Posting the same thing twice is a repeat. Posting it three times is a tradition.
At various points this quarter we'll be talking about the origin of life, the early history of the earth and the importance of asteroid impacts.
For everyone who has ever wondered what it would be like when a 500km diameter asteroid crashes into the earth. If you go to YouTube to watch it you can click a little link to watch it in high def. (highly recommended). You might also want to wait until you can crank up the speakers. The perfect soundtrack to the end of the world. Or the beginning...
Kamis, 30 Desember 2010
Rabu, 15 Desember 2010
Why Did Swine Flu Kill Healthy Adults?
One of the most intriguing questions about the swine flu epidemic last year was why most of the deaths occurred in healthy young adults. Why were the very young and the very old generally spared?
A recent paper in Nature Medicine provides a clue, according to a news article in Science magazine. The gist of it is that the immune system of most adults is not very effective against first exposure to the H1N1-type virus. Unable to kill the virus initially with just a normal first immune response, the immune system in some patients mounted an all-out “do or die” effort to kill the virus. The result was a severe inflammatory reaction in the lungs that ultimately killed the patient instead of the virus.
The theory of a hyperactive but ineffective immune system would explain why the very young and the very old were spared by swine flu. The very young do not have a fully developed immune system with which to mount even a normal immune response, much less an exaggerated one. And many older persons may have had at least some effective antibodies against H1N1 by virtue of having been exposed to the previous H1N1 strain that was around until the late 1950’s.
A recent paper in Nature Medicine provides a clue, according to a news article in Science magazine. The gist of it is that the immune system of most adults is not very effective against first exposure to the H1N1-type virus. Unable to kill the virus initially with just a normal first immune response, the immune system in some patients mounted an all-out “do or die” effort to kill the virus. The result was a severe inflammatory reaction in the lungs that ultimately killed the patient instead of the virus.
The theory of a hyperactive but ineffective immune system would explain why the very young and the very old were spared by swine flu. The very young do not have a fully developed immune system with which to mount even a normal immune response, much less an exaggerated one. And many older persons may have had at least some effective antibodies against H1N1 by virtue of having been exposed to the previous H1N1 strain that was around until the late 1950’s.
Minggu, 12 Desember 2010
Does Aspirin Reduce the Risk of Cancer?
In addition to its known blood anticoagulant properties, aspirin might also help prevent cancer, according to an article soon to be published in The Lancet. The authors of the study examined past data from the medical charts of over 25,000 patients in eight different studies who were taking aspirin to reduce their risk of a cardiovascular event. They found that daily doses of at least 75 mg of aspirin for at least five years reduced the overall death rate due to cancer by an astonishing 21%.
So should we all start popping aspirin? Not necessarily, says the Deputy Chief Medical Officer for the national office of the American Cancer Society in his blog post of Dec. 6. Although he finds no fault with the reported results as an interesting observation, he points out that the study was a retrospective (in the past) examination of cancer deaths in studies originally designed for other purposes – far better would be a randomized prospective (looking into the future) trial, in which both the risks and benefits of aspirin could be studied together. But such a study would take another 20 years! Who wants to wait that long?
It’s a quandary often faced in medicine – what to do when there’s tantalizing new information that seems to point in a certain direction, but no way to know for sure. No doubt, some of you will start taking aspirin as a result of this new study. Before you do, consider carefully that taking aspirin may be a double-edged sword; risks associated with taking aspirin include (in some people) gastrointestinal bleeding and bleeding in the brain. It’s your call.
So should we all start popping aspirin? Not necessarily, says the Deputy Chief Medical Officer for the national office of the American Cancer Society in his blog post of Dec. 6. Although he finds no fault with the reported results as an interesting observation, he points out that the study was a retrospective (in the past) examination of cancer deaths in studies originally designed for other purposes – far better would be a randomized prospective (looking into the future) trial, in which both the risks and benefits of aspirin could be studied together. But such a study would take another 20 years! Who wants to wait that long?
It’s a quandary often faced in medicine – what to do when there’s tantalizing new information that seems to point in a certain direction, but no way to know for sure. No doubt, some of you will start taking aspirin as a result of this new study. Before you do, consider carefully that taking aspirin may be a double-edged sword; risks associated with taking aspirin include (in some people) gastrointestinal bleeding and bleeding in the brain. It’s your call.
Selasa, 07 Desember 2010
Cellulosic Ethanol? Not Any Time Soon
Old conventional wisdom: ethanol made from farm and forest organic wastes (cellulosic ethanol) would soon be powering our cars and trucks. New conventional wisdom: cellulosic ethanol is dead, at least for now.
Not five years ago the government was pouring money and tax credits into various cellulosic biofuels projects. Although there were technical hurdles still to be overcome in extracting ethanol efficiently from cellulose and lignin (the primary energy storage molecules in most plants), there was optimism that the problems would be solved in short order. Today, plans for large-scale demonstration plants have been shelved, venture capital has dried up, and the industry is producing just 10% of the production goal once set by the Environmental Protection Agency. What happened?!
Lots of things happened, it turns out. Ethanol production from corn (technically easier) increased four-fold and is at an all-time high. Oil got cheaper again, technical problems in producing ethanol from cellulosic feedstocks have not yet been overcome, and investors are worried that government support (i.e., subsidies) for the developing cellulosic biofuels industry may dry up. Unless something changes, don’t expect to hear much about cellulosic biofuels for a while.
Not five years ago the government was pouring money and tax credits into various cellulosic biofuels projects. Although there were technical hurdles still to be overcome in extracting ethanol efficiently from cellulose and lignin (the primary energy storage molecules in most plants), there was optimism that the problems would be solved in short order. Today, plans for large-scale demonstration plants have been shelved, venture capital has dried up, and the industry is producing just 10% of the production goal once set by the Environmental Protection Agency. What happened?!
Lots of things happened, it turns out. Ethanol production from corn (technically easier) increased four-fold and is at an all-time high. Oil got cheaper again, technical problems in producing ethanol from cellulosic feedstocks have not yet been overcome, and investors are worried that government support (i.e., subsidies) for the developing cellulosic biofuels industry may dry up. Unless something changes, don’t expect to hear much about cellulosic biofuels for a while.
Senin, 06 Desember 2010
Evolutionary Ecology Internship Opportunities in the Mazer Lab
The Mazer lab tests predictions and develops hypotheses concerning the process and outcome of evolution by natural selection in wild plant species. In our current work, we’re examining the causes and consequences of the evolution of plant mating behaviors (yes, plants behave!). The "mating system" of wild plant and animal populations refers to the ways in which sperm and egg unite within and between individuals. In plants, outcrossing occurs when pollen is transferred (often by insects or by wind) from one plant's flowers to another's. In contrast, self-fertilization (selfing) is an extreme form of inbreeding that occurs when a single plant pollinates itself; the united egg and sperm originate from the same individual! Just as in humans and other animals, inbreeding in plants can have harmful effects on their offspring. Nevertheless, the evolution of selfing (from outcrossing ancestors) is quite common in plants. Indeed fully 20-25% of living plant species regularly engage in selfing. Detecting the “costs” and “benefits” of self-fertilization — especially in a stressful and changing climate, where pollinators may become a highly limiting resource — and predict the ecological conditions under which selfing evolves are the central goals of our research.
We would like to recruit undergraduates into the Mazer lab to help with a supervised research project on mating system evolution in several species of the California native wildflower, Clarkia. Undergraduate researchers will work with Professor Mazer, graduate students, postdocs, other undergraduates in the lab to learn a variety of lab, greenhouse, and computing techniques that we’ve developed to study:
1) The physiological performance of selfers vs. outcrossers under stressful conditions
2) Genetically based associations between mating system, physiology, and fitness
3) The ways in which natural selection operates under field conditions
Time Commitment: 8-10 hours per week, including a weekly meeting. Students who work for at least two full quarters will be eligible for paid positions in future quarters (pending available funding).
Current Lab Members:
• Dr. Susan Mazer, Principal Investigator (mazer@lifesci.ucsb.edu)
• Dr. Leah Dudley, Post-doc (dudley@lifesci.ucsb.edu)
• Alisa Hove: PhD Student (hove@lifesci.ucsb.edu)
• Brian Haggerty: PhD Student (haggerty@lifesci.ucsb.edu)
Please contact Leah Dudley (dudley@lifesci.ucsb.edu) if you are interested in joining our research group. Also describe why you are interested in this project and what preparation you’ve had that might help you to be an excellent co-worker (Examples: course work in ecology or evolution, organizational skills, statistical experience, data entry, lab work, chemistry, camping, wilderness experience, or field work). We will meet
Tuesday, January 4, 2010, the first week of the new quarter in LSB 4301 2-3pm to introduce ourselves and chat about schedules and possible projects. However, please contact me beforehand if you are interested in the lab and especially if you cannot make it to this meeting time.
We would like to recruit undergraduates into the Mazer lab to help with a supervised research project on mating system evolution in several species of the California native wildflower, Clarkia. Undergraduate researchers will work with Professor Mazer, graduate students, postdocs, other undergraduates in the lab to learn a variety of lab, greenhouse, and computing techniques that we’ve developed to study:
1) The physiological performance of selfers vs. outcrossers under stressful conditions
2) Genetically based associations between mating system, physiology, and fitness
3) The ways in which natural selection operates under field conditions
Time Commitment: 8-10 hours per week, including a weekly meeting. Students who work for at least two full quarters will be eligible for paid positions in future quarters (pending available funding).
Current Lab Members:
• Dr. Susan Mazer, Principal Investigator (mazer@lifesci.ucsb.edu)
• Dr. Leah Dudley, Post-doc (dudley@lifesci.ucsb.edu)
• Alisa Hove: PhD Student (hove@lifesci.ucsb.edu)
• Brian Haggerty: PhD Student (haggerty@lifesci.ucsb.edu)
Please contact Leah Dudley (dudley@lifesci.ucsb.edu) if you are interested in joining our research group. Also describe why you are interested in this project and what preparation you’ve had that might help you to be an excellent co-worker (Examples: course work in ecology or evolution, organizational skills, statistical experience, data entry, lab work, chemistry, camping, wilderness experience, or field work). We will meet
Tuesday, January 4, 2010, the first week of the new quarter in LSB 4301 2-3pm to introduce ourselves and chat about schedules and possible projects. However, please contact me beforehand if you are interested in the lab and especially if you cannot make it to this meeting time.
Minggu, 05 Desember 2010
Dinosaur Proteins Found in Fossils
Paleontologists have generally assumed that the only useful information that could be obtained from ancient fossils was in the sizes and shapes of the organism’s bones. The prevailing view has been that the soft tissues and any organic molecules or cellular structures within the bones themselves would have long since disappeared, leaving behind only fossils comprised of the same minerals found in rocks.
That view is slowly changing. It now appears that under the right conditions of fossilization, organic molecules may still remain in some fossils. So far, researchers have identified molecules that appear to be collagen and even fossilized osteocytes (bone-forming cells) and red blood cells, from the bones of dinosaurs as old as 80 million years.
No one is suggesting that we could ever resurrect dinosaurs from these ancient materials – cloning dinosaurs is still in the realm of science fiction. However if we could identify the precise sequences of certain ancient proteins, we’d have a better understanding of the function of these proteins within the organism. We might also be able to more accurately map out the evolutionary relationships between organisms, both ancient and living.
Reference: Schweitzer, Mary. Blood From Stone. Scientific American Dec. 2010, pp. 62-69.
That view is slowly changing. It now appears that under the right conditions of fossilization, organic molecules may still remain in some fossils. So far, researchers have identified molecules that appear to be collagen and even fossilized osteocytes (bone-forming cells) and red blood cells, from the bones of dinosaurs as old as 80 million years.
No one is suggesting that we could ever resurrect dinosaurs from these ancient materials – cloning dinosaurs is still in the realm of science fiction. However if we could identify the precise sequences of certain ancient proteins, we’d have a better understanding of the function of these proteins within the organism. We might also be able to more accurately map out the evolutionary relationships between organisms, both ancient and living.
Reference: Schweitzer, Mary. Blood From Stone. Scientific American Dec. 2010, pp. 62-69.
Kamis, 02 Desember 2010
Sanford-Burnham
Learn about Sanford-Burnham's Core facilities: THURSDAY, Dec 2, 3:30-4:30pm, Rathmann Auditorium (ie 1001LSB)
This week's MCDB seminar is a departure from our normal form and represents a unique opportunity to learn more about the Core facilities and research resources of the Sanford-Burnham Medical Research Institute. The purpose is to provide faculty, staff, and students with information on what these facilities are and how they can access them in supporting research projects here at UCSB. The speaker is Dr. Craig Hauser, the VP for Scientific Resources at SBMRI.
