test tube.

Virus Engineered To Kill Deadly Brain Tumors

Yale Lab Engineers Virus That Can Kill Deadly Brain Tumors

A laboratory-engineered virus that can find its way through the vascular system and kill deadly brain tumors has been developed by Yale School of Medicine researchers, it was reported this week in the Journal of Neuroscience.

Each year 200,000 people in the United States are diagnosed with a brain tumor, and metastatic tumors and glioblastomas make up a large part of these tumors. There currently is no cure for these types of tumors, and they generally result in death within months.
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“Three days after inoculation, the tumors were completely or almost completely infected with the virus and the tumor cells were dying or dead,” van den Pol said. “We were able to target different types of cancer cells. Within the same time frame, normal mouse brain cells or normal human brain cells transplanted into mice were spared. This underlines the virus’ potential therapeutic value against multiple types of brain cancers.”

Pretty cool. Too bad these press releases never quite live up to the initial promise. Still this one is very cool, if it can succeed in helping even a small percentage of people it will be a great breakthrough. It is also just cool – using a virus to kill tumors – how cool is that?

Scientists Search for Clues To Bee Mystery

Honey Bees Give Clues on Virus Spread by Carl Zimmer

Now, as farmers wait anxiously to see if the honeybees will suffer again this spring, the true cause of CCD remains murky. Skeptics have raised many reasons to doubt that Australian viruses are to blame. In Australia, bees that get Israeli acute paralytic virus don’t get sick, and the country has had no reports of CCD. And in places where honeybee colonies are collapsing — Greece, Poland, Spain — there are no imported Australian bees. These are not the sort of patterns you’d expect, the skeptics say, if Australian viruses were killing American bees.
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Whether scientists look inside a honeybee or look at the entire biosphere, nature is proving to be awesomely intricate. In the oceans and the soil, metagenomics is revealing millions of different kinds of microbes, with an almost inconceivable diversity of viruses shuttling between them, carrying genes from host to host. But we have almost no idea how these menageries work together, either in the biosphere or inside a host like a honeybee — or a human. Many of the microbes that metagenomics is revealing are entirely new to science. As genetic databases fill with DNA sequences from millions of new species, our scientific wisdom lags far behind.

How true. Watching as scientists try to work out what is going on with Colony Collapse Disorder is a great lesson in how scientists search for answers. As I stated earlier much of science is not about simple obvious truths but a search through confusing signs to try and determine what is going on. Answering why, is not always so easy as it appears when someone has already found the answer and posted it online.

Electron Filmed for the First Time

Now it is possible to see a movie of an electron. The movie shows how an electron rides on a light wave after just having been pulled away from an atom. This is the first time an electron has ever been filmed. Previously it has been impossible to photograph electrons since their extremely high velocities have produced blurry pictures. In order to capture these rapid events, extremely short flashes of light are necessary, but such flashes were not previously available.

With the use of a newly developed technology for generating short pulses from intense laser light, so-called attosecond pulses, scientists at the Lund University Faculty of Engineering in Sweden have managed to capture the electron motion for the first time. “It takes about 150 attoseconds for an electron to circle the nucleus of an atom. An attosecond is 10-18 seconds long, or, expressed in another way: an attosecond is related to a second as a second is related to the age of the universe,” says Johan Mauritsson, an assistant professor in atomic physics at the Faculty of Engineering, Lund University.

Scientists also hope to find out more about what happens with the rest of the atom when an inner electron leaves it, for instance how and when the other electrons fill in the gap that is created. “What we are doing is pure basic research. If there happen to be future applications, they will have to be seen as a bonus,” adds Johan Mauritsson. The length of the film corresponds to a single oscillation of the light, but the speed has then been ratcheted down considerably so that we can watch it. The filmed sequence shows the energy distribution of the electron and is therefore not a film in the usual sense.

