Posts about Science

Explaining the Higgs Boson Particle Again

comic illustration explaining the Higgs-boson particle

Excerpt from Piled Higher and Deeper by Jorge Cham – go see the entire illustration.

Related: 5% of the Universe is Normal Matter, What About the Other 95%?At the Heart of All MatterThe god of small thingsCERN Pressure Test FailureNinja ProfessorsFriday Fun, CERN Version

Math Education Results Show China, Singapore, Korea and Japan Leading

The most comprehenvise comparison of student achievement in math and science around the globe undertaken by the Organisation for Economic Co-operation and Development (OECD). The 2012 Program for International Student Assessment (PISA) focuses on math understanding of 15 year olds (the 2014 report will focus on science). The 2009 report focused on the results of science education student achievement around the globe.

2012 results for the math portion (rank – country – mean score)(I am not listing all countries):

  • 1 – Singapore – 573
  • 2 – Korea – 554
  • 3 – Japan – 536
  • 5 – Switzerland – 531
  • 6 – Netherlands – 523
  • 7 – Estonia – 521
  • 8 – Finland – 519
  • 9 – Canada – 518
  • 12 – Germany – 514
  • 24 – UK – 494 (this is also the OECD average)
  • 34 – USA – 481
  • 49 – Malaysia – 421
  • 50 – Mexico – 413

All 34 OECD member countries and 31 partner countries and economies participated in PISA 2012, representing more than 80% of the world economy. Portions of China participated and did very well including Shanghai-China (highest mean score of 613 points – if you ranked that as a country, I ignored these “regional results” in the ranks I shown here), Hong Kong-China (561, 3rd if including countries and regions together), Chinese Taipei [Taiwan] (560, 4th), Macao-China (538, 6th).

Boys perform better than girls in mathematics in 38 out of the 65 countries and economies that participated in PISA 2012, and girls outperform boys in 5 countries.

Related: Playing Dice and Children’s NumeracyNumeracy: The Educational Gift That Keeps on GivingMathematicians Top List of Best OccupationsThe Economic Consequences of Investing in Science EducationCountry H-index Ranking for Science PublicationsEconomic Strength Through Technology Leadership

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How Wolves Changed the Yellowstone Ecosystem

A great short video explaining the dramatic changes to the Yellowstone ecosystem with the re-introduction of wolves. Even the rivers changed.

Related: Light-harvesting Bacterium Discovered in YellowstoneFishless FutureThe Sea Otter storyYellowstone Youth Conservation Corps Polar Bears Playing with HuskiesCurious Cat travel photos of Yellowstone National Park

Why Don’t All Ant Species Replace Queens in the Colony, Since Some Do

My response to: There are other species of ants that do replace the queen, so why did some species not do this?

Basically the method they evolved copes well with losing the queen. Out of various ways of dealing with having a dominant Queen some may lead to replacement if she dies.

There are lots of examples of method is very effective at creating lots of successful offspring but happens to be less than ideal in some situations. Natural selection is pretty amazing and awesome at creating effective genes but we certainly can look at the results sometimes and see improvements that would be useful.

Likely if losing the queen was very common a good way of dealing with that would be found (or that species would be disadvantaged and at risk). If the queen happens to evolve to being very reliable coping with her death becomes less important. If they produce lots of useful offspring but have a less than ideal method of coping with their home colony losing her it is entirely sensible to imagine that species could flourish.

I would imagine species with queens that had shorter lifespans, that invested more in the home colony, that were less effective at setting up new colonies… would be more likely to have better queen replacement strategies/results.

Related: Ants, Ants, AntsE.O. Wilson: Lord of the AntsAmazonian Ant Species is All Female, Reproduces By CloningRoyal Ant GenesHuge Ant Nest

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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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

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

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

graph of earnings by college-major

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.

Related: No Surprise – Engineering Graduates Continue to Reign SupremeEngineering Again Dominates The Highest Paying College Degree ProgramsEngineering Majors Hold 8 of Top 10 Highest Paid MajorsThe Labor Market for Software Developers

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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