Dr. Hauser will present some background on the other two Sanford-Burnham sites (La Jolla, California and Orlando, Florida) and describe the somewhat unique philosophy and operations of the Institute’s many core facilities at these sites. In addition to presenting the capabilities of these cores, he will describe how Sanford-Burnham’s partners, such as UCSB, can access the core services.
This week's MCDB seminar is a departure from our normal form and represents a unique opportunity to learn more about the Core facilities and research resources of the Sanford-Burnham Medical Research Institute. The purpose is to provide faculty, staff, and students with information on what these facilities are and how they can access them in supporting research projects here at UCSB. The speaker is Dr. Craig Hauser, the VP for Scientific Resources at SBMRI.
Dr. Hauser is of the UC system, having done his undergraduate studies at UC Davis, Ph.D. at UC Irvine, and postdoctoral studies at UC Berkeley. He was then recruited to the Sanford-Burnham faculty in La Jolla in 1989. His research has centered on the interplay between the regulation of gene expression and oncogenic transformation, focusing on the Ets family of transcription factors. In 2005, he became an adjunct faculty member and assumed a full-time administrative position, currently serving as Vice President for Scientific Resources. His responsibilities include overseeing the operations of the Institute’s Shared Resources (cores), scientific equipment, and scientific regulatory compliance.
Dr. Hauser will present some background on the other two Sanford-Burnham sites (La Jolla, California and Orlando, Florida) and describe the somewhat unique philosophy and operations of the Institute’s many core facilities at these sites. In addition to presenting the capabilities of these cores, he will describe how Sanford-Burnham’s partners, such as UCSB, can access the core services.
Minggu, 28 November 2010
New Uses for DNA Identification
It’s now possible to synthesize a nearly infinite number of unique DNA sequences. It’s also possible to identify the sequence of even a small sample of DNA quickly and cheaply. Taken together, these two advances are likely to lead to some interesting new uses of DNA technology.
According to an article in The New York Times, in Rotterdam, the Netherlands, police are experimenting with synthetic “DNA sprays” as a way to discourage robberies or to catch robbers of local businesses. When a store is robbed, the store clerk activates a security system that sprays the robber with a fine mist containing a unique synthetic DNA sequence as the robber departs. The system also notifies police that a robbery is in progress. Suspects who are apprehended within a certain time frame can then be tested for that specific DNA sequence.
Another idea: “DNA crayons” - each with a different DNA sequence - to mark valuable items that belong to you. Items suspected of having been stolen could then be tested and returned to their rightful owners. We’ll probably hear about other practical uses of DNA technology in the future. Have YOU got any good ideas?
According to an article in The New York Times, in Rotterdam, the Netherlands, police are experimenting with synthetic “DNA sprays” as a way to discourage robberies or to catch robbers of local businesses. When a store is robbed, the store clerk activates a security system that sprays the robber with a fine mist containing a unique synthetic DNA sequence as the robber departs. The system also notifies police that a robbery is in progress. Suspects who are apprehended within a certain time frame can then be tested for that specific DNA sequence.
Another idea: “DNA crayons” - each with a different DNA sequence - to mark valuable items that belong to you. Items suspected of having been stolen could then be tested and returned to their rightful owners. We’ll probably hear about other practical uses of DNA technology in the future. Have YOU got any good ideas?
Rabu, 24 November 2010
Obesity and Body Size Misperception
According to a recent report in the Archives of Internal Medicine, about 8% of obese individuals don’t recognize that they need to lose weight. Researchers call the phenomenon “body size misperception”. Obese individuals who misperceive their body size tend to be more satisfied with their overall health and are more likely to believe that they have a low lifetime risk of chronic diseases related to obesity, than are those who acknowledge that they are obese. Two-thirds of them actually believe that they are at low risk of developing obesity in their lifetimes, even though they already ARE obese according to the standard government definition.
But are there other possibilities for these people’s failure to acknowledge their obesity besides body size misperception? Perhaps these individuals do know that they are obese, but because they don’t think they can lose weight or don’t want to try, they are unwilling to acknowledge it even on a survey. It’s called denial. Or perhaps they just don’t accept the current definition of obesity (a Body Mass Index of 30 or above) and/or its health consequences.
How people perceive obesity and its consequences need to be explored further if we wish stem the rising tide of obesity in the U.S. and around the world.
But are there other possibilities for these people’s failure to acknowledge their obesity besides body size misperception? Perhaps these individuals do know that they are obese, but because they don’t think they can lose weight or don’t want to try, they are unwilling to acknowledge it even on a survey. It’s called denial. Or perhaps they just don’t accept the current definition of obesity (a Body Mass Index of 30 or above) and/or its health consequences.
How people perceive obesity and its consequences need to be explored further if we wish stem the rising tide of obesity in the U.S. and around the world.
Selasa, 23 November 2010
Summer research opportunities
Caltech is excited to announce two summer research opportunities available to continuing undergraduate students. Questions about these programs can be directed to Carol Casey at casey@caltech.edu or (626) 395-2887.
MURF UNDERGRADUATE RESEARCH FELLOWSHIPS
The MURF program aims to increase the participation of underrepresented students (such as African American, Hispanic, and Native American, females who are underrepresented in their discipline, and first-generation college students) in science and engineering Ph.D. or M.D./Ph.D. programs and to make
Caltech's programs more visible to students not traditionally exposed to Caltech.
Eligibility: Students must be current sophomores through non-graduating seniors and must be U.S. citizens or U.S. permanent residents. A minimum GPA of 3.0 is required.
Support: MURF students will receive a $6000 award for the ten-week program.
Additional housing and travel support may be provided.
Application: Online applications are due January 12, 2011.
For more information, please visit www.murf.caltech.edu
AMGEN SCHOLARS PROGRAM
Caltech's Amgen Scholars Program is geared towards students in biology, chemistry, and biotechnology fields. Some of these fields include biology, biochemistry, bioengineering, chemical and biomolecular engineering, and chemistry.
Eligibility: Students must be current sophomores through non-graduating seniors, must be attending a four-year university, and must be U.S. citizens or U.S. permanent residents. A minimum GPA of 3.2 is required.
Support: Amgen Scholars will receive a $5500 award, round-trip air transportation, a generous housing allowance, and a food allowance.
Application: Online applications are due February 15, 2011.
For more information, please visit www.amgenscholars.caltech.edu
Carol Casey
Associate Director
Student-Faculty Programs
California Institute of Technology
Mail Code 330-87
Pasadena, CA 91125
(626) 395-2887
casey@caltech.edu
MURF UNDERGRADUATE RESEARCH FELLOWSHIPS
The MURF program aims to increase the participation of underrepresented students (such as African American, Hispanic, and Native American, females who are underrepresented in their discipline, and first-generation college students) in science and engineering Ph.D. or M.D./Ph.D. programs and to make
Caltech's programs more visible to students not traditionally exposed to Caltech.
Eligibility: Students must be current sophomores through non-graduating seniors and must be U.S. citizens or U.S. permanent residents. A minimum GPA of 3.0 is required.
Support: MURF students will receive a $6000 award for the ten-week program.
Additional housing and travel support may be provided.
Application: Online applications are due January 12, 2011.
For more information, please visit www.murf.caltech.edu
AMGEN SCHOLARS PROGRAM
Caltech's Amgen Scholars Program is geared towards students in biology, chemistry, and biotechnology fields. Some of these fields include biology, biochemistry, bioengineering, chemical and biomolecular engineering, and chemistry.
Eligibility: Students must be current sophomores through non-graduating seniors, must be attending a four-year university, and must be U.S. citizens or U.S. permanent residents. A minimum GPA of 3.2 is required.
Support: Amgen Scholars will receive a $5500 award, round-trip air transportation, a generous housing allowance, and a food allowance.
Application: Online applications are due February 15, 2011.
For more information, please visit www.amgenscholars.caltech.edu
Carol Casey
Associate Director
Student-Faculty Programs
California Institute of Technology
Mail Code 330-87
Pasadena, CA 91125
(626) 395-2887
casey@caltech.edu
Senin, 22 November 2010
I don’t know what to believe…
If they find out you are a biologist chances are you'll get asked about topics ranging from global warming to this week's cancer scare. Here's a handy dandy resource for putting people straight about why they shouldn't necessarily believe it when they hear that cell phone towers are killing plants,
Have a safe Thanksgiving.
Genital Herpes Vaccine Fails
An experimental vaccine designed to protect against herpes simplex virus type-2 (HSV-2) has failed completely in clinical trials, according to a news article in Science. HSV-2, also known as genital herpes, is transmitted via sexual contact. It causes painful blisters that may recur at various times in life after initial infection (see Figure 16.17 in Johnson’s Human Biology, 5th ed.). Approximately half a million people worldwide currently are infected with genital herpes.
At the moment there is no known cure for HSV-2 infection, and other than the vaccine that just failed there was no major effort directed at finding one. Genital herpes is considered to be a rather trivial disease by pharmaceutical companies because although it can cause irritating and painful blisters, it is not particularly dangerous. Given the negative result from this vaccine and several others tried before it, there may not be much of an effort put into finding a cure in the near future. We may just have to live with genital herpes for a while longer.
At the moment there is no known cure for HSV-2 infection, and other than the vaccine that just failed there was no major effort directed at finding one. Genital herpes is considered to be a rather trivial disease by pharmaceutical companies because although it can cause irritating and painful blisters, it is not particularly dangerous. Given the negative result from this vaccine and several others tried before it, there may not be much of an effort put into finding a cure in the near future. We may just have to live with genital herpes for a while longer.
Sabtu, 20 November 2010
Why is Global Warming Such a Hot-Button Issue?
Why can’t we hold a civilized conversation about global warming any more without the feeling that everyone’s minds are already made up? Some people argue that global warming is an established fact, and that human activities (most notably the burning of fossil fuels) are responsible. Others insist that the evidence in support of global warming is either not convincing, deliberately misleading, or even just plain false. It’s getting to be almost as bad as talking about abortion. How did it come to this?
One science writer suggests that part of the problem lies with a failure of climate scientists to communicate the meaning of scientific uncertainty adequately to the public. Predicting climate change far into the future IS an inexact science at the moment, but that does not mean that the climate isn’t changing. Not knowing everything is not the same as knowing nothing. I’m reminded of the common anti-evolutionist argument that evolution can’t be true because (gasp) “there are GAPS in the fossil record!”
In addition, scientists may sometimes come across as having a “we know best” attitude toward dissent, rather than a willingness to engage the dissenters in a dialogue. Scientists may need to acknowledge openly that there are things about climate change that they do not know yet. But rather than representing a failure of the scientific method, these uncertainties represent an opportunity to develop better methods and testable hypotheses so that in the future we CAN be more certain.
One science writer suggests that part of the problem lies with a failure of climate scientists to communicate the meaning of scientific uncertainty adequately to the public. Predicting climate change far into the future IS an inexact science at the moment, but that does not mean that the climate isn’t changing. Not knowing everything is not the same as knowing nothing. I’m reminded of the common anti-evolutionist argument that evolution can’t be true because (gasp) “there are GAPS in the fossil record!”
In addition, scientists may sometimes come across as having a “we know best” attitude toward dissent, rather than a willingness to engage the dissenters in a dialogue. Scientists may need to acknowledge openly that there are things about climate change that they do not know yet. But rather than representing a failure of the scientific method, these uncertainties represent an opportunity to develop better methods and testable hypotheses so that in the future we CAN be more certain.
Senin, 15 November 2010
Monday's EEMB seminar
Today's EEMB seminar speaker is Mike Ryan from the University of Texas.
Mike integrates behavioral ecology, physiology and biogeography within a phylogenetic approach to study mate signaling and sexual selection in túngara frogs and swordtail fishes. Please join us at 4pm in the MSRB auditorium for his talk, "Sexual Selection and Communication in Tungara Frogs: Brian, Behavior & Evolution". Refreshments will be served prior to the talk.
Kamis, 11 November 2010
Friday seminar
Nov 12 @ 1:00pm, 1132 HFH - Harold Frank Hall also known as Engineering I
Professor Cherie Briggs,
"Models of host-pathogen dynamics"
A recently discovered chytrid fungus, Batrachochytrium dendrobatidis (Bd), is having devastating effects on amphibian populations in the California Sierra Nevada, and throughout the world. In the Sierra Nevada, Bd has led to hundreds of local extinctions of frog populations, but a few populations are persisting with Bd. Efforts are currently underway, both in the Sierra Nevada and worldwide, to attempt to control this pathogen and/or limit its impact on amphibian populations. Herpetologists and ecologists are actively seeking the advice of modelers and theoreticians about what control strategies are likely to be most effective against this pathogen. In this talk, I will describe our efforts to date to develop models of the Bd/frog system, which involve models that differ from standard microparasite disease models because of the unique biology of Bd. I will discuss mechanisms by which control strategies might be effective, and areas in which further modeling work is needed.
