Category Archives: Life Science

Big Drug Research and Development on Campus

Merck and Harvard just signed an agreement to develop treatments for the bone disease osteoporosis. On Apr. 25 rival Pfizer (PFE) invested $14 million in an alliance with four universities to study diabetes and obesity.

Drugmakers are counting on these deals to solve a persistent problem: underperforming product pipelines. Merck, Pfizer, and others have been losing sales of one blockbuster drug after another as patents expire and competitors charge in with generics. Big drug companies have fought back by spending more on research, yet the number of new medicines approved each year is falling. In the last week of April alone, the U.S. Food & Drug Administration rejected two of Merck’s experimental drugs, prompting the company to lay off 1,200 salespeople.
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Past deals between industry and academia have been hampered by patent disputes and tussles over publication rights, as companies tried to thwart academics who want to share their discoveries with colleagues around the world. So now the companies have devised policies allowing their Ivory Tower partners to patent and publish their discoveries, even as they draw the professors more deeply into corporate affairs.

Funding university activities this way can lead to conflicts and problems but realistically huge amounts of funding are entangled with possible conflicts of interest. The biggest concern I is that universities will bow to the almighty dollar instead of their missions. And inadequate oversight can damage their credibility (not one failure, most likely, but if a pattern emerges). For example: Researchers Fail to Reveal Full Drug Pay (“The Harvard group’s consulting arrangements with drug makers were already controversial because of the researchers’ advocacy of unapproved uses of psychiatric medicines in children.”). Then find out the companies were paying them well, the professors failed to disclose that and the advocacy is rightfully questioned.

Big Fat Lie

Big fat lie

‘I got actively attacked, but I guess I had to be,’ Taubes says. ‘What are the chances of writing an article that says the entire medical establishment is wrong, and them going, ” Good point, thank you, Gary. Can we give you an award?” When people challenge the establishment, 99.9 per cent of the time they are wrong. If I was writing about me, I’d begin from the assumption that I am both wrong and a quack.’

At least he is right on this. You challenge the accepted scientific understanding and this is what will happen. But if the evidence is there scientists will be won over by the evidence over time.

‘Reading the research was a reawakening for me,’ he says. ‘I did all the things that the rest of us did. I ate a low-fat diet, went to the gym and was getting heavier anyway. But once you flip your way of thinking about it, it seems so absurd: the idea that what you put in minus what you expend equals how fat you are. Our bodies don’t work like a car. We are not thermodynamic black boxes; we are biological organisms and we have evolved complex systems of hormones and enzymes and proteins. That’s how we are regulated.’

The obesity epidemic began in America during the late 1970s, which is also when the low-fat, high-carb diet-and-exercise revolution began. ‘You have a starting point,’ says Taubes. ‘The question is what is causing it? Then I realised that we were first told to eat less fat in the late 1970s, and, if you eat less fat, you start to eat more carbohydrates – it’s a trade-off.’

The whole healthy eating debate is sure not easy to figure out. But I think some things are clear. Eating too many calories and not exercising enough are problems. And it also makes sense that it is not only the number of calories that matter but what type. We are biological beings and how we process food is not just by a count of the calories. It seems the evidence of bad effects of too much carbohydrates is growing.

It also makes perfect sense that our bodies evolved to store energy for worse times (and some of us have bodies better at doing that). Now we are in a new environment where (at least for many people alive today) finding enough calories is not going to be a problem so it would be nice if we could tell our bodies to get less efficient at storing fat for bad times ahead. But we can’t so we need to take actions to remain healthy given the how our body reacts to what we eat and do. And it seems one of those actions might mean we have to eat less than we might want to.

The Science Barge

The Science Barge is a prototype, sustainable urban farm and environmental education center. It is the only fully functioning demonstration of renewable energy supporting sustainable food production in New York City. The Science Barge grows tomatoes, cucumbers, and lettuce with zero net carbon emissions, zero chemical pesticides, and zero runoff.

From May to October 2007, the Science Barge hosted over 3,000 schoolchildren from all five New York boroughs as well as surrounding counties as part of our environmental education program. In addition, over 6,000 adult visitors visited the facility along with press from around the world.

NY Sun Works: The Science Barge

Limited growing space means growing upwards, with stacked pots for strawberries, and vines that grow up to the ceiling and are then folded over to grow back down. Instead of using pesticides, pests are kept in check using ladybugs, parasitic wasps, and other predators as needed. Environmentally friendly substrates such as rice husks, coconut shells, and Earth Stone (recycled glass), are used to aerate the root systems for the plants.

Most fascinating of all was the Aquaponic system for providing nutrients to the plants using catfish. Nutrients from the plants and worms feed the catfish, who produce nitrogen-rich waste, which feeds the plants. Tilapia were originally used, but eventually replaced with catfish, which were better suited to the climate. The result of all this effort is a bounty of fresh fruits and vegetables given out to all the children who visit the barge.

