Tue, 20 Nov 2007 01:46:03 GMT

Deppea splendens

van swearingen@Flickr is the contributor of today''s photograph from Huntington Botanical Gardens in California (original | BPotD Flickr Group Pool). Thank you!

Golden fuchsia seems to be the common name for this plant (though it''s not a fuchsia). On the related topic of its scientific name, a team of Hungarian taxonomists have suggested it be renamed Csapodya splendens, but the GRIN Taxonomy Database has retained Deppea splendens (so far).

Despite the cosmopolitan distribution of its family, the Rubiaceae (madder or coffee family), Deppea splendens was “only known from a canyon on the south slope of Cerro Mozotal in southern Chiapas, where it naturally occurred as a fifteen- to twenty-five-foot shrub or small tree in pine-oak cloud forest within sight of the Pacific Ocean.” This site was cleared for farmland in 1986; Deppea splendens is now presumed extinct in the wild (though some hope exists that it may be rediscovered on other nearby mountains in Chiapas, Mexico and neighbouring Guatemala). Its original discovery by Western science occurred in 1972, though it remained unrecognized as a novel species for a long time; in fact, it was not published and described in the scientific literature until 1987, a year after its possible demise in the wild.

The quote above is from an account of the species in the April 2000 issue of Pacific Horticulture magazine, available online via San Francisco Botanical Garden: Deppea splendens (PDF) by Kathy Musial. If you have the time to read the article, I can find no better written piece about the species. If you''ve only a short amount of time, a brief article is available from the Mildred E. Mathias Botanical Garden newsletter: Deppea splendens by Rand Plewak.

A photograph of the foliage is available via frequent BPotD contributor Eric in SF''s PlantWorld site: Deppea splendens. Posted by: Daniel Mosquin      Read more     Source

Tue, 20 Nov 2007 01:43:33 GMT

Still Rising

This is a new weekend with plenty of posts from the field of personalized genetics. After my review about companies focusing on individualized medicine, I got several positive comments, so I’m going to write other reviews soon. Until then, here are some interesting news, announcements:

• Personalized Medicine: Against the Odds (Epidemix): Shocking statistics to promote personalized medicine.

• deCODE Offers Personal Genomic Sequencing Test for $985: Another company to write about. Coverage at The Genetic Genealogist and DNA Direct Talk.

• Highlights from the Burrill Personalized Medicine Meeting at DNA Direct Talkand The Gene Sherpa:

“Early medical testing and treatment could save patients and healthcare providers a ton of money, but nobody wants to pay for unproven and often expensive new lab work. FDA approval is not required for laboratory tests, but it is an indicator that products are actually beneficial to doctors and patients.” - Wired

• DNA Direct Talk (PredictER): The problem of DTC genetic testing is still unsolved.

• DNA Direct Talk (Reuters):

While advances are being made in a few areas, so-called pharmacogenetics will not change the commercial landscape for the bulk of pharmaceuticals for several years, drugmakers told the Reuters Health Summit in New York this week.

• DNA Direct Talk (US News):

But let’s not wait until we have a hearing room filled with victims before taking action. As Collins warns, “The strategy to offer individual personalized medicine has a big cloud over its horizon. If we want a brighter healthcare future, we need to blow that cloud away.” He’s right. It’s time to get GINA out of the holding pen, one way or the other.

I finish this resume with a funny video which tries to answer the question: Why Personalized Medicine? Especially with drugs such as Antidepressants which are often prescribed based on trial-and-error and objective criteria for succesful treatment outcome are lacking. (This movie is from a Dutch commercial from Eiffel) Posted by: Bertalan      Read more     Source

Tue, 20 Nov 2007 01:35:33 GMT

Conforming to the Norm

Solomon Asch''s classic ) had found that when people were faced with making a judgement on an ambiguous test, they used other people''s judgements as a reference point.

This makes perfect sense. If I''m not sure about something, I''ll check with someone else. But this is only when I''m not sure. The situation is quite different when I have unambiguous information, such as when I can clearly see the answer myself. Other people''s judgement should then have no effect - or at least that''s what Asch thought.

The experiment
To test his theory he brought male undergraduates, one at a time, into a room with eight other people who were passed off as fellow participants (Asch, 1951). They were then shown three lines with another for comparison, similar to the figure above. Participants were asked to call out which line - A, B or C - was the same length as the reference line. This procedure was repeated 12 times with participants viewing variations of the above figure.

What the participants didn''t realise was that all the other people sat around the table were in on the game. They were all confederates who had been told by the experimenter to give the wrong answer. On half of the trials they called out the line that was too short, and on the other half the line that was too long.

The real experimental participant, who knew nothing of this, was actually the sixth to call out their answer after five other confederates of the experimenter had given the wrong answer.

Surprising findings
The results were fascinating, and not at all what Asch had been expecting:

• 50% of people gave the same wrong answer as the others on more than half of the trials.
• Only 25% of participants refused to be swayed by the majority''s blatantly false judgement on all of the 12 trials.
• 5% always conformed with the majority incorrect opinion (we all know people like that, right?!)
• Over all the trials the average conformity rate was 33%.

