Posts about university research

80% of the Antibiotics in the USA are Used in Agriculture and Aquaculture

Citing an overabundance in the use of antibiotics by the agriculture and aquaculture industries that poses a threat to public health, economics professor Aidan Hollis has proposed a solution in the form of user fees on the non-human use of antibiotics.

In a newly released paper published (closed science, sadly, so no link provide), Hollis and co-author Ziana Ahmed state that in the United States 80% of the antibiotics in the country are consumed in agriculture and aquaculture for the purpose of increasing food production.

This flood of antibiotics released into the environment – sprayed on fruit trees and fed to the likes of livestock, poultry and salmon, among other uses – has led bacteria to evolve, Hollis writes. Mounting evidence cited in the journal shows resistant pathogens are emerging in the wake of this veritable flood of antibiotics – resulting in an increase in bacteria that is immune to available treatments.

If the problem is left unchecked, this will create a health crisis on a global scale, Hollis says.

Hollis suggest that the predicament could be greatly alleviated by imposing a user fee on the non-human uses of antibiotics, similar to the way in which logging companies pay stumpage fees and oil companies pay royalties.

“Modern medicine relies on antibiotics to kill off bacterial infections,” explains Hollis. “This is incredibly important. Without effective antibiotics, any surgery – even minor ones – will become extremely risky. Cancer therapies, similarly, are dependent on the availability of effective antimicrobials. Ordinary infections will kill otherwise healthy people.”

Bacteria that can effectively resist antibiotics will thrive, Hollis adds, reproducing rapidly and spreading in various ways.

“It’s not just the food we eat,” he says. “Bacteria is spread in the environment; it might wind up on a doorknob. You walk away with the bacteria on you and you share it with the next person you come into contact with. If you become infected with resistant bacteria, antibiotics won’t provide any relief.”

While the vast majority of antibiotic use has gone towards increasing productivity in agriculture, Hollis asserts that most of these applications are of “low value.”

“It’s about increasing the efficiency of food so you can reduce the amount of grain you feed the cattle,” says Hollis. “It’s about giving antibiotics to baby chicks because it reduces the likelihood that they’re going to get sick when you cram them together in unsanitary conditions.

“These methods are obviously profitable to the farmers, but that doesn’t mean it’s generating a huge benefit. In fact, the profitability is usually quite marginal.

“The real value of antibiotics is saving people from dying. Everything else is trivial.”

While banning the use of antibiotics in food production is challenging, establishing a user fee makes good sense, according to Hollis.

Such a practice would deter the low-value use of antibiotics, with higher costs encouraging farmers to improve their animal management methods and to adopt better substitutes for the drugs, such as vaccinations.

Hollis also suggests that an international treaty could ideally be imposed. “Resistant bacteria do not respect national borders,” he says. He adds that such a treaty might have a fair chance of attaining international compliance, as governments tend to be motivated by revenue collection.

Hollis notes that in the USA, a move has been made to control the non-human use of antibiotics, with the FDA recently seeking voluntary limits on the use of antibiotics for animal growth promotion on farms.

Related: Raising Food Without AntibioticsOur Dangerous Antibiotic Practices Carry Great RisksWhat Happens If the Overuse of Antibiotics Leads to Them No Longer Working?Antibiotics Too Often Prescribed for Sinus Woes

DNA Contains Gene Control Instructions

Scientists discover double meaning in genetic code

Scientists have discovered a second code hiding within DNA. This second code contains information that changes how scientists read the instructions contained in DNA and interpret mutations to make sense of health and disease.

“For over 40 years we have assumed that DNA changes affecting the genetic code solely impact how proteins are made,” said Stamatoyannopoulos. “Now we know that this basic assumption about reading the human genome missed half of the picture. These new findings highlight that DNA is an incredibly powerful information storage device, which nature has fully exploited in unexpected ways.”

The genetic code uses a 64-letter alphabet called codons. The UW team discovered that some codons, which they called duons, can have two meanings, one related to protein sequence, and one related to gene control. These two meanings seem to have evolved in concert with each other. The gene control instructions appear to help stabilize certain beneficial features of proteins and how they are made.

The discovery of duons has major implications for how scientists and physicians interpret a patient’s genome and will open new doors to the diagnosis and treatment of disease.

“The fact that the genetic code can simultaneously write two kinds of information means that many DNA changes that appear to alter protein sequences may actually cause disease by disrupting gene control programs or even both mechanisms simultaneously,” said Stamatoyannopoulos.

The wonder of DNA continues to amaze.

