Category Archives: Education

Antigen Shift in Influenza Viruses

Antigenic shift is the process by which at least two different strains of a virus, (or different viruses), especially influenza, combine to form a new subtype having a mixture of the surface antigens of the two original strains.

Pigs can be infected with human, avian and swine influenza viruses. Because pigs are susceptible to all three they can be a breeding ground for antigenic shift (as in the recent case of H1N1 Flu – Swine Flu) allowing viruses to mix and create a new virus.

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Merck and Elsevier Publish Phony Peer-Review Journal

Elsevier is one of those publishers fighting open science. They try to claim that the government publishing government funded research in an open way will tarnish science. The argument makes no sense to me. Here is another crazy action on their part: they published a “journal” funded by Merck to promote Merck products. Merck Makes Phony Peer-Review Journal:

Merck cooked up a phony, but real sounding, peer reviewed journal and published favorably looking data for its products in them. Merck paid Elsevier to publish such a tome, which neither appears in MEDLINE or has a website, according to The Scientist.
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What’s sad is that I’m sure many a primary care physician was given literature from Merck that said, “As published in Australasian Journal of Bone and Joint Medicine, Fosamax outperforms all other medications….” Said doctor, or even the average researcher wouldn’t know that the journal is bogus. In fact, knowing that the journal is published by Elsevier gives it credibility!

As I have said the journals fighting open science should have their credibility questioned. They are putting their outdated business model above science. We should not see organizations that are focused on closing science research through deceptive publicity efforts and lobbying efforts as credible.

New Largest Known Cave

photo of world's largest known cave, in Vietnam

The world’s largest cave

A British caving team believe they have discovered the world’s largest cave passage in the heart of the Vietnamese jungle. The rocky passage is 150metres long and measures a towering 200metres in height – seven times as high as the vaulted ceiling of York Cathedral.
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Called Hang Son Doong (Mountain River Cave) it is believed to be almost twice the size of the current record holder
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The cave was originally discovered in 1991 by a Vietnamese Jungle man called Ho Khanh. However Mr Spillane said no-one had entered if before because ‘it emitted a frightful wind and noise which was due to a large underground river’.

Friday Cat Fun #15: Curious Cat Hat

Maru, a Scottish Fold, in Japan has his own cat blog. This is a second post on Maru: Friday Cat Fun #7: Curious Cat and Boxes

Influenza Pandemic Alert Raised to Level 5 (of 6)

WHO Director-General, Dr Margaret Chan, announced today that she has “decided to raise the current level of influenza pandemic alert from phase 4 to phase 5.” And she further comments:

Let me remind you. New diseases are, by definition, poorly understood. Influenza viruses are notorious for their rapid mutation and unpredictable behaviour. WHO and health authorities in affected countries will not have all the answers immediately, but we will get them.

WHO will be tracking the pandemic at the epidemiological, clinical, and virological levels. All countries should immediately activate their pandemic preparedness plans. Countries should remain on high alert for unusual outbreaks of influenza-like illness and severe pneumonia.

At this stage, effective and essential measures include heightened surveillance, early detection and treatment of cases, and infection control in all health facilities.

I have reached out to companies manufacturing antiviral drugs to assess capacity and all options for ramping up production. I have also reached out to influenza vaccine manufacturers that can contribute to the production of a pandemic vaccine.

The biggest question, right now, is this: how severe will the pandemic be, especially now at the start?

It is possible that the full clinical spectrum of this disease goes from mild illness to severe disease. We need to continue to monitor the evolution of the situation to get the specific information and data we need to answer this question.

From past experience, we also know that influenza may cause mild disease in affluent countries, but more severe disease, with higher mortality, in developing countries.

No matter what the situation is, the international community should treat this as a window of opportunity to ramp up preparedness and response.

Above all, this is an opportunity for global solidarity as we look for responses and solutions that benefit all countries, all of humanity. After all, it really is all of humanity that is under threat during a pandemic.

As I have said, we do not have all the answers right now, but we will get them.
—- end of her remarks —-
The latest WHO Epidemic and Pandemic Alert and Response release puts the total number of confirmed cases at 148, in 9 countries, with 8 deaths. Mexico has many more suspected cases but just 26 confirmed cases. The CDC Swine Influenza site, puts the total number of confirmed cases in the USA at 91, in 10 states, with 1 death.

Lenz’s Law in Action: Eddy Current Tubes

Eddy Current Tubes — Drop the Magnets down the tube. An eddy current is set up in a conductor in response to a changing magnetic field. Lenz’s law predicts that the current moves in such a way as to create a magnetic field opposing the change; to do this in a conductor, electrons swirl in a plane perpendicular to the changing magnetic field.

Because the magnetic fields of the eddy currents oppose the magnetic field of the falling magnet; there is attraction between the two fields. Energy is converted into heat. This principle is used in damping the oscillation of the lever arm of mechanical balances.

Engineering Students Increasing at Universities

Engineering suddenly hot at universities

Across the United States, enrollment in engineering programs has risen to levels not seen in three decades. The recession appears to be one factor, as students and their parents look for dependable careers. But some education officials detect a shift in opinion about the profession itself, as global warming and stem-cell research make fields like chemical and bioengineering more than just wise choices for job-seekers – but fashionable ones, too.

Many students are bringing to engineering a heightened sense of social responsibility and a desire “to go out and make a difference in the world,” says Joseph Helble, dean of the Thayer School of Engineering at Dartmouth College in Hanover, N.H., where enrollment in introductory undergraduate courses is 30 percent above the five-year average.