Intrigued as to why participants had gone along with the majority, Asch interviewed them after the experiment. Their answers are probably very familiar to all of us:

• All felt anxious, feared disapproval from others and became self-conscious.
• Most explained they saw the lines differently to the group but then felt the group was correct.
• Some said they went along with the group to avoid standing out, although they knew the group was wrong.
• A small number of people actually said they saw the lines in the same way as the group.

The findings of this study were so startling they inspired many psychologists to investigate further. Here are a few of their findings:

• Asch himself found that if the participant only had to write down their answer (while others called theirs out) conformity was reduced to 12.5%.
• Deutsch and Gerard (1955) still found conformity rates of 23% even in conditions of high anonymity and high certainty about the answer.
• Those who are ''conformers'' typically have high levels of anxiety, low status, high need for approval and often authoritarian personalities.
• Cultural differences are important in conformity. People from cultures which view conformity more favourably - typically Eastern societies - are more likely to conform.

A mixed blessing
The variations on the original theme go on and on, examining many possible experimental permutations, but the basic finding still remains solid. While there''s no surprise that we copy each other, it''s amazing that some people will conform despite the evidence from their own eyes. Imagine how much easier it is to encourage conformity when ambiguity levels are much higher, as they often are in everyday life. Posted by: Jerry      Read more     Source

November 18, 2007, 8:50 PM CT

genomes of 12 fly species

In work that reveals important clues in the evolution of genes, an international consortium of MIT researchers and his colleagues has analyzed the genomes of twelve species of the fruit fly Drosophila in one of the first large-scale comparisons of multiple animal genomes.

The researchers' approach may also help unlock the secrets of other genomes, including our own.

The work appears in the Nov. 8 issue of Nature and in more than 40 accompanying papers in Genome Research and other journals.

"Having the sequences of a number of closely related species allows us to study the evolutionary forces that have shaped the fruit fly's family tree, and to discover the working parts of the fly genome in a systematic way," said Manolis Kellis, associate member of the Broad Institute of MIT and Harvard and one of the project leaders. Kellis is also the Karl Van Tassel Career Development Assistant Professor of Electrical Engineering and Computer Science at MIT, and is affiliated with the Institute's Computer Science and Artificial Intelligence Laboratory.

On one hand, the scientists studied the differences across species to help elucidate how evolution has shaped fly biology over millions of years. Their analysis revealed that while a number of attributes of Drosophila genomes are in fact conserved across multiple species, each species has novel features not seen in any other. For example, the genes involved in interactions with the environment and in reproduction showed signs of adaptive evolution, meaning that they likely provided some survival advantage to the organism......... Posted by: Beverly      Read more         Source

November 18, 2007, 8:49 PM CT

Study sees potential for acceleration in U.S. emissions

U.S. greenhouse gas emissions could grow more quickly in the next 50 years than in the prior half-century, even with technological advances and current energy-saving efforts, as per a new study by MIT's Richard Eckaus, the Ford International Professor of Economics, emeritus, and his co-author, Ian Sue Wing (Ph.D. 2001).

What's more, technology itself may be more the stuff that dreams are made on than the most available tool for reducing CO2 emissions or solving the global energy crisis, cautions Eckaus.

"There is no a priori reason to think technology has the potential for reducing energy use while meeting the tests of economics. It's politically unappetizing in the U.S., but in Europe, gas costs six dollars a gallon. Make energy more expensive: People will use less of it," Eckaus says.

In their paper, "The Implications of the Historical Decline in U.S. Energy Intensity for Long-Run CO2 Emission Projections," reported in the recent issue of Energy Policy, Eckaus and Wing portray the changing interplay among technology, energy use and CO2 emissions, based on a simulation of the U.S. economy.

"We observed that, in spite of increasing energy prices, technological change has not been responsible for much reduction in energy use, and that it may have had the reverse effect," Eckaus says of their results......... Posted by: Beverly      Read more         Source

November 15, 2007, 10:08 PM CT

New Theory Of Brain Flexibility

Carnegie Mellon University neuroscientist Marcel Just and Stanford postdoctoral fellow Sashank Varma have put forward a new computational theory of brain function that provides answers to one of the central questions of modern science: How does the human brain organize itself to give rise to complex cognitive tasks such as reading, problem solving and spatial reasoning? Just and Varmas theory, called 4CAPS, is described in the fall issue of the journal Cognitive, Affective, and Behavioral Neuroscience.

More than a decade of research involving functional Magnetic Resonance Imaging brain scans in hundreds of laboratories has yielded a tremendous amount of information about what parts of the brain are activated when a person performs various tasks. Some scientists have been tempted to conclude that a simple one-to-one relationship exists between high-level mental tasks and brain areas. For example, some think that a specific brain area is responsible for a specific cognitive task, such as identifying a face.