Related: Epigenetic Effects on DNA from Living Conditions in Childhood Persist Well Into Middle AgeDNA Passed to Descendants Changed by Your LifeDNA based Algorithmic Self-Assembly

Better Health Through: Exercise, Not Smoking, Low Weight, Healthy Diet and Low Alcohol Intake

These 5 activities/state reduce the risk of chronic diseases: regular exercise, not smoking, healthy bodyweight, healthy diet and low alcohol intake. How these were defined

  • not smoking
  • body mass index (BMI): 18 to under 25
  • diet: target was to be 5 portions of fruit and/or vegetables a day, but since almost no one meet that target they reduced the acceptable rate to 3 as accepted as ‘healthy.” Also a diet with less than 30% of calories from fat was required.
  • physical activity: walking two or more miles to work each day, or cycling ten or more miles to work each day, or ‘vigorous’ exercise described as a regular habit
  • alcohol: three or fewer units per day, with abstinence not treated as a healthy behaviour.

Healthy Lifestyles Reduce the Incidence of Chronic Diseases and Dementia: Evidence from the Caerphilly Cohort Study (PLoS open science publication).

The numbers of men judged to be following a healthy lifestyle were as follows: 179 (8%) followed none of the five behaviours, 702 (31%) followed one behaviour, 814 (36%) followed two, 429 (19%) followed three, 111 (5%) followed four or five behaviours and only two (0.1%) followed all five behaviors.

Within a representative sample of middle-aged men, the following of increasing numbers of healthy behaviours was associated with increasing reductions in several important chronic diseases and mortality: an estimated 50% reduction in diabetes, 50% in vascular disease and 60% for all-cause mortality. These results therefore confirm previous studies and provide further data on the association of lifestyle with cognitive impairment and dementia, with a reduction of about 60% in cognitive impairment and about the same in dementia. These reductions, and especially those in cognitive function, are of enormous importance in an ageing population.

Healthy habits reduce dementia risk (Cardiff University press release):

The people who consistently followed four or five of these behaviors exp
experienced a 60 per cent decline in dementia and cognitive decline – with exercise being the strongest mitigating factor – as well as 70 per cent fewer instances of diabetes, heart disease and stroke, compared with people who followed none.

Principle Investigator Professor Peter Elwood from Cardiff University’s School of Medicine. “What the research shows is that following a healthy lifestyle confers surprisingly large benefits to health – healthy behaviours have a far more beneficial effect than any medical treatment or preventative procedure.

Christopher Allen, Senior Cardiac Nurse at the British Heart Foundation, which part-funded the study, said:

“The results of this study overwhelmingly support the notion that adopting a healthy lifestyle reduces your risk of cardiovascular disease and dementia.

Related: Examining the Scientific Basis Around Exercise and Diet ClaimsHealthy Diet, Healthy Living, Healthy WeightStudy Finds Obesity as Teen as Deadly as SmokingPhysical Activity for Adults: Inactivity Leads to 5.3 Million Early Deaths a YearToday, Most Deaths Caused by Lifetime of Action or Inaction

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

Anti-Science Politics in Australia, Canada and the UK

Age of Unreason by George Monbiot

The governments of Britain, Canada and Australia are trying to stamp out scientific dissent.

in Canada… scientists with government grants working on any issue that could affect industrial interests – tar sands, climate change, mining, sewage, salmon farms, water trading – are forbidden to speak freely to the public(17,18,19). They are shadowed by government minders and, when they must present their findings, given scripts to memorise and recite(20). Dozens of turbulent research programmes and institutes have either been cut to the bone or closed altogether(21).

In Australia, the new government has chosen not to appoint a science minister(22). Tony Abbott, who once described manmade climate change as “absolute crap”(23), has already shut down the government’s Climate Commission and Climate Change Authority(24).

Follow the link for sources. Sadly governments are fighting for the crown of how anti-science they can be. It isn’t a matter of the countries that are doing a good job and a better job of using scientific understanding to aid in policy decisions. It is a matter of how extreme the anti-science crowds are in each country.

Trashing the scientific method and the use of scientific knowledge to pursue a pre-determined political agenda is a foolhardy action putting political expediency above effectiveness. Making political judgement, considering the available scientific research is fine, and will result in some people being upset. But the extremely bad process behind ignoring and intentionally sabotaging the use of data and scientific thinking is extremely harmful to society.

Every man has a right to his own opinion, but no man has a right to be wrong in his facts.
– Bernard Baruch (Daniel Patrick Moynihan said something very similar later)

Related: The Politics of Anti-Science (USA focus)Science and Engineering in PoliticsStand with Science: Late is Better than NeverScience and Engineering in Global Economics

Mechanical Gears Found in Jumping Insects

A natural example of a functioning gear mechanism has been discovered in a common insect – the plant-hopper Issus – showing that evolution developed interlocking cogs long before we did.

The gears in the Issus hind-leg bear remarkable engineering resemblance to those found on every bicycle and inside every car gear-box. Each gear tooth has a rounded corner at the point it connects to the gear strip; a feature identical to man-made gears such as bike gears – essentially a shock-absorbing mechanism to stop teeth from shearing off.

