Tag Archives: biology

2011 MacArthur Fellows

Elodie Ghedin (in video) is a biomedical researcher who is harnessing the power of genomic sequencing techniques to generate critical insights about human pathogens. A major focus of her work has been parasites that cause diseases endemic to tropical climates, such as leishmaniasis, sleeping sickness, Chagas disease, elephantiasis, and river blindness.

More scientists given the $500,000 award: Markus Greiner, Condensed Matter Physicist, Harvard University; Sarah Otto, Evolutionary Geneticist, University of British Columbia; Shwetak Patel, Sensor Technologist & Computer Scientist, University of Washington; Kevin Guskiewicz, Department of Exercise & Sport Science, University of North Carolina; Melanie Sanford, Organometallic Chemist, University of Michigan; Matthew Nock, Clinical Psychologist, Harvard University; Yukiko Yamashita, Developmental Biologist, University of Michigan; William Seeley, Neurologist, University of California, San Francisco.

Science Explained: Cool Video of ATP Synthase, Which Provides Usable Energy to Us

[I replaced the webcast – as so often happen the non-Youtube video embed failed to work as time passed]

This webcast shows animations of ATP synthase structure and the mechanism for synthesizing ATP. Biology is incredibly cool. Too bad they didn’t have stuff like this when I was in school, instead biology was mainly about memorizing boring lists of stuff.

ATP (adenosine tri-phosphate) transports chemical energy within cells. When one of the phosphates is released by ATP energy is given off (and ATP becomes ADP (adenosine di-phosphate) + Pi (inorganic phosphate). And then the synthase structure can then turn it back into ATP to be used again.

The human body, which on average contains only 250 grams of ATP, turns over its own body weight equivalent in ATP each day.

Antibiotics fuel obesity by creating microbe upheavals

We aren’t single individuals, but colonies of trillions. Our bodies, and our guts in particular, are home to vast swarms of bacteria and other microbes. This “microbiota” helps us to harvest energy from our food by breaking down the complex molecules that our own cells cannot cope with. They build vitamins that we cannot manufacture. They ‘talk to’ our immune system to ensure that it develops correctly, and they prevent invasions from other more harmful microbes. They’re our partners in life.

What happens when we kill them?

Farmers have been doing that experiment in animals for more than 50 years. By feeding low doses of antibiotics to healthy farm animals, they’ve found that they could fatten up their livestock by as much as 15 percent.
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Ilseung Cho from the New York University School of Medicine has confirmed that hypothesis. By feeding antibiotics to young mice, he has shown that the drugs drastically change the microscopic communities within their guts, and increase the amount of calories they harvest from food. The result: they became fatter.

I continue to believe we are far to quick to medicate. We tremendously overuse anti-biotis and those costs are huge. They often are delays and systemic and given our current behavior we tend to ignore delayed and systemic problems.

The link between the extremely rapid rise in obesity and the overuse of anti-biotics is in need of much more study. It seems a possible contributing factor but there is much more data needed to confirm such a link. And other factors still seem dominant to me: increase in caloric intake and decrease in physical activity.

Great Webcast Explaining the Digestive Systems

You will learn things like why it is so important to chew your food well (increase the surface area for enzymes to get at the food). Our bodies also have adapted to provide a huge surface area for the digestive system to work; the small intestine alone has a surface area of 250 square meters (larger than the size of most apartments). Your small intestine is 4.5 to 10.5 meters long.

Science PhD Job Market in 2012

The too-big-to-fail-bank crisis continues to produce huge economic pain throughout the economy. Science PhDs are not immune, though they are faring much better than others.

U.S. pushes for more scientists, but the jobs aren’t there

Since 2000, U.S. drug firms have slashed 300,000 jobs, according to an analysis by consulting firm Challenger, Gray & Christmas. In the latest closure, Roche last month announced it is shuttering its storied Nutley, N.J., campus — where Valium was invented — and shedding another 1,000 research jobs.
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Largely because of drug industry cuts, the unemployment rate among chemists now stands at its highest mark in 40 years, at 4.6 percent, according to the American Chemical Society, which has 164,000 members. For young chemists, the picture is much worse. Just 38 percent of new PhD chemists were employed in 2011, according to a recent ACS survey.
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Two groups seem to be doing better than other scientists: physicists and physicians. The unemployment rate among those two groups hovers around 1 to 2 percent, according to surveys from NSF and other groups. Physicists end up working in many technical fields — and some go to Wall Street — while the demand for doctors continues to climb as the U.S. population grows and ages.

But for the much larger pool of biologists and chemists, “It’s a particularly difficult time right now,” Stephan said.
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From 1998 to 2003, the budget of the National Institutes of Health doubled to $30 billion per year. That boost — much of which flows to universities — drew in new, young scientists. The number of new PhDs in the medical and life sciences boomed, nearly doubling from 2003 to 2007, according to the NSF.

The current overall USA unemployment rate is 8.2%.

The current economy doesn’t provide for nearly guaranteed success. The 1960’s, in the USA, might have come close; but that was a very rare situation where the richest country ever was at the prime of economic might (and even added on top of that science was seen as key to promote continued economic success). Today, like everyone else (except trust fund babies), scientists and engineers have to make their way in the difficult economy: and that should be expected to be the case in the coming decades.

Right now, physicians continue to do very well but the huge problems in the USA health system (we pay double what other rich countries do for not better outcomes) make that a far from a certain career. They likely will continue to do very well, financially, just not as well as they have been used to.

