Posts about Research

How Lysozyme Protein in Our Tear-Drops Kill Bacteria

A disease-fighting protein in our teardrops has been tethered to a tiny transistor, enabling UC Irvine scientists to discover exactly how it destroys dangerous bacteria. The research could prove critical to long-term work aimed at diagnosing cancers and other illnesses in their very early stages.

Ever since Nobel laureate Alexander Fleming found that human tears contain antiseptic proteins called lysozymes about a century ago, scientists have tried to solve the mystery of how they could relentlessly wipe out far larger bacteria. It turns out that lysozymes have jaws that latch on and chomp through rows of cell walls like someone hungrily devouring an ear of corn.

“Those jaws chew apart the walls of the bacteria that are trying to get into your eyes and infect them,” said molecular biologist and chemistry professor Gregory Weiss, who co-led the project with associate professor of physics & astronomy Philip Collins.

The researchers decoded the protein’s behavior by building one of the world’s smallest transistors – 25 times smaller than similar circuitry in laptop computers or smartphones. Individual lysozymes were glued to the live wire, and their eating activities were monitored.

“Our circuits are molecule-sized microphones,” Collins said. “It’s just like a stethoscope listening to your heart, except we’re listening to a single molecule of protein.”

It took years for the UCI scientists to assemble the transistor and attach single-molecule teardrop proteins. The scientists hope the same novel technology can be used to detect cancerous molecules. It could take a decade to figure out but would be well worth it, said Weiss, who lost his father to lung cancer.

“If we can detect single molecules associated with cancer, then that means we’d be able to detect it very, very early,” Weiss said. “That would be very exciting, because we know that if we treat cancer early, it will be much more successful, patients will be cured much faster, and costs will be much less.”

The project was sponsored by the National Cancer Institute and the National Science Foundation. Co-authors of the Science paper are Yongki Choi, Issa Moody, Patrick Sims, Steven Hunt, Brad Corso and Israel Perez.

Related: full press releaseWhy ‘Licking Your Wounds’ WorksHow Bleach Kills BacteriaAlgorithmic Self-Assembly

Royal Society Journal Embraces Open Access

Royal Society journal archive made permanently free to access

The Royal Society…journal archive – which includes the first ever peer-reviewed scientific journal – has been made permanently free to access online.

Around 60,000 historical scientific papers are accessible via a fully searchable online archive, with papers published more than 70 years ago now becoming freely available.

reasures in the archive include Isaac Newton’s first published scientific paper, geological work by a young Charles Darwin, and Benjamin Franklin’s celebrated account of his electrical kite experiment.

The move is being made as part of the Royal Society’s ongoing commitment to open access in scientific publishing.

Good for them. Slowly more and more are realizing clinging to old fashion publishing models are contrary to promoting science and scientific literacy.

Related: 340 Years of Royal Society Journals OnlineBritain’s Royal Society Experiments with Open Access (2006)8-10 Year Olds Research Published in Royal Society Journal

Study of the Colony Collapse Disorder Continues as Bee Colonies Continue to Disappear

I can understand why people get complacent. We have a pretty remarkable run of science and technology finding solutions for whatever peril we face.

Also, quite often, future risks are over-blown. Then, people get habituated to reading ominous predictions, followed by a future doesn’t seem to reach those dramatic predictions. But this is a risky pattern to just expect – that no matter what we will figure out some way to avoid the consequences.

Risks actually do come true. The obvious result of overfishing, just as predicted, has resulted in collapses of fish populations over and over creating great hardship for those who had fallen victim to that prediction. If people don’t vaccinate themselves (and their kids) we will have ever increasing numbers of deaths and sickness. If we fail to use anti-biotics is a long term sustainable way, our actions will result in many deaths.

I am not sure why we find it so easy to ignore the evidence of bad consequences but we do. Partially I would imagine that as problems begin to be manifest countermeasures take affect. So in the fishing example, many people leave that line of work and so the numbers in the industry after a collapse, who are suffering in the present, are reduced. Still I find it odd how easily we ignore the risks in the future.

