Category Archives: Science

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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Study After Study Find No Benefits to Multivitamins

The largest study of its kind concludes that long-term multivitamin use has no impact on the risk of common cancers, cardiovascular disease or overall mortality in postmenopausal women.

“Dietary supplements are used by more than half of all Americans, who spend more than $20 billion on these products each year. However, scientific data are lacking on the long-term health benefits of supplements,” said lead author Marian L. Neuhouser, Ph.D., an associate member of the Public Health Sciences Division at the Hutchinson Center.

The study focused the effects of multivitamins because they are the most commonly used supplement. “To our surprise, we found that multivitamins did not lower the risk of the most common cancers and also had no impact on heart disease,” she said.

The study assessed multivitamin use among nearly 162,000 women enrolled in the Women’s Health Initiative, one of the largest U.S. prevention studies of its kind designed to address the most common causes of death, disability and impaired quality of life in postmenopausal women. The women were followed for about eight years.

Nearly half of the study participants – 41.5 percent – reported using multivitamins on a regular basis. Multivitamin users were more likely to be white, live in the western United States, have a lower body-mass index, be more physically active and have a college degree or higher as compared to non-users.

The study found no significant differences in risk of cancer, heart disease or death between the multivitamin users and non-users.

These findings are consistent with most previously published results regarding the lack of health benefits of multivitamins, Neuhouser said, but this study provides definitive evidence. Since the study did not include men, Neuhouser cautions that the results may not apply to them.

So what advice do Neuhouser and colleagues offer to women who want to make sure they’re getting optimal nutrition? “Get nutrients from food,” she said. “Whole foods are better than dietary supplements. Getting a wide variety of fruits, vegetables and whole grains is particularly important.”

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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.

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.

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.
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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.

Silicon Valley Shows Power of Global Science and Technology Workforce

Even with the challenges created by the culture in Washington DC against non-European foreigners the last 15 years Silicon Valley continues to prosper due to the talents of a pool of global science and engineering talent. Other countries continue to fumble the opportunity provided by the USA’s policies (largely a combination of security theater thinking and a lack of scientific literacy); and the strength of Silicon Valley’s ecosystem has proven resilient.

Software Is Reorganizing the World

an incredible 64% of the Valley’s scientists and engineers hail from outside the U.S., with 43.9% of its technology companies founded by emigrants.

5 things to know about the Silicon Valley economy

64 percent of college-educated professionals working in Silicon Valley science and engineering positions were born outside the U.S. as of 2011. That’s compared to the national average of 26 percent.

The Kauffman foundation’s recent study America’s New Immigrant Entrepreneurs: Then and Now shows evidence the anti-global culture in Washington DC is negatively impacting the economy in the USA.

The drop is even more pronounced in Silicon Valley, where the percentage of immigrant-founded startups declined from 52.4 percent to 43.9 percent.
…
The Immigrant Exodus: Why America Is Losing the Global Race to Capture Entrepreneurial Talent, draws on the research to show that the United States is in the midst of a historically unprecedented halt in high-growth, immigrant-founded startups.

… launched a website — ImmigrantExodus.com — as a resource for journalists and a voice for immigrant entrepreneurs.

As I have written for years, I expected the USA’s relative position to decline. The huge advantages we had were not sustainable. But the very bad policies of the last 15 years have negatively impacted the USA. The only thing not making the results much worse is no strong competitors have stepped into the void created by the policies of the last 2 USA administrations. It isn’t easy to create a strong alternative for technology startups but the economic value of doing so is huge.

The USA has created the opportunity for others to grow much faster, now some just have to step into the void. Will Brazil, Norway, Korea, Chile, Malaysia, Finland, New Zealand, Singapore, Germany, India… step up and create conditions for entrepreneurial scientists and engineers? Each country has been doing some good things but also continue to miss many opportunities. Some countries also have more challenges to overcome – it is much easier if the economy is already rich (say in top 20 in the world), speaks English, has a strong science and technology workforce… The innovation stiffing legal system in place in the USA is absolutely horrible and presents a huge opportunity to anyone willing to stand up to the USA’s continuing pressure to force countries to burden themselves with equally bad (or even worse) policies (such as the Trans-Pacific Partnership). It is possible to succeed with numerous weaknesses it just requires even more offsetting benefits to attract technology entrepreneurs.

Some things are probably absolutely required: rule of law, strong technology infrastructure (internet, etc.), good transportation links internationally, stable politically, freedom of expression (technology entrepreneurs expect to be able to try and say crazy things if you want to control what people say and publish that is very counter to the technology entrepreneurial spirit – especially around internet technology)…

Search for Antibiotic Solutions Continues: Killing Sleeper Bacteria Cells

Killing Sleeper Cells and Superbugs with Assassin Janitors

Discovered in 2005 by scientists from Bayer Healthcare in Germany, ADEP4 killed a variety of different bacteria and cured lethal infections in mice and rats.

Here’s how it works. Proteins need to fold into very precise shapes to do their jobs, and misfolded proteins are wastes of space. Bacteria dispose of these useless molecules with ClpP—a janitorial protein that digests other proteins. It works with a partner, which recognises misfolded proteins, unfolds them, and threads them through a hole in the middle of ClpP so they can be broken down. But ADEP4 opens ClpP up so it no longer needs its partner. The janitor now becomes an assassin, running amok and chopping up any protein it comes across, misfolded or not.

The Bayer scientists showed that ADEP4 can force fast-growing cells to self-destruct, but Lewis suspected that it would do the same to persisters. Afterall, ClpP’s partner requires energy to do its job, but ClpP itself doesn’t. Once ADEP4 opens it up, it should go about its fatal business even in a dormant cell.

