Posts about Research

Beehive Fence Protects Farms from Elephants

photo of farmer in front of beehive fence in Botswana

Another cool use of appropriate technology. One of the problems with Elephants in Africa is when they go into farm fields and eat crops and destroy crops. The elephants and bees project is helping farmers deal with that problem.

By doing so they eliminate the need of farmers to protect their crops by killing elephant. The project uses bees natural behavior and elephants natural desire to avoid bees to create a fence that works to keep elephants out.

The beehives are hung on wires stretched between fenceposts around the farm. If an elephant bumps into the wires to try and enter the farm the bees will swarm and the elephants will run away (and the elephants will send an warning to other elephants to stay away). The fences are being used in Africa and India.

And this fence also produces honey. You can donate to the project to help elephants, bees and people.

Related: Insightful Problem Solving in an Asian ElephantElephant Underpass in KenyaUsing Drones to Deliver Medical Supplies in Roadless AreasFighting Elephant Poaching With Science (2007)Europe Bans Certain Pesticides, USA Just Keeps Looking, Bees Keep Dying (2013)

Fighting Superbugs with Superhero Bugs

As concerns over deadly antibiotic-resistant strains of ‘superbug’ bacteria grow, scientists at the Salk Institute are offering a possible solution to the problem: ‘superhero’ bacteria that live in the gut and move to other parts of the body to alleviate life-threatening side effects caused by infections.

Salk researchers reported finding a strain of microbiome Escherichia coli bacteria in mice capable of improving the animals’ tolerance to infections of the lungs and intestines by preventing wasting–a common and potentially deadly loss of muscle tissue that occurs in serious infections. If a similarly protective strain is found in humans, it could offer a new avenue for countering muscle wasting, which afflicts patients suffering from sepsis and hospital-acquired infections, many of which are now antibiotic resistant.

images of E. coli bacteria, salmonella typhimurium and burkholderia thailandensis

Salk scientists found a strain of E. coli bacteria (left) that were able to stop muscle wasting in mice infected with either Salmonella Typhimurium (center) and Burkholderia thailandensis (right). Image courtesy the Salk Institute.

“Treatments for infection have long focused on eradicating the offending microbe, but what actually kills people aren’t the bacteria themselves–it’s the collateral damage it does to the body,” says Janelle Ayres, a Salk assistant professor in the Nomis Foundation Laboratories for Immunobiology and Microbial Pathogenesis and senior researcher on the study.

“Our findings suggest that preventing the damage–in this case muscle wasting–can stave off the most life-threatening aspects of an infection,” she adds. “And by not trying the kill the pathogen, you’re not encouraging the evolution of the deadly antibiotic-resistant strains that are killing people around the world. We might be able to fight superbugs with ‘superhero’ bugs.”

Once the most powerful and revolutionary of drugs, antibiotics appear to have reached their limits, due to the ability of bacteria to rapidly evolve resistance to the medicines. The rise of antibiotic resistance presents a grave threat to people around the world, as diseases once easily controlled repel all attempts at treatment. A recent study found that up to half of the bacteria that cause infections in US hospitals after a surgery are resistant to standard antibiotics.

In the United States alone, two million people annually become infected with bacteria that are resistant to antibiotics and at least 23,000 people die each year as a direct result of these infections, according to the U.S. Centers for Disease Control.

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Funding Sources for Independent Postdoctoral Research Projects in Biology

Here is a nice list of funding sources for independent postdoctoral research projects in biology.

Some examples:

Directory of select science and engineering scholarships and fellowships for undergraduates, graduates and faculty on our blog.

Related: Science, Engineering and Math Fellowships (2008)Proposal to Triple NSF GFRP Awards and the Size of the Awards by 33% (2007)HHMI Expands Support of Postdoctoral ScientistsNSF Graduate Research Fellow Profiles (Sergy Brin, Google co-founder)

Lexus Has Built a Working Hoverboard

Toyota continues to do some fun and interesting research while they produce great cars (and make a lot of money doing so that allows them resources to do interesting research). Some past posts on their engineering exploits: Toyota Develops Thought-controlled Wheelchair (2009), Toyota Engineering Development Process, Innovation at Toyota, How to Develop Products like Toyota, Toyota IT Overview.

Toyota is teasing with the hoverboard announcement but it seems they have actually created it (though it isn’t ready to be in stores this year.

Liquid nitrogen cooled superconductors and permanent magnets combine to power the Lexus Hoverboard.