I do understand if there are short term benefits to ignoring the risks (or pretending they don’t exist): so you have fisherman that don’t want to take steps in advance to avoid collapse. Or you have industries and politicians that want to pretend ignoring global warming is a strategy to avoid the consequences. Or you have parents that say, well today we don’t have many risks of sicknesses people get vaccinated against (yes, because people have been vaccinated – if you stop vaccinating your children they we get to experience the avoidable pain and suffering).

I have been following the honeybee colony collapse disorder for several years (see the end of the posts for links to posts from 2006 – 2010, like this one The Study of Bee Colony Collapses Continues from 2007). It is a great example of the scientific inquiry process. It is messy and confusing and full of studies that have trouble finding what the actually causes are or what solutions will work.

There are occasionally mentions of how devestating things could get if the trend continues. In fact stories that seem so devestating that they just don’t seem real. surely either that won’t happen or if it started to some countermeasure would be found to deal with the problem and avoid the most severe consequences. That is basially how I have felt about it. But that is not because of some scientific understanding but just a feeling that hey that couldn’t really happen. Well that isn’t exactly solid evidence that it can’t.

Honeybee problem nearing a ‘critical point’

In addition to continued reports of CCD — a still somewhat mysterious phenomenon in which entire bee colonies literally disappear, alien-abduction style, leaving not even their dead bodies behind — bee populations are suffering poor health in general, and experiencing shorter life spans and diminished vitality. And while parasites, pathogens, and habitat loss can deal blows to bee health, research increasingly points to pesticides as the primary culprit.

farmers use these chemicals to protect their crops from destructive insects, but in so doing, they harm other insects essential to their crops’ production — a catch-22 that Hackenberg said speaks to the fact that “we have become a nation driven by the chemical industry.” In addition to beekeeping, he owns two farms, and even when crop analysts recommend spraying pesticides on his crops to kill an aphid population, for example, he knows that “if I spray, I’m going to kill all the beneficial insects.” But most farmers, lacking Hackenberg’s awareness of bee populations, follow the advice of the crop adviser — who, these days, is likely to be paid by the chemical industry, rather than by a state university or another independent entity.

I believe this is the latest advise of the Unites States Department of Agriculture (though their web site doesn’t make it nearly as obvious as it should that this is in fact the current advice – the document seems to indicate it is but if someone were to say no, that is outdated, it wouldn’t be hard to believe)

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Journal of Emerging Investigators Will Publish Middle and High School Student Research Papers

The Journal of Emerging Investigators is a new journal for publishing research paper and reviews of research papers by middle school and high school students from any country.

The Journal of Emerging Investigators strives to provide students with as much access to original scientific writing as possible. With this in mind, all submissions are covered by an attribution non-commercial, no derivative license. This means that anyone is free to share, copy and distribute an unaltered article for non-commercial purposes.

Graduate students with substantial research experience will review the manuscripts.

All hypothesis driven science is acceptable for research articles. This includes, but is not limited to, life science, physics, chemistry, health, psychology, and physiology. Engineering articles are also accepted as long as there is a clear question and hypothesis being tested.

Hopefully this will encourage some students to give research a try. Advisors may submit items for publication (students have to have an mentor/teacher do the submitting.

Similar journals: The Journal of Experimental Secondary Science, open science :-)Canadian Young Scientist, closed science :-(

Related: 8-10 Year Olds Research Published in Royal Society JournalYouTube SpaceLab Experiment CompetitionOpen Access Engineering JournalsKids on Scientists: Before and After

Using a Virus to Improve Solar-cell Efficiency Over 30%

Solar and wind energy are making great strides, and are already contributing significantly to providing relatively clean energy.

Researchers at MIT have found a way to make significant improvements to the power-conversion efficiency of solar cells by enlisting the services of tiny viruses to perform detailed assembly work at the microscopic level.