Rabu, 10 November 2010
Patenting Human Genes - An Update
In April of this year a U.S. District Court judge issued an order invalidating the patents on several human genes held by a company called Myriad Genetics. (See this blog, April 5, 2010.) The company promptly appealed, sending the issue to the next judicial level, the U.S. Court of Appeals.
Last month the U.S. Department of Justice filed a friend-of-the-court brief with the Court of Appeals, supporting the position that human genes should not be patentable. In its brief the Justice Department stated that “The chemical nature of native human genes is a product of nature, and it is no less a product of nature when that structure is ‘isolated’ from its natural environment than are cotton fibers that have been separated from cotton seeds or coal that has been extracted from the earth.” (The defendants in the case had tried to argue that their method of gene isolation had somehow fundamentally changed the genes, making them patentable.) However, in a bit of a compromise, the Justice Department’s brief also suggested that human DNA that is altered in some way (i.e. is not the original human gene sequence) could still be patented.
The U.S. Patent and Trademark Office has been issuing patents for human genes for years, but the legality of the patents has never been challenged in court. The outcome of the court case could affect the commercial use of numerous human genes and gene products. For now, we await the decision of the U.S. Court of Appeals.
Last month the U.S. Department of Justice filed a friend-of-the-court brief with the Court of Appeals, supporting the position that human genes should not be patentable. In its brief the Justice Department stated that “The chemical nature of native human genes is a product of nature, and it is no less a product of nature when that structure is ‘isolated’ from its natural environment than are cotton fibers that have been separated from cotton seeds or coal that has been extracted from the earth.” (The defendants in the case had tried to argue that their method of gene isolation had somehow fundamentally changed the genes, making them patentable.) However, in a bit of a compromise, the Justice Department’s brief also suggested that human DNA that is altered in some way (i.e. is not the original human gene sequence) could still be patented.
The U.S. Patent and Trademark Office has been issuing patents for human genes for years, but the legality of the patents has never been challenged in court. The outcome of the court case could affect the commercial use of numerous human genes and gene products. For now, we await the decision of the U.S. Court of Appeals.
Selasa, 09 November 2010
Carcinonemertes kurisi
UCSB zoology professor Armand Kuris has received one of the greatest honors biologists can hope for — having a newly discovered species named after him.
Carcinonemertes kurisi, a species of ribbon worm, was first found and documented by Kuris and Patricia Sadeghian, one of his former students. Sadeghian wrote her Master’s thesis on the species in 2003 and then named the ribbon worm after Kuris in an October 2010 issue of the Journal of Natural History after producing a formal description of the worm.
Senin, 08 November 2010
EEMB Seminar time and location change
NOTE: Today's EEMB seminar is at 3:30 PM in the third floor conference room of the MSI building- 3322 MSRB
Mark Vellend, an ecologist from the University of British Columbia will be giving the EEMB departmental seminar today, "Integrating ecology and genetics: patterns, experiments, and ideas." Mark is an interactive and broad thinking population and community ecologist, who focuses on plants. His website is: http://www.botany.ubc.ca/vellend/
Mark Vellend, an ecologist from the University of British Columbia will be giving the EEMB departmental seminar today, "Integrating ecology and genetics: patterns, experiments, and ideas." Mark is an interactive and broad thinking population and community ecologist, who focuses on plants. His website is: http://www.botany.ubc.ca/vellend/
Minggu, 07 November 2010
Alcohol and Caffeine - a Potent Mix
Last year the Food and Drug Administration sent warning letters to 27 manufacturers of alcoholic beverages containing caffeine (see this blog Nov. 15, 2009), asking the companies to justify the safety of their products. But apparently the agency has not yet followed through with its promises to review the safety information requested from the companies and then to take appropriate action if it was not forthcoming.
One of the companies selling caffeine-and-alcohol drinks was in the news again last month after students at two universities ended up in emergency rooms with alcohol poisoning. The drinks in question, called Four Loko, contain 23.5 ounces of 12% alcohol laced with caffeine. Allegedly the caffeine overrides the natural sleepiness effect of alcohol, causing the user to underestimate how drunk he/she really is.
The company says that it is being unfairly singled out.
Some college students will abuse alcohol no matter what form it is in. But are packaged caffeine-and-alcohol drinks GRAS (Generally Recognized As Safe) or not? It should be up to the FDA to decide, and so far it hasn’t.
Meanwhile, states and municipalities are taking action. Last Thursday Michigan became the first state to ban alcohol-and-caffeine drinks. The city of Chicago is considering a similar ban.
One of the companies selling caffeine-and-alcohol drinks was in the news again last month after students at two universities ended up in emergency rooms with alcohol poisoning. The drinks in question, called Four Loko, contain 23.5 ounces of 12% alcohol laced with caffeine. Allegedly the caffeine overrides the natural sleepiness effect of alcohol, causing the user to underestimate how drunk he/she really is.
The company says that it is being unfairly singled out.
Some college students will abuse alcohol no matter what form it is in. But are packaged caffeine-and-alcohol drinks GRAS (Generally Recognized As Safe) or not? It should be up to the FDA to decide, and so far it hasn’t.
Meanwhile, states and municipalities are taking action. Last Thursday Michigan became the first state to ban alcohol-and-caffeine drinks. The city of Chicago is considering a similar ban.
Kamis, 04 November 2010
Geeky science students wanted
As CCS students you should not restrict yourself to those labs that actively advertise for undergraduates. But if research on the molecular mechanisms underlying polycystic kidney disease and mechanisms of epithelial cell function and kidney physiology sound like your thing then this is a great opportunity.
Geeky science students invited to apply for undergraduate research internships in the Weimbs lab in MCDB
Do you have a passion for research? Did you spend your childhood looking at dirt samples under a microscope or mixing concoctions with a beefed-up chemistry set? Are you serious about a career in research and attending a PhD program in a top graduate school? Do you want to make a real contribution to research on a human disease that affects millions? Do you want to be intellectually involved, read research papers, come up with new ideas and test them yourself? Are you unafraid of learning new scientific techniques, tinkering with experiments over and over until you get them to work, spending long hours in the lab, reading papers all night long, presenting your findings in front of the research team?
If this sounds like you, we want you in the lab!
You would be teamed up with and trained by an experienced scientist in the lab. You would be expected to work more and more independently over time, manage your own experiments and schedule, plan and interpret experiments, understand what you are doing, be productive, move your research project forward.
Look up our research on the web to see if this excites you. If it does, send your resume and list of grades to:
Thomas Weimbs, PhD
Associate Professor, Department of Molecular, Cellular & Developmental Biology
weimbs@lifesci.ucsb.edu
Associate Professor, Department of Molecular, Cellular & Developmental Biology
weimbs@lifesci.ucsb.edu
Yearly courses
GOLD is your best source of information about what courses are running next quarter but what about the one after that? The two biology departments at UCSB plan at least a year in advance and publish their list of planned courses online. They aren't however, that easy to find. Go to the EEMB website, click on Academic Programs - Undergraduate Studies and then on the menu on the left hand side click 'current students'. Scroll down and you'll see a link to:
Updated list of the proposed courses for the year
Updated list of the proposed courses for the year
- EEMB Proposed Courses (2010-11)
- MCDB Proposed Courses (2010-11)
Senin, 01 November 2010
EEMB seminar
Today's EEMB seminar should be of interest to those with an interest in marine biology, ecology or global change
Dr. Jonathan Shurin from UCSD will be giving this Monday's EEMB seminar. Dr. Shurin works in aquatic ecosystems investigating local and regional controls of species diversity, consumer-resource dynamics and food web energetics. The title of his talk is "Plankton ecosystem dynamics in a warmer, wilder world"
Dr. Jonathan Shurin from UCSD will be giving this Monday's EEMB seminar. Dr. Shurin works in aquatic ecosystems investigating local and regional controls of species diversity, consumer-resource dynamics and food web energetics. The title of his talk is "Plankton ecosystem dynamics in a warmer, wilder world"
Assessing the Long-Term Risks of Drugs
Here’s a dilemma for you; drugs that prevent or treat chronic diseases and that therefore will probably be taken for the rest of the patient’s life are generally only tested for a only a couple of years (for safety and efficacy) before they are approved. What if the drugs have adverse effects that only become apparent when they have been taken for many years?
This concern has been raised recently by the discovery that two blockbuster drugs do in fact have long-term negative effects not seen in their initial safety studies. The class of drugs known as bisphosphonates (Fosamax, Actonel, and Boniva) widely used to prevent osteoporosis can, on rare occasion, lead to degeneration of the jawbone or to thigh fractures. And a drug called Avandia, often prescribed for diabetics to prevent heart disease, has been shown to increase the risk of heart disease in certain cases.
I'm not saying that FDA approval of these drugs in the first place was a mistake, because in some cases the benefits may still outweigh the risks. Still, it would be nice to know the long-term risks as soon as possible so that patient treatment decisions can be made with full information. The question becomes, then, how to reduce the potential long-term risk without making the drug approval process even longer than it already is. Requiring 30 years of clinical trials before a drug can be approved is clearly impractical.
Once a drug is approved, currently there is no method for effectively tracking the incidence of adverse side effects over time. Some health officials are suggesting that we develop a national drug-use database and require physicians to report all adverse effects, so that long-term effects can be determined as soon as possible. But that raises concerns over confidentiality of patient information.
What do you think?
This concern has been raised recently by the discovery that two blockbuster drugs do in fact have long-term negative effects not seen in their initial safety studies. The class of drugs known as bisphosphonates (Fosamax, Actonel, and Boniva) widely used to prevent osteoporosis can, on rare occasion, lead to degeneration of the jawbone or to thigh fractures. And a drug called Avandia, often prescribed for diabetics to prevent heart disease, has been shown to increase the risk of heart disease in certain cases.
I'm not saying that FDA approval of these drugs in the first place was a mistake, because in some cases the benefits may still outweigh the risks. Still, it would be nice to know the long-term risks as soon as possible so that patient treatment decisions can be made with full information. The question becomes, then, how to reduce the potential long-term risk without making the drug approval process even longer than it already is. Requiring 30 years of clinical trials before a drug can be approved is clearly impractical.
Once a drug is approved, currently there is no method for effectively tracking the incidence of adverse side effects over time. Some health officials are suggesting that we develop a national drug-use database and require physicians to report all adverse effects, so that long-term effects can be determined as soon as possible. But that raises concerns over confidentiality of patient information.
What do you think?
Selasa, 26 Oktober 2010
Drug Safety in the Workplace
Should a company be permitted to fire a worker for taking a drug that is legally prescribed by a physician to treat a medical condition? That’s what happened to a worker on an auto-parts assembly line who was taking hydrocodone for back pain, according to an article in The New York Times.
You might say, “That’s not fair!”, but it’s not that simple. After all, companies have a responsibility to maintain a safe work environment. Companies can be held responsible for accidents on the job and for product defects caused by impaired workers. And in “safety-sensitive” jobs, such as airline pilot, the public has a right to expect that the employee is not impaired.
The question becomes, then, how does society achieve the right balance between the rights of workers and the responsibilities of employers? At present we know very little about just how safe various prescription drugs are in the workplace, because testing for workplace safety is not part of the normal approval process for pharmaceutical drugs.
More and more companies are requiring drug tests of their employees. Employees who test positive are sometimes fired, in part because companies aren’t sure whether or not the drug creates a safety issue and just aren’t willing to take the risk. It’s a societal problem that needs to be addressed by valid scientific research into drug safety in the workplace.
You might say, “That’s not fair!”, but it’s not that simple. After all, companies have a responsibility to maintain a safe work environment. Companies can be held responsible for accidents on the job and for product defects caused by impaired workers. And in “safety-sensitive” jobs, such as airline pilot, the public has a right to expect that the employee is not impaired.
The question becomes, then, how does society achieve the right balance between the rights of workers and the responsibilities of employers? At present we know very little about just how safe various prescription drugs are in the workplace, because testing for workplace safety is not part of the normal approval process for pharmaceutical drugs.
More and more companies are requiring drug tests of their employees. Employees who test positive are sometimes fired, in part because companies aren’t sure whether or not the drug creates a safety issue and just aren’t willing to take the risk. It’s a societal problem that needs to be addressed by valid scientific research into drug safety in the workplace.