Still Just a Lizard

Still just a lizard by PZ Myers

in 1971, scientists started an experiment. They took 5 male lizards and 5 female lizards of the species Podarcis sicula from a tiny Adriatic island called Pod Kopiste, 0.09km2, and they placed them on an even tinier island, Pod Mrcaru, 0.03km2, which was also inhabited by another lizard species, Podarcis melisellensis. Then a war broke out, the Croatian War of Independence, which went on and on and meant the little islands were completely neglected for 36 years, and nature took its course. When scientists finally returned to the island and looked around, they discovered that something very interesting had happened.

The original population of P. sicula was still present on Pod Kopiste, so we have a nice control population. These lizards are small, fast, insect-eaters in which the males defend territories. Sadly, P. melisellensis on Pod Mrcaru had been extirpated. So we had a few innocent casualties of the experiment.

The transplanted P. sicula thrived and swarmed over the island of Pod Mrcaru, but they were different, and they had evolved in multiple ways.

The original P. sicula were insectivores who occasionally munched on a leaf; approximately 4-7% of their diet was vegetation. The P. sicula of Pod Mrcaru, though, had adopted a more vegetarian diet: examining their gut contents revealed that 34% of their diet was plants in the spring, climbing to 61% in the summer…and much of this diet was hard-to-digest stuff, high in cellulose. This is a fairly radical shift.

There were concomitant changes. The lizards’ skulls were wider, deeper, and longer, and they had stronger bites — a necessity for chomping off bits of tough plants, instead of soft mosquitos. Instead of chasing bugs, they’re browsing stationary plants, and their legs are shorter and they are slower. Population densities are higher. The Pod Mrcaru lizards no longer seem to defend territories, so there have been behavioral changes.

Still just a lizard, I know.

Now here’s something really cool, though: these lizards have evolved cecal valves. What those are are muscular ridges in the gut that allow the animal to close off sections of the tube to slow the progress of food through them, and to act as fermentation chambers where plant material can be broken down by commensal organisms like bacteria and nematodes — and the guts of Pod Mrcaru P. sicula are swarming with nematodes not found in the guts of their Pod Kopiste cousins.

Nobel Laureate Initiates Symposia for Student Scientists

The video shows a portion of Oliver Smithies’ Nobel acceptance lecture. See the rest of the speech, and more info, on the Nobel Prize site.

As an undergraduate student at Oxford University in the 1940s, Oliver Smithies attended a series of lectures by Linus Pauling, one of the most influential chemists of the 20th century. It was a powerful experience, one that sparked the young scientist’s ambitions and helped launch his own eminent career.

“It was tremendously inspiring,” says Smithies, one of three scientists who shared the Nobel Prize in Medicine in 2007. “People were sitting in the aisles to listen to him.”

Now Smithies, who was a genetics professor at the University of Wisconsin-Madison from 1960-88, is taking it upon himself to expose a new generation of undergraduates to this sort of experience. Using the prize money that came with his Nobel Prize, Smithies is funding symposia at all four universities he has been affiliated with throughout his scientific career: Oxford, the University of Toronto, UW-Madison and the University of North Carolina, where he is currently the Excellence Professor of Pathology and Laboratory Medicine. Each university will receive about $130,000 to get things started.

“He wants the symposium to be a day when we bring the very best in biology to campus to interact with the students,” says geneticist Fred Blattner, who is in charge of organizing the symposium at UW-Madison and who collaborated with Smithies when their careers paths overlapped in Wisconsin.

The first of two speakers at the UW-Madison’s inaugural Oliver Smithies Symposium will be Leroy Hood, director of the Institute for Systems Biology, located in Seattle. Hood is a pioneer of high-throughput technologies and was instrumental in developing the technology used to sequence the human genome. More recently, Hood has focused his efforts on systems biology, the field of science in which researchers create computer models to describe complex biological processes, such as the development of cancer in the body. He is also at the forefront of efforts to use computer models to help doctors tailor drugs and dosages to an individual’s genetic makeup.
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Robotic Prosthetic Arms for People

Dean Kamen latest invention was funded by DARPA. Once again he is doing amazing stuff. It is great what engineers can do (many worked together to get the progress so far) when given the opportunity. We need many more such efforts.

Dean Kamen Lends a Hand, or Two (August 2007):

DARPA has spent almost $25 million funding two independent teams, Mr. Kamen’s DEKA Research & Development Corp. and a group at Johns Hopkins’ University in an effort they hope will ultimately lead to commercial prosthesis that can be controlled from the human brain.

The innovation in the DEKA arm lies in its ultra light weight carbon shell, giving the user an exoskeleton with which to gain the leverage necessary to do some of the extraordinary things the system makes possible, such as lifting a 40 lb. weight.

To make the system function, the DEKA engineers coated the inside of the shell with a mosaic of thin air bladders that can be individually filled with air to offer padding and rigidity necessary to make possible normally ordinary tasks such as operating a portable power drill. When the arm is not in use the system deflates, or can even alternately fill and empty to offer a massage effect, so that it is not painful to wear for long periods.

The DEKA system is controlled by a joystick that is moved by the remaining portion of the user’s arm and by a second control mechanism in the user’s shoe. Mr. Kamen said that despite the complexity of controlling an ensemble of motors and mechanical servo devices, a user can gain basic functional control in just one day.

