Posts about Research

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)

Another Bee Study Finds CCD is Likely Due to Combination of Factors Including Pesticides

Abstract of open access science paper funded by the United States Department of Agriculture (USDA) Crop Pollination Exposes Honey Bees to Pesticides Which Alters Their Susceptibility to the Gut Pathogen Nosema ceranae:

Recent declines in honey bee populations and increasing demand for insect-pollinated crops raise concerns about pollinator shortages. Pesticide exposure and pathogens may interact to have strong negative effects on managed honey bee colonies. Such findings are of great concern given the large numbers and high levels of pesticides found in honey bee colonies. Thus it is crucial to determine how field-relevant combinations and loads of pesticides affect bee health.

We collected pollen from bee hives in seven major crops to determine 1) what types of pesticides bees are exposed to when rented for pollination of various crops and 2) how field-relevant pesticide blends affect bees’ susceptibility to the gut parasite Nosema ceranae. Our samples represent pollen collected by foragers for use by the colony, and do not necessarily indicate foragers’ roles as pollinators. In blueberry, cranberry, cucumber, pumpkin and watermelon bees collected pollen almost exclusively from weeds and wildflowers during our sampling.

Thus more attention must be paid to how honey bees are exposed to pesticides outside of the field in which they are placed. We detected 35 different pesticides in the sampled pollen, and found high fungicide loads. The insecticides esfenvalerate and phosmet were at a concentration higher than their median lethal dose in at least one pollen sample. While fungicides are typically seen as fairly safe for honey bees, we found an increased probability of Nosema infection in bees that consumed pollen with a higher fungicide load.

Our results highlight a need for research on sub-lethal effects of fungicides and other chemicals that bees placed in an agricultural setting are exposed to.

The attempts to discover the main causes of bee colony deaths and find solutions continues to prove difficult years after the problems became major. The complex interaction of many variables makes it difficult. And special interest groups pushing pesticides and the like, which have seemed to be major contributors to the problem for years, make it even more difficult (by preventing restrictions on potentially damaging pesticide use).

The challenges in determining what is killing bees are similar to the challenges of discovering what practices are damaging human health. The success of studying complex biological interactions (to discover threats to human health) is extremely limited. I am concerned we are far too caviler about using large numbers of interventions (drugs, pesticides, massive antibiotics use in factory farms, pollution…).

Related: Europe Bans Certain Pesticides, USA Just Keeps Looking, Bees Keep DyingGermany Bans Chemicals Linked to Bee Deaths (2008)Virus Found to be One Likely Factor in Bee Colony Colapse Disorder (2007)Study of the Colony Collapse Disorder Continues as Bee Colonies Continue to Disappear

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.

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Europe Bans Certain Pesticides, USA Just Keeps Looking, Bees Keep Dying

For years the bee colony collapse disorder has been showing the difficulty of the scientific inquiry process. And that difficulty often becomes more difficult if interests with lots of money at stake want to block certain conclusions.

One-Third of U.S. Honeybee Colonies Died Last Winter, Threatening Food Supply

Multiple factors — pesticides, fungicides, parasites, viruses and malnutrition — are believed to cause the losses, which were officially announced today by a consortium of academic researchers, beekeepers and Department of Agriculture scientists.

“We’re getting closer and closer to the point where we don’t have enough bees in this country to meet pollination demands,” said entomologist Dennis vanEngelstorp of the University of Maryland, who led the survey documenting the declines.

Beekeepers lost 31 percent of their colonies in late 2012 and early 2013, roughly double what’s considered acceptable attrition through natural causes. The losses are in keeping with rates documented since 2006, when beekeeper concerns prompted the first nationwide survey of honeybee health. Hopes raised by drop in rates of loss to 22 percent in 2011-2012 were wiped out by the new numbers.

Most losses reported in the latest survey, however, don’t actually fit the CCD profile. And though CCD is largely undocumented in western Europe, honeybee losses there have also been dramatic. In fact, CCD seems to be declining, even as total losses mount. The honeybees are simply dying.

“Even if CCD went away, we’d still have tremendous losses,” said entomologist Diana Cox-Foster at Pennsylvania State University. “CCD losses are like the straw that breaks the camel’s back. The system has many other issues.”

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People are Superorganisms With Microbiomes of Thousands of Species

In a recent article in National Geographic Carl Zimmer has again done a good job of explaining the complex interaction between our bodies and the bacteria and microbes that make us sick, and keep us healthy.