Minggu, 24 Oktober 2010
Long Beach Bans Smoking in Public Outdoor Areas
The City Council of Long Beach, California voted unanimously last week to ban smoking in nearly all public outdoor areas, including parks, hiking trials, and biking paths. Supporters of the ban argued that the ban was necessary to protect children’s health.
The ban exempts public golf courses because of a potential loss of income to Long Beach (and because not many children golf). It also makes exceptions for special events like filming. Does anybody else see the double standard being applied here - that smoking is banned in public places in Long Beach unless it’s in Long Beach’s financial best interests to allow it?
Disclaimer: I’m not a smoker. I am convinced that the evidence is pretty solid that smoking is harmful for the smoker, and I wish that smokers would see the wisdom of quitting for their own good. But let’s be clear about one thing; banning smoking in public places outdoors is not likely to improve children’s health. There is no scientific evidence to support the notion that a brief whiff of smoke causes any damage to children or to adults. A better way to improve children’s health would be to encourage them to exercise more, even if they occasionally smelled a whiff of smoke while doing it.
If we’re going to ban smoking in public places, let’s at least be honest with smokers about why we’re doing it.
The ban exempts public golf courses because of a potential loss of income to Long Beach (and because not many children golf). It also makes exceptions for special events like filming. Does anybody else see the double standard being applied here - that smoking is banned in public places in Long Beach unless it’s in Long Beach’s financial best interests to allow it?
Disclaimer: I’m not a smoker. I am convinced that the evidence is pretty solid that smoking is harmful for the smoker, and I wish that smokers would see the wisdom of quitting for their own good. But let’s be clear about one thing; banning smoking in public places outdoors is not likely to improve children’s health. There is no scientific evidence to support the notion that a brief whiff of smoke causes any damage to children or to adults. A better way to improve children’s health would be to encourage them to exercise more, even if they occasionally smelled a whiff of smoke while doing it.
If we’re going to ban smoking in public places, let’s at least be honest with smokers about why we’re doing it.
Minggu, 17 Oktober 2010
Canada Declares BPA Plastic to be Toxic
Canada recently declared a plastic called BPA (bisphenol A) to be a toxic substance. BPA is commonly used in the manufacture of refillable polycarbonate water bottles and in the linings of metal food and beverage cans.
BPA falls into a category of substances known as endocrine disruptors. As a group, endocrine disruptors either mimic or block the action of hormones, thereby disrupting the body’s functions. In laboratory animals, high concentrations of BPA have been shown to mimic the female hormone estrogen. Several studies reported by The Endocrine Society, a well-known scientific group, suggest that endocrine disruptors such as BPA may have adverse health affects that include infertility and cancer.
Canada and about half a dozen states in the U.S. have already banned the use of BPA in children’s products. Canada’s recent action paves the way for future bans on the use of BPA in food and beverage containers for adults as well, and for increased control over manufacturing processes involving BPA.
So far the U.S. government has taken no action, saying there is not enough evidence that the substance harms humans. But research is underway, and time will tell.
BPA falls into a category of substances known as endocrine disruptors. As a group, endocrine disruptors either mimic or block the action of hormones, thereby disrupting the body’s functions. In laboratory animals, high concentrations of BPA have been shown to mimic the female hormone estrogen. Several studies reported by The Endocrine Society, a well-known scientific group, suggest that endocrine disruptors such as BPA may have adverse health affects that include infertility and cancer.
Canada and about half a dozen states in the U.S. have already banned the use of BPA in children’s products. Canada’s recent action paves the way for future bans on the use of BPA in food and beverage containers for adults as well, and for increased control over manufacturing processes involving BPA.
So far the U.S. government has taken no action, saying there is not enough evidence that the substance harms humans. But research is underway, and time will tell.
Jumat, 15 Oktober 2010
Lab opportunity
Subject: Freshman/Sophomore Lab Position Available in Collin's Lab
Research Project:
The overall research is to determine the influence of environmental and hormonal factors on the constituent phase of embryo and larval development as they occur within the ovaries of viviparous nearshore rockfish(Sebastes spp)
Undergraduate Contribution:
The undergraduate will be responsible for validating protocols for incubating embryos and larvae aspirated from the ovaries of rockfish at various stages of development. The student will carry out incubations at different osmolalities and in the presence of various potential growth promoting factors. The student will assess development by morphometric analysis of fresh specimens and histological sections.
If you are interested, please contact Adam Karevoll at
akarevoll at umail.ucsb.edu
Research Project:
The overall research is to determine the influence of environmental and hormonal factors on the constituent phase of embryo and larval development as they occur within the ovaries of viviparous nearshore rockfish(Sebastes spp)
Undergraduate Contribution:
The undergraduate will be responsible for validating protocols for incubating embryos and larvae aspirated from the ovaries of rockfish at various stages of development. The student will carry out incubations at different osmolalities and in the presence of various potential growth promoting factors. The student will assess development by morphometric analysis of fresh specimens and histological sections.
If you are interested, please contact Adam Karevoll at
akarevoll at umail.ucsb.edu
Rabu, 13 Oktober 2010
HPV Vaccination Rates in College Women
It’s been more than three years since the FDA approved Gardasil, the vaccine against the sexually transmitted Human Papilloma Virus (HPV) that is responsible for most cases of cervical cancer. How is the vaccine being accepted by young college-age women?
To find out, researchers conducted a survey of 972 female college students at a large Midwestern state university. Most of the women were freshmen or sophomores. Sixty-five % of the women reported being sexually active, and by the Spring of 2009 57% had already received at least the first of the three shots required by the vaccination protocol for Gardasil. (The vaccine was available on request at the university student health center, at a cost of $360).
Vaccination coverage of 57% in this age group within three years of vaccine availability is welcome news, considering that these college-age women were already 15 or 16 years old when the vaccine first became available. Current recommendations are that girls should be vaccinated as early as 11-12 years of age. Significantly, young women who believed that their mothers would approve of their receiving the vaccine were more likely to have been vaccinated or to have an interest in being vaccinated.
More than a third of the women reported having had three or more sexual partners, and over 25% had had vaginal sex with a casual partner (not a serious or steady dating partner) without using protection against sexually transmitted diseases. All the more reason they should be vaccinated…
To find out, researchers conducted a survey of 972 female college students at a large Midwestern state university. Most of the women were freshmen or sophomores. Sixty-five % of the women reported being sexually active, and by the Spring of 2009 57% had already received at least the first of the three shots required by the vaccination protocol for Gardasil. (The vaccine was available on request at the university student health center, at a cost of $360).
Vaccination coverage of 57% in this age group within three years of vaccine availability is welcome news, considering that these college-age women were already 15 or 16 years old when the vaccine first became available. Current recommendations are that girls should be vaccinated as early as 11-12 years of age. Significantly, young women who believed that their mothers would approve of their receiving the vaccine were more likely to have been vaccinated or to have an interest in being vaccinated.
More than a third of the women reported having had three or more sexual partners, and over 25% had had vaginal sex with a casual partner (not a serious or steady dating partner) without using protection against sexually transmitted diseases. All the more reason they should be vaccinated…
Senin, 11 Oktober 2010
Dance your Ph.D.
"The dreaded question. "So, what's your Ph.D. research about?" You could bore them with an explanation. Or you could dance.
That's the idea behind "Dance Your Ph.D." Over the past 3 years, scientists from around the world have teamed up to create dance videos based on their graduate research."
Thought you all might enjoy this! A good way to both relieve stress and study science at the same time... Enjoy :)
Minggu, 10 Oktober 2010
Cell Phones Can't Cause Cancer?
One of the limitations of the scientific method is that it is virtually impossible to prove that something doesn’t exist or could never happen based on empirical data alone. And if that “something” has the potential for great harm, then common sense would dictate that we should err on the side of caution and continue to assume that it could exist, or might happen. It’s what’s known as the precautionary principle.
Take cell phones and cancer, for example. Despite tens of millions of dollars spent on research, no one has ever proven that mobile phones cause brain cancer. And yet, researchers (and the public) are still unwilling to conclude that they don’t. Even the authors of a major study that once again showed no relationship between cell phones and cancer concluded: “The possible effects of long-term heavy use of mobile phones require further investigation”. Of course, that might mean more funding for their laboratory….
Physicist Bernard Leikind has taken an entirely different approach. He claims that, based on well-accepted physical principles, cell phones cannot cause cancer. He argues that the energy emitted by cell phones is not strong enough to disrupt the chemical bonds in biological molecules, period. Indeed, he claims that if it were possible for radiation energy of this type to disrupt cellular biochemical processes, there would be no life on earth because of natural sources of similar radiation energy in the environment.
Dr. Leikind has taken a lot of heat (no pun intended) from readers – see the reader-response thread after the article. But I have yet to find the flaw in his logic.
Take cell phones and cancer, for example. Despite tens of millions of dollars spent on research, no one has ever proven that mobile phones cause brain cancer. And yet, researchers (and the public) are still unwilling to conclude that they don’t. Even the authors of a major study that once again showed no relationship between cell phones and cancer concluded: “The possible effects of long-term heavy use of mobile phones require further investigation”. Of course, that might mean more funding for their laboratory….
Physicist Bernard Leikind has taken an entirely different approach. He claims that, based on well-accepted physical principles, cell phones cannot cause cancer. He argues that the energy emitted by cell phones is not strong enough to disrupt the chemical bonds in biological molecules, period. Indeed, he claims that if it were possible for radiation energy of this type to disrupt cellular biochemical processes, there would be no life on earth because of natural sources of similar radiation energy in the environment.
Dr. Leikind has taken a lot of heat (no pun intended) from readers – see the reader-response thread after the article. But I have yet to find the flaw in his logic.
Rabu, 06 Oktober 2010
Seeing is believing
I know at least one of you mentioned an interest in stem cells. The MCDB seminar looks like it might be of interest:
MCDB Seminar
Speaker: Pete Coffey
Head of Ocular Biology & Therapeutics
Professor, Cellular Therapy and Visual Sciences
Director, London Project to Cure Blindness
Title: "Stemming Vision Loss Using Stem Cells - Seeing Is Believing"
Location: Rathmann Auditorium, LSB 1001
Thursday October 7th 3:30 p.m. - 4:30 p.m.
MCDB Seminar
Speaker: Pete Coffey
Head of Ocular Biology & Therapeutics
Professor, Cellular Therapy and Visual Sciences
Director, London Project to Cure Blindness
Title: "Stemming Vision Loss Using Stem Cells - Seeing Is Believing"
Location: Rathmann Auditorium, LSB 1001
Thursday October 7th 3:30 p.m. - 4:30 p.m.
Popular Joint Pain Supplements Don't Work
The popular joint-pain supplements glucosamine and chondroitin are ineffective in reducing knee or hip pain due to osteoarthritis, according to a recent report in the British Medical Journal. The latest meta-analysis reviewed 10 previous large, randomized, controlled studies. The authors conclude that the two supplements have no effect on either patient perception of joint pain or minimum width of joint space (a clinical measure of improvement) when compared to a placebo.
Glucosamine and chondroitin are among the most popular over-the-counter supplements, with annual sales of nearly $2 billion per year. Some people swear by the two supplements because they genuinely do feel better when taking them, and I sincerely believe they’re telling the truth. But the improvements could be due to the well-known placebo effect, or to the fact that in some patients, joint pain declines over time due to natural healing processes. Anecdotal evidence can’t be generalized to a larger population.
The authors of the study see no harm in patients continuing to take the supplements if it makes them feel better. They say that neither supplement does any harm (except to lighten your wallet a little).
Glucosamine and chondroitin are among the most popular over-the-counter supplements, with annual sales of nearly $2 billion per year. Some people swear by the two supplements because they genuinely do feel better when taking them, and I sincerely believe they’re telling the truth. But the improvements could be due to the well-known placebo effect, or to the fact that in some patients, joint pain declines over time due to natural healing processes. Anecdotal evidence can’t be generalized to a larger population.
The authors of the study see no harm in patients continuing to take the supplements if it makes them feel better. They say that neither supplement does any harm (except to lighten your wallet a little).
Jumat, 01 Oktober 2010
Texting and Fatal Driving Accidents
Text messages sent per month from hand-held phones increased more than 15-fold from 2002 to 2008. Over the same years the percentage of fatalities in which distracted driving was listed as a possible contributing factor increased from about 12% to nearly 16%.
Based on these data, the authors of a recent report speculate that texting while driving may have contributed to 16,000 additional driving fatalities between 2001 and 2007. The claim was reported in the Los Angeles Times and other papers, but is it true?