Mapping the Human Proteome

The human genome is old news. Next stop: the human proteome

Unlike the genome, which remains essentially static between cell types and over time, the proteome is tremendously dynamic, changing constantly in response to cell-cell signalling and environmental stimuli. Thus even though -with some small exceptions – every cell in your body carries the same genome, the proteome can be wildly different between different tissues and can change rapidly over time
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At the very least, large-scale analysis of the human proteome should allow researchers to tentatively place many of our currently anonymous genes into functional pathways. That’s a step forward for personal genomics: knowing that you have a loss-of-function mutation in a gene that may be involved in cholesterol biosynthesis is a lot more useful (in terms of guiding further clinical testing) than simply knowing that you have a mutation in hypothetical gene C11orf68.

Using Cameras Monitoring To Aid Conservation Efforts

photo of Jaguar

How Hidden Cameras Aid Conservation Efforts for Jaguars and Other Rare Animals

Tobler and his fellow authors write that “despite years of research throughout the Amazon, there are few complete mammal inventories and our knowledge of the distributions of rare and elusive species is still poor.” They explain further that traditional techniques for inventorying which animals are present in a given ecosystem, such as identification of tracks and scat, direct observations, and trapping of animals often do not account for species of animals that are rare and/or low in their numbers in a certain area. For these reasons, they wanted to test out how well cameras could document animals in the rainforest, where cover is dense and many species are hard to observe.
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Over the two years of the study, some of the more photographed animals included the Lowland tapir, which was caught on camera 102 times and also the White-lipped Peccary (seen 210 times). Among cat species, jaguars were photographed 51 times, ocelots 46 times, pumas 25 times, margays 15 times, and jaguarundis proved the most elusive, only being photographed twice.

The four species of animals that were not photographed included the pacarana, the grison, the Southern naked-tailed armadillo, and the Bush dog.
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Given the recent lowering of costs and improvements in camera technology, hopefully their example and those of others will help other conservationists around the world to better understand the location of important and rare animals in their respective ecosystems. Given the large range of jaguars and their need for connected habitat, this study gives us hope to think that little hidden cameras might help us better understand where these charismatic cats and other rare animals roam, and consequently give us better information with which to help protect them.

Photo Credit: purplegrum at Flickr under a Creative Commons attribution license

Bacteria “Feed” on Earth’s Ocean-Bottom Crust

Once considered a barren plain dotted with hydrothermal vents, the seafloor’s rocky regions appear to be teeming with microbial life, say scientists
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“Initial research predicted that life could in fact exist in such a cold, dark, rocky environment,” said Santelli. “But we really didn’t expect to find it thriving at the levels we observed.” Surprised by this diversity, the scientists tested more than one site and arrived at consistent results, making it likely, according to Santelli and Edwards, that rich microbial life extends across the ocean floor. “This may represent the largest surface area on Earth for microbes to colonize,” said Edwards.
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Santelli and Edwards also found that the higher microbial diversity on ocean-bottom rocks compared favorably with other life-rich places in the oceans, such as hydrothermal vents. These findings raise the question of where these bacteria find their energy, Santelli said.

“We scratched our heads about what was supporting this high level of growth,” Edwards said. With evidence that the oceanic crust supports more bacteria than overlying water, the scientists hypothesized that reactions with the rocks themselves might offer fuel for life.

Why doesn’t this stuff make the news over what some celebrity did or politician said… (well I must admit I am just guessing since I don’t actually watch the news or read the mass media much – other than some science, investing or economics content). Oh well, at least you get to read the Curious Cat Science blog and find out about some of the cool stuff being learned every day.

Learning from Leprosy Diagnosis

A Scary Diagnosis Hits Home

The diagnosis that ultimately resulted — leprosy — turned the Blanchards’ world upside down and rippled through the lives of many people they knew or had contact with. It also raised issues that are often confronted when any contagious disease is diagnosed, particularly one with scary connotations: What precautions should be taken to protect the rights of the affected individual as well as the health of the community?
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For the Blanchards, some of the answers lay almost literally in their back yard. Baton Rouge is home to the National Hansen’s Disease (Leprosy) Clinical Center, part of the U.S. Public Health Service.
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About 300,000 new cases of leprosy are diagnosed annually, according to the World Health Organization. Now known as Hansen’s disease, after the Norwegian scientist who discovered the mycobacterium that causes the illness, it affects about 2 million to 3 million people worldwide.

Where it is left untreated, Hansen’s disease is a leading cause of disability and devastating deformity. It remains endemic in Bangladesh, India, Brazil and elsewhere. In the United States, roughly 6,000 people have the disease. One hundred to two hundred new cases are reported annually, and, like BB Blanchard, about two dozen of those new patients have never been beyond U.S. borders.
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How transmission occurs is a mystery. Humans and the armadillo are the only two creatures known to get the disease. No one knows where the microbe hides in nature, although the suspicion is that the leprosy mycobacterium may be airborne like its bacterial cousin, tuberculosis.

Most people think of leprosy as a skin disease. But the rash that BB Blanchard had and the disfiguring lesions often associated with it are just a symptom. The mycobacteria burrow into nerves, where they often remain undetected for years or even decades.