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?

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.

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

I don’t know what to believe…

Thanksgiving and Christmas are times where we traditionally meet with family, eat too much and have awkward conversations with relatives we barely know and realize we have very little in common with.

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, will cure/cause cancer, or how scientists are all faking global warming. 

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.

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.

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.

Friday seminar

This talk should be more accessible to undergraduates than most modelling talks. The photograph above is from one of Cherie's field sites and was taken by Joel Sartore, a National Geographic photographer. It recently won a prize in the prestigious Wildlife Photographer of the Year awards.

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.

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.

Carcinonemertes kurisi

In case you didn't see the Nexus today:  New Nemertean Worm Species Named After UCSB Scientist


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.

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/

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.

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

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

• EEMB Proposed Courses (2010-11)
• MCDB Proposed Courses (2010-11)

This is a list, updated yearly, of what courses the two departments are actually planning on running. It isn't a guarantee but it's as good as you are going to get. I use it all the time to find out what is happening.

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"

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?