There are several problems with this report. First, the authors defined a fatality as caused by driver distraction whenever a distraction was merely listed as present. Other factors such as equipment failure, alcohol, or driver age were not considered. Second, distractions are anything that takes the driver’s attention away from driving, including texting or talking on a hand-held phone, reading an on-board navigation system (also increasingly popular these days), reaching for something, eating, drinking, putting on makeup, etc. Searching for street signs or rubbernecking another accident are also distractions. None of these were factored out in this study.
All the report really shows is that text-messaging volumes (in and out of cars) and the number of fatal accidents due to all distractions are both going up. The authors call it a correlation, but so what? A correlation does not prove causation. I’m reminded of the example presented by my thesis advisor years ago of the tight correlation between the rise in the number of telephones in the U.S. and the decline in the incidence of tuberculosis. Do telephones prevent tuberculosis? Hardly.
Is texting while driving a problem? Probably yes. Does this paper convince me that texting while driving has caused 16,000 additional fatalities? Sadly, no.
Based on these data, the authors of a recent report speculate that texting while driving may have contributed to 16,000 additional driving fatalities between 2001 and 2007. The claim was reported in the Los Angeles Times and other papers, but is it true?
There are several problems with this report. First, the authors defined a fatality as caused by driver distraction whenever a distraction was merely listed as present. Other factors such as equipment failure, alcohol, or driver age were not considered. Second, distractions are anything that takes the driver’s attention away from driving, including texting or talking on a hand-held phone, reading an on-board navigation system (also increasingly popular these days), reaching for something, eating, drinking, putting on makeup, etc. Searching for street signs or rubbernecking another accident are also distractions. None of these were factored out in this study.
All the report really shows is that text-messaging volumes (in and out of cars) and the number of fatal accidents due to all distractions are both going up. The authors call it a correlation, but so what? A correlation does not prove causation. I’m reminded of the example presented by my thesis advisor years ago of the tight correlation between the rise in the number of telephones in the U.S. and the decline in the incidence of tuberculosis. Do telephones prevent tuberculosis? Hardly.
Is texting while driving a problem? Probably yes. Does this paper convince me that texting while driving has caused 16,000 additional fatalities? Sadly, no.
Biomechanics
Swimming and filtration in the ocean by jet-propelled salps
Dr. Kelly R. Sutherland
Postdoctoral Scholar in Bioengineering, California Institute of Technology
MECHANICAL ENGINEERING SEMINAR
Engineering Sciences Building, ESB 1001
Thursday, October 4th, 4.00 p.m.
Salps are barrel-shaped marine organisms that are common in the open ocean and swim using a pulsed jet. Among salp species, there are a variety of body shapes and swimming styles that correspond to differences in ecological function. Dye visualization via bluewater SCUBA techniques and laboratory Digital Particle Image Velocimetry (DPIV) were used to describe jet wake structure and swimming performance variables including thrust, drag and propulsive efficiency among three salp species (Pegea confoederata, Weelia (Salpa) cylindrica, Cyclosalpa sp.). Locomotion by each species was achieved using vortex ring ring propulsion. Different combinations of swimming speed and hydrodynamic efficiency were observed and can be considered in light of metabolic constraints and ecological roles. Though nature does not strive for optimality, this work shows the value of a comparative approach for understanding how underlying structure and mechanism influence performance.
During swimming, the same fluid that propels the salp forward also contains food particles, which are captured on a mucous mesh as fluid passes through the mostly hollow body. Though salps are centimeters in length and swim at speeds of ~1-10 cm s-1, filtration occurs on a fine, mucous mesh (fiber diameter ~0.1 μm) at low velocity (1.6 cm s−1) and is thus a low Reynolds number (Re ~10−3) process. A model of particle capture efficiency by a rectangular mesh was used to estimate particle capture rates on the salp filtering mesh based on realistic oceanic particle concentrations. Particle feeding experiments using 0.5, 1 and 3 µm fluorescent polystyrene microspheres were then performed to test the theoretical model. Results from both the model and from experiments showed that smaller particles are captured at considerably higher rates than larger particles. Though particles smaller than mesh openings (1.4 µm) are expected to supply substantially less carbon than larger particles, they can still completely satisfy salp energetic needs. By removing different sized particles with nonuniform efficiency and packaging them into fast-sinking fecal pellets, salps have the potential to structure oceanic particle size spectra.
Rabu, 29 September 2010
Labwork opportunity
Contact Tom directly if you are interested.
From Silent Spring to Silent Night
Tyrone Hayes, Professor, UC Berkeley
"From Silent Spring to Silent Night: What happens if our canary stops singing?"
Hosted by Bren Professor Patricia Holden as part of the Seminar in Ecotoxicology
Friday, Oct. 8, 2010
11:00 a.m. - 12:00 p.m.
Bren Hall 1414
Abstract
The herbicide atrazine is a potent endocrine disrupter that chemically castrates and feminizes exposed male amphibians. Further, when combined with other pesticides, exposure results in a hormonal stress response that leads to retarded growth and development, and immuno-suppression. The immuno-suppression results in increased disease rates and mortality. Though many factors likely contribute to amphibian declines, pesticides likely play an important role even in populations that appear to decline for other reasons, such as disease. Pesticides like atrazine are ubiquitous, persistent contaminants. Effects of exposure have been shown in every vertebrate class examined (fish, amphibians, reptiles, and mammals) via common mechanisms. These observations demonstrate the critical impact that pesticides have on environmental health. Furthermore, reproductive cancers and birth defects associated with exposure to many of these same chemicals (e.g. atrazine) via identical mechanisms demonstrate that the impact on environmental health is an indicator of a negative impact on public health. Many of these mechanisms are being revealed only now in the scientific literature and agencies (such as the Environmental Protection Agency) are ill-equipped to deal with this emergent science and translate it efficiently into health-protective policies. Given the importance of this science and relevance to public health, there is a strong need to translate this information and provide public access to this knowledge. In particular, minority populations, more likely to be exposed to these chemicals, more likely to suffer health effects associated with exposure, less likely to have access to adequate health care and less likely to have access to this information, need to be informed. It is especially incumbent upon research scientists to make accurate accounts of these data available when industry and agency representatives (e.g. the EPA) provide inaccurate information to the public.
CCS distinguished lecturer
This will be of interest to CCS Literature and Science students, as Mary writes about science, particularly biology - "Stiff" looks into "the curious lives of human cadavers", "Spook" into claims of the afterlife and "Bonk" into the somewhat whackier aspects of the physiology of sex (see reviews).
She will be available to talk with CCS students in the Gallery on Monday October 4th at 4:00 PM and will be giving an arts & lectures address in Campbell Hall at 8:00 that evening. (General $10, Students $6)
This is an opportunity to converse with a successful and off-the-beaten track author who is noted for a combination of insight & humor. Be sure to visit her website and read her biography.
Sabtu, 25 September 2010
Thimerosal, Vaccines, and Autism
The tenth scientific study showing that autism spectrum disorders in children are not linked to thimerosal, a mercury-containing preservative once used in vaccines, has just been published in the journal of the American Academy of Pediatrics, adding one more to the nine others already published. In addition, the initial report that there is a link have been largely discredited. According to an article in the LA Times earlier this year, the doctor who first alleged that there was a link between autism and thimerosal has been rebuked by the British General Medical Council for the way his research was conducted, and the journal in which published his work declared that it should not have published the report.
And yet, one in four parents still persist in believing that vaccinations increase the likelihood of a child developing autism. Is there anything that could convince them otherwise?
Perhaps not. Resistance based on emotion (fear), may not be able to be overcome by scientific evidence, no matter how clear and convincing the evidence is. It’s too bad, really. It would be a shame if diseases like measles, mumps, or even polio made a comeback because not enough children had been vaccinated against them.
And yet, one in four parents still persist in believing that vaccinations increase the likelihood of a child developing autism. Is there anything that could convince them otherwise?
Perhaps not. Resistance based on emotion (fear), may not be able to be overcome by scientific evidence, no matter how clear and convincing the evidence is. It’s too bad, really. It would be a shame if diseases like measles, mumps, or even polio made a comeback because not enough children had been vaccinated against them.
Selasa, 21 September 2010
Testing Athletes for Gene Doping
Ever since winning athletic competitions has meant a lot of money, athletes have tried to increase their odds of winning by using performance-enhancing drugs. And for just as long, sports associations have tried to catch the athletes who cheat. In most cases the athletes have stayed one jump ahead by using newer-generation harder-to-detect “designer” drugs as soon as sports associations developed tests to detect the older-generation ones.
Sports associations and many athletes thought that the next level of sophistication in athletic performance enhancement through artificial means (i.e., cheating) was going to be “gene doping” – using genetic engineering techniques to introduce foreign genes into the body that would cause the body to produce performance-enhancing hormones naturally. But the athletes may have lost the detection battle before it even began. Scientists in Germany have already developed a test that they say can conclusively prove with 100% certainty that gene doping has occurred, using a blood sample as small as 200ul. The test looks for the presence of the foreign gene itself, not the protein or hormone product produced by the gene.
It’ll take about two more years for independent laboratories to validate the test, and so it may not be ready by the 2012 Olympics. But even if it’s not, blood samples could be stored and tested later.
Score one for the sports authorities, for once.
Sports associations and many athletes thought that the next level of sophistication in athletic performance enhancement through artificial means (i.e., cheating) was going to be “gene doping” – using genetic engineering techniques to introduce foreign genes into the body that would cause the body to produce performance-enhancing hormones naturally. But the athletes may have lost the detection battle before it even began. Scientists in Germany have already developed a test that they say can conclusively prove with 100% certainty that gene doping has occurred, using a blood sample as small as 200ul. The test looks for the presence of the foreign gene itself, not the protein or hormone product produced by the gene.
It’ll take about two more years for independent laboratories to validate the test, and so it may not be ready by the 2012 Olympics. But even if it’s not, blood samples could be stored and tested later.
Score one for the sports authorities, for once.
Minggu, 19 September 2010
Biodiesel Fuel from Sunlight and CO2
From time to time I like to highlight innovations that have the potential to be real game-changers; good ideas still in the development stage that could alter our lives significantly within our lifetimes. So here’s one; a tiny start-up company called Joule Unlimited announced last week that it had received a patent on a bacterium that has been genetically engineered to produce diesel fuel using only sunlight, water and CO2. It’s similar to how plants produce hydrocarbons, but in this instance the hydrocarbon is diesel fuel, not a sugar or a starch.
The company expects that the process could be scaled up to produce 15,000 gallons of diesel fuel per acre, using water that is unfit for drinking (it could be wastewater or brackish water) and land that is unsuitable for farming. The process is not yet efficient enough to use the very limited amount of CO2 available in air (air is only 0.04% CO2), but it has been shown to work using the kinds of CO2 concentrations found in the effluent of coal-fired energy facilities. The company expects to begin production at a pilot plant in Texas by 2012.
Imagine a future in which the very CO2 that we’re trying so hard to get rid of these days (because it’s a greenhouse gas) becomes an asset – the raw material for creating diesel fuel. That would make CO2 an endlessly renewable energy source and solve most of the global warming problem at the same time.
With a few more good ideas like this, maybe there’s hope for our planet (smile).
The company expects that the process could be scaled up to produce 15,000 gallons of diesel fuel per acre, using water that is unfit for drinking (it could be wastewater or brackish water) and land that is unsuitable for farming. The process is not yet efficient enough to use the very limited amount of CO2 available in air (air is only 0.04% CO2), but it has been shown to work using the kinds of CO2 concentrations found in the effluent of coal-fired energy facilities. The company expects to begin production at a pilot plant in Texas by 2012.
Imagine a future in which the very CO2 that we’re trying so hard to get rid of these days (because it’s a greenhouse gas) becomes an asset – the raw material for creating diesel fuel. That would make CO2 an endlessly renewable energy source and solve most of the global warming problem at the same time.
With a few more good ideas like this, maybe there’s hope for our planet (smile).
Kamis, 16 September 2010
Electronic Cigarette Manufacturers Warned
The Food and Drug Administration (FDA) sent letters last week to five manufacturers of electronic cigarettes (e-cigs), warning the companies that they were making unsubstantiated medical claims about their products, including the claim that the products were an aid to stopping smoking – a medical claim prohibited by the Federal Food, Drug, and Cosmetic Act. The FDA also signaled its intent to regulate e-sigs as a drugs or drug-delivery devices.