The gear teeth on the opposing hind-legs lock together like those in a car gear-box, ensuring almost complete synchronicity in leg movement – the legs always move within 30 ‘microseconds’ of each other, with one microsecond equal to a millionth of a second.

This is critical for the powerful jumps that are this insect’s primary mode of transport, as even miniscule discrepancies in synchronisation between the velocities of its legs at the point of propulsion would result in “yaw rotation” – causing the Issus to spin hopelessly out of control.

“This precise synchronisation would be impossible to achieve through a nervous system, as neural impulses would take far too long for the extraordinarily tight coordination required,” said lead author Professor Malcolm Burrows, from Cambridge’s Department of Zoology.

“By developing mechanical gears, the Issus can just send nerve signals to its muscles to produce roughly the same amount of force – then if one leg starts to propel the jump the gears will interlock, creating absolute synchronicity.

Interestingly, the mechanistic gears are only found in the insect’s juvenile – or ‘nymph’ – stages, and are lost in the final transition to adulthood. These transitions, called ‘molts’, are when animals cast off rigid skin at key points in their development in order to grow.

It may also be down to the larger size of adults and consequently their ‘trochantera’ – the insect equivalent of the femur or thigh bones. The bigger adult trochantera might allow them to can create enough friction to power the enormous leaps from leaf to leaf without the need for intermeshing gear teeth to drive it, say the scientists.

It’s not yet known why the Issus loses its hind-leg gears on reaching adulthood. The scientists point out that a problem with any gear system is that if one tooth on the gear breaks, the effectiveness of the whole mechanism is damaged. While gear-teeth breakage in nymphs could be repaired in the next molt, any damage in adulthood remains permanent. It is amazing what evolution results in, not only gears but a system that changes to a different solution (maybe, who knows the real “reason”) when the gears solution lack of robustness would create a problem for survivability.

While there are examples of apparently ornamental cogs in the animal kingdom – such as on the shell of the cog wheel turtle or the back of the wheel bug – gears with a functional role either remain elusive or have been rendered defunct by evolution.

Related: Using Bacteria to Power Microscopic MachinesWebcast of a T-cell Killing a Cancerous CellBuilding A Better Bed Bug Trap Using Bean Leaves

In the video above, Professor Malcolm Burrows talks about finding the bugs that led to the science, and working with artists Elizabeth Hobbs and Emily Tracy and members of the community in the London borough of Hackney to produce the film ‘Waterfolk’.

Full press release

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)

Exercise Reduces Anxiety While Also Promoting the Growth of New Neurons

Exercise reorganizes the brain to be more resilient to stress

These findings potentially resolve a discrepancy in research related to the effect of exercise on the brain — namely that exercise reduces anxiety while also promoting the growth of new neurons in the ventral hippocampus. Because these young neurons are typically more excitable than their more mature counterparts, exercise should result in more anxiety, not less. The Princeton-led researchers, however, found that exercise also strengthens the mechanisms that prevent these brain cells from firing.

From an evolutionary standpoint, the research also shows that the brain can be extremely adaptive and tailor its own processes to an organism’s lifestyle or surroundings, Gould said. A higher likelihood of anxious behavior may have an adaptive advantage for less physically fit creatures. Anxiety often manifests itself in avoidant behavior and avoiding potentially dangerous situations would increase the likelihood of survival, particularly for those less capable of responding with a “fight or flight” reaction, she said.

The anxiety-reducing effect of exercise was canceled out when the researchers blocked the GABA receptor that calms neuron activity in the ventral hippocampus.

Interesting research (with mice) that explores how exercise makes us more resilient to stress. I know for me, exercise seems to help relieve stress.

Related: Feed your Newborn NeuronsNew Neurons are Needed for New MemoriesRegular Aerobic Exercise for a Faster Brain (2007)Inactivity Leads to 5.3 Million Early Deaths a YearHow Aerobic Exercise Suppresses Appetite

Tropical Lizards Can Solve Novel Problems and Remember the Solutions

Brainy Lizards Pass Tests for Birds

[Duke biologist Manuel Leal] tested the lizards using a wooden block with two wells, one that was empty and one that held a worm but was covered by a cap. Four lizards, two male and two female, passed the test by either biting the cap or bumping it out of the way.

The lizards solved the problem in three fewer attempts than birds need to flip the correct cap and pass the test, Leal said. Birds usually get up to six chances a day, but lizards only get one chance per day because they eat less. In other words, if a lizard makes a mistake, it has to remember how to correct it until the next day

Leal’s experiment “clearly demonstrates” that when faced with a situation the lizards had never experienced, most of them were able to devise a way to solve the problem. Their ability to “unlearn” a behavior, a skill that some mammalian species have difficulty in, is the mark of a cognitively advanced animal, said Jonathan Losos, a biologist at Harvard who was not involved in the study.

