Tag Archives: scientific inquiry

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.

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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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

New Iron Based Superconductors

Research Suggests Novel Superconductor Is in a Powerful Class All its Own

discovered surprising magnetic properties in the new superconductors that suggest they may have very powerful applications — from improved MRI machines and research magnets, to a new generation of superconducting electric motors, generators and power transmission lines. The research also adds to the long list of mysteries surrounding superconductivity, providing evidence that the new materials, which scientists are calling “doped rare earth iron oxyarsenides,” develop superconductivity in quite a new way
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Early this year, Japanese scientists who had been developing iron-based superconducting compounds for several years, finally tweaked the recipe just right with a pinch of arsenic. The result: a superconductor, also featuring oxygen and the rare earth element lanthanum, performing at a promising -413 degrees F (26 K). The presence of iron in the material was another scientific stunner: Because it’s ferromagnetic, iron stays magnetized after exposure to a magnetic field, and any current generates such a field. As a rule, magnetism’s effect on superconductivity is not to enhance it, but to kill it.

Iron based superconductors might resist magnetic fields over 100 Tesla

The new superconductors seem like they will be able to make improved MRI machines and research magnets, a new generation of superconducting electric motors, generators and power transmission lines. Tesla is a unit of magnetic field strength; the Earth’s magnetic field is one twenty thousandth of a tesla.

Challenging the Science Status Quo

Challenging Science

When scientists question facets of existing theories or propose new ones, they present the best evidence available and make the strongest arguments they can to their colleagues. Colleagues in turn challenge that evidence and reasoning. The rigor of this process is what makes science such a powerful tool.
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Lynn Margulis wrote a paper, “The Origin of Mitosing Eukaryotic Cells,” which argued that eukaryotic cells – those with a true nucleus – arose when cells with no nucleus symbiotically incorporated other such cells to make new cells that could perform more functions. The paper was rejected by many journals, and when eventually published by The Journal of Theoretical Biology it was highly criticized. Margulis spent decades defending her work, but scientists now accept her suggested mechanism through which organelles such as mitochondria and chloroplasts evolved. Her suggestions about other organelles have not stood up to experimental tests, and are not as widely accepted.
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In 1982, Stanley Prusiner published an article on his research into scrapie – a disease in sheep related to Creutzfeldt-Jakob disease – which argued that the infectious agent was not a virus but a protein, which Prusiner called a “prion”. Because no one had heard of a protein replicating without a nucleic acid like DNA or RNA, many virologists and scrapie researchers reacted to the article with incredulity. When the media picked up the story, “the personal attacks of the naysayers at times became very vicious,” according to Prusiner. However, his critics failed to find the nucleic acid they were sure existed, and less than two years later, Prusiner’s lab had isolated the protein. Subsequent research provided even more support for prions, and in 1997 Prusiner was awarded the Nobel Prize in Physiology or Medicine.

Molecular Action May Help Keep Birds on Course

Four decades after scientists showed that migratory birds use Earth’s magnetic field to orient themselves during their seasonal journeys, researchers have at last found a molecular mechanism that may explain how they do it.

If the hypothesis is true, the planet’s magnetic field lines — which arch around Earth from north to south — may be plainly visible to birds, like the dashed line in the middle of a road.

The work, described online yesterday in the journal Nature, was conducted in a test tube and does not prove that birds actually use the mechanism. And researchers aligned with a competing model say they are not convinced.

But by identifying for the first time a molecule that reacts to very weak magnetic fields, the experiments prove the plausibility of a long-hypothesized method of avian navigation that has had a credibility problem because no one had ever found a molecule with the required sensitivity.

Colony Collapse Disorder Continues

1.1 Million Bee Colonies Dead This Year

The information provided here was generated by a survey conducted by the Apiary Inspectors of America. They took the survey in January and February this year, and in the process, gathered information from 18% of the colonies in the U.S.

The survey found that about 35% of all the colonies in the U.S. died last winter. Of those that died, 71% died of natural causes, 29% from symptoms that are suspect colony collapse disorder. Doing the math that comes to at least 10% of all the bees in the U.S. last year died of Colony Collapse Disorder.
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Considering all these factors, undue concern over IAPV detection is not warranted. While IAPV’s role in colony losses remains a priority in ongoing research, we do know that high levels of other common bee viruses, such as KBV, DWV, and ABPV, have also been linked with certain incidences of high colony mortality or decline in worker numbers. We also know that nearly all bee colonies are infected with at least one type of virus and that all these viruses are potentially pathogenic.

The research continues. As I have said before this is a great example of scientists in action trying to figure out what is happening.

Vanishing Giant Nests of Yellow-jackets

Giant wasp nest

Vanishing Nests

Only a year ago, an Auburn University research entomologist encountered a phenomenon that beggared description – 16 super-sized yellow jacket nests throughout central and south Alabama.

By the end of the summer, the number of reported nests increased to more than 80. Auburn researcher Dr. Charles Ray speculates there probably were hundreds more undetected nests throughout the state. One nest collector spotted 10 of these nests in Lowndes County alone, while an Alabama Cooperative Extension System agent in Covington County reported as many as 25 nests.

Why were these gigantic nests considered such oddities? Because entomologists such as Ray could go an entire career without seeing scarcely one of these huge nests. This year, though, the nests seem to have vanished as quickly as dissipating clouds. Working closely with Alabama Extension agents and other monitors throughout the state, Ray hasn’t turned up so much as one nest this year.

“The summer of 2006 may prove to be a once in a lifetime opportunity,” say Ray, who considers the discovery of the nests one of the high points of his career. So what accounts for this once in a lifetime occurrence? Ray speculates it had to do with an unusually mild 2006 winter. “The mid-20s was about as cold as it got that year – only about a day or two of really cold weather,” says Ray, adding that this extremely mild winter probably established optimal conditions for the yellow jackets the following spring.