The damage done by our indiscriminate use of antibiotics is not just the long term resistance that we create in bacteria (making the future more dangerous for people) that I have written about numerous times but it also endangers the person taking the anti-biotics in the short term. Sometimes the other damage is a tradeoff that should be accepted. But far too often we ignore the damage taking antibiotics too often does.

When You Swallow A Grenade

While antibiotics can discriminate between us and them, however, they can’t discriminate between them and them–between the bacteria that are making us sick and then ones we carry when we’re healthy. When we take a pill of vancomycin, it’s like swallowing a grenade. It may kill our enemy, but it kills a lot of bystanders, too.

If you think of the human genome as all the genes it takes to run a human body, the 20,000 protein-coding genes found in our own DNA are not enough. We are a superorganism that deploys as many as 20 million genes.

Before he started taking antibiotics, the scientists identified 41 species in a stool sample. By day 11, they only found 13. Six weeks after the antibiotics, the man was back up to 38 species. But the species he carried six weeks after the antibiotics did not represent that same kind of diversity he had before he took them. A number of major groups of bacteria were still missing.

They found that children who took antibiotics were at greater risk of developing inflammatory bowel disease later in life. The more antibiotics they took, the greater the risk. Similar studies have found a potential link to asthma as well.

The human body contains trillions of microorganisms — outnumbering human cells by 10 to 1. Because of their small size, however, microorganisms make up only about 1% to 3% of the body’s mass, but play a vital role in human health.

Where doctors had previously isolated only a few hundred bacterial species from the body, Human Microbiome Project (HMP) researchers now calculate that more than 10,000 microbial species occupy the human ecosystem. Moreover, researchers calculate that they have identified between 81% and 99% of all microorganismal genera in healthy adults.

“Humans don’t have all the enzymes we need to digest our own diet,” said Lita Proctor, Ph.D., NHGRI’s HMP program manager. “Microbes in the gut break down many of the proteins, lipids and carbohydrates in our diet into nutrients that we can then absorb. Moreover, the microbes produce beneficial compounds, like vitamins and anti-inflammatories that our genome cannot produce.” Anti-inflammatories are compounds that regulate some of the immune system’s response to disease, such as swelling.

“Enabling disease-specific studies is the whole point of the Human Microbiome Project,” said Barbara Methé, Ph.D., of the J. Craig Venter Institute, Rockville, MD, and lead co-author of the Nature paper on the framework for current and future human microbiome research. “Now that we understand what the normal human microbiome looks like, we should be able to understand how changes in the microbiome are associated with, or even cause, illnesses.”

Read the full NIH press release on the normal bacterial makeup of the body

Related: Tracking the Ecosystem Within UsWhat Happens If the Overuse of Antibiotics Leads to Them No Longer Working?Antibacterial Products May Do More Harm Than GoodAntibiotics Too Often Prescribed for Sinus Woes

Homing Pigeons May Use Low Frequency Sound Maps To Locate Home

Mystery of Lost Homing Pigeons Finally Solved

Prior research had shown that birds hear incredibly low-frequency sound waves of about 0.1 Hertz, or a tenth of a cycle per second. These infrasound waves may emanate from in the ocean and create tiny disturbances in the atmosphere. Hagstrum began to think the birds used infrasound for navigation.

on the odd day when the birds reached home from Jersey Hill without problems, the infrasound traveled between the two locations. At the other locations where pigeons headed off in the wrong direction, he showed that wind currents channeled the infrasound waves in that direction.

The explanation may solve other mysteries about pigeons — for instance, why they circle around before heading off in one direction. Because the sound waves are so long, but the birds’ ear canals are tiny, they need to circle to reconstruct the wave and figure out which way they are oriented, he said.

More interesting scientific inquiry. It is very interesting to learn what scientists are learning about our world – even when the conclusions are still preliminary and may be adjusted or refuted.

Related: Pigeon Solves Box and Banana ProblemCool Research on CrowsBird Using Bait to FishMoth Jams Bat Sonar

Evolution Follows a Predictable Genetic Pattern

Far from random, evolution follows a predictable genetic pattern

The researchers carried out a survey of DNA sequences from 29 distantly related insect species, the largest sample of organisms yet examined for a single evolutionary trait. Fourteen of these species have evolved a nearly identical characteristic due to one external influence — they feed on plants that produce cardenolides, a class of steroid-like cardiotoxins that are a natural defense for plants such as milkweed and dogbane.

