Category Archives: Science

2012 Nobel Prize in Chemistry to Robert Lefkowitz and Brian Kobilka

The Royal Swedish Academy of Sciences has decided to award the Nobel Prize in Chemistry for 2012 to

Robert J. Lefkowitz, Howard Hughes Medical Institute and Duke University Medical Center, Durham, NC, USA
and Brian K. Kobilka, Stanford University School of Medicine, Stanford, CA, USA

for studies of G-protein–coupled receptors.

Your body is a fine-tuned system of interactions between billions of cells. Each cell has tiny receptors that enable it to sense its environment, so it can adapt to new situtations. Robert Lefkowitz and Brian Kobilka are awarded the 2012 Nobel Prize in Chemistry for groundbreaking discoveries that reveal the inner workings of an important family of such receptors: G-protein–coupled receptors.

For a long time, it remained a mystery how cells could sense their environment. Scientists knew that hormones such as adrenalin had powerful effects: increasing blood pressure and making the heart beat faster. They suspected that cell surfaces contained some kind of recipient for hormones. But what these receptors actually consisted of and how they worked remained obscured for most of the 20th Century.

Lefkowitz started to use radioactivity in 1968 in order to trace cells’ receptors. He attached an iodine isotope to various hormones, and thanks to the radiation, he managed to unveil several receptors, among those a receptor for adrenalin: Î²-adrenergic receptor. His team of researchers extracted the receptor from its hiding place in the cell wall and gained an initial understanding of how it works.

The team achieved its next big step during the 1980s. The newly recruited Kobilka accepted the challenge to isolate the gene that codes for the Î²-adrenergic receptor from the gigantic human genome. His creative approach allowed him to attain his goal. When the researchers analyzed the gene, they discovered that the receptor was similar to one in the eye that captures light. They realized that there is a whole family of receptors that look alike and function in the same manner.

Today this family is referred to as G-protein–coupled receptors. About a thousand genes code for such receptors, for example, for light, flavour, odour, adrenalin, histamine, dopamine and serotonin. About half of all medications achieve their effect through G-protein–coupled receptors.

The studies by Lefkowitz and Kobilka are crucial for understanding how G-protein–coupled receptors function. Furthermore, in 2011, Kobilka achieved another break-through; he and his research team captured an image of the Î²-adrenergic receptor at the exact moment that it is activated by a hormone and sends a signal into the cell. This image is a molecular masterpiece – the result of decades of research.

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.
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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.
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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.

Did a massive comet explode over Canada 12,900 years ago and start an ice age?

I think it is important to increase scientific literacy. One thing that is greatly misunderstood is the process for new scientific explanations being accepted by the scientific community. It is often quite a drawn out process over years (and for the explanation provided in this paper the debate is certainly still ongoing). And for issues that really shake up past explanations it can take decades and be quite contentious. I think posts tagged with “scientific inquiry” are a very interesting collection to explore.

It is important to understand the difficulty in providing evidence that satisfies the overwhelming majority of the scientific experts in any area. And it is important to understand the claims in one (or numerous papers) are not the accepted proven wisdom of the scientific community. Thankfully the process is rigorous. While mistakes can still be made, the evidence needed to substantiate a scientific hypothesis is significant. Their is still plenty of room for position to color accepted scientific wisdom. A respected professor is often able to make a claim that is more readily accepted and even more-so for to insist the new claims do not provide enough evidence in support of them to accept the new claims and have there position accepted (even when it really shouldn’t be looking just at the facts).

Topper site in middle of comet controversy

Firestone found concentrations of spherules (micro-sized balls) of metals and nano-sized diamonds in a layer of sediment dating 12,900 years ago at 10 of 12 archaeological sites that his team examined. The mix of particles is thought to be the result of an extraterrestrial object, such as a comet or meteorite, exploding in the earth’s atmosphere. Among the sites examined was USC’s Topper, one of the most pristine U.S. sites for research on Clovis, one of the earliest ancient peoples.
“This independent study is yet another example of how the Topper site with its various interdisciplinary studies has connected ancient human archaeology with significant studies of the Pleistocene,” said Goodyear, who began excavating Clovis artifacts in 1984 at the Topper site in Allendale, S.C. “It’s both exciting and gratifying.”
Younger-Dryas is what scientists refer to as the period of extreme cooling that began around 12,900 years ago and lasted 1,300 years. While that brief ice age has been well-documented – occurring during a period of progressive solar warming after the last ice age – the reasons for it have long remained unclear.

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Key Indicator for Malignant Melanoma Found

Skin cancer detection breakthrough

The researchers found that certain biochemical elements in the DNA of normal pigment-producing skin cells and benign mole cells are absent in melanoma cells. Loss of these methyl groups — known as 5-hmC — in skin cells serves as a key indicator for malignant melanoma. Loss corresponded to more-advanced stages of melanoma as well as clinical outcome.

Strikingly, researchers were able to reverse melanoma growth in preclinical studies. When the researchers introduced enzymes responsible for 5-hmC formation to melanoma cells lacking the biochemical element, they saw that the cells stopped growing.

“It is difficult to repair the mutations in the actual DNA sequence that are believed to cause cancer,” said Christine Lian, a physician-scientist in the Department of Pathology at BWH and one of the lead authors. “So having discovered that we can reverse tumor cell growth by potentially repairing a biochemical defect that exists — not within the sequence but just outside of it on the DNA structure — provides a promising new melanoma treatment approach for the medical community to explore.”