Nationally, enrollment in undergraduate engineering programs rose 3 percent in 2007 and 4.5 percent 2008, according to the American Association of Engineering Education. Meanwhile, enrollment in masters’ degree programs rose 7 percent in 2007 and 2 percent in 2008. In the fall of 2008, 91,489 masters degree students and 403,193 undergraduates were studying engineering at US universities and colleges.

Skeptics note that engineering remains a low priority for US students: Among the 25 top engineer-producing countries, the United States ranks No. 22 on a per capita basis.

Increased engineering education is good news for future economic growth. Hopefully this trend can continue.

Swine Flu: a Quick Overview

World Health Organization on Swine influenza

After reviewing available data on the current situation, Committee members identified a number of gaps in knowledge about the clinical features, epidemiology, and virology of reported cases and the appropriate responses. The Committee advised that answers to several specific questions were needed to facilitate its work.

The Committee nevertheless agreed that the current situation constitutes a public health emergency of international concern.

Based on this advice, the Director-General has determined that the current events constitute a public health emergency of international concern, under the Regulations.

Swine flu: a quick overview–and new New York and Kansas cases by Tara Smith

while the cases in the US have been mild and no deaths have occurred that we’re aware of, it seems in Mexico that young people are dying from this–a group that is typically not hard-hit by seasonal influenza viruses. Readers familiar with influenza and know the history of the 1918 influenza pandemic will recall that the “young and healthy” were disproportionally struck by that virus as well–so this knowledge is currently disconcerting and worrisome, but there are so many gaps in our information as far as what’s really going on in Mexico that it’s difficult to make heads or tails out of this data right now.

Third, is this really a new virus? So few influenza isolates are actually analyzed each year (in proportion to the number of people infected) that we aren’t sure yet whether this is something brand-new, or something that has been circulating at a low level for awhile, but just hadn’t been picked up. After all, H1N1 is a common serotype, so additional molecular testing is needed to determine that it’s “swine flu” versus “human” H1N1.
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this is a fast-developing story, and it will take much more investigation and field work to determine the true extent of the virus’s spread in the population; to figure out… how efficiently it’s transmitted…

This is very early in the scientific inquiry process looking into what exactly is going on. It is too early to tell how serious a threat this is. The reaction of WHO, CDC though shows they are taking the threat seriously. By far the biggest danger in such situations, is reacting too slowly to serious and contagious threats. If you wait to react until proof exists that the situation is very serious the situation can be almost impossible to control. So you need to react quickly to shut down the spread of the threat, hopefully before it has spread too far.

Evolutionary Robotics

Evolutionary Robotics, chapter of Handbook of Robotics, is interesting and includes a good explanation of the difference between evolution and learning:

Evolution and learning (or phylogenetic and ontogenetic
adaptation) are two forms of biological adaptation that differ in space and time. Evolution is a process of selective reproduction and substitution based on the existence of a population of individuals displaying variability at the genetic level. Learning, instead, is a set of modifications taking place within each single individual during its own life time.

Evolution and learning operate on different time scales. Evolution is a form of adaptation capable of capturing relatively slow environmental changes that

might encompass several generations (e.g., the perceptual characteristics of food sources for a given species). Learning, instead, allows an individual to adapt to environmental modifications that are unpredictable at the generational level. Learning might include a variety of mechanisms that produce adaptive changes in an individual during its lifetime, such as physical development, neural maturation, variation of the connectivity between neurons, and synaptic plasticity. Finally, whereas evolution operates on the genotype, learning affects only the phenotype and phenotypic modifications cannot directly modify the genotype.
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Recent research showed that teams of evolved robots can: (a) develop robust and effective behavior, (b) display an ability to differentiate their behavior so
to better cooperate; (c) develop communication capabilities and a shared communication system.

Iron-breathing Species Isolated in Antarctic for Millions of Years

Graphic showing environment of Antarctic subglacial microbes

Graphic of Blood Falls showing microbial community environment in the Antarctic by Zina Deretsky at NSF)

A reservoir of briny liquid buried deep beneath an Antarctic glacier supports hardy microbes that have lived in isolation for millions of years, researchers report this week. The discovery of life in a place where cold, darkness, and lack of oxygen would previously have led scientists to believe nothing could survive comes from a team led by researchers at Harvard University and Dartmouth College.

Despite their profound isolation, the microbes are remarkably similar to species found in modern marine environments, suggesting that the organisms now under the glacier are the remnants of a larger population that once occupied an open fjord or sea.

“It’s a bit like finding a forest that nobody has seen for 1.5 million years,” says Ann Pearson, Thomas D. Cabot Associate Professor of Earth and Planetary Sciences in Harvard’s Faculty of Arts and Sciences. “Intriguingly, the species living there are similar to contemporary organisms, and yet quite different — a result, no doubt, of having lived in such an inhospitable environment for so long.”

“This briny pond is a unique sort of time capsule from a period in Earth’s history,” says lead author Jill Mikucki, now a research associate in the Department of Earth Sciences at Dartmouth and visiting fellow at Dartmouth’s Dickey Center for International Understanding and its Institute of Arctic Studies. “I don’t know of any other environment quite like this on Earth.”

Chemical analysis of effluent from the inaccessible subglacial pool suggests that its inhabitants have eked out a living by breathing iron leached from bedrock with the help of a sulfur catalyst. Lacking any light to support photosynthesis, the microbes have presumably survived by feeding on the organic matter trapped with them when the massive Taylor Glacier sealed off their habitat an estimated 1.5 to 2 million years ago.
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