In a solar cell, sunlight hits a light-harvesting material, causing it to release electrons that can be harnessed to produce an electric current. The research, is based on findings that carbon nanotubes — microscopic, hollow cylinders of pure carbon — can enhance the efficiency of electron collection from a solar cell’s surface.

Previous attempts to use the nanotubes, however, had been thwarted by two problems. First, the making of carbon nanotubes generally produces a mix of two types, some of which act as semiconductors (sometimes allowing an electric current to flow, sometimes not) or metals (which act like wires, allowing current to flow easily). The new research, for the first time, showed that the effects of these two types tend to be different, because the semiconducting nanotubes can enhance the performance of solar cells, but the metallic ones have the opposite effect. Second, nanotubes tend to clump together, which reduces their effectiveness.

And that’s where viruses come to the rescue. Graduate students Xiangnan Dang and Hyunjung Yi — working with Angela Belcher, the W. M. Keck Professor of Energy, and several other researchers — found that a genetically engineered version of a virus called M13, which normally infects bacteria, can be used to control the arrangement of the nanotubes on a surface, keeping the tubes separate so they can’t short out the circuits, and keeping the tubes apart so they don’t clump.

The system the researchers tested used a type of solar cell known as dye-sensitized solar cells, a lightweight and inexpensive type where the active layer is composed of titanium dioxide, rather than the silicon used in conventional solar cells. But the same technique could be applied to other types as well, including quantum-dot and organic solar cells, the researchers say. In their tests, adding the virus-built structures enhanced the power conversion efficiency to 10.6% from 8% — almost a one-third improvement.

Read the full press release

Related: Using Virus to Build BatteriesUsing Viruses to Construct ElectrodesUsing Bacteria to Carry Nanoparticles Into Cells

Rats Show Empathy-driven Behavior

Rats free trapped companions, even when given choice of chocolate instead

The experiments, designed by psychology graduate student and first author Inbal Ben-Ami Bartal with co-authors Decety and Peggy Mason, placed two rats that normally share a cage into a special test arena. One rat was held in a restrainer device — a closed tube with a door that can be nudged open from the outside. The second rat roamed free in the cage around the restrainer, able to see and hear the trapped cagemate but not required to take action.

The researchers observed that the free rat acted more agitated when its cagemate was restrained, compared to its activity when the rat was placed in a cage with an empty restrainer. This response offered evidence of an “emotional contagion,” a frequently observed phenomenon in humans and animals in which a subject shares in the fear, distress or even pain suffered by another subject.

While emotional contagion is the simplest form of empathy, the rats’ subsequent actions clearly comprised active helping behavior, a far more complex expression of empathy. After several daily restraint sessions, the free rat learned how to open the restrainer door and free its cagemate. Though slow to act at first, once the rat discovered the ability to free its companion, it would take action almost immediately upon placement in the test arena.

“We are not training these rats in any way,” Bartal said. “These rats are learning because they are motivated by something internal. We’re not showing them how to open the door, they don’t get any previous exposure on opening the door, and it’s hard to open the door. But they keep trying and trying, and it eventually works.”

To control for motivations other than empathy that would lead the rat to free its companion, the researchers conducted further experiments. When a stuffed toy rat was placed in the restrainer, the free rat did not open the door. When opening the restrainer door released his companion into a separate compartment, the free rat continued to nudge open the door, ruling out the reward of social interaction as motivation. The experiments left behavior motivated by empathy as the simplest explanation for the rats’ behavior.

“There was no other reason to take this action, except to terminate the distress of the trapped rats,” Bartal said. “In the rat model world, seeing the same behavior repeated over and over basically means that this action is rewarding to the rat.”

As a test of the power of this reward, another experiment was designed to give the free rats a choice: free their companion or feast on chocolate. Two restrainers were placed in the cage with the rat, one containing the cagemate, another containing a pile of chocolate chips. Though the free rat had the option of eating all the chocolate before freeing its companion, the rat was equally likely to open the restrainer containing the cagemate before opening the chocolate container.