Sadly they haven’t bothered to hire a decent web designer. They have a pretty but broken website, with essentially no information. It is sad when interesting stories are keep to nearly no information using poorly designed websites created by people obviously more concerned with old fashion paper design thinking than how the web can be used to be clear and useful (not just pretty).

Pretty much for the last 10 years Toyota has had pretty but web hostile design for their web sites. It is a shame they can’t hire people that know how to properly create good web sites. Thankfully they hire good engineers and use good processes to actually develop products.

We Have Thousands of Viruses In Us All the Time

Biology and the amazing interactions within a human body are amazing. Our bodies are teeming with other life (and almost life – viruses). All these microbes have a drastic impact on our health and those impacts are not always bad.

A Virus In Your Mouth Helps Fight The Flu

Hidden inside all of us are likely thousands of viruses — maybe more. They just hang out, harmlessly. We don’t even know they’re there.

But every once in a while, one of these viral inhabitants might help us out.

Young people infected with a type of herpes virus have a better immune response to the flu vaccine than those not infected, scientists at Stanford University report Wednesday. In mice, the virus directly stops influenza itself.

We’re talking about a ubiquitous critter, called cytomegalovirus. About half of all Americans carry it. And so do nearly 100 percent of people in developing countries.

In younger people, CMV had the opposite effect that Davis had predicted: “The virus ramped up the immune system to give better protection from pathogens,” Mark Davis says. “We tested only for the flu, but I speculate it protects against everything.”

So should we all go out and get infected with CMV? No way! Davis exclaims.

You see, CMV has a dark side. It can become dangerous if the immune system is suppressed, which happens after an organ transplant or during treatments for autoimmune disorders. CMV is also a concern for pregnant woman. It’s the top viral cause of birth defects worldwide.

The human microbiome is incredible and teams with thousands of species (bacteria, viruses, members of domain Archaea, yeasts, single-celled eukaryotes, helminth parasites and bacteriophages). The complexity of interactions between all the elements of what is in our bodies and cells is one of the things that makes health care so challenging. It is also fascinating how these interactions provide benefits and costs as they work within our bodies.

The fact that we have evolved in concert with all these interactions is one of the big problems with anti-biotics. Antibiotics are miraculous when they work, but they can also decimate our natural micro-biomes which does create risks.

I would have thought Stanford wasn’t still supporting closed science 🙁 Sadly this research is not published in an open science manner.

Related: Foreign Cells Outnumber Human Cells in Our BodiesMicrobes Flourish In Healthy PeopleTracking the Ecosystem Within UsPeople Have More Bacterial Cells than Human CellsCats Control Rats With ParasitesSkin Bacteria

Leslie Lamport Receives 2013 ACM Turing Award

Leslie Lamport, a Principal Researcher at Microsoft Research, has been named as the recipient of the 2013 ACM A.M. Turing Award for imposing clear, well-defined coherence on the seemingly chaotic behavior of distributed computing systems, in which several autonomous computers communicate with each other by passing messages. He devised important algorithms and developed formal modeling and verification protocols that improve the quality of real distributed systems. These contributions have resulted in improved correctness, performance, and reliability of computer systems.

ACM (Association for Computing Machinery) announced that the funding level for the ACM Turing Award is now $1,000,000 (to be provided by Google). The new amount is four times its previous level. It seems to me the 14th of November 2014 is a bit late to announce the 2013 award winner, but for an extra $750,000 I would gladly wait a year (or a decade for that matter).

The new award level brings the computer science award to the level of Nobel Prizes and the Fields medal.

Leslie Lamport’s 1978 paper, “Time, Clocks, and the Ordering of Events in a Distributed System,” one of the most cited in the history of computer science.

Read more about the work of Leslie Lamport.

Related: Barbara Liskov wins Turing Award (2009)Donald Knuth, Computer Scientist (2006)Google 2006 Anita Borg Scholarship2008 Draper Prize for Engineering

Epigenetics, Scientific Inquiry and Uncertainty

Science is full of fascinating ideas. Epigenetics is one area I find particularly interesting. This previous post has a few links to learning more: DNA Passed to Descendants Changed by Your Life.

Angela Saini is one 109 people I follow on Twitter. I don’t see the point in “following” people on Twitter that you have no interest in, I only follow the small number of people that post Tweets I want to read.

In, Epigenetics: genes, environment and the generation game, Angela Saini looks at the confused state of current scientific understand now. It is very difficult to tell if, and if so, to what extent, epigenetic inheritance happens in people.