Lewis’ team found that ADEP4 did effectively kills persister populations of Staphylococcus aureus, but the bacteria bounce back. ClpP isn’t essential, so the bacteria just inactivated it to evolve their way around ADEP4. This, says Lewis, is why Bayer stopped working on the drug.

His solution was to pair ADEP4 with another antibiotic called rifampycin. ADEP4 would kill off the majority of the persisters, and if any of the rest started growing again, rifampycin would finish them off. He predicted that the double-whammy would leave very few survivors, maybe just a thousand cells or so.

“That’s not what we saw,” he says. “What we saw was complete sterilisation.”

This is a very nice effort. As our efforts fail to find “magic bullet” antibiotics fail and antibiotic resistance increases combo drug solutions offer some hope. While this is good news, the overall state of our ability to treat bacterial infections continues to decline as our misuse of antibiotics has greatly increased the speed at which antibiotic resistance has developed in bacteria.

This solution only works on gram positive antibiotics. ADEP4 is too big to pass through the extra outer layers of the gram-negative bacteria like ecoli and salmonella.

Related: Entirely New Antibiotic Developed, Platensimycin (2006) (2013 update: Platensimycin is a very effective antibiotic in vivo when continuously administered to cells, however this efficacy is reduced when administered by more conventional means. Efforts continue to find a way to create delivery options that are successful in treating people.) – New Family of Antibacterial Agents Discovered (2009) – Potential Antibiotic Alternative to Treat Infection (2012)

Earnings by College Major – Engineers and Scientists at the Top

Median annual income by major based on data from the Georgetown Center On Education And The Workforce – via blog post: The Most And Least Lucrative College Majors.

As we have posted about for years engineers do very well financially. This chart shows the median income by college major (the data includes those who went on to get advanced degrees) based on data for the USA. See the data on those that only have bachelors degrees. Also see a detailed post from the Curious Cat Economics blog looking at the value of college degrees based on the Georgetown data.

Engineering holds 6 of the top spots in the graph shown above and 8 of the top spots for those that didn’t earn an advanced degree. Pharmacy-sciences-and-administration and Math-and-computer-sciences made the top 10 of both lists. Pharmacology and health-and-medical-prepatory-programs make the list when advanced degrees are included.

The highest earning major, petroleum engineering, with $120,000 doesn’t have an increase for those with advanced degrees. The 10th spot goes to electrical engineering with a $94,000 median income.

Outdoor Air Pollution Resulted in 223,000 Cancer Deaths in 2010

The specialized cancer agency of the World Health Organization, the International Agency for Research on Cancer (IARC), announced today that it has classified outdoor air pollution as carcinogenic to humans.

After thoroughly reviewing the latest available scientific literature, the world’s leading experts convened by the IARC Monographs Programme concluded that there is sufficient evidence that exposure to outdoor air pollution causes lung cancer. They also noted a positive association with an increased risk of bladder cancer.

Particulate matter, a major component of outdoor air pollution, was evaluated separately and was also classified as carcinogenic to humans.

The IARC evaluation showed an increasing risk of lung cancer with increasing levels of exposure to particulate matter and air pollution. Although the composition of air pollution and levels of exposure can vary dramatically between locations, the conclusions of the Working Group apply to all regions of the world.

Air pollution is already known to increase risks for a wide range of diseases, such as respiratory and heart diseases. Studies indicate that in recent years exposure levels have increased significantly in some parts of the world, particularly in rapidly industrializing countries with large populations. The most recent data indicate that in 2010, 223,000 deaths from lung cancer worldwide resulted from air pollution.

“The air we breathe has become polluted with a mixture of cancer-causing substances,” says Dr Kurt Straif.

The stories of amazingly high (and persistent) air pollution levels in China have been continuing for years. But, while China, likely represents several of the worst existing air pollution conditions hundreds of thousands have died outside China due to air pollution just in the last 5 years.

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Deadly Trio of Acidification, Warming and Deoxygenation Threaten Our Oceans

An international panel of marine scientists is demanding urgent remedies to halt ocean degradation based on findings that the rate, speed and impacts of change in the global ocean are greater, faster and more imminent
than previously thought.

Professor Dan Laffoley, International Union for Conservation of Nature, said: “What these latest reports make absolutely clear is that deferring action will increase costs in the future and lead to even greater, perhaps irreversible, losses. The UN climate report confirmed that the ocean is bearing the brunt of human-induced changes to our planet. These findings give us more cause for alarm – but also a roadmap for action. We must use it.“

Results from the latest International Programme on the State of the Ocean (IPSO)/IUCN review of science on anthropogenic stressors on the ocean go beyond the conclusion reached last week by the UN climate change panel the IPCC that the ocean is absorbing much of the warming and unprecedented levels of carbon dioxide and warn that the cumulative impact of this with other ocean stressors is far graver than previous estimates.

Decreasing oxygen levels in the ocean caused by climate change and nitrogen runoff, combined with other chemical pollution and rampant overfishing are undermining the ability of the ocean to withstand these so-called ‘carbon perturbations’, meaning its role as Earth’s ‘buffer’ is seriously compromised.

Professor Alex Rogers of Somerville College, Oxford, and Scientific Director of IPSO said: “The health of the ocean is spiraling downwards far more rapidly than we had thought. We are seeing greater change, happening faster, and the effects are more imminent than previously anticipated. The situation should be of the gravest concern to everyone since everyone will be affected by changes in the ability of the ocean to support life on Earth.”

Among the latest assessments of factors affecting ocean health, the panel identified the following areas as of greatest cause for concern:
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