An “e-cig” (since you forgot to ask) is a battery-powered cigarette-shaped device that can be loaded with a cartridge of nicotine and other additives. When the user inhales through the device, the battery vaporizes the liquid so that it can be inhaled into the lungs. The product contains no tobacco. A wisp of “smoke” appears, but it’s just water vapor.
Several of the e-cig products contain herbal ingredients in addition to nicotine. One of the e-cig companies even sells other drugs in liquid form for use in the devices, including an erectile dysfunction drug (tadalafil) and a weight-loss drug not approved in the U.S. (rimonabant).
The names of the companies and copies of the FDA’s letters to them can be found on the FDA web site in a press announcement dated Sept. 9th. Whether this is the end of e-cigs isn’t clear.
An “e-cig” (since you forgot to ask) is a battery-powered cigarette-shaped device that can be loaded with a cartridge of nicotine and other additives. When the user inhales through the device, the battery vaporizes the liquid so that it can be inhaled into the lungs. The product contains no tobacco. A wisp of “smoke” appears, but it’s just water vapor.
Several of the e-cig products contain herbal ingredients in addition to nicotine. One of the e-cig companies even sells other drugs in liquid form for use in the devices, including an erectile dysfunction drug (tadalafil) and a weight-loss drug not approved in the U.S. (rimonabant).
The names of the companies and copies of the FDA’s letters to them can be found on the FDA web site in a press announcement dated Sept. 9th. Whether this is the end of e-cigs isn’t clear.
Minggu, 12 September 2010
Stem Cell Research Continues (Temporarily)
In the long-standing battle between opponents and proponents of research involving stem cells derived from human embryos, last month a U.S. District judge issued a temporary injunction against the use of federal funds for such research (see this blog, Sept. 1). The injunction not only halted funding for future research projects that would have used stem cells derived from embryos, but also threw the funding for all current research projects into doubt. Researchers wondered whether their experimental animals would have to be euthanatized and their laboratory workers laid off.
To prevent that from happening, last week the U.S. Court of Appeals (the next step up the judicial ladder) issued a temporary injunction against the lower court’s ruling. The injunction will allow the National Institutes of Health to continue funding stem cell research temporarily, until an appeal is heard by the higher court. It also gives Congress time to act to change the law, but of course that depends on whether proponents of stem cell research can muster the votes to do so.
So now it’s in the hands of the U.S. Court of Appeals and Congress. Researchers, patient advocacy groups, and opponents of embryonic stem cell research will be watching closely. It’s time to lobby your congressman, if you have an opinion.
To prevent that from happening, last week the U.S. Court of Appeals (the next step up the judicial ladder) issued a temporary injunction against the lower court’s ruling. The injunction will allow the National Institutes of Health to continue funding stem cell research temporarily, until an appeal is heard by the higher court. It also gives Congress time to act to change the law, but of course that depends on whether proponents of stem cell research can muster the votes to do so.
So now it’s in the hands of the U.S. Court of Appeals and Congress. Researchers, patient advocacy groups, and opponents of embryonic stem cell research will be watching closely. It’s time to lobby your congressman, if you have an opinion.
Selasa, 07 September 2010
Pre-run Streching Doesn't Prevent Injuries
I reported last year on this blog that the U.S.A. Track & Field association (USATF) was recruiting runners for a study to try to determine whether pre-run stretching prevents running injuries. Coaches and trainers often recommend stretching before exercise, but whether it’s helpful, harmful, or neutral has remained essentially an untested hypothesis.
To test the hypothesis that pre-run stretching reduces the incidence of injuries to runners, the USATF recruited 2,729 runners, defined as persons who ran over 10 miles a week. Each runner was randomly assigned to either a “stretch” or a “no-stretch” group. “No-stretch” runners were instructed not to stretch before running even if they had been in the habit of doing so before. “Stretch” runners were instructed to follow a specific stretch routine before running. All runners were instructed to continue their normal running routine for three months and to report any injuries that caused them to stop running for at least three days.
The results of the study were released last month. Just over half of the runners complied with their assigned group protocol and successfully completed the three months of the study. The results - injury rates were precisely 16% in both groups. In other words, pre-run stretching had no effect on injury rates.
One intriguing finding was that runners who normally stretched before running but were assigned to the “no-stretch” group had a higher injury rate than those who normally didn’t stretch and were in the same group. One hypothesis is that just changing their routine (stopping stretching) may have been enough to predispose them to injury.
So if you’ve always stretched before you run and like doing it, by all means keep doing it. But if you haven’t been in the habit of stretching before running, don’t feel that you have to start.
To test the hypothesis that pre-run stretching reduces the incidence of injuries to runners, the USATF recruited 2,729 runners, defined as persons who ran over 10 miles a week. Each runner was randomly assigned to either a “stretch” or a “no-stretch” group. “No-stretch” runners were instructed not to stretch before running even if they had been in the habit of doing so before. “Stretch” runners were instructed to follow a specific stretch routine before running. All runners were instructed to continue their normal running routine for three months and to report any injuries that caused them to stop running for at least three days.
The results of the study were released last month. Just over half of the runners complied with their assigned group protocol and successfully completed the three months of the study. The results - injury rates were precisely 16% in both groups. In other words, pre-run stretching had no effect on injury rates.
One intriguing finding was that runners who normally stretched before running but were assigned to the “no-stretch” group had a higher injury rate than those who normally didn’t stretch and were in the same group. One hypothesis is that just changing their routine (stopping stretching) may have been enough to predispose them to injury.
So if you’ve always stretched before you run and like doing it, by all means keep doing it. But if you haven’t been in the habit of stretching before running, don’t feel that you have to start.
Minggu, 05 September 2010
Vaginal Gel is Effective Against HIV
Finally, there’s an HIV prevention method that’s controlled by women. This is especially important for women who are not in a mutually monogamous relationship and who cannot convince their men to use a condom. (In Africa, over 60% of HIV-infected persons are women who contracted the disease via heterosexual sex.)
In a study published last week in Science, nearly 900 sexually active women in a high-risk area in South Africa were supplied with either a vaginal gel containing the antiviral drug tenofovir, or just the gel alone as a control, over a thirty-month period. Women who received the drug were 39% less likely to become infected with HIV, compared to women in the control group.
Why wasn’t the treatment 100% effective? Part of the reason may be that some study participants may not have used the gel properly and consistently. Among women who used the gel as advised (both before and after sex) more than 80% of the time, the reduction in HIV infections was 54%. When the gel was used less than half the time the reduction in infections was only 28%. No one should be surprised; after all condoms, too, only work if you use them!
AIDS researchers are cheering. Although prevention wasn’t perfect, they’ve proved that pre-exposure prophylaxis controlled by women is at least partially effective. The next step will be to find more potent drugs or a more effective delivery method – perhaps a vaginal ring that releases the drug over longer periods of time.
By the way, would you like to know how the researchers monitored compliance to the study protocol (participant’s actual use of the gels)? They counted the used gel applicators returned by the women in the study and compared that number to the 181,340 gel applicators they gave out. Obviously the researchers suspected in advance that compliance might be a problem. You have to admire the researchers’ advance planning and their willingness to do what was necessary to improve the validity of their results.
In a study published last week in Science, nearly 900 sexually active women in a high-risk area in South Africa were supplied with either a vaginal gel containing the antiviral drug tenofovir, or just the gel alone as a control, over a thirty-month period. Women who received the drug were 39% less likely to become infected with HIV, compared to women in the control group.
Why wasn’t the treatment 100% effective? Part of the reason may be that some study participants may not have used the gel properly and consistently. Among women who used the gel as advised (both before and after sex) more than 80% of the time, the reduction in HIV infections was 54%. When the gel was used less than half the time the reduction in infections was only 28%. No one should be surprised; after all condoms, too, only work if you use them!
AIDS researchers are cheering. Although prevention wasn’t perfect, they’ve proved that pre-exposure prophylaxis controlled by women is at least partially effective. The next step will be to find more potent drugs or a more effective delivery method – perhaps a vaginal ring that releases the drug over longer periods of time.
By the way, would you like to know how the researchers monitored compliance to the study protocol (participant’s actual use of the gels)? They counted the used gel applicators returned by the women in the study and compared that number to the 181,340 gel applicators they gave out. Obviously the researchers suspected in advance that compliance might be a problem. You have to admire the researchers’ advance planning and their willingness to do what was necessary to improve the validity of their results.
Selasa, 31 Agustus 2010
Injunction Against Human Stem Cell Research
In March of 2009 President Obama issued an executive order permitting the use of federal funds for research on stem cells lines derived previously from human embryos, arguing that the researchers had not destroyed the embryos themselves. The Obama executive order effectively overturned the ban of the Bush administration on the use of human embryonic stem cells for research. At the time, I reported in this blog that the Obama order might still face a legal challenge, based on a federal law called the Dickey-Wicker Amendment of 1999.
Last week it finally happened. As the result of a lawsuit filed by several Christian groups and two doctors opposed to human stem cell research, a U.S. District Court judge issued an injunction which blocks the National Institutes of Health (NIH) from implementing the Obama order. The judge argued that the Obama executive order clearly violates the language of the Dickey-Wicker Amendment, and even some supporters of the Omama order grudgingly agree. According to Harvard ethicist Louis Guenin, allowing research on cell lines merely derived from human embryonic stem cells would be like allowing research on dead bald eagles. It’s illegal to kill bald eagles, and therefore anyone doing research on bald eagles killed by someone else would be considered complicit in the crime.
If research on stem cells derived from human embryos is to continue, it appears that Congress will have to overturn the Dickey-Wicker Amendment. Whether there are sufficient votes in both houses of Congress to do so is anybody’s guess. In the meantime, funding for future projects is on hold. And while NIH’s interpretation is that currently-funded research projects can continue for now, not everyone seems to agree. We’ll have to see how this one shakes out. For starters, I’m sure we can expect the ruling to be appealed.
Last week it finally happened. As the result of a lawsuit filed by several Christian groups and two doctors opposed to human stem cell research, a U.S. District Court judge issued an injunction which blocks the National Institutes of Health (NIH) from implementing the Obama order. The judge argued that the Obama executive order clearly violates the language of the Dickey-Wicker Amendment, and even some supporters of the Omama order grudgingly agree. According to Harvard ethicist Louis Guenin, allowing research on cell lines merely derived from human embryonic stem cells would be like allowing research on dead bald eagles. It’s illegal to kill bald eagles, and therefore anyone doing research on bald eagles killed by someone else would be considered complicit in the crime.
If research on stem cells derived from human embryos is to continue, it appears that Congress will have to overturn the Dickey-Wicker Amendment. Whether there are sufficient votes in both houses of Congress to do so is anybody’s guess. In the meantime, funding for future projects is on hold. And while NIH’s interpretation is that currently-funded research projects can continue for now, not everyone seems to agree. We’ll have to see how this one shakes out. For starters, I’m sure we can expect the ruling to be appealed.
Rabu, 25 Agustus 2010
The Benefits of Human Breast Milk
Colonization of the human infants’ gastrointestinal tract by bacteria occurs only after birth. It is known that human breast milk encourages colonization of the newborn’s gut by beneficial bacteria and discourages colonization by harmful ones, but how exactly does it do that? An article in the Proceedings of the National Academy of Sciences provides a tantalizing glimpse into the likely mechanisms.
About 4-12% of the macronutrient composition of human milk consists of a structurally diverse group of complex sugars called oligosaccharides. These oligosaccharides are indigestible by the infant, and so for many years scientists thought they had no function. It turns out that they are digestible by a particular group of beneficial bacteria called bifidobacteria. The presence of these oligosaccharides in human milk gives the bifidobacteria a nutritional advantage over less desirable bacteria in the human infant’s gut. In other words, these oligosaccharides are produced in human milk specifically to provide nutrients to beneficial bacteria, rather than to nourish the infant.
Some of these oligosaccharides have another interesting property; they bind to certain harmful bacteria, thus preventing them from attaching to the epithelial cells lining the gut. Researchers think that these oligosaccharides may flush out harmful bacteria during that very vulnerable time in early life when the infant’s immune system has not yet developed fully.
About 4-12% of the macronutrient composition of human milk consists of a structurally diverse group of complex sugars called oligosaccharides. These oligosaccharides are indigestible by the infant, and so for many years scientists thought they had no function. It turns out that they are digestible by a particular group of beneficial bacteria called bifidobacteria. The presence of these oligosaccharides in human milk gives the bifidobacteria a nutritional advantage over less desirable bacteria in the human infant’s gut. In other words, these oligosaccharides are produced in human milk specifically to provide nutrients to beneficial bacteria, rather than to nourish the infant.