Professor Azim Surani, a leading developmental biologist and geneticist at the University of Cambridge, adds that while there is good evidence that epigenetic inheritance happens in plants and worms, mammals have very different biology. Surani’s lab carried out thorough studies on how epigenetic information was erased in developing mouse embryos and found that “surprisingly little gets through” the reprogramming process.

Professor Timothy Bestor, a geneticist at Columbia University in New York, is far more damning, claiming that the entire field has been grossly overhyped. “It’s an extremely fashionable topic right now. It’s very easy to get studies on transgenerational epigenetic inheritance published,” he says, adding that all this excitement has lowered critical standards.

Related: Epigenetic Effects on DNA from Living Conditions in Childhood Persist Well Into Middle AgeMedical Study Findings too Often Fail to Provide Us Useful KnowledgeScientific Inquiry Process Finds That Komodo Dragons Don’t have a Toxic Bite After All

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Refusal to Follow Scientific Guidance Results in Worms Evolving to Eat Corn Designed to Kill The Worms

An understanding of natural selection and evolution is fundamental to understanding science, biology, human health and life. Scientists create wonderful products to improve our lives: vaccines, antibiotics, etc.; if we don’t use them or misuse them it is a great loss to society.

There is also great value in genetic enhanced seeds and thus plants (through natural human aided processes such as breeding and providing good genetic material over a wide area – distances that would not be covered naturally, at least not in a time that helps us much). Genetic Modified Organisms (GMO) food, in which we tinker with the genes directly also holds great promise but has risks, especially if we forget basic scientific principles such as biodiversity.

Voracious Worm Evolves to Eat Biotech Corn Engineered to Kill It

First planted in 1996, Bt corn quickly became hugely popular among U.S. farmers. Within a few years, populations of rootworms and corn borers, another common corn pest, had plummeted across the midwest. Yields rose and farmers reduced their use of conventional insecticides that cause more ecological damage than the Bt toxin.

By the turn of the millennium, however, scientists who study the evolution of insecticide resistance were warning of imminent problems. Any rootworm that could survive Bt exposures would have a wide-open field in which to reproduce; unless the crop was carefully managed, resistance would quickly emerge.

Key to effective management, said the scientists, were refuges set aside and planted with non-Bt corn. Within these fields, rootworms would remain susceptible to the Bt toxin. By mating with any Bt-resistant worms that chanced to evolve in neighboring fields, they’d prevent resistance from building up in the gene pool.

But the scientists’ own recommendations — an advisory panel convened in 2002 by the EPA suggested that a full 50 percent of each corn farmer’s fields be devoted to these non-Bt refuges — were resisted by seed companies and eventually the EPA itself, which set voluntary refuge guidelines at between 5 and 20 percent. Many farmers didn’t even follow those recommendations.

Using extremely powerful tools like GMO requires society to have much better scientific literacy among those making decisions than any societies have shown thus far. The failure of our governments to enforce sensible scientific constraints on such use of genetic engineering creates huge risks to society. It is due to this consistent failure of our government to act within sensible scientific constraints that causes me to support efforts (along with other reasons – economic understanding – the extremely poor state of patent system, risk reduction…) to resist the widespread adoption of GMO, patenting of life (including seeds and seeds produced by seeds).

Wonderful things are possible. If we grow up and show a long term track record of being guided by scientific principles when the risks of not doing so are huge then I will be more supportive of using tactics such as GMO more easily. But I don’t see us getting their anytime soon. If anything we are much less scietifically minded and guided than we were 50 years ago: even while we bask in the glorious wonders science has brought us on a daily basis.

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Country H-index Ranking for Science Publications

The SCImago Journal and Country Rank provides journal and country scientific indicators developed from the information contained in the Scopus database (this site also lets you look at these ranking by very specific categories (I think 313 categories), for example biotechnology #1 USA, #2 Germany, #3 UK, #4 Japan, #9 China or Theoretical Computer Science #1 USA, #2 UK, #3 Canada, #6 China). I posted about this previously (in 2008 and 2011) and take a look at the updated picture in this post.

I like looking at data and country comparisons but in doing so it is wise to remember this is the results of a calculation that is interesting but hardly definative. We don’t have the ability to have exact numbers on haw the true scientific knowledge output by countries are. I think you can draw the conclusion that the USA is very influential, and along with other data make the case even that the USA is the leading scientific publication center.

The table shows the top 6 countries by h-index and then some others I chose to list.