To see if the lizards could reverse this association, Leal next placed the worm under the other cap. At first, all the lizards bumped or bit the formerly lucrative blue cap. But after a few mistakes, two of the lizards figured out the trick. “We named these two Plato and Socrates,” Leal said.

It is very cool to see what scientists keep learning about animals.

Related: Insightful Problem Solving in an Asian ElephantBird Using Bread as Bait to Catch FishCrows Transferring Their Understanding to Novel ProblemDolphins Using Tools to Hunt

Research on Ancient Roman Concrete Will Allow the Creation of More Durable and Environmentally Friendly Concrete

Analysis of samples of ancient Roman concrete pinpointed why the best Roman concrete was superior to most modern concrete in durability, why its manufacture was less environmentally damaging – and how these improvements could be adopted in the modern world.

“It’s not that modern concrete isn’t good – it’s so good we use 19 billion tons of it a year,” says Paulo Monteiro (U.S. Department of Energy’s Lawrence Berkeley National Laboratory). “The problem is that manufacturing Portland cement accounts for seven percent of the carbon dioxide that industry puts into the air.”

Portland cement is the source of the “glue” that holds most modern concrete together. But making it releases carbon from burning fuel, needed to heat a mix of limestone and clays to 1,450 degrees Celsius (2,642 degrees Fahrenheit) – and from the heated limestone (calcium carbonate) itself. Monteiro’s team found that the Romans, by contrast, used much less lime and made it from limestone baked at 900˚ C, or lower, requiring far less fuel than Portland cement.

Cutting greenhouse gas emissions is one powerful incentive for finding a better way to provide the concrete the world needs; another is the need for stronger, longer-lasting buildings, bridges, and other structures. Roman harbor installations have survived 2,000 years of chemical attack and wave action underwater. We now expect our construction to last 50 to 100 years.

The Romans made concrete by mixing lime and volcanic rock. For underwater structures, lime and volcanic ash were mixed to form mortar, and this mortar and volcanic tuff were packed into wooden forms. The seawater instantly triggered a hot chemical reaction. The lime was hydrated – incorporating water molecules into its structure – and reacted with the ash to cement the whole mixture together.

Continue reading

Human Gene Origins: 37% Bacterial, 35% Animal, 28% Eukaryotic

The percent of human genes that emerged in various stages of evolution: 37% bacterial, 28% eukaryotic, 16% animal, 13% vertebrate, 6% primate. The history that brought us to where we are is amazing. Eukaryotes include animals, plants, amoebae, flagellates, amoeboflagellates, fungi and plastids (including algae). So eukaryotic genes are those common to us and other non-animal eukaryotes while those classified as animal genes are shared by animals but not non-animal eukaryotes.

We are living in a bacterial world, and it’s impacting us more than previously thought by Lisa Zyga

Bacterial signaling is not only essential for development, it also helps animals maintain homeostasis, keeping us healthy and happy. As research has shown, bacteria in the gut can communicate with the brain through the central nervous system. Studies have found that mice without certain bacteria have defects in brain regions that control anxiety and depression-like behavior. Bacterial signaling also plays an essential role in guarding an animal’s immune system. Disturbing these bacterial signaling pathways can lead to diseases such as diabetes, inflammatory bowel disease, and infections. Studies also suggest that many of the pathogens that cause disease in animals have “hijacked” these bacterial communication channels that originally evolved to maintain a balance between the animal and hundreds of beneficial bacterial species.

Scientists have also discovered that bacteria in the human gut adapts to changing diets. For example, most Americans have a gut microbiome that is optimized for digesting a high-fat, high-protein diet, while people in rural Amazonas, Venezuela, have gut microbes better suited for breaking down complex carbohydrates. Some people in Japan even have a gut bacterium that can digest seaweed. Researchers think the gut microbiome adapts in two ways: by adding or removing certain bacteria species, and by transferring the desired genes from one bacterium to another through horizontal gene transfer. Both host and bacteria benefit from this kind of symbiotic relationship, which researchers think is much more widespread than previously thought.

We want badly for the message in ‘Animals in a bacterial world,’ to be a call for the necessary disappearance of the old boundaries between life science departments (e.g., Depts of Zoology, Botany, Microbiology, etc.) in universities, and societies (e.g., the American Society for Microbiology, etc.). We also want the message disseminated in college and university classes from introductory biology to advanced courses in the various topic areas of our paper.”

Very cool stuff. This amazing facts scientists discover provide an amazing view of the world we live in and how interconnected we are to other life forms in ways we don’t normally think of.

Related: People’s Bodies Carry More Bacterial Cells than Human CellsMicrobes Flourish In Healthy PeopleTracking the Ecosystem Within UsForeign Cells Outnumber Human Cells in Our BodiesBacteria Beneficial to Human Health

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