Some of these oligosaccharides have another interesting property; they bind to certain harmful bacteria, thus preventing them from attaching to the epithelial cells lining the gut. Researchers think that these oligosaccharides may flush out harmful bacteria during that very vulnerable time in early life when the infant’s immune system has not yet developed fully.
Selasa, 24 Agustus 2010
Oral Immunotherapy for Food Allergies
Some people have food allergies so severe that even the slightest contact with the food can lead to a life-threatening allergic response. A rare but potentially fatal allergic response to peanuts, for example, is why most airlines no longer serve peanuts on their flights. Other sufferers are equally allergic to milk or to eggs, commonly used as ingredients in many food products and recipes. Is there anything that can be done for people with life-threatening food allergies aside from having them try to avoid the food?
Current research efforts are focused on oral immunotherapy (OIT). OIT consists of exposing the patient to miniscule quantities of the allergen in a supervised research setting (under close medical supervision), and then if an allergic reaction fails to occur or remains mild, slowly increasing the dose over days or months to “desensitize” the patient.
Researchers caution that the technique is not yet ready for widespread clinical use, however. The risk of an adverse reaction to the first dose is fairly high, and little is known about the safety of OIT when done at home under a variety of conditions. In addition, it is not known how long desensitization lasts if/when regular desensitizing dosing is ended. There is a danger that desensitized patients might develop a false sense of security once they become partially desensitized or quit their therapy altogether.
Nevertheless, OIT might become a useful therapy for severe food allergies in the future, once we better understand how to perform it safely. For sufferers of truly severe food allergies, the risks associated with desensitization would have to be balanced against the risk of accidental exposure to the allergen and perhaps even death.
Current research efforts are focused on oral immunotherapy (OIT). OIT consists of exposing the patient to miniscule quantities of the allergen in a supervised research setting (under close medical supervision), and then if an allergic reaction fails to occur or remains mild, slowly increasing the dose over days or months to “desensitize” the patient.
Researchers caution that the technique is not yet ready for widespread clinical use, however. The risk of an adverse reaction to the first dose is fairly high, and little is known about the safety of OIT when done at home under a variety of conditions. In addition, it is not known how long desensitization lasts if/when regular desensitizing dosing is ended. There is a danger that desensitized patients might develop a false sense of security once they become partially desensitized or quit their therapy altogether.
Nevertheless, OIT might become a useful therapy for severe food allergies in the future, once we better understand how to perform it safely. For sufferers of truly severe food allergies, the risks associated with desensitization would have to be balanced against the risk of accidental exposure to the allergen and perhaps even death.
Minggu, 22 Agustus 2010
Kidney Disease and African Sleeping Sickness
Natural selection can actually favor an otherwise harmful allele of a gene, if that allele somehow confers a survival advantage in some individuals and populations. The one textbook example of this phenomenon has always been sickle cell disease, a genetically inherited disease that results in deformed red blood cells and can lead to early death. Sickle cell disease is prevalent in persons of African ancestry because the allele that causes sickle cell disease also protects the person with that allele from malaria, a disease which is widespread in Africa.
Now there’s a second example of this phenomenon. Researchers have found that two different alleles for a gene involved in the production of a blood protein can; a) lead to kidney disease, and b) protect against the parasite that causes African sleeping sickness. Not surprisingly, the two abnormal alleles and the kidney diseases they cause are four to five times more common in African Americans than in persons of European descent.
Researchers are wondering how many other genetic diseases we’ll find that also confer protective advantages against certain infectious diseases. Researchers are also hoping to develop new treatments for African sleeping sickness that are based on the proteins these abnormal alleles produce.
Now there’s a second example of this phenomenon. Researchers have found that two different alleles for a gene involved in the production of a blood protein can; a) lead to kidney disease, and b) protect against the parasite that causes African sleeping sickness. Not surprisingly, the two abnormal alleles and the kidney diseases they cause are four to five times more common in African Americans than in persons of European descent.
Researchers are wondering how many other genetic diseases we’ll find that also confer protective advantages against certain infectious diseases. Researchers are also hoping to develop new treatments for African sleeping sickness that are based on the proteins these abnormal alleles produce.
Sabtu, 14 Agustus 2010
Maximum Heart Rate for Women
Many serious exercisers pay close attention to their heart rates while exercising. That’s because they generally are advised to keep their heart rates within 65-85% of their maximum heart rate for a safe but relatively strenuous workout designed to improve aerobic capacity and endurance.
According to a formula for maximum heart rate that is now 40 years old (it was developed in the 17970s), your maximum heart rate should be around 220 beats per minute (bpm) minus your age. The formula is a population average, of course, and shouldn’t be taken as an absolute number for each individual. More importantly, the old formula was based solely on men subjects. Now a new study of over 5,000 healthy women indicates that a better population-based formula for women is:
Maximum Heart Rate for Women = 206 – (0.88 x age)
Admittedly the new formula has the disadvantage that it can’t be calculated in your head, but it’s easy enough to do with a calculator. And the difference may be significant: By the old formula, a 40-year-old’s 65-85% target range would have been 117-153 bpm. By the new formula, the target range for a 40-yr-old woman would be 111-145 bpm. Six to eight beats per minute might not sound like much, but over an hour’s workout it could make the difference between pushing yourself too far and getting discouraged, and just getting a good healthy workout.
The new study focused only on women subjects. Perhaps someone ought to confirm or revise the old formula for men, too!
Reference: Gulati, M. et al., Heart Rate Response to Exercise Stress Testing in Asymptomatic Women: The St. James Women Take Heart Project. Circulation 122:130-137, 2010.
According to a formula for maximum heart rate that is now 40 years old (it was developed in the 17970s), your maximum heart rate should be around 220 beats per minute (bpm) minus your age. The formula is a population average, of course, and shouldn’t be taken as an absolute number for each individual. More importantly, the old formula was based solely on men subjects. Now a new study of over 5,000 healthy women indicates that a better population-based formula for women is:
Maximum Heart Rate for Women = 206 – (0.88 x age)
Admittedly the new formula has the disadvantage that it can’t be calculated in your head, but it’s easy enough to do with a calculator. And the difference may be significant: By the old formula, a 40-year-old’s 65-85% target range would have been 117-153 bpm. By the new formula, the target range for a 40-yr-old woman would be 111-145 bpm. Six to eight beats per minute might not sound like much, but over an hour’s workout it could make the difference between pushing yourself too far and getting discouraged, and just getting a good healthy workout.
The new study focused only on women subjects. Perhaps someone ought to confirm or revise the old formula for men, too!
Reference: Gulati, M. et al., Heart Rate Response to Exercise Stress Testing in Asymptomatic Women: The St. James Women Take Heart Project. Circulation 122:130-137, 2010.
Minggu, 08 Agustus 2010
Rapid Eye Movement (REM) Sleep
Humans go through several stages of sleep during a typical night. One of them is the period during which we have complex dreams, called rapid eye movement (REM) sleep. During REM sleep our eyes move about rapidly beneath closed eyelids, even though our bodies typically remain completely motionless.
The explanation for rapid eye movement during REM sleep has always remained somewhat of a mystery - until now. In the June issue of Brain, researchers report that the most likely explanation is that our eyes are trying to follow the action in our dreams. They came to this conclusion after studying the direction of eye movements in a group of subjects who have a particular sleep disorder in which they physically act out their dreams while sleeping. The patients’ eye movements tracked their physical actions with a consistency of nearly 90%. The eye movements in these patients were no different than in normal subjects who did not move physically during sleep, leading the authors to suggest that the “follow-the-dream-action” explanation for REM activity may hold for normal subjects as well.
The explanation for rapid eye movement during REM sleep has always remained somewhat of a mystery - until now. In the June issue of Brain, researchers report that the most likely explanation is that our eyes are trying to follow the action in our dreams. They came to this conclusion after studying the direction of eye movements in a group of subjects who have a particular sleep disorder in which they physically act out their dreams while sleeping. The patients’ eye movements tracked their physical actions with a consistency of nearly 90%. The eye movements in these patients were no different than in normal subjects who did not move physically during sleep, leading the authors to suggest that the “follow-the-dream-action” explanation for REM activity may hold for normal subjects as well.
Kamis, 05 Agustus 2010
Dietary Supplements Deceptive Sales Practices
Dietary supplements are regulated as food products, not as drugs. Manufacturers are free to make vague claims of effectiveness, such as “improves heart health” or “boosts brain function”, but they cannot make medical claims such as “lowers high blood pressure” or “prevents Alzheimer’s”. And although their products are supposed to be safe, they’re not required to submit any data to prove it.
Now a Senate document reveals that even though the products may be labelled correctly, in sales conversations (“off-label”, so to speak) retail sales representatives of dietary supplements products are openly engaging in “deceptive and questionable sales tactics” – in other words, they’re lying to make a sale.
In testimony before a U.S. Senate committee, the General Accounting Office (GAO) reported that it had staff members ask questions of sales representatives such as: Is ginkgo biloba safe to take with aspirin? Can ginseng cure cancer? Is it okay to replace my blood pressure medication with garlic supplements? All too often they got “yes” answers when the correct answers are “no”. These answers are not just harmless sales advice – they are potentially dangerous advice and they are against the law. Action may be taken against some sellers as a result of the investigation. But for all practical purposes, it’s still “buyer beware” when it comes to the safety and efficacy of dietary supplements.
You can hear clips of some of the undercover calls at http://www.gao.gov/products/GAO-10-662T.
Now a Senate document reveals that even though the products may be labelled correctly, in sales conversations (“off-label”, so to speak) retail sales representatives of dietary supplements products are openly engaging in “deceptive and questionable sales tactics” – in other words, they’re lying to make a sale.
In testimony before a U.S. Senate committee, the General Accounting Office (GAO) reported that it had staff members ask questions of sales representatives such as: Is ginkgo biloba safe to take with aspirin? Can ginseng cure cancer? Is it okay to replace my blood pressure medication with garlic supplements? All too often they got “yes” answers when the correct answers are “no”. These answers are not just harmless sales advice – they are potentially dangerous advice and they are against the law. Action may be taken against some sellers as a result of the investigation. But for all practical purposes, it’s still “buyer beware” when it comes to the safety and efficacy of dietary supplements.
You can hear clips of some of the undercover calls at http://www.gao.gov/products/GAO-10-662T.
Minggu, 01 Agustus 2010
First Human Stem Cell Therapy Trial
The first clinical trial of a therapy based on human stem cells has received final approval from the Food and Drug Administration (FDA) and will get underway shortly, according to a press release from Geron Corporation, the company sponsoring the research. During the first phase of the trial, researchers will inject precursor cells to neural support cells called oligodendrocytes into the spinal cords of patients who have suffered recent spinal cord injuries and who have almost no chance of recovery of function otherwise. The hope is that the precursor cells will differentiate into mature oligodendrocytes (the cells that produce myelin) and that the myelin will form new sheaths around damaged nerves.
The trial was planned several years ago but held up by the FDA over concerns that the therapy could increase the risk of tumors forming in the spinal cord if the injected cells were not free of embryonic stem cells. The first phase of the trial is designed to test the safety of the procedure. It will be years before the technique becomes widely available for the repair of spinal cord injuries, even if it does eventually prove to be both safe and effective.
Stem cell researchers will be holding their breath. A failure in this first approved trial could set back the whole field of stem cell therapy research for years.
The trial was planned several years ago but held up by the FDA over concerns that the therapy could increase the risk of tumors forming in the spinal cord if the injected cells were not free of embryonic stem cells. The first phase of the trial is designed to test the safety of the procedure. It will be years before the technique becomes widely available for the repair of spinal cord injuries, even if it does eventually prove to be both safe and effective.
Stem cell researchers will be holding their breath. A failure in this first approved trial could set back the whole field of stem cell therapy research for years.
Senin, 26 Juli 2010
Familial DNA Searches
DNA testing is a modern way to positively match DNA left at a crime scene to a suspect. But what if police have DNA from a crime scene but no suspect? Most states have DNA banks only of convicted felons already in prison, so a criminal with no prior record would almost certainly go undetected.
One method being used in California is to look for partial matches between DNA from a crime scene and the state’s database of DNA from convicted criminals. A partial match, while not implicating the criminal himself, would suggest that a close relative might have carried out the crime. California used the method this month to identify a person previously convicted on a weapons charge as “probably related” to a long-sought-after Los Angeles serial killer known as the Grim Sleeper. The person’s father eventually was arrested and charged with ten murders.
This is new ethical ground for us all. As a society we need to understand the costs vs. benefits of these types of searches. The benefits are obvious – another killer identified. But the costs will be freedom lost – the freedom, for example, not to be put under suspicion and investigated for a crime unless there is reason to suspect you of an offense. Suspicion of relatives based on partial DNA matches is likely to fall disproportionately on African Americans, since they already represent a disproportionate fraction of the prison population.