Country h-index 2007
h-index
% of World
Population
% of World GDP total cites
USA 1,389 793     4.4%   22.4% 129,540,193
United Kingdom 851 465  0.9  3.4 31,393,290
Germany 740 408  1.2  4.7  25,848,738
France 681 376  0.9  3.6  5,795,531
Canada 658 370  0.5  2.5 15,696,168
Japan 635 372  1.8  8.2 20,343,377
Additional countries of interest
16) China 385 161  19.2  11.3  11,253,119
19) South Korea 343 161    .7  1.8  4,640,390
22) Brazil 305 148  2.8  3.1 3,362,480
24) India 301 146  17.6  2.5 4,528,302

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Nobel Prize Winner Criticizes Role of Popular Science Journals in the Scientific Process

Randy Schekman, 2013 Nobel Prize winner in physiology or medicine has written another critique of the mainstream, closed-science journals. How journals like Nature, Cell and Science are damaging science

Mine is a professional world that achieves great things for humanity. But it is disfigured by inappropriate incentives. The prevailing structures of personal reputation and career advancement mean the biggest rewards often follow the flashiest work, not the best. Those of us who follow these incentives are being entirely rational – I have followed them myself – but we do not always best serve our profession’s interests, let alone those of humanity and society.

We all know what distorting incentives have done to finance and banking. The incentives my colleagues face are not huge bonuses, but the professional rewards that accompany publication in prestigious journals – chiefly Nature, Cell and Science.

There is a better way, through the new breed of open-access journals that are free for anybody to read, and have no expensive subscriptions to promote. Born on the web, they can accept all papers that meet quality standards, with no artificial caps. Many are edited by working scientists, who can assess the worth of papers without regard for citations. As I know from my editorship of eLife, an open access journal funded by the Wellcome Trust, the Howard Hughes Medical Institute and the Max Planck Society, they are publishing world-class science every week.

Just as Wall Street needs to break the hold of the bonus culture, which drives risk-taking that is rational for individuals but damaging to the financial system, so science must break the tyranny of the luxury journals. The result will be better research that better serves science and society.

Very well said. The closed access journal culture is damaging science in numerous ways. We need to stop supporting those organizations and instead support organizations focused more on promoting great scientific work for the good of society.

Related: Fields Medalist Tim Gowers Takes Action To Stop Cooperating with Anti-Open Science CartelScience Journal Publishers Stay StupidHarvard Steps Up Defense Against Abusive Journal PublishersThe Future of Scholarly Publication (2005)The Trouble with Incentives: They WorkWhen Performance-related Pay BackfiresRewarding Risky Behavior

Scientific Research Spending Cuts in the USA and Increases Overseas are Tempting Scientists to Leave the USA

Unlimited Potential, Vanishing Opportunity

Globally, the United States invests more real dollars in research and development than any other country. However, in terms of percentage of gross domestic product, the United States is reducing its investment in scientific research. In fact, of the 10 countries investing the most money in scientific research, the United States is the only country that has reduced its investment in scientific research as a percentage of GDP since 2011.

The study by 16 scientific societies surveyed 3,700 scientists in the USA. As a result of the difficult research funding environment 20% of the scientists are considering going overseas to continue their research careers.

I have written about the likelihood of the USA’s leadership position in science, engineering and technology diminishing. As I stated (see links below), it seemed obvious many other countries were more committed to investing in science now than the USA was (which is different than decades ago when the USA was the country most committed). Various factors would determine how quickly others would shrink the USA’s lead including whether they could setup the infrastructure (scientific, social and economic) and how much damage the anti-science politicians elected in the USA do.

The advantages of being the leader in scientific and engineering research and development are huge and long term. The USA has been coasting on the advantages built up decades ago and the benefits still poor into the USA economy. However, the USA has continued to take economically damaging actions due to the anti-science politics of many who we elect. That is going to be very costly for the USA. The losses will also accelerate sharply when the long term investments others are making bear significant fruit. Once the economic impact is obvious the momentum will continue in that direction for a decade or two even if the USA finally realizes the mistake and learns to appreciate the importance of investing in science.

The good news is that many other countries are making wise investments in science. Humanity will benefit from those investments. The downside of the decisions to cut investments in science (and to actively ignore scientific knowledge) in the USA are largely to move much of the economic gains to other countries, which is regrettable for the future economy of the USA.

Related: Economic Strength Through Technology LeadershipScience, Engineering and the Future of the American EconomyGlobal Scientific LeadershipCompetition to Create Scientific Centers of ExcellenceEngineering the Future EconomyWorldwide Science and Engineering Doctoral Degree Data (2005)

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