Photo: Experimental results obtained in helium at an intensity of 1:2 x 1013 W=c/m2 are shown. The results are
distinctively different from those taken in argon (Fig. 1).With this higher intensity, more momentum is transferred to the electrons, and in combination with the lower initial energy, some electrons return to the atomic potential for further interaction. In the first panel, we compare the experimental results (right) with theoretical calculations (left) obtained for the same conditions.
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Superconducting Surprise

Assistant Professor of Physics Eric Hudson transfers liquid helium to cool the scanning tunneling microscope

Research Finds Superconducting Surprise

Most superconductors only superconduct at temperatures near absolute zero, but about 20 years ago, it was discovered that some ceramics can superconduct at higher temperatures (but usually still below 100 Kelvin, or -173 Celsius). Such high-temperature superconductors are now beginning to be used for many applications, including cell-phone base stations and a demo magnetic-levitation train. But their potential applications could be much broader. “If you could make superconductors work at room temperature, then the applications are endless,” said Hudson.

Superconductors are superior to ordinary metal conductors such as copper because current doesn’t lose energy as wasteful heat as it flows through them, thus allowing larger current densities. Once a current is set in motion in a closed loop of superconducting material, it will flow forever.
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The new MIT study shows that scattering by impurities occurs in the pseudogap state as well as the superconducting state. That finding challenges the theory that the pseudogap is only a precursor state to the superconductive state, and offers evidence that the two states may coexist.

This method of comparing the pseudogap and superconducting state using STM could help physicists understand why certain materials are able to superconduct at such relatively high temperatures, said Hudson. “Trying to understand what the pseudogap state is is a major outstanding question,” he said.

Photo: Assistant Professor of Physics Eric Hudson transfers liquid helium to cool the scanning tunneling microscope he is using in his research on high-temperature superconductivity. Photo by Donna Coveney.

Dead Zones in the Ocean

Oceanic Dead Zones Off West Coast are the ‘New Normal’

Ever since it was first noticed by crab fishermen who hauled up hundreds of dead and dying crabs in 2002, the “dead zone” that popped up in the waters along the northwestern coastal shelf just off the coast of Oregon has claimed unknown millions of lives. This oxygen-depleted region has transformed formerly rich seafloor communities teeming with life into vast graveyards filled with the bodies of crabs, echinoderms, molluscs, sea worms and other creatures.
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a low-oxygen zone appears each spring off the coast of Louisiana due to fertilizers in farm runoff and sewage present in the Mississippi River. When the Mississippi flows into the sea, it creates a nutrient-rich area that triggers huge but short-lived algal blooms that soon die, sink to the seafloor and are decomposed by bacteria that produce toxic sulfide gases.
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the dead zone off the West Coast of North America has another cause: global warming. Here’s how it works: Winds cause the oceanic rivers of nutrients, such as the California Current in this case, to flow upwards from the deep, carrying nutrients and phyoplankton into the sunlight, which triggers the phytoplankton to reproduce, to “bloom”. This is the normal state of things, but since global warming has been causing land temperatures to increase, these winds have become stronger and more persistent. This is not normal because it prolongs the oceanic upwelling, producing a surplus of phytoplankton that isn’t consumed and subsequently dies, and sinks to the seafloor to decay. As the bacterial-mediated breakdown occurs, dissolved oxygen in the surrounding water is depleted to dangerously low levels

One Step Closer to Holographic TV

UA team creates new holographic display

A 3-D holographic image that can be updated and viewed without special glasses may soon find its way from a UA optics lab to operating rooms and battlefield command centers.
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That holographic bird on your credit card can’t turn into something else every few minutes, but Tay’s display can take an image rendered in three dimensions — initially photographed or computer-generated — and display it on the display surface, followed by another and another.

In addition, the device requires no special glasses or headgear to see the image, unlike present-day virtual-reality systems.
The scientists who worked on the device first speak of using it as an aid in brain surgery or as a close-to-real-time battlefield display, but Tay and UA optical sciences professor Nasser Peyghambarian are not unaware of its much more commercial potential.
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The heart of the innovation, says Tay, is the photorefractive polymer — a thin plastic film that reacts to light — that can hold an image indefinitely and be updated. Tay says the method that allowed the polymer to hold the image and update it came to him “out of the blue” while at a meeting about that very problem.
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Cramming the pinball- machine-size collection of equipment into a “table-top” commercial unit is also possible, Tay says, but a challenge. Tay says the work, which started about two years ago, was done in collaboration with Nitto Denko Technical Corp. and was funded by the U.S. Air Force Office of Scientific Research.