Because cancer is traditionally regarded as a genetic disease involving permanent defects that directly affect the DNA sequence, this new finding of a potentially reversible abnormality that surrounds the DNA (thus termed “epigenetic”) is a hot topic in cancer research, according to the researchers.

In the United States, melanoma is the fifth most common type of new cancer diagnosis in men and the seventh most common type in women. The National Cancer Institute estimates that in 2012 there will be 76,250 new cases and 9,180 deaths in the United States owing to melanoma.

Thankfully scientists keep making great progress in understanding and finding potential clues to treating cancer. And big gains have been made in treating some cancers over the last few decades. But the research successes remain difficult to turn into effective solutions in treating patients.

I am thankful we have so many scientists doing good work in this difficult and important area (cancer).

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.

Man in Coma for 7 Years was Given a Sleeping Pill and Woke Up

Lazarus pill miracle for E Cape man, 9 September 2012

After reading a report in City Press last month, his wife, Nomfundo, insisted that he be given a prescription for the sleeping pill Stilnox, which has the opposite effect on those with brain injuries.

It worked – and brought him out of a seven-year coma.
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But on August 12, family friend Nceba Mokoena came across an article in City Press about a miracle recovery made by another car crash victim, hundreds of kilometres away in Gauteng.

Louis Viljoen was given the sleeping pill by chance by his mother, Sienie.

She had noticed he wasn’t sleeping peacefully and asked her doctor if she could give him half a sleeping tablet. After she did, Louis opened his eyes and said “Hello Mamma”, his first words in five years.

Very cool anecdote and example that modern medicine has many miraculous cures but the medical system can’t always use them as well as we would hope. Even with all the knowledge we have today just getting that information into the right doctor’s minds is very hard. And the complexity of diagnoses and interactions makes medical care still an art as well as a science.

So is this just some freak accident. Partially, in the mother giving her son a sleeping pill to reduce his seeming restlessness in the coma. But the effect of Stilnox in bringing coma victims out of a coma has been documented previously.

Reborn from persistent vegetative state, 12 September 2006

Four three years, Riaan Bolton has lain motionless, his eyes open but unseeing. After a devastating car crash doctors said he would never again see or speak or hear. Now his mother, Johanna, dissolves a pill in a little water on a teaspoon and forces it gently into his mouth. Within half an hour, as if a switch has been flicked in his brain, Riaan looks around his home in the South African town of Kimberley and says, “Hello.” Shortly after his accident, Johanna had turned down the option of letting him die.

Three hundred miles away, Louis Viljoen, a young man who had once been cruelly described by a doctor as “a cabbage”, greets me with a mischievous smile and a streetwise four-move handshake. Until he took the pill, he too was supposed to be in what doctors call a persistent vegetative state.

Across the Atlantic in the United States, George Melendez, who is also brain-damaged, has lain twitching and moaning as if in agony for years, causing his parents unbearable grief. He, too, is given this little tablet and again, it’s as if a light comes on. His father asks him if he is, indeed, in pain. “No,” George smiles, and his family burst into tears.

It all sounds miraculous, you might think. And in a way, it is. But this is not a miracle medication, the result of groundbreaking neurological research. Instead, these awakenings have come as the result of an accidental discovery by a dedicated – and bewildered – GP. They have all woken up, paradoxically, after being given a commonly used sleeping pill.

Medical care is still today an extremely difficult area where highly trained and continuously learning doctors still have a great deal of trouble keeping up with the latest medical knowledge.

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.

The Eagle Has Landed

Neil Armstrong and Buzz Aldren land on the moon: July 20, 1969. As Neil Armstrong took humanity’s first step onto the Moon he said:

That’s one small step for man, one giant leap for mankind.

The Science Behind Hummingbird Flight

Aerodynamics of the hovering hummingbird

Hummingbirds and insects have evolved for sustained hovering ï¬‚ight from vastly different ancestral directions, and their distinct phylogenies underlie the differences in their aerodynamic styles. In all other birds—and, presumably, hummingbird ancestors—the downstroke provides 100% of weight support during slow ï¬‚ight and hovering. Given that many birds possess the mass-speciï¬c power (using anaerobic metabolism) to hover for short periods, the selective pressure on hummingbird ancestors was probably for increased efï¬ciency (resulting in stiff wings with greatly simpliï¬ed
kinematics), and an upstroke muscle (the supracoracoideus) that makes the recovery stroke rapid, while contributing enough to the hovering power requirements to allow the downstroke muscle (the pectoralis) to operate within its aerobic limits.

In other words, this pseudosymmetrical wingbeat cycle is good enough, and although hummingbirds do not exhibit the elegant aerodynamic symmetry of insects, natural selection rewards ‘good enough’ as richly as it does our aesthetic ideals

A single spot in the Sahara that provides huge amounts of nutrients to the Amazon

About 40 million tons of dust are transported annually from the Sahara to the Amazon basin. Saharan dust has been proposed to be the main mineral source that fertilizes the Amazon basin, generating a dependence of the health and productivity of the rain forest on dust supply from the Sahara. Here we show that about half of the annual dust supply to the Amazon basin is emitted from a single source: the BodÃ©lÃ© depression located northeast of Lake Chad, approximately 0.5% of the size of the Amazon or 0.2% of the Sahara. Placed in a narrow path between two mountain chains that direct and accelerate the surface winds over the depression, the BodÃ©lÃ© emits dust on 40% of the winter days, averaging more than 0.7 million tons of dust per day.

Even understanding how connected the global ecosystem is, research like this provides amazing reminders of those connections.