Just and Varma, however, propose that the evidence reveals a more complex picture in which thinking is a network function a collaboration of several brain areas that is constantly adapting itself, based on the task at hand and the brains own resources and biological limitations. The collaborating parts of the brain, as per Just, are like members of a sports team whose players substitute in and out of the action. 4CAPS (an acronym for Capacity Constrained Concurrent Cortical Activation-based Production System), proposes a decentralized process by which members of the cortical team volunteer themselves when their strengths are called for, but also permits less efficient but capable members to step forward when the primary player is injured or disabled, as might occur as a result of a stroke. Just and Varma have constructed many computational models to demonstrate this process, such as a model that understands English sentences......... Posted by: Beverly      Read more         Source

November 14, 2007, 9:16 PM CT

How Water "Lubricates" Proteins

Scientists are one more step closer to understanding how proteins move when they perform functions essential for supporting life.

For the first time, researchers have directly observed how water lubricates the movements of protein molecules to enable different functions to happen.

In a paper reported in the online early edition of the Proceedings of the National Academy of Sciences, Ohio State University scientists report using ultra-fast light pulses to reveal how water molecules link up with proteins and enable them to move and function.

The finding could one day help scientists find new therapys for diseases such as Alzheimer's, Parkinson's, cataracts, cystic fibrosis, and diabetes.

Proteins are complex molecules that form the main support structure for plant and animal cells, and they also regulate biochemical reactions. The shape and movements of a protein molecule determine its function, and researchers have long known that proteins can't function unless they are immersed in water.

"Protein-water interactions are a central, long-standing, unsolved problem in protein science," said Dongping Zhong, associate professor of physics at Ohio State and leader of the study. "We think that we are making a major step to answer these fundamental questions, and the final results will be very important for a number of biological applications"......... Posted by: Beverly      Read more         Source

November 14, 2007, 8:41 PM CT

Speed plays crucial role in breaking protein's H-bonds

Scientists at MIT studying the architecture of proteins have finally explained why computer models of proteins' behavior under mechanical duress differ dramatically from experimental observations. This work could have vast implications in bioengineering and medical research by advancing our understanding of the relationship between structure and function in these basic building blocks of life.

In a paper published as the cover article of the Oct. 16 issue of the Proceedings of the National Academies of Science (PNAS), the scientists, who work with atomistic models--accurate representations of nature that use fundamental laws of atomistic interactions as their basis--show for the first time the basic rupture mechanisms of protein structures when protein strands unfold in response to pressure.

"We have for the first time simulated the behavior of protein structures under conditions that correspond to those in living biological systems," said Markus Buehler, the Esther and Harold E. Edgerton Assistant Professor in MIT's Department of Civil and Environmental Engineering and lead researcher on the team. "All the different types of proteins we studied exhibit two distinct fracture modes that are dependent on the speed at which force is applied. Now we understand that what seemed unrealistic in the earlier computer simulations was actually a consequence of deformation rates and a change in the way hydrogen bonds respond to pressure"......... Posted by: Beverly      Read more         Source

November 13, 2007, 9:34 PM CT

Changing environment organizes genetic structure

What is the fundamental creative force behind life on Earth" It's a question that has vexed mankind for millennia, and thanks to theory and almost a year's worth of number-crunching on a supercomputer, Rice University physicist and bioengineer Michael Deem thinks he has the answer: A changing environment may organize the structure of genetic information itself.

Deem's research is available online and slated to appear next month in Physical Review Letters.

"Our results suggest that the beautiful, intricate and interrelated structures observed in nature may be the generic result of evolution in a changing environment," Deem said. "The existence of such structure need not necessarily rest on intelligent design or the anthropic principle".

The information that allows all living things to survive and reproduce is encoded in genes. Deem's theory probed the structure of this genetic information, looking for patterns that were created over time.

The study by Deem and postdoctoral fellow Jun Sun found the structure of genetic information becomes increasingly modular when two conditions are taken as givens: horizontal gene transfer (HGT) and a changing environment. Like modular furniture that can be rearranged in different functional patterns, modular genes are standardized components that lend themselves to flexible rearrangement, and this genetic modularity arises spontaneously because of the selective pressure of a changing environment and the existence of horizontal gene transfer......... Posted by: Beverly      Read more         Source

November 12, 2007, 10:28 PM CT

Health professionals responding to ethnic diversity

Guidelines and training for doctors have tried to address the problems they face when dealing with patients who come from cultures and ethnic groups different to their own. However, new research published in PLoS Medicine suggests that a number of British doctors and other health professionals still have profound difficulties when caring for such patients. More still needs to be done to improve their confidence.

Professor Joe Kai, a family physician, and his team from University of Nottingham, interviewed over 100 doctors, nurses and other health professionals in focus groups across the Midlands of the UK. They asked them to describe their experiences of caring for people from ethnic minority backgrounds. They were encouraged to recall actual cases and to identify what they saw as problems and strengths in their interaction with these patients.

The scientists observed that health professionals wrestled with a number of challenges such as problems with language and communication. But an equally powerful challenge was health professionals feeling very uncertain about what to do (for example, deciding when it was acceptable to touch a patient to show empathy).This was because they felt they didnt know enough about different cultures and wanted to avoid causing affront or appearing racist. This uncertainty, the scientists report, disempowered health professionals, sometimes making them hesitate or fail to do what may be best for their patient......... Posted by: Beverly      Read more         Source