Science and engineering education prepare people well for economic success but it is not sufficient to guarantee the easy life. Just like everyone else, the ability to adapt to current market conditions is important in the current economic climate – and will likely continue to be hugely important going forward.

The reason to get a undergraduate or graduate science or engineering education is because you are interested in science and engineering. The economic prospects are likely to continue to be above average (compared to other education choices) but those choosing this path should do so because they are interested. It makes sense to me to factor in how your economic prospects will be influenced by your choices but no matter what choices are made a career is going to take hard work and likely many frustrations and obstacles. But hopefully a career will provide much more joy than hardship.

The Appendix Serves As a Reservoir of Beneficial Bacteria

This is an interesting explanation for the purpose of the appendix.

The appendix does have a use – re-booting the gut

The US scientists found that the appendix acted as a “good safe house” for bacteria essential for healthy digestion, in effect re-booting the digestive system after the host has contracted diseases such as amoebic dysentery or cholera, which kill off helpful germs and purge the gut.

This function has been made obsolete by modern, industrialised society; populations are now so dense that people pick up essential bacteria from each other, allowing gut organisms to regrow without help from the appendix, the researchers said.

But in earlier centuries, when vast tracts of land were more sparsely populated and whole regions could be wiped out by an epidemic of cholera, the appendix provided survivors with a vital individual stockpile of suitable bacteria.

Wonderful Views of Life Using Micro-photography

The Olympus BioScapes 2011 Winners Gallery is full of great photos and videos of micro bioscapes.

Floschularia Ringerns Rotifer feeding by Charles Crebs

Winning photo by Mr. Charles Krebs, Issaquah, Washington, USA
Specimen: Rotifer Floscularia ringens feeding. Its rapidly beating cilia (hair-like structures) bring water containing food to the rotifer
Technique: Differential interference contrast microscopy

The photo shows the microscopic animal’s self-made reddish tube-shaped home, with a building block in the process of being formed inside the rotifer’s body.

Scientists Singing About Science

Fun video with scientists singing about science.

More scientists singing science songs: Friday Fun, Large Hadron Rap – Cambrian Explosion Song – The Sun is a Miasma of Incandescent Plasma – Protein Synthesis: 1971 Video

Today, Most Deaths Caused by Lifetime of Action or Inaction

Chart of the Leading Causes of Death in 1900 and 2010

Our instincts lead us to fear the unknown and immediate threats (probably so we can be ready to run – or maybe fight). But today the biggest risks to an untimely dealt are not lions, other people out to get us, or even just random infection. We have to adapt to the new risks by taking action to eat healthfully and exercise, in the same way we we have evolved to avoid becoming a meal for a hungry beast.

Today the largest causes of death are heart disease and cancer (which account for more than 60% of the deaths causes by the top 10 leading causes of death). The next leading causes are non-infectious airways diseases, cerebrovascular diseases and accidents. Alzheimer’s, diabetes, nephropathies, pneumonia or influenza and suicide make of the rest of the top 10 leading causes.

In 1900 Pneumonia or influenza and tuberculosis took as many lives (per 100,000 people) and cancer and heart disease take today. We have done well decreasing the incidents of death (fewer deaths per 100,000) by greatly reducing and nearly eliminating some causes of death (the 2 leading causes from 1900 are good examples).

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Modeling Weight Loss Over the Long Term

Researchers at the National Institutes of Health have created a mathematical model of what happens when people of varying weights, diets and exercise habits try to change their weight. The findings challenge the commonly held belief that eating 3,500 fewer calories, or burning them off exercising, will result in a pound of weight loss.

Instead, the researchers’ computer simulations indicate that this assumption overestimates weight loss because it fails to account for how metabolism changes. The computer simulations show how these metabolic changes can significantly differ among people.

However, the computer simulation of metabolism is meant as a research tool and not as a weight-loss guide for the public. The computer program can run simulations for changes in calories or exercise that would never be recommended for healthy weight loss. The researchers hope to use the knowledge gained from developing the model and from clinical trials in people to refine the tool for everyone.

“This research helps us understand why one person may lose weight faster or slower than another, even when they eat the same diet and do the same exercise,” said Kevin Hall, Ph.D., an obesity researcher and physicist at the NIH’s National Institute of Diabetes and Digestive and Kidney Diseases. “Our computer simulations can then be used to help design personalized weight management programs to address individual needs and goals.”

The online simulation tool based on the model enables researchers to accurately predict how body weight will change and how long it will likely take to reach weight goals based on a starting weight and estimated physical activity. The tool simulates how factors such as diet and exercise can alter metabolism over time and thereby lead to changes of weight and body fat.

The team found that people’s bodies adapt slowly to changes in dietary intake. They also found heavier people can expect greater weight change with the same change in diet, though reaching a stable body weight will take them longer than people with less fat.

The model also points to a potential simplified method to approximate weight loss in an average overweight person. An adult who has a body mass index (a measure of a person’s weight in relation to his or her height) between 25 and 29.9 is considered overweight. One example: For every pound you want to lose, permanently cut 10 calories from your current intake per day. At that rate, it will take about one year to achieve half of the total weight loss, and almost all of the weight loss will have occurred by three years. This calculation shows how long it takes to achieve a weight-loss goal for a single permanent change of diet or exercise.

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