“That was very compelling,” said Mason, Professor in Neurobiology. “It said to us that essentially helping their cagemate is on a par with chocolate. He can hog the entire chocolate stash if he wanted to, and he does not. We were shocked.”

Now that this model of empathic behavior has been established, the researchers are carrying out additional experiments. Because not every rat learned to open the door and free its companion, studies can compare these individuals to look for the biological source of these behavioral differences. Early results suggested that females were more likely to become door openers than males, perhaps reflecting the important role of empathy in motherhood and providing another avenue for study…

Interesting study. My guess is this is the kind of thing those that don’t like science would deride. I believe in the value of science. I believe in the value of learning. I believe that such experiments are what drives science forward. I believe if you want your economy to benefit from investing in science you should be encouraging hundreds and thousands of such experiments. Funding for this study was provided by The National Science Foundation (NSF), and others.

I am thankful that more and more countries are willing to invest in science, especially since the USA is showing an increasing anti-science attitude. I would rather the USA continue to believe in the value of science and other countries looked to increase investments. But, it is much better that other countries increase their interest in science, and willingness to invest in science, to more than make up for the USA’s decisions to reduce the appreciation for science than for the world to just lose do to a decrease in investments in science.

Related: Insightful Problem Solving in an Asian ElephantPigeon Solves Box and Banana ProblemStand with ScienceEliminating NSF Program to Aid K-12 Science EducationThe Importance of Science Education

Stand with Science – Late is Better than Never

The USA public has made very bad decisions in who to send to Washington DC to spend our money (and the money of our children and grandchildren). We have wasted hundreds of billions that could have been spent more wisely. I happen to think investing in science and engineering is important for a societies economic health. The problem the USA has is we have chosen to waste lots of money for decades, at some point you run out of money (yes the USA government doesn’t really, as they can print it, but essentially they do – in practical terms).

I would certainly eliminate tax breaks for trust fund babies and trust fund grandchildren (while your grandchildren are going to be left holding the bag for the spending those elected by us, the grandchildren of the rich often get huge trust funds with no taxes being paid at all). But most of the people we have elected want to give trust fund babies huge payoffs. I would cut much spending in government – spending 5% less in 2020 than we did this year would be fine with me. But we don’t elect people that support that. I would support not adding new extensions to tax cuts sold with false claims and again supported by those we continue to elect. I wouldn’t allow the financial industry subverting of markets. But again we elect people that do allow that. And when the bill comes due for letting them take tens and hundreds of millions in individual profits in the good years, we can either let the economy go into a depression (maybe) or spend hundreds of billions to trillions bailing out those institutions our politicians let threaten the economy.

It might not seem fair, but there are consequences to allowing our political system to waste huge amounts of money paying of special interests for decades. And investing in science and engineering has been a casualty and will likely continue to be. Eventually you run out of money, even for the stuff that matters. Trying to fight for politicians that will put the interests of the country ahead of their donors is not something you can do effectively only when your interests are directly threatened. At that point things may already be too bad to be saved.

I have been writing about the failed political system for quite awhile now. I wrote awhile back that Hillary Clinton’s idea to tripple the number of GRFP awards was something I thought was very smart economically. But even then I questioned if we could afford it, if we refused to do anything else different (just adding new spending isn’t what the country needed).

Even in the state the politicians we continue to elect (we elect the same people election after election – there is no confusion about what they will do) we can debate what to cut and for something we spend so little on as investing science and engineering we can even easily increase that spending and not have any real impact on cutting overall spending. But those we have elected don’t show much interest in investing in science and engineering overall.

The USA continues to invest a good deal in science and engineering. But the difference in focus today versus the 1960′s is dramatic. The USA will continue to do well in the realm of science. The advantages gained over decades leave us in a hugely beneficial position – and one that takes other countries decades to catch up to. Now some countries have been working on that for decades now, and are doing very well. China, hasn’t been at it quite as long but has been making amazingly fast progress (similar to the amazing economic story).