Though separated by 300 million years of evolution, these diverse insects — which include beetles, butterflies and aphids — experienced changes to a key protein called sodium-potassium adenosine triphosphatase, or the sodium-potassium pump, which regulates a cell’s crucial sodium-to-potassium ratio. The protein in these insects eventually evolved a resistance to cardenolides, which usually cripple the protein’s ability to “pump” potassium into cells and excess sodium out.

Andolfatto and his co-authors examined the sodium-potassium pump protein because of its well-known sensitivity to cardenolides. In order to function properly in a wide variety of physiological contexts, cells must be able to control levels of potassium and sodium. Situated on the cell membrane, the protein generates a desired potassium to sodium ratio by “pumping” three sodium atoms out of the cell for every two potassium atoms it brings in.

Cardenolides disrupt the exchange of potassium and sodium, essentially shutting down the protein, Andolfatto said. The human genome contains four copies of the pump protein, and it is a candidate gene for a number of human genetic disorders, including salt-sensitive hypertension and migraines. In addition, humans have long used low doses of cardenolides medicinally for purposes such as controlling heart arrhythmia and congestive heart failure.

Cool stuff. It makes sense to me which is nice (it is nice to get confirmation that I find what actually exists is sensible). When things that are true just seem crazy it is a bit disconcerting – like quantum mechanics. It is fun to read stuff that totally shakes up preconceived notions, but even then it is nice once I think understand it to find it sensible.

Related: All present-day Life on Earth Has A Single AncestorCambrian Explosion SongBacteriophages: The Most Common Life-Like Form on EarthMicrocosm by Carl Zimmer

Add Over-Fishing to the Huge Government Debt as Examples of How We Are Consuming Beyond Our Means

Fish are hidden under the water so the unsustainable harvesting isn’t quite as obvious as the unsustainable government debt but they both are a result of us living beyond our sustainable production. You can live well by consuming past wealth and condemning your decedents to do without. That is the way we continue to live. Over-fishing a century ago was not as obviously dangerous as it is today. But we have witnessed many instances of overfishing devastating the fishing economy (when the fishing is unsustainable the inevitable result is collapse and elimination of the vast majority of the food and income that previous generations enjoyed).

The normal pattern has been to turn to more aggressive fishing methods and new technology to try and collect fish as over-fishing devastates yields. This, of course, further devastates the state of the resources and makes it so recovery will take much much longer (decades – or more).

New research shows the existing problems and the potential if we apply science and planning to manage fisheries effectively.

Using new methods to estimate thousands of unassessed fisheries, a new comprehensive study provides a new view of global fish stocks. The results show that the overall state of fisheries is worse than previously thought. Unassessed stocks, which are often left out of global analyses because of a lack of data, are declining at disturbing rates. When these fisheries are taken into account, the results indicate that over 40 percent of fisheries have crashed or are overfished, producing economic losses in excess of $50 billion per year.

The good news is that this decline is not universal: fisheries are starting to rebound in many areas across the globe and we can learn from these examples. Recovery trends are strongest for fisheries where data on the status of the fishery exists, and in which managers and fishermen have made science-based decisions and stuck with them in the face of political pressure.

The amount of fish brought to shore could increase 40 percent on average – and double in some areas – compared to yields predicted if we continue current fishing trends.

The management solutions to overfishing are well known, tested and proven to work. While these solutions are not “one-size-fits-all” for fisheries, there are common themes. Specifically, managers and fishermen must: 1. Reduce fishing to allow stocks to rebuild; 2. Set catches at a sustainable level that is based on the best available scientific and economic information rather than short-term political pressures; and 3. Prevent dangerous fishing activities that destroy habitat, wildlife, or breeding fish.

The over fishing problem is difficult because our nature is to ignore problems that are not immediate. But the costs of doing so are very large. If we don’t behave more wisely our children will pay the price. And, in fact, this problem is so acute now that those of us that expect to live a couple decades can expect to pay the price. In rich countries this will be tolerable, a bit less fish at much higher prices. In rich countries food prices are a minor expense compared to the billions of those not living in rich countries. They will suffer the most. As will those that have jobs directly dependent on fishing.

Related: Fishless FutureEuropean Eels in Crisis After 95% Decline in Last 25 yearsLet the Good Times Roll (using Credit)SelFISHingRunning Out of FishThe State of the Oceans is Not GoodChinook Salmon Vanish Without a Trace

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