Because of these concerns, California wisely put some safeguards in place for familial DNA searches. Currently, such searches require that all other investigative leads have been exhausted, that the crime is murder or rape, and that the criminal is still committing crimes – i.e. is still a threat to society. Other states considering familial DNA searches should consider similar safeguards.
One method being used in California is to look for partial matches between DNA from a crime scene and the state’s database of DNA from convicted criminals. A partial match, while not implicating the criminal himself, would suggest that a close relative might have carried out the crime. California used the method this month to identify a person previously convicted on a weapons charge as “probably related” to a long-sought-after Los Angeles serial killer known as the Grim Sleeper. The person’s father eventually was arrested and charged with ten murders.
This is new ethical ground for us all. As a society we need to understand the costs vs. benefits of these types of searches. The benefits are obvious – another killer identified. But the costs will be freedom lost – the freedom, for example, not to be put under suspicion and investigated for a crime unless there is reason to suspect you of an offense. Suspicion of relatives based on partial DNA matches is likely to fall disproportionately on African Americans, since they already represent a disproportionate fraction of the prison population.
Because of these concerns, California wisely put some safeguards in place for familial DNA searches. Currently, such searches require that all other investigative leads have been exhausted, that the crime is murder or rape, and that the criminal is still committing crimes – i.e. is still a threat to society. Other states considering familial DNA searches should consider similar safeguards.
Jumat, 23 Juli 2010
Cotton Pests Infest GM Cotton
It was bound to happen, given enough time. In western India, a species of cotton bollworm has now developed the ability to infest genetically modified (GM) cotton that was specifically engineered to resist bollworm infestation.
GM cotton has become increasingly popular with farmers – so popular that approximately 50% of all cotton planted worldwide is now GM cotton. The largest users (and cotton growers) are China, India, and the United States, in that order. With so much GM cotton being planted, we could have anticipated that the cotton pests would adapt eventually. But it’s surprising how quickly it happened – bollworm-resistant cotton was only first planted in India in 2002.
Realistically, we can expect the current generation of GM crops to remain useful for several more decades. In the meantime I’m sure that researchers at Monsanto will be working on new ways to thwart the pests, just as the pests will be slowly adapting. It’s just part of the ongoing battle between species for survival.
GM cotton has become increasingly popular with farmers – so popular that approximately 50% of all cotton planted worldwide is now GM cotton. The largest users (and cotton growers) are China, India, and the United States, in that order. With so much GM cotton being planted, we could have anticipated that the cotton pests would adapt eventually. But it’s surprising how quickly it happened – bollworm-resistant cotton was only first planted in India in 2002.
Realistically, we can expect the current generation of GM crops to remain useful for several more decades. In the meantime I’m sure that researchers at Monsanto will be working on new ways to thwart the pests, just as the pests will be slowly adapting. It’s just part of the ongoing battle between species for survival.
Rabu, 21 Juli 2010
A New (Extinct) Human Ancestor
Scientists have discovered two partial skeletons of a new species of the genus Australopithecus near Johannesburg, South Africa, which they named Australopithecus sediba. The new australopithecines, nearly 1.95 million years old, appear to be closely related to both A. Afarensis and A. africanus.
Of course, paleoanthropologists are already debating where to place A. sediba in the human family tree; direct human ancestor, or evolutionary dead end? Regardless of the outcome, the new find is significant in that it fills some gaps in our understanding of evolutionary processes leading to humans. For instance, it appears that changes in the shape of the pelvis occurred before brain enlargement, and that the legs underwent adaptive changes for upright walking before the arms took on smaller, more human-like proportions.
Of course, paleoanthropologists are already debating where to place A. sediba in the human family tree; direct human ancestor, or evolutionary dead end? Regardless of the outcome, the new find is significant in that it fills some gaps in our understanding of evolutionary processes leading to humans. For instance, it appears that changes in the shape of the pelvis occurred before brain enlargement, and that the legs underwent adaptive changes for upright walking before the arms took on smaller, more human-like proportions.
Minggu, 18 Juli 2010
Using Bacteria to Fight Bacteria
A recent article in the New York Times is a good primer on the astonishing variety of bacteria that colonize our bodies, and what they may be doing there. It turns out that our individual microbiomes (all of the microbes in a defined environment within our bodies) are quite different. And at any one time, each of us probably has only about 20% of the species of bacteria that can inhabit the human body.
An interesting new idea is that the “good” bacteria in certain people’s microbiomes might actually be used to treat certain diseases. Doctors have actually cured several stubborn cases of severe diarrhea caused by a particularly difficult bacterium to treat (Clostridium difficile) by transplanting human fecal matter from a healthy person into the patients’ colons! Granted, having a fecal transplant in order to cure disease sounds a bit strange. But apparently the “good” bacteria in the fecal transplant outcompete the C. difficile and wipe them out.
Someday maybe there’ll be ointments or pills containing especially “good” bacteria for treating certain antibiotic-resistant infections such as flesh-eating Staphylococcus aureus or diarrhea-causing C. difficile. Using bacteria to kill bacteria – like using fire to fight fire.
Reference: Zimmer, C., How Microbes Defend and Define Us. New York Times, July 13, 2010.
An interesting new idea is that the “good” bacteria in certain people’s microbiomes might actually be used to treat certain diseases. Doctors have actually cured several stubborn cases of severe diarrhea caused by a particularly difficult bacterium to treat (Clostridium difficile) by transplanting human fecal matter from a healthy person into the patients’ colons! Granted, having a fecal transplant in order to cure disease sounds a bit strange. But apparently the “good” bacteria in the fecal transplant outcompete the C. difficile and wipe them out.
Someday maybe there’ll be ointments or pills containing especially “good” bacteria for treating certain antibiotic-resistant infections such as flesh-eating Staphylococcus aureus or diarrhea-causing C. difficile. Using bacteria to kill bacteria – like using fire to fight fire.
Reference: Zimmer, C., How Microbes Defend and Define Us. New York Times, July 13, 2010.
Selasa, 13 Juli 2010
Heritable, Non-Genetic Behavioral Patterns
Why do abused children grow up to be abusive parents? Why do people raised in lower socio-economic environments tend to have more long-term health problems? Why is it so hard for drug addicts to kick their habit?
For possible answers, behavioral neuroscientists are turning to a hot new field called behavioral epigenetics. Behavioral epigenetics is the study of inherited changes in behavior or gene expression that are caused by factors other than changes in DNA, i.e., that are epi- (Greek: over, above) genetics.
According to epigenetics theory, environmental factors such as the degree of nurturing (or lack of it) by one’s parents early in life can alter the chemical structure of DNA (specifically, the degree of methylation of DNA and its associated histones). This in turn affects how and when certain genes are turned on and off. In theory, such chemical alterations in DNA could last for multiple generations (i.e., be heritable) even though the nucleotide sequence of the genes themselves hasn’t changed.
So far, there’s very little evidence to suggest that epigenetic mechanisms influence human behavior, mostly because human brain tissue is not readily available for research. However, laboratory studies show that rats raised by less-nurturing mothers tend to be more prone to stress as adults and to exhibit increased methylation of certain genes. It’s worth keeping an eye on this developing field to see where it leads.
For possible answers, behavioral neuroscientists are turning to a hot new field called behavioral epigenetics. Behavioral epigenetics is the study of inherited changes in behavior or gene expression that are caused by factors other than changes in DNA, i.e., that are epi- (Greek: over, above) genetics.
According to epigenetics theory, environmental factors such as the degree of nurturing (or lack of it) by one’s parents early in life can alter the chemical structure of DNA (specifically, the degree of methylation of DNA and its associated histones). This in turn affects how and when certain genes are turned on and off. In theory, such chemical alterations in DNA could last for multiple generations (i.e., be heritable) even though the nucleotide sequence of the genes themselves hasn’t changed.
So far, there’s very little evidence to suggest that epigenetic mechanisms influence human behavior, mostly because human brain tissue is not readily available for research. However, laboratory studies show that rats raised by less-nurturing mothers tend to be more prone to stress as adults and to exhibit increased methylation of certain genes. It’s worth keeping an eye on this developing field to see where it leads.
Rabu, 07 Juli 2010
It's Official: She Can Compete
It took more than 10 months for a committee of the IAAF, international track and field’s governing body, to decide that Caster Semenya could compete in track and field events as a woman. As you may recall, Ms. Semenya’s gender was called into question after she completely dominated the 800-meter event in the world championships last August in Berlin (see this blog, Sept. 7, 2009.) A statement released yesterday by the IAFF on their Web site (www.IAAF.org) reads in full:
Caster Semenya May Compete. “The process initiated in 2009 in the case of Caster Semenya (RSA) has been completed. The IAFF accepts the panel of medical experts that she can compete with immediate effect. Please note that the medical details of the case remain confidential and the IAAF will make no further comment on the matter.” (IAFF statement)
Remember the old “Where’s the beef?” commercials for Wendy’s chain of restaurants? One might ask, “Where’s the proof?” Out of fairness to all athletes in sports, sports governing bodies should develop understandable policies, guidelines, or criteria for gender assignment in sports. But it won’t be easy (gender IS ambiguous, sometimes), so I’m betting the IAAF won’t even attempt it.
The Wendy’s commercial ended with the remark, “(I don’t think there’s anybody back there…)” IAAF, are you listening?
Caster Semenya May Compete. “The process initiated in 2009 in the case of Caster Semenya (RSA) has been completed. The IAFF accepts the panel of medical experts that she can compete with immediate effect. Please note that the medical details of the case remain confidential and the IAAF will make no further comment on the matter.” (IAFF statement)
Remember the old “Where’s the beef?” commercials for Wendy’s chain of restaurants? One might ask, “Where’s the proof?” Out of fairness to all athletes in sports, sports governing bodies should develop understandable policies, guidelines, or criteria for gender assignment in sports. But it won’t be easy (gender IS ambiguous, sometimes), so I’m betting the IAAF won’t even attempt it.
The Wendy’s commercial ended with the remark, “(I don’t think there’s anybody back there…)” IAAF, are you listening?
Jumat, 02 Juli 2010
Studying Human Behavior
What drives human behavior? In a provocative paper published online in Behavioral and Brain Sciences last week, it is argued that much of what we believe we know about human behavior is skewed by the fact that most psychological studies are performed on WIERDs – subjects from Western, Educated, Industrialized, Rich, Democratic societies. Indeed, most human subjects used in psychological studies are from the United States, according to an article published several years ago in American Psychologist by Jeffrey Arnett. And most of the subjects are psychology undergraduate students – hardly representative of the world’s cultures as a whole.
How might this affect the results? Take for example, perception of self. Textbooks generally describe people has having a tendency to rate their own abilities as above average and to be motivated to maintain a positive image of themselves. But this may not necessarily be true for non-WEIRD cultures, who may place more emphasis on family relationships and less on personal choice or ability.
There’s nothing inherently wrong with studying WEIRDs, of course, as long as it is understood that the conclusions may not generalize to all cultures.
Reference: Henrich, Joseph et al. The Weirdest People in the World? Behavioral and Brain Sciences 33 pp. 61-83.
How might this affect the results? Take for example, perception of self. Textbooks generally describe people has having a tendency to rate their own abilities as above average and to be motivated to maintain a positive image of themselves. But this may not necessarily be true for non-WEIRD cultures, who may place more emphasis on family relationships and less on personal choice or ability.
There’s nothing inherently wrong with studying WEIRDs, of course, as long as it is understood that the conclusions may not generalize to all cultures.
Reference: Henrich, Joseph et al. The Weirdest People in the World? Behavioral and Brain Sciences 33 pp. 61-83.
Lucy's Older Brother
Remember “Lucy”, the first nearly complete skeleton of Australopithecus afarensis, an extinct species of early human ancestor? Well, now partial remains of her older “big brother” have been found, though technically he’s not her brother because he lived nearly half a million years earlier. But at 5 – 5 ½ feet tall he is big by early human ancestor standards. Kadanuumuu, or “big man”, as he was nicknamed, had a rib cage and shoulder blade (scapula) more like a modern human than a chimpanzee. In addition, his legs were long compared to his arms, another feature that is more humanlike than apelike.
This second Australopithecus afarensis partial skeleton strengthens the hypothesis that although early human ancestors were not entirely humanlike, they also did not resemble modern apes or chimpanzees.
Details were published online on June 21 in the Proceedings of the National Academy of Science, ahead of the print version.
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