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Russia Launches Mars Moon Probe

Russians launch Mars moon probe

Russia has launched an audacious bid to scoop up rock and dust samples from the Martian moon Phobos and bring them back to Earth for study.

Moscow has despatched a total of 16 missions to the Red Planet since the 1960s. None has successfully completed its goals, with the most recent endeavour – the sophisticated Mars-96 spacecraft – being destroyed in a failed launch.

Once on the surface, a robotic arm will pick up samples of the regolith (“soil”). Some of this material will be analysed there and then, but a portion of it – about 200g – will be transferred to a canister for return to Earth.

This canister and its departure stage should be sent home within a few days of Phobos-Grunt’s arrival on the moon. All being well, the canister should fall to Earth in the Kazakh desert in August 2014.

Potato-shaped Phobos is a fascinating target. Although it has been studied extensively by passing satellites, it still holds many secrets – not just about itself, but also the planet below.

The mission also is carrying a Chinese satellite that will be launched into orbit around Mars. This mission shows the future of space exploration. The USA continues to reduce the funding for space exploration while countries such as China are greatly increasing their funding.

I expect the leading space exploration will become much more global and the USA will take a less prominent role as the USA decides to spend funds elsewhere instead of scientific missions in space. Politicians in the USA have also stopped NASA from collaborating internationally which further reduces the USA role in the future of scientific research in space.

Russia seems to be making a new push to invest in space after a period of reduced funding. Russia’s economy still has many weaknesses, but in the last decade the oil wealth has provided some wealth and Russia is interested in using some of those funds for space exploration.

Update: This attempt failed also, making Russia 0 for 17 on Mars attempts. In the last few years Russia has shown a renewed interest in investing in space exploration. But their struggles show that it isn’t easy to in effect restart a program. Space exploration requires a great deal of very complex work. I hope they can get back on track and efforts in other countries also do well: China, Japan…

Related: NASA’s Mars Curiosity RoverMagnetic Portals Connect Sun and EarthGreat Astronaut Self Portrait

Epigenetic Effects on DNA from Living Conditions in Childhood Persist Well Into Middle Age

Family living conditions in childhood are associated with significant effects in DNA that persist well into middle age, according to new research by Canadian and British scientists.

The team, based at McGill University in Montreal, University of British Columbia in Vancouver and the UCL Institute of Child Health in London looked for gene methylation associated with social and economic factors in early life. They found clear differences in gene methylation between those brought up in families with very high and very low standards of living. More than twice as many methylation differences were associated with the combined effect of the wealth, housing conditions and occupation of parents (that is, early upbringing) than were associated with the current socio-economic circumstances in adulthood. (1252 differences as opposed to 545).

I find Epigenetics to be a very interesting area. My basic understanding as I grew up was that you inherited your genes. But epigenetics explores how your genes change over time. This has been a very active area of research recently. Your DNA remains the same during your life. But the way those genes are expressed changes.

I don’t know of any research supporting the idea I mention in this example, but, to explain the concept in a simple way: you may carry genes in your DNA for processing food in different ways. If you have very limited diet the way your body reacts could be to express genes that specialize in maximizing the acquisition of nutrition from food. And it could be that your body sets these expressions based on your conditions when young; if later, your diet changes you may have set those genes to be expressed in a certain way. Again this is an example to try and explain the concept, not something where I know of research that supports evidence for this example.

The findings by these universities, were unfortunately published in a closed way. Universities should not support the closing of scientific knowledge. Several universities, that support open science, require open publication of scientific research. It is unfortunate some universities continue to support closed science.

The research could provide major evidence as to why the health disadvantages known to be associated with low socio-economic position can remain for life, despite later improvement in living conditions. The study set out to explore the way early life conditions might become ‘biologically-embedded’ and so continue to influence health, for better or worse, throughout life. The scientists decided to look at DNA methylation, a so-called epigenetic modification that is linked to enduring changes in gene activity and hence potential health risks. (Broadly, methylation of a gene at a significant point in the DNA reduces the activity of the gene.)

Related: DNA Passed to Descendants Changed by Your LifeBlack Raspberries Alter Hundreds of Genes Slowing CancerBreastfeeding Linked to More Intelligent Kids

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2011 Nobel Prize in Chemistry

photo of Dan Shechtman

Dan Shechtman, Israel Institute of Technology, 2011 Nobel Laurette in Chemistry

The Royal Swedish Academy of Sciences has decided to award the Nobel Prize in Chemistry for 2011 to Dan Shechtman, Technion – Israel Institute of Technology, Haifa, Israel for the discovery of quasicrystals.

In quasicrystals, we find the fascinating mosaics reproduced at the level of atoms: regular patterns that never repeat themselves. However, the configuration found in quasicrystals was considered impossible, and Dan Shechtman had to fight a fierce battle against established science. The Nobel Prize in Chemistry 2011 has fundamentally altered how chemists conceive of solid matter.

On the morning of 8 April 1982, an image counter to the laws of nature appeared in Dan Shechtman’s electron microscope. In all solid matter, atoms were believed to be packed inside crystals in symmetrical patterns that were repeated periodically over and over again. For scientists, this repetition was required in order to obtain a crystal.

Shechtman’s image, however, showed that the atoms in his crystal were packed in a pattern that could not be repeated. Such a pattern was considered just as impossible as creating a football using only six-cornered polygons, when a sphere needs both five- and six-cornered polygons. His discovery was extremely controversial. In the course of defending his findings, he was asked to leave his research group. However, his battle eventually forced scientists to reconsider their conception of the very nature of matter.

Aperiodic mosaics, such as those found in the medieval Islamic mosaics of the Alhambra Palace in Spain and the Darb-i Imam Shrine in Iran, have helped scientists understand what quasicrystals look like at the atomic level. In those mosaics, as in quasicrystals, the patterns are regular – they follow mathematical rules – but they never repeat themselves.

When scientists describe Shechtman’s quasicrystals, they use a concept that comes from mathematics and art: the golden ratio. This number had already caught the interest of mathematicians in Ancient Greece, as it often appeared in geometry. In quasicrystals, for instance, the ratio of various distances between atoms is related to the golden mean.

Following Shechtman’s discovery, scientists have produced other kinds of quasicrystals in the lab and discovered naturally occurring quasicrystals in mineral samples from a Russian river. A Swedish company has also found quasicrystals in a certain form of steel, where the crystals reinforce the material like armor. Scientists are currently experimenting with using quasicrystals in different products such as frying pans and diesel engines.

Related: 2009 Nobel Prize in Chemistry: the Structure and Function of the RibosomeThe Nobel Prize in Chemistry 2008Nobel Prize in Chemistry (2006)

Read more on the science he has worked on. Our understanding of science is built on the discoveries of our predecessors and on the discoveries that counter what we thought we knew.
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Driving Via Direct Signals from the Brain

Last year we learned of Google’s Self Driving Car, which is actually making great progress in the real world (cool). And a few years ago I wrote about Toyota’s wheelchair you control with your mind. Now Nissan is looking at cars that you drive aided by accessing brain signals.

This idea is a bit scary to me, the self driving car is less so. But it is great to see us pushing the engineering boundaries forward. It is such a shame that the huge economic failures in the USA, Europe and Japan are rightly grabbing much of the attention these days. If we just reduced the waste and corruption in the political and financial systems it would allow us to take more joy is the great time we do for awesome engineering breakthroughs. Still, if we can try to block out those painful economic realities, these types of breakthroughs are really cool.

The webcast shows the work of the Artificial Intelligence Group of the Freie Universität Berlin in Germany (BrainDriver).

Related: Nissan’s Cars Will Read Your MindResearching Direct Brain Interfaces for Text EntryWave Disk Engine Could Increase Efficiency 5 Times

And Nissan is collaborating with the École Polytechnique Fédérale de Lausanne in Switzerland (EPFL) on a car that uses your brain signals (along with signals the computer gets via its own